Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Vol. 58, No. 4 MICROBIOLOGICAL REVIEWS, Dec. 1994, p. 700-754 0146-0749/94/$04.00+0 Copyright © 1994, American Society for Microbiology Chloroplast Ribosomes and Protein Synthesis ELIZABETH H. HARRIS,`* JOHN E. BOYNTON,' AND NICHOLAS W. GILLHAM2 DCMB Group, Departments of Botany' and Zoology,2 Duke University, Durham, North Carolina 27708-1000 .700 ORIGIN OF CHLOROPLASTS................................................................ CHLOROPLAST GENOME STRUCTURE AND GENE CONTENT.. THE PROCESS OF CHLOROPLAST PROTEIN SYNTHESIS........... -s F' - .................. 704 Phylogenetic Conservation ........................ General Characteristics of Chloroplast rRNA Gene Organization .........................................*707 ........................... .................. 707 16S rRNA ..................................................................... 23S rRNA ..................................................................... 709 5S rRNA ..................................................................o.. 709 709 Introns in rRNA Genes ..................................................................... 712 The 16S-23SSpacer .................................................................... 712 tRNAs Flanking the rRNA Operons..................................................................... ...2.0..................712 Antibiotic Resistance Mutations in the Chloroplast rRNA Genes ......................1.. 714 RIBOSOMAL PROTEINS ..................................... 714 Number and Nomenclature ..................................................................... 715 Organization of Chloroplast Ribosomal Protein Genes ....................................... ............*................. 716 Correspondence of Chloroplast Ribosomal Proteins to Bacterial Ribosomal Proteins ................ ............... 716 Proteins of the Small Subunit................................ 726 Proteins of the Large Subunit. Chloroplast Ribosomal Proteins with No Obvious Homology to Those of E. coli . 729 ........................30 Comparative Analysis of Ribosomal Proteins ............................... ASSEMBLY OF CHLOROPLAST RIBOSOMES ..................................................................... 730 SYNTHESIS OF THE COMPONENTS OF CHLOROPLAST RIBOSOMES .............................................., 731 731 Transcription of rRNA Transcription of Chloroplast Genes Encoding Ribosomal Proteins ..................................................................... 732 ..........733 Posttranscriptional Regulatory Mechanisms Affecting Chloroplast mRNAs .......................... Membrane Binding of Chloroplast Ribosomes ..................................................................... 733 734 HOW ESSENTIAL IS CHLOROPLAST PROTEIN SYNTHESIS?...........-..................'............... 735 CONCLUSIONS ..................................................................... 735 ....................... ACKNOWLEDGMENTS. 73 REFERENCES .................... ..................... ........... ..................................... ........................................... .......................... ................ .. Genes.................................................................. .......... ........................... ................... ................................I............"o .. among these various taxa have produced intriguing directions for future evolutionary studies, while analysis of ribosomal protein sequences, particularly among the diverse algal groups, promises. to be a valuable tool for determining conserved regions likely to have essential functions in ribosome assembly or protein synthesis. ORIGIN OF CHLOROPLASTS Chloroplasts and mitochondria contain protein synthesizingsystems more similar to those of bacteria than to those of the eukaryotic cytoplasm, consistent with the hypothesis that these organelles had xenogenous (endosymbiotic) rather than autogenous (intracellular differentiation) origins (see. references 5, 205, 220-223, 274, 633, and 694 for discussions). Phylogenies based mostly on rRNA sequences indicate that the cyanobacteria are ancestral to chloroplasts while the members of the alpha subdivision of the purple sulfur bacteria are the likely progenitors of mitochondria (221, 222). Whether the, chlorophyte algae and land plants on the one hand, and the rhodophyte, chromophyte, and euglenoid algae on the other represent more than one endosymbiotic event remains unresolved (130, 403, 434). Comparisons of gene order and arrangement CHLOROPLAST GENOME STRUCTURE AND GENE CONTENT Unlike their prokaryotic ancestors, neither chloroplasts nor mitochondria are genetically autonomous, and information specifying components of the organelle protein synthesizing systems is divided between organelle and nucleus. Separation of the genes encoding these RNAs and proteins between two discrete cellular compartments suggests that mechanisms must have evolved to coordinate expression of these genes so that protein synthesis in the organelle can proceed efficiently. Whereas chloroplast genomes of land plants usually have a common organization and gene content, a great deal more variability is encountered among the algae, particularly with * Corresponding author. Mailing address: DCMB, Duke University Box 91000, Durham, NC 27708-1000. Phone: (919) 613-8164. Fax: (919) 613-8177. Electronic mail address: [email protected]. 700 Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV ..700 ..702 .....................................................................................................................................t.a..i.....n.... ... .....1....'rnl Initiation kElongation.........417d 0304 A 704 Chloroplast tRNAs and Aminoacyl-tRNA Synthetases ..................................................................... 704 PLASTID GENES FOR rRNAs ................................................... CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS VOL. 58, 1994 encoding ribosomal proteins. Gene locations are from reference 560. regard to the ribosomal protein genes that have been retained in the organelle. In this section we review the chloroplast genome structure of land plants and the algal genera that have been investigated to date with respect to composition and organization of genes encoding rRNAs and ribosomal proteins. Chloroplasts are highly polyploid organelles containing circular DNA molecules of 85 to 200 kb organized into discrete membrane-associated nucleoids (see references 50, 206, 260, 337, 482, 483, 558, 613, and 614 for reviews). Three land plant chloroplast genomes have been completely sequenced: the dicotyledon tobacco (Nicotiana tabacum, 156 kb [560, 561]), the monocotyledon rice (Oryza sativa, 135 kb [265]); and a liverwort (Marchantia polymorpha, 121 kb [471-473]). Each contains 110 to 120 genes (482, 614). These sequences, as well as restriction maps and partial sequences from many other species, indicate that the basic chloroplast genome structure and overall gene order in land plants are highly conserved. Although green algae (Chlorophyta) are regarded as ancestral to land plants, modern green algae often show substantial rearrangements in chloroplast gene order (see below). Other of algae (Rhodophyta, Euglenophyta, Chromophyta) show even more diversity in gene content and organization. In the typical land plant chloroplast genome, unique sequence regions of 15 to 25 kb and 80 to 100 kb are separated groups by the two copies of an inverted repeat, which is usually 20 to 30 kb in size and contains genes encoding the chloroplast rRNAs, certain tRNAs, and often one or more genes specifying proteins (Fig. 1) (see references 482 and 614 for reviews). Within the inverted repeat, the rRNA operon is usually oriented with the 23S rRNA gene closer to the small singlecopy region and the 16S rRNA gene closer to the large single-copy region. The two repeats are identical in sequence as a consequence of an active copy correction system (50). Nearly two-thirds of the variation in size among land plant chloroplast genomes (120 to 216 kb) is accounted for by expansion or contraction of the inverted repeat (482). The smallest chloroplast genomes among land plants are seen in conifers (355, 600, 695) and in six tribes of the legume family Fabaceae (314, 482, 487), which have lost the inverted repeat and thus contain only a single copy of each of the rRNA genes. Black pine (Pinus thunbergii) chloroplast DNA does possess a short inverted repeat sequence, which contains a tRNA gene and part of the 3' portion of the psbA gene, but not the rRNA genes (654). In contrast, species with the largest chloroplast genomes often have expanded inverted repeats (e.g., Pelargonium hortorum has a 76-kb inverted repeat encompassing nearly half of the 216-kb chloroplast genome, in which many genes normally in the single-copy region have been duplicated [482]). Chloroplast genomes from land plants specify a relatively constant set of components for the protein-synthesizing machinery of the organelle (4 rRNAs, 30 to 31 tRNAs, 21 ribosomal proteins, and 4 RNA polymerase subunits) and for photosynthesis (28 thylakoid proteins plus 1 soluble protein, the ribulose-1,5-bisphosphate carboxylase/oxygenase [Rubisco] large subunit). In addition, homologs of 11 subunits of mammalian mitochondrial complex I (the ndh genes) have now been found to be encoded by chloroplast DNA in flowering plants and Marchantia species (9,713). Chloroplast genomes of gymnosperms, liverworts, and algae (e.g., Chlamydomonas reinhardtii) which synthesize chlorophyll in darkness possess genes encoding three subunits of a light-independent protochlorophyllide reductase that is also found in photosynthetic prokaryotes (see reference 367 for a summary). These genes are absent from the tobacco and rice chloroplast genomes. Mapping and sequencing studies of chloroplast genomes from widely different algal taxa reveal that these are much more variable in organization and gene content than those of land plants. The well-characterized chloroplast genomes of three species of unicellular green algae in the genus Chlamydomonas are substantially larger (C. reinhardtii, 196 kb; C. eugametos, 243 kb; C. moewusii, 292 kb) than the chloroplast genomes of land plants (42, 43, 50, 247). In these species the two copies of the large inverted repeat encoding the rRNAs are separated by unique sequence regions of roughly equal size. Chloroplast genes in Chlamydomonas species are also extensively rearranged between distantly related species and with respect to land plants (43). The green alga Spirogyra maxima, in the charophyte lineage presumed to be ancestral to land plants, lacks an inverted repeat and shows altered gene order relative to land plants (352, 393). The organization, structure, and gene content of the completely sequenced 145-kb chloroplast genome of Euglena gracilis Z (243) depart markedly from the chloroplast genomes of chlorophyte algae or land plants. In this Euglena strain and in its colorless relative Astasia longa, the plastid genome contains three tandemly repeated rRNA operons plus an additional 16S gene or fragment thereof (288, 289, 315-317, 478, 569). Euglena gracilis var. bacillaris has only a single complete rRNA operon (720). Most of the Euglena chloroplast tRNA genes are grouped in tight clusters of two to five genes, whereas they tend to be scattered in plastid genomes of land plants. While most protein-coding chloroplast genes in land plants or Chlamydomonas species are uninterrupted or contain at most one or two introns, comparable genes in Euglena gracilis each contain multiple introns (243, 482). However, several chloroplast tRNA genes that have introns in land plants lack introns in Euglena or Chlamydomonas species (331). A number of other genes found in land plant chloroplast genomes, including three genes encoding ribosomal proteins, are missing from the Euglena chloroplast genome (see below), but this algal genome also contains some genes not found in plastid genomes of land plants. The plastid of Cyanophora paradoxa is often referred to as Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV FIG. 1. Schematic diagram of a typical land plant chloroplast showing the positions of the inverted repeat, rRNA genome (tobacco), genes, and genes 701 702 HARRIS ET AL. MICROBIOL. REV. chloroplast protein synthesis has been presented by Steinmetz and Weil (593). has now been sequenced (32, 598). This genome contains an inverted repeat which encodes the cyanelle rRNAs and several other genes. Although the gene content of the cyanelle generally resembles that of land plant chloroplasts, there are about 30% more genes, including 11 additional genes encoding components of the translational apparatus. So far, only a single type I intron has been found in Cyanophora paradoxa, in a tRNAIeU gene (162). The same intron is found in cyanobacteria. Cryptomonad algae contain a plastid and residual nucleus or nucleomorph enclosed within the endoplasmic reticulum of the cytoplasm and thus effectively separated from the normal cell nucleus (see 123, 386). Distinctly different 18S rRNAs are encoded by the nucleus and nucleomorph of Cryptomonas (D and are spatially separated within the cell (129, 414). The nucleomorph rRNA genes are related to those of red algae, while the nuclear rRNA genes are clustered separately in the phylogenetic branch containing land plants and green algae. This suggests that cryptomonad algae may have arisen through a second endosymbiotic event in which a eukaryotic symbiont from the red algal lineage was taken up by a unicellular host more closely related to the green algae (129, 130, 386). Partial sequencing of the plastid genome of Cryptomonas (D has revealed the presence of several novel genes, including four genes for ribosomal proteins not found in chloroplast genomes of land plants (122, 124, 680; also see below). In the red alga Porphyra purpurea, over 125 genes have been identified in the ca. 60% sequenced chloroplast genome (514, 515), suggesting that the entire genome may contain as many as 200 to 220 genes, about twice as many as found in the completely sequenced genomes of land plant chloroplasts. These include at least seven photosynthesis and nine ribosomal protein genes not present in land plants. Introns have not been found in any of the 80 genes sequenced to date. The chloroplast genome of P. yezoensis possesses an inverted repeat containing the rRNA genes (353, 562, 563), but the related red algae P. purpurea and Grijflthsia pacifica lack this invertedrepeat structure. In P. purpurea the rRNA genes are encoded in direct repeats which are not identical in sequence (514, 516, 563). The unicellular red alga Cyanidium caldarium possesses an inverted repeat containing only the rRNA genes, but gene order appears to be more similar overall to that of Cryptomonas (D than to that of P. yezoensis or Griffithsia pacifica (385). Inverted repeats containing rRNA genes are also found in the plastid genomes of the brown alga Dictyota dichotoma (330) and the golden-brown algae Olisthodiscus luteus and Ochromonas danica (108, 563). The plastid genome of the brown alga Pylaiella littoralis contains two different circular DNA molecules (369, 370, 404, 405). The larger (133 kb) molecule resembles a typical land plant chloroplast genome, with two rRNA operons in an inverted repeat. The smaller (58 kb) molecule contains a 16S pseudogene sequence, which is 65% homologous to the functional 16S genes of the large molecule, and a complex region that hybridizes with a 23S rRNA probe (369, 370). Initiation THE PROCESS OF CHLOROPLAST PROTEIN SYNTHESIS We begin this brief review of chloroplast protein synthesis with a comparison with the process as it occurs in bacteria. This section will be followed by discussion of the tRNAs and aminoacyl-tRNA synthetases. A more detailed discussion of In prokaryotes, protein synthesis begins with formation of a preinitiation complex from the 30S ribosomal subunit and tRNAIMetUAC, with the 30S subunit binding to the purine-rich Shine-Dalgarno sequence 7 ± 2 nucleotides (nt) upstream of the initiator AUG (230, 261, 323). The canonical ShineDalgarno sequence, GGAGG, or a variant, pairs with a pyrimidine-rich complementary sequence, the anti-Shine-Dalgarno sequence, near the 3' end of the 16S rRNA molecule. Addition of a 50S ribosomal subunit converts the preinitiation complex to an initiation complex that can enter the elongation phase of protein synthesis. These reactions are promoted by the three initiation factors, IF-1, IF-2, and IF-3. IF-1 enhances the rates of ribosome dissociation and association and the activities of the other initiation factors (261). IF-2 is involved in initiator tRNA binding and GTP hydrolysis, while IF-3 prevents ribosomal subunit association in the absence of mRNA and appears to stabilize mRNA binding by promoting the conversion of a preternary ribosome-mRNA-fMet tRNA complex into a ternary complex in which codon-anticodon interaction has occurred. IF-3 also is thought to proofread the AUG-anticodon interaction. Chloroplast equivalents of IF-2 and IF-3Chl, have been characterand IF-3, designated ized from Euglena gracilis (212, 324, 325, 375,527, 678). Roney et al. 527) confirmed that IF-2Chl is required for binding of tRNA et to chloroplast 30S subunits, as is prokaryotic IF-2. IF-2,hl occurs in several complex forms, varying in molecular mass from 200 to 800 kDa (375). Subunits of 97 to >200 kDa have been observed in these preparations. IF-3,hl promotes Alinitiation complex formation in the presence of though IF-3Chl will replace Escherichia coli IF-3 in initiation complex formation, there is some evidence that its function may be modified (527). A DNA sequence with homology to the E. coli infA gene encoding initiation factor IF-1 has been identified in the chloroplast genomes of land plants, including the colorless parasite Epifagus virginiana (558, 714), but is apparently absent from the completely sequenced chloroplast genome of Euglena gracilis (243). The tobacco infA gene, in contrast to the spinach gene (571), lacks the ATG translation initiation codon and thus may be a pseudogene. Reading frames with homology to the genes encoding IF-2 and IF-3 have not been detected in the sequenced plastid genomes of green plants, Epifagus virginiana, or Euglena gracilis, and inhibitor experiments suggest that the Euglena genes specifying these factors are nuclear in location. However, homologs of the infB gene encoding IF-2 have been found in the chloroplast genomes of the red algae P. purpurea (514) and Galdieria sulphuraria (322). Lin et al. (359) have recently reported characterization of a cDNA clone encoding IF-3Chl in Euglena gracilis. This nuclear gene appears to be present in about four copies, one of which is probably a pseudogene. The putative protein contains two acidic regions with no homology to other known sequences, in addition to a 175-amino-acid region with 31 to 37% homology to other IF-3 proteins. Shine-Dalgarno-like sequences are present in the untranslated leader regions of many but not all chloroplast mRNAs (35, 44, 318, 532, 593, 746). Ruf and Kossel (532) reported that 37 of 41 chloroplast genes examined in tobacco have such sequences if one extends the anti-Shine-Dalgarno sequence in the 16S rRNA beyond the canonical CCUCC to include the adjacent unpaired ACUAG sequence. Bonham-Smith and IF-2Ch, IF-2Chi. Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV the cyanelle because of its secondary peptidoglycan wall and photosynthetic apparatus with phycobiliproteins typical of cyanobacteria and red algae. Most of the 133-kb cyanelle genome CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS VOL. 58, 1994 Elongation Elongation of the peptide chain requires three steps, i.e., aminoacyl-tRNA binding, peptide bond formation, and translocation, and involves three binding sites for tRNA (261, 460, 518, 690). The aminoacylated tRNA combines with elongation factor EF-Tu and GTP to form a ternary complex, which then associates with a ribosome complexed to mRNA and peptidyl- tRNA. The specific ternary complex is selected on the basis of codon-anticodon recognition at the A site and is followed by GTP hydrolysis and the release of an EF-Tu-GDP complex. Peptide bond formation takes place with transfer of the growing peptide chain to the aminoacyl-tRNA in the A site. Translocation is promoted by EF-G and GTP hydrolysis, and involves movement of the peptidyl-tRNA-mRNA complex from the A to the P site. The process is then repeated, and the deacylated tRNA moves from the P to the E site. The A and E sites themselves are allosterically linked in a negative sense so that occupation of the A site by aminoacylated tRNA reduces the affinity of the E site for deacylated tRNA and vice versa. Regeneration of the active EF-Tu-GTP complex from EF-TuGDP is mediated by elongation factor EF-Ts. All three elongation factors have been characterized from Euglena chloroplasts by Spremulli and colleagues (53, 145, 173, 341, 585), and the structure of the guanine nucleotide-binding domain of EF-Tu has been modeled by Lapadat et al. (341). EF-Tu has also been purified from pea and tobacco chloroplasts (445, 589). Reading frames with homology to the bacterial genes encoding the three elongation factors EF-Tu, EF-G, and EF-Ts are absent from the three completely sequenced land plant chloroplast genomes (482, 558), but some of these genes have been retained in the plastid genomes of certain algae (see below). Two distinct nuclear genes encoding chloroplast EF-Tu have been identified in tobacco (445, 611, 661). A nuclear EF-G gene has been cloned and sequenced from soybean (650), and a partial clone obtained from pea (2). Early inhibitor experiments with Euglena gracilis indicated that EF-Ts and EF-G were nuclear gene products but that EF-Tu might be encoded in the chloroplast (52, 173). These predictions were confirmed by identification of a chloroplast tufA gene encoding EF-Tu (429) and by failure to find genes encoding EF-Ts or EF-G in the recently completed Euglena chloroplast genome sequence (243). The Euglena tufA gene is split into three exons separated by two introns (429). An uninterrupted sequence with homology to the E. coli tufA gene has been reported from the chloroplast genome of C. reinhardtii (15, 684). The tufA gene sequence is also found in the Cyanophora cyanelle genome (32, 598) and in the chloroplast genomes of representative green algae in the families Ulvophyceae, Chlorophyceae, and Charophyceae, the latter group being the presumed ancestors of land plants (14, 15). However, tufA is absent from the chloroplast genome of the liverwort Marchantia polymorpha, representative of the earlier land plant lineages (472, 473). Baldauf and Palmer (15) concluded that transfer of this gene to the nucleus probably occurred in the charophycean lineage prior to the emergence of land plants. Reith and Munholland (514) have reported that the chloroplast genome of the red alga P. purpurea not only possesses a reading frame corresponding to tufA but also possesses one corresponding to tsf which encodes EF-Ts in prokaryotes. This gene has also been found in the chloroplast genome of the thermophilic red alga Galdieria sulphuraria (322). In prokaryotes, mutations to fusidic acid resistance can occur in the structural gene for EF-G (fus) (357). A nuclear mutation in C. reinhardtii has been reported to confer fusidic acid resistance on chloroplast EF-G, but the gene encoding this factor has not yet been identified (74; also see 247). Production of chloroplast protein synthesis factors appears to be light regulated. Spremulli and coworkers have shown that activities of Euglena IF-2, IF-3, EF-Tu, EF-G, and EF-Ts all increase on transfer of cells from dark growth to light (52, 173, 324, 585). In Chlamydomonas synchronous cultures, transcription rates for four chloroplast-encoded photosynthetic genes Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV Bourque (35) observed that 181 of 196 chloroplast-encoded transcripts examined possessed a Shine-Dalgarno sequence within 100 bp 5' to the initiation codon. However, spacing of Shine-Dalgarno sequences in chloroplast mRNAs is less uniform than in bacteria. Frequency distributions of the most common individual positions potentially involved in base pairing with 16S rRNA ranged from -2 to -29, with a major peak (ca. 40%) at -7 to -8, a smaller peak at -15 to -16, and a third small peak at -21 to -23 (35, 532). Thus, chloroplast ribosomes may be able to accommodate larger distances between the ribosome recognition site and translational start sites than bacterial ribosomes. For example, in the Chlamydomonas rpsl2 gene, a canonical Shine-Dalgarno sequence is found at position -55 upstream of the initiator codon (364). The variability of the Shine-Dalgarno sequence raises the question whether initiation from this sequence proceeds as in eubacteria for Shine-Dalgarno sequences close to the AUG codon and occurs by transient binding and "scanning" for more-distant Shine-Dalgarno sequences (306). In tobacco the mRNAs for those chloroplast genes lacking Shine-Dalgarno sequences either show only a trinucleotide sequence for potential base pairing (atpB) or contain out-of-frame initiator codons between the potential recognition sites and the respective in-frame start codons (rpsl6, rpoB, and petD [532]). In Euglena chloroplasts, mRNA-rRNA recognition seems to proceed by somewhat different rules, because the putative anti-Shine-Dalgarno sequence CUCCC differs from the canonical CCUCC sequence and actually forms the 3' terminus of the 16S rRNA rather than being located several bases from the end (592). Since only about half of the Euglena chloroplast mRNAs contain Shine-Dalgarno sequences, two modes of initiation complex formation have been postulated (527, 677). In one class of mRNAs, complex formation is facilitated by a Shine-Dalgarno-like sequence. However, in the second class the A+U content of the region 5' to the initiator AUG is 90% or greater and this portion of the mRNA is relatively unstructured, making potential start sites in this region readily accessible to small subunits. Koo and Spremulli (318, 319) have studied formation of initiation complexes in vitro with transcripts containing the 5' untranslated leader region of the Euglena rbcL mRNA, which is A+U rich and contains no Shine-Dalgarno sequence. Introducing a Shine-Dalgarno sequence into this region enhanced initiation only slightly. Deletion and/or modification of the leader region demonstrated that a minimum of about 20 nt is required to form the initiation complex in vitro and that the full 55-nt length is necessary for full activity in complex formation (318). The primary sequence of the region seems less important for initiation than does its length. The native 55-nt sequence has only weak secondary structure, and modification of the sequence to create increased secondary structure within about 10 nt of the AUG codon diminished formation of the initiation complex significantly (319). Koo and Spremulli concluded that the major determinant of initiation in those Euglena mRNAs with no Shine-Dalgarno sequence is presence of the AUG codon in an unstructured region of mRNA that is accessible to the 30S subunit. 703 704 MICROBIOL. REV. HARRIS ET AL. and for the tufA gene were all found to be maximal at the beginning of the light period (51, 350). However, EF-Tu mRNA decreased to almost undetectable levels in the second half of the light period. Activity of the pea chloroplast EF-G, encoded by a nuclear gene, is also light regulated but at the level of translation (1). Termination Chloroplast tRNAs and Aminoacyl-tRNA Synthetases The properties of chloroplast aminoacyl-tRNA synthetases have been summarized by Steinmetz and Weil (593). These enzymes are encoded in the nucleus. Most are distinguishable from their cytoplasmic counterparts and will charge only chloroplast or prokaryotic tRNAs efficiently. These enzymes have unusually high molecular masses (75 kDa or greater) and can be found as monomers, homodimers, heterodimers, or heterotetramers depending on the enzyme. The structure and codon recognition patterns of chloroplast tRNAs and the organization of their cognate genes have been extensively reviewed elsewhere (397-399, 593, 616). Genes encoding individual chloroplast tRNAs are highly conserved in different species of land plants and are similar in structure and sequence (ca. 70% sequence identity) to prokaryotic tRNA genes but have low homology to those of eukaryotic cells. However, the 3'-terminal CCA triplets of chloroplast tRNAs are added posttranscriptionally, as occurs for all eukaryotic cytoplasmic tRNAs but for only about one-third of bacterial tRNAs. Isoaccepting tRNAs for a given amino acid are encoded by different chloroplast genes, but these tRNAs are charged by the same chloroplast tRNA synthetases. Some chloroplast tRNA genes are preceded by prokaxyotic-like promoter sequences, but such sequences are absent upstream of other chloroplast tRNA genes, which may thus possess alternative promoters, possibly internal to the coding region (227, 229, 616). The tobacco chloroplast genome contains 30 tRNA genes, 23 of which are single and 7 of which are duplicated in the inverted repeat. Rice has the same set of tRNA genes as tobacco, but the inverted repeat extends through the tRNAH1S gene, found in the single-copy region adjacent to the inverted repeat in tobacco. In liverwort there are 31 chloroplastencoded tRNA genes, with the extra gene being tRNAAxgCCG, but in Euglena gracilis there are only 27 (243, 558, 616). (444). One tRNAGlUuc has a special function in chlorophyll biosynthesis as well as participating in protein synthesis, while the other two species have a U*UG anticodon specific for glutamine and are converted from Glu-tRNA01n to GlntRNAGJn by a specific amidotransferase activity present in chloroplast extracts (398, 616). This mischarging mechanism has also been described in several gram-positive bacteria (398). The chloroplast genomes sequenced to date encode a typical initiator tRNA"cICAu, and all employ the three classical termination codons (UAA, UAG, and UGA). However, genes for tRNAs recognizing the codons CUU/C (Leu), CCU/C (Pro), GCU/C (Ala), and CGC/A/G (Arg) are absent from the chloroplast genomes of tobacco and rice. Since all 61 sense codons are used in the three sequenced land plant chloroplast genomes, this deficit in specific tRNAs requires that the tRNAs either be imported or be read by the "two-of-three" mechanism used in animal mitochondria (174, 716) or by four-way wobble (480). In the absence of import in Euglena chloroplasts, one of the last two mechanisms would have to pertain to seven of the eight codon families (243). In land plant chloroplasts, two-of-three or four-way wobble seems to be used for tRNAMIaUda,GC, tRNAProU*GC, and tRNAA`gICG, which can read respectively all four alanine (GCN), proline (CCN), and arginine (CGN) codons (488). The first two tRNAs contain a modified U (U*) in the anticodon. The problem of decoding the six leucine codons is solved somewhat differently. Two of the leucyl-tRNAs translate the UUA and UUG codons (488). The remaining tRNAeUUAM7G translates all four CUN codons for leucine apparently by a U * N wobble mechanism (489). In tobacco, rice, and liverwort, six of the chloroplast-encoded tRNA genes possess introns which must be removed from the primary transcript during processing (398). In tobacco these introns range in size from 503 bp (tRNAeuuAA) to 2,526 bp (tRNALYSJuu) (616). Many land plant chloroplast tRNAs are singly transcribed, although a cotranscribed, tricistronic tRNA gene cluster has been identified in tobacco (398) and the two tRNAs found in the spacer between the 16S and 23S rRNA genes are transcribed as part of the rRNA operon precursor (see below). Cotranscription of tRNA gene operons is the usual case in Euglena gracilis. RNase activities thought to be involved specifically in tRNA processing have been identified in chloroplast extracts (225, 226, 727). PLASTID GENES FOR rRNAs Phylogenetic Conservation All chloroplast genomes examined contain genes for the 16S, 23S, and 5S RNAs of the chloroplast ribosome. Table 1 lists species for which sequences have been published. Chloroplast rRNAs are highly conserved at the sequence level and are most closely related to eubacterial sequences, which include those of cyanobacteria (210, 219, 236, 512, 709). For Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV Termination of translation in bacteria involves the hydrolysis of peptidyl-tRNA and release of the completed protein from the ribosome when the ribosome reaches one of the three termination codons (261). Termination requires the action of two release factors, RF-1, which is specific for UAA and UAG, and RF-2, which is specific for UAA and UGA. A third release factor, RF-3, stimulates the activities of RF-1 and RF-2. The same three codons are used for translation termination in chloroplasts (35, 36), with UAA being by far the most frequent (70% in land plant sequences surveyed by Bonham-Smith and Bourque [36]) and UGA being rare (9%). UAA is also overwhelmingly preferred as the stop codon in Chlamydomonas chloroplast genes (247). Bonham-Smith and Bourque (35) noted that UGA was never used as a stop codon in Marchantia chloroplast genes and proposed that a modification of the 16S rRNA in this species prevents recognition of UGA as a termination signal. No reading frame with homology to any of the genes encoding bacterial termination factors has been identified in a chloroplast genome, nor has isolation of these factors been reported. Several chloroplast tRNAs have unusual features. TIwo different tRNAIle species are found in plant chloroplasts. The major species (tRNAIle1, encoded in the spacer between the 16S and 23S genes) recognizes the codons AUU and AUC, while a minor species (tRNAIle2) recognizes AUA. However, the gene encoding the latter tRNA contains a CAU anticodon, which normally would recognize AUG for methionine. One possible explanation is that the C residue is modified in some way posttranscriptionally. In E. coli the C of the homologous tRNA is modified to lysidine, a novel type of cytidine with a lysine residue, which allows it to recognize the AUA codon VOL. 58, 1994 CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS 705 TABLE 1. Plastid and cyanobacterial rRNA sequences published or submitted to GenBank Taxon 16S rRNA Anabaena sp. Anacystis nidulans Antithamnion sp. Astasia longa Chlamydomonas moewusii Cyanophora paradoxa Daucus carota Epifagus virginiana Euglena gracilis Euglena gracilis bacillaris Glycine max Helianthus annuus Marchantia polymorpha Nanochlorum eucaryotum Nicotiana plumbaginifolia Nicotiana tabacum Ochromonas danica Ochrosphaera sp. Olisthodiscus luteus Oryza sativa Oscillatoria sp. Palmaria palmata Pisum sativum Porphyra purpurea Porphyridium sp. Prochloron sp. Pylaiella littoralis Pyrenomonas salina Sinapis alba Spinacia oleracea Spirodela oligorhiza Synechococcus lividus Zea mays 23S rRNA Alnus incana Anacystis nidulans Antihamnion sp. Astasia longa Chlamydomonas eugametos Chlamydomonas frankii Chlamydomonas gelatinosa Chlamydomonas geitleri Chlamydomonas humicola Chlamydomonas indica Chlamydomonas iyengarii Chlamydomonas komma Chlamydomonas mexicana Chlamydomonas moewusii Chlamydomonas pallidostigmatica Chlamydomonas peterfii Chlamydomonas pitschmanii X59559 X03538; X00346, K01983 (partial) X54299 X14386 X15850 J01395, X03269 X12742, X05694, X03848 X65099 X65100 X65688 X65689 X16579 X58864 X56806 X52985 M63813, M63814 M62775, M62776 M64522, M64526, M64531, M64536 M19493 (partial) X73670 M81884, X62099 V00159, X12890, X05005, X70810 X00536 (partial) X07675, X06428, M37149 (partial) X73893 X04465 X76084 M82900, X70938 J01452, J01453, V00165, V00166, Z00044 X53183 X65101 M82860, X15768 X15901 X58359, X58360, X58361 (partial) Z18289 M37430 X51598 M16874, M16862, M30826 (partial) L07257, L07258 X63141 M21373, X14873, X14874 X55015 M15915, X04182 J01440, M21453 (partial) X00014, X00015 (partial) X67091, X67092, X67093 (partial) M10720, Z00028 M75722 X00512, X00343 (partial) X54299 (partial) X14386 Z17234 X68905-X68909 Z15151 X68891, X68892 X68921, X68922 X68893-X68898 X68886, X68886 X68927-X68929 X68910-X68912 X68913-X68918 X68899-X68904 X68887, X68888 Z15152 Reference(s) 356 333, 647, 697 384 569 140 137 722, 724, 725 281 281 280 280 279 702, 703 130 383 63 681-683, 692 548 287 395 435, 712, 714 217, 243, 529, 530, 549 152 110, 673 77 312, 472, 473 553 476, 729 560, 561, 645, 646 705 281 108, 109 265 698, 699 573 602 79 557, 617, 618 516 34 555, 660, 665 404, 405 382 502 56, 409 302 38 554 351 126, 334 384 569 200, 657, 658 658 658 658 658 658 658 658 658 658 658 658 658 Continued on following page Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV Chlamydomonas reinhardtii Chlorella ellipsoidea Chlorella kessleri Chlorella mirabilis Chlorella protothecoides Chlorella sorokiniana Chlorella vulgaris Conopholis americana Cryptomonas 1 Cyanidium caldarium Cyanobacteria (miscellaneous spp.) GenBank accession no(s). 706 MICROBIOL. REV. HARRIS ET AL. TABLE 1-Continued Epifagus virginiana Euglena gracilis Marchantia polymorpha Nicotiana tabacum Olisthodiscus luteus Oryza sativa Palmaria palmata Pisum sativum Pylaiella littoralis Spinacia oleracea Spirodela oligorhiza Zea mays 4.5S rRNA Acorus calamus Allium tuberosum Alnus incana Apium graveolus Codium fragile Commelia communis Conopholis americana Dryopteris acuminata Gossypium hirsutum Hordeum vulgare Jungermannia subulata Ligularia calthifolia Lycopersicon esculentum Marchantia polymorpha Marsilia quadrifolia Mnium rugicum Nicotiana tabacum Oryza sativa Osmunda regalis Pisum sativum Spinacia oleracea Spirodela oligorhiza Triticum aestivum Zea mays J01398, X01977, X16687, X16686 X68889, X68890 X68919, X68920 X68923-X68926 M36158; X05693, X03848 (partial) X52737 (partial) X59768 X14504 (partial) X54300 (partial) M19493 (partial) M81884, X62099 X13310, X12890 M13809, X04465, X01647 J01446, Z00044 X15768 (partial) X15901 Z18289 M37430 X61179, M21373 (partial) M21453, X04977 (partial) X00012, X00013 (partial) Z00028, X01365 M36166 M35406 M75719 M35404 M35276 M35407 X58863 X01523 X63124 M35405, M57605 M13808 M36165 M33098 X04465, M13809 X51641 M35056 J01446, V00161, J01891, J01451, X01277, Z00044 X15901 X51978 M37430 M10757, X04977 J01439 M10541 M19943, Z00028, X01365 346, 521 658 658 658 726 394 703 128 384 287 435, 712, 714 549, 730 312, 473 560, 561, 627 108 265 573 602 405, 581 11, 409 304 148 31 738 284 738 176 738 703 623 440 80, 738 691 31 739 472, 473, 691 421 652 560, 561, 624, 625 265 421 602 11, 332 303 696 147, 148, 601 5S rRNA Alnus incana Anacystis nidulans Astasia longa X00343, X00757, M23834 X14386 Chlamydomonas reinhardtii Chlorella ellipsoidea Conopholis americana Cyanophora paradoxa Cycas revoluta Dryopteris acuminata Euglena gracilis bacillaris Euglena gracilis Ginkgo biloba Glycine max Gossypium hirsutum Jungermannia subulata Juniperus media X03271 X04978 X58863 M32451, M33030 X12787 X00758 X00536 K02483, X12890 X51979 X16736 X63124 X00667 Lemna minor Lupinus albus Marchantia polymorpha X02714 X65030 M75719 X00666, X04465 284 94, 125 569 550 724 703 411, 412 743 629 152 243, 296 421 23 440 728 663 144 327 472, 473, 728 Continued on following page Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV Chlamydomonas reinhardtii Chlamydomonas starrii Chlamydomonas zebra Chlamydomonas sp. Chlorella ellipsoidea Coleochaete orbicularis Conopholis americana Cryptomonas (F Cyanidium caldarium Cyanophora paradoxa Reference(s) GenBank accession no(s). Taxon VOL. 58, 1994 CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS 707 TABLE 1-Continued Taxon Spirodela oligorhiza Synechococcus lividus Vicia faba Zea mays J01451, M10360, M15995, X01277, Z00044 X15901 X63200 X05551 M37430 L07259, L07260 144, 265 421 146 602 516 664 380 580 112, 303 111, 663 147, K03159, X02637 X61179 V00169, X05876 J01439 X02731 M19943, Z00028 example, primary sequence homology is generally over 70% for chloroplast or cyanobacterial 16S rRNAs compared with that of E. coli and greater than 80% for chloroplast 16S rRNA compared with cyanobacterial 16S rRNAs. Gray (219) recognized eight noncontiguous conserved primary sequences in 16S rRNA interspersed among nonconserved sequences. The predicted secondary structures of these molecules are even more conserved, and virtually all of the approximately 45 helices postulated for the E. coli 16S rRNA (62, 462) are present in chloroplast 16S rRNAs of Euglena gracilis, Chlamydomonas species, tobacco, and maize (232, 512; also see below). Compensating base substitutions are often seen on the complementary sides of predicted stem structures, strengthening the supposition that these structures are functional in vivo. Because of this high degree of structural conservation, rRNA genes have found extensive use in phylogenetic studies (78, 219, 232, 235, 236, 342, 710). Comparative analyses of 16S (54, 210) and 5S (144, 380, 663, 743) rRNA sequences support both the probable origin of chloroplasts from endosymbiotic cyanobacteria and the hypothesis that land plants derive from one branch of chlorophyte algae. Van de Peer et al. (665) have compared 16S and 18S sequences from eukaryotic, archaebacterial, eubacterial, plastid, and mitochondrial ribosomes. Although their analysis focused largely on mitochondrial origins, their data also support the common ancestry of cyanobacteria and plastids. General Characteristics of Chloroplast rRNA Gene Organization As in the eubacteria, chloroplast rRNA genes are normally arranged in an operon transcribed in the order 16S-23S-5S (Fig. 2) (114, 320). In land plants, including some but not all ferns, approximately 95 nt homologous to the 3' terminus of the E. coli 23S molecule constitutes a 4.5S rRNA molecule, separated from the remainder of the 23S gene by a transcribed spacer, whereas in prokaryotes, all algae so far examined, mosses, and the liverwort Marchantia polymorpha, the equivalent sequence is part of the 23S gene (47, 320). In C. reinhardtii, the sequences homologous to the 5' portion of the 23S gene of bacteria and plants are divided into 7S and 3S rRNAs, separated by short spacers that are removed from the precursor rRNA posttranscriptionally (137). The large subunit rRNA of C. eugametos comprises species (a and ,B) equivalent to the C. reinhardtii 7S and 3S rRNAs and two larger species (ry and 8) which together are equivalent to the remainder of the 23S molecule (656). 560, 561, 624-626 491, 492 113 601 16S rRNA The secondary-structure model of 16S rRNA based on comparative sequence analysis (231, 232, 236, 449, 463, 468) suggests a functional division into distinct 5', central, and 3' domains, corresponding in E. coli to residues 26 to 557, 564 to 912, and 926 to 1391, respectively, followed by a "3' minor domain" from ca. 1401 to 1542 (Fig. 3; for a numbered E. coli sequence diagram in similar format to the tobacco sequence shown in Fig. 3, see references 231 and 235). Each of these domains comprises helices and loops whose secondary structure is phylogenetically conserved (219, 236). Models for the tertiary structure of the E. coli 30S subunit have been constructed based on studies of RNA-RNA and RNA-protein cross-linking, immunoelectron microscopy, and neutron diffraction (58-61, 463, 465, 596). Functional analyses involving mutants, binding of tRNA and antibiotics, and assembly of ribosomal proteins with RNA in vitro indicate that codonanticodon recognition involves the 3' domain and terminal 3' minor domain. Three regions of the 16S molecule (E. coli nt 518 to 533, 1394 to 1408, and 1492 to 1505) that show a particularly high degree of primary sequence conservation appear to have tertiary interactions related to decoding (468). tRNA bound in the A site interacts specifically with the 3' domain and with residues in the "530 loop" (see reference 465 for review), whereas P-site-bound tRNA protects five sites in the central and 3' domains that are proposed to be clustered in tRNA 168 lie Al 23S _uI tRNA 165 5s IE cyanobacteria, most algae 23S I 4.5S 5S land plants tRNA 165 IleAla 7S 38 23S 5' 23S 3' 5S C. relnhardtll FIG. 2. Arrangement of the rRNA operons in land plants and algae, showing conservation of tRNAIle and tRNAMa within the spacer between the 16S and 23S genes and variation in the species that constitute the 23S molecule. In land plants, the tRNA genes are split by introns, whereas in all algae examined to date they are uninterrupted. The region corresponding to the 3' end of the eubacterial 23S rRNA is a separate 4.5S rRNA in angiosperms, gymnosperms, and some (but not all) ferns. Internal transcribed sequences and one or more introns interrupt the 23S genes of Chlamydomonas species (658). Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV Nicotiana tabacum Oryza sativa Picea excelsa Pelargonium zonale Pisum sativum Porphyra purpurea Porphyra umbilicalis Prochloron sp. Pylaiella littoralis Spinacia oleracea Reference(s) GenBank accession no(s). 708 MICROBIOL. REV. HARRIS ET AL. UA a^o GA a central domain AA a CMnGAA A c^^c GUc 'aGGUGGCCUUUAAGGG-cCA CGA A U a-C A U -a ca0-C spr GO 0 U.G G-C C - GA U - AC 0-C u a C-Q c-a U AA ACA cc ACCC GGCGOUGGA CU A AAGC AACCCUG0 I .II I .II II IIIIIlIi 11I1II1I1 UCGOGACC CU CUGCCGCCU A UAA GA UUUUUC A a A 3' domain CAC 0. G~~~~~A GU /.UAG A0! A helix 17 5' domain i sr 0 5, nr A GUC ACOGGAAGUG I - I I In I I I I- a COO U0ACCUUUoU a G a C helix 6 3' minor domain tobacco 16S rRNA FIG. 3. Secondary structure of tobacco 16S rRNA, showing the major functional domains and sites of antibiotic resistance (Table 2; sr, streptomycin; spr, spectinomycin; nr, neamine/kanamycin). Sequence from the Ribosomal Database Project, courtesy of Robin Gutell. the tertiary structure. Many of the same sites, which are all in highly conserved regions of the 16S molecule, also interact with antibiotics that block protein synthesis at the level of the 30S subunit (424, 467, 537; also see below). The principal regions in which the secondary structures of chloroplast 16S rRNAs deviate from the E. coli model are in the 5' domain between nt 198 and 220 (numbering according to the E. coli sequence [462]), where chloroplast rRNAs have a shorter helix 10 than E. coli does, and between 455 and 477, where E. coli has a well-defined helix (the upper part of helix Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV ^Aa GA G G AaUUCUCCU~AA A-U C - CHLOROPLAST RIBOSOMES AND VOL. 58, 1994 17 of Brimacombe et al. [59]) that is lacking in cyanobacteria and chloroplasts. Helix 6 is also shorter in chloroplast and cyanobacterial 16S rRNAs than inE. coli. Raue et al. (512) noted eight regions where secondary structure is conserved but primary sequence is highly variable. These eight regions are also sites of variation in secondary structure when the 16S rRNAs of chloroplasts and eubacteria on the one hand are compared with small-subunit rRNAs of mitochondria and eukaryotic cytoplasmic ribosomes on the other. 23S rRNA 709 teria and plastid rRNAs, as does domain V. The break between the 23S rRNA and 4.5S rRNA of land plants occurs in domain VI. 5S rRNA Their short length and relatively high degree of evolutionary conservation have madeSS rRNA molecules frequent subjects for phylogenetic studies (see e.g., references 117, 270, 580, 663, 664). They have also proved useful for computer modeling of secondary and tertiary structure, including chemical reactivity and accessibility of bases, and possible protein binding (67, 524, 525, 693). A numbering scheme applicable to both prokaryotic and eukaryoticSS rRNAs, proposed by Erdmann and Wolters (157), defines five loops (a to e) and five helices (A to E). In a compilation of sequences in the Berlin RNA Databank, Specht et al. (583) included representations of the common secondary structure of eukaryotic and prokaryotic SS rRNAs, which are differentiated into five structural groups primarily on the basis of variability in one (D) of the five helices. PlastidSS rRNAs are grouped in this classification with those of eubacteria and land plant mitochondria (mitochondria of other taxa lackSS rRNA). Plastid and cyanobacterial SS rRNAs are distinguished from those of most other eubacteria and mitochondria by a single-base insertion in helix C and a deleted base in loop c (157). Of the 121 nt of the typical SS rRNA, 110 are identical in nearly all angiosperms and gymnosperms, 73 are conserved in ferns and liverworts as well, and 29 are identical in all plastids so far sequenced with a few singular exceptions. The colorless flagellate Astasia longa and the red alga P. umbilicalis are somewhat divergent compared with Euglena gracilis and P. purpurea, respectively; 4 nt are altered in one or both of the two parasitic plants Conopholis americana and Epifagus virginiana compared with all other angiosperms; and the sequence submitted to GenBank for cotton, Gossypium hirsutum (440), is missing 2 nt but is otherwise identical to that of tobacco in all but two residues. Vogel et al. (671) reported that SS rRNA from spinach chloroplasts could be incorporated into biologically active 50S ribosomal subunits assembled in vitro from Bacillus stearothermophilus proteins and 23S rRNA. Introns in rRNA Genes A survey of 23S rRNA genes from 17 Chlamydomonas species representing most of the taxonomic groups defined on morphological and biochemical grounds (159, 538) revealed a total of 39 group I introns inserted at 12 different positions, some of which were unique to Chlamydomonas species (656658). However, no correlation was found between intron distribution and a phylogeny for these 17 species based on primary sequence of their 23S genes. Most of the intron insertion sites identified in this study are in highly conserved regions of the genome, which tend to be exposed in the assembled ribosome. This is also true of the single intron in the 16S gene of C. moewusii, which lies within the 530 loop, a part of the translational fidelity domain. In contrast, internal transcribed spacers, which have also been identified in rRNA genes of bacteria and organelles, occur within regions of variable primary sequence and secondary structure (224). When these sequences are processed out of the pre-rRNA molecule, the mature sequence is not religated, resulting in a fragmented rRNA. Three internal transcribed spacers, found at equivalent positions in the Chlamydomonas taxa studied by Turmel et al. (656-658), result in fragmentation of the 23S rRNA into four mature rRNA species, ao, ,, -y, and &. The single group I intron in the 23S gene of C. reinhardtii Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV The secondary-structure model for the E. coli 23S rRNA published by Gutell and Fox (233) consists of six domains comprising a total of 95 helices (Fig. 4; for a numberedE. coli sequence diagram in similar format to the tobacco sequence shown in Fig. 4, see references 234 and 235). Domain V is the principal site of tRNA binding to the 50S subunit (60, 426). The central loop of this domain is involved in the peptidyltransferase center and is the site of mutations conferring resistance to erythromycin, lincomycin, and chloramphenicol (see below). Some tRNA interactions are found in domains II and IV. When bound to the P site, tRNA also interacts with the 3' terminus of the 23S molecule (426). EF-G binds specifically to position 1067 in the 23S molecule, a region identified with GTP hydrolysis (465). EF-Tu protects residues in the 2660 loop. Rau6 et al. (512) identified 18 variable regions in 23S RNAs based on comparisons of eubacterial, organelle, archaebacterial, and eukaryotic large-subunit rRNAs, including the cyanobacterium Anacystis nidulans and chloroplast 23S rRNA from Chlorella ellipsoidea, Marchantia polymorpha, tobacco and maize. Of these 18 variable regions,5 are significantly different in chloroplasts compared with E. coli, while in the remaining 13 regions, chloroplast rRNAs resemble those of eubacteria but may differ from those of archaebacteria, mitochondria, and eukaryotic cytoplasmic ribosomes. Somerville et al. (581) have published a secondary-structure map of the 23S rRNA from the brown alga Pylaiella littoralis which resembles the cyanobacterial (Anacystis) molecule much more closely than it resembles those of land plants or green algae. Cladistic analysis of the 23S rRNA sequence produced a tree in which cyanobacterial and plastid sequences were clearly delineated from all other eubacterial sequences and in which the chromophyte algae (as represented by Pylaiella littoralis) and Euglena gracilis formed a common branch. In domain I, cyanobacterial and chloroplast 23S rRNAs lack helix 8 of E. coli (nt 131 to 148, variable region V1) and have an insertion between helices 13 and 14 (E. coli nt 271 to 365, variable region V2) which can be folded into a helix (512). In domain II, variable regions V4 and V7 (nt 636 to 655 and 1020 to 1029, respectively) are highly conserved among eubacteria and chloroplasts, while 3 nt (nt 931 to 933) in E. coli V6 are replaced by a loop of 5 to 20 nt in chloroplasts. Region V8 (nt 1164 to 1185) is conserved in E. coli, Anacystis nidulans, and most chloroplast 23S rRNAs but is the site of a possible 243-nt intron in Chlorella ellipsoidea (726). Gutell and Fox (233) have suggested that this insertion may actually be a part of the rRNA rather than the only known instance of an intron inserted in a variable rRNA region. Domain III comprises variable regions V9 to V12, of which Vii (E. coli nt 1521 to 1542) is the most diverse in chloroplast 23S rRNAs. Some (but not all) chloroplast rRNAs have lost part of helix 54, and helix 55 in Chlorella ellipsoidea and Z. mays contains insertions compared with E. coli; however, in other chloroplast genomes, this helix is similar in size to that of E. coli. Domain IV shows strong conservation among eubac- PROTEIN SYNTHESIS 710 MICROBIOL. REV. HARRIS ET AL. AAAUUac cu A AB BAA U-A G eUAAGAAG I II I I *I VI I tcc A AUUUC a A I II I I - AcUoUUUC%cccuu OGAAUBCAAA A u c c GTPase center Ue c a UUA UCOB G UA ABCC a OAA Cu AGGCGC ,,|"III 0UC0CB _UBAAG A U-A U A u-C -c u~~~~~~~~~ A~~~~~~~~ a u Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV A A AU aAU u u 0-C 0-C O-C A-U -1 B 6-C A A 0 U0 ViOA BA% GOCC BUC CC0ABzG0ACQ%%.IA ZqGCCCCCUUBUUBa °scU r Buu CUC AcC IIIIII,I*I I I1111 I AA CA V9 0AU aa4AusUC UBUC GBOA AAABBCPUA Aa CCBA CUAAAU UG.LCACAG A ACC A A AAAf GU CAU V7 C II UUBG 111111- A 'ac GUUUA u AB-U AAC 1G1 A[q OCCUCCU' AAC U A UB' C-B V12 III ~~~domain C A A .UE C CA _sC-B c U AA uuC-Gc UI-C _ _Ca I f 3'fn bAA V6 domain I V3 domain 11 e AA Aa CAA c u C=U a-B AA U-A B-C C-B tobacco 23S rRNA, 5' V2 AAC-BGBUUBU a oil 11|1 A -QU 11, AAA' 0-2 ._ FIG. 4. Secondary structure of tobacco 23S rRNA, showing major functional domains and sites of antibiotic resistance (Table 2). Variable regions are numbered according to the system of Raue et al. (512). Sequence from the Ribosomal Database Project, courtesy of Robin Gutell. VOL. 58, 1994 CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS 711 UC U * G C-a C-C UCG-C a-C A AG C uu V5 AICUA LL C,1 3UGG A G-CA domainIV UCACCTf C CU U- UAGAG c-a U-A U-A C-a c-a G GGA GA a-Cu G GA 0U u U-A V13 A A u.G tu a V16 a G-CUA Accuu U UCUCGGAC G-CC C I I * I°I -II G U -UGACAG A G0-Cc aC U-A - c-a C - a G aa A CCA o A A A A cC-O cU G U-A GC Gu UC- aU GOA AG CG U-A C I-C U AA- U Uuca c U: U-A U -c C II C a G AU C 1 G*U GU c -Ga U G A-AA AU : : C U-A U-A0 G G-CUA U-A CG-C U AGUC CAa U-AA A A aUu A A C AUA GaO A ACG GU aUUC AC UGC. I III ACG aC G_.C CC AC-G GAU AU C AA C A peptidyl GGCUGAUCUUCCCCACCU It C 1I. 1i1i1iI transferase caUC GAAC A a domain VI Ac UU u C u 3A Ac cA UC 5' 4.5S A UC CAUGG UGUGGCUG U AAGCCACC UUAU A-UA BC-U A CAUU -U C-G a-*U 'A UtU G0GACCUUGUA U C A U-A tobacco 23S rRN IA, 3 a Ua-C C-a A A c CA- U U%GCCGA Gc CC--G U. a C=a ACGGCGAG 11111 A A aG G A G-C _A a ~~~U C Aa-c u GUaA a 0C -GU Ac .A 'C C-G C=G C' CU UUG Aa C0 A U GA A-U U aG C-C U-A CGU (522) is mobile (142) and encodes a double-stranded nuclease (I-CreI) which has been purified and shown to have a 19- to 24-bp recognition sequence in this gene (143, 638). The enzyme makes a 4-bp staggered cut just downstream of the intron insertion site and will tolerate single- and even multiplebase-pair changes (143). This intron can undergo autocatalytic splicing in vitro (637). The ac-20 nuclear gene mutant of C. reinhardtii, which was initially characterized as deficient in chloroplast ribosomes (see reference 247 and references therein), has been found to accumulate unspliced precursor rRNA molecules, as well as unspliced precursors of the chloroplastencoded psbA gene (258, 259). Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV domain IV A -C 712 HARRIS ET AL. The 23S rRNA gene of C. eugametos, a species now thought to be only distantly related to C. reinhardtii, contains six group I introns and three internal transcribed spacers (657). One optional 955-bp group I intron in the 23S gene of C. eugametos also appears to be mobile and is transmitted to all progeny of crosses with the interfertile species C. moewusii, which lacks this intron (347). The 402-bp group I intron in the 16S rRNA gene of C. moewusii likewise can be transmitted in crosses to The 16S-23S Spacer The spacer regions between the 16S and 23S rRNA genes in chloroZlasts and cyanobacteria contain tRNAIleGAU and as do the E. coli rmA, mD, and rmH operons tRNA aUGcm (301, 436, 697, 735). In E. coli and cyanobacteria, the 16S-23S spacer is short (<550 bp), but in land plants and charophyte algae it is 1 to 2 kb or more, largely because of the presence of type II introns in the two spacer tRNA genes (110, 311, 320, 394, 628). In all other algae so far examined, these spacer tRNAs are uninterrupted (108, 216, 384, 405, 551, 725). In C. 1,100-bp region between the 3' end of the 16S dispersed repeat elements in direct and inverted orientations, which are capable of pairing to generate extensive secondary structure in the precursor RNA (551). Similar repeat elements are found elsewhere in intergenic regions of the chloroplast genomes of C. reinhardtii and the interfertile species C. smithii, and variations in their numbers are responsible for most of the restriction fragment length polymorphisms between the chloroplast genomes of these isolates (50, 250, 486). The absence of these repeats in chloroplast rRNA operons of other organisms, including C. eugametos and C. moewusii, and their variation in number in the 16S-23S spacer region between C. reinhardtii and C. smithii suggest they are not essential for processing of the rRNA reinhardtii, an gene and tRNAIle contains short precursor. Although the 16S and 23S rRNA genes in the plastid euglenoid flagellate Astasia longa are highly homologous to those of Euglena gracilis, the spacer between these genes appears to lack tRNAIle and tRNAAla (569). The chloroplast genome of Chlorella ellipsoidea was also reported to lack the spacer tRNAAla (724), but subsequent analysis has shown that the rRNA operon in this alga has been genome of the colorless disrupted by an inversion of a 5-kb region with a breakpoint between the two tRNAs, so that the 5S, 23S, and tRNAMa genes constitute a second operon on the opposite strand from the 16S and tRNAIle genes (723, 725). tRNAs Flanking the rRNA Operons Genes encoding tRNAs are also often found in regions flanking the rRNA operons, but their presence and identity are much more variable than for the two tRNA genes in the 16S-23S spacer. There is a tRNAVa" proximal to the 5' end of the 16S rRNA gene in all land plants examined (114). This gene, which precedes the promoter for the rRNA operon, is not present in C. reinhardtii or C. moewusii, nor is it found upstream of any of the E. coli rm operons or in any of the cyanobacterial sequences to date. In Euglena gracilis, the equivalent tRNAVal is in a gene cluster distant from the rRNA operons (477), and a pseudo-tRNAIle is found 5' to the 16S gene (479). In land plants the 5S rRNA gene is typically followed by a tRNAN9 gene in the same orientation and by a tRNA,sn gene on the opposite strand (118, 297, 298, 305, 557). In maize, primer extension experiments have shown that the tRNA'9 gene, which is separated from the 5S gene by a 252-bp spacer, is cotranscribed with the rRNA operon (118). This operon and the tRNA In gene, which is distal to tRNAArg by 253 bp on the opposite strand, are thought to share a common terminator region consisting of a palindromic sequence which can be folded into hairpin structures on both strands. Antibiotic Resistance Mutations in the Chloroplast rRNA Genes Many antibiotics that inhibit bacterial protein synthesis bind specifically to the 16S or 23S rRNA molecules (102, 424, 425), and mutants resistant to these antibiotics have been shown to result from single-base-pair changes in evolutionarily conserved regions of the genes encoding these RNAs in bacteria, mitochondria, and chloroplasts (Table 2). Streptomycin resistance can result from changes at several nucleotides clustered in three sites in the 16S chloroplast rRNA molecule of land plants and green algae (equivalent to E. coli residues 13, 523 to 525, and 912 to 915). Although these three sites are widely separated in the primary sequence, they interact with the same subset of ribosomal proteins and are thought to be in close proximity in the assembled 30S subunit of E. coli (603). Spectinomycin resistance has been shown to result from mutations at the bases of the chloroplast 16S rRNA equivalent to E. coli residues 1191 to 1193 and at the base equivalent to residue 1064, which pairs with 1192. Neamine and kanamycin resistance in C. reinhardtii can result from mutations at the chloroplast 16S rRNA nucleotides equivalent to E. coli residues 1408 and 1409. In E. coli, binding of aminoglycoside antibiotics to this region has been demonstrated (424, 717), and site-directed mutagenesis of these and neighboring bases has been used to obtain a number of mutants (116). Because the E. coli genome has seven rm operons, antibiotic resistance mutations must be selected by expression of cloned rRNA operons on high-copy-number plasmids (570, 603). In contrast, an efficient copy correction mechanism involving the inverted repeat ensures that newly occurring 16S mutations can spread to both rRNA cistrons in the chloroplast genome (50). Erythromycin resistance mutations in the large subunit rRNA are known in bacteria, in mitochondria of Saccharomyces cerevisiae and mammalian cells, and chloroplasts at the Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV isolates of the sibling species C. eugametos that lack this intron (140). Transmission of these introns is often accompanied by coconversion of flanking DNA polymorphisms. The mobile intron in the 23S gene encodes a double-stranded DNA endonuclease activity (I-CeuI) which has a 19-bp recognition site centered around the insertion site. I-CeuI produces a staggered cut 5 bp down from the insertion site (200, 406, 407). The 23S rRNA gene of C. humicola has a group I intron, ChLSU-1, inserted at a site in the peptidyltransferase loop and encoding a putative 218-amino-acid endonuclease (96). Introns have been found at this site only in a few Chlamydomonas species (658). Turmel et al. (658) discuss the alternative possibilities for transfer of group I introns from one site to another within a genome. Intron-encoded endonucleases could effect such a transfer at the DNA level (139); alternatively, a reversal of self-splicing followed by reverse transcription of the recombined RNA could occur, followed by integration into DNA by homologous recombination. The latter mechanism requires only a short target site that can pair with the 5' intron sequence called the internal guide sequence (718) and would be consistent with the position of intron insertion sites in exposed rRNA regions in the ribosome in the Chlamydomonas species examined by Turmel et al. (658). MICROBIOL. REV. VOL. 58, 1994 CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS 713 TABLE 2. Antibiotic resistance mutations in chloroplast rRNA and ribosomal protein genes compared with analogous mutations in E. coli and mitochondria Taxon' Nucleotides Reference(s) 16S rRNA mutations to streptomycin resistance E. coli wild type E. coli mutant E. coli mutant C. reinhardtii wild type C. reinhardtii mutant E. coli wild type E. coli mutant Nicotiana plumbaginifolia wild type N. plumbaginifolia mutant Nicotiana tabacum wild type N. tabacum mutant C. reinhardtii wild type C. reinhardtii mutant C. eugametos wild type C. eugametos mutant E. coli wild type E. coli mutant E. coli mutant E. coli mutant E. coli mutant E. coli mutant E. coli mutant Euglena gracilis wild type E. gracilis mutant Mycobacterium tuberculosis M. tuberculosis resistant isolate Nicotiana plumbaginifolia wild type N. plumbaginifolia mutant N. tabacum wild type N. tabacum mutant N. tabacum mutant C. reinhardtii wild type C. reinhardtii mutant C. reinhardtii mutant C. reinhardtii mutant 905 UAAAACUCAAAUGA 905 . . 905. G. 905 . U 905 . C 905 . ... G 905 . ... 869 UGAAACUCAAAGGA 869. U. 858 UAAAACUCAAAGGA 858. G. 854 UGAAACUCAAAGGA 854. U. 853 UGAAACUCAAAGGA 853. A. 853. U. 849 UGAAACUCAAAGGA 849. U. 849 . C 849 .G 16S rRNA mutations to spectinomycin resistance N. tabacum wild type N. tabacum mutant N. tabacum wild type N. tabacum mutant N. tabacum mutant N. tabacum mutant C. reinhardtii wild type C. reinhardtii mutant C reinhardtii mutant C. reinhardtii mutant E. coli wild type E. coli mutant E. coli mutant E. coli mutant Zea mays (naturally resistant) N. tabacum wild type N. tabacum mutant 1006 1006 1133 1133 1133 1133 1118 1118 1118 1118 1186 1186 1186 1186 1132 1326 1326 16S rRNA mutations to neamine and kanamycin resistance C. reinhardtii wild type C. reinhardtii mutant C. reinhardtii mutant 1332 CGCCCGUCACACCAUGGA 1349 137 251 1332 ...............G.1349 1332 251 1349 ........ 23S rRNA mutations to erythromycin and/or lincomycin resistance C. reinhardtii wild type C reinhardtii mutant C. reinhardtii mutant E. coli wild type E. coli mutant 2007 CUGGACAGAAAGACCC 2022 2007 2022 2007 2022 2050 CAAGACGGAAAGACCC 2065 2050 2065 . ......... ...... 21 21 21 22 22 534 534 482 482 481 481 485 485 .....C ...... 918 918 918 918 918 918 918 882 882 871 871 867 867 866 866 866 862 862 862 862 66 493 493 137 251 66 420 729 643, 644 646 184 137 251 199 199 66 431 343 493 37 493 343 217 428 131 131 729 643, 644 646 160 184 137 251 251 251 GCUGUCGUCAGC 1017 646 ...... 1017 182 GGAUGACGUCAAGU 1146 646 ..... 1146 620 ...........U.1146 620 ....... 182 1146 GGAUGACGUCAAGU 1131 137 1131 ....... 249, 251 1131 ....... 249, 251 ....... 1131 249, 251 GGAUGACGUCAAGU 1199 64 ...........U.1199 26, 387, 570 ...... .. ...G .1199 26, 387 ...........A.1199 26, 387 GGAUGAGGCCAAGU 1145 554 GUUCCCGGGCCUUGUAC 1341 646 ....... ... .. 620 1341 .... .. ..... ..... ......... ....... ..... ........ ...... ....... ..... 346 251 251 65 158 Continued on following page Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV JUGAAGAGUUUGAUCAUG A. . C. AUGGAGAGUUUGAUCCUG 5 . G. 517 GCCAGCAGCCGCGGUAAU 517 ......C........... 465 GCCAGCAGCCGCGGUAAU 465. U. 464 GCCAGCAGCCGCGGUAAU U 464 . ....... 468 GCCAGCAGCCGCGGUAAU 468 C. .......... GCCAGCAGCCGCGGUAAU 4 4 4 5 714 HARRIS ET AL. TABLE 2-Continued .. Reference(s) 2 570 . .............. 2065 132 . .............. 2065 99 CUGGACAGAAAGACCC 99 ........G..... ......99 See 100 GCAGACGGAAAGACCC 1958 See 100 . . G....... 1958 65 CAGUUCGGUCCCUAUC 2616 667 2616 ..........u 346 CAGUUUGGUCCAUAUC 2574 251 2574 ..........U 251 ..........G..... 2574 199 CAGUUUGGUCCAUAUC 199 .......... See 100 CAGUAUGGUUCCUAUC 2790 2790 See 100 . ........ G 100 2790 .......... Nucleotides Taxona 2050 2050 1943 1943 2601 2601 2559 2559 2559 ..... ..... ..... 2775 2775 2775 ..... Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV E. coli mutant E. coli mutant Nicotiana plumbaginifolia wild type N. plumbaginifolia mutant N. plumbaginifolia mutant Saccharomyces cerevisiae mitochondria wild type S. cerevisiae mutant E. coli wild type E. coli mutant C. reinhardtii wild type C. reinhardtii mutant C. reinhardtii mutant C. moewusii wild type C. moewusii wild type S. cerevisiae mitochondria wild type S. cerevisiae mutant S. cerevisiae mutant MICROBIOL. REV. 23S rRNA mutations to chloramphenicol resistance E. coli wild type E. coli mutant C. reinhardtii wild type C. reinhardtii mutant S. cerevisiae mitochondria wild type S. cerevisiae mutant S. cerevisiae mutant 65 2499 CUCGAUGUCGG 2509 158, 425 2509 .... 2499 346 2509 CUCGAUGUCGG 2519 2519 208 2509 ..... See 158 2672 CUCGAUGUCGA 2682 .2682 See 158 .. 2672 See 158 2682 2672 ..... S12 mutations to streptomycin resistance and dependence E. coli wild type E. coli mutant (sr) E. coli mutant (sr) E. coli mutant (sr) E. coli mutant (sr) C. reinhardtii wild type C. reinhardtii mutant (sr) E. coli wild type E. coli mutant (sd) E. coli mutant (sr) E. coli mutant (sd) E. coli mutant (sd) C. reinhardtii wild type C. reinhardtii mutant (sd) N. plumbaginifolia wild type N. plumbaginifolia mutant (sr) N. tabacum wild tpe N. tabacum mutant (sr) 38 TTTPKKPNSA 38 .... N. Q. 38 . Q.. 38 .... R. 38 .... T. 38 TVTPKKPNSA 38 .... T. 83 GGRVKDLPGV .. 83 .S 83 .... R. L 83 . D. 83. 83 GGRVKDLPGV L 83 . 83 GGRVKDLPGV 83 .... R. 83 GGRVKDLPGV .S 83 a .... .. .... ... 47 47 47 47 47 47 47 92 92 92 92 92 92 92 92 92 92 92 707 188 190 188 190 364 364 707 285 188 662 285 364 364 276 276 561 191 sr, streptomycin resistance; sd, streptomycin dependence. positions equivalent to E. coli nt 2057 to 2058 (the yeast rib3 locus) and 2611 (yeast rib2) (Table 2). Some of the erythromycin-resistant mutants of C. reinhardtii are cross-resistant to lincomycin. A lincomycin-resistant mutant of Nicotiana plumbaginifolia has also been identified at the base equivalent to E. coli nt 2032. Chloramphenicol resistance in C. reinhardtii results from a nucleotide substitution at a position equivalent to E. coli nt 2504 (208). Chloramphenicol resistance mutations at this site are also known in mitochondria of yeast (the rbl locus) and mammals. All three regions of conserved sequence together form a loop known to be involved in peptidyltransferase activity in E. coli (464). Chloroplast antibiotic resistance mutations have been used as markers in generation of transgenic tobacco plants by using somatic cell fusions (427) and in chloroplast transformation of Chlamydomonas species (48, 49, 453) and of tobacco (390, 619) by using biolistic techniques. RIBOSOMAL PROTEINS Number and Nomenclature Recent reviews provide an overview of chloroplast ribosomal proteins and the genes that encode them (36, 377, 379, 606, 608, 609, 615). For a concise summary of structure and function of individual ribosomal proteins, with emphasis on the E. coli ribosome, see the review by Liljas (358). Lindahl and Zengel (360) provide a review of bacterial genes for ribosomal proteins. Chloroplast ribosomal proteins were initially identified from various plants and algae by one-dimensional and two-dimensional gel electrophoresis and were numbered according to their migration on these gels, a function of charge and/or molecular mass, depending on the gel system. Natural variations in the physical properties of ribosomal proteins themselves, together with differing electrophoretic conditions used for their separation, have meant that no two numbering VOL. 58, 1994 CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS Organization of Chloroplast Ribosomal Protein Genes The first suggestion that chloroplast genomes might encode chloroplast ribosomal proteins came from labeling experiments carried out in the presence of inhibitors specific for either chloroplast or cytoplasmic protein synthesis. These studies led to the then remarkable conclusion that in land plants, Euglena gracdiis, and C. reinhardtii about one-third of the chloroplast ribosomal proteins were themselves synthesized- on chloroplast ribosomes, with the remainder being made on cytoplasmic ribosomes and imported (121, 156, 181, 239, 495, 547). With a few notable exceptions, the same subset of ribosomal proteins is encoded in the chloroplast genome of each land plant examined, while marked variations occur in certain algal groups (see below). The genes encoding many of these proteins are arranged in clusters that are clearly remnants of the ribosomal protein operons of eubacteria (Fig. 5) (see references 36, 377, 606, and 608 for additional discussion). The Porphyra plastid genome has the most complete version of these operons found to date (Fig. 5; Table 3) (514, 517). Most of the same genes are also present in the cyanelle genome, but the operon has been broken into three pieces (598). In land plant chloroplasts the largest cluster contains the genes for ribosomal proteins L23, L2, S19, L22, S3, L16, L14, S8, L36, and S11 and the RNA polymerase gene rpoA in the same order that they appear in the E. coli S10, spc and a operons, which are part of the str cluster (Fig. 5; see Table 3 for references). A similar organization of genes encoding ribosomal proteins is seen in the Marchantia mitochondrial genome (630). The rps4 and rpsl4 genes are also found in chloroplast genomes of land plants but are relocated outside the ribosomal protein cluster. In some legumes, rp122 has been removed from this cluster and relocated to the nucleus (193), and in a number of dicots the chloroplast rp123 gene is disrupted and probably nonfunctional (see below). The rp122 gene is also missing from this operon in Chlamydomonas species (43, 277). In Euglena gracilis (242) and in both C. reinhardtii and C. moewusii (43, 277), the ribosomal protein gene cluster also contains rplS, which does not appear to be present in the chloroplast genomes of land plants. However, the Euglena operon lacks rpsll, which is now in a separate operon with rps4 (242, 597). The Chlamydomonas operons lack rps3, but open reading frames with homology to rps3 are found elsewhere in the chloroplast genome (see below). In C. moewusii, the large ribosomal protein cluster has been disrupted by a rearrangement such that rp123, rpl2, and rpsl9 are separated from rplJ6, rpll4, rplS, and rps8 by about 42 kb (43). The genes encoding S17, L24, and L15, which are part of these operons in bacteria, have been identified in the nuclear genomes of certain land plants (153, 196, 640). The remaining genes of these E. coli ribosomal protein operons (encoding proteins L17 and L30) have not been identified with plastid equivalents thus far. In E. coli, the genes encoding S12, S7, and the elongation factors EF-G and EF-Tu constitute a fourth operon in the str cluster (Fig. 5). This operon has undergone several alterations in the course of plant evolution. It persists intact in cyanobacteria (422, 641), but the fiusA gene encoding EF-G is absent from all chloroplast genomes analyzed so far and has presumably been relocated to the nucleus. In Cyanophora paradoxa, the cyanelle str operon includes rpsl2, rps7, tufA, and rpslO, which are processed from a primary transcript into two dicistronic mRNAs (68, 69, 368). The rpslO gene is also downstream from tufA in Porphyra and Cryptomonas species (517). In the Euglena chloroplast, the rpsl2 and rps7 genes constitute one operon and the tufA gene remains adjacent but is separately transcribed (430). In land plants, where tufA is a nuclear gene (15), the rpsl2 gene has been split, with the second and third exons remaining proximal to rps7 and the first exon encoded separately downstream from rpl20 (183, 187, 649). Lew and Manhart (352) have recently reported that the rpsl2 gene is also split in a green alga, Spirogyra maxima. This alga is believed to represent a relatively early stage in the charophyte lineage leading to land plants. The rpsl2 mRNA is assembled by trans-splicing (264, 313, 737). In three species of the angiosperm genus Anemone, the second rpsl2 intron has been lost secondarily, in conjunction with expansion of the inverted repeat and several inversions within the chloroplast genome (269). In two Chlamydomonas species, the rpsl2 operon has been further disrupted. In C. reinhardtii, the uninterrupted rpsl2 gene (364) is separated from tufA by about 40 kb and is cotranscribed with the psbJ and atpI genes encoding photosynthetic proteins (253, 572). The entire rps7 gene is located in the other single-copy region about 50 kb away, 5' to and cotranscribed with the atpE gene (253). In C. moewusii, rpsl2, rps7, and tufA are also widely separated; both rps7 and rpsl2 have been completely sequenced and are uninterrupted (655). Most of the remaining chloroplast-encoded genes for ribosomal proteins are transcribed either separately or in operons that also contain genes for photosynthetic proteins (606, 608). The rp133 and rpsl8 genes are cotranscribed in land plants, whereas the corresponding genes in E. coli are each part of a different operon. The rpl21 gene, which is monocistronic in the Marchantia chloroplast genome (312), has not been found in Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV schemes are the same. Even the well-characterized ribosomal proteins of E. coli are not numbered according to their migration on two-dimensional sodium dodecyl sulfate-polyacrylamide gels. Since most of the chloroplast ribosomal proteins identified on gels have not yet been correlated with sequenced genes, organism-specific terminologies are sometimes used, e.g., the numbering system of Mache et al. (378) and Dorne et al. (119, 120) for spinach, the system of Capel and Bourque (73) for tobacco, and that of Schmidt et al. (547) for C. reinhardtii. When used here, such designations will be given in quotation marks as "L-13," etc. However, in cases in which equivalence has been established, designations of the chloroplast ribosomal proteins and the genes encoding these proteins have been changed to indicate the E. coli ribosomal proteins to which they correspond. For example, seven of the ribosomal proteins from chloroplast ribosomes of spinach have been purified by Schmidt et al. (540) and shown by N-terminal sequencing to be equivalent to seven E. coli proteins (S12, S16, S19, L20, L32, L33, and L36), whose homologs are encoded by chloroplast DNA. Those chloroplast and nuclear genes encoding chloroplast ribosomal proteins corresponding to those of E. coli are designated rps- or rpl- followed by numbers equivalent to the similar bacterial ribosomal protein designation (S1 to S21 for small-subunit ribosomal proteins and Li to L36 for large-subunit ribosomal proteins [241, 606]). Thus, rps4 encodes protein S4 and corresponds to E. coli rpsD, rpl2 encodes protein L2 (E. coli rplB), etc. Previous estimates of the number of chloroplast ribosomal proteins in the small and large subunits have been in the range of 22 to 31 and 32 to 36, respectively (73, 119, 156, 495, 547), i.e., at least as many as in E. coli, in which 21 and 33 proteins have been identified in the small and large subunits, respectively. Part of the variability in these estimates is undoubtedly the result of differing isolation and electrophoretic conditions. In some circumstances these factors may cause certain proteins, particularly those of higher molecular weight, to be excluded from gels (see references 510 and 547 for discussion). 715 716 MICROBIOL. REV. HARRIS ET AL. S10 str E. coil operons 812 LI fE tf 18D 810 123 810L225183 IL16 Cyanophora L EJuf 812D 810 L3 L2 81L22 Porphyra 81 IEI 810 18 L4 L23 L2 Euglena C. relnhardtll 83 I L16 8 A EjJiJ1 83 16 12 A 812j[E E.J i] Ri~JEE] Marchantla 812' 1! Nicotlana 8 i 819 1 alpha apC 814 88 16118 15ER| Porphyra 114 Euglons E1 rEli 88 16 116 85 IE130 &K1S lIlI 136 I 1~~~~ 8131111 || S4 IiFPOAII 117 I ElbElJ_rpo 85 88 188 ELE16 E 1L16 123123T12~J[ 19[GITi S i3 | 16 i~jr~I3I j1 E coil operons EjE7 83 EREEJ~~ rpo _JE C. relnhardtll EE1 Marchantla _136 | Epifagus Nicotlana ES FIG. 5. Conservation of ribosomal protein gene clusters in chloroplast genomes, showing retention of some (but not all) genes of the closely adjacent str, S10, spc, and a operons of E. coli (12), in Cyanophora paradoxa (598), P. purpurea (514, 517), Euglena gracilis (243), C reinhardtii (43, 277), Marchantia polymorpha (471), Epifagus virginiana (712, 714), and Nicotiana tabacum (560). Shaded boxes indicate genes that have been lost from the corresponding operon but have been identified elsewhere in a given plastid genome. For example, rps7 and tuf4 are present in the C reinhardtii chloroplast genome but have become separated from rpsl2. In Cyanophora paradoxa and P. purpurea, the operon begins with the rpl3 gene (A) and ends with the rpsl2, rps7, tufA, and rpslO genes (517, 598). The rpsl2 gene in land plants is split, and the 3' portion of the gene remains proximal to rps7. the Euglena, rice, or tobacco chloroplast genomes (243, 265, 560) and has been identified as a nuclear gene in spinach (408, 578). Conversely, rpsl6 is a chloroplast gene in all angiosperms so far examined and in Euglena, Cyanophora, and Porphyra species (Table 3) but is absent from the Marchantia and Pinus thunbergii chloroplast genomes (614, 654). In E. coli and Bacillus subtilis, as well as in the cyanobacterium Synechocystis sp., the genes encoding Li, L10, Lll, and L12 are clustered (539, 564). The rpll, rplll, and rp112 genes also form a cluster in the cyanelle genome, but rpllO is apparently missing (32). The rpoB and rpoC genes, which are part of the same cluster in E. coli, were found elsewhere in the Synechocystis genome and in the cyanelle genome. None of these four ribosomal protein genes has been found in any land plant chloroplast genome, but rpl12 is now known to be a chloroplast gene in Euglena gracilis, located some distance from the rpoB and rpoC genes (243). Correspondence of Chloroplast Ribosomal Proteins to Bacterial Ribosomal Proteins Of the 54 ribosomal proteins that constitute the E. coli ribosome, the chloroplast equivalents of 44 have been identified by sequencing of nuclear or chloroplast genes from one or more organisms (Table 3). Derived amino acid sequence identities for these proteins with their equivalents in E. coli are mostly in the range of 35 to 55%, with S12 showing considerably greater conservation (Table 3). In addition, at least three distinct genes for chloroplast ribosomal proteins that show no obvious sequence similarity with any bacterial ribosomal protein have been found in the nuclear genomes of pea and spinach (192, 290, 741). In general, the chloroplast-encoded ribosomal proteins show greater immunological cross-reactivity with bacterial ribosomal proteins than those encoded in nuclear genes (510). The chloroplast-encoded proteins also show somewhat greater sequence identity to their counterparts fromE. coli than do the nucleus-encoded ones (Table 3). Subramanian et al. (608) made the interesting point that of 15 ribosomal proteins that can be individually eliminated by mutation in E. coli without total loss of viability (103, 104), the equivalent of only one, L33, is chloroplast encoded in land plants. They suggest that location of particular chloroplast ribosomal protein genes to the nuclear or chloroplast genome may be related to the essential roles of these proteins in ribosome assembly or function. In the following section we discuss each ribosomal protein in turn, briefly describing what is known about its function and structure in bacteria and indicating the chloroplast equivalents that have been identified. Table 3 provides a summary of references for sequence information to complement this text. Proteins of the Small Subunit Protein SI is essential for mRNA binding in E. coli and may play an important role in initiation of translation of mRNAs that lack a Shine-Dalgarno sequence (604, 666). The gene Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV Epifagus Cyanophora 129 VOL. 58, 1994 CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS 717 TABLE 3. Chloroplast and cyanobacterial ribosomal proteins that have been identified by gene or protein sequence Proteina Taxon GenBank accession no(s). E. Locationa colib N. tabacumb Reference(s) %S %I %S Si S2 Porphvra purpurea -a oeraea Spinacia oleracea -Spra X16004, X75651 X64567 (partial) X61798, M81884 X70810, Z11874 X04465 Z00044 X15901 X05917, X03912 X05916 X53651 M35396 X17318, X52270 49 26 59c 38c 517 48 22 100 100 178 C C C C C C C C C C C 52 31 56 C C 66 58 57 63 61 58 61 66 61 84 59 59 48 38 35 45 41 37 42 47 40 71 39 39 65 92 60 83 100 87 94 70 95 60 86 87 33 566 634 49 598 85 435,712,714 40 88, 243 73 659 100 560, 561 79 265 87 97, 278 50 517 92 278 42 536 78 267 79 282, 587, 588 S3 Chlamydomonas reinhardtii 5' X66250 Chlamydomonas reinhardtii 3' X66250 M30487 Cyanophora paradoxa M81884 Epifagus virginiana Euglena gracilis X70810, Z11874, M37463 Gracilaria tenuistipitata M32638 Marchantia polymorpha X04465 Nicotiana tabacum Z00044 X15901 Oryza sativa Porphyra purpurea X13336 Spinacia oleracea Zea mays Y00340, M31336 C C C C C C C C C C C C 44 57 72 60 69 64 67 64 66 68 65 65 25 36 51 35 51 46 43 39 40 51 42 40 49 25 172, 366 56 34 172, 366 67 47 423 84 75 712,714 58 35 88, 243 65 43 294 76 62 186 100 100 560, 561 83 70 265 69 46 517 95 89 742 84 72 417 S4 Chlamydomonas reinhardtii Chlorella ellipsoidea Cryptomonas 4) Cyanophora paradoxa C C C C C C C C C C C C 59 65 64 63 56 56 61 58 61 62 58 59 38 44 44 41 35 35 38 36 38 38 38 38 64 48 277, 511 66 52 734 72 58 127 74 59 32 85 76 712, 714 70 51 243 83 76 659 100 100 560, 561 89 80 265 72 56 517 95 92 22, 742 88 79 610 C C 64 42 65 39 423 517 C 57 28 517 Epifagus virginiana Euglena gracilis Marchantia polymorpha Nicotiana tabacum Oryza sativa Porphyra purpurea Spinacia oleracea Zea mays S5 Cyanophora paradoxa Porphyra purpurea S6 Porphyra purpurea S7 Anacystis nidulans Astasia longa Chlamydomonas moewusii Chlamydomonas reinhardtii Cryptomonas 4) Cuscuta reflexa Cyanophora paradoxa Epifagus virginiana Euglena gracilis Glycine max Marchantia polymorpha Nicotiana tabacum Oryza sativa Porphyra purpurea Spirodela oligorhiza Spirogyra maxima Spirulina platensis D10997 X51511 M81884 X70810, Z11874, M22010 X04465 Z00044 X15901 M16878 X01608 M30487 X17442 X14385, X75652 X53977 (partial; see text) X52912 X72584 X52497 M81884 X70810, X06254, X00480 X07675, X05013 X04465 Z00044, M19073 X15901 X04508 (partial) L07932 X15646 C C C C C C C C C C C C C C C 69 48 60 56 69 62 67 62 62 63 66 62 60 67 54 26 38 37 49 43 49 43 40 43 43 43 43 48 72 50 64 63 70 100 71 95 62 99 88 100 92 72 66 48 82 69 55 72 52 29 42 44 55 98 53 91 41 97 78 100 85 58 422 565 655 509, 519 122 237 326 712, 714 243, 430 672 659 560,561 265 517 498 71 352 54 72 Continued on following page Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV Astasia longa Conopholis americana Cyanophora paradoxa Epifagus vitginiana Euglena gracilis Marchantia polymorpha Nicotiana tabacum Oryza sativa Pisum sativum Porphyra purpurea Spinacia oleracea Spirulina platensis Triticum aestivum Zea mays X66135, M82923 %I C N 718 MICROBIOL. REV. HARRIS ET AL. TABLE 3-Continued N. E. GenBank accession no(s). Taxon Protein' Location" colib tabacumb Reference(s) %S %I %S %I S8 Zea mays M17841 C 60 43 92 Astasia longa X16004, X75651 C C C C C C C C c C C C C 60 65 69 68 62 62 67 65 34 44 46 46 38 48 46 42 62 72 53 62 41 51 37 41 c c c c 62 42 62 41 64 44 122 598 243 517 C C C 71 52 71 50 72 49 122 68, 451, 452 517 C C C C C C C C C C 72 71 58 72 71 72 72 72 72 72 S9 S10 Sil X13336 X06734 Cryptomonas 4D Cyanophora paradoxa Euglena gracilis Porphyra purpurea X52912 (partial) Cryptomonas 4D Cyanophora paradoxa Porphyra purpurea X52912 Cyanophora paradoxa Epifagus virginiana Euglena gracilis Marchantia polymorpha Nicotiana tabacum Oryza sativa Pisum sativum Porphyra purpurea Spinacia oleracea Zea mays S12 X16548 M30487 M81884 X70810, Z11874 X04465 Z00044 M60180 (partial) X15901 Anacystis nidulans Chlamydomonas reinhardtii Cryptomonas 4D Cuscuta reflea Cyanophora paradoxa Epifagus virginiana Euglena gracilis Glycine max Marchantia polymorpha Nicotiana plumbaginifolia Nicotiana tabacum Oryza sativa Pinus contorta Porphyra purpurea Spinacia oleracea Spirodela oligorhiza Spirogyra maxima Spinulina platensis Triticum aestivum Zea mays X70810 X52143, M35206 M81884 X70810, Z11874, M22010 X04465 Z00044 X15901 X15645, X05029 X03496 M35831 X17442 M29284 X52912 X72584 (partial) X52497 M81884 X70810, X00480, X06254 X07675, X05013 X04465, X03661, X03698 L12250, L12366 X03481, Z00044 X15901 L28807 (partial) (partial) X04508 (partial) L07931, L07932 X15646 X54484 (partial) X60548, M17841, M17842 S13 Cyanophora paradoxa Porphyra purpurea S14 Astasia longa Chlorella ellipsoidea Chlorella-like alga Cyanophora paradoxa X16004, X75651 D10997 M74441, M81884 Epifagus virginiana X61798 X70810, Z11874, X15240 Euglena gracilis C C C C C C C C C C C C C C C C 53 54 38 51 55 52 54 55 54 52 64 38 69 53 67 47 67 47 89 84 64 44 78 59 100 100 86 68 89 86 72 55 598 90 83 712, 714 69 44 243, 477 89 79 186, 659 100 100 560, 561 87 74 265 93 84 504, 506 74 55 517 99 90 571 88 73 401 82 74 89 76 68 84 82 73 90 83 77 82 78 81 79 79 79 77 67 69 70 71 71 71 67 88 92 85 98 94 100 - d 94 80 73 88 81 73 90 82 74 88 C C 79 67 93 C C 71 54 73 52 C C C C C C 62 65 64 65 56 61 76 47 79 79 566 277 69 423 712, 714 88, 243 186 560, 561 715 265 517 742 400 46 68 50 67 48 65 46 71 39 94 42 61 81 422 78 364 84 122 238 84 326 90 712, 714 73 243, 430 98 672 92 187, 659 100 276 d 183, 560, 561 89 265 89 80 517 540 498 87 352 81 72 218 89 204, 687 598 517 566 734 6 598 435, 712, 714 88, 243 Continued on following page 55 52 52 54 90 46 Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV Chlamydomonas reinhardtii Cyanophora paradoxa Cyanophora paradoxa Epifagus virginiana Euglena gracilis Marchantia polymorpha Nicotiana tabacum Oenothera ammophila Oryza sativa Porphyra purpurea Spinacia oleracea Zea mays 85 204 VOL. 58, 1994 CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS 719 TABLE 3-Continued E. Proteina Taxon GenBank accession no(s). X04465 Z00044 X15901, X13208 X05394 S15 S16 Reference(s) X04131 Y00359, M16559 C C C C C C C 58 56 56 57 56 54 56 44 41 40 38 40 40 40 82 75 659 100 100 560, 561 92 87 95, 265 85 79 344 70 56 517 90 90 307 92 87 523,586 Marchantia polymorpha Nicotiana tabacum Oryza sativa Secale cereale Zea mays X04465 Z00044 X15901 X14811 X52614 C C C C C 53 61 58 59 60 36 36 36 38 41 72 58 312 100 100 560, 561 82 71 265 81 69 501 86 77 170 Cyanidium caldarium Hordeum vulgare Nicotiana tabacum Oryza sativa Porphyra purpurea Sinapis alba Solanum tuberosum Zea mays X62578 X52765 C C C C C C C C 59 62 60 66 58 62 39 38 37 39 42 39 S17 Arabidopsis thaliana Pisum sativum Porphyra purpurea J05215, Z11151 M31025 N N C 61 34 72e 55e 196, 640 54 29 100 100 195, 196 69 49 54e 39e 517 S18 Chlamydomonas reinhardtii Cyanophora paradoxa X17498 M81884 X70810, Z11874 X04465 Z00044 X15901 C C C C C C C C C 53 69 58 61 58 56 55 69 55 34 47 34 37 38 37 34 48 34 63 41 348 68 54 163 86 81 712, 714 70 48 134 88 74 186 100 100 560, 561 79 72 265 72 51 517 75 70 686 C C C C C C C C C C C C C C C C 63 78 83 65 71 75 77 75 75 65 44 67 70 47 57 54 62 56 56 45 76 57 65 45 66 43 211 81 62 277 85 68 163 84 83 712, 714 72 54 88, 243 97 92 584 88 80 186 100 100 745 100 100 560, 561, 612 84 70 265 3 88 84 448 76 60 517 454 97 92 635, 745 82 70 415 Cyanophora paradoxa Porphyra purpurea C C 53 34 51 33 32 517 Cyanophora paradoxa C C N 65 62 64 61 32 517 300 539 Epifagus viginiana Euglena gracilis Marchantia polymorpha Nicotiana tabacum Oryza sativa Porphyra purpurea Zea mays S19 Astasia longa Chlamydomonas reinhardtii Cyanophora paradoxa Epifagus virginiana Euglena gracilis Glycine max Marchantia polymorpha Nicotiana debneyi Nicotiana tabacum Oryza sativa Petunia hybrida Pisum sativum Porphyra purpurea Sinapis alba Spinacia oleracea Zea mays S20 Z00044, X03415 X15901 X13609 Z11741 (partial) X60823 X56673 X75653 X17498 M81884 X70810, Z11874, M37463 X06429 X04465 Z00044, V00163 X15901 M35955, M37322 (partial) X59015 X17331 (partial) X13336, X00797 Y00141 63 41 385 90 86 556 100 100 560, 561 87 82 265 71 51 517 87 81 450 138 63 37 90 84 293 73 55 78 62 S2lf Ll Porphyra purpurea Spinacia oleracea Synechocystis strain PCC X73005 45 41 43 46 6803 L2 Astasia longa X75653 C 66 51 71 53 211 Continued on following page Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV Marchantia polymorpha Nicotiana tabacum Oryza sativa Pisum sativum Porphyra purpurea Spinacia oleracea Zea mays N. tabacumb Locationa col %S %I %S %I 720 HARRIS ET AL. MICROBIOL. REV. TABLE 3-Continued Proteina Taxon X17498 M81884 X70810, Z11874, M37463 X06429 (partial) X04465 X00798 Z00044 X15901 M35944, M37322 (partial) X59015 X65615 X00797 (partial) Zea mays X53066, X12851, X62070 L3 Cyanophora paradoxa Porphyra purpurea X17498 L4 L5 L6 no(s). Locationa C C C C C C C C C C C C C C C C E. colib N. tabacumb Reference(s) %S %I %S %I 70 68 64 68 53 52 47 52 60 61 93 55 64 60 66 64 49 43 48 49 68 67 66 63 50 50 48 44 65 49 75 76 96 72 277 163 712, 714 88, 243 584 81 73 186 91 88 745 100 100 560, 561 93 90 265 3 94 93 448 73 59 517 97 97 455 90 85 745 46 93 90 299 C C 62 45 63 45 161 517 Porphyra purpurea C 60 38 517 Astasia longa X16004, X14384, X75651 Chlamydomonas reinhardtii X16548 Cyanophora paradoxa Cyanophora paradoxa M30487 Euglena gracilis X70810, Z11874, X17051 Porphyra purpurea C C C C C C 66 76 76 76 69 74 44 51 51 52 44 54 566 277 69 423 517 Cyanophora paradoxa Porphyra purpurea X16548, M30487 C C 63 38 58 41 517 Arabidopsis thaliana Z11509, Z11129 X14019 N N C 88, 243 69, 423 L7 (see L12) L8 (see L10) L9 L10 Pisum sativum Porphyra purpurea Synechococcus sp. Synechocystis strain PCC 6803 X63765 D10716 53 54 61 56 57 Synechocystis strain PCC X53178 53 26 32 34 30 36 34 82e 100 55e 58e 69e 100 33e 34e 640 192 517 439 62~ 38e 388 539, 564 6803 Lll Arabidopsis thaliana Cyanophora paradoxa Porphyra purpurea Spinacia oleracea Synechocystis strain PCC N C C X56615 X73005 N X68046 (a) X68046 (b) X68046 (c) N N N 6803 L12 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Cyanophora paradoxa Euglena gracilis Nicotiana sylvestris Nicotiana tabacum Nicotiana tabacum Porphyra purpurea Secale cereale Secale cereale Spinacia oleracea C X70810 S93166 X62368 X62339 N N N X68325 X68340 J02849 N N N C C 63 71 70 63 75 51 55 54 52 61 93C 75C 80c 100 82C 69 64 69 68 66 69 70 70 74 70 69 75 46 40 86 71 86 46 47 63 47 48 48 49 58 45 44 53 88C 63c 65c 100 69C 543 32 517 579 539 75 543, 689 59 543, 689 75 543, 689 39 32 63 44 243 99 99 354 99 99 155 100 100 155 70 49 517 82 70 544 80 68 544 89 78 201 Continued on following page Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV Chlamydomonas reinhardtii Cyanophora paradoxa Epifagus virginiana Euglena gracilis Glycine max Marchantia polymorpha Nicotiana debneyi Nicotiana tabacum Oryza sativa Petunia hybrida Pisum sativum Porphyra purpurea Sinapis alba Spinacia oleracea Triticum aestivum GenBank accession CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS VOL. 58, 1994 721 TABLE 3-Continued Proteina GenBank accession no(s). Taxon Synechocystis strain PCC Locationa X53178, X67516 E. N. coli' tabacumb Reference(s) %S %I %S %I 78 62 70 45 539, 564 6803 L13 Porphyra purpurea Spinacia oleracea J04461 66 51 69C 57C 517 71 54 100 100 490 77 80 76 83 80 Chlamydomonas reinhardtii Cyanophora paradoxa Euglena gracilis Marchantia polymorpha Nicotiana tabacum Oenothera ammophila Oryza sativa Porphyra purpurea Spinacia oleracea Vigna unguiculata Zea mays X14062 M30487 X70810, Z11874 X04465 Z00044 M60179, M60180 (partial) X15901 X13336 M80799 (partial) X06734 C C C C C C C C C C C L15 Arabidopsis thaliana Pisum sativum Z11507, Z11508 Z11510 N N 61 41 76e 68e 640 63 44 100 100 640 L16 Chlamydomonas reinhardtii Cyanophora paradoxa Epifagus virginiana Euglena gracilis Gracilaria tenuistipitata Marchantia polymorpha Nicotiana tabacum Oenothera ammophila 0ryza sativa Porphyra purpurea Spinacia oleracea Spirodela oligorhiza Vigna unguiculata Zea mays M13931 M30487 M81884 C C C C C C C C C C C C C C 79 76 76 73 72 75 78 57 54 50 53 60 56 56 76 72 76 75 54 55 53 54 L18 Cyanophora paradoxa Porphyra purpurea M30487 C C 62 49 65 45 423 517 L19 Cyanophora paradoxa Porphyra purpurea Synechocystis strain PCC C C 69 46 69 47 72 56 598 517 542 C C C C C C C C C C C 56 66 72 60 55 33 46 53 41 29 55 68 71 81 54 27 44 52 77 31 54 58 54 62 60 26 31 29 33 32 54C 57C 55C 52C 32C 385 30C 598 53 31 60 62 44 70 L14 X70810, Z11874 M32638 X04465 Z00044 M60179 (partial) X15901 X13336 X03834 M80799 (partial) Y00375, X06734 (partial) 57 58 60 58 55 88 71 89 69 85 63 94 80 100 100 80 54 93 80 60 85 82 58 94 85 67 88 80 53 92 81 82 69 88 70 90 81 77 65 77 65 90 79 100 100 90 81 96 90 86 68 90 85 372 423 88, 243 186 560, 561 715 265 517 742 8 400 373 423 712, 714 88, 243 294 186 560, 561 715 265 517 742 497 8 400, 418 L17f X72627 6803 L20 Astasia longa Chlamydomonas reinhardtii Cyanophora paradoxa Epifagus virginiana Euglena gracilis Glycine max Marchantia polymorpha Nicotiana tabacum Oryza sativa Porphyra purpurea Zea mays L21 L22 X75653 X62566 X17063 M81884 X70810, Z11874, Y00143 X07676 (partial) X04465 Z00044 X15901 X60548 Spinacia oleracea M57413, M64682 C C C C N Astasia longa X75653 M30487, X17498 C C Cyanidium caldarium Cyanophora paradoxa Marchantia polymorpha Porphyra purpurea Cyanophora paradoxa X04465 211 736 69 712,714 243, 396 673 64 45 76 57 186 63 41 100 100 560, 561 59 41 78 67 265 69 47 64 46 517 58 41 81 71 687 30c 312 32C 517 100 100 340, 578 34 211 47 163, 423 Continued on following page Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV C N 722 MICROBIOL. REV. HARRIS ET AL. TABLE 3-Continued N. E. Proteina GenBank accession Taxon no(s). Locationa colib tabacumb Reference(s) %S %I %S %I X70810, Z11874, M37463 M32638 X04465 Z00044 X15901 M60953 M60951, M60952 Arabidopsis thaliana Astasia longa Chlamydomonas reinhardtii Euglena gracilis Marchantia polymorpha Nicotiana tabacum Oryza sativa Porphyra purpurea Sinapis alba Spinacia oleracea X66414 X75653 Triticum aestivum Zea mays L24 Nicotiana tabacum Pisum sativum Spinacia oleracea Porphyra purpurea C C C C C C N C C 59 59 59 54 53 50 58 66 47 38 40 41 36 32 35 43 49 28 C C C C C C C C C C C C 50 38 53 42 46 48 51 46 50 25 18 31 17 25 23 26 28 25 97 95 374 42 21 211 55 39 277 53 32 88, 243 77 55 186 100 100 560, 561 94 84 265 63 36 517 98 96 455 635 51 26 94 83 46 51 26 93 84 419 N N N C 64 56 58 51 38 34 34 33 C D26101 (partial) C C C C 185 363 185 185 185 73 59 100 100 154 77 58 77 61 185 185 74 61 69 57 517 185 X68078 N 57 36 731 Y00329 X70810, Z11874, M37463 X04465 Z00044 X15901 X65615 X07462 (pseudogene?) X12850 X07864 X14020 M58522 52 42 64 42 68 54 100 100 70 54 78 67 72 53 66 48 66 52 100 100 86 78 76 61 61 49 88, 243 295 186 560, 561 265 193 193 517 416 153 192 75 517 L25f L27 Calyptrosphaera sphaeroidea Chlamydomonas reinhardtii Chrysochromulina alifera Chrysochromulina hirta Cyanidium caldarium Nicotiana tabacum Pleurochrysis carterae Pleurochrysis haptonemofera Porphyra purpurea Porphyridium cruentum D26097 (partial) N-terminal amino acid sequence only D26096 (partial) D26099 (partial) D26098 (partial) M75731 D26100 D26102 (partial) N C C C N L28 Nicotiana tabacum L29 Porphyra purpurea C 51 24 517 L31 Porphyra purpurea C 60 37 517 L32 Astasia longa Brassica rapa Euglena gracilis Lycopersicon esculentum Marchantia polymorpha Nicotiana tabacum Oryza sativa Porphyra purpurea Vicia faba Zea mays L30f L33 Cyanophora paradoxa Epifagus virginiana Marchantia polymorpha Nicotiana tabacum Oryza sativa Porphyra purpurea X16004, X75651 Z26332 X70810 D17805 (partial) X04465 Z00044 (as ORF55) X15901 C C C C C C C C X51471 X64099 X17498 M81884 X04465 Z00044 X15901 C C C C C C C C 56 38 55 45 568 48 15 85 83 582 48 30 50 35 243 668 43 18 74 61 186 46 18 100 100 733 47 22 67 56 265 44 20 57 48 517 52 26 83 68 256 43 18 74 61 688 60 52 56 52 60 59 42 37 44 37 42 43 78 62 93 85 80 71 100 100 82 73 67 50 163 712,714 186 560, 561 265 517 Continued on following page Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV L23 Euglena gracilis Gracilaria tenuistipitata Marchantia polymorpha Nicotiana tabacum Oryza sativa Pelargonium zonale Pisum sativum Porphyra purpurea Zea mays CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS VOL. 58, 1994 723 TABLE 3. Chloroplast and cyanobacterial ribosomal proteins that have been identified by gene or protein sequence E. Proteina Taxon GenBank accession no(s). Locationa N. colib tabacumb Reference(s) %S %I %S %I Zea mays X56673 Cyanophora paradoxa Porphyra purpurea L35 Cyanophora paradoxa Porphyra purpurea Spinacia oleracea X17063 Astasia longa Cryptomonas 'F Cyanophora paradoxa Epifagus virginiana Euglena gracilis Marchantia polymorpha Nicotiana tabacum Oryza sativa Pisum sativum Porphyra purpurea Spinacia oleracea Zea mays X16004, X75651 X62348 (partial) L36 CS-S5, PSrp-1, "S22" or "S30"g Spinacia oleracea Spinacia oleracea M60449 57 38 81 C C 49 40 60 49 C C N 55 38 61C 45c 69 52 36 67C 50c 517 64 42 100 100 577 C 68 46 73 X03496 M35956 C C C C C C C C C X59270, X15344 M55322 598 517 C C M81884 X70810, Z11874 X04465 Z00044 X15901 Y00468, X15645 N N 78 81 73 86 86 89 84 81 84 89 62 57 51 62 62 68 62 59 62 68 75 686 92 95 84 95 100 95 97 95 97 95 57 566 124 76 598 92 712, 714 65 88, 243 86 186 100 560, 561 92 265 86 505, 506 70 517 95 571 92 402 28, 741 290 "S31" or SCS239" Spinacia oleracea PsCL189 Pisum sativum X14021 N 192 "L40999 Spinacia oleracea M58523 N 75 541, 674 PsCL25M Pisum sativum X14022 N 192 a Proteins Si through S21 and LI through 136 are named by reference to similar sequences in E. coli, and the location of the gene encoding them (N, nuclear; C, chloroplast or cyanelle) is given for all eukaryotic species. A few additional chloroplast ribosomal proteins with no obvious similarity to E. coli proteins have been identified and appear at the end of the table. b The percent similarity (%S) and percent identity (%I) to the E. coli and tobacco proteins or other reference land plant proteins were calculated by the gap routine of the Genetics Computer Group sequence analysis package. c Tobacco sequence not available; spinach used instead for comparison. d The complete tobacco genome sequence (Z00044) has a stop codon in the terminal exon encoding the S12 protein, whereas the sequence by Fromm et al. (183) (X03481) shows a full-length protein comparable to that from other chloroplast genes. The Swissprot sequence (P06309) omits the terminal residue (Tyr) of the first exon of this protein. The composite sequence with these corrections made is identical to that for N. plumbaginifolia and was used for the comparisons given here. I Tobacco sequence not available; pea used instead for comparison. f No equivalent found so far in chloroplasts. g Proteins for which no equivalent appears to exist in E. coli. h Small, basic protein found in spinach ribosome preparations. encoding this protein is absent from the completely sequenced chloroplast genomes of tobacco, rice, Marchantia polymorpha, and Euglena gracilis (243, 558) but appears in the Porphyra purpurea chloroplast genome (514). A nuclear gene encoding this protein has been identified in spinach (178, 179) and shown to have a light-independent, leaf-specific pattern of expression under the control of a negative nuclear factor, SlF, that down-regulates its promoter (740). Hahn et al. (240) reported that monoclonal antisera to E. coli Si reacted with a chloroplast protein of spinach. Polyclonal antisera to two chloroplast-synthesized ribosomal proteins of C. reinhardtii ("S-7" and "S-11" [547]) reacted with E. coli Si (510), as did antisera to mixed chloroplast ribosomal proteins of spinach (119). Subramanian et al. (608) also suggested the presence of a chloroplast Si homolog in maize on the basis of affinitybinding experiments with a matrix-bound poly(U) column. In E. coli the S2 protein interacts primarily with the 3' domain of the 16S rRNA in the 960 loop region and can be cross-linked to proteins S3, S5, and S8 (500, 595, 599). The rps2 gene encoding a ribosomal protein homologous to E. coli S2 has been found in chloroplast genomes from diverse species (Table 3), typically mapping between the rpoB and rpoC genes encoding subunits of RNA polymerase and the atpI and atpH genes encoding ATP synthase subunits. The deduced amino sequences of S2 proteins from land plants are highly conserved (Table 3), and those of three monocots (wheat, rice, and maize) are nearly identical to one another. A nuclear DNA sequence in spinach with substantial homology to a portion of the chloroplast rps2 gene is thought to be an example of "promiscuous DNA," i.e., a DNA sequence found in more than one genetic compartment (85). Protein S3, like S2, interacts with nucleotides in the 960 and Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV L34 C 724 HARRIS ET AL. ending with rps8 (Fig. 5) but is separated from this operon by exon 1 of the psaA gene and two tRNA genes, tmM and trnG (277). In Euglena gracilis, rps4 is transcribed together with rpsll (242, 597). In the alga Cryptomonas 'F, rps4 is close to rbcL on the same strand and is flanked by tRNAArg on the opposite strand (127), whereas in Cyanophora paradoxa, tRNA et and tRNAG'Y are adjacent to rps4 but on the opposite strand (32, 598). In E. coli, the S5 protein is part of the recognition complex (466) and is the first protein of the small subunit whose crystal structure has been determined (from B. stearothermophilus [507, 508]). The protein appears to be a somewhat elongated molecule with two distinct domains. Mutations affecting amino acids 20 to 22 of E. coli S5 can confer spectinomycin resistance, whereas mutations at amino acids 104 and 112 have a ram phenotype and suppress streptomycin dependence mutations in protein S12 (508). Some of the latter class of mutants are also neamine resistant (721). These two conserved regions of the S5 protein are thought to be the sites of its interaction with rRNA (508). Genes encoding a protein with homology to E. coli S5 have been sequenced from the cyanelle genome of Cyanophora paradoxa (368, 423) and from the P. purpurea chloroplast genome (517). No equivalent gene has been found in any land plant chloroplast genome, however, nor does it appear in the chloroplast genome of Euglena gracilis. The S6 ribosomal protein of E. coli is implicated in mRNA and tRNA binding and in termination (465, 632), and it appears to be a component of the platform region of the 30S particle (432, 622). A plastid equivalent of S6 is known so far only from Porphyra purpurea (517). In E. coli, protein S7 interacts with several clusters of nucleotides in the 3' domain of 16S rRNA, in proximity to S9, S1O, and S19 (57, 136, 465, 499), and is one of the initiating proteins of 30S assembly (255). Binding of S7 to 16S riRNA is a prerequisite to assembly of S9 and S19. As discussed above, the gene encoding S7 is transcribed together with that for S12 in bacteria and in the chloroplast genomes of most plants and algae examined (Fig. 5), the principal exceptions so far being Chlamydomonas species. In C. reinhardtii, the protein encoded by rps7 corresponds immunologically to the protein that Schmidt et al. (547) identified as "S-20" (509). Although derived amino acid sequence identity between chloroplasts and bacteria is lower for S7 than for S12 (Table 3), antibodies to E. coli S7 do cross-react with a corresponding small-subunit protein from spinach chloroplast ribosomes (18). In E. coli, S8 is an RNA-binding protein that is essential early in assembly of the 30S subunit and interacts with a highly conserved site in the central domain of 16S rRNA, designated by Oakes et al. (466) as the platform ring (also see references 141, 437, 465, and 622). It is associated with proteins S15 and S17 (57). It also has a key role in translational regulation of the spc operon in E. coli (719). S8 is moderately conserved phylogenetically and can be identified with equivalents in eukaryotic ribosomes (410, 708). The rps8 gene is chloroplast encoded (Table 3) and is one of at least three genes of the bacterial spc operon that remain linked in chloroplast genomes (Fig. 5). Most plastid S8 proteins have a central 4- to 7-aminoacid insertion compared with the E. coli protein, followed by a highly conserved C-terminal region. Protein S9 interacts with S7 and S19 in the 3' domain of the E. coli ribosome (57, 499). Bartsch (18) obtained cross-reactivity of antibody to E. coli S9 with a spinach chloroplast ribosomal protein, but the gene encoding this protein has not been found in any of the land plant chloroplast genomes so far sequenced and is presumed to be nucleus encoded. However, an rps9 gene does appear in the chloroplast genomes of Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV 1050/1200 regions of E. coli 16S rRNA (465) and appears from immunoelectron microscopy studies of the 70S ribosome to reside near the site to which the polypeptide release factor RF-2 binds (632). The rps3 gene encoding the equivalent protein has been sequenced from several chloroplast genomes (Table 3), where it has been found between rp122 and rp116, as is true for the corresponding genes in the S10 operon of E. coli (Fig. 5). In most algae and plants the rps3 gene is uninterrupted, but in Euglena gracilis it contains two introns, one (102 nt) belonging to the group III class (as defined by Christopher and Hallick [87]; also see reference 86) and the other (409 bp) being a "twintron" consisting of a 311-nucleotide group II intron within a 98-nt group III intron (92). Splicing proceeds sequentially, with the internal 311-nt intron being excised first. In the chloroplast genome of C. reinhardtii, there is no gene equivalent to rps3 in the expected location between rp122 and rp116 (277). However, Fong and Surzycki (172) found a long open reading frame between the rpoB and rpoC genes, whose 5' and 3' ends would encode a protein with substantial homology to S3. The central portion of the predicted product of this open reading frame has no homology to S3, however, and the DNA sequence does not contain recognizable splice junctions that would suggest that this region is in fact an intron. Liu et al. (366) found that this open reading frame is also present in several other Chlamydomonas species. After transformation of C. reinhardtii cells with a construct containing this open reading frame interrupted by the bacterial aad antibiotic resistance gene, the only resistant cells recovered were heteroplasmic for the interrupted and native forms of the gene. In contrast to transformants in which the same construct was inserted into other regions of the genome, no homoplasmic cells containing only the interrupted gene could be obtained, strongly suggesting that this gene is not only functional but also essential to cell growth. No single transcript spanning the whole gene could be detected, however, and the gene product has not been identified (366). In E. coli, S4 is one of the primary rRNA-binding proteins that initiate assembly of the 30S subunit (255, 465) and is associated with the 5' domain of 16S rRNA, at a junction of several helices. Together with S5 and S12, S4 participates in a region designated by Oakes et al. (466) as the recognition complex on the basis of its demonstrated involvement in codon-anticodon recognition and translational accuracy. This region involves the 530 loop, the 900 loop region, and the 5' end of the 16S molecule which pairs with the region around residue 912 (Fig. 3). Homologs of all three of these proteins have been identified in yeast cytoplasmic ribosomes and appear to have similar functions (4). Mutations in the gene encoding S4 in E. coli suppress streptomycin dependence mutations in the gene for S12 and increase translational ambiguity (ram mutants [7, 189, 335, 336, 475). The chloroplast gene encoding ribosomal protein S4 has been sequenced from a number of plants and algae (Table 3) and shows a high degree of conservation in its first 25 amino acid residues and in a large block of approximately 120 residues in the central portion of the protein. The C. reinhardtii S4 protein is somewhat longer than all others examined so far, having two internal insertions and a 22-amino-acid C-terminal extension (511). In land plants, rps4 appears to be transcribed singly under control of its own promoter and is not part of an operon with other ribosomal protein genes (608). In tobacco, rice, and Marchantia polymorpha, the rps4 gene is in the large singlecopy region and is preceded by tRNAThr on the same strand and followed by tRNAser on the opposite strand. In C. reinhardtii, rps4 follows the large ribosomal protein operon MICROBIOLE REV. VOL. 58, 1994 CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS the 16S rRNA and is probably close to S4 in the assembled 30S subunit (594). Montesano-Roditis et al. (432) have localized S16 to the 30S body near its junction with the platform, on the surface facing the 50S particle. In various angiosperms, S16 is encoded by a chloroplast gene (Table 3), but the rps16 gene is absent from the Marchantia chloroplast genome (471). It is found, however, in the plastid genome of the red alga Cyanidium caldarium (385). In tobacco, the rpsl6 gene has an 860-bp intron with boundary sequences similar to the introns in rpsl2, rp12, and several tobacco tRNA genes (559). The rpsl6 genes of mustard (450), barley (556), and maize (293) also contain introns, but that of Cyanidium caldarium is uninterrupted (385). S17 is one of the primary assembly proteins in E. coli and binds to 16S rRNA in the 5' domain (213, 255, 465, 594). It is one of only three chloroplast ribosomal proteins of the small subunit to date for which a nucleus-encoded gene has been cloned and sequenced (Table 3) (606). This protein contains a highly conserved region which can be identified in both bacterial (S17) and eukaryotic (Sli) ribosomal proteins. Comparison of the deduced amino acid sequences of the equivalent chloroplast S17 and cytosolic Sli ribosomal proteins from Arabidopsis thaliana with E. coli S17 supports the notion that chloroplast S17 is derived from a prokaryotic endosymbiont and not from duplication of the eukaryotic S11 gene (196). The presence of an rpsl7 gene in the cyanelle genome of Cyanophora paradoxa (368) and in the chloroplast genome of Porphyra purpurea (514) is consistent with this hypothesis. Proteins S18 and S6 assemble coordinately in the bacterial ribosome to form part of the platform ring in the central domain (432, 466, 622). The chloroplast gene encoding S18 has been found to be part of an operon with rp133 in the completely sequenced chloroplast genomes of tobacco, rice, and Marchantia polymorpha, as well as in Cyanophora paradoxa, but it is absent from this operon in Euglena gracilis (Fig. 5). The angiosperm S18 proteins have N-terminal extensions compared with E. coli, Marchantia polymorpha, and Cyanophora paradoxa, containing various numbers of repeats of a hydrophilic heptapeptide (686). A C-terminal extension found in the S18 proteins of rice and maize is missing from this protein in tobacco (561, 686). The S19 protein of E. coli interacts with proteins S7, S9, and S14 and with several helices in the 3' domain of the 16S rRNA molecule (57). The gene encoding S19 was the first chloroplast-encoded ribosomal protein gene to be identified and sequenced (612, 745). In plants with the "typical" chloroplast inverted-repeat structure, the rpsl9 gene and the adjacent rp12 and rp122 genes are located at or near the boundary between the inverted repeat and the large single-copy region. In tobacco (560) and Marchantia polymorpha (186), rpsl9 is entirely within the large single-copy region but near the inverted-repeat junction, whereas in rice (433) the whole gene is within the inverted repeat. Zurawski et al. (746) found that the first 48 codons of rpsl9 in spinach were in the inverted repeat, with 44 codons homologous to the 3' end of the E. coli gene being present only on one side of the large single-copy region. Thomas et al. (635, 636) showed that this complete copy of the gene was expressed, whereas the rpsl9' sequences beginning in the other side of the inverted repeat and extending for 66 codons into the adjoining unique sequence region (745) were not transcribed. The rpsl9 gene also straddles the boundary of the inverted repeat in Spirodela oligorhiza (494) and in mustard (454). S20, which was also identified in early ribosome studies in E. coli as L26, is a primary RNA-binding protein that interacts with the 5' domain of the 16S rRNA (255,594). Deletion of the Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV Euglena (243), Porphyra (517), and Cryptomonas (122) species and in the cyanelle genome (598). Overall, the C-terminal portions of the S9 proteins appear more highly conserved than the N-terminal portions. S10 is a late-assembly ribosomal protein of the 3' domain in E. coli 16S rRNA (465). A gene encoding a homolog of S10 has been found in the cyanelle genome (68, 451, 452), where it maps downstream of the petFI gene. Sequences encoding an S10 protein have also been found in Cryptomonas D (122) and in Porphyra purpurea downstream of the tufA gene (517). In E. coli, Sl1 interacts with S6 and S18 in the platform region of the 30S subunit (466). S11 is highly conserved phylogenetically, with homologs also identified in eukaryotic ribosomes (401, 708). There is some variability in length among Sli proteins, localized to the N-terminal regions. In chloroplast genomes of land plants, the rpsll gene is part of the large ribosomal protein operon that terminates in rpoA (Fig. 5). In Euglena gracilis, in which it is in a separate operon with rps4, the rpsll gene contains two group III introns (597). S12 appears to be the most highly conserved of all the small subunit proteins. The C. reinhardtii S12 protein is sufficiently similar to its bacterial counterpart that the rpsl2 gene from this alga can be expressed in E. coli cells and the resulting protein can assemble and function in the E. coli ribosome (364). In E. coli, S12 interacts with two regions of the 16S rRNA, the 530 loop and 900 stem-loop. Mutations affecting either the S12 protein or the 16S rRNA regions with which it associates can confer streptomycin resistance in E. coli by reducing misreading induced by the drug (Table 2). Streptomycin resistance mutations have also been found at evolutionarily conserved sites in the S12 proteins or 16S rRNA of Chlamydomonas species, Euglena gracilis, and tobacco, and streptomycin dependence mutations affecting the S12 protein have been found in bacteria and in C. reinhardtii (Table 2). Streptomycin-dependent E. coli mutants exhibit hyperaccurate proofreading and reduced efficiency of binding of EF-Tu (25, 102, 150). In E. coli, S13 appears to be located at the head of the 30S subunit, near the center of the surface that faces the 50S subunit (432). It has been reported to cross-link to S7 and S19 in the 3' domain of the 16S rRNA (599). Genes encoding a cognate protein have been identified in the cyanelle genome (598) and in the Porphyra chloroplast genome (517) but have so far not been reported to occur in other algae or land plants. The late-assembly ribosomal protein S14 interacts with the 3' domain of 16S rRNA in E. coli (465). The chloroplastencoded Euglena rpsl4 gene is part of the large ribosomal protein cluster as it is in E. coli, downstream from rp136 and a tRNAIle gene (457), whereas in other chloroplast genomes it is found outside this cluster. In land plants, the rpsl4 gene is located in the chloroplast genome downstream from the psaA and psaB genes encoding reaction center proteins of photosystem 1 (81, 82, 307, 496, 560). In Cyanophora paradoxa, the rpsl4 gene is upstream of open reading frame ORF512 andpsaA and is transcribed divergently from these two genes (598). In Porphyra purpurea, rpsl4 is flanked by petF and petG (514). S15 is an early-assembly protein in E. coli that interacts with the central domain of the 16S rRNA, together with S6, S8, and S18 in the platform ring (57, 151, 438, 465, 466, 622). In tobacco and liverwort, the rpsl5 gene is in the small single-copy region of the chloroplast genome (312, 560), whereas in three monocots (rice [265], rye [501], and maize [170]) it is in the inverted repeat, very close to the boundary with the small single-copy region. This gene is missing from the chloroplast genomes of Euglena gracilis (243) and Porphyra purpurea (517) and from the cyanelle genome (32, 598). In E. coli, S16 is a protein associated with the 5' domain of 725 726 HARRIS ET AL. rpsT gene encoding S20 in E. coli results in increased misreading of all three nonsense codons and a deficiency in assembly of 30S and 50S subunits to form 70S monomers (534). An rps2O gene has been identified in the cyanelle genome (32) and in the Porphyra chloroplast (517). E. coli S21 interacts with the central domain in the platform ring (466). No equivalent protein has been identified so far in the chloroplast ribosome. families and documented six independent losses of this intron among dicotyledons. The L3 and L4 proteins of E. coli both bind to the 23S rRNA molecule and have been identified with analogous proteins in archaebacterial and eukaryotic ribosomes (215, 708). Genes encoding an L3 protein have been sequenced from the Cyanophora cyanelle genome (161) and from the Porphyra chloroplast genome (517). Neither an rp13 nor an rpl4 gene has been found in the completely sequenced chloroplast genomes of tobacco, rice, Marchantia polymorpha, or Euglena gracilis Bartsch (18) found a cross-reaction between antibody to E. coli L3 and a spinach chloroplast ribosomal protein which has not been further characterized. Genes encoding a protein corresponding to the 5S RNAbinding protein LS of E. coli have been found in the Euglena, C. reinhardtii, Porphyra, Astasia, and Cyanophora plastid genomes (Table 3). However, no equivalent gene has been found in any land plant chloroplast genome. Antibody to Chlamydomonas chloroplast ribosomal protein "L-13" (547) reacts with E. coli LS and with a ribosomal protein of Anabaena sp. (510). A weak reaction was also seen to a spinach protein ("LIO"), whose site of synthesis is uncertain (121). The Chlamydomonas "L-13" protein is known to be synthesized in the chloroplast (547), suggesting that this is the product of the chloroplastencoded rplS gene sequenced by Huang and Liu (277). TheE. coli L6 protein binds to domain VI of 23S rRNA (90). Genes encoding an equivalent protein have been found in the cyanelle genome of Cyanophora paradoxa (69) and the Porphyra chloroplast genome (514). The protein originally identified as L7 in E. coli is in fact the aminoacetylated form of L12, and L8 is a complex of L7/L12 and L10 (358). Protein L9 of E. coli is an elongated protein with distinct terminal domains which is associated with the protuberance formed by protein Li and the region of the 23S rRNA to which it binds (57, 213, 266). Genes encoding a protein equivalent to E. coli L9 have been sequenced from the nuclear genomes of pea (192) and Arabidopsis thaliana (640) and from the Porphyra chloroplast genome (517). The E. coli L9 protein crossreacts slightly with antibody to the acidic chloroplast ribosomal protein "L-30" from C. reinhardtii (510). E. coli protein L10 (L8) forms the base of the ribosomal stalk in a pentameric complex with two dimers of L7/L12 and, like L7/L12, appears to be a universal constituent of eubacterial, eukaryotic, and archaebacterial ribosomes (708). A cyanobacterial gene encoding this protein has been found (539, 564) but no chloroplast equivalent has yet been identified. Presumably, chloroplast L10 is encoded by a nuclear gene in plants. L1i is an early-assembly protein that constitutes part of the GTPase center in the E. coli ribosome (528) and also has been identified in eubacterial, eukaryotic, and archaebacterial ribosomes (708). Nuclear genes encoding a chloroplast L1 homolog have been cloned from spinach andArabidopsis thaliana (543, 579, 606), while plastid genes have been identified in Porphyra purpurea (517) and Cyanophora paradoxa (32). In E. coli, L1i has the most extensive posttranslational modification (nine methyl groups) of all ribosomal proteins (708); the same modifications occur in the spinach chloroplast Lii in the corresponding amino acid residues, located in conserved sequence contexts (607). Mutations in Bacillus megaterium and B. subtilis conferring resistance to the antibiotic thiostrepton cause the loss of Lii from the ribosomes (16, 101). Lli does not bind thiostrepton itself in solution but enhances thiostrepton binding to 23S rRNA (102, 639). Bacterial thiostreptonresistant mutants with altered 23S rRNA have also been found Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV Proteins of the Large Subunit In E. coli, ribosomal protein Li forms a prominent ridge on the large subunit (177, 466, 599) and has been demonstrated to bind to nt 2100 to 2200 on the E. coli 23S rRNA, a region that shows a high degree of conservation among chloroplast 23S sequences. The gene encoding this protein is present in the cyanelle genome (32) and in the Porphyra chloroplast genome (517) but is absent from the completely sequenced plastid genomes of land plants. Antibodies to E. coli Ll cross-reacted with a spinach chloroplast ribosomal protein (8). cDNAs encoding chloroplast Li have been cloned from the nuclear genomes of pea, spinach, and Arabidopsis thaliana, and the nuclear gene has been isolated and characterized from Arabidopsis thaliana (300). In E. coli, the L2 protein binds to domain IV of the 23S rRNA molecule, and cross-links specifically to nt 1818 to 1823 (744), in a stem-loop structure that is part of the peptidyltransferase center and is conserved in chloroplast 23S rRNAs. Site-directed mutagenesis of a conserved region in the E. coli L2 protein outside the 23S binding site has been used to produce temperature-sensitive mutants that are impaired in assembly of the 50S subunit (526). The L2 protein is encoded in the chloroplast genomes of all land plants and algae so far examined (Table 3). The L2 protein itself is moderately conserved, and its equivalent has been identified in eukaryotic ribosomes (708). The C. reinhardtii protein "L-1," which is synthesized in the chloroplast (547), appears to be encoded by the rpl2 gene since "L-1" antibodies cross-react with E. coli L2 (510). Kamp et al. (292) showed that the N-terminal amino acid of the L2 protein in spinach is N-methylalanine, the first demonstration of methylation of a chloroplast ribosomal protein. Several ribosomal proteins of E. coli are methylated, but L2 is not among these. The maize rpl2 gene begins with an ACG codon, which is edited to AUG at the transcript level (321). The 3'-terminal ends of the deduced L2 amino acid sequences for spinach and Nicotiana debneyi published by Zurawski et al. (745) appear to lack homology to the corresponding regions from other chloroplast and bacterial L2 proteins. However, if a single-base insertion is made after the amino acid 226 of the spinach gene (changing the sequence CCC ACG GGG GTG GTG ... .[Pro Thr Gly Val Val.1..].. to CCN CAC GGG GGT GGT ... .[Pro His Gly Gly Gly... .], the reading frame is shifted to specify 45 additional amino acids that resemble the consensus sequence much more closely. The corresponding change in the N. debneyi sequence produces a C terminus identical to that of N. tabacum as determined by Shinozaki et al. (561). The rp12 genes of tobacco, spinach, rice, and maize are located in the inverted-repeat region, but those of Marchantia polymorpha and C. reinhardtii are in single-copy DNA. The spinach, C. reinhardtii, and Euglena genes are uninterrupted, whereas those of many other land plants contain a single group II intron (133). The intron insertion sites are identical in the Nicotiana, rice, and Marchantia genes, and the introns themselves have a high degree of nucleotide sequence identity. Downie et al. (133) determined the distribution of the rpl2 intron in 390 species from 116 angiosperm MICROBIOL. REV. VOL. 58, 1994 CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS protease digestion, suggesting that it remained on the ribosome surface (203). L14 in E. coli is a late-assembly protein and does not bind directly to 23S rRNA (458). Antibody-binding studies suggest that in B. stearothermophilus this protein is located on the surface of the 50S subunit (599). Genes encoding proteins with a high degree of homology to E. coli L14 have been found in chloroplast genomes of all plants and algae examined, except in the parasitic plant Epifagus virginiana, in which a pseudogene is present instead (714) (Table 3). In E. coli, both L15 and L16 are late-assembly proteins that are associated with the peptidyltransferase center but seem to be nonessential for ribosome function. Fully active ribosomes lacking both these proteins, as well as L30, can be reconstituted in vitro by modifying the conditions of the reconstitution procedure (175). Nuclear genes encoding chloroplast ribosomal protein L15 have been reported from Arabidopsis thaliana and pea (640), and no rpll5 sequences have been identified in any chloroplast genome to date (Table 3). The spinach chloroplast homolog of L15 is significantly larger than its counterpart in E. coli, owing to extensions at the N-terminal and probably also the C-terminal ends (291). In contrast to L15, ribosomal protein L16 is encoded by a chloroplast gene located in a conserved operon in all species examined (Table 3; Fig. 5). In land plants, the rpll6 gene is split into two exons (e.g., 498), whereas in Chlamydomonas reinhardtii (373) and Gracilaria tenuistipitata (294), it is uninterrupted. The Euglena gene contains three introns (86, 93). Antibodies to a chloroplast-encoded Chlamydomonas protein ("L-17") cross-react with E. coli L16, with spinach "L24," and with an Anabaena protein that comigrates with E. coli L16 (510). Protein L17 of E. coli has been shown to bind 23S rRNA (358). A mitochondrial homolog has been identified in Saccharomyces cerevisiae (708), but no corresponding chloroplast protein has been found. However, proteins of similar charge and size were seen on two-dimensional electrophoresis of ribosomal proteins from C. reinhardtii and Anabaena sp. (510). Antibodies to E. coli L17 were also observed to cross-react with a chloroplast ribosomal protein from spinach (18). Protein L18, which is highly conserved in bacteria, binds to 5S rRNA and is associated with the peptidyltransferase center (91). Genes encoding a ribosomal protein equivalent to E. coli L18 have been found in the cyanelle genome of Cyanophora paradoxa (423) and in the Porphyra chloroplast genome (517). Spinach ribosomal protein "CS-L13" is a homolog of E. coli L22 (see below), with N- and C-terminal extensions that have no sequence homology with the 5S-binding proteins of E. coli but show some structural similarity to L18 (651). A gene encoding a protein equivalent to E. coli L19 has been found in the Porphyra chloroplast genome (514) and in the cyanelle genome (598). Little is known about the function of this protein in either bacterial or chloroplast ribosomes. An equivalent of the early-assembly, RNA-binding protein L20 of E. coli is encoded in chloroplast genomes of plants and algae and in the cyanelle genome of Cyanophora paradoxa (Table 3). Protein L21 of E. coli can be cross-linked to the 5' domain of the 23S rRNA molecule and, together with L4, may have a second contact to the 23S molecule in the adjacent domain (57, 481). The gene encoding L21 is chloroplast encoded in Marchantia polymorpha and in the red algae Cyanidium caldarium and P. purpurea (Table 3) but is absent from the chloroplast genomes of rice, tobacco, and Euglena gracilis. A spinach nuclear gene encoding L21 has been found to contain four introns in its central region (340, 578). Two transcription start Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV (149, 533). McElwain et al. (413) have isolated a thiostreptonresistant mutant of C. reinhardtii whose chloroplast ribosomes are resistant to the drug in vitro. The large subunits of the mutant ribosomes lack a cytoplasmically synthesized protein ("L-23") that, on the basis of size and immunological criteria, appears to be the equivalent of the E. coli L1i protein. In pulse-labeling experiments, this Chlamydomonas mutant synthesizes small amounts of protein "L-23," but the protein fails to assemble into chloroplast ribosomes. The mutation shows Mendelian inheritance, suggesting that rplll is a nuclear gene in C. reinhardtii. The acidic protein L7/L12 is one of the most intensively studied ribosomal components (57, 474, 708). Four L12 molecules are present in each ribosome of E. coli, together with one L10 polypeptide, forming the stalk of the 50S subunit and interacting with elongation factor EF-G which binds near the base of the stalk. The homologous protein was identified in spinach chloroplasts by direct sequencing of tryptic peptides (19) and was predicted to have a tertiary structure similar to that of its counterpart in E. coli (271, 345). cDNA clones encoding this protein have been isolated and sequenced from the nuclear genomes of several land plants (Table 3), and the gene has been cloned and characterized from Arabidopsis thaliana and spinach (689). In Arabidopsis thaliana (689), L12 is encoded by a multigene family with one silent and two functional genes, the functional genes both being closely linked to cytosolic tRNA genes (this is the first such case identified for a chloroplast ribosomal protein [607]). However, L12 is encoded by a chloroplast gene in Euglena gracilis and by a cyanelle gene in Cyanophora paradoxa. The derived amino acid sequence of the cloned spinach gene includes three amino acids that were apparently overlooked in the primary sequence of the corresponding protein published by Bartsch et al. (19). Sibold and Subramanian (564) have compared the spinach and bacterial sequences with the L12 protein of the cyanobacterium Synechocystis sp. Like the E. coli protein, spinach L12 is present in multiple copies per ribosome, but it lacks the N-terminal acetylation seen in the bacterial protein (19). Giese and Subramanian (202) reported that the transit peptide sequence of a spinach gene for L12 contains two ATG codons, each in a consensus initiation context, that would yield the same mature peptide after transport into chloroplast and N-terminal cleavage. Genes for L13, L35, and the novel protein Psrp-1 have similar duplicated ATGs. Experiments in which the 5' part of the L12 gene was fused to a reporter gene demonstrated that both codons can be used in vitro and in spinach protoplasts, with about 25% of initiations occurring at the second codon. Such an arrangement may enhance translational efficiency. However, Elhag et al. (155) found that both L12 cDNAs from tobacco had only a single ATG, corresponding to the first ATG of the spinach gene. The L13 protein of E. coli interacts with the 5' domain of the 23S rRNA molecule, in proximity to L4, L21, L28, and L29 (57). A nuclear cDNA clone encoding a chloroplast ribosomal protein equivalent to E. coli L13 has been identified in spinach (490, 609), and a chloroplast gene for this protein has been found in Porphyra purpurea (517). The spinach protein has 54% deduced amino acid identity with that of E. coli over the 142 amino acid residues that can be aligned, but it is preceded by 52 residues at the N terminus with no homology to any known protein. Upstream of this sequence are 47 amino acids which appear to be a transit peptide. The chloroplast protein also has a C-terminal extension with no homology to E. coli L13. However, spinach L13 translated in E. coli from cDNA constructs was found to be incorporated into functional ribosomes (203). The N-terminal extension was removable by mild 727 728 HARRIS ET AL. L23 are found in ribosomes from eubacteria, organelles, archaebacteria, and cytoplasmic ribosomes of eukaryotes (513, 708). The equivalent cytoplasmic ribosomal proteins (called L25 proteins) have an extended amino terminus and a carboxy terminus that resembles the archaebacterial L23 protein more than the eubacterial one. Sequences with relatively low homology to the gene encoding E. coli L23 have been found in the "S1O"-like operons in chloroplast genomes of a number of plants (Table 3; Fig. 5). While these rp123 sequences are in the same position as the E. coli gene for L23 in this operon, not all the chloroplast sequences form continuous open reading frames and some may be pseudogenes (45, 732, 746). The rp123 genes of spinach and four related dicots appear to have sustained a 14-bp deletion approximately in the center of the coding sequence, creating two overlapping open reading frames with homology to the two halves of the tobacco gene (635, 746). Transcripts for both reading frames could be detected in vivo by S1 mapping in spinach (635). However, no radioactive peptides corresponding to these transcripts were seen on two-dimensional electrophoresis of the products of a coupled transcription-translation system. Furthermore, when chloroplast ribosomal proteins of a size close to those expected for the chloroplast rpl23 gene products, either singly or spliced, were subjected to N-terminal sequencing, none of the sequences obtained corresponded to the predicted sequence of the split rp123 gene. Bubunenko et al. (70) have recently reported that chloroplast ribosomes of spinach contain no protein that cross-reacts with the product of the functional chloroplast rpl23 gene of maize but do contain a protein with strong homology to the L23 equivalent of eukaryotic cytoplasmic ribosomes. This is the first suggestion that a nuclear gene encoding a cytoplasmic ribosomal protein has been substituted for a nonfunctional chloroplast gene. In Epifagus virginiana the plastid rpl23 sequence is also a pseudogene (714). However, Yokoi et al. (732) found that the tobacco rpl23 gene, which does have a continuous open reading frame, appears to be functional, since the N-terminal sequence of a 13-kDa protein from the 50S ribosomal subunit exactly matches that predicted from the chloroplast rp123 gene. The rp123 genes from three monocots (rice, wheat, and maize) are also uninterrupted, and their derived amino acid sequences are virtually identical to one another. In rice an rp123 gene is located in the inverted repeat, but an open reading frame with homology to rpl23 is also present in the large single-copy region between rbcL and petA (265). Analysis of the corresponding region in wheat (Triticum aestivum) and two closely related plants,Aegilops squarrosa andA. crassa, has revealed an apparent rp123 pseudogene in wheat andA. crassa but not inA. squarrosa, whose chloroplast genome seems to have sustained a deletion in this region as a result of illegitimate recombination between short direct repeats (45, 46, 469). Wheat has a length polymorphism just downstream of this gene compared with A. crassa, also apparently the result of an illegitimate recombination event between relics of short repeats. Sequences with strong homology to the chloroplast rpl23 genes and pseudogenes have also been detected in mitochondrial DNA of rice and maize (45). The rpl23 gene is missing from the corresponding operon of the cyanelle genome (32, 598). In Euglena gracilis, the rp123 gene is in the expected position at the start of the "S10" operon but is interrupted by three group III introns (243). An uninterrupted rp123 gene has been sequenced from the chloroplast genome of C. reinhardtii, in the expected position at the start of the "S10" operon (277). However Randolph-Anderson et al. (510) found that antibody to C. reinhardtii "L-29," a cytoplas- Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV sites were identified, one which appears to be constitutive and the other which appears to be induced only in leaf tissue (340). The spinach L21 protein (formerly "CS-L7" [378]) is considerably longer than its homologs from E. coli and Marchantia polymorpha, having extensions at both the N and C termini. The carboxyl-terminal extension contains seven Ala-Glu repeats, creating a region of high negative charge, and the protein as a whole is acidic, in contrast to E. coli L21, which is basic. However, this protein can be incorporated into E. coli ribosomes assembled in vivo (71, 685). The spinach L21 protein shows greater homology to E. coli L21 than it does to the chloroplast-encoded Marchantia protein, prompting Martin et al. (408) to hypothesize that spinach L21 arose either by duplication of a nuclear gene for a corresponding protein of the cytoplasmic ribosome or by transfer of a mitochondrial gene, rather than by transfer of a chloroplast gene to the nucleus. A mitochondrial origin seems unlikely, since no gene encoding the equivalent of L21 has so far been identified in a mitochondrial genome of any plant (371). Protein L22 binds to 23S rRNA early in assembly of the 50S particle in E. coli and is one of only five proteins both necessary and sufficient to formation of the core precursor particle RI* (459). Equivalent proteins have been identified in archaebacteria and cytoplasmic ribosomes (381, 708). The rp122 gene is found in chloroplast genomes of all land plants so far examined, with the exception of two unrelated groups of angiosperms, the legumes and the parasitic plant Epifagus virginiana (193, 485) (Table 3). A nuclear gene encoding L22 has been cloned from pea (193). In this gene, the exon encoding the putative N-terminal transit peptide is separated by an intron from the conserved structural gene. Gantt et al. (193) speculated that the transit peptide sequence may have been acquired by a form of exon shuffling. The rp122 gene is also missing from the relic of the S10 operon in the C. reinhardtii chloroplast genome (277) but is found in the expected location in the plastid genomes of Euglena gracilis and the red algae Gracilaria tenuistipitata and Porphyra purpurea (86, 295, 514) and in the cyanelle genome (163, 423). The spinach rp122 gene encodes a protein with a central region homologous to all L22 proteins but has N-terminal and C-terminal extensions with structural similarity to the E. coli L18 and L25 proteins on the basis of hydropathy profiles (651, 741). The spinach L22 protein binds to SS rRNA, protecting three nonoverlapping binding sites (76, 651). In E. coli, however, L22 does not bind SS rRNA but L18 and L25 do. These observations suggest the interesting possibility that the spinach L22 protein ("CS-L13") serves the composite functions of all three of these proteins. Carol et al. (76) have shown that the L22-like central domain of the spinach protein is required for SS binding, so that this domain appears to have a function lacking in the E. coli protein. However, both the spinach and E. coli L22 proteins bind erythromycin. The monocots rice and maize have L22 proteins with similar 29-residue N-terminal extensions, which, however, have little homology to the spinach extension. N-terminal extensions are lacking in the L22 proteins of tobacco, Marchantia, Euglena, and Gracilaria species; the tobacco protein has a C terminus that is longer than that of Marchantia polymorpha but considerably shorter than that of spinach. The position of L23 in the E. coli ribosome has been controversial, with cross-linking and immunoelectron microscopy studies giving conflicting results (91, 447). Kruft et al. (328) propose that it has an elongated structure, with the N-terminal domain close to L29 at the base of the 50S subunit and the C-terminal domain on the ribosomal surface close to the peptidyltransferase center. Proteins equivalent to E. coli MICROBIOL. REV. VOL. 58, 1994 CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS tive (103). A nuclear gene encoding a protein with sequence similarity to E. coli protein L28 has been isolated from tobacco (731). The "L-31" protein of C. reinhardtii chloroplast ribosomes was observed to comigrate with E. coli L28, but immunological cross-reactivity was not tested (510). E. coli protein L29 also can be cross-linked to the 5' domain of the 23S molecule (57) but associates with the ribosomal particle early in the assembly process (459). L29 appears in the same ribosomal neighborhood as proteins L2, L4, L15, and L34 (676). A gene encoding an equivalent chloroplast protein has so far been found only in Porphyra purpurea (514). Protein L30 of E. coli assembles late and can be eliminated by mutation (103, 459). An equivalent protein has been identified in archaebacteria (708) but so far not in chloroplasts. L31 is a late-assembly protein in E. coli (358, 459) and is known so far only from the Porphyra chloroplast genome. E. coli L32 also associates with the ribosome late in the assembly process (459). Genes encoding L32 have been found in the chloroplast genomes of several plants and algae (Table 3). However, this gene is missing from the Epifagus chloroplast genome (714). Deduced amino acid similarity to the E. coli gene is low (Table 3), but hydropathy plots suggest that the plant and bacterial proteins are similar in conformation (733). The N-terminal portions of the chloroplast L32 proteins are highly conserved in amino acid sequence, whereas the Cterminal ends are variable in sequence and in length. The E. coli L33 protein can be cross-linked to 23S rRNA at positions 2422 to 2424 (481) and to proteins Li and L27 (676). Mutants of E. coli lacking L33 are viable but cold sensitive (103). The rp133 gene is chloroplast encoded in land plants and Porphyra purpurea and has also been sequenced from the cyanelle genome (Table 3) but is missing from the Euglena chloroplast genome (243). Protein L34 has been characterized in a number of eubacterial species but has not yet been identified in chloroplasts except for those in Cyanophora and Porphyra purpurea. In the E. coli ribosome, it is found in a neighborhood with proteins L2, IA, L15, and L29 (676). Protein L35, formerly designated ribosomal protein A in E. coli (675), is encoded in the nuclear genome of spinach (577) but in the chloroplast genome of P. purpurea (514) and in the cyanelle genome of Cyanophora paradocxa (69). L36, the product of the E. coli gene formerly designated secX (675), is chloroplast encoded in all plants and algae so far examined (Table 3). The high degree of conservation of the amino acid sequence of the chloroplast L36 proteins compared with E. coli (Table 3) suggests that this small protein may have an important but as yet unknown role in the ribosome. Chloroplast Ribosomal Proteins with No Obvious Homology to Those of E. coli Zhou and Mache (741) reported that spinach chloroplasts contain relatively large amounts of a unique ribosomal protein, "CS-S5." The deduced amino acid sequence of a full-length cDNA clone for the nuclear gene encoding this ribosomal protein shows no sequence similarity to any bacterial ribosomal protein (28, 741). Working independently, Johnson et al. (290) characterized a 26-kDa protein from spinach chloroplast ribosomes ("PSrp-1"), which appears to be identical to "CSSS." The DNA sequences determined by the two groups differ in three nucleotides, one of which creates a frame shift that changes the predicted C-terminal sequence. Direct sequencing of protease-generated internal peptides supports the 236amino-acid sequence published by Johnson et al. (290). The precursor form of this protein contains 302 amino acids. Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV mically synthesized protein, cross-reacts with E. coli L23 and with spinach ribosomal protein "L28." This antibody showed no cross-reaction with Anabaena "L24," a protein which comigrates with E. coli L23 on two-dimensional gels. L24 is an early-assembly rRNA-binding protein in bacteria, which, together with L3, is essential for initiation of assembly of the 50S subunit but seems not to be essential either for late stages of ribosome assembly or for translation in vivo. An E. coli mutant lacking L24 can grow, albeit very slowly (257, 461). A reading frame specifying L24 has been found in the chloroplast genome of P. purpurea, in the position expected based on similarity to the E. coli spc operon (514), but this protein appears to be nucleus encoded in land plants, and cDNAs encoding it have been sequenced from pea (192), spinach (75, 339), and tobacco (153). The plant sequences have transit peptides of about 70 amino acids, as well as highly conserved C-terminal extensions. L25 is a 5S-binding protein in E. coli (57). No exact homolog has been identified in chloroplast ribosomes. However, in spinach two chloroplast ribosomal proteins, L22 and "CS-12," have been shown to bind SS rRNA and may thus together serve the same function as E. coli L5, L18, and L25 (76, 651) (see above). The 5S-binding domain of spinach "CS-12" shows structural similarity to that of L25. The protein formerly designated as L26 of E. coli is now identified as S20 (706). L27 is a conserved protein that maps by immunoelectron microscopy to the base of the central protuberance of the 50S subunit of the E. coli ribosome and appears to be associated with the peptidyltransferase center (57, 744). Plastid genes encoding this protein have been sequenced from chromophyte and rhodophyte algae (185, 517), but the gene appears to be nucleus encoded in green algae and in land plants. Two cDNAs encoding a protein homologous to E. coli L27 have been sequenced from tobacco (154) and found to have differing 3'-flanking sequences, suggesting that the tobacco nuclear genome encodes more than one L27 gene. The identity of these cDNAs was confirmed by comparing the predicted amino acid sequences with that determined for the purified L27 protein (154). N-terminal amino acid sequencing of the cytoplasmically synthesized ribosomal protein designated "L-18" in C. reinhardtii (547) indicates that this protein is the E. coli L27 homolog (363), but the gene has not yet been cloned. Schmidt et al. (545, 546) found that C. reinhardtii "L-18" is synthesized as an 18.5-kDa precursor that undergoes a two-step processing reaction. Conversion of the 17-kDa intermediate identified in pulse-labeling experiments to the mature 15.5-kDa form requires chloroplast protein synthesis. Liu et al. (363) showed that the 17-kDa intermediate specifically associates with a ribosomal complex that migrates with the ribosomal large subunit before being processed to the mature protein. This suggests that the second processing step may be required for maturation of the 50S ribosomal subunit. Antibody to C. reinhardtii "L-18" cross-reacts with E. coli L27, with spinach "L22" (terminology of Mache et al. [378]), and with an Anabaena protein ("L23" [510]). Elhag and Bourque (154) show the alignments of the tobacco L27 sequence with the partial L27 sequences of C. reinhardtii (547) and spinach (607), and with that of the yeast mitochondrial ribosomal protein MRP7 (167). Elhag and Bourque (154) note that this is the first example of a chloroplast ribosomal protein for which the sequence of a presumably homologous mitochondrial ribosomal protein is known. L28, which cross-links to the 5' domain of the 23S rRNA, is added to the E. coli ribosome relatively late in assembly (57, 459), and mutants lacking L28 are viable although cold sensi- 729 730 HARRIS ET AL. Lagrange et al. (339) proposed to designate this ribosomal protein S22, since S21 is the highest-numbered protein of the E. coli small subunit. Schmidt et al. (541) have proposed alternatively that the numbers 22 to 29 be skipped and that this protein be named S30 instead. Schmidt et al. (541) and Wada et al. (674) have independently identified another novel protein in preparations of spinach chloroplast ribosomes. Schmidt et al. described a basic protein of about 7.5 kDa and gave it the designation S31. A Comparative Analysis of Ribosomal Proteins Sequence comparisons across phylogenetic lines can reveal essential structural features of both RNAs and proteins. This technique has been beautifully exploited in establishing conserved loops and helices in 16S and 23S rRNAs (see, e.g., reference 236) but has been less well developed to date in analysis of ribosomal proteins. Golden et al. (213) have recently reported the three-dimensional structure of ribosomal protein S17 from B. stearothermophilus, based on nuclear magnetic resonance spectroscopy, and Hoffman et al. (266) have solved the crystal structure for protein L9 from this bacterium. The comparative analysis presented in both these papers includes the sequences for the homologous proteins from pea and Arabidopsis thaliana, as well as the Cyanophora S17 and Synechocystis L9 sequences. Conserved structural residues and proposed rRNA-binding sites can be identified in both proteins. Conservation of the length of an al-helix in the L9 protein, for example, suggests that this helix has a structural role, whereas variability in the central region of the protein sequence is consistent with its occupying an exposed position in the ribosome. Similar analyses should be possible with other ribosomal proteins. ASSEMBLY OF CHLOROPLAST RIBOSOMES Subramanian (606) points out that the ribosomal proteins encoded in land plant chloroplast genomes share the following properties: (i) all are important proteins in early steps in ribosome assembly as judged from comparison with assembly maps of the E. coli 30S and 50S subunits (see, e.g., reference 707); (ii) their loss is likely to be lethal, since no E. coli mutants lacking any of these proteins, with the exception of L33, have been isolated; and (iii) all are basic or highly basic ribosomal proteins, even though chloroplast ribosomes contain a much larger number of acidic ribosomal proteins than E. coli ribosomes do. The limited data available on chloroplast ribosome assembly have been summarized for land plants by Mache (377). The main observations on land plants and C. reinhardtii are as follows. (i) Seven chloroplast ribosomal proteins, four of which are made in the chloroplast, bind to chloroplast or E. coli 16S rRNA, in agreement with the seven E. coli ribosomal proteins known to bind to 16S rRNA (531). (ii) Two 5S rRNA-binding proteins have been detected in spinach (L22 and "CS-12" [651]), in contrast to three in E. coli (L5, L18, L25). However, one of these chloroplast proteins, encoded by the rp122 gene, has a central region of homology to other L22 proteins flanked by long N- and C-terminal extensions (76). (iii) In C. reinhardtii, the second step of processing of "L-18," a homolog of E. coli L27, occurs during ribosome assembly and may be required for maturation of the 50S ribosome subunit (363). (iv) The nucleus-encoded ribosomal protein "L-29" of C. reinhardtii is required for assembly of chloroplast-encoded ribosomal protein "L-13" (see below and reference 446). Mutants with defects in chloroplast ribosome assembly have been identified in C reinhardtii and map to seven nuclear and two chloroplast loci (see reference 247 for a summary). Two phenotypic classes are seen, one in which small subunits are deficient but large subunits accumulate and one in which both subunits are deficient. No mutant specifically deficient in large subunits has been identified. Analysis of double-mutant combinations of five nonallelic nuclear mutations led to the proposal that mutants deficient in both subunits were blocked in steps common to the assembly of the two subunits, while the mutants that accumulated large subunits were blocked only in the assembly of small subunits (248). One of the mutants deficient in both subunits, ac-20, has subsequently been shown to be defective in its ability to splice an intron present in the precursor of 23S rRNA (259). Since expression of the mutant defect apparently occurs after processing of the primary rRNA transcript, these observations suggest that inability to process pre-23S rRNA properly results in a deficiency of large subunits, which in turn prevents small subunit assembly. Two Chlamydomonas allelic nuclear mutations, cr-6 and cr-7, cause production of ribosomal large subunits that sediment abnormally on sucrose gradients, assemble into monomers less efficiently than those from wild-type cells, and show reduced capacity for protein synthesis in vivo (446). Large subunits of chloroplast ribosomes from these two mutants lack two proteins, one of which ("L-29") is made in the cytoplasm and the other ("L-13") is made in the chloroplast. The primary defect appears to be an inability to make "L-29," which prevents assembly of "L-13" into the 50S subunit. Immunologically, "L-29" is related to E. coli L23 and to a lesser extent to L7/L12, while "L-13" is related to E. coli L5 (see above and reference 510). Assembly of L5 into the E. coli 50S subunit Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV sequence of 43 of the estimated 60 amino acids constituting this protein showed no homology to any known E. coli ribosomal protein or to any other sequence available in public databases, nor did it correspond to the derived amino acid sequence of any coding region in a published chloroplast DNA sequence. However, the sequenced region was shown to have 42% identity to the unpublished sequence of a small basic protein isolated from the bacterium Thermus thermophilus. Wada et al. (674) described a 5-kDa protein, SCS23, with no apparent homology or immunological cross-reactivity to any E. coli ribosomal protein. The N-terminal sequence of this protein is similar to that published by Schmidt et al. (541). Two cDNAs isolated from pea encode ribosomal proteins of moderate size with no recognizable similarity to any ribosomal protein of E. coli (192). The PsCL18 gene encodes a protein of 145 amino acids, including a transit sequence of approximately 50 amino acids, and the PsCL25 gene specifies a protein of 104 amino acids, of which about 30 amino acids constitute a transit sequence. Typical of ribosomal proteins, the deduced amino acid sequences of both PsCL18 and PsCL25 have a high content of lysine and arginine residues, and a consequent high net positive charge, but differ in the distribution of these charged amino acids. PsCL18 has a highly charged, highly basic carboxyl end, whereas the carboxyl terminal of PsCL25 contains mostly uncharged amino acids with four aspartic acid residues constituting the only charged species. No E. coli ribosomal protein has a carboxyl terminus resembling either of these nucleus-encoded chloroplast ribosomal proteins from pea. A protein similar to PsCL18 has been isolated from spinach and designated L40 (75, 339). This protein appears to be encoded by a single-copy nuclear gene and to contain 142 amino acids with 54% sequence identity to pea CsL18. This is a slightly lower sequence identity than is seen between other nucleus-encoded ribosomal proteins of higher plants, e.g., S17, L12, and L15 (Table 3). MICROBIOL. REV. CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS VOL. 58, 1994 origin. SYNTHESIS OF THE COMPONENTS OF CHLOROPLAST RIBOSOMES Biogenesis of chloroplast ribosomes requires expression of both nuclear and chloroplast genes encoding different ribosomal proteins, as well as chloroplast genes encoding the component rRNAs. The mechanisms by which the appropriate stoichiometry of these components is achieved from genes present in vastly different copy numbers remain poorly understood (229, 377, 379). In general, nuclear gene expression in plants tends to be controlled at the level of transcription and to be subject to light regulation, whereas chloroplast gene expression is largely regulated posttranscriptionally. Pool sizes of some components may also be controlled by proteolysis. Furthermore, chloroplast genes encoding ribosomal components appear to be regulated differently from those encoding proteins of the photosynthetic apparatus (207, 253, 365). In this section we will discuss transcription and splicing of rRNAs, transcription and translation of genes encoding ribosomal proteins, and posttranscriptional and translational regulation of chloroplast gene expression. Transcription of rRNA Genes As in bacteria, chloroplast rRNA genes are thought to be transcribed as large precursor molecules that subsequently undergo several processing steps to generate the mature rRNAs (114). Relatively little is known, however, about the specific enzymes and cleavage steps that are involved. Although 5S rRNA sequences are not detected in the primary transcript, S1 and primer extension experiments suggest that the 5S gene is indeed cotranscribed with the 16S and 23S genes and that the 5S rRNA is rapidly cleaved from the initial precursor (10, 601). Possible promoter sequences have been found between the 4.5S and 5S rRNA genes in some plants, suggesting that separate 5S transcription might occur, but these sequences are not present in many plants and do not seem to be active in vitro (10, 146). Likewise, the tRNA'g following the 5S gene in land plants is thought to be cotranscribed with the rRNAs (118). However, the tRNAVal upstream of the 16S gene in many plants lies distal to the identified transcription start sites for the rRNA operon and thus is not part of the primary transcript. Possible processing sites of the primary rRNA transcript have been identified by Si and reverse transcriptase mapping (118, 601; see also reference 114). Experiments so far suggest that cleavage at the various sites does not occur in a precise order. The 5'- and3'-terminal precursor sequences of the 16S and 23S RNAs can form double-stranded stem structures similar to those of the E. coli rRNA genes, leading to the suggestion that these molecules may be processed by an RNase III-like endonucleolytic cleavage (114). Vera et al. (669) have found that tobacco chloroplast ribosomes contain a minor fraction of 16S rRNA molecules in which a 30-nt leader sequence containing the putative RNase III site is still present, suggesting that the final maturation of the 16S rRNA may actually take place within the ribosome. Processing of the tRNAs of the spacer between the 16S and 23S genes requires the ribozyme RNase P (679), but other processing reactions specific to plant chloroplast rRNAs have not been well characterized to date. Additional processing of the mature 23S rRNA of land plants may occur, leading to hidden breaks at specific stem-loop sites. Thus 23S rRNA isolated under denaturing conditions typically appears as several short species rather than a single intact molecule. Delp and Kossel (114) suggest that this fragmentation is real, not an artifact of preparation, and that it may be necessary for some structural or functional requirement of the chloroplast ribosome. There are conflicting data regarding whether chloroplast rRNA genes are transcribed by a different RNA polymerase from that used to produce mRNAs (229, 283, 320, 349, 642). Chloroplast genomes typically contain genes homologous to the rpoA, rpoB, and rpoC genes, which encode RNA polymerase subunits of bacteria, but appear to lack a gene for rpoD, which encodes the principal cr factor of the bacterial RNA polymerase (24, 171, 614, 653). However, immunological studies suggest that the chloroplast RNA polymerase complexes do contain a-like factors (642, 653). Expression of the chloroplastencoded RNA polymerase genes in Euglena chloroplasts resulted in activity of a soluble RNA polymerase fraction capable of transcribing tRNA and mRNA genes, whereas transcription of rRNA genes required a membrane-bound fraction (226, 244, 361). However, soluble RNA polymerase from spinach chloroplasts appears to be able to transcribe both rRNA and protein-coding genes in vitro (55). Fractionation of RNA polymerase activities from spinach suggests that a 110-kDa component may represent a core enzyme active as a single polypeptide chain, which shows no immunological similarity to E. coli RNA polymerase subunits and is thus probably not the product of the chloroplast rpoB gene (349). Further evidence for a second, presumably nucleus-encoded RNA polymerase activity in chloroplasts comes from the observation that the plastid genome of the parasitic plant Epifagus virginiana lacks the rpo genes but is nevertheless transcribed (115, 435, 713, 714). Also, some plastid genes in heat-bleached leaves of rye and barley plants and the albostiians mutant of barley are transcribed, although these leaves lack functional chloroplast Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV does not depend directly on the presence of either L7/L12 or L23 (707). Chloroplast and nuclear mutations causing complete or nearly complete loss of chloroplast ribosomes from white tissues and seedlings have also been identified in land plants (39) and have been very useful in probing the function of the chloroplast protein-synthesizing system. Barkan (17) has recently described transposon-induced nuclear mutations in maize that impair chloroplast protein synthesis. Seedlings of these mutants are paler green than those of the wild type and are photosynthetically inactive, although they do accumulate nucleus-encoded proteins of the light-harvesting complex. One mutant appears to be blocked specifically in processing of 16S rRNA. Complete assembly of ribosomal subunits has been detected in isolated spinach chloroplasts, implying either that a pool of unassembled nucleus-encoded ribosomal proteins exists in plastids or that ribosomal proteins can be released from preexisting ribosomes and reutilized (121). Certain proteins, e.g., the CS-S5 protein of spinach, can be found in high concentrations in the chloroplast stroma (741). When rye plants are grown at high temperature (32°C), plastid ribosome formation is severely impaired (168, 169). Pools of a few unassembled plastid ribosomal proteins were detected when soluble extracts from leaves deficient in 70S ribosomes were examined with antibodies raised against purified 50S and 30S subunits. These antibodies were shown to react with about 17 of the 33 polypeptides of the 50S subunit and 10 of the 25 proteins of the 30S subunit. Feierabend and Berberich (168) believe that these observations confirm the absence of plastid ribosomes following bleaching and that the unassembled proteins detected by the antibodies are probably of cytoplasmic 731 732 HARRIS ET AL. ribosomes and are thus unable to translate the mRNAs for the rRNA gene and has a conserved and essential -35 sequence. A 14-bp sequence that is recognized by polypeptides of 33 and 35 kDa has also been identified upstream of the 16S rRNA initiation start site in spinach (13). This sequence is not found upstream of chloroplast genes encoding mRNAs or tRNAs and thus may have a role in differential regulation of rRNA and protein-coding genes during chloroplast development. Expression of rRNA genes appears to depend on both light and developmental stage in plant seedlings (309, 442), but steady-state levels of rRNA seem to be controlled more by the rate of breakdown than by transcriptional regulation (114). Bendich (21) has suggested that rRNA transcription is regulated primarily by gene dosage. However, in cells of C. reinhardtii grown in the presence of 5-fluorodeoxyuridine, the reduction in chloroplast DNA copies was mirrored by a reduction in accumulation of chloroplast rRNA (208, 272). There is indirect evidence that conserved stem-loop structures and short open reading frames found between the promoter and the start of the 16S coding sequence could be involved in regulation of rRNA operon expression in spinach chloroplasts (338). Bisanz-Seyer et al. (27) observed the accumulation of 16S rRNA and mRNAs for several chloroplast ribosomal proteins during early development of spinach. The 16S rRNA, already present in dry seeds, began to increase at the time of seed germination 5 days after planting and continued to accumulate thereafter. Most ribosomal protein mRNAs appeared at the beginning of germination (5 days), but the rpsl9 and rp123 mRNAs appeared 2 days earlier. These two genes belong to a large chloroplast ribosomal protein operon including parts of the S10, spc, and a operons of E. coli. Interestingly, mRNAs for several other ribosomal protein genes in this operon, including rps3 and rp116, did not begin to accumulate until germination. One explanation of these results is that the first three genes in this operon, rp123-rp12-rpsl9, are transcribed early and the whole operon is transcribed later. This hypothesis predicts that rp12 transcripts should also be detected early, but this was not examined with appropriate probes. Alternatively, the entire operon may be transcribed early, but transcripts distal to rpsl9 are initially degraded. Gantt et al. (194) have presented additional evidence that nuclear genes encoding chloroplast ribosomal proteins are subject to light regulation. Pea seedlings grown in bright light in the presence of the inhibitor norflurazon, which blocks carotenoid synthesis, showed greatly decreased levels of mRNA for nucleus-encoded ribosomal proteins compared with seedlings grown with or without norflurazon in the dark. Levels of mRNAs for other chloroplast components were similarly diminished, but mRNAs for cytoplasmic ribosomal proteins, histones, and other nonphotosynthetic proteins were not affected. Transcription of Chloroplast Genes Encoding Ribosomal Proteins Nuclear and plastid genes which cooperate in controlling chloroplast biogenesis and function appear to be regulated by very different mechanisms, although their gene products often occur in equal stoichiometry within the multimeric thylakoid complexes or chloroplast ribosomes. This may reflect the way in which plant cells cope with large differences in ploidy levels between nuclear genes (present in single copies or small gene families) and chloroplast genes (present in hundreds or thousands of copies per cell). Nuclear genes encoding chloroplast polypeptides are regulated largely at the transcriptional level in response to environmental and developmental signals (for reviews, see references 209, 329, and 443). In contrast, most plastid genes appear to be transcribed at all times during plastid development, and posttranscriptional regulatory mechanisms are thought to play major roles in modulating their expression (see below). All 21 of the ribosomal protein genes in the rice, tobacco, maize, and Marchantia chloroplast genomes have been demonstrated to be transcribed (540), but not all have been shown unequivocally to be translated into the corresponding polypeptides. N-terminal sequencing indicates that ribosomal proteins S12, S16, S19, L2, L20, L32, L33, and L36 of spinach chloroplasts do indeed appear to be products of the corresponding chloroplast genes (540). Most of the clusters of chloroplastencoded ribosomal protein genes that show striking homology to bacterial ribosomal protein operons (631) (Fig. 5) are probably functional transcriptional units (540). Multiple transcripts are typically found for individual ribosomal protein genes in these clusters, and these may arise from processing of larger polycistronic transcripts (470, 605). In C. reinhardtii, no single large mRNA has been detected for the ribosomal protein gene cluster that begins with the rp123 gene, but, rather, a series of transcripts of different lengths have been observed, including some probably monocistronic transcripts and others corresponding to two or more genes (362; see also reference 253). Christopher and Hallick (87, 88) published a detailed characterization of the organization and transcription of the large ribosomal protein operon in Euglena gracilis. The primary transcript of this operon includes 11 genes encoding ribosomal proteins, a tRNA gene, and an open reading frame encoding a highly basic protein of unknown function (88, 243). An 8.3-kb mRNA from which all introns have been removed by splicing is then processed stepwise into transcripts containing one or more genes. Tonkyn and Gruissem (648) examined the relative expression levels of the intact S10 operon from spinach and the partial S10 operon that begins in the opposite inverted repeat but ends in an rpsl9' pseudogene as discussed above. Because the upstream regulatory regions of these two operons are included in the inverted repeat in spinach and are therefore identical, Tonkyn and Gruissem predicted that these operons Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV plastid-encoded rpo genes (164, 262, 263). In land plant chloroplasts, promoter sequences preceding the transcription start sites of rRNA operons do not differ significantly from the -10 and -35 consensus sequences of plastid protein-coding genes and are typically 50 to 200 bp upstream of the 16S rRNA genes (229). The resemblance to promoter sequences of protein-coding genes implies that a single-core RNA polymerase might be able to transcribe all classes of RNAs, a notion that is also supported by the demonstration that a chimeric gene consisting of the 16S promoter fused to the bacterial aadA gene encoding spectinomycin and streptomycin resistance is expressed in chloroplast transformants of tobacco (621). This construct was edited by site-directed mutagenesis to eliminate upstream AUGs in the mRNA, and a synthetic leader sequence containing a ribosome-binding site was attached. The aadA gene was followed by the 3' region of the chloroplast psbA gene. However, deletion analysis with chloroplast transformants in which putative promoter regions were fused to a reporter gene has led to the identification of two classes of chloroplast promoters in C. reinhardtii (310). Promoters of the first class, such as atpB, lack a conserved -35 sequence, and deletion of this region has no effect on relative rates of transcription or the transcription initiation site. The second class of promoters includes the 16S MICROBIOL. REV. VOL. 58, 1994 CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS Posttranscriptional Regulatory Mechanisms Affecting Chloroplast mRNAs Recent reviews by Rochaix (520), Gruissem and Schuster (228), and Gruissem and Tonkyn (229) provide excellent summaries of the current literature dealing with the processing, stability, and translational control of chloroplast mRNAs in general, although relatively little of this literature is specific to genes encoding ribosomal proteins. Two generalizations emerge from these reviews. First, nuclear gene products control expression of chloroplast-encoded mRNAs. On the basis of analysis of nuclear nonphotosynthetic mutants of C. reinhardtii, several different gene products may be required for expression of a given chloroplast mRNA (520). Second, specific proteins bind to inverted repeat regions present in the 5' and 3' untranslated leaders of chloroplast mRNAs that are capable of forming thermodynamically stable stem-loop structures (105, 229). Although the 3' untranslated leaders appear to function in stabilization and processing of mRNAs rather than as transcript terminators in land plants, there is some evidence that they serve as terminators for chloroplast transcripts in C. reinhardtii (30). Experiments are currently under way in several laboratories to demonstrate the functional role of individual binding proteins in mRNA stability and translation as well as to decipher the signal transduction pathway leading to the expression of these proteins. For example, Nickelsen and Link (456) have described a 54-kDa protein from mustard chloroplasts that binds to a conserved sequence in the 3'-flanking regions of the tmK and rpsl6 genes and appears to have endonucleolytic activity that may be involved in RNA 3'-end formation and mRNA stability. Development of reliable protocols for chloroplast transformation in C. reinhardtii (48) and tobacco (390), coupled with the ability to express foreign reporter sequences in the chloroplast, has allowed the functional dissection of the 5' and 3' untranslated leaders for the first time (84, 214, 535, 591, 621). Detailed consideration of the genetic basis for translational regulation in chloroplasts and mitochondria and a model depicting the role of a multiprotein translation complex bound to the 5' untranslated leaders of organelle mRNAs in modulating the translational regulation are presented in a recent review (207). Membrane Binding of Chloroplast Ribosomes Thylakoid-bound polysomes have been characterized in chloroplasts with respect to their physical status and physiological function (see references 40, 41, and 286 for reviews). High-salt washes of isolated thykakoids remove 30 to 45% of the membrane-bound RNA while addition of puromycin releases up to 80% of the bound RNA. By analogy with the rough endoplasmic reticulum, these results suggest that between one-third and one-half of the polysomes found on thylakoids are attached electrostatically to the membranes and the rest are held by both electrostatic forces and nascent polypeptide chains. The electrostatic binding of chloroplast polysomes predicts the presence of a ribosome receptor similar to the ribophorin-containing receptor found on the rough endoplasmic reticulum (503) but missing from the bacterial cytoplasmic membrane. Other components of the system for synthesizing eukaryotic secretory proteins, such as a signal recognition particle and a docking protein, have not been demonstrated in chloroplasts. The fraction of membranebound polysomes observed can be markedly enhanced by pretreating the cells with antibiotics such as chloramphenicol and erythromycin that inhibit transpeptidation. Freimann and Hachtel (180) examined the distribution of mRNAs on free and membrane-bound chloroplast polysomes of broad bean (Vicia faba). They used the criteria of release of the associated mRNA by high salt alone or high salt plus puromycin, together with gene-specific probes, to distinguish mRNAs electrostatically bound to thylakoids from those engaged in cotranslational protein synthesis. Three classes of mRNA were recognized. (i) The rbcL mRNA encoding the large subunit of Rubisco was the only mRNA associated solely with stromal polysomes. However, other authors have reported that rbcL mRNA is also found associated with thylakoid membranes (252). (ii) Thylakoid polysomes containing mRNAs for six genes encoding integral membrane proteins appeared to synthesize their products in a cotranslational fashion. These mRNAs were released only by high salt plus puromycin. (iii) Thylakoid polypeptides encoded by seven other genes were assumed to be incorporated posttranslationally because their mRNAs were found on stromal polysomes or polysomes bound electrostatically to the thylakoid membranes. Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV might be expressed at the same level and that a nonfunctional product of the rpsl9' gene might accumulate. In fact, they found that the rpsl9' transcript was present at very low levels if at all and that the rp12 mRNA that is translated appears to be transcribed from the gene copy located in the complete operon. However, transcription of the intact operon can be initiated from several different promoters, suggesting that it may be subject to developmental regulation. A number of genes encoding ribosomal proteins are part of mixed clusters that also contain genes encoding components of the photosynthetic apparatus. Stahl et al. (587) demonstrated that such a mixed chloroplast gene cluster in maize containing genes encoding four subunits of the ATP synthase (atpI, atpH, atpF, and atpA) and the gene encoding ribosomal protein S2 (rps2) produces a total of 12 transcripts, including a major species of 6,200 nt containing mRNAs of all five genes. They suggest that this plastid gene cluster is "functionally organized as an operon with additional regulatory features to allow for increased accumulation of mRNAs for the thylakoid components." The analogous operon in Euglena gracilis, containing rps2, atpI, atpH, atpF, atpA, and rpsl8, was analyzed by Drager and Hallick (134). Of these genes, all but atpH contain one or more introns, comprising in aggregate nine introns of the group III class unique to the genus Euglena and its colorless relative Astasia (87, 565), seven introns with group II structure, and one intron that matched neither category. Drager and Hallick (134) found that all 17 introns are removed to yield a 5.5-kb mRNA spanning all six genes, from which monocistronic transcripts are then generated, presumably by endonucleolytic cleavage. The unique 434-nt intron in the rpsl8 gene is a complex twintron, consisting of four group III introns which are removed in four sequential splicing reactions, some of which can use multiple splice sites (135). Chen et al. (83) found that the psaA, psaB, and rpsl4 genes in rice are organized into a single transcriptional unit. A 5.2-kb transcript hybridizing to probes for all three genes was observed in leaf tissue. Ribosomal protein L32 of the tobacco chloroplast has been shown to be encoded by the gene formerly identified as open reading frame ORF55 (733), located in the small single-copy region. A primary transcript of 1,550 nt contains no other open reading frames and overlaps the ndhF gene on the opposite strand (668). Vera et al. (668) demonstrated that the rp132 promoter is located within the ndhF coding region, the first instance so far of an internal divergent promoter in the chloroplast genome. 733 734 HARRIS ET AL. HOW ESSENTUIL IS CHLOROPLAST PROTEIN SYNTHESIS? Chloroplast protein synthesis has long been known to be indispensable for survival of plants and algae that depend on CO2 as their sole carbon source, since numerous proteins required for photosynthesis are plastid gene products. However, as we learn more about the genes encoded in the plastid genomes of algae such as Cyanophora, Cryptomonas, and Porphyra species, some of which specify proteins required for amino acid or fatty acid biosynthesis, the likelihood is increasing that chloroplast protein synthesis is also required for the production of one or more essential proteins not involved in photosynthesis. This viewpoint is supported by some, but not all, analyses of plastid genome function in colorless plants. We begin with cases that support the hypothesis that chloroplast protein synthesis is essential and then turn to evidence that makes the converse argument. The colorless heterotroph Astasia longa is closely related to Euglena gracilis and possesses a circular 73-kb plastid genome. This genome is the counterpart of the larger (145-kb) Euglena chloroplast genome, and the genes identified include the rRNAs, tufA, and several tRNAs and ribosomal proteins (565-569). The rbcL gene encoding the large subunit of the enzyme Rubisco is the only photosynthetic gene so far detected in the Astasia plastid genome. This polypeptide has been immunoprecipitated from Astasia longa, suggesting that the rbcL gene is transcribed and translated and that the plastid protein-synthesizing system of this colorless flagellate must be functional. Colorless, heterotrophic algae of the genus Polytoma, closely related to or derived from the genus Chlamydomonas, contain a plastid genome (ca. 200 kb) similar in size to the C. reinhardtii chloroplast genome (574, 670). Plastid rRNA genes are present and expressed in Polytoma species, leukoplast ribosomes have been isolated, and the tufA gene has been identified. These results suggest that Polytoma species too have a functioning plastid protein-synthesizing system (575, 576, 670). Plastid genomes of the colorless plants Epifagus virginiana (beechdrops) and Conopholis americana in the Orobranchaceae family of root-parasitic angiosperms have also been examined (115, 702-704, 711, 712, 714). The 70-kb Epifagus plastid genome has been completely sequenced and contains only 42 genes (714). At least 38 of these genes encode components of the plastid gene expression system (rRNAs, tRNAs, and ribosomal proteins). Functional photosynthesis genes and genes of the NADH dehydrogenase complex are absent, although several photosynthetic pseudogenes have been found. The Epifagus plastid genome contains only 17 tRNAs, suggesting that tRNAs must be imported if this plastid protein-synthesizing system is to function. Genes specifying the four RNA polymerase subunits encoded in the chloroplast genomes of green plants are also absent. Although no experiments with Epifagus virginiana demonstrating synthesis of a specific plastid-encoded protein have been reported, there are several lines of indirect evidence suggesting that the plastid protein-synthesizing system is functional. Wolfe et al. (714) reported transcription of all eight rRNA and protein-encoding genes so far examined and cited the following three evolutionary arguments in favor of function. (i) Plastid gene deletions in Epifagus virginiana are not random but are skewed toward photosynthetic genes. Although only 5% of photosynthetic sequences have been retained with respect to tobacco, 80% of the ribosomal protein sequences are present. (ii) Large open reading frames are retained in the Epifagus plastid genome. If these genes were nonfunctional, mutations, truncations, and internal deletions would have been expected to occur, as is true of pseudogenes in the Epifagus plastid genome. (iii) The genera Conopholis and Epifagus share the loss of the photosynthetic and ndh genes, but their rRNA genes are strongly conserved, suggesting that the evolution of these genes is constrained by natural selection because they are functional. Why might the protein-synthesizing systems of Epifagus virginiana and other colorless plants be essential? The argument of Howe and Smith (275) that plastid protein synthesis was retained in Epifagus species for the sole purpose of making the chloroplast-encoded RNA polymerase subunits required for transcription of the tRNAGIU gene necessary for porphyrin synthesis (see, e.g., references 20 and 552) is invalidated by the finding that the RNA polymerase subunit genes are absent from the Epifagus plastid genome (714). However, one or more other proteins essential for survival might be encoded and translated in the Epifagus chloroplast. The best candidate is clpP, which specifies one subunit of the plastid homolog of the ATP-dependent Clp protease of E. coli. Perhaps this protease is involved in processing chloroplast protein precursors into an active form or in protein degradation. The thesis that chloroplast protein synthesis is essential is also supported by work on the genus Plasmodium, the malaria parasite. This protozoan contains, in addition to its tiny (6-kb) linearly reiterated mitochondrial genome, a 35-kb circular DNA molecule that seems to be a residual plastid genome (see references 273, 484, 700, and 701 for reviews). The 35-kb circle possesses inverted repeats containing continuous rRNAs with secondary structures quite similar to those predicted for E. coli (166, 197, 198). It also encodes tRNAs, two subunits of a eubacterial-type RNA polymerase, and at least four ribosomal proteins (165). Genetic evidence suggests that chloroplast protein synthesis in C. reinhardtii is essential for survival. Hanson and Bogorad (245) showed that cells carrying a nuclear mutation conferring erythromycin resistance on chloroplast ribosomes underwent a marked reduction in chloroplast ribosome content when shifted from 25 to 15°C. Ribosome loss was accompanied by loss of the ability of the mutant to grow at 15°C under all conditions. Also, although several Chlamydomonas mutants which have a reduced content of chloroplast ribosomes have been isolated, none is completely deficient in chloroplast protein synthesis (247-249, 446). Lastly, mutations with symmetric deletions of the psbA gene encoded within the inverted Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV Other supporting evidence exists that such chloroplast-synthesized proteins as Dl, the reaction center polypeptide encoded by the psbA gene, and the alpha and beta subunits of the CF1 portion of the ATP synthase are made, at least in part, on thylakoid-bound polysomes (see reference 286 for a summary). Membrane binding of polysomes may play an additional role in translational regulation of chloroplast gene expression. In C. reinhardtii, the distribution of chloroplast mRNAs varied between the thylakoid and soluble fractions in cells growing synchronously on a light-dark cycle (41). Thus, a striking increase in the fraction of membrane-bound polysomes was observed for both rbcL and psbA mRNAs in the light period. Thylakoid binding may occur in the light phase because translation is initiated. In contrast, Klein et al. (308) found that the psaA, psaB, and psbA transcripts are primarily membrane associated in dark-grown barley plants. The protein products of these genes are made in the dark but are unstable in the absence of chlorophyll (441). Jagendorf and Michaels (286) correctly point out that the possible role of the thylakoid membrane itself in translational regulation requires further investigation. MICROBIOL. REV. VOL. 58, 1994 CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS calli (98, 392). Experiments with calli cultured from roots of haploid rice plants derived from pollen grains provide convincing evidence that plastid protein synthesis is not essential in this system (246). Albino plants obtained in this way from barley and wheat have long been known to contain large deletions in the plastid genome (106, 107), but the deleted molecules form a heterogeneous collection. By inducing callus cultures from roots of albino rice plants, Harada et al. (246) obtained isolates that were homoplasmic for different large deletions. Of five that were characterized, four lacked the inverted repeat and the plastid rRNA genes, so that none of these callus cultures could carry out chloroplast protein synthesis, yet all five retained one region in common which contained the tRNAGlu gene. Harada et al. (246) suggest that this gene has been retained because the tRNAGlu encoded by the gene is essential for porphyrin biosynthesis. Similarly, heat-bleached leaves of rye and oat lack chloroplast ribosomes but have substantial amounts of tRNAGlU and chlorophyll synthetase activity despite their low chlorophyll level (262). Obviously, expression of the tRNAGlU gene would require functioning of a nucleusencoded plastid RNA polymerase. Retention of small amounts of plastid DNA in bleached Euglena mutants (254) is probably not related to a general requirement for tRNAG'U in porphyrin synthesis, since mitochondrial heme in this flagellate is made via the animal-type 8-aminolevulinic synthetase pathway which does not require tRNAGlU (268). In fact, the rRNA genes were the only ones detected in these deleted plastid genomes. The existing data currently suggest that chloroplast protein synthesis may be essential for survival in Chlamydomonas and Epifagus species but possibly not in other plants such as tobacco, at least in tissue culture. The plastid-encoded tRNAGlu gene is essential for synthesis of all porphyrins in plants and algae examined to date, with the exception of Euglena gracilis, so transcription of this gene is crucial to survival. However, the Epifagus results suggest that in this plant, at least, transcription of tRNAGlU depends on a nucleus-encoded RNA polymerase. CONCLUSIONS Analysis of chloroplast sequences has been invaluable in determining variable and conserved regions of the 16S and 23S rRNA molecules and in predicting their secondary and tertiary structures. Similar comparisons of ribosomal protein sequences are just beginning but will doubtless prove important in years to come. Specific domains conserved over a wide variety of organisms are likely to be important in ribosome function or assembly. Sequence analysis of ribosomal proteins in a diverse array of algae and land plants will allow further refinements in understanding which domains are important for ribosome function. Although no analysis of mitochondrial ribosomal proteins has been included here, these will also be a valuable comparative tool in such research. We hope that this review will provide a useful starting point for investigations on these topics. ACKNOWLEDGMENTS We thank Hans Bohnert, Donald Bryant, Robin Gutell, Claude Lemieux, Xiang-Qin Liu, Michael Reith, Alap Subramanian, and Monique Turmel for sharing unpublished data. Our work described in this review was supported by NIH grant GM-19427. REFERENCES 1. Akkaya, M. S., and C. A. Breitenberger. 1992. Light regulation of protein synthesis factor EF-G in pea chloroplasts. Plant Mol. Biol. 20:791-800. 2. Akkaya, M. S., P. L. Welsch, M. A. Wolfe, B. K. Duerr, W. J. Becktel, and C. A. Breitenberger. 1994. Purification and Nterminal sequence analysis of pea chloroplast protein synthesis factor EF-G. Arch. Biochem. Biophys. 308:109-117. 3. Aldrich, J., B. W. Cherney, E. Merlin, and L. Christopherson. 1988. The role of insertions/deletions in the evolution of the intergenic region between psbA and trnH in one chloroplast genome. Curr. Genet. 14:137-146. 4. Alksne, L, E., R A. Anthony, S. W. Liebman, and J. R. Warner. 1993. An accuracy center in the ribosome conserved over 2 billion years. Proc. Natl. Acad. Sci. USA 90:9538-9541. 5. Allen, J. R 1993. Control of gene expression by redox potential and the requirement for chloroplast and mitochondrial genomes. J. Theor. Biol. 165:609-631. 6. Amberg, S. M., and R. H. Meints. 1991. Nucleotide sequence of the genes for ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit and ribosomal protein S14 from a Chlorella-like green alga. J. Phycol. 27:753-758. 7. Andersson, D. I., S. G. E. Andersson, and C. G. Kurland. 1986. Functional interactions between mutated forms of ribosomal proteins S4, S5 and S12. Biochimie 68:705-713. Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV repeat are frequently isolated, but the only known deletion mutation affecting the rRNA gene region of the repeat removed only one set of rRNA genes (486). Many years ago, Blamire et al. (29) reported that treatment of wild-type cells with antibiotics blocking translation on chloroplast ribosomes inhibited replication of nuclear but not chloroplast DNA. Inhibition did not occur in mutant strains with chloroplast ribosomes resistant to these antibiotics. These intriguing experiments have never been repeated. The notion that chloroplast protein synthesis is indispensable is challenged by several other findings. Cuscuta reflexa (Convolvulaceae) is a colorless parasitic plant, unrelated to the genus Epifagus, that contains residual thylakoids and traces of chlorophylls a and b (376). The plant also possesses very low levels of light-stimulated CO2 fixation and Rubisco activity, although the Rubisco large subunit is undetectable by immunological methods (237, 376). Partial sequence analysis of the Cuscuta reflewa plastid genome (33, 237, 238) revealed that although many photosynthesis genes are intact (e.g., atpB, atpE, rbcL, and psbA), a large deletion has removed certain protein synthesis genes (rpl2, rp123, and several tRNA genes), and the ndh genes appear to be nonfunctional. Transcription analysis showed that rbcL was weakly transcribed while psbA was transcribed strongly. Bommer et al. (33) hypothesized that the translational apparatus of Cuscuta reflexa is nonfunctional based on the absence of specific protein synthesis genes from the plastid genome and their inability to detect Rubisco large subunit using immunological techniques. Alternatively, the plastid protein-synthesizing system of Cuscuta reflexa might be functional, with the missing tRNAs and ribosomal proteins encoded in the nucleus. In tobacco, antibacterial antibiotics such as streptomycin and lincomycin cause bleaching, but they do not cause death of callus in tissue culture (389). The bleached antibiotic-sensitive cells continue to divide at a reduced rate, using sucrose as the carbon source. Mutants resistant to these antibiotics are green in tissue culture. Streptomycin-resistant mutants result from specific base pair changes in the 16S rRNA or rpsl2 genes, while those resistant to lincomycin arise because of a specific base pair alteration in the gene encoding the 23S rRNA (391, 590) (Table 2). The ability of bleached antibiotic-sensitive cells to continue to divide implies that chloroplast protein synthesis may be required only for the manufacture of photosynthetic and ribosomal proteins in Nicotiana species. However, tobacco calli containing a chloroplast mutation to streptomycin resistance grow better in the dark on antibiotic than do sensitive 735 736 MICROBIOL. REV. HARRIS ET AL. 8. Arief, L., B. Entsch, and R E. Wicks. 1991. Unpublished Chlamydomonas chloroplast rbcL and psaB genes. Mol. Gen. se- quence submission. Genet. 238:339-349. 31. Bobrova, V. K., A. V. Troitsky, A. G. Ponomarev, and A. S. Antonov. 1987. Low-molecular weight rRNAs sequences and plant phylogeny reconstruction: nucleotide sequences of chloroplast 4.5S rRNAs from Acorus calamus (Araceae) and Ligulana calthifolia (Asteraceae). Plant Syst. Evol. 156:13-27. 32. Bohnert, H. Unpublished data. 33. Bommer, D., G. Haberhausen, and K. Zetsche. 1993. A large deletion in the plastid DNA of the holoparasitic flowering plant Cuscuta reflexa concerning two ribosomal proteins (rp12, rp123), one transfer RNA (tmI) and an ORF 2280 homologue. Curr. Genet. 24:171-176. 34. Bonen, L, W. F. Doolittle, and G. E. Fox. 1979. Cyanobacterial evolution: results of 16S ribosomal ribonucleic acid sequence analyses. Can. J. Biochem. 57:879-888. 35. Bonham-Smith, P. C., and D. P. Bourque. 1989. Translation of chloroplast-encoded mRNA: potential initiation and termination signals. Nucleic Acids Res. 17:2057-2080. 36. Bonham-Smith, P. C., and D. P. Bourque. 1990. The chloroplast genome and regulation of its expression, p. 179-216. In K Adolph (ed.), Chromosomes: eucaryotic, prokaryotic, and viral, vol. II. CRC Press, Inc., Boca Raton, Fla. 37. Bonny, C., P.-E. Montandon, S. Marc-Martin, and E. Stutz. 1991. Analysis of streptomycin-resistance of Escherichia coli mutants. Biochim. Biophys. Acta 1089:213-219. 38. Borbely, G., and A. Simoncsits. 1981. 3'-terminal conserved loops 39. 40. 41. 42. 43. 44. 45. 46. forms of S12. J. Mol. Biol. 224:1011-1037. 26. Bilgin, N., A. A. Richter, M. Ehrenberg, A. E. Dahlberg, and C. G. Kurland. 1990. Ribosomal RNA and protein mutants resistant to spectinomycin. EMBO J. 9:735-739. 27. Bisanz-Seyer, C., Y.-F. Li, P. Seyer, and R Mache. 1989. The components of the plastid ribosome are not accumulated synchronously during the early development of spinach plants. Plant Mol. Biol. 12:201-211. 28. Bisanz-Seyer, C., and R Mache. 1992. Organization and expression of the nuclear gene coding for the plastid-specific S22 ribosomal protein from spinach. Plant Mol. Biol. 18:337-344. 29. Blamire, J., V. R Flechtner, and R. Sager. 1974. Regulation of nuclear DNA replication by the chloroplast in Chlamydomonas. Proc. Natl. Acad. Sci. USA 71:2867-2871. 30. Blowers, A. D., U. Klein, G. S. Ellmore, and L. Bogorad. 1993. Functional in vivo analyses of the 3' flanking sequences of the 47. 48. 49. of 16S rRNAs from the cyanobacterium Synechococcus AN PCC 6301 and maize chloroplast differ only in two bases. Biochem. Biophys. Res. Commun. 101:846-852. Borner, T., and B. B. Sears. 1986. Plastome mutants. Plant Mol. Biol. Rep. 4:69-92. Boschetti, A., R. Blattler, and E. Breidenbach. 1991. Regulation of protein synthesis in chloroplasts of Chlamydomonas reinhardii. NATO ASI Ser. Ser. H 55:229-238. Boschetti, A., E. Breidenbach, and R. Blattler. 1990. Control of protein formation in chloroplasts. Plant Sci. 68:131-149. Boudreau, E., C. Lemieux, C. Otis, and M. Turmel. 1993. Plastid genomes of the interfertile green algae Chlamydomonas eugametos and Chlamydomonas moewusii, p. 2.154-2.156. In S. J. O'Brien (ed.), Genetic maps. Locus maps of complex genomes, 6th ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. Boudreau, E., C. Otis, and M. Turmel. 1994. Conserved gene clusters in the highly rearranged chloroplast genomes of Chlamydomonas moewusii and Chlamydomonas reinhardtii. Plant Mol. Biol. 24:585-602. Bourque, D. P., G. Elhag, P. Bonham-Smith, F. Thomas, T. McCreery, and B. Glinsmann-Gibson. 1991. Expression of nuclear and chloroplast genes coding for tobacco chloroplast ribosomal proteins. NATO ASI Ser. Ser. H 55:85-93. Bowman, C. M. 1991. The evolution of genes and pseudogenes for some chloroplast ribosomal proteins. Transposition and recombination lead to different fates in different genomes. NATO ASI Ser. Ser. H 55:71-83. Bowman, C. M., R. F. Barker, and T. A. Dyer. 1988. In wheat ctDNA, segments of ribosomal protein genes are dispersed repeats, probably conserved by nonreciprocal recombination. Curr. Genet. 14:127-136. Bowman, C. M., and T. A. Dyer. 1979. 4.5S ribonucleic acid, a novel ribosome component in the chloroplasts of flowering plants. Biochem. J. 183:605-613. Boynton, J. E., and N. W. Gillham. 1993. Chloroplast transformation in Chlamydomonas. Methods Enzymol. 217:510-536. Boynton, J. E., N. W. Gillham, E. H. Harris, S. M. Newman, B. L Randolph-Anderson, A. M. Johnson, and A. R. Jones. 1990. Manipulating the chloroplast genome of Chlamydomonas-molecular genetics and transformation. Curr. Res. Photosynth. m:509-516. 50. Boynton, J. E., N. W. Gillham, S. M. Newman, and E. H. Harris. 1992. Organelle genetics and transformation in Chlamydomonas, p. 3-64. In R. Herrmann (ed.), Cell organelles. Advances in plant gene research, vol. 6. Springer-Verlag KG, Vienna. Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV 9. Arizmendi, J. M., M. J. Runswick, J. M. Skehel, and J. E. Walker. 1992. NADH:ubiquinone oxidoreductase from bovine heart mitochondria. A fourth nuclear encoded subunit with a homologue encoded in chloroplast genomes. FEBS Lett. 301:237-242. 10. Audren, H., C. Bisanz-Seyer, J.-F. Briat, and R Mache. 1987. Structure and transcription of the 5S rRNA gene from spinach chloroplasts. Curr. Genet. 12:263-269. 11. Audren, H., and R Mache. 1986. Nucleotide sequence of the spinach chloroplast 4.5S ribosomal RNA gene and of its 5' flanking region including the 3' end of the 23S rRNA gene. Nucleic Acids Res. 14:9533. 12. Bachmann, B. J. 1993. Linkage map of Escherichia coli K-12, edition 8, p. 2.1-2.33. In S. J. O'Brien (ed.), Genetic maps, locus maps of complex genomes, 6th ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. 13. Baeza, L., A. Bertrand, R Mache, and S. Lerbs-Mache. 1991. Characterization of a protein binding sequence in the promoter region of the 16S rRNA gene of the spinach chloroplast genome. Nucleic Acids Res. 19:3577-3581. 14. Baldauf, S. L., J. R Manhart, and J. D. Palmer. 1990. Different fates of the chloroplast tufA gene following its transfer to the nucleus in green algae. Proc. Natl. Acad. Sci. USA 87:5317-5321. 15. Baldauf, S. L., and J. D. Palmer. 1990. Evolutionary transfer of the chloroplast tufA gene to the nucleus. Nature (London) 344:262-265. 16. Ballesta, J. P. G. 1991. The structure of the antibiotic binding sites in bacterial ribosomes. NATO ASI Ser. Ser. H 55:179-195. 17. Barkan, A. 1993. Nuclear mutants of maize with defects in chloroplast polysome assembly have altered chloroplast RNA metabolism. Plant Cell 5:389-402. 18. Bartsch, M. 1985. Correlation of chloroplast and bacterial ribosomal proteins by cross-reactions of antibodies specific to purified Escherichia coli ribosomal proteins. J. Biol. Chem. 260:237241. 19. Bartsch, M., M. Kimura, and A.-R Subramanian. 1982. Purification, primary structure, and homology relationships of a chloroplast ribosomal protein. Proc. Natl. Acad. Sci. USA 79:68716875. 20. Beale, S. I. 1976. The biosynthesis of 8-amino-levulinic acid in plants. Philos. Trans. R. Soc. London Ser. B 273:99-108. 21. Bendich, A. J. 1987. Why do chloroplasts and mitochondria contain so many copies of their genome? Bioessays 6:279-282. 22. Ben Tahar, S., W. Bottomley, and P. R Whitfeld. 1986. Characterization of the spinach chloroplast genes for the S4 ribosomal protein, tRNAThr (UGU) and tRNAser (GGA). Plant Mol. Biol. 7:63-70. 23. Benzinger, E. A., and A. G. Hepburn. 1989. The sequence of the chloroplast 5S ribosomal RNA gene of soybean (Glycine max Merr.). Nucleic Acids Res. 17:10124. 24. Bergsland, K. J., and R Haselkorn. 1991. Evolutionary relationships among eubacteria, cyanobacteria, and chloroplasts: evidence from the rpoCl gene of Anabaena sp. strain PCC 7120. J. Bacteriol. 173:3446-3455. 25. Bilgin, N., F. Claesens, H. Pahverk, and M. Ehrenberg. 1992. Kinetic properties of Escherichia coli ribosomes with altered VOL. 58, 1994 CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS 71. Bubunenko, M. G., and A. R Subramanian. 1994. Recognition of novel and divergent higher plant chloroplast ribosomal proteins by Escherichia coli ribosome during in vivo assembly. J. Biol. Chem. 269:18223-18231. 72. Buttarelli, F. R, R A. Calogero, 0. Tiboni, C. 0. Gualerzi, and C. L. Pon. 1989. Characterization of the str operon genes from Spirulina platensis and their evolutionary relationship to those of other prokaryotes. Mol. Gen. Genet. 217:97-104. 73. Capel, M. S., and D. P. Bourque. 1982. Characterization of Nicotiana tabacum chloroplast and cytoplasmic ribosomal proteins. J. Biol. Chem. 257:7746-7755. 74. Carbonera, D., S. Sora, G. Riccardi, G. Camerino, and 0. Ciferri. 1981. Characterization of a mutant of Chlamydomonas reinhardtii resistant to fusidic acid. FEBS Lett. 132:227-230. 75. Carol, P., Y. F. Li, and R Mache. 1991. Conservation and evolution of the nucleus-encoded and chloroplast-specific ribosomal proteins in pea and spinach. Gene 103:139-145. 76. Carol, P., C. Rozier, E. Lazaro, J. P. G. Ballesta, and R. Mache. 1993. Erythromycin and SS rRNA binding properties of the spinach chloroplast ribosomal protein CL22. Nucleic Acids Res. 21:635-639. 77. Ceci, R 1993. Unpublished sequence submission. 78. Cedergren, R, M. W. Gray, Y. Abel, and D. Sankoff. 1988. The evolutionary relationships among known life forms. J. Mol. Evol. 28:98-112. 79. Cerutti, H., and A. T. Jagendorf. 1991. Nucleotide sequence of the chloroplast 16S rRNA gene from pea (Pisum sativum L.). Plant Mol. Biol. 17:125-126. 80. Chang, H., T.-C. Cheng, and P. Lee. 1986. Barley chloroplast 4.5S rRNA sequence determination and comparison with other chloroplast 4.5S rRNA sequences. Acta Genet. Sin. 13:411-416. 81. Chen, M., M. Cheng, and S. G. Chen. 1993. Characterization of the promoter of rice plastid psaA-psaB-rpsl4 operon and the DNA-specific binding proteins. Plant Cell Physiol. 34:577-584. 82. Chen, S. G., M. Cheng, J. Chen, and L. Hwang. 1990. Organization of the rice chloroplast psaA-psaB-rpsl4 gene and the presence of sequence heterogeneity in this gene cluster. Plant Sci. 68:218-221. 83. Chen, S. G., M. Cheng, K. Chung, N. Yu, and M. Chen. 1992. Expression of the rice chloroplast psaA-psaB-rpsl4 gene cluster. Plant Sci. 81:93-102. 84. Chen, X., K. Kindle, and D. Stern. 1993. Initiation codon mutations in the Chlamydomonas chloroplastpetD gene result in temperature-sensitive photosynthetic growth. EMBO J. 12:36273635. 85. Cheung, W. Y., and N. S. Scott. 1989. A contiguous sequence in spinach nuclear DNA is homologous to three separated sequences in chloroplast DNA. Theor. Appl. Genet. 77:625-633. 86. Christopher, D. A., J. C. Cushman, C. A. Price, and R. B. Hallick. 1988. Organization of ribosomal protein genes rp123, rp12, rpsl9, rp122 and rps3 on the Euglena gracilis chloroplast genome. Curr. Genet. 14:275-286. 87. Christopher, D. A., and R B. Hallick. 1989. Euglena gracilis chloroplast ribosomal protein operon: a new chloroplast gene for ribosomal protein L5 and description of a novel organelle intron category designated group III. Nucleic Acids Res. 17:7591-7608. 88. Christopher, D. A., and R B. Hallick. 1990. Complex RNA maturation pathway for a chloroplast ribosomal protein operon with an internal tRNA cistron. Plant Cell 2:659-671. 89. Clarke, A. K., J. Lidholm, R. P. Bhalerao, and P. Gustafsson. 1994. Unpublished sequence submission. 90. Cooperman, B. S., P. Muralikrishna, and R W. Alexander. 1993. Photolabile oligodeoxyribonucleotide probes of E. coli ribosome structure, p. 465-476. In K. H. Nierhaus, F. Franceschi, A. R. Subramanian, V. A. Erdmann, and B. Wittmann-Liebold (ed.), The translational apparatus. Structure, function, regulation, evolution. Plenum Press, New York. 91. Cooperman, B. S., C. J. Weitzmann, and C. L. Fernandez. 1990. Antibiotic probes of Escherichia coli ribosomal peptidyltransferase, p. 491-501. In W. E. Hill, A. Dahlberg, G. A. Garrett, P. B. Moore, D. Schlessinger, and J. R. Warner (ed.), The ribosome. Structure, function, and evolution. American Society for Microbiology, Washington, D.C. Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV 51. Breidenbach, E., S. Leu, A. Michaels, and A. Boschetti. 1990. Synthesis of EF-Tu and distribution of its mRNA between stroma and thylakoids during the cell cycle of Chlamydomonas reinhardtii. Biochim. Biophys. Acta 1048:209-216. 52. Breitenberger, C. A., M. C. Graves, and L. L, Spremulli. 1979. Evidence for the nuclear location of the gene for chloroplast elongation factor G. Arch. Biochem. Biophys. 194:265-270. 53. Breitenberger, C. A., and L, L. Spremulli. 1980. Purification of Euglena gracilis chloroplast elongation factor G and comparison with other prokaryotic and eukaryotic translocases. J. Biol. Chem. 255:9814-9820. 54. Bremer, B., and K. Bremer. 1989. Cladistic analysis of blue-green procaryote interrelationships and chloroplast origin based on 16S rRNA oligonucleotide catalogues. J. Evol. Biol. 2:13-30. 55. Briat, J.-F., C. Bisanz-Seyer, and A.-M. Lescure. 1987. In vitro transcription initiation of the rDNA operon of spinach chloroplast by a highly purified soluble homologous RNA polymerase. Curr. Genet. 11:259-263. 56. Briat, J.-F., M. Dron, S. Loiseaux, and R. Mache. 1982. Structure and transcription of the spinach chloroplast rDNA leader region. Nucleic Acids Res. 10:6865-6878. 57. Brimacombe, R. 1991. RNA-protein interactions in the Escherichia coli ribosome. Biochimie 73:927-936. 58. Brimacombe, R. 1992. Structure-function correlations (and discrepancies) in the 16S ribosomal RNA from Escherichia coli. Biochimie 74:319-326. 59. Brimacombe, R., J. Atmadja, W. Stiege, and D. Schuler. 1988. A detailed model of the three-dimensional structure of Escherichia coli 16S ribosomal RNA in situ in the 30S subunit. J. Mol. Biol. 199:115-136. 60. Brimacombe, R., T. Doring, B. Greuer, N. Junke, P. Mitchell, F. Muller, M. Osswald, J. Rinke-Appel, and K. Stade. 1993. Mapping the functional centre of the Escherichia coli ribosome, p. 433-444. In K. H. Nierhaus, F. Franceschi, A. R. Subramanian, V. A. Erdmann, and B. Wittmann-Liebold (ed.), The translational apparatus. Structure, function, regulation, evolution. Plenum Press, New York. 61. Brimacombe, R., B. Greuer, P. Mitchell, M. Osswald, J. RinkeAppel, D. Schuler, and K. Stade. 1990. Three-dimensional structure and function of Eschenichia coli 16S and 23S rRNA as studied by cross-linking techniques, p. 93-106. In W. E. Hill, A. Dahlberg, G. A. Garrett, P. B. Moore, D. Schlessinger, and J. R. Warner (ed.), The ribosome. Structure, function, and evolution. American Society for Microbiology, Washington, D.C. 62. Brimacombe, R, and W. Stiege. 1985. Structure and function of ribosomal RNA. Biochem. J. 229:1-17. 63. Britschgi, T. B., and S. J. Giovannoni. 1991. Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing. Appl. Environ. Microbiol. 57:1707-1713. 64. Brosius, J., T. Dull, D. D. Sleeter, and H. F. Noller. 1981. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J. Mol. Biol. 148:107-127. 65. Brosius, J., T. J. Dull, and H. F. Noller. 1980. Complete nucleotide sequence of a 23S ribosomal RNA gene from Escherichia coli. Proc. Natl. Acad. Sci. USA 77:201-204. 66. Brosius, J., M. L. Palmer, P. J. Kennedy, and H. F. Noller. 1978. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc. Natl. Acad. Sci. USA 75:4801-4805. 67. Brunel, C., P. Romby, E. Westhof, C. Ehresmann, and B. Ehresmann. 1991. Three-dimensional model of Escherichia coli ribosomal 5 S RNA as deduced from structure probing in solution and computer modeling. J. Mol. Biol. 221:293-308. 68. Bryant, D. A., W. M. Schluchter, and V. L Stirewalt. 1991. Ferredoxin and ribosomal protein S10 are encoded on the cyanelle genome of Cyanophora paradoxa. Gene 98:169-175. 69. Bryant, D. A., and V. L. Stirewalt. 1990. The cyanelle genome of Cyanophora paradoxa encodes ribosomal proteins not encoded by the chloroplast genomes of higher plants. FEBS Lett. 259:273280. 70. Bubunenko, M. G., J. Schmidt, and A. R. Subramanian. 1994. Protein substitution in chloroplast ribosome evolution: a eukaryotic cytosolic protein has replaced its organelle homologue (L23) in spinach. J. Mol. Biol. 240:28-41. 737 738 HARRIS ET AL. Structure, function, and evolution. American Society for Microbiology, Washington, D.C. 103. Dabbs, E. R. 1986. Mutant studies on the prokaryotic ribosome, p. 733-748. In B. Hardesty and G. Kramer (ed.), Structure, function and genetics of ribosomes, Springer-Verlag, New York. 104. Dabbs, E. R. 1991. Mutants lacking individual ribosomal proteins as a tool to investigate ribosomal properties. Biochimie 73:639645. 105. Danon, A., and S. P. Y. Mayfield. 1991. Light regulated translational activators: identification of chloroplast gene specific mRNA binding proteins. EMBO J. 10:3993-4001. 106. Day, A., and T. H. N. Ellis. 1984. Chloroplast DNA deletions associated with wheat plants regenerated from pollen: possible basis for maternal inheritance of chloroplasts. Cell 39:359-368. 107. Day, A., and T. H. N. Ellis. 1985. Deleted forms of plastid DNA in albino plants from cereal anther culture. Curr. Genet. 9:671678. 108. Delaney, T. P., and R. A. Cattolico. 1989. Chloroplast ribosomal DNA organization in the chromophytic alga Olisthodiscus luteus. Curr. Genet. 15:221-229. 109. Delaney, T. P., and R. A. Cattolico. 1991. Sequence and secondary structure of chloroplast 16S rRNA from the chromophyte alga Olisthodiscus luteus, as inferred from the gene sequence. Nucleic Acids Res. 19:6328. 110. de Lanversin, G., and D. T. N. Pillay. 1988. Primary structure and sequence organization of the 16S-23S spacer in the ribosomal operon of soybean (Glycine max L.) chloroplast DNA. Theor. Appl. Genet. 76:443-448. 111. Delihas, N., J. Andersen, and D. Berns. 1985. Phylogeny of the SS ribosomal RNA from Synechococcus lividus. II. The cyanobacterial/chloroplast SS RNAs form a common structural class. J. Mol. Evol. 21:334-337. 112. Delihas, N., J. Andersen, H. M. Sprouse, and B. Dudock 1981. The nucleotide sequence of the chloroplast 5S ribosomal RNA from spinach. Nucleic Acids Res. 9:2801-2805. 113. Delihas, N., W. Andresini, J. Andersen, and D. Berns. 1982. Structural features unique to the 5S ribosomal RNAs of the thermophilic cyanobacterium Synechococcus lividus III and the green plant chloroplasts. J. Mol. Biol. 162:721-727. 114. Delp, G., and H. Kossel. 1991. rRNAs and rRNA genes of plastids. Cell Cult. Somatic Cell Genet. Plants 7A.-139-167. 115. dePamphilis, C. W., and J. D. Palmer. 1990. Loss of photosynthetic and chlororespiratory genes from the plastid genome of a parasitic flowering plant. Nature (London) 348:337-339. 116. De Stasio, E. A., and A. E. Dahlberg. 1990. Effects of mutagenesis of a conserved base-paired site near the decoding region of Escherichia coli 16S ribosomal RNA. J. Mol. Biol. 212:127-133. 117. Devereux, R., A. R. Loeblich III, and G. E. Fox. 1990. Higher plant origins and the phylogeny of green algae. J. Mol. Evol. 31:18-24. 118. Dormann-Przybyl, D., G. Strittmatter, and H. Kossel. 1986. The region distal to the rRNA operon from chloroplasts of maize contains genes coding for tRNAM9(ACG) and tRNAIn(GUU). Plant Mol. Biol. 7:419-431. 119. Dorne, A. M., J. Eneas-Filho, P. Heizmann, and R. Mache. 1984. Comparison of ribosomal proteins of chloroplast from spinach and of E. coli. Mol. Gen. Genet. 193:129-134. 120. Dorne, A. M., P. Heizmann, J. Alt, and R Mache. 1985. Spinach chloroplast genes coding for three ribosomal proteins. Mol. Gen. Genet. 198:512-524. 121. Dorne, A. M., A. M. Lescure, and R. Mache. 1984. Site of synthesis of spinach chloroplast ribosomal proteins and formation of incomplete ribosomal particles in isolated chloroplasts. Plant Mol. Biol. 3:83-90. 122. Douglas, S. E. 1991. Unusual organization of a ribosomal protein operon in the plastid genome of Cryptomonas (: evolutionary considerations. Curr. Genet. 19:289-294. 123. Douglas, S. E. 1992. Eukaryote-eukaryote endosymbioses: insights from studies of a cryptomonad alga. BioSystems 28:57-68. 124. Douglas, S. E. 1992. A secY homologue is found in the plastid genome of Cryptomonas Phi. FEBS Lett. 298:93-96. 125. Douglas, S. E., and W. F. Doolittle. 1984. Nucleotide sequence of the 5S rRNA gene and flanking regions in the cyanobacterium, Anacystis nidulans. FEBS Lett. 166:307-310. 126. Douglas, S. E., and W. F. Doolittle. 1984. Complete nucleotide sequence of the 23S rRNA gene of the cyanobacterium Anacystis nidulans. Nucleic Acids Res. 12:3373-3386. 127. Douglas, S. E., and D. G. Durnford. 1990. Nucleotide sequence of the genes for ribosomal protein S4 and tRNA'g from the chlorophyll c-containing alga Cryptomonas (. Nucleic Acids Res. 18:1903. 128. Douglas, S. E., and D. G. Durnford. 1990. Sequence analysis of the plastid rDNA spacer region of the chlorophyll c-containing alga Cryptomonas. DNA Seq. 1:55-62. 129. Douglas, S. E., C. A. Murphy, D. F. Spencer, and M. W. Gray. 1991. Cryptomonad algae are evolutionary chimaeras of two phylogenetically distinct unicellular eukaryotes. Nature (London) 350:148-151. 130. Douglas, S. E., and S. Turner. 1991. Molecular evidence for the origin of plastids from a cyanobacterium-like ancestor. J. Mol. Evol. 33:267-273. 131. Douglass, J., and L. M. Steyn. 1993. A ribosomal gene mutation in streptomycin-resistant Mycobacterium tuberculosis isolates. J. Infect. Dis. 167:1505-1506. 132. Douthwaite, S., and C. Aagaard. 1993. Erythromycin binding is reduced in ribosomes with conformational alterations in the 23S rRNA peptidyl transferase loop. J. Mol. Biol. 232:725-731. 133. Downie, S. R., R G. Olmstead, G. Zurawski, D. E. Soltis, P. S. Soltis, J. C. Watson, and J. D. Palmer. 1991. Six independent losses of the chloroplast DNA rpl2 intron in dicotyledons: molecular and phylogenetic implications. Evolution 45:12451259. 134. Drager, R G., and R. B. Hallick. 1993. A novel Euglena gracilis chloroplast operon encoding four ATP synthase subunits and two ribosomal proteins contains 17 introns. Curr. Genet. 23:271-280. 135. Drager, R G., and R B. Hallick 1993. A complex twintron is excised as four individual introns. Nucleic Acids Res. 21:2389-2394. Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV 92. Copertino, D. W., D. A. Christopher, and R. B. Hallick 1991. A mixed group IV/group III twintron in the Euglena gracilis chloroplast ribosomal protein S3 gene: evidence for intron insertion during gene evolution. Nucleic Acids Res. 19:6491-6497. 93. Copertino, D. W., S. Shigeoka, and R. B. Halliclk 1992. Chloroplast group III twintron excision utilizing multiple 5'- and 3'splice sites. EMBO J. 11:5041-5050. 94. Corry, M. J., P. I. Payne, and T. A. Dyer. 1974. The nucleotide sequence of 5S rRNA from the blue-green alga Anacystis nidulans. FEBS Lett. 46:63-66. 95. C6te, J.-C., and R. Wu. 1989. Sequence of the chloroplast rps14 gene encoding the chloroplast ribosomal protein S14 from rice. Nucleic Acids Res. 17:1780. 96. Cote, V., J.-P. Mercier, C. Lemieux, and M. Turmel. 1993. The single group-I intron in the chloroplast rmL gene of Chlamydomonas humicola encodes a site-specific DNA endonuclease (IChuI). Gene 129:69-76. 97. Cozens, A. L., and J. E. Walker. 1986. Pea chloroplast DNA encodes homologues of Eschenichia coli ribosomal subunit S2 and the f3'-subunit of RNA polymerase. Biochem. J. 236:453-460. 98. Cseplo, A., L. Eigel, G. V. Horvath, P. Medgyesy, R. G. Herrmann, and H.-U. Koop. 1993. Subcellular location of lincomycin resistance in Nicotiana mutants. Mol. Gen. Genet. 236:163-170. 99. Cseplo, A., T. Etzold, J. Schell, and P. H. Schreier. 1988. Point mutations in the 23S rRNA genes of four lincomycin resistant Nicotiana plumbaginifolia mutants could provide new selectable markers for chloroplast transformation. Mol. Gen. Genet. 214: 295-299. 100. Cui, Z., and T. L. Mason. 1989. A single nucleotide substitution at the rib2 locus of the yeast mitochondrial gene for 21S rRNA confers resistance to erythromycin and cold-sensitive ribosome assembly. Curr. Genet. 16:273-279. 101. Cundliffe, E. 1986. Involvement of specific portions of ribosomal RNA in defined ribosomal functions: a study utilizing antibiotics, p. 586-604. In B. Hardesty and G. Kramer (ed.), Structure, function and genetics of ribosomes, Springer-Verlag, New York. 102. Cundliffe, E. 1990. Recognition sites for antibiotics within rRNA, p. 479-490. In W. E. Hill, A. Dahlberg, G. A. Garrett, P. B. Moore, D. Schlessinger, and J. R. Warner (ed.), The ribosome. MICROBIOL. REV. VOL. 58, 1994 CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS quence and analysis of mRNA and genes. Biochemistry 21:68566864. 155. Elhag, G. A., F. J. Thomas, T. P. McCreery, and D. P. Bourque. 1992. Nuclear-encoded chloroplast ribosomal protein L12 of Nicotiana tabacum: characterization of mature protein and isolation and sequence analysis of cDNA clones encoding its cytoplasmic precursor. Nucleic Acids Res. 20:689-697. 156. Eneas-Filho, J., M. R. Hartley, and R. Mache. 1981. Pea chloroplast ribosomal proteins: characterization and site of synthesis. Mol. Gen. Genet. 184:484-488. 157. Erdmann, V. A., and J. Wolters. 1986. Collection of published SS, 5.8S, and 4.5S ribosomal RNA sequences. Nucleic Acids Res. 14(Suppl.):rl-r59. 158. Ettayebi, M., S. M. Prasad, and E. A. Morgan. 1985. Chloramphenicol-erythromycin resistance mutations in a 23S rRNA gene of Escherichia coli. J. Bacteriol. 162:551-557. 159. Etti, H. 1976. Die Gattung Chlamydomonas Ehrenberg. Beih. Nova Hedwigia 49:1-1122. 160. Etzold, T., C. C. Fritz, J. Schell, and P. H. Schreier. 1987. A point mutation in the chloroplast 16S rRNA gene of a streptomycin resistant Nicotiana tabacum. FEBS Lett. 219:343-346. 161. Evrard, J.-L., C. Johnson, I. Janssen, W. Loffelhardt, J.-H. Weil, and M. Kuntz. 1990. The cyanelle genome of Cyanophora paradoxa, unlike the chloroplast genome, codes for the ribosomal L3 protein. Nucleic Acids Res. 18:1115-1119. 162. Evrard, J.-L., M. Kuntz, N. A. Straus, and J.-H. Weil. 1988. A class-I intron in a cyanelle tRNA gene from Cyanophora paradoxa: phylogenetic relationship between cyanelles and chloroplasts. Gene 71:115-122. 163. Evrard, J. L., M. Kuntz, and J. H. Weil. 1990. The nucleotide sequence of five ribosomal protein genes from the cyanelles of Cyanophora paradoxa: implications concerning the phylogenetic relationship between cyanelles and chloroplasts. J. Mol. Evol. 30:16-25. 164. Falk, J., A. Schmidt, and K. Krupinska. 1993. Characterization of plastid DNA transcription in ribosome deficient plastids of heat-bleached barley leaves. J. Plant Physiol. 141:176-181. 165. Feagin, J. E. 1994. The extra-chromosomal DNAs of apicomplexan parasites. Annu. Rev. Microbiol. 48:81-104. 166. Feagin, J. E., E. Werner, M. J. Gardner, D. H. Williamson, and R. J. M. Wilson. 1992. Homologies between the contiguous and fragmented rRNAs of the two Plasmodium falciparum extrachromosomal DNAs are limited to core sequences. Nucleic Acids Res. 20:879-887. 167. Fearon, K., and T. L. Mason. 1988. Structure and regulation of a nuclear gene in Saccharomyces cerevisiae that specifies MRP7, a protein of the large subunit of the mitochondrial ribosome. Mol. Cell. Biol. 8:3636-3646. 168. Feierabend, J., and T. Berberich. 1991. Heat-induced ribosomedeficiency of plastids-mechanism and applications. NATO ASI Ser. Ser. H 55:215-227. 169. Feierabend, J., W. Schluter, and K. Tebartz. 1988. Unassembled polypeptides of the plastidic ribosome in heat-treated 70Sribosome-deficient rye leaves. Planta 174:542-550. 170. Fitzky, B., and A. R. Subramanian. 1990. Nucleotide sequence and map positions of the duplicated gene for chloroplast ribosomal protein S15 in Zea mays (maize). Nucleic Acids Res. 18:3407. 171. Fong, S. E., and S. J. Surzycki. 1992. Chloroplast RNA polymerase genes of Chlamydomonas reinhardii exhibit an unusual structure and arrangement. Curr. Genet. 21:485-497. 172. Fong, S. E., and S. J. Surzycki. 1992. Organization and structure of plastome psbF, psbL, petG and 0RF712 genes in Chlamydomonas reinhardtii. Curr. Genet. 21:527-530. 173. Fox, L., J. Erion, J. Tarnowski, L. Spremulli, N. Brot, and H. Weissbach. 1980. Euglena gracilis chloroplast EF-Ts: evidence that it is a nuclear-coded gene product. J. Biol. Chem. 255:60186019. 174. Fox, T. D. 1987. Natural variation in the genetic code. Annu. Rev. Genet. 21:67-91. 175. Franceschi, F. J., and K. H. Nierhaus. 1990. Ribosomal proteins L15 and L16 are mere late assembly proteins of the large ribosomal subunit. Analysis of an Escherichia coli mutant lacking Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV 136. Dragon, F., and L. Brakier-Gingras. 1993. Interaction of Escherichia coli ribosomal protein S7 with 16S rRNA. Nucleic Acids Res. 21:1199-1203. 137. Dron, M., M. Rahire, and J.-D. Rochaix. 1982. Sequence of the chloroplast 16S rRNA gene and its surrounding regions of Chlamydomonas reinhardii. Nucleic Acids Res. 10:7609-7620. 138. Du Jardin, P. 1992. Unpublished sequence submission. 139. Dujon, B. 1989. Group I introns as mobile genetic elements: facts and mechanistic speculations-a review. Gene 82:91-114. 140. Durocher, B., A. Gauthier, G. Bellemare, and C. Lemieux. 1989. An optional group I intron between the chloroplast small subunit rRNA genes of Chlamydomonas moewusii and C. eugametos. Curr. Genet. 15:277-282. 141. Durovic, P., D. Liao, S. Mylvaganam, and P. P. Dennis. 1993. The evolution of ribosomal protein and ribosomal RNA operons: coding sequences, regulatory mechanisms and processing pathways, p. 679-688. In K. H. Nierhaus, F. Franceschi, A. R. Subramanian, V. A. Erdmann, and B. Wittmann-Liebold (ed.), The translational apparatus. Structure, function, regulation, evolution. Plenum Press, New York. 142. Durrenberger, F., and J.-D. Rochaix. 1991. Chloroplast ribosomal intron of Chlamydomonas reinhardtii: in vitro self-splicing, DNA endonuclease activity and in vivo mobility. EMBO J. 10:3495-3501. 143. Durrenberger, F., and J.-D. Rochaix. 1993. Characterization of the cleavage site and the recognition sequence of the I-Crel DNA endonuclease encoded by the chloroplast ribosomal intron of Chlamydomonas reinhardtii. Mol. Gen. Genet. 236:409-414. 144. Dyer, T. A., and C. M. Bowman. 1979. Nucleotide sequences of chloroplast 5S ribosomal ribonucleic acid in flowering plants. Biochem. J. 183:595-604. 145. Eberly, S. L., G. H. Spremulli, and L. L. Spremulli. 1986. Light induction of the Euglena chloroplast protein synthesis elongation factors: relative effectiveness of different wavelength ranges. Arch. Biochem. Biophys. 245:338-347. 146. Eck, R., C. M. Lazarus, F. Baldauf, M. Metzlaf, and R. Hagemann. 1987. Sequence analysis and Escherichia coli minicell transcription test of Pelargonium plastid SS rDNA. Mol. Gen. Genet. 207:514-516. 147. Edwards, K, J. Bedbrook, T. Dyer, and H. Kossel. 1981. 4.5S rRNA from Zea mays chloroplasts shows structural homology with the 3' end of prokaryotic 23S rRNA. Biochem. Int. 2:533538. 148. Edwards, K., and H. Kossel. 1981. The rRNA operon from Zea mays chloroplasts: nucleotide sequence of 23S rDNA and its homology with E. coli 23S rDNA. Nucleic Acids Res. 9:28532869. 149. Egebjerg, J., S. Douthwaite, and R. A. Garrett. 1989. Antibiotic interactions at the GTPase-associated centre within Escherichia coli 23S rRNA. EMBO J. 8:607-611. 150. Ehrenberg, M., A.-M. Rojas, I. Diaz, N. Bilgin, J. Weiser, F. Claesens, and C. G. Kurland. 1990. New aspects of elongation factor Tu function in translation, p. 373-379. In W. E. Hill, A. Dahlberg, G. A. Garrett, P. B. Moore, D. Schlessinger, and J. R. Warner (ed.), The ribosome. Structure, function, and evolution. American Society for Microbiology, Washington, D.C. 151. Ehresmann, B., C. Ehresmann, P. Romby, M. Mougel, F. Baudin, E. Westhof, and J.-P. Ebel. 1990. Detailed structures of rRNAs: new approaches, p. 148-159. In W. E. Hill, A. Dahlberg, G. A. Garrett, P. B. Moore, D. Schlessinger, and J. R. Warner (ed.), The ribosome. Structure, function, and evolution. American Society for Microbiology, Washington, D.C. 152. El-Gewely, M. R., R. B. Helling, and J. G. T. Dibbits. 1984. Sequences and evolution of the regions between the nm operons in the chloroplast genome of Euglena gracilis bacillaris. Mol. Gen. Genet. 194:432-443. 153. Elhag, G. A., and D. P. Bourque. 1992. Nuclear-encoded tobacco chloroplast ribosomal protein L24. Protein identification, sequence analysis of cDNAs encoding its cytoplasmic precursor, and mRNA and genomic DNA analysis. J. Biol. Chem. 267: 21705-21711. 154. Elhag, G. A., and D. P. Bourque. 1992. Nuclear-encoded chloroplast ribosomal protein L27 of Nicotiana tabacum: cDNA se- 739 740 HARRIS ET AL. L15. J. Biol. Chem. 265:16676-16682. 176. Francis, M. A., R. F. Balint, and B. S. Dudock 1987. A novel variety of 4.5 S RNA from Codium fragile chloroplasts. J. Biol. Chem. 262:1848-1854. 177. Frank, J., A. Verschoor, M. Radermacher, and T. Wagenknecht. 1990. Morphologies of eubacterial and eucaryotic ribosomes as determined by three-dimensional electron microscopy, p. 107113. In W. E. Hill, A. Dahlberg, G. A. Garrett, P. B. Moore, D. Schlessinger, and J. R. Warner (ed.), The ribosome. Structure, function, and evolution. American Society for Microbiology, Washington, D.C. 178. Franzetti, B., P. Carol, and R Mache. 1992. Characterization and RNA-binding properties of a chloroplast S1-like ribosomal proFranzetti, B., D.-X. Zhou, and R Mache. 1992. Structure and expression of the nuclear gene coding for the plastid CS1 ribosomal protein from spinach. Nucleic Acids Res. 20:4153- 4157. 180. Freimann, A., and W. Hachtel. 1988. Chloroplast messenger RNAs of free and thylakoid-bound polysomes from Vicia faba L. Planta 175:50-59. 181. Freyssinet, G. 1978. Determination of the site of synthesis of some Euglena cytoplasmic and chloroplast ribosomal proteins. Exp. Cell Res. 115:207-219. 182. Fromm, H., M. Edelman, D. Aviv, and E. Galun. 1987. The molecular basis for rRNA-dependent spectinomycin resistance in Nicotiana chloroplasts. EMBO J. 6:3233-3237. 183. Fromm, H., M. Edelman, B. Koller, P. Goloubinof, and E. Galun. 1986. The enigma of the gene coding for ribosomal protein S12 in the chloroplasts of Nicotiana. Nucleic Acids Res. 14:883-898. 184. Fromm, H., E. Galun, and M. Edelman. 1989. A novel site for streptomycin resistance in the "530 loop" of chloroplast 16S ribosomal RNA. Plant Mol. Biol. 12:499-505. 185. Fujiwara, S., M. Kawachi, I. Inouye, and J. Someya. 1994. The gene for ribosomal protein L27 is located on the plastid rather than the nuclear genome of the chlorophyll c-containing alga Pleurochrysis carterae. Plant Mol. Biol. 24:253-257. 186. Fukuzawa, H., T. Kohchi, T. Sano, H. Shirai, K. Umesono, H. Inokuchi, H. Ozeki, and K. Ohyama. 1988. Structure and organization of Marchantia polymorpha chloroplast genome. III. Gene organization of the large single copy region from rbcL to trnl(CAU). J. Mol. Biol. 203:333-351. 187. Fukuzawa, H., T. Kohchi, H. Shirai, KI Ohyama, K. Umesono, H. Inokuchi, and H. Ozeki. 1986. Coding sequences for chloroplast ribosomal protein S12 from the liverwort, Marchantia polymorpha, are separated far apart on the different DNA strands. FEBS Lett. 198:11-15. 188. Funatsu, G., K. Nierhaus, and H. G. Wittmann. 1972. Ribosomal proteins. XXXVII. Determination of allele types and amino acid exchanges in protein S-12 of three streptomycin-resistant mutants of Escherichia coli. Biochim. Biophys. Acta 287:282-291. 189. Funatsu, G., W. Puls, E. Schiltz, J. Reinbolt, and H. G. Wittmann. 1972. Ribosomal proteins. XXXI. Comparative studies on altered proteins S4 of six Escherichia coli revertants from streptomycin dependence. Mol. Gen. Genet. 115:131-139. 190. Funatsu, G., and H. G. Wittmann. 1972. Ribosomal proteins XXXIII. Location of amino acid replacements in protein S12 isolated from Eschenichia coli mutants resistant to streptomycin. J. Mol. Biol. 68:547-550. 191. Galili, S., H. Fromm, D. Aviv, M. Edelman, and E. Galun. 1989. Ribosomal protein S12 as a site for streptomycin resistance in Nicotiana chloroplasts. Mol. Gen. Genet. 218:289-292. 192. Gantt, J. S. 1988. Nucleotide sequences of cDNAs encoding four complete nuclear-encoded plastid ribosomal proteins. Curr. Genet. 14:519-528. 193. Gantt, J. S., S. L. Baldauf, P. J. Calie, N. F. Weeden, and J. D. Palmer. 1991. Transfer of rp122 to the nucleus greatly preceded its loss from the chloroplast and involved the gain of an intron. EMBO J. 10:3073-3078. 194. Gantt, J. S., A. Gupta, and M. D. Thompson. 1991. The effects of chlorophyll photooxidation on nuclear-encoded plastid ribosomal protein mRNAs in norflurazon-treated pea seedlings. NATO ASI Ser. Ser. H 55:207-213. 195. Gantt, J. S., and J. L. Key. 1986. Isolation of nuclear encoded plastid ribosomal protein cDNAs. Mol. Gen. Genet. 202:186193. 196. Gantt, J. S., and M. D. Thompson. 1990. Plant cytosolic ribosomal protein Sli and chloroplast ribosomal protein CS17. Their primary structures and evolutionary relationships. J. Biol. Chem. 265:2763-2767. 197. Gardner, M. J., J. E. Feagin, D. J. Moore, K. Rangachari, D. H Williamson, and R J. M. Wilson. 1993. Sequence and organization of large subunit rRNA genes from the extrachromosomal 35 kb circular DNA of the malaria parasite Plasmodium falciparum. Nucleic Acids Res. 21:1067-1071. 198. Gardner, M. J., J. E. Feagin, D. J. Moore, D. F. Spencer, M. W. Gray, D. H. Williamson, and R J. M. Wilson. 1991. Organisation and expression of small subunit ribosomal RNA genes encoded by a 35-kilobase circular DNA in Plasmodium falciparum. Mol. Biochem. Parasitol. 48:77-88. 199. Gauthier, A., M. Turmel, and C. Lemieux. 1988. Mapping of chloroplast mutations conferring resistance to antibiotics in Chlamydomonas: evidence for a novel site of streptomycin resistance in the small subunit rRNA. Mol. Gen. Genet. 214:192-197. 200. Gauthier, A., M. Turmel, and C. Lemleux 1991. A group I intron in the chloroplast large subunit rRNA gene of Chlamydomonas eugametos encodes a double-strand endonuclease that cleaves the homing site of this intron. Curr. Genet. 19:43-47. 201. Giese, K., and A. R Subramanian. 1989. Chloroplast ribosomal protein L12 is encoded in the nucleus: construction and identification of its cDNA clones and nucleotide sequence including the transit peptide. Biochemistry 28:3525-3529. 202. Giese, K., and A. R Subramanian. 1990. Enhanced translational utilization of chloroplast ribosomal protein mRNAs from two AUG codons shown by site-directed mutation. Biochemistry 29:10562-10566. 203. Giese, K., and A. R Subramanian. 1991. Expression and functional assembly into bacterial ribosomes of a nuclear-encoded chloroplast ribosomal protein with a long NH2-terminal extension. FEBS Lett. 288:72-76. 204. Giese, K., A. R Subramanian, L. M. rinua, and L. Bogorad. 1987. Nucleotide sequence, promoter analysis, and linkage mapping of the unusually organized operon encoding ribosomal proteins S7 and S12 in maize chloroplast. J. Biol. Chem. 262: 15251-15255. 205. GilHham, N. W. 1994. Organelle genes and genomes. Oxford University Press, Oxford. 206. Gillham, N. W., J. E. Boynton, and E. H. Harris. 1991. Transmission of plastid genes. Cell Cult. Somatic Cell Genet. Plants 7A.-55-92. 207. Gillham, N. W., J. E. Boynton, and C. R Hauser. 1994. Translational regulation of gene expression in chloroplasts and mitochondria. Annu. Rev. Genet. 28:71-93. 208. Gillham, N. W., E. H. Harris, B. L Randolph-Anderson, J. E. Boynton, C. K Hauser, K. B. McElwain, and S. M. Newman. 1991. Molecular genetics of chloroplast ribosomes in Chlamydomonas. NATO ASI Ser. Ser. H 55:127-144. 209. Gilmartin, P. M., L Sarokin, J. Memelink, and N.-H. Chua. 1990. Molecular light switches for plant genes. Plant Cell 2:369378. 210. Giovannoni, S. J., S. Turner, G. J. Olsen, S. Barns, D. J. Lane, and N. R Pace. 1988. Evolutionary relationships among cyanobacteria and green chloroplasts. J. Bacteriol. 170:3584-3592. 211. Gockel, G., S. Baier, and W. Hachtel. 1994. Plastid ribosomal protein genes from the nonphotosynthetic flagellate Astasia longa. Plant Physiol. 105:1443-1444. 212. Gold, J. C., and L L Spremulli. 1985. Eugena gracils chloroplast initiation factor 2 (IF-2Chl): identification and initial characterization. J. Biol. Chem. 260:14897-14900. 213. Golden, B. L, D. W. Hoffinan, V. Ramakrishnan, and S. W. White. 1993. Ribosomal protein S17: characterization of the three-dimensional structure by 'H and 15N NMR. Biochemistry 32:12812-12820. 214. Goldschmidt-Clermont, M. 1991. Transgenic expression of aminoglycoside adenine transferase in the chloroplast: a selectable marker for site-directed transformation of Chlamydoimonas. Nu- Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV tein. J. Biol. Chem. 267:19075-19081. 179. MICROBIOL. REV. VOL. 58, 1994 CHLOROPLAST RIBOSOMES AND SYNTHESIS 741 genome of the holoparasitic flowering plant Cuscuta reflexa. Mol. Gen. Genet. 232:154-161. 238. Haberhausen, G., and K. Zetsche. 1994. Functional loss of all ndh genes in an otherwise relatively unaltered plastid genome of the holoparasitic flowering plant Cuscuta reflexa. Plant Mol. Biol. 24:217-222. 239. Hachtel, W. 1985. Biosynthesis and assembly of chloroplast ribosomal proteins in isolated chloroplasts from Vicia faba L. Biochem. Physiol. Pflanz. 180:115-124. 240. Hahn, V., A. M. Dorne, R. Mache, J. P. Ebel, and P. Stiegler. 1988. Identification of an Escherichia coli S1-like protein in the spinach chloroplast ribosome. Plant Mol. Biol. 10:459-464. 241. Hallick, R. B., and W. Bottomley. 1983. Proposals for the naming of chloroplast genes. Plant. Mol. Biol. Rep. 1:38-43. 242. Hallick, R. B., D. A. Christopher, D. W. Copertino, R. G. Drager, K. P. Jenkins, and J. K Stevenson. 1991. Chloroplast ribosomal protein operons of Euglena gracilis. NATO ASI Ser. Ser. H 55:145-153. 243. Hallick, R. B., L. Hong, R. G. Drager, M. R. Favreau, A. Monfort, B. Orsat, A. Spielmann, and E. Stutz. 1993. Complete sequence of Euglena gracilis chloroplast DNA. Nucleic Acids Res. 21:35373544. 244. Hallick, R. B., C. Lipper, 0. C. Richards, and W. Rutter. 1976. Isolation of a transcriptionally active chromosome from chloroplasts of Euglena gracilis. Biochemistry 15:3039-3045. 245. Hanson, M. R., and L. Bogorad. 1978. The ery-M2 group of Chlamydomonas reinhardtii: cold-sensitive, erythromycin-resis246. 247. 248. 249. 250. 251. 252. tant mutants deficient in chloroplast ribosomes. J. Gen. Microbiol. 105:253-262. Harada, T., R. Ishikawa, M. Niizeki, and K. Saito. 1992. Pollenderived rice calli that have large deletions in plastid DNA do not require protein synthesis in plastids for growth. Mol. Gen. Genet. 233:145-150. Harris, E. H. 1989. The Chlamydomonas sourcebook. Academic Press, Inc., San Diego, Calif. Harris, E. H., J. E. Boynton, and N. W. Gillham. 1974. Chloroplast ribosome biogenesis in Chlamydomonas. Selection and characterization of mutants blocked in ribosome formation. J. Cell Biol. 63:160-179. Harris, E. H., J. E. Boynton, and N. W. Gillham. 1987. Interaction of nuclear and chloroplast mutations in biogenesis of chloroplast ribosomes in Chlamydomonas, p. 142-149. In W. Wiessner, D. G. Robinson, and R. C. Starr (ed.), Molecular and cellular aspects of algal development. Springer-Verlag KG, Berlin. Harris, E. H., J. E. Boynton, N. W. Gillham, B. D. Burkhart, and S. M. Newman. 1991. Chloroplast genome organization in Chlamydomonas. Arch. Protistenkd. 139:183-192. Harris, E. H., B. D. Burkhart, N. W. Gillham, and J. E. Boynton. 1989. Antibiotic resistance mutations in the chloroplast 16S and 23S rRNA genes of Chlamydomonas reinhardtii: correlation of genetic and physical maps of the chloroplast genome. Genetics 123:281-292. Hattori, T., and M. Margulies. 1986. Synthesis of large subunit of ribulose-bisphosphate carboxylase by thylakoid-bound polyribosomes from spinach chloroplasts. Arch. Biochem. Biophys. 244: 630-640. 253. Hauser, C. R., B. L. Randolph-Anderson, T. M. Hohl, E. H. Harris, J. E. Boynton, and N. W. Gillham. 1993. Molecular genetics of chloroplast ribosomes in Chlamydomonas reinhardtii, p. 545-554. In K. H. Nierhaus, F. Franceschi, A. R. Subramanian, V. A. Erdmann, and B. Wittmann-Liebold (ed.), The translational apparatus. Structure, function, regulation, evolution. Plenum Press, New York. 254. Heizmann, P., Y. Doly, Y. Hussein, P. Nicolas, V. Nigon, and G. Bernardi. 1981. The chloroplast genome of bleached mutants of Euglena gracilis. Biochim. Biophys. Acta 653:412-415. 255. Held, W. A., B. Ballou, S. Mizushima, and M. Nomura. 1974. Assembly mapping of 30S ribosomal proteins from Escherichia coli. J. Biol. Chem. 249:3103-3111. 256. Herdenberger, F., D. T. N. Pillay, and A. Steinmetz. 1990. Sequence of the tmH gene and the inverted repeat structure deletion site of the broad bean chloroplast genome. Nucleic Acids Res. 18:1297. Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV cleic Acids Res. 19:4083-4089. 215. Graack, H.-R., L. Grohmann, M. Kitakawa, K.-L. Schafer, and V. Kruft. 1992. YmL9, a nucleus-encoded mitochondrial ribosomal protein of yeast, is homologous to L3 ribosomal proteins from all natural kingdoms and photosynthetic organelles. Eur. J. Biochem. 206:373-380. 216. Graf, L., H. Kossel, and E. Stutz. 1980. Sequencing of 16S-23S spacer in a ribosomal RNA operon of Euglena gracilis chloroplast DNA reveals two tRNA genes. Nature (London) 286:908-910. 217. Graf, L., E. Roux, and W. Stutz. 1982. Nucleotide sequence of a Euglena gracilis chloroplast gene coding for the 16S rRNA: homologies to E. coli and Zea mays chloroplast 16S rRNA. Nucleic Acids Res. 10:6369-6381. 218. Gray, J. C., S. M. Hird, and T. A. Dyer. 1990. Nucleotide sequence of the wheat chloroplast gene encoding the proteolytic subunit of an ATP-dependent protease. Plant Mol. Biol. 15:947950. 219. Gray, M. W. 1988. Organelle origins and ribosomal RNA. Biochem. Cell Biol. 66:325-348. 220. Gray, M. W. 1991. Origin and evolution of plastid genomes and genes. Cell Cult. Somatic Cell Genet. Plants 7A:303-330. 221. Gray, M. W. 1992. The endosymbiont hypothesis revisited. Int. Rev. Cytol. 141:233-357. 222. Gray, M. W. 1993. Origin and evolution of organelle genomes. Curr. Opin. Genet. Dev. 3:884-890. 223. Gray, M. W., and W. F. Doolittle. 1982. Has the endosymbiont hypothesis been proven? Microbiol. Rev. 46:1-42. 224. Gray, M. W., and M. N. Schnare. 1990. Evolution of the molecular structure of rRNA, p. 589-597. In W. E. Hill, A. Dahlberg, G. A. Garrett, P. B. Moore, D. Schlessinger, and J. R. Warner (ed.), The ribosome. Structure, function, and evolution. American Society for Microbiology, Washington, D.C. 225. Greenberg, B. M., and R. B. Hallick 1986. Accurate transcription and processing of 19 Euglena chloroplast tRNAs in a Euglena soluble extract. Plant Mol. Biol. 6:89-100. 226. Greenberg, B. M., J. 0. Narita, C. DeLuca-Flaherty, W. Gruissem, K. A. Rushlow, and R. B. Hallick. 1984. Evidence for two RNA polymerase activities in Euglena gracilis chloroplasts. J. Biol. Chem. 259:14880-14887. 227. Gruissem, W., C. Elsner-Menzel, S. Latshaw, J. 0. Narita, M. A. Schaffer, and G. Zurawski. 1986. A subpopulation of spinach chloroplast tRNA genes does not require upstream promoter elements for transcription. Nucleic Acids Res. 14:7541-7556. 228. Gruissem, W., and G. Schuster. 1993. Control of mRNA degradation in organelles, p. 329-365. In G. Brawerman and J. Belasco (ed.), Control of mRNA stability. Academic Press, Inc., Orlando, Fla. 229. Gruissem, W., and J. C. Tonkyn. 1993. Control mechanisms of plastid gene expression. Crit. Rev. Plant Sci. 12:19-55. 230. Gualerzi, C. O., and C. L. Pon. 1990. Initiation of mRNA translation in prokaryotes. Biochemistry 29:5881-5889. 231. Gutell, R. R. 1993. Collection of small subunit (16S- and 16S-like) ribosomal RNA structures. Nucleic Acids Res. 21:3051-3054. 232. Gutell, R. R. 1993. The simplicity behind the elucidation of complex structure in ribosomal RNA, p. 477-488. In K. H. Nierhaus, F. Franceschi, A. R. Subramanian, V. A. Erdmann, and B. Wittmann-Liebold (ed.), The translational apparatus. Structure, function, regulation, evolution. Plenum Press, New York. 233. Gutell, R. R., and G. E. Fox. 1988. A compilation of large subunit RNA sequences presented in a structural format. Nucleic Acids Res. 16(Suppl.):r175-r269. 234. Gutell, R. R., M. W. Gray, and M. N. Schnare. 1993. A compilation of large subunit (23S and 23S-like) ribosomal RNA structures. Nucleic Acids Res. 21:3055-3074. 235. Gutell, R. R., N. Larsen, and C. R. Woese. 1994. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol. Rev. 58:10-26. 236. Gutell, R. R., B. Weiser, C. R. Woese, and H. F. Noller. 1985. Comparative anatomy of 16-S-like ribosomal RNA. Prog. Nucleic Acid Res. Mol. Biol. 32:155-216. 237. Haberhausen, G., K. Valentin, and K. Zetsche. 1992. Organization and sequence of photosynthetic genes from the plastid PROTEIN 742 HARRIS ET AL. 277. 278. 279. 280. 281. 282. 283. 284. 285. 286. 287. 288. 289. 290. 291. 292. 293. 294. 295. 296. 297. 298. Nicotiana plumbaginifolia confers streptomycin resistance. Plant Mol. Biol. 23:179-283. Huang, C., and X.-Q. Liu. Unpublished data. Hudson, G. S., J. G. Mason, T. A. Holton, B. Koller, G. B. Cox, P. R Whitfeld, and W. Bottomley. 1987. A gene cluster in the spinach and pea chloroplast genomes encoding one CF1 and three CFo subunits of the H+-ATP synthase complex and the ribosomal protein S2. J. Mol. Biol. 196:283-298. Huss, V. A. R, and S. J. Giovannoni. 1989. Primary structure of the chloroplast small subunit ribosomal RNA from Chlorella vulgaris. Nucleic Acids Res. 17:9487. Huss, V. A. R., F. Hatzack, and G. E. Fox. 1992. Unpublished sequence submission. Huss, V. A. R, E. Hirsch, and S. J. Giovannoni. 1992. Unpublished sequence submission. Igloi, G. L., I. Dory, and H. Kossel. 1990. Nucleotide and derived amino acid sequence of rps2 from maize chloroplasts. Nucleic Acids Res. 18:663. Igloi, G. L., and H. Kossel. 1992. The transcriptional apparatus of chloroplasts. Crit. Rev. Plant Sci. 10:525-558. Imbeault, J.-C., and D. A. Johnson. 1991. Unpublished sequence submission. Itoh, T., and H. G. Wittmann. 1973. Amino acid replacements in proteins S5 and S12 of two Escherichia coli revertants from streptomycin dependence to independence. Mol. Gen. Genet. 127:19-32. Jagendorf, A. T., and A. Michaels. 1990. Rough thylakoids: translation on photosynthetic membranes. Plant Sci. 71:137145. Janssen, I., H. Mucke, W. L6ffelhardt, and H. J. Bohnert. 1987. The central part of the cyanelle rDNA unit of Cyanophora paradoxa: sequence comparison with chloroplasts and cyanobacteria. Plant Mol. Biol. 9:479-484. Jenni, B., and E. Stutz. 1978. Physical mapping of the ribosomal DNA region of Euglena gracilis chloroplast DNA. Eur. J. Biochem. 88:127-134. Jenni, B., and E. Stutz. 1979. Analysis of Euglena gracilis chloroplast DNA. Mapping of a DNA sequence complementary to 16S rRNA outside of the three rRNA gene sets. FEBS Lett. 102:9599. Johnson, C. H., V. Kruft, and A. R Subramanian. 1990. Identification of a plastid-specific ribosomal protein in the 30S subunit of chloroplast ribosomes and isolation of the cDNA clone encoding its cytoplasmic precursor. J. Biol. Chem. 265:1279012795. Johnson, C. H., and A. R Subramanian. 1991. Chloroplast ribosomal protein L15, like Ll, L13 and L21, is significantly larger than its E. coli homologue. FEBS Lett. 282:268-272. Kamp, R M., B. R Srinivasa, K. von Knoblauch, and A. R Subramanian. 1987. Occurrence of a methylated protein in chloroplast ribosomes. Biochemistry 26:5866-5870. Kanakari, S., G. Timmier, K. von Knoblauch, and A. R Subramanian. 1992. Nucleotide sequence, map position and transcript pattern of the intron-containing gene for maize chloroplast ribosomal protein S16. Plant Mol. Biol. 18:419-422. Kao, J., M. Wu, and Y.-M. Chiang. 1990. Cloning and characterization of chloroplast ribosomal protein-encoding genes, rp116 and rps3, of the marine macro-algae, Gracilaria tenuistipitata. Gene 90:221-226. Kao, J.-S., and M. Wu. 1990. The sequence of the plastid encoded rp122 protein in marine macroalgae, Gracilaria tenuistipitata. Nucleic Acids Res. 18:3067. Karabin, G. D., J. 0. Narita, J. R Dodd, and R B. Hallick. 1983. Euglena gracilis chloroplast ribosomal RNA transcription units. Nucleotide sequence polymorphism in 5S rRNA genes and 5S rRNAs. J. Biol. Chem. 258:14790-14796. Kato, A., H. Shimada, M. Kusuda, and M. Sugiura. 1981. The nucleotide sequences of two tRNAASN genes from tobacco chloroplast. Nucleic Acids Res. 9:5601-5607. Kato, A., F. Takaiwa, K. Shinozaki, and M. Sugiura. 1985. Location and nucleotide sequence of the genes for tobacco chloroplast tRNAM9(ACG) and tRNAL-U(UAG). Curr. Genet. 9:405-409. Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV 257. Herold, M., V. Nowotny, E. R. Dabbs, and K. H. Nierhaus. 1986. Assembly analysis of ribosomes from a mutant lacking the assembly-initiator protein L24: lack of L24 induces temperature sensitivity. Mol. Gen. Genet. 203:281-287. 258. Herrin, D. L., Y. Bao, A. J. Thompson, and Y.-F. Chen. 1991. Self-splicing of the Chlamydomonas chloroplast psbA introns. Plant Cell 3:1095-1107. 259. Herrin, D. L., Y.-F. Chen, and G. W. Schmidt. 1990. RNA splicing in Chlamydomonas chloroplasts: self-splicing of 23S preRNA. J. Biol. Chem. 265:21134-21140. 260. Herrmann, R. G., P. Westhoff, and G. Link 1992. Biogenesis of plastids in higher plants, p. 276-349. In R. Herrmann (ed.), Cell organelles. Advances in plant gene research, vol. 6. SpringerVerlag KG, Vienna. 261. Hershey, J. B. 1987. Protein synthesis, p. 613-647. In F. C. Neidhardt, J. L. Ingraham, K. B. Low, B. Magasanik, M. Schaechter, and H. E. Umbarger (ed.), Eschenchia coli and Salmonella typhimurium: cellular and molecular biology. American Society for Microbiology, Washington, D.C. 262. Hess, W. R, M. Blank-Huber, B. Fieder, T. Borner, and W. Rudiger. 1992. Chlorophyll synthetase and chloroplast tRNASlU are present in heat-bleached, ribosome-deficient plastids. J. Plant Physiol. 139:427-430. 263. Hess, W. R., A. Prombona, B. Fieder, A. R. Subramanian, and T. Borner. 1993. Chloroplast rpsl5 and the rpoB/C1/C2 gene cluster are strongly transcribed in ribosome-deficient plastids: evidence for a functioning non-chloroplast-encoded RNA polymerase. EMBO J. 12:563-571. 264. Hildebrand, M., R. B. Hallick, C. W. Passavant, and D. P. Bourque. 1988. Trans-splicing in chloroplasts: the rpsl2 loci of Nicotiana tabacum. Proc. Natl. Acad. Sci. USA 85:372-376. 265. Hiratsuka, J., H. Shimada, R Whittier, T. Ishibashi, M. Sakamoto, M. Mori, C. Kondo, Y. Honji, C.-R. Sun, B.-Y. Meng, Y.-Q. Li, A. Kanno, Y. Nishizawa, A. Hirai, K. Shinozaki, and M. Sugiura. 1989. The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Mol. Gen. Genet. 217:185194. 266. Hoffman, D. W., C. Davies, S. E. Gerchman, J. H. Kycia, S. J. Porter, S. W. White, and V. Ramakrishnan. 1994. Crystal structure of prokaryotic ribosomal protein L9: a bi-lobed RNAbinding protein. EMBO J. 13:205-212. 267. Hoglund, A. S., and J. C. Gray. 1987. Nucleotide sequence of the gene for ribosomal protein S2 in wheat chloroplast DNA. Nucleic Acids Res. 15:10590. 268. Hoober, J. K. 1987. The molecular basis of chloroplast development, p. 1-74. In M. D. Hatch and N. K Boardman (ed.), The biochemistry of plants, vol. 10. Academic Press, Inc., Orlando, Fla. 269. Hoot, S. B., and J. D. Palmer. 1994. Structural rearrangements, including parallel inversions, within the chloroplast genome of Anemone and related genera. J. Mol. Evol. 38:274-281. 270. Hori, H., B.-L. Lim, and S. Osawa. 1985. Evolution of green plants as deduced from 5S rRNA sequences. Proc. Natl. Acad. Sci. USA 82:820-823. 271. Horjales, E., J. Aqvist, M. LeUonmarck, and 0. Tapia. 1987. Aspects of model building applied to the C-terminal domain of the L12 protein from chloroplast ribosomes: a molecular dynamics study. Biochem. Biophys. Res. Commun. 148:954-961. 272. Hosler, J. P., E. A. Wurtz, E. H. Harris, N. W. Gillham, and J. E. Boynton. 1989. Relationship between gene dosage and gene expression in the chloroplast of Chlamydomonas reinhardtii. Plant Physiol. 91:648-655. 273. Howe, C. J. 1992. Plastid origin of an extrachromosomal DNA molecule from Plasmodium, the causative agent of malaria. J. Theor. Biol. 158:199-205. 274. Howe, C. J., T. J. Beanland, A. W. D. Larkum, and P. J. Lockhart. 1992. Plastid origins. Trends Ecol. Evol. 7:378-383. 275. Howe, C. J., and A. G. Smith. 1991. Plants without chlorophyll. Nature (London) 349:109. 276. Hsu, C.-M., W.-P. Yang, C.-C. Chen, Y.-K. Lai, and T.-Y. Lin. 1993. A point mutation in the chloroplast rpsl2 gene from MICROBIOL. REV. VOL. 58, 1994 CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS bisphosphate carboxylase/oxygenase (rbcL) messenger RNA. J. Biol. Chem. 269:7494-7500. 319. Koo, J. S., and L. L. Spremulli. 1994. Effect of the secondary structure in the Euglena gracilis chloroplast ribulose-bisphosphate carboxylase/oxygenase messenger RNA on translational initiation. J. Biol. Chem. 269:7501-7508. 320. 321. Kossel, H. 1991. Structure and expression of rRNA genes. NATO ASI Ser. Ser. H 55:1-17. Kossel, H., B. Hoch, G. L. Igloi, R. M. Maier, and S. Ruf. 1993. Editing creates the initiator codon of the rpl2 transcript from maize chloroplasts, p. 609-616. In K. H. Nierhaus, F. Franceschi, A. R. Subramanian, V. A. Erdmann, and B. Wittmann-Liebold (ed.), The translational apparatus. Structure, function, regulation, evolution. Plenum Press, New York. 322. Kostrzewa, M., and K. Zetsche. 1993. Organization of plastidencoded ATPase genes and flanking regions including homologues of infB and tsf in the thermophilic red alga Galdieria sulphuraria. Plant Mol. Biol. 23:67-76. 323. Kozak, M. 1983. Comparison of initiation of protein synthesis in procaryotes, eucaryotes and organelles. Microbiol. Rev. 47:1-45. 324. Kraus, B. L., and L. L. Spremulli. 1986. Chloroplast initiation factor 3 from Euglena gracilis. J. Biol. Chem. 261:4781-4784. 325. Kraus, B. L., and L L. Spremulli. 1988. Evidence for the nuclear location of the genes for chloroplast IF-2 and IF-3 in Euglena. Plant Physiol. 88:993-995. 326. Kraus, M., M. Gotz, and W. L6ffelhardt. 1990. The cyanelle str operon from Cyanophora paradoxa: sequence analysis and phylogenetic implications. Plant Mol. Biol. 15:561-573. 327. Krayevski, Y., M. Nalaskowska, Y. Ciesiohka, Y. Barciszweski, and W. Krizosiak 1992. Unpublished sequence submission. 328. Kruft, V., 0. Bischof, U. Bermann, E. Herfurth, and B. Wittmann-Liebold. 1993. Towards ribosomal structure at peptide level: use of crosslinking, antipeptide antibodies and limited proteolysis, p. 509-520. In K. H. Nierhaus, F. Franceschi, A. R. Subramanian, V. A. Erdmann, and B. Wittmann-Liebold (ed.), The translational apparatus. Structure, function, regulation, evolution. Plenum Press, New York. 329. Kuhlemeier, C. 1992. Transcriptional and post-transcriptional regulation of gene expression in plants. Plant Mol. Biol. 19:1-14. 330. Kuhsel, M., and K. V. Kowallik 1987. The plastome of a brown alga, Dictyota dichotoma. II. Location of structural genes coding for ribosomal RNAs, the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase and for polypeptides of photosystems I and II. Mol. Gen. Genet. 207:361-368. 331. Kuhsel, M., R Strickland, and J. D. Palmer. 1990. An ancient group I intron shared by eubacteria and chloroplasts. Science 250:1570-1573. 332. Kumagai, I., T. Pieler, A. R Subramanian, and V. A. Erdmann. 1982. Nucleotide sequence and secondary structure analysis of spinach chloroplast 4.5S RNA. J. Biol. Chem. 257:1292412928. 333. Kumano, M., N. Tomioka, K. Shinozaki, and M. Sugiura. 1986. Analysis of the promoter region in the rmA operon from a blue-green alga, Anacystis nidulans 6301. Mol. Gen. Genet. 202:173-178. 334. Kumano, M., N. Tomioka, and M. Sugiura. 1983. The complete nucleotide sequence of a 23S rRNA gene from a blue-green alga, Anacystis nidulans. Gene 24:219-225. 335. Kurland, C. G. 1992. Translational accuracy and the fitness of bacteria. Annu. Rev. Genet. 26:29-50. 336. Kurland, C. G., F. Jorgensen, A. Richter, M. Ehrenberg, N. Bilgin, and A.-M. Rojas. 1990. Through the accuracy window, p. 513-526. In W. E. Hill, A. Dahlberg, G. A. Garrett, P. B. Moore, D. Schlessinger, and J. R. Warner (ed.), The ribosome. Structure, function, and evolution. American Society for Microbiology, Washington, D.C. 337. Kuroiwa, T. 1991. The replication, differentiation, and inheritance of plastids with emphasis on the concept of organelle nuclei. Int. Rev. Cytol. 128:1-62. 338. Laboure, A.-M., A.-M. Lescure, and J.-F. Briat. 1988. Evidence for a translation-mediated attenuation of a spinach rDNA operon. Biochimie 70:1343-1352. 339. Lagrange, T., P. Carol, C. Bisanz-Seyer, and R. Mache. 1991. chloroplast Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV 299. Kavousi, M., K. Giese,I. M. Larrinua, W. R. McLaughlin, and A. R. Subramanian. 1990. Nucleotide sequence and map position of the gene for maize (Zea mays) chloroplast ribosomal protein L2. Nucleic Acids Res. 18:4244. 300. Kavousi, M., C. Webster, W. Weglohner, J. C. Gray, and A. R. Subramanian. Unpublished data. 301. Keller, M., G. Burkard, H. J. Bohnert, M. Mubumbila, K. Gordon, A. Steinmetz, D. Heiser, E. J. Crouse, and J. H. Weil. 1980. Transfer RNA genes associated with the 16S and 23S rRNA genes of Euglena chloroplast DNA. Biochem. Biophys. Res. Commun. 95:47-54. 302. Keus, R. J. A., A. F. Dekker, M. A. van Roon, and G. S. P. Groot. 1983. The nucleotide sequences of the regions flanking the genes coding for 23S, 16S and 4.5S ribosomal RNA on chloroplast DNA from Spirodela oligorhia. Nucleic Acids Res. 11:6465-6474. 303. Keus, R. J. A., D. J. Roovers, A. F. Dekker, and G. S. P. Groot. 1983. The nucleotide sequence of the 4.5S and 5S rRNA genes and flanking regions from Spirodela oligorhiza chloroplasts. Nucleic Acids Res. 11:3405-3410. 304. Keus, R. J. A., D. J. Roovers, H. Van Heerikhuizen, and G. S. P. Groot. 1983. Molecular cloning and characterization of the chloroplast ribosomal RNA genes from Spirodela oligorhiza. Curr. Genet. 7:7-12. 305. Keus, R. J. A., N. J. Stam, T. Zwiers, H. T. de Hei, and G. S. P. Groot. 1984. The nucleotide sequences of the genes coding for tRNAArgUCU, tRNAArgACG and tRNAInGUU on Spirodela oligorhiza chloroplast DNA. Nucleic Acids Res. 12:5639-5646. 306. Kim, J., and J. E. Mullet. 1994. Ribosome binding sites on chloroplast rbcL and psbA mRNAs and light-induced initiation of Dl translation. Plant Mol. Biol. 25:437-448. 307. Kirsch, W., P. Seyer, and R G. Herrmann. 1986. Nucleotide sequence of the clustered genes for two P700 chlorophyll a apoproteins of the photosystem I reaction center and the ribosomal protein S14 of the spinach plastid chromosome. Curr. Genet. 10:843-855. 308. Klein, R R, H. S. Mason, and J. E. Mullet. 1988. Light-regulated translation of chloroplast proteins. I. Transcripts of psaA-psaB, psbA and rbcL are associated with polysomes in dark-grown and illuminated barley seedlings. J. Cell Biol. 106:289-301. 309. Klein, R. R., and J. E. Mullet. 1990. Light-induced transcription of chloroplast genes. J. Biol. Chem. 265:1895-1902. 310. Klein, U., J. D. De Camp, and L. Bogorad. 1992. Two types of chloroplast gene promoters in Chlamydomonas reinhardtii. Proc. Natl. Acad. Sci. USA 89:3453-3457. 311. Koch, W., K. Edwards, and H. Kossel. 1981. Sequencing of the 16S-23S spacer in a ribosomal RNA operon of Zea mays chloroplast DNA reveals two split tRNA genes. Cell 25:203-213. 312. Kohchi, T., H. Shirai, H. Fukuzawa, T. Sano, T. Komano, K. Umesono, H. Inokuchi, H. Ozeki, and K. Ohyama. 1988. Structure and organization of Marchantia polymorpha chloroplast genome. IV. Inverted repeat and small single copy regions. J. Mol. Biol. 203:353-372. 313. Kohchi, T., K. Umesono, Y. Ogura, Y. Komine, K. Nakahigashi, T. Komano, Y. Yamada, H. Ozeki, and K. Ohyama. 1988. A nicked group II intron and trans-splicing in liverwort, Marchantia polymorpha, chloroplasts. Nucleic Acids Res. 16:10025-10036. 314. Koller, B., and H. Delius. 1980. Vicia faba chloroplast DNA has only one set of ribosomal RNA genes as shown by partial denaturation mapping and R-loop analysis. Mol. Gen. Genet. 178:261-269. 315. Koller, B., and H. Delius. 1982. Parts of the sequence between the complete rRNA operons are repeated on either side of the extra 16S rRNA gene in chloroplast DNA of Euglena gracilis strain Z. FEBS Lett. 140:198-202. 316. Koller, B., H. Delius, and R B. Helling. 1984. Structure and rearrangements of rRNA genes in chloroplast DNA in two strains of Euglena gracilis. Plant Mol. Biol. 3:127-136. 317. Koller, B., E. Roux, P.-E. Montandon, and E. Stutz. 1988. A chimeric transcript containing a 16S rRNA and a potential mRNA in chloroplasts of Euglena gracilis. Plant Mol. Biol. 10:339-347. 318. Koo, J. S., and L. L. Spremulli. 1994. Analysis of the translational initiation region on the Euglena gracilis chloroplast ribulose- 743 744 340. 341. 343. 344. 345. 346. 347. 348. 349. 350. 351. Comparative analysis of four different cDNA clones encoding chloroplast ribosomal proteins. NATO ASI Ser. Ser. H 55:107115. Lagrange, T., B. Franzetti, M. Axelos, R. Mache, and S. LerbsMache. 1993. Structure and expression of the nuclear gene coding for the chloroplast ribosomal protein L21: developmental regulation of a housekeeping gene by alternative promoters. Mol. Cell. Biol. 13:2614-2622. Lapadat, M., D. W. Deerfield II, L. G. Pedersen, and L. L. Spremulli. 1990. Generation of potential structures for the G-domain of chloroplast EF-Tu using comparative molecular modeling. Proteins 8:237-250. Larsen, N. 1992. Higher order interactions in 23S rRNA. Proc. Natl. Acad. Sci. USA 89:5044-5048. Leclerc, D., P. MelanVon, and L. Brakier-Gingras. 1991. Mutations in the 915 region of Escherichia coli 16S ribosomal RNA reduce the binding of streptomycin to the ribosome. Nucleic Acids Res. 19:3973-3977. Lehmbeck, J., B. M. Stummann, and K. W. Henningsen. 1987. Sequence of two regions of pea chloroplast DNA, one with the genes rpsl4, tmfM and tmG-GCC, and one with the genes tmP-UGG and tmW-CCA. Nucleic Acids Res. 15:3630. Leijonmarck, M., A. Lilias, and A. R Subramanian. 1984. Computed spatial homology between the L12 protein of chloroplast ribosome and 1.7 A structure of Escherichia coli L12 domain. Biochem. Int. 8:69-76. Lemieux, C., J. Boulanger, C. Otis, and M. Turmel. 1989. Nucleotide sequence of the chloroplast large subunit rRNA gene from Chlamydomonas reinhardtii. Nucleic Acids Res. 17:7997. Lemieux, C., and R W. Lee. 1987. Nonreciprocal recombination between alleles of the chloroplast 23S rRNA gene in interspecific Chlamydomonas crosses. Proc. Natl. Acad. Sci. USA 84:4166-4170. Lemieux, C., C. Otis, and M. Turmel. Unpublished data. Lerbs-Mache, S. 1993. The 110-kDa polypeptide of spinach plastid DNA-dependent RNA polymerase: single-subunit enzyme or catalytic core of multimeric enzyme complexes? Proc. Natl. Acad. Sci. USA 90:5509-5513. Leu, S., D. White, and A. Michaels. 1990. Cell cycle-dependent transcriptional and post-transcriptional regulation of chloroplast gene expression in Chlamydomonas reinhardtii. Biochim. Biophys. Acta 1049:311-317. Lavesque, M., and D. A. Johnson. 1992. Nucleotide sequence of the chloroplast 23S rRNA gene from alder (Alnus incana). Plant Mol. Biol. 18:601-602. 352. Lew, K. A., and J. R. Manhart. 1993. The rpsl2 gene in Spirogyra maxima (Chlorophyta) and its evolutionary significance. J. Phycol. 29:500-505. 353. Li, N., and R. A. Cattolico. 1987. Chloroplast genome characterization in the red alga Griffithsia pacifica. Mol. Gen. Genet. 209:343-351. 354. Li, Y., H. Itadani, M. Sugita, and M. Sugiura. 1992. cDNA cloning and sequencing of tobacco chloroplast ribosomal protein L12. FEBS Lett. 300:199-202. 355. Lidholm, J., A. E. Szmidt, J.-E. Hallgren, and P. Gustafsson. 1988. The chloroplast genomes of conifers lack one of the rRNA-encoding inverted repeats. Mol. Gen. Genet. 212:6-10. 356. Ligon, P. J. B., K. G. Meyer, J. A. Martin, and S. E. Curtis. 1991. Nucleotide sequence of a 16S rRNA gene from Anabaena sp. strain PCC 7120. Nucleic Acids Res. 19:4553. 357. Liljas, A. 1990. Some structural aspects of elongation, p. 309-317. In W. E. Hill, A. Dahlberg, G. A. Garrett, P. B. Moore, D. Schlessinger, and J. R. Warner (ed.), The ribosome. Structure, function, and evolution. American Society for Microbiology, Washington, D.C. 358. Lilias, A. 1991. Comparative biochemistry and biophysics of ribosomal proteins. Int. Rev. Cytol. 124:103-136. 359. Lin, Q., L. Ma, W. Burkhart, and L. L. Spremulli. 1994. Isolation and characterization of cDNA clones for chloroplast translational initiation factor-3 from Euglena gracilis. J. Biol. Chem. 269:9436-9444. 360. Lindahl, L., and J. M. Zengel. 1986. Ribosomal genes in Escherichia coli. Annu. Rev. Genet. 20:297-326. 361. Little, M. C., and R B. Hallick 1988. Chloroplast rpoA, rpoB, and 362. 363. 364. 365. 366. 367. 368. 369. 370. 371. 372. 373. 374. 375. 376. 377. 378. 379. 380. 381. rpoC genes specify at least three components of a chloroplast DNA-dependent RNA polymerase active in tRNA and mRNA transcription. J. Biol. Chem. 263:14302-14307. Liu, X.-Q. Unpublished data. Liu, X.-Q., N. W. Gillham, and J. E. Boynton. 1988. Chloroplast ribosomal protein L-18 in Chlamydomonas reinhardtii is processed during ribosome assembly. Mol. Gen. Genet. 214:588-591. Liu, X.-Q., N. W. Gillham, and J. E. Boynton. 1989. Chloroplast ribosomal protein gene rps12 of Chlamydomonas reinhardtii. Wild-type sequence, mutation to streptomycin resistance and dependence, and function in Escherichia coli. J. Biol. Chem. 264:16100-16108. Liu, X.-Q., J. P. Hosler, J. E. Boynton, and N. W. Gillham. 1989. mRNAs for two ribosomal proteins are preferentially translated in the chloroplast of Chlamydomonas reinhardtii under conditions of reduced protein synthesis. Plant Mol. Biol. 12:385-394. Liu, X.-Q., C. Huang, and H. Xu. 1993. The unusual rps3-like orf712 is functionally essential and structurally conserved in Chlamydomonas. FEBS Lett. 336:225-230. Liu, X.-Q., H. Xu, and C. Huang. 1993. Chloroplast chlB gene is required for light-independent chlorophyll accumulation in Chlamydomonas reinhardtii. Plant Mol. Biol. 23:297-308. LWfelhardt, W., C. Michalowski, M. Kraus, B. Pfanzagl, C. Neumann-Spallart, J. Jakowitzch, M. Brandtner, and H. J. Bohnert. 1991. rpslO and 6 other ribosomal protein genes from the S10/spc-operon not encountered on higher plant plastid DNA are located on the cyanelle genome of Cyanophora paradoxa. NATO ASI Ser. Ser. H 55:155-165. Loiseaux-de Goer, S., Y. Markowicz, J. Dalmon, and H. Andren. 1988. Physical maps of the two circular plastid DNA molecules of the brown alga Pylaiella littoralis (L.) Kjellm. Curr. Genet. 14:155-162. Loiseaux-de Goer, S., Y. Markowicz, and C. C. Somerville. 1991. Ribosomal RNA genes and pseudogenes of the bi-molecular plastid genome of the brown alga Pylaiella littoralis. NATO ASI Ser. Ser. H. 55:19-29. Lonsdale, D. M., and J. M. Grienenberger. 1992. The mitochondrial genome of plants, p. 183-218. In R. Herrmann (ed.), Cell organelles. Advances in plant gene research, vol. 6. SpringerVerlag KG, Vienna. Lou, J. K., F. D. Cruz, and M. Wu. 1989. Nucleotide sequence of the chloroplast ribosomal protein gene L14 in Chlamydomonas reinhardtii. Nucleic Acids Res. 17:3587. Lou, J. K., M. Wu, C. H. Chang, and A. J. Cutiechia. 1987. Localization of a r-protein gene within the chloroplast DNA replication origin of Chlamydomonas. Curr. Genet. 11:537-541. Luschnig, C., and D. Schweizer. 1992. Nucleotide sequence of ml(CAU) and rp123 from Arabidopsis thaliana chloroplast genome. Nucleic Acids Res. 20:3511. Ma, L., and L. L Spremulli. 1992. Immunological characterization of the complex forms of chloroplast translational initiation factor 2 from Euglena gracilis. J. Biol. Chem. 267:18356-18360. Machado, M. A., and K. Zetsche. 1990. A structural, functional and molecular analysis of plastids of the holoparasites Cuscuta reflexa and Cuscuta europaea. Planta 181:91-96. Mache, R. 1990. Chloroplast ribosomal proteins and their genes. Plant Sci. 72:1-12. Mache, R., A. M. Dorne, and R. M. Batlle. 1980. Characterization of spinach plastid ribosomal proteins by two dimensional -gel electrophoresis. Mol. Gen. Genet. 177:333-338. Mache, R., D.-X. Zhou, B. Franzetti, T. Lagrange, S. LerbsMache, and C. Bisanz-Seyer. 1993. The spinach plastid ribosome: protein properties and aspects of ribosome biosynthesis, p. 565-574. In K H. Nierhaus, F. Franceschi, A. R. Subramanian, V. A. Erdmann, and B. Wittmann-Liebold (ed.), The translational apparatus. Structure, function, regulation, evolution. Plenum Press, New York. MacKay, R. M., D. Salgado, L. Bonen, E. Stackebrandt, and W. F. Doolittle. 1982. The 5S ribosomal RNAs of Paracoccus denitnficans and Prochloron. Nucleic Acids Res. 10:2963-2970. Madsen, L H., J. D. Kreiberg, and K. Gausing. 1991. A small gene family in barley encodes ribosomal proteins homologous to yeast YL17 and L22 from archaebacteria, eubacteria, and chlo- Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV 342. MICROBIOL. REV. HARRIS ET AL. VOL. 58, 1994 CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS 404. Markowicz, Y., S. Loiseaux-de Goer, and R Mache. 1988. Presence of a 16S rRNA pseudogene in the bi-molecular plastid genome of the primitive brown alga Pylaiella littoralis. Evolutionary implications. Curr. Genet. 14:599-608. 405. Markowicz, Y., R Mache, and S. Loiseaux-de Goer. 1988. Sequence of the plastid rDNA spacer region of the brown alga Pylaiella littoralis (L.) Kjellm. Evolutionary significance. Plant Mol. Biol. 10:465-469. 406. Marshall, P., and C. Lemieux. 1991. Cleavage pattern of the homing endonuclease encoded by the fifth intron in the chloroplast large subunit rRNA-encoding gene of Chlamydomonas eugametos. Gene 104:241-245. 407. Marshall, P., and C. Lemieux. 1992. The I-Ceul endonuclease recognizes a sequence of 19 base pairs and preferentially cleaves the coding strand of the Chlamydomonas moewusii chloroplast large subunit rRNA gene. Nucleic Acids Res. 20:6401-6407. 408. Martin, W., T. Lagrange, Y. F. Li, C. Bisanz-Seyer, and R. Mache. 1990. Hypothesis for the evolutionary origin of the chloroplast ribosomal protein L21 of spinach. Curr. Genet. 18:553-556. 409. Massenet, O., P. Martinez, P. Seyer, and J.-F. Briat. 1987. Sequence organization of the chloroplast ribosomal spacer of Spinacia oleracea including the 3' end of the 16S rRNA and the 5' end of the 23S rRNA. Plant Mol. Biol. 10:53-63. 410. Matheson, A. T., J. Auer, C. Ramirez, and A. Bock. 1990. Structure and evolution of archaebacterial ribosomal proteins, p. 617-635. In W. E. Hill, A. Dahlberg, G. A. Garrett, P. B. Moore, D. Schlessinger, and J. R. Warner (ed.), The ribosome. Structure, function, and evolution. American Society for Microbiology, Washington, D.C. 411. Maxwell, E. S., J. Liu, and J. M. Shiveley. 1986. Nucleotide sequences of Cyanophora paradoxa cellular and cyanelle-associated 5S ribosomal RNAs: the cyanelle as a potential intermediate in plastid evolution. J. Mol. Evol. 23:300-304. 412. Maxwell, E. S., J. Liu, and J. M. Shively. 1987. Nucleotide sequence of Cyanophora paradoxa cellular and cyanelle-associated 5S ribosomal RNAs. Ann. N. Y. Acad. Sci. 503:559-561. 413. McElwain, K. B., J. E. Boynton, and N. W. Gillham. 1993. A nuclear mutation conferring thiostrepton resistance in Chlamydomonas reinhardtii affects a chloroplast ribosomal protein related to Escherichia coli ribosomal protein L1i. Mol. Gen. Genet. 241:564-572. 414. McFadden, G. I., P. R Gilson, and S. E. Douglas. 1994. The photosynthetic endosymbiont in cryptomonad cells produces both chloroplast and cytoplasmic-type ribosomes. J. Cell Sci. 107:649-657. 415. McLaughlin, W. E., and I. M. Larrinua. 1987. The sequence of the maize locus and the inverted repeat/unique region junctions. Nucleic Acids Res. 15:3932. 416. McLaughlin, W. E., and I. M. Larrinua. 1987. The sequence of the maize plastid encoded rpl22 locus. Nucleic Acids Res. 15: 4356. 417. McLaughlin, W. E., and I. M. Larrinua. 1987. The sequence of the maize plastid encoded rps3 locus. Nucleic Acids Res. 15:4689. 418. McLaughlin, W. E., and I. M. Larrinua. 1987. The sequence of the first exon and part of the intron of the maize plastid encoded rpll6 locus. Nucleic Acids Res. 15:5896. 419. McLaughlin, W. E., and I. M. Larrinua. 1988. The sequence of the maize plastid encoded rpl23 locus. Nucleic Acids Res. 16: 8183. 420. Melancon, P., C. Lemieux, and L. Brakier-Gingras. 1988. A mutation in the 530 loop of Escherichia coli 16S ribosomal RNA causes resistance to streptomycin. Nucleic Acids Res. 16:96319639. 421. Melekhovets, Y. F. 1993. Unpublished sequence submission. 422. Meng, B. Y., K Shinozaki, and M. Sugiura. 1989. Genes for the ribosomal proteins S12 and S7 and elongation factors EF-G and EF-Tu of the cyanobacterium, Anacystis nidulans: structural homology between 16S rRNA and S7 mRNA. Mol. Gen. Genet. 216:25-30. 423. Michalowski, C. B., B. PfEanzagl, W. LOfelhardt, and H. J. Bohnert. 1990. The cyanelle S10 spc ribosomal protein gene operon from Cyanophora paradoxa. Mol. Gen. Genet. 224:222-231. rpsl9 Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV roplasts. Curr. Genet. 19:417-422. 382. Maerz, M., J. Wolters, C. J. B. Hoffmann, P. Sitte, and U.-G. Maier. 1992. Plastid DNA from Pyrenomonas salina (Cryptophyceae): physical map, genes and evolutionary implications. Curr. Genet. 21:73-81. 383. Maid, U., and K. Zetsche. 1990. Nucleotide sequence of the plastid 16S rRNA gene of the red alga Cyanidium caldanum. Nucleic Acids Res. 18:3996. 384. Maid, U., and K. Zetsche. 1991. Structural features of the plastid ribosomal RNA operons of two red algae: Antithamnion sp. and Cyanidium caldarium. Plant Mol. Biol. 16:537-546. 385. Maid, U., andKI Zetsche. 1992. A 16 kb small single-copy region separates the plastid DNA inverted repeat of the unicellular red alga Cyanidium caldarium: physical mapping of the IR-flanking regions and nucleotide sequences of the psbD-psbC, rpsl6, 5S rRNA and rp121 genes. Plant Mol. Biol. 19:1001-1010. 386. Maier, U.-G. 1992. The four genomes of the alga Pyrenomonas salina (Cryptophyta). BioSystems 28:69-73. 387. Makosky, P. C., and A. E. Dahlberg. 1987. Spectinomycin resistance at site 1192 in 16S ribosomal RNA of E. coli: an analysis of three mutants. Biochimie 69:885-889. 388. Malakhov, M. P., H. Wada, D. A. Los, T. Sakamoto, and N. Murata. 1993. Structure of a cyanobacterial gene encoding the 50S ribosomal protein L9. Plant Mol. Biol. 21:913-918. 389. Maliga, P. 1984. Isolation and characterization of mutants in plant cell culture. Annu. Rev. Plant Physiol. 35:519-542. 390. Maliga, P. 1993. Towards plastid transformation in flowering plants. Tibtech 11:101-107. 391. Maliga, P., B. Moll, and Z. Svab. 1990. Towards manipulation of plastid genes in higher plants, p. 133-143. In I. Zelitch (ed.), Perspectives in biochemical and genetic regulation of photosynthesis, Alan R. Liss, Inc., New York. 392. Malone,R, G. V. Horvath, A. Cseplo, B. Buzas, P. J. Dix, and P. Medgyesy. 1992. Impact of the stringency of cell selection on plastid segregation in protoplast fusion-derived Nicotiana regenerates. Theor. Appl. Genet. 84:866-873. 393. Manhart, J. R, R. W. Hoshaw, and J. D. Palmer. 1990. Unique chloroplast genome in Spirogyra maxima (Chlorophyta) revealed by physical and gene mapping. J. Phycol. 26:490-494. 394. Manhart, J. R, and J. D. Palmer. 1990. The gain of two chloroplast tRNA introns marks the green algal ancestors of land plants. Nature (London) 345:268-270. 395. Manna, F. 1993. Unpublished sequence submission. 396. Manzara, T., and R B. Hallick 1987. Nucleotide sequence of the Euglena gracilis chloroplast gene for ribosomal protein L20. Nucleic Acids Res. 15:3927. 397. Marechal-Drouard, L., P. Guillemaut, H. Pfitzingzer, and J. H. Weil. 1991. Chloroplast tRNAs and tRNA genes: structure and function. NATO ASI Ser. Ser. H 55:45-57. 398. Marechal-Drouard, L., M. Kuntz, and J. H. Weil. 1991. tRNAs and tRNA genes of plastids. Cell Cult. Somatic Cell Genet. 7A.169-189. 399. Marechal-Drouard, L., J. H. Weil, and A. Dietrich. 1993. Transfer RNAs and transfer RNA genes in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 44:13-32. 400. Markmann-Mulisch, U., and A. R Subramanian. 1988. Nucleotide sequence and linkage map position of the genes for ribosomal proteins L14 and S8 in the maize chloroplast genome. Eur. J. Biochem. 170:507-514. 401. Markmann-Mulisch, U., and A. R Subramanian. 1988. Nucleotide sequence of maize chloroplast rpsll with conserved amino acid sequence between eukaryotes, bacteria and plastids. Biochem. Int. 17:655-664. 402. Markmann-Mulisch, U., K. von Knoblauch, A. Lehmann, and A. R Subramanian. 1987. Nucleotide sequence and linkage map position of the secX gene in maize chloroplast and evidence that it encodes a protein belonging to the 50S ribosomal subunit. Biochem. Int. 15:1057-1067. 403. Markowicz, Y., and S. Loiseaux-de Goe~r. 1991. Plastid genomes of the Rhodophyta and Chromophyta constitute a distinct lineage which differs from that of the Chlorophyta and have a composite phylogenetic origin, perhaps like that of the Euglenophyta. Curr. Genet. 20:427-430. 745 746 HARRIS ET AL. 1993. Purification of chloroplast elongation factor Tu and cDNA analysis in tobacco: the existence of two chloroplast elongation factor Tu species. Plant Mol. Biol. 22:767-774. 446. Myers, A. M., E. H. Harris, N. W. Gillham, and J. E. Boynton. 1984. Mutations in a nuclear gene of Chlamydomonas cause the loss of two chloroplast ribosomal proteins, one synthesized in the chloroplast and the other in the cytoplasm. Curr. Genet. 8:369378. 447. Nagano, K., M. Harel, and M. Takezawa. 1988. Prediction of three-dimensional structure of Escherichia coli ribosomal RNA. J. Theor. Biol. 134:199-256. 448. Nagano, Y., H. Ishikawa, R. Matsuno, and Y. Sasaki. 1991. Nucleotide sequence and expression of the ribosomal protein L2 gene in pea chloroplasts. Plant Mol. Biol. 17:541-545. 449. Neefs, J.-M., Y. Van de Peer, P. De Rijk, S. Chapelle, and R. De Wachter. 1993. Compilation of small ribosomal subunit RNA structures. Nucleic Acids Res. 21:3025-3049. 450. Neuhaus, H., A. Scholz, and G. Linlk 1989. Structure and expression of a split chloroplast gene from mustard (Sinapis alba): ribosomal protein gene rpsl6 reveals unusual transcriptional features and complex RNA maturation. Cuff. Genet. 15:63-70. 451. Neumann-Spallart, C., M. Brandtner, M. Kraus, J. Jakowitsch, M. G. Bayer, T. L. Maier, H. E. A. Schenk, and W. Lofelhardt. 1990. The petFI gene encoding ferredoxin I is located close to the str operon on the cyanelle genome of Cyanophora paradoxa. FEBS Lett. 268:55-58. 452. Neumann-Spallart, C., J. Jakowitsch, M. Kraus, M. Brandtner, H. J. Bohnert, and W. Lofelhardt. 1991. rpslO, unreported for plastid DNAs, is located on the cyanelle genome of Cyanophora paradoxa and is cotranscribed with the str operon genes. Curr. Genet. 19:313-315. 453. Newman, S. M., J. E. Boynton, N. W. Gillham, B. L RandolphAnderson, A. M. Johnson, and E. H. Harris. 1990. Transformation of chloroplast ribosomal RNA genes in Chiamydomonas: molecular and genetic characterization of integration events. Genetics 126:875-888. 454. Nickelsen, J., and G. Link 1990. Nucleotide sequence of the mustard chloroplast genes tmH and rpsl9'. Nucleic Acids Res. 18:1051. 455. Nickelsen, J., and G. Link 1992. Unpublished sequence submission. 456. Nickelsen, J., and G. Link. 1993. The 54kDa RNA-binding protein from mustard chloroplasts mediates endonucleolytic transcript 3' end formation in vitro. Plant J. 3:537-544. 457. Nickoloff, J. A., D. A. Christopher, R. G. Drager, and R B. Hallick. 1989. Nucleotide sequence of the Euglena gracilis chloroplast genes for isoleucine, phenylalanine and cysteine transfer RNAs and ribosomal protein S14. Nucleic Acids Res. 17:4882. 458. Nierhaus, K. H. 1982. Structure, assembly, and function of ribosomes. Curr. Top. Microbiol. Immunol. 97:81-155. 459. Nierhaus, K. H. 1991. The assembly of prokaryotic ribosomes. Biochimie 73:739-755. 460. Nierhaus, K. H., R Adlung, T.-P. Hausner, S. Schilling-Bartetzko, T. Twardowski, and F. Triana. 1993. The allosteric three-site model and the mechanism of action of both elongation factors EF-Tu and EF-G, p. 263-272. In K H. Nierhaus, F. Franceschi, A. R. Subramanian, V. A. Erdmann, and B. Wittmann-Liebold (ed.), The translational apparatus. Structure, function, regulation, evolution. Plenum Press, New York. 461. Nishi, K., M. Muller, and J. Schnier. 1987. Spontaneous missense mutations in the rplX gene for ribosomal protein L24 from Eschenichia coli. J. Bacteriol. 169:.4854-4856. 462. Noller, H. F. 1984. Structure of ribosomal RNA. Annu. Rev. Biochem. 53:119-162. 463. Noller, H. F. 1991. Ribosomal RNA and translation. Annu. Rev. Biochem. 60:191-227. 464. Noller, H. F. 1993. Peptidyl transferase: protein, ribonucleoprotein, or RNA? J. Bacteriol. 175:5297-5300. 465. Noller, H. F., D. Moazed, S. Stern, T. Powers, P. N. Allen, J. M. Robertson, B. Weiser, and K. Triman. 1990. Structure of rRNA and its functional interactions in translation, p. 73-92. In W. E. Hill, A. Dahlberg, G. A. Garrett, P. B. Moore, D. Schlessinger, Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV 424. Moazed, D., and H. F. Noller. 1987. Interaction of antibiotics with functional sites in 16S ribosomal RNA. Nature (London) 327: 389-394. 425. Moazed, D., and H. F. Noller. 1987. Chloramphenicol, erythromycin, carbomycin and vemamycin B protect overlapping sites in the peptidyl transferase region of 23S ribosomal RNA. Biochimie 69:879-884. 426. Moazed, D., and H. F. Noller. 1989. Interaction of tRNA with 23S rRNA in the ribosomal A, P, and E sites. Cell 57:585-597. 427. Moll, B., L. Polsby, and P. Maliga. 1990. Streptomycin and lincomycin resistances are selective plastid markers in cultured Nicotiana cells. Mol. Gen. Genet. 221:245-250. 428. Montandon, P.-E., P. Nicolas, P. Schurmann, and E. Stutz. 1985. Streptomycin-resistance of Euglena gracilis chloroplasts: identification of a point mutation in the 16S rRNA gene in an invariant position. Nucleic Acids Res. 13:4299-4310. 429. Montandon, P.-E., and E. Stutz. 1983. Nucleotide sequence of a Euglena gracilis chloroplast genome region coding for the elongation factor Tu: evidence for a spliced mRNA. Nucleic Acids Res. 11:5877-5892. 430. Montandon, P.-E., and E. Stutz. 1984. The genes for the ribosomal proteins S12 and S7 are clustered with the gene for the EF-Tu protein on the chloroplast genome of Euglena gracilis. Nucleic Acids Res. 12:2851-2859. 431. Montandon, P.-E., R. Wagner, and E. Stutz. 1986. E. coli ribosomes with a C912 to U base change in the 16S rRNA are streptomycin resistant. EMBO J. 5:3705-3708. 432. Montesano-Roditis, L., R. McWilliams, D. G. Glitz, T. V. Olah, A. R. Perrault, and B. S. Cooperman. 1993. Placement of dinitrophenyl-modified ribosomal proteins in totally reconstituted Escherichia coli 30S subunits. Localization of proteins S6, S13, S16, and S18 by immune electron microscopy. J. Biol. Chem. 268:18701-18709. 433. Moon, E., and R. Wu. 1988. Organization and nucleotide sequence of genes at both junctions between the two inverted repeats and the large single-copy region in the rice chloroplast genome. Gene 70:1-12. 434. Morden, C. W., C. F. Delwiche, M. Kuhsel, and J. E. Palmer. 1992. Gene phylogenies and the endosymbiotic origin of plastids. BioSystems 28:7590. 435. Morden, C. W., K. H. Wolfe, C. W. DePamphilis, and J. D. Palmer. 1991. Plastid translation and transcription genes in a non-photosynthetic plant: intact, missing and pseudo genes. EMBO J. 10:3281-3288. 436. Morgan, E. A., T. Ikemura, and M. Nomura. 1977. Identification of spacer tRNA genes in individual ribosomal RNA transcription units of Escherichia coli. Proc. Natl. Acad. Sci. USA 74:27102714. 437. Mougel, M., C. Alimang, F. Eyermann, C. Cachia, B. Ehresmann, and C. Ehresmann. 1993. Minimal 16S rRNA binding site and role of conserved nucleotides in Escherichia coli ribosomal protein S8 recognition. Eur. J. Biochem. 215:787-792. 438. Mougel, M., C. Philippe, J.-P. Ebel, B. Ehresmann, and C. Ehresmann. 1988. The E. coli 16S rRNA binding site of ribosomal protein S15: higher-order structure in the absence and in the presence of the protein. Nucleic Acids Res. 16:2825-2839. 439. Muehlenhoff, U., W. Haehnel, H. T. Witt, and R. G. Herrmann. 1992. Unpublished sequence submission. 440. Mukhamedov, R. S. 1991. Unpublished sequence submission. 441. Mullet, J. E., P. G. Klein, and R. R. Klein. 1990. Chlorophyll regulates accumulation of the plastid-encoded chlorophyll apoproteins CP43 and Dl by increasing apoprotein stability. Proc. Natl. Acad. Sci. USA 87:4038-4043. 442. Mullet, J. E., and R. R. Klein. 1987. Transcription and RNA stability are important determinants of higher plant chloroplast RNA levels. EMBO J. 6:1571-1579. 443. Mural, R. J. 1991. Fundamentals of light-regulated gene expression in plants. Subcell. Biochem. 17:191-211. 444. Muramatsu, T., K. Nishihawa, F. Nemoto, Y. Kuchino, S. Nishimura, T. Miyazawa, and S. Yokoyama. 1988. Codon and amino acid specificities of a transfer RNA are both converted by a single post-transcriptional modification. Nature (London) 336:179-181. 445. Murayama, Y., T. Matsubayashi, M. Sugita, and M. Sugiura. MICROBIOL. REV. VOL. 58, 1994 CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS 482. Palmer, J. D. 1991. Plastid chromosomes: structure and evolution. Cell Cult. Somatic Cell Genet. Plants 7A:55-92. 483. Palmer, J. D. 1992. Comparison of chloroplast and mitochondrial genome evolution in plants, p. 99-133. In R. Herrmann (ed.), Cell organelles. Advances in plant gene research, vol. 6. SpringerVerlag, KG, Vienna. 484. Palmer, J. D. 1992. Green ancestry of malarial parasites? Curr. Biol. 2:318-320. 485. Palmer, J. D., S. L. Baldauf, P. J. Calie, and C. W. dePamphilis. 1990. Chloroplast gene instability and transfer to the nucleus, p. 97-106. In M. T. Clegg and S. J. O'Brien (ed.), Molecular evolution. Alan R. Liss, Inc., New York. 486. Palmer, J. D., J. E. Boynton, N. W. Gillham, and E. H. Harris. 1985. Evolution and recombination of the large inverted repeat in Chlamydomonas chloroplast DNA, p. 269-278. In K. E. Steinback, S. Bonitz, C. J. Arntzen, and L. Bogorad (ed.) The molecular biology of the photosynthetic apparatus. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. 487. Palmer, J. D., and W. F. Thompson. 1982. Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost. Cell 29:537-550. 488. Pfitzinger, H., P. Guillemaut, J.-H. Weil, and D. T. N. Pillay. 1987. Adjustment of the tRNA population to the codon usage in chloroplasts. Nucleic Acids Res. 15:1377-1386. 489. Pfitzinger, H., J.-H. Weil, D. T. N. Pillay, and P. Guillemaut. 1990. Codon recognition mechanisms in plant chloroplasts. Plant Mol. Biol. 14:805-814. 490. Phua, S. H., B. R. Srinivasa, and A. R. Subramanian. 1989. Chloroplast ribosomal protein L13 is encoded in the nucleus and is considerably larger than its bacterial homologue. Construction, immunoisolation, and nucleotide sequence (including transit peptide) of its cDNA clone from an angiosperm. J. Biol. Chem. 264:1968-1971. 491. Pieler, T., M. Digweed, M. Bartsch, and V. A. Erdmann. 1983. Comparative structural analysis of cytoplasmic and chloroplastic 5S rRNA from spinach. Nucleic Acids Res. 11:591-604. 492. Pieler, T., V. A. Erdmann, M. Digweed, and N. Delihas. 1982. Size heterogeneity in Spinacia oleracea (spinach) chloroplast 5S ribosomal RNA. Nucleic Acids Res. 10:6579-6580. 493. Pinard, R., C. Payant, P. Melanson, and L. Brakier-Gingras. 1993. The 5' proximal helix of 16S rRNA is involved in the binding of streptomycin to the ribosome. FASEB J. 7:173-176. 494. Posno, M., D. J. Torenvliet, H. Lustig, M. van Noort, and G. S. P. Groot. 1985. Localization of three chloroplast ribosomal protein genes at the left junction of the large single copy region and the inverted repeat of Spirodela oligorhiza chloroplast DNA. Curr. Genet. 9:211-219. 495. Posno, M., M. van Noort, R. Debise, and G. S. P. Groot. 1984. Isolation, characterization, phosphorylation and site of synthesis of Spinacia chloroplast ribosomal proteins. Curr. Genet. 8:147154. 496. Posno, M., A. van Vliet, and G. S. P. Groot. 1986. Localization of chloroplast ribosomal protein genes on Spirodela oligorhiza chloroplast DNA. Curr. Genet. 10:923-930. 497. Posno, M., A. van Vliet, and G. S. P. Groot. 1986. The gene for Spirodela oligorhiza chloroplast ribosomal protein homologous to E. coli ribosomal protein L16 is split by a large intron near its 5' end: structure and expression. Nucleic Acids Res. 14:3181-3195. 498. Posno, M., W. R. Verweij, I. C. Dekker, P. M. de Waard, and G. S. P. Groot. 1986. The genes encoding chloroplast ribosomal proteins S7 and S12 are located in the inverted repeat of Spirodela oligorhiza chloroplast DNA. Curr. Genet. 11:25-34. 499. Powers, T., L.-M. Changchien, G. R. Craven, and H. F. Noller. 1988. Probing the assembly of the 3' major domain of 16S ribosomal RNA. Quaternary interactions involving ribosomal proteins S7, S9 and S19. J. Mol. Biol. 200:309-319. 500. Powers, T., S. Stern, L.-M. Changchien, and H. F. Noller. 1988. Probing the assembly of the 3' major domain of 16S rRNA. Interactions involving ribosomal proteins S2, S3, S10, S13 and S14. J. Mol. Biol. 201:697-716. 501. Prombona, A., and A. R. Subramanian. 1989. A new rearrangement of angiosperm chloroplast DNA in rye (Secale cereale) involving translocation and duplication of the ribosomal rpsl5 Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV and J. R. Warner (ed.), The ribosome. Structure, function, and evolution. American Society for Microbiology, Washington, D.C. 466. Oakes, M. I., A. Scheinman, T. Atha, G. Shankweiler, and J. A. Lake. 1990. Ribosome structure: three-dimensional locations of rRNA and proteins, p. 180-193. In W. E. Hill, A. Dahlberg, G. A. Garrett, P. B. Moore, D. Schlessinger, and J. R. Warner (ed.), The ribosome. Structure, function, and evolution. American Society for Microbiology, Washington, D.C. 467. O'Connor, M., H. U. Goringer, and A. E. Dahlberg. 1992. A ribosomal ambiguity mutation in the 530 loop of E. coli 16S rRNA. Nucleic Acids Res. 20:4221-4227. 468. Ofengand, J., A. Bakin, and K. Nurse. 1993. The functional role of conserved sequences of 16S ribosomal RNA in protein synthesis, p. 489-500. In K. H. Nierhaus, F. Franceschi, A. R. Subramanian, V. A. Erdmann, and B. Wittmann-Liebold (ed.), The translational apparatus. Structure, function, regulation, evolution. Plenum Press, New York. 469. Ogihara, Y., T. Terachi, and T. Sasakuma. 1988. Intramolecular recombination of chloroplast genome mediated by short directrepeat sequences in wheat species. Proc. Natl. Acad. Sci. USA 85:8573-8577. 470. Ohto, C., K. Torazawa, M. Tanaka, K. Shinozaki, and M. Sugiura. 1988. Transcription of ten ribosomal protein genes from tobacco chloroplasts: a compilation of ribosomal protein genes found in the tobacco chloroplast genome. Plant Mol. Biol. 11:589-600. 471. Ohyama, K., H. Fukuzawa, T. Kohchi, T. Sano, S. Sano, H. Shirai, K. Umesono, Y. Shiki, M. Takeuchi, Z. Chang, S. Aota, H. Inokuchi, and H. Ozeki. 1988. Structure and organization of Marchantia polymorpha chloroplast genome. I. Cloning and gene identification. J. Mol. Biol. 203:281-298. 472. Ohyama, K., H. Fukuzawa, T. Kohchi, H. Shirai, T. Sano, S. Sano, K. Umesono, Y. Shiki, M. Takeuchi, Z. Chang, S. Aota, H. Inokuchi, and H. Ozeki. 1986. Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature (London) 322:572-574. 473. Ohyama, K., H. Fukuzawa, T. Kohchi, H. Shirai, T. Sano, S. Sano, K. Umesono, Y. Shiki, M. Takeuchi, Z. Chang, S. Aota, H. Inokuchi, and H. Ozeki. 1986. Complete nucleotide sequence of liverwort Marchantia polymorpha chloroplast DNA. Plant Mol. Biol. Rep. 4:148-175. 474. Oleinikov, A. V., B. Perroud, B. Wang, and R R. Traut. 1993. Structural and functional domains of Escherichia coli ribosomal protein L7/L12. J. Biol. Chem. 268:917-922. 475. Olsson, M. O., and L. A. Isaksson. 1979. Analysis of rpsD mutations in Escherichia coli. I. Comparison of mutants with various alterations in ribosomal protein S4. Mol. Gen. Genet. 169:251-257. 476. O'Neill, C., V. G. Horvath, E. Horvath, P. J. Dix, and P. Medgyesy. 1993. Chloroplast transformation in plants: polyethylene glycol (PEG) treatment of protoplasts in an alternative to biolistic delivery systems. Plant J. 3:729-738. 477. Orozco, E. M., and R B. Hallick 1982. Euglena gracilis chloroplast transfer RNA transcription units. II. Nucleotide sequence analysis of a tRNAVa_tRNAASn-tRNAAr9-tRNAL`U gene cluster. J. Biol. Chem. 257:3265-3275. 478. Orozco, E. M., Jr., P. W. Gray, and R B. Hallick 1980. Euglena gracilis chloroplast ribosomal RNA transcription units. I. The location of transfer RNA, SS, 16S, and 23S ribosomal RNA genes. J. Biol. Chem. 255:10991-10996. 479. Orozco, E. M., Jr., K. E. Rushlow, J. R Dodd, and R B. Hallick 1980. Euglena gracilis chloroplast ribosomal RNA transcription units. II. Nucleotide sequence homology between the 16S-23S ribosomal RNA spacer and the 16S ribosomal RNA leader regions. J. Biol. Chem. 255:10997-11003. 480. Osawa, S., T. H. Jukes, K. Watanabe, and A. Muto. 1992. Recent evidence for evolution of the genetic code. Microbiol. Rev. 56:229-264. 481. Osswald, M., B. Greuer, and R Brimacombe. 1990. Localization of a series of RNA-protein cross-link sites in the 23S and SS ribosomal RNA from Escherichia coli, induced by treatment of 50S subunits with three different bifunctional reagents. Nucleic Acids Res. 18:6755-6760. 747 748 HARRIS ET AL. gene. J. Biol. Chem. 264:19060-19065. 502. Przybyl, D., E. Fritzsche, K. Edwards, H. Kossel, H. Falk, J. A. Thompson, and G. Link. 1984. The ribosomal RNA genes from chloroplasts of mustard (Sinapis alba L.): mapping and sequencing of the leader region. Plant Mol. Biol. 3:147-158. 503. Pugsley, A. R. 1989. Protein targeting. Academic Press, Inc., San Diego, Calif. 522. Rochaix, J.-D., M. Rahire, and F. Michel. 1985. The chloroplast ribosomal intron of Chlamydomonas reinhardii codes for a polypeptide related to mitochondrial maturases. Nucleic Acids Res. 13:975-984. 523. Rodermel, S., P. Orlin, and L. Bogorad. 1987. The transcription termination region between two convergently-transcribed photoregulated operons in the maize plastid chromosome contains rpsl4, tmR (UCU) and a putative tmnjM pseudogene. Nucleic Acids Res. 15:5493. 524. Romby, P., C. Brunel, E. Westhof, F. Baudin, P. J. Romaniuk, R. Mache, C. Ehresmann, and B. Ehresmann. 1991. The solution structure of spinach chloroplast and of Xenopus laevis oocyte SS rRNAs. NATO ASI Ser. Ser. H 55:31-44. 525. Romby, P., E. Westhof, R. Toukifimpa, R. Mache, H. P. Ebel, C. Ehresmann, and B. Ehresmann. 1988. Higher order structure of chloroplastic SS ribosomal RNA from spinach. Biochemistry 27:4721-4730. 526. Romero, D. P., J. A. Arredondo, and R. R. Traut. 1990. Identification of a region of Escherichia coli ribosomal protein L2 required for the assembly of L16 into the 50S ribosomal subunit. J. Biol. Chem. 265:18165-18191. 527. Roney, W. B., L. Ma, C.-C. Wang, and L. L. Spremulli. 1991. Recent progress on understanding the initiation of translation in the chloroplasts of Euglena gracilis. NATO ASI Ser. Ser. H 55:197-205. 528. Rosendahl, G., and S. Douthwaite. 1993. Ribosomal proteins Li1 and L10.(L12)4 and the antibiotic thiostrepton interact with overlapping regions of the 23S rRNA backbone in the ribosomal GTPase centre. J. Mol. Biol. 234:1013-1020. 529. Roux, E., L. Graf, and E. Stutz. 1983. Nucleotide sequence of a truncated rRNA operon of the Euglena gracilis chloroplast genome. Nucleic Acids Res. 11:1957-1968. 530. Roux, E., and E. Stutz. 1985. The chloroplast genome of Euglena gracilis: the mosaic structure of a DNA segment linking the extra 16S rRNA gene with the rm operon A. Curr. Genet. 9:221-227. 531. Rozier, C., and R. Mache. 1984. Binding of 16S rRNA to chloroplast 30S ribosomal proteins blotted on nitrocellulose. Nucleic Acids Res. 19:7293-7304. 532. Ruf, M., and H. Kossel. 1988. Occurrence and spacing of ribosome recognition sites in mRNAs of chloroplasts from higher plants. FEBS Lett. 240:41-44. 533. Ryan, P. C., M. Lu, and D. E. Draper. 1991. Recognition of the highly conserved GTPase center of 23S ribosomal RNA by ribosomal protein Lii and the antibiotic thiostrepton. J. Mol. Biol. 221:1257-1268. 534. Ryden-Aulin, M., Z. Shaoping, P. Kylsten, and L. A. Isaksson. 1993. Ribosome activity and modification of 16S RNA are influenced by deletion of ribosomal protein S20. Mol. Microbiol. 7:983-992. 535. Sakamoto, W., K. L. Kindle, and D. B. Stern. 1993. In vivo analysis of Chlamydomonas chloroplast petD gene expression using stable transformation of beta-glucuronidase translational fusions. Proc. Natl. Acad. Sci. USA 90:497-501. 536. Sanangelantoni, A. M., R. C. Calogero, F. R. Buttarelli, C. 0. Gualerzi, and 0. Tiboni. 1990. Organization and nucleotide sequence of the genes for ribosomal protein S2 and elongation factor Ts in Spirulina platensis. FEMS Microbiol. Lett. 66:141146. 537. Santer, M., U. Santer, A. Bakin, P. Cunningham, M. Zain, D. O'Connell, and J. Ofengand. 1993. Functional effects of a G to U base change at position 530 in a highly conserved loop of Escherichia coli 16S RNA. Biochemistry 32:5539-5547. 538. Schlosser, U. G. 1984. Species-specific sporangium autolysins (cell-wall-dissolving enzymes) in the genus Chlamydomonas, p. 409-418. In D. E. G. Irvine and D. M. John (ed.), Systematics of the green algae. Academic Press, Inc., New York. 539. Schmidt, J., M. Bubunenko, and A. R. Subramanian. 1993. A novel operon organization involving the genes for chorismate synthase (aromatic biosynthesis pathway) and ribosomal GTPase center proteins (Lii, Li, L10, L12: rplKAJL) in cyanobacterium Synechocystis PCC 6803. J. Biol. Chem. 268:27447-27457. 540. Schmidt, J., E. Herfurth, and A. R. Subramanian. 1992. Purification and characterization of seven chloroplast ribosomal pro- Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV 504. Purton, S., and J. C. Gray. 1987. Nucleotide sequence of the gene for ribosomal protein S11 in pea chloroplast DNA. Nucleic Acids Res. 15:1873. 505. Purton, S., and J. C. Gray. 1987. Nucleotide sequence of the gene for ribosomal protein L36 in pea chloroplast DNA. Nucleic Acids Res. 15:9080. 506. Purton, S., and J. C. Gray. 1989. The plastid rpoA gene encoding a protein homologous to the bacterial RNA polymerase alpha subunit is expressed in pea chloroplasts. Mol. Gen. Genet. 217:77-84. 507. Ramakrishnan, V., S. E. Gerchman, B. L Golden, D. W. Hofman, J. H. Kycia, S. J. Porter, and S. W. White. 1993. Structural studies on prokaryotic ribosomal proteins, p. 533-544. In K H. Nierhaus, F. Franceschi, A. R. Subramanian, V. A. Erdmann, and B. WittmannLiebold (ed.), The translational apparatus. Structure, function, regulation, evolution. Plenum Press, New York. 508. Ramakrishnan, V., and S. W. White. 1992. The structure of ribosomal protein S5 reveals sites of interaction with 16S rRNA. Nature (London) 358:768-771. 509. Randolph-Anderson, B. L. Unpublished data. 510. Randolph-Anderson, B. L., J. E. Boynton, and N. W. Gillham. 1989. Electrophoretic and immunological comparisons of chloroplast and prokaryotic ribosomal proteins reveal that certain families of large subunit proteins are evolutionarily conserved. J. Mol. Evol. 29:68-88. 511. Randolph-Anderson, B. L., J. E. Boynton, N. W. Gillham, C. Huang, and X.-Q. Liu. The chloroplast gene encoding ribosomal protein S4 in Chiamydomonas reinhardtii spans an inverted repeat-unique sequence junction and can be mutated to suppress a streptomycin dependence mutation in the chloroplast gene encoding S12. Submitted for publication. 512. Raue, H. A., J. Klootwi%k, and W. Musters. 1988. Evolutionary conservation of structure and function of high molecular weight ribosomal RNA. Prog. Biophys. Mol. Biol. 51:77-129. 513. Raue, H. A., E. Otaka, and K. Suzuki. 1989. Structural comparison of 26S rRNA-binding ribosomal protein L25 from two different yeast strains and the equivalent proteins from three eubacteria and two chloroplasts. J. Mol. Evol. 28:418-426. 514. Reith, M., and J. Munholland. 1993. A high-resolution gene map of the chloroplast genome of the red alga Porphyra purpurea. Plant Cell 5:465-475. 515. Reith, M., and J. Munholland. 1993. Two amino-acid biosynthetic genes are encoded on the plastid genome of the red alga Porphyra umbilicalis. Curr. Genet. 23:59-65. 516. Reith, M., and J. Munholland. 1993. The ribosomal RNA repeats are non-identical and directly oriented in the chloroplast genome of the red alga Porphyra purpurea. Curr. Genet. 24:443-450. 517. Reith, M., and J. Munholland. Unpublished data. 518. Rheinberger, H.-J., U. Geigenmuller, A. Gnirke, T. P. Hausner, J. Remme, H. Saruyama, and K. H. Nierhaus. 1990. Allosteric three-site model for the ribosomal elongation cycle, p. 318-330. In W. E. Hill, A. Dahlberg, G. A. Garrett, P. B. Moore, D. Schlessinger, and J. R. Warner (ed.), The ribosome. Structure, function, and evolution. American Society for Microbiology, Washington, D.C. 519. Robertson, D., J. E. Boynton, and N. W. Gillham. 1990. Cotranscription of the wild type chloroplast atpE gene encoding the CF1/CFO epsilon subunit with the 3' half of the rps7 gene in Chlamydomonas reinhardtii and characterization of frameshift mutations in atpE. Mol. Gen. Genet. 221:155-163. 520. Rochaix, J.-D. 1992. Post-transcriptional steps in the expression of chloroplast genes. Annu. Rev. Cell Biol. 8:1-28. 521. Rochaix, J.-D., and J.-L. Darlix. 1982. Composite structure of the chloroplast 23S ribosomal RNA genes of Chlamydomonas reinhardii. Evolutionary and functional implications. J. Mol. Biol. 159:383-395. MICROBIOL. REV. VOL. 58, 1994 CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS 560. Shinozaki, K, M. Ohme, M. Tanaka, T. Wakasugi, N. Hayashida, T. Matsubayashi, N. Zaita, J. Chunwongse, J. Obokata, K. Yamaguchi-Shinozaki, C. Ohto, K. Torazawa, B. Y. Meng, M. Sugita, H. Deno, T. Kamogashira, K. Yamada, J. Kusuda, F. Takaiwa, A. Kato, N. Tohdoh, H. Shimada, and M. Sugiura. 1986. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 5:2043-2049. 561. Shinozaki, K., M. Ohme, M. Tanaka, T. Wakasugi, N. Hayashida, T. Matsubayashi, N. Zaita, J. Chunwongse, J. Obokata, K. 562. 563. 564. 565. 566. Yamaguchi-Shinozaki, C. Ohto, K. Torazawa, B. Y. Meng, M. Sugita, H. Deno, T. Kamogashira, K. Yamada, J. Kusuda, F. Takaiwa, A. Kato, N. Tohdoh, H. Shimada, and M. Sugiura. 1986. The complete nucleotide sequence of the tobacco chloroplast genome. Plant Mol. Biol. Rep. 4:111-147. Shivji, M.S. 1991. Organization of the chloroplast genome in the red alga Porphyra yezoensis. Curr. Genet. 19:49-54. Shivji, M. S., N. Li, and R A. Cattolico. 1992. Structure and organization of rhodophyte and chromophyte plastid genomes: implications for the ancestry of plastids. Mol. Gen. Genet. 232:65-73. Sibold, C., and A. R Subramanian. 1990. Cloning and characterization of the genes for ribosomal proteins L10 and L12 from Synechocystis sp. PCC 6803: comparison of gene clustering pattern and protein sequence homology between cyanobacteria and chloroplasts. Biochim. Biophys. Acta 1050:61-68. Siemeister, G., C. Buchholz, and W. Hachtel. 1990. Genes for the plastid elongation factor Tu and ribosomal protein S7 and six tRNA genes on the 73 kb DNA fromAstasia longa that resembles the chloroplast DNA of Euglena. Mol. Gen. Genet. 220:425-432. Siemeister, G., C. Buchholz, and W. Hachtel. 1990. Genes for ribosomal proteins are retained on the 73 kb DNA from Astasia longa that resembles Euglena chloroplast DNA. Curr. Genet. 18:457-464. 567. Siemeister, G., and W. Hachtel. 1989. A circular 73 kb DNA from the colourless flagellate Astasia longa that resembles the chloroplast DNA of Euglena: restriction and gene map. Curr. Genet. 15:435-441. 568. Siemeister, G., and W. Hachtel. 1990. Structure and expression of a gene encoding the large subunit of ribulose-1,5-bisphosphate carboxylase (rbcL) in the colourless euglenoid flagellate Astasia longa. Plant Mol. Biol. 14:825-833. 569. Siemeister, G., and W. Hachtel. 1990. Organization and nucleotide sequence of ribosomal RNA genes on a circular 73 kbp DNA from the colourless flagellate Astasia longa. Curr. Genet. 17:433-438. 570. Sigmund, C. D., M. Ettayebi, and E. A. Morgan. 1984. Antibiotic 571. 572. 573. 574. 575. 576. 577. resistance mutations in 16S and 23S ribosomal RNA genes of Escherichia coli. Nucleic Acids Res. 12:4653-4663. Siben-Muller, G., R Hallick, J. Alt, P. Westhoff, and R. G. Herrmann. 1986. Spinach plastid genes coding for initiation factor IF-1, ribosomal protein Sl and RNA polymerase Ca-subunit. Nucleic Acids Res. 14:1029-1044. Silk, G. W., and M. Wu. 1993. Posttranscriptional accumulation of chloroplast tufA (elongation factor gene) mRNA during chloroplast development in Chlamydomonas reinhardtii. Plant Mol. Biol. 23:87-96. Singh, R. K. 1993. Unpublished sequence submission. Siu, C.-H., K.-S. Chiang, and H. Swift. 1975. Characterization of cytoplasmic and nuclear genomes in the colorless alga Polytoma. V. Molecular structure and heterogeneity of leucoplast DNA. J. Mol. Biol. 98:369-391. Siu, C.-H., K.-S. Chiang, and H. Swift. 1976. Characterization of cytoplasmic and nuclear genomes in the colorless alga Polytoma. III. Ribosomal RNA cistrons of the nucleus and leucoplast. J. Cell Biol. 69:383-392. Siu, C.-H., H. Swift, and K.-S. Chiang. 1976. Characterization of cytoplasmic and nuclear genomes in the colorless alga Polytoma. II. General characterization of organelle nucleic acids. J. Cell Biol. 69:371-382. Smooker, P. M., T. Choli, and A. R. Subramanian. 1990. Ribosomal protein L35: identification in spinach chloroplasts and isolation of a cDNA clone encoding its cytoplasmic precursor. Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV teins: evidence that organelle ribosomal protein genes are functional and that NH2-terminal processing occurs via multiple pathways in chloroplasts. Plant Mol. Biol. 20:459-465. 541. Schmidt, J., B. Srinivasa, W. Weglohner, and A. R. Subramanian. 1993. A small novel chloroplast ribosomal protein (S31) that has no apparent counterpart in the E. coli ribosome. Biochem. Mol. Biol. Int. 29:25-31. 542. Schmidt, J., and A. R. Subramanian. 1993. Sequence of the cyanobacterial tRNA-W in Synechocystis PCC6803: requirement of 3' CCA attachment to the acceptor stem. Nucleic Acids Res. 21:2519. 543. Schmidt, J., W. Weglohner, and A.R Subramanian. 1993. The nuclear genes for chloroplast ribosomal proteins Lii and L12 in higher plants, p. 555-564. In K. H. Nierhaus, F. Franceschi, A. R. Subramanian, V. A. Erdmann, and B. Wittmann-Liebold (ed.), The translational apparatus. Structure, function, regulation, evolution. Plenum Press, New York. 544. Schmidt, M., L. Pichl, M. Lepper, and J. Feierabend. 1993. Identification of the nuclear-encoded chloroplast ribosomal protein L12 of the monocotyledonous plant Secale cereale and sequencing of two different cDNAs with strong codon bias. Biochimn. Biophys. Acta 1172:349-352. 545. Schmidt,R J., N. W. Gillham, and J. E. Boynton. 1985. Processing of the precursor to a chloroplast ribosomal protein made in the cytosol occurs in two steps, one of which depends on a protein made in the chloroplast. Mol. Cell. Biol. 5:1093-1099. 546. Schmidt, R J., A. M. Myers, N. W. Gillham, and J. E. Boynton. 1984. Chloroplast ribosomal proteins of Chlamydomonas synthesized in the cytoplasm are made as precursors. J. Cell Biol. 98:2011-2018. 547. Schmidt, R J., C. B. Richardson, N. W. Gillham, and J. E. Boynton. 1983. Sites of synthesis of chloroplast ribosomal proteins in Chlamydomonas. J. Cell Biol. 96:1451-1463. 548. Schmidt, T. M., E. F. DeLong, and N. R Pace. 1991. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J. Bacteriol. 173:4371-4378. 549. Schnare, M. N., G. M. Yepiz-Plascencia, D. W. Copertino, R B. Hallick, and M. W. Gray. 1992. 5'- and 3'-terminal sequences of the chloroplast 16S and 23S ribosomal RNAs of Euglena gracilis. Nucleic Acids Res. 20:1421. 550. Schneider, M., J.-L. Darlix, J. Erickson, and J.-D. Rochaix. 1985. Sequence organization of repetitive elements in the flanking regions of the chloroplast ribosomal unit of Chlamydomonas reinhardii. Nucleic Acids Res. 13:8531-8541. 551. Schneider, M., and J.-D. Rochaix. 1986. Sequence organization of the chloroplast ribosomal spacer of Chlamydomonas reinhardii: uninterrupted tRNAile and tRNAala genes and extensive secondary structure. Plant Mol. Biol. 6:265-270. 552. Schon, A., G. Krupp, S. Gough, S. Berry-Lowe, C. G. Kannangara, and D. Soil. 1986. The RNA required in the first step in chlorophyll biosynthesis is a chloroplast glutamate tRNA. Nature (London) 322:281-284. 553. Schreiner, M. 1993. Unpublished sequence submission. 554. Schwarz, Z., and H. Kossel. 1980. The primary structure of 16S rDNA from Zea mays chloroplast is homologous to E. coli 16S rRNA. Nature (London) 283:739-742. 555. Seewaldt, E., and E. Stackebrandt. 1982. Partial sequence of 16S ribosomal RNA and the phylogeny of Prochloron. Nature (London) 295:618-620. 556. Sexton, T. B., J. T. Jones, and J. E. Mullet. 1990. Sequence and transcriptional analysis of the barley ctDNA region upstream of psbD-psbC encoding tmK(UUU), rpsl6, trnQ(UUG),psbK,psbl, and tmS(GCU). Curr. Genet. 17:445-454. 557. Shapiro, D. R., and K. K. Tewari. 1986. Nucleotide sequences of transfer RNA genes in the Pisum sativum chloroplast DNA. Plant Mol. Biol. 6:1-12. 558. Shimada, H., and M. Sugiura. 1991. Fine structural features of the chloroplast genome: comparison of the sequenced chloroplast genomes. Nucleic Acids Res. 19:983-995. 559. Shinozaki, K., H. Deno, M. Sugita, S. Kuramitsu, and M. Sugiura. 1986. Intron in the gene for the ribosomal protein S16 of tobacco chloroplast and its conserved boundary sequences. Mol. Gen. Genet. 202:1-5. 749 750 MICROBIOL. REV. HARRIS ET AL. 18(Suppl.):2215-2230. 584. Spielmann, A., E. Rouz, J.-M. von Allmen, and E. Stutz. 1988. The soybean chloroplast genome: complete sequence of the rpsl9 gene, including flanking parts containing exon 2 of rp12 (upstream) but lacking rp122 (downstream). Nucleic Acids Res. 16:1199. 585. Sreedharan, S. P., C. M. Beck, and L. L. Spremulli. 1985. Euglena gracilis chloroplast elongation factor Tu: purification and initial characterization. J. Biol. Chem. 260:3126-3131. 586. Srinivasa, B. R, and A. R Subramanian. 1987. Nucleotide sequence and linkage map position of the gene for maize chloroplast ribosomal protein S14. Biochemistry 26:3188-3192. 587. Stahl, D. J., S. R Rodermel, L. Bogorad, and A. R Subramanian. 1993. Cotranscription pattern of an introgressed operon in the maize chloroplast genome comprising four ATP synthase subunit genes and the ribosomal rps2. Plant Mol. Biol. 21:1069-1076. 588. Stahl, D., S. R. Rodermel, A. R Subramanian, and L. Bogorad. 1990. Nucleotide sequence of a 3.46 kb region of maize chloroplast DNA containing the gene cluster rpoC2-rps2-atpI-atpH. Nucleic Acids Res. 18:3073-3074. 589. Stanzel, M., A. Schon, and M. Sprinzl. 1994. Discrimination against misacylated tRNA by chloroplast elongation factor Tu. Eur. J. Biochem. 219:435-439. 590. Staub, J. M., and P. Maliga. 1992. Long regions of homologous DNA are incorporated into the tobacco plastid genome by transformation. Plant C&.l 4:39-45. 591. Staub, J. M., and P. Maliga. 1993. Accumulation of Dl polypeptide in tobacco plastids is regulated via the untranslated region of the psbA mRNA. EMBO J. 12:601-606. 592. Steege, D. A., M. C. Graves, and L. L. Spremulli. 1982. Euglena gracilis chloroplast small subunit rRNA: sequence and base pairing potential of the 3' terminus, cleavage by colicin E3. J. Biol. Chem. 257:10430-10439. 593. Steinmetz, A., and J.-H. Weil. 1989. Protein synthesis in chloroplasts, p. 193-227. In A. Marcus (ed.), The biochemistry of plants, vol. 15. Academic Press, Inc., San Diego, Calif. 594. Stern, S., L.-M. Changchien, G. R Craven, and H. F. Noller. 1988. Interaction of proteins S16, S17 and S20 with 16S ribosomal RNA. J. Mol. Biol. 200:291-299. 595. Stern, S., T. Powers, L.-M. Changchien, and H. F. Noller. 1989. RNA-protein interactions in 30S ribosomal subunits: folding and function of 16S rRNA. Science 244:783-790. 596. Stern, S., B. Weiser, and H. F. Noller. 1988. Model for the three-dimensional folding of 16 S ribosomal RNA. J. Mol. Biol. 204:447-481. 597. Stevenson, J. K., R. G. Drager, D. W. Copertino, D. A. Christopher, K P. Jenkins, G. Yepiz-Plascencia, and R B. Hallick. 1991. Intercistronic group III introns in polycistronic ribosomal protein operons of chloroplasts. Mol. Gen. Genet. 228:183-192. 598. Stirewalt, V. L., and D. A. Bryant. Unpublished data. 599. Stoller-Meilicke, M., and G. Stoffler. 1990. Topography of the 600. 601. 602. 603. 604. 605. 606. 607. 608. 609. 610. 611. 612. 613. 614. 615. ribosomal proteins from Escherichia coli within the intact subunits as determined by immunoelectron microscopy and proteinprotein cross-linking, p. 123-133. In W. E. Hill, A. Dahlberg, G. A. Garrett, P. B. Moore, D. Schlessinger, and J. R. Warner (ed.), The ribosome. Structure, function, and evolution. American Society for Microbiology, Washington, D.C. Strauss, S. H., J. D. Palmer, G. T. Howe, and A. H. Doerksen. 1988. Chloroplast genomes of two conifers lack a large inverted repeat and are extensively rearranged. Proc. Natl. Acad. Sci. USA 85:3898-3902. Strittmatter, G., and H. Kossel. 1984. Cotranscription and processing of 23S, 4.5S and 5S rRNA in chloroplasts from Zea mays. Nucleic Acids Res. 12:7633-7647. Stummann, B. M., J. Lehmbeck, G. Bookjans, and K. W. Henningsen. 1988. Nucleotide sequence of the single ribosomal RNA operon of pea chloroplast DNA. Physiol. Plant. 72:139146. Stutz, E., and C. Bonny. 1991. Interaction of streptomycin with 16S rRNA of chloroplasts and E. coli. NATO ASI Ser. Ser. H 55:167-177. Subramanian, A. R 1983. Structure and functions of ribosomal protein S1. Prog. Nucleic Acid Res. Mol. Biol. 28:101-142. Subramanian, A. R 1991. Nuclear-coded chloroplast r-proteins, precursor cDNA clones and transit sequences. NATO ASI Ser. Ser. H 55:95-105. Subramanian, A. R 1993. Molecular genetics of chloroplast ribosomal proteins. Trends Biochem. Sci. 18:177-180. Subramanian, A. R Unpublished data. Subramanian, A. R, P. M. Smooker, and K. Giese. 1990. Chloroplast ribosomal proteins and their genes, p. 655-663. In W. E. Hill, A. Dahlberg, G. A. Garrett, P. B. Moore, D. Schlessinger, and J. R. Warner (ed.), The ribosome. Structure, function, and evolution. American Society for Microbiology, Washington, D.C. Subramanian, A. R, D. Stahl, and A. Prombona. 1991. Ribosomal proteins, ribosomes, and translation in plastids. Cell Cult. Somatic Cell Genet. Plants 7A.-191-215. Subramanian, A. R, A. Steinmetz, and L. Bogorad. 1983. Maize chloroplast DNA encodes a protein sequence homologous to the bacterial ribosome assembly protein S4. Nucleic Acids Res. 11:5277-5286. Sugita, M., Y. Murayama, and M. Sugiura. 1994. Structure and differential expression of two distinct genes encoding the chloroplast elongation factor Tu in tobacco. Curr. Genet. 25:164-168. Sugita, M., and M. Sugiura. 1983. A putative gene of tobacco chloroplast coding for ribosomal protein similar to E. coli ribosomal protein S19. Nucleic Acids Res. 11:1913-1918. Sugiura, M. 1991. Transcript processing in plastids: trimming, cutting, splicing. Cell Cult. Somatic Cell Genet. Plants 7A.-125137. Sugiura, M. 1992. The chloroplast genome. Plant Mol. Biol. 19:149-168. Sugiura, M., K. Torazawa, and T. Wakasugi. 1991. Chloroplast genes coding for ribosomal proteins in land plants. NATO ASI Ser. Ser. H 55:59-69. 616. Sugiura, M., and T. Wakasugi. 1989. Compilation and comparison of transfer RNA genes from tobacco chloroplasts. Crit. Rev. Plant Sci. 8:89-101. 617. Sun, E., D. R Shapiro, B. W. Wu, and K. K. Tewari. 1986. Specific in vitro transcription of 16S rRNA gene by pea chloroplast RNA polymerase. Plant Mol. Biol. 6:429-439. 618. Sun, E., B.-W. Wu, and K. K. Tewari. 1989. In vitro analysis of the pea chloroplast 16S rRNA gene promoter. Mol. Cell. Biol. 9:5650-5659. 619. Svab, Z., P. Hajdukiewicz, and P. Maliga. 1990. Stable transformation of plastids in higher plants. Proc. Natl. Acad. Sci. USA 87:8526-8530. 620. Svab, Z., and P. Maliga. 1991. Mutation proximal to the tRNA binding region of the Nicotiana plastid 16S rRNA confers resistance to spectinomycin. Mol. Gen. Genet. 228:316-319. 621. Svab, Z., and P. Maliga. 1993. High-frequency plastid transformation in tobacco by selection for a chimeric aadA gene. Proc. Natl. Acad. Sci. USA 90:913-917. Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV Biochemistry 29:9733-9736. 578. Smooker, P. M., V. Kruft, and A. R Subramanian. 1990. A ribosomal protein is encoded in the chloroplast DNA in a lower plant but in the nucleus in angiosperms. Isolation of the spinach L21 protein and cDNA clone with transit and an unusual repeat sequence. J. Biol. Chem. 265:16699-16703. 579. Smooker, P. M., J. Schmidt, and A. R. Subramanian. 1991. The nuclear:organelle distribution of chloroplast ribosomal proteins genes. Features of a cDNA clone encoding the cytoplasmic precursor of Lll. Biochimie 73:845-851. 580. Somerville, C. C., S. Jouannic, and S. Loiseaux-de Gojer. 1992. Sequence, proposed secondary structure, and phylogenetic analysis of the chloroplast 5S rRNA gene of the brown alga Pylaiella littoralis (L.) Kjellm. J. Mol. Evol. 34:246-253. 581. Somerville, C. C., S. Jouannic, W. F. Martin, B. Kloareg, and S. Loiseaux-de Goer. 1993. Secondary structure and phylogeny of the chloroplast 23S rRNA gene from the brown alga Pylaiella littoralis. Plant Mol. Biol. 21:779-787. 582. Song, S., C. Shin, and Y. Choi. 1993. Unpublished sequence submission. 583. Specht, T., J. Wolters, and V. A. Erdmann. 1990. Compilation of SS rRNA and SS rRNA gene sequences. Nucleic Acids Res. VOL. 58, 1994 CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS 643. To, K.-Y., Y.-K. Lai, T.-Y. Feng, and C.-C. Chen. 1992. Restriction endonuclease analysis of chloroplast DNA from streptomycin-resistant mutants of Nicotiana plumbaginifolia. Genome 35: 220-224. 644. To, K.-Y., C.-I. Lieu, S.-T. Liu, and Y.-S. Chang. 1993. Detection of point mutations in the chloroplast genome by single-stranded conformation polymorphism analysis. Plant J. 3:183-186. 645. Tohdoh, N., K. Shinozaki, and M. Sugiura. 1981. Sequence of a putative promoter region for the rRNA genes of tobacco chloroplast DNA. Nucleic Acids Res. 9:5399-5406. 646. Tohdoh, N., and M. Sugiura. 1982. The complete nucleotide sequence of a 16S ribosomal RNA gene from tobacco chloroplasts. Gene 17:213-218. 647. Tomioka, N., and M. Sugiura. 1983. The complete nucleotide sequence of a 16S ribosomal RNA gene from a blue-green alga, Anacystis nidulans. Mol. Gen. Genet. 191:46-50. 648. Tonkyn, J. C., and W. Gruissem. 1993. Differential expression of the partially duplicated chloroplast S10 ribosomal protein operon. Mol. Gen. Genet. 241:141-152. 649. Torazawa, K., N. Hayashida, J. Obokata, K. Shinozaki, and M. Sugiura. 1986. The 5' part of the gene for ribosomal protein S12 is located 30 kbp downstream from its 3' part in tobacco chloroplast genome. Nucleic Acids Res. 14:3143. 650. Torres, J. H., C. A. Breitenberger, A. Spielmann, and E. Stutz. 1993. Cloning and sequencing of a soybean nuclear gene coding for a chloroplast translation elongation factor EF-G. Biochim. Biophys. Acta 1174:191-194. 651. Toukifimpa, R, P. Romby, C. Rozier, C. Ehresmann, B. Ehresmann, and R. Mache. 1989. Characterization and footprint analysis of two SS rRNA binding proteins from spinach chloroplast ribosomes. Biochemistry 28:5840-5846. 652. Troitsky, A. V., V. K. Bobrova, A. G. Ponomarev, and A. S. Antonov. 1984. The nucleotide sequence of chloroplast 4.5 S rRNA from Mnium rugicum (Bryophyta): mosses also possess this type of RNA. FEBS Lett. 176:105-109. 653. Troxier, R F., F. Zhang, J. Hu, and L. Bogorad. 1994. Evidence that cr factors are components of chloroplast RNA polymerase. Plant Physiol. 104:753-759. 654. Tsudzuki, J., K. Nakashima, T. Tsudzuki, J. Hiratsuka, M. Shibata, T. Wakasugi, and M. Sugiura. 1992. Chloroplast DNA of black pine retains a residual inverted repeat lacking rRNA genes: nucleotide sequences of tmQ, trnK, psbA, trmI and trnH and the absence of rps16. Mol. Gen. Genet. 232:206-214. 655. Turmel, M. Unpublished data. 656. Turmel, M., E. Boudreau, J. Boulanger, J.-P. Mercier, C. Otis, and C. Lemieux. 1991. Chloroplast DNA evolution and phylogenetic relationships in Chlamydomonas, p. 816-827. In E. C. Dudley (ed.). The unity of evolutionary biology, vol. 1 and 2. Fourth International Congress of Systematic and Evolutionary Biology. Dioscorides Press, Portland, Oreg. 657. Turmel, M., J. Boulanger, M. N. Schnare, M. W. Gray, and C. Lemieux. 1991. Six group I introns and three internal transcribed spacers in the chloroplast large subunit ribosomal RNA gene of the green alga Chlamydomonas eugametos. J. Mol. Biol. 218:293311. 658. Tunnel, M., R R Gutell, J.-P. Mercier, C. Otis, and C. Lemieux. 1993. Analysis of the chloroplast large subunit ribosomal RNA gene from 17 Chlamydomonas taxa. Three internal transcribed spacers and 12 group I intron insertion sites. J. Mol. Biol. 232:446467. 659. Umesono, K., H. Inokuchi, Y. Shiki, M. Takeuchi, Z. Chang, H. Fukuzawa, T. Kohchi, H. Shirai, K. Ohyama, and H. Ozeki. 1988. Structure and organization of Marchantia polymorpha chloroplast genome. II. Gene organization of the large single copy region from rps'12 to atpB. J. Mol. Biol. 203:299-331. 660. Urbach, E., D. L. Robertson, and S. W. Chisholm. 1992. Multiple evolutionary origins of prochlorophytes within the cyanobacterial radiation. Nature (London) 355:267-269. 661. Ursin, V. M., C. K. Becker, and C. K. Shewmaker. 1993. Cloning and nucleotide sequence of a tobacco chloroplast translational elongation factor, EF-Tu. Plant Physiol. 101:333-334. 662. van Acken, U. 1975. Proteinchemical studies on ribosomal proteins S4 and S12 from ram (ribosomal ambiguity) mutants of Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV 622. Svensson, P., L.-M. Changchien, G. R. Craven, and H. F. Noller. 1988. Interaction of ribosomal proteins, S6, S8, S15 and S18 with the central domain of 16S ribosomal RNA. J. Mol. Biol. 200:301308. 623. Takaiwa, F., M. Kusuda, and M. Sugiura. 1982. The nucleotide sequence of chloroplast 4.5S rRNA from a fern, Dryopteris acuminata. Nucleic Acids Res. 10:2257-2260. 624. Takaiwa, F., and M. Sugiura. 1980. Nucleotide sequences of the 4.5S and 5S ribosomal RNA genes from tobacco chloroplasts. Mol. Gen. Genet. 180:1-4. 625. Takaiwa, F., and M. Sugiura. 1980. The nucleotide sequence of 4.5S ribosomal RNA from tobacco chloroplasts. Nucleic Acids Res. 8:4125-4129. 626. Takaiwa, F., and M. Sugiura. 1981. Heterogeneity of SS RNA species in tobacco chloroplasts. Mol. Gen. Genet. 182:385-389. 627. Takaiwa, F., and M. Sugiura. 1982. The complete nucleotide sequence of a 23S rRNA gene from tobacco chloroplasts. Eur. J. Biochem. 124:13-19. 628. Takaiwa, F., and M. Sugiura. 1982. Nucleotide sequence of the 16S-23S spacer region in an rRNA gene cluster from tobacco chloroplast DNA. Nucleic Acids Res. 10:2665-2676. 629. Takaiwa, F., and M. Sugiura. 1982. The nucleotide sequence of chloroplast 5S ribosomal RNA from a fern, Dryopteris acuminata. Nucleic Acids Res. 10:5369-5373. 630. Takemura, M., K. Oda, K. Yamato, E. Ohta, Y. Nakamura, N. Nozato, K. Adashi, and K. Ohyama. 1992. Gene clusters for ribosomal proteins in the mitochondrial genome of a liverwort, Marchantia polymorpha. Nucleic Acids Res. 20:3199-3205. 631. Tanaka, M., T. Wakasugi, M. Sugita, K. Shinozaki, and M. Sugiura. 1986. Genes for the eight ribosomal proteins are clustered on the chloroplast genome of tobacco (Nicotiana tabacum): similarity to the S10 and spc operons of Escherichia coli. Proc. Natl. Acad. Sci. USA 83:6030-6034. 632. Tate, W. P., C. M. Brown, and B. Kastner. 1990. Codon recognition by the polypeptide release factor, p. 393-401. In W. E. Hill, A. Dahlberg, G. A. Garrett, P. B. Moore, D. Schlessinger, and J. R. Warner (ed.), The ribosome. Structure, function, and evolution. American Society for Microbiology, Washington, D.C. 633. Taylor, F. J. R. 1987. An overview of the status of evolutionary cell symbiosis theories. Ann. N. Y. Acad. Sci. 503:1-16. 634. Taylor, G. W., K. H. Wolfe, C. W. Morden, C. W. dePamphilis, and J. D. Palmer. 1991. Lack of a functional plastid tRNAc'y gene is associated with loss of photosynthesis in a lineage of parasitic plants. Curr. Genet. 20:515-518. 635. Thomas, F., 0. Massenet, A. M. Dorne, J. F. Briat, and R Mache. 1988. Expression of the rp123, rpl2 and rpsl9 genes in spinach chloroplasts. Nucleic Acids Res. 16:2461-2472. 636. Thomas, F., G.-Q. Zeng, R. Mache, and J.-F. Briat. 1988. Transcription study of the genes encoded in the region of the junction between the large single copy and the inverted repeat A of spinach chloroplast DNA. Plant Mol. Biol. 10:447-457. 637. Thompson, A. J., and D. L. Herrin. 1991. In vitro self-splicing reactions of the chloroplast group I intron Cr.LSU from Chlamydomonas reinhardtii and in vivo manipulation via gene-replacement. Nucleic Acids Res. 19:6611-6618. 638. Thompson, A. J., X. Yuan, W. Kudlicki, and D. L. Herrin. 1992. Cleavage and recognition pattern of a double-strand-specific endonuclease (I-Crel) encoded by the chloroplast 23S rRNA intron of Chlamydomonas reinhardtii. Gene 119:247-251. 639. Thompson, J., and E. Cundliffe. 1991. The binding of thiostrepton to 23S ribosomal RNA. Biochimie 73:1131-1135. 640. Thompson, M. D., C. M. Jacks, T. R. Lenvik, and J. S. Gantt. 1992. Characterization of rpsl7, rpl9 and rpllS: three nucleusencoded plastid ribosomal protein genes. Plant Mol. Biol. 18: 931-944. 641. Tiboni, O., and G. Di Pasquale. 1987. Organization of genes for ribosomal proteins S7 and S12, elongation factors EF-Tu and EF-G in the cyanobacterium Spirulina platensis. Biochim. Biophys. Acta 908:113-122. 642. Tiller, K., A. Eisermann, and G. Linlk 1991. The chloroplast transcription apparatus from mustard (Sinapis alba L.). Evidence for three different transcription factors which resemble bacterial a factors. Eur. J. Biochem. 198:93-99. 751 752 HARRIS ET AL. in nature. Adv. Microb. Ecol. 12:219-286. 682. Ward, D. M., E. D. Kopczynski, B. K. Heimbuch, M. M. Bateson, and R Weller. 1992. Uncultivated cyanobacteria, Chloroflexuslike inhabitants and Spirochete-like inhabitants of a hot spring microbial mat. Appl. Environ. Microbiol. 58:3964-3969. 683. Ward, D. M., R. Weller, and M. M. Bateson. 1990. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature (London) 345:63-65. 684. Watson, J. C., and S. J. Surzycki. 1982. Extensive sequence homology in the DNA coding for elongation factor Tu from Escherichia coli and the Chlamydomonas reinhardtii chloroplast. Proc. Natl. Acad. Sci. USA 79:2264-2267. 685. Weglohner, W., J. Schmidt, K. Giese, and A. R. Subramanian. 1993. Expression and assembly of chloroplast ribosomal proteins in E. coli, p. 701-711. In K. H. Nierhaus, F. Franceschi, A. R. Subramanian, V. A. Erdmann, and B. Wittmann-Liebold (ed.), The translational apparatus. Structure, function, regulation, evolution. Plenum Press, New York. 686. Weglohner, W., and A. R Subramanian. 1991. A heptapeptide repeat contributes to the unusual length of chloroplast ribosomal protein S18. Nucleotide sequence and map position of the rp133-rps18 gene cluster in maize. FEBS Lett. 279:193-197. 687. Weglohner, W., and A. R Subramanian. 1992. Nucleotide sequence of a region of maize chloroplast DNA containing the 3' end of clpP, exon 1 of rpsl2 and rpl20 and their cotranscription. Plant Mol. Biol. 18:415-418. 688. Weglohner, W., and A. R Subramanian. 1993. Nucleotide sequence of maize chloroplast rpl32: completing the apparent set of plastid ribosomal protein genes and their tentative operon organization. Plant Mol. Biol. 21:543-548. 689. Weglohner, W., and A. R Subramanian. 1994. Multicopy GTPase center protein L12 of Arabidopsis chloroplast ribosome is encoded by a clustered nuclear gene family with the expressed members closely linked to tRNAPrO genes. J. Biol. Chem. 269: 7330-7336. 690. WeUland, A., and A. Parmeggiani. 1993. Toward a model for the interaction between elongation factor Tu and the ribosome. Science 259:1311-1314. 691. Weil, J. H., T. Kohchi, H. Fukuzawa, K. Ohyama, and T. Komano. 1985. Nucleotide sequences of chloroplast 4.5 S ribosomal RNA from a leafy liverwort, Jungermannia subulata, and a thalloid liverwort, Marchantia polymorpha. FEBS Lett. 185:203207. 692. Weller, R., J. W. Weller, and D. M. Ward. 1991. 16S rRNA sequences of uncultivated hot spring cyanobacterial mat inhabitants retrieved as randomly primed cDNA. Appl. Environ. Microbiol. 57:1146-1151. 693. Westhof, E., P. Romby, P. J. Romaniuk, J.-P. Ebel, C. Ehresmann, and B. Ehresmann. 1989. Computer modeling from solution data of spinach chloroplast and of Xenopus laevis somatic and oocyte SS rRNAs. J. Mol. Biol. 207:417-431. 694. Whatley, J. M. 1993. The endosymbiotic origin of chloroplasts. Int. Rev. Cytol. 144:259-299. 695. White, E. E. 1990. Chloroplast DNA in Pinus monticola. 1. Physical map. Theor. Appl. Genet. 79:119-124. 696. Wildeman, A. G., and R N. Nazar. 1980. Nucleotide sequence of wheat chloroplastid 4.5S ribonucleic acid. Sequence homologies in 4.5S RNA species. J. Biol. Chem. 255:11896-11900. 697. Williamson, S. E., and W. F. Doolittle. 1983. Gene for tRNAI"e and tRNAM"a in the spacer between the 16S and 23S rRNA genes of a blue-green alga: strong homology to chloroplast tRNA genes and tRNA genes of the Escherichia coli rmnD gene cluster. Nucleic Acids Res. 11:225-235. 698. Willmotte, A., S. Turner, Y. Van de Peer, and N. R Pace. 1992. Taxonomic study of marine Oscillatoriacean strains (Cyanobacteria) with narrow trichomes. II. Nucleotide sequence analysis of the 16S ribosomal RNA. J. Phycol. 28:828-838. 699. Willmotte, A., G. Van der Auwera, and R De Wachter. 1993. Structure of the 16S ribosomal RNA of the thermophilic cyanobacterium Chlorogloeopsis HTF ('Mastigocladus laminosus HTF') strain PCC7518, and phylogenetic analysis. FEBS Lett. 317:96-100. 700. Wilson, R. J. M., M. Fry, M. J. Gardner, J. E. Feagin, and D. H. Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV Escherichia coli. Mol. Gen. Genet. 140:61-68. 663. Van den Eynde, H., R De Baere, E. De Roeck, Y. Van de Peer, A. Vandenberghe, P. Willekens, and R De Wachter. 1988. The 5S ribosomal RNA sequences of a red algal rhodoplast and a gymnosperm chloroplast. Implications for the evolution of plastids and cyanobacteria. J. Mol. Evol. 27:126-132. 664. Van den Eynde, H., R. De Baere, and R De Wachter. 1988. Sequence and secondary structure of Porphyra umbilicalis SS rRNA. Relevance for the evolutionary origin of red algae. Nucleic Acids Res. 16:10919. 665. Van de Peer, Y., J.-M. Neefs, and R. De Wachter. 1990. Small ribosomal subunit RNA sequences, evolutionary relationships among different life forms, and mitochondrial origins. J. Mol. Evol. 30:463-476. 666. Van Knippenberg, P. H. 1990. Aspects of translation initiation in Escherichia coli, p. 265-274. In W. E. Hill, A. Dahlberg, G. A. Garrett, P. B. Moore, D. Schlessinger, and J. R. Warner (ed.), The ribosome. Structure, function, and evolution. American Society for Microbiology, Washington, D.C. 667. Vannuffel, P., M. Di Giambattista, E. A. Morgan, and C. Cocito. 1992. Identification of a single base change in ribosomal RNA leading to erythromycin resistance. J. Biol. Chem. 267:83778382. 668. Vera, A., T. Matsubayashi, and M. Sugiura. 1992. Active transcription from a promoter positioned within the coding region of a divergently oriented gene: the tobacco chloroplast rp132 gene. Mol. Gen. Genet. 233:151-156. 669. Vera, A., F. Yokoi, and M. Sugiura. 1993. The existence of pre-mature 16S rRNA species in plastid ribosomes. FEBS Lett. 327:29-31. 670. Vernon-Kipp, D., S. A. Kuhl, and C. W. Birky, Jr. 1989. Molecular evolution of Polytoma, a non-green chlorophyte, p. 284-286. In C. D. Boyer, J. C. Shannon, and R. C. Hardison (ed.), Physiology, biochemistry and genetics of nongreen plastids. American Society of Plant Physiologists, Rockville, Md. 671. Vogel, D. W., R. K. Hartmann, M. Bartsch, A. R Subramanian, W. Kleinow, T. W. O'Brien, T. Pieler, and V. A. Erdmann. 1984. Reconstitution of 50S ribosomal subunits from Bacillus stearothernophilus with 5S RNA from spinach chloroplasts and low-Mr RNA from mitochondria of Locusta migratonia and bovine liver. FEBS Lett. 169:67-72. 672. Von Alimen, J. M., and E. Stutz. 1987. Complete sequence of 'divided' rps12 (r-protein S12) and rps7 (r-protein S7) gene in soybean chloroplast DNA. Nucleic Acids Res. 15:2387. 673. Von Allmen, J.-M., and E. Stutz. 1988. The soybean chloroplast genome: nucleotide sequence of a region containing tRNA-Val (GAC) and 16S rRNA gene. Nucleic Acids Res. 16:1200. 674. Wada, A., K. Koyama, Y. Maki, Y. Shimoi, A. Tanaka, and H. Tsuji. 1993. A 5 kDa protein (SCS23) from the 30S subunit of the spinach chloroplast ribosome. FEBS Lett. 319:115-118. 675. Wada, A., and T. Sako. 1987. Primary structures of and genes for new ribosomal proteins A and B in Escherichia coli. J. Biochem. 101:817-820. 676. Walleczek, J., D. Schuler, M. Stodlier-Meilicke, R. Brimacombe, and G. Stfflfer. 1988. A model for the spatial arrangement of the proteins in the large subunit of the Escherichia coli ribosome. EMBO J. 7:3571-3576. 677. Wang, C. C., W. B. Roney, R L. Alston, and L. L. Spremulli. 1989. Initiation complex formation on Euglena chloroplast 30 S subunits in the presence of natural mRNAs. Nucleic Acids Res. 17:9735-9747. 678. Wang, C.-C., and L. L. Spremulli. 1991. Chloroplast translational initiation factor 3. Purification and characterization of multiple forms from Euglena gracilis. J. Biol. Chem. 266:17079-17083. 679. Wang, M. J., N. W. Davis, and P. Gegenheimer. 1988. Novel mechanisms for maturation of chloroplast transfer RNA precursors. EMBO J. 7:1567-1574. 680. Wang, S., and X.-Q. Liu. 1991. The plastid genome of Cryptomonas (D encodes an hsp70-like protein, a histone-like protein, and an acyl carrier protein. Proc. Natl. Acad. Sci. USA 88:1078310787. 681. Ward, D. M., M. M. Bateson, KL Weller, and A. L. Ruff-Roberts. 1992. Ribosomal RNA analysis of microorganisms as they occur MICROBIOL. REV. VOL. 58, 1994 CHLOROPLAST RIBOSOMES AND PROTEIN SYNTHESIS 721. Yaguchi, M., H. G. Wittmann, T. Cabezon, M. DeWilde, B. Villarroel, A. Herzog, and A. Bollen. 1975. Cooperative control of translational fidelity by ribosomal proteins in Escherichia coli. II. Localization of amino acid replacements in proteins S5 and S12 altered in double mutants resistant to neamine. Mol. Gen. Genet. 142:35-43. 722. Yamada, T. 1988. Nucleotide sequence of the chloroplast 16S rRNA gene from the unicellular green alga Chlorella ellipsoidea. Nucleic Acids Res. 16:9865. 723. Yamada, T. 1991. Repetitive sequence-mediated rearrangements in Chlorella ellipsoidea chloroplast DNA. Completion of nucleotide sequence of the large inverted repeat. Curr. Genet. 19:139-148. 724. Yamada, T., and M. Shimaji. 1986. Peculiar feature of the organization of rRNA genes of the Chlorella chloroplast DNA. Nucleic Acids Res. 14:3827-3839. 725. Yamada, T., and M. Shimaji. 1987. Splitting of the ribosomal RNA operon on chloroplast DNA from Chlorella ellipsoidea. Mol. Gen. Genet. 208:377-383. 726. Yamada, T., and M. Shimaji. 1987. An intron in the 23S rRNA gene of the Chlorella chloroplast: complete nucleotide sequence of the 23S rRNA gene. Curr. Genet. 11:347-352. 727. Yamaguchi-Shinozaki, K., K. Shinozaki, and M. Sugiura. 1987. Processing of precursor tRNAs in a chloroplast lysate. FEBS Lett. 215:132-136. 728. Yamano, Y., K. Ohyama, and T. Komano. 1984. Nucleotide sequences of chloroplast SS ribosomal RNA from cell suspension cultures of the liverworts Marchantia polymorpha and Jungermannia subulata. Nucleic Acids Res. 12:4621-4624. 729. Yeh, K.-C., K.-Y. To, M. Wu, and C.-C. Chen. 1991. Unpublished sequence submission. 730. Yepiz-Plascencia, G. M., M. E. Jenkins, and R B. Hallick. 1988. 731. 732. 733. 734. 735. 736. 737. 738. 739. 740. 741. Nucleotide sequence of the Euglena gracilis chloroplast 23S rRNA gene of the rnC operon. Nucleic Acids Res. 16:9340. Yokoi, F., and M. Sugiura. 1992. Tobacco chloroplast ribosomes contain a homologue of E. coli ribosomal protein L28. FEBS Lett. 308:258-260. Yokoi, F., M. Tanaka, T. Wakasugi, and M. Sugiura. 1991. The chloroplast gene for ribosomal protein CL23 is functional in tobacco. FEBS Lett. 281:64-66. Yokoi, F., A. Vassileva, N. Hayashida, K. Torazawa, T. Wakasugi, and M. Sugiura. 1990. Chloroplast ribosomal protein L32 is encoded in the chloroplast genome. FEBS Lett. 276:88-90. Yoshinaga, K., T. Ohta, Y. Suzuki, and M. Sugiura. 1988. Chlorella chloroplast DNA sequence containing a gene for the large subunit of ribulose-1,5-bisphosphate carboxylase and a part of a possible gene for the beta' subunit of RNA polymerase. Plant Mol. Biol. 10:245-250. Young, R, R. Macklis, and J. Steitz. 1979. Sequence of the 16S-23S spacer region in two ribosomal operons of E. coli. J. Biol. Chem. 254:3264-3271. Yu, W., D. Zhang, and R J. Spreitzer. 1992. Sequences of the Chlamydomonas reinhardtii chloroplast genes encoding tRNASer and ribosomal protein L20. Plant Physiol. 100:1079-1080. Zaita, N., K. Torazawa, K. Shinozaki, and M. Sugiura. 1987. Trans splicing in vivo: joining of transcripts from the "divided" gene for ribosomal protein S12 in the chloroplasts of tobacco. FEBS Lett. 210:153-156. Zhen-Qi, C., Z. Hong, L. Guo-Ya, and L. Xiao-Yang. 1986. The nucleotide sequences of chloroplast 4.5 S rRNAs from four species of plants, celery (Apium graveoleus), barley (Hordeum vulgare), Chinese chive (Allium tuberosum) and dayflower (Commelina communis). FEBS Lett. 200:193-196. Zhen-Qi, C., X. Xiao, and W. E. Sheng. 1986. The nucleotide sequence of 4.5 S rRNA from tomato chloroplasts. Biochim. Biophys. Acta 866:89-91. Zhou, D.-X., Y.-F. Li, M. Rocipon, and R. Mache. 1992. Sequence-specific interaction between SlF, a spinach nuclear factor, and a negative cis-element conserved in plastid-related genes. J. Biol. Chem. 267:23515-23519. Zhou, D.-X., and R. Mache. 1989. Presence in the stroma of chloroplasts of a large pool of a ribosomal protein not structurally related to any Escherichia coli ribosomal protein. Mol. Gen. Genet. 219:204-208. Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV Williamson. 1991. Have malaria parasites three genomes? Parasitol. Today 7:136-138. 701. Wilson, R. J. M., M. Fry, M. J. Gardner, J. E. Feagin, and D. H. Williamson. 1992. Subcellular fractionation of the two organelle DNAs of malaria parasites. Curr. Genet. 21:405-408. 702. Wimpee, C. F., R. Morgan, and R. L. Wrobel. 1992. Loss of transfer RNA genes from the plastid 16S-23S ribosomal RNA gene spacer in a parasitic plant. Curr. Genet. 21:417-422. 703. Wimpee, C. F., R. Morgan, and R. Wrobel. 1992. An aberrant plastid ribosomal RNA gene cluster in the root parasite Conopholis americana. Plant Mol. Biol. 18:275-285. 704. Wimpee, C. F., R. L. Wrobel, and D. K. Garvin. 1991. A divergent plastid genome in Conopholis americana, an achlorophyllous parasitic plant. Plant Mol. Biol. 17:161-166. 705. Witt, D., and E. Stackebrandt. 1988. Disproving the hypothesis of a common ancestry for the Ochromonas danica chrysoplast and Heliobacterium chlorum. Arch. Microbiol. 150:244-248. 706. Wittmann, H. G., J. A. Littlechild, and B. Wittmann-Liebold. 1980. Structure of ribosomal proteins, p. 51-88. In G. Chambliss, G. R. Craven, J. Davies, K. Davis, L. Kahan, and M. Nomura (ed.), Ribosomes. Structure, function, and genetics. University Park Press, Baltimore. 707. Wittmann-Liebold, B. 1986. Ribosomal proteins: their structure and evolution, p. 326-361. In B. Hardesty and G. Kramer (ed.), Structure, function, and genetics of ribosomes. Springer-Verlag, New York. 708. Wittmann-Liebold, B., A. K. E. Kopke, E. Arndt, W. Kramer, T. Hatakeyama, and H.-G. Wittmann. 1990. Sequence comparison and evolution of ribosomal proteins and their genes, p. 598-616. In W. E. Hill, A. Dahlberg, G. A. Garrett, P. B. Moore, D. Schlessinger, and J. R. Warner (ed.), The ribosome. Structure, function, and evolution. American Society for Microbiology, Washington, D.C. 709. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221271. 710. Woese, C. R., L. J. Magrum, R. Gupta, R. B. Siegel, D. A. Stahl, J. Kop, N. Crawford, J. Brosius, R. Gutell, J. J. Hogan, and H. F. Noller. 1990. Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence. Nucleic Acids Res. 8:2275-2293. 711. Wolfe, K H., D. S. Katz-Downie, C. W. Morden, and J. D. Palmer. 1992. Evolution of the plastid ribosomal RNA operon in a nongreen parasitic plant: accelerated sequence evolution, altered promoter structure, and tRNA pseudogenes. Plant Mol. Biol. 18:1037-1048. 712. Wolfe, K. H., C. W. Morden, S. C. Ems, and J. D. Palmer. 1992. Rapid evolution of the plastid translational apparatus in a nonphotosynthetic plant: loss or accelerated sequence evolution of tRNA and ribosomal protein genes. J. Mol. Evol. 35:304317. 713. Wolfe, K. H., C. W. Morden, and J. D. Palmer. 1991. Ins and outs of plastid genome evolution. Curr. Opin. Genet. Dev. 1:523-529. 714. Wolfe, K. H., C. W. Morden, and J. D. Palmer. 1992. Function and evolution of a minimal plastid genome from a nonphotosynthetic plant. Proc. Natl. Acad. Sci. USA 89:10648-10652. 715. Wolfson, R., K. G. Higgins, and B. B. Sears. 1991. Evidence for replication slippage in the evolution of Oenothera chloroplast DNA. Mol. Biol. Evol. 8:709-720. 716. Wolstenholme, D. R 1992. Animal mitochondrial DNA: structure and evolution. Int. Rev. Cytol. 141:173-216. 717. Woodcock, J., D. Moazed, M. Cannon, J. Davies, and H. F. Noller. 1991. Interaction of antibiotics with A- and P-site-specific bases in 16S ribosomal RNA. EMBO J. 10:3099-3103. 718. Woodson, S. A., and T. R Cech. 1989. Reverse self-splicing of the Tetrahymena group I intron: implication for the directionality of splicing and for intron transposition. Cell 57:335-345. 719. Wu, H., I. Wower, and R A. Zimmermann. 1993. Mutagenesis of ribosomal protein S8 from Escherichia coli: expression, stability, and RNA-binding properties of S8 mutants. Biochemistry 32: 4761-4768. 720. Wurtz, E. A., and D. E. Buetow. 1981. Intraspecific variation in the structural organization and redundancy of chloroplast ribosomal DNA cistrons in Euglena gracilis. Curr. Genet. 3:181-187. 753 754 HARRIS ET AL. 742. Zhou, D.-X., F. Quigley, 0. Massenet, and R. Mache. 1989. Cotranscription of the S10- and spc-like operons in spinach chloroplasts and identification of three of their gene products. Mol. Gen. Genet. 216:439-445. 743. Zhou, X., W. Liu, and M. Wang. 1988. Comparative study on the evolution of chloroplast ribosomal 5S RNA of a living fossil plant, Cycas revoluta Thunb. FEBS Lett. 235:30-34. 744. Zimmermann, R A., C. L Thomas, and J. Wower. 1990. Structure and function of rRNA in the decoding domain and at the peptidyltransferase center, p. 331-347. In W. E. Hill, A. Dahlberg, G. A. Garrett, P. B. Moore, D. Schlessinger, and J. R. MICROBIOL. REV. Warner (ed.), The ribosome. Structure, function, and evolution. American Society for Microbiology, Washington, D.C. 745. Zurawski, G., W. Bottomley, and P. R. Whitfeld. 1984. Junctions of the large single copy region and the inverted repeats in Spinacia oleracea and Nicotiana debneyi chloroplast DNA: sequence of the genes for tRNAH1S and the ribosomal proteins S19 and L2. Nucleic Acids Res. 12:6547-6558. 746. Zurawski, G., and M. T. Clegg. 1987. Evolution of higher-plant chloroplast DNA-encoded genes: implications for structure-function and phylogenetic studies. Annu. Rev. Plant Physiol. 38:391-418. Downloaded from http://mmbr.asm.org/ on March 6, 2016 by PENN STATE UNIV