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Gene Loss and Organelle Genome Evolution Level 3 Molecular Evolution and Bioinformatics Jim Provan References Race HL, Herrmann RG, Martin W (1999) “Why have organelles retained genomes?” Trends in Genetics 15: 364-370 Lang BF, Gray MW, Burger G (1999) “Mitochondrial genome evolution and the origin of eukaryotes” Annual Review of Genetics 33: 351-397 Gene loss in early organelle evolution Rickettsia prowazeki (1,111kb - 834 genes) Synechocystis sp. (3,573kb - 3000 genes) Reclinomonas americana mtDNA (69kb - 97 genes) Porphyra purpurea cpDNA (201kb - 250 genes) Types of genes in organelles and their ancestors 160 140 120 100 80 60 40 20 0 Synechocystis Plastids Rickettsia Mitochondria Genes encoded in plastid genomes Electron transport / related processes Gene expression PSII Cyt b6 PSI ATPase CO2 fix Synechocystis 25 8 12 9 Any plastid genome All plastid genomes 16 13 7 2 12 4 8 5 Other Total RNA pol rRNA 24 12 53 3025 3168 2 1 4 3 48 16 159 2 2569 46 Evolution of the spc (spectinomycin) operon L14 E. coli H. influenzae B. subtilis Synechocystis P. purpurea O. sinensis C. paradoxa M. polymorpha N. tabacum L24 L5 S14 S8 L6 L18 S5 L30 L15 Where did the genes go? Obsolete genes eliminated early on: Nucleotide, lipid and amino acid biosynthesis genes not found in mitochondria Still found in some chloroplasts: ancient mitochondrial genomes may exist which contain these genes cf. Porphyra vs. angiosperm chloroplasts Takeover of corresponding function by nuclear genes: Protozoan Paramecium mtDNA contains only three tRNA genes To translate all codons, tRNAs are imported from cytosol The mitochondrial RNA polymerase Most eukaryote mtDNAs use a nucleus-encoded single-subunit polymerase similar to T3/T7 phages Jakobid protists J. libera and R. americana mtDNA contains genes for multisubunit RNA polymerase like that in bacteria Original RNA polymerase has been superseded by phage-like enzyme Phylogeny of green algae Chlorophyceae Chlorophyta Trebouxiophyceae Ulvophyceae Charophyceae Embryophyta Charales Streptophyta Prasinophyceae Closest relatives to land plants (Embryophyta) are Charophyceae Complete chloroplast DNA sequence available for Trebouxiophyte Chlorella Green algae chloroplast structure highly variable difficult to predict ancestral structure Nephroselmis olivacea chloroplast structure Quadripartite structure: 92,126bp LSC 16,399bp SSC 46,137bp IR IRs also found in: Cyanophora Odontella Guillardia Land plants (mostly) but not in: Chlorella Porphyra Nephroselmis olivacea gene content Total of 127 genes: largest among green lineage: Marchantia - 120; Chlorella - 111; Euglena - 85 May represent “primitive” green plastid Seven genes not found in other green chloroplasts: rnpB, trnS(cga), ftsW, rne, ycf62 found in non-green algae ycf81 and ftsI found in bacteria ftsW and ftsI involved in formation of peptidoglycan: — — Cell wall only found in glaucocystophyte Cyanophora May be more prevalent than first thought Ten subunits of NADH:ubiquinone oxidoreductase: ndh genes found in four of five land plants Pseudogenes in Pinus - transferred to nucleus Nephroselmis olivacea gene content Atypical codon usage and AT-composition: Suggests that majority of IR has been gained by lateral transfer Also noted in green alga Chlamydomonas No introns cf. Porphyra, Odontella and Guillardia: Suggests ancestral plastid genome contained very few introns Intron proliferation seems to be a feature of higher plants trnL intron in Chlorella seems to have been vertically transmitted from cyanobacteria: — — Found in Cyanophora Found in plants Phylogenetic position of Nephroselmis chloroplasts Nicotiana * Marchantia * Chlamydomonas * Chlorella * Euglena * Nephroselmis Porphyra * Guillardia Odontella Cyanophora Synechocystis Tree based on 37 cpDNA proteins Agrees with 18S-rRNA (nuclear) phylogenies Nephroselmis represents basal branch of Chlorophyta Euglena included in Chlorophyta Patterns of gene loss in chloroplast genomes Euglena (85) chlB chlL chlN cysA cysT psaM rpl21 ycf12 ycf66 R(ccg) Chlorella (111) Nicotiana rpl22 accD ccsA cemA chlB chlL chlN clpP cysA cysT ftsI ftsW ndhA ndhB ndhC ndhD (111) rps16 Marchantia ftsH infA minD minE petA petD petL psaI psbM ndhE ndhF ndhG ndhH ndhI ndhK rpl19 rpoA ycf1 ycf3 I(gau) L(gag) S(gga) T(ggu) R(ccg) rne rmpB ycf6 ycf62 ycf81 S(cga) Nephroselmis (127) (120) chlI ftsI ftsW minD minE rne rnpB rpl5 rpl12 rpl19 rps9 tufA ycf62 ycf81 L(gag) S(cga) Ancestral Green Alga (137) ndhJ rpl21 rpl33 rps15 rps16 ycf66 V(gac) minE psaM rpl22 Gene partitioning All but one genes located in single-copy regions in Nephroselmis are found in corresponding region in Marchantia: Exception is trnL(UAG) Suggests that ancestral green algal plastid genome had IR Some genes adjacent to IR in Marchantia have been “subsumed” into the IR in Nephroselmis In smaller region delineated by rRNA operons (cf. SSC), only four of thirteen genes have been transferred to large region (cf. LSC) between “red” / “green” lineages: Suggests that transfer between LSC and SSC regions is rare Further evidence for single origin of all plastid genomes