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Comparative analysis of ribosomal proteins in complete genomes: ribosome “striptease” in Archaea Odile Lecompte, Raymond Ripp, Jean-Claude Thierry, Dino Moras and Olivier Poch Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS, INSERM, ULP), BP163, 67404 Illkirch Cedex, France Abstract A comprehensive investigation of ribosomal genes in complete genomes from 66 different species allows us to address the distribution of r-proteins between and within the three primary domains. 34 r-protein families are represented in all domains but 33 families are specific to Archaea and Eucarya, providing evidence for specialisation at an early stage of evolution between the bacterial lineage and the lineage leading to archaea and eukaryotes. With only one specific r-protein, the archaeal ribosome appears to be a small-scale model of the eukaryotic one in term of protein composition. However, the mechanism of evolution of the protein component of the ribosome appears dramatically different in Archaea. In Bacteria and Eucarya, a restricted number of ribosomal genes can be lost with a bias toward losses in intracellular pathogens. In Archaea, losses implicate 15% of the ribosomal genes revealing an unexpected plasticity of the translation apparatus and the pattern of gene losses indicates a progressive elimination of ribosomal genes in the course of archaeal evolution. This first documented case of reductive evolution at the domain scale provides a new framework for discussing the shape of the universal tree of life and the selective forces directing the evolution of prokaryotes. Genes often missed during annotation process Ribosomal gene detection : cross-validation needed ! Small size and biased composition of r-proteins An initial set of ribosomal proteins classified into 102 families was obtained at http://www.expasy.ch/cgi-bin/lists?ribosomp.txt. For each family, representatives of various lineages across Bacteria, Archaea and Eucarya were used as probes and systematically compared to a nonredundant protein database consisting of SwissProt, SpTrEMBL and SpTrEMBLNEW using the BlastP program (1) with a cut-off of E<0.001. The results of the BlastP comparison were cross-validated by a TBlastN search against a complete genome database including 66 different species. The putative new gene sequences detected by the TBlastN searches were examined in the light of their genomic context to eliminate false-positives “hits”. For each r-protein family, the likely r-protein sequences obtained by the BlastP and TBlastN searches were included in a multiple alignment constructed by MAFFT (2). All alignments were refined by RASCAL (3) and their quality assessed by NorMD (4). These alignments were manually examined to remove false-positives observed in some ribosomal protein families, in particular those containing ubiquitous RNA-binding domains. BlastP Hit between RL40_METJA (Query) and RL40_HUMAN >SW:RL40_HUMAN P14793 60S RIBOSOMAL PROTEIN L40 (CEP52). 10/2001 Length = 52 Score = 31.6 bits (70), Expect = 1.8 Identities = 18/34 (52%), Positives = 20/34 (57%), Gaps = 3/34 (8%) Query: 13 KKICMRCNARNPWRATKCR--KCGY-KGLRPKAK 43 K IC +C AR RA CR KCG+ LRPK K Sbjct: 17 KMICRKCYARLHPRAVNCRKKKCGHTNNLRPKKK 50 Difficulty of protein detection by similarity search Protocol of ribosomal gene detection R-protein families Complete genomes 102 r-protein families Genomic context analysis Several representatives for each protein family Pa, Ph, Pf, Mj 45 Bacteria Ap 14 Archaea Proteins 66 Complete complete genomes L14E SECY ADK Hyp GATA L34E CMK L14E L14E ... L19E L18P S5P L30P L15P SECY ADK Hyp L34E CMK Ss, St ... L19E L18P S5P L30P L15P SECY ADK Hyp L34E CMK L14E L19E L18P S5P L30P L15P SECY ADK Hyp L34E CMK L14E GATA L34E CMK L14E Py TBlastN CMK Mt Mk BlastP L34E TRUB TRUBa TRUBb TRUB Multiple alignment of complete sequences 7 Eucarya Homology Detection Analysis)) Creation of 24 missed genes Protein detected by : 100% of the family representatives in >50% of the family representatives in <50% of the family representatives in 0% of the family representatives in 0% of the family representatives in (gene missed during annotation both blastp and tblastn blastp blastp both blastp and tblastn blastp but detected by tblastn process) • Coherence of the protein family • Elimination of false-positives • Correction of protein sequences Validation of protein sequences for each family All the alignments are available at http://www-igbmc.u-strasbg.fr/BioInfo/Rproteins A complex Last Universal Common Ancestor ? Interdomain distribution Ribosomal protein losses in each of the three domains Animals Eucarya: 78 (32;46) Archaea: 68 (28;40) AE: 33 (13;20) E: 11 (4;7) BE: 0 BAE: 34 (15;19) Bacteria Bacteria A: 1 (0;1) Archaea 1 23 Fungi Eucarya 11 Archaeoglobus Gram positives 33 Proteobacteria Cyanobacteria 34 B: 23 (8;15) Plants Ciliates* Thermoplasma Methanococcus Pyrococcus Pyrobaculum Chlamydia Halobacterium Methanobacterium Spirochaetes BA: 0 Eucarya Archaea Methanopyrus Flagellates* Trichomonads* Sulfolobus Deinococcus Aeropyrum Thermotoga Bacteria: 57 (23;34) Diplomonads* Microsporidia Aquifex • Prevalence of r-proteins within the universal pool that may be present in the last universal common ancestor (LUCA) • specialization of bacterial versus archaeal/eukaryotic ribosomes • the majority of archeal and eucaryotic r-proteins appears before the split between Archaea and Eucarya, suggesting a complex cenancestor S22p S1p L25p S21p L30p L38e L13e S25e S26e S30e S21e L35ae L14e L34e L30e LXa L28e Full circles indicate proteins absent in all complete genomes investigated in the indicated taxon. Empty circles stand for proteins absent in some complete genomes of the indicated taxon Localisation in the 3D structures Bacteria-specific proteins (colored in different shades of red) are preferentially located at the periphery of the ribosome Progressive elimination of 10 r-proteins (15%) in the course of archaeal evolution S6p S18p S2p S11p S15p S7p S8p S17p S9p Thx First example of reductive evolution at domain-scale S20p S13p S16p S19p S3p S5p S10p S12p S4p S14p the 30S ribosomal subunit of Thermus thermophilus (5) (back side) L5p L25p L30p L16p L21p L11p L20p Reductive evolution as a general trend in Archaea ? In Procaryotes ? L18p L27p L35p A complex Last Universal Common Ancestor (LUCA) ? L33p L15p L4p/L4e L28p L6p Which evolutionary scenario ? L9p L31p L2p L24p L36p L13p L3p E B A A B E i E A B o L29p References: L14p L19p L17p L32p L23p L22p L34p the 50S ribosomal subunit of Deinococcus radodurans (6) (crown view rotated by 180°) 1 2 3 4 5 6 Simple ancestor(s) Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Nucleic Acids Res., 25, 3389-3402. Katoh,K., Misawa,K., Kuma,K. and Miyata,T. (2002) Nucleic Acids Res., 30, 3059-3066. Bacterial Thompson,J.D., Thierry,J.C., Poch,O. (2003) Bioinformatics, 19, 1155-61. Thompson,J.D., Plewniak,F., Ripp,R., Thierry,J.C. and Poch,O. (2001) J. Mol. Biol., 314, 937-951. Wimberly,B.T., Brodersen,D.E., Clemons,W.M., Jr., Morgan-Warren,R.J., Carter,A.P., Vonrhein,C., Hartsch,T. and Ramakrishnan,V. (2000) Nature, 407, 327-339. Harms,J., Schluenzen,F., Zarivach,R., Bashan,A., Gat,S., Agmon,I., Bartels,H., Franceschi,F. and Yonath,A. (2001) Cell, 107, 679-688. rooting Simple ancestor(s) Complex ancestor(s) Symbiosis Eucarya rooting