Genes optimized by evolution for accurate and fast translation encode in Archaea and Bacteria a broad and characteristic spectrum of protein functions

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  von Mandach, Conrad ^a   Merkl, Rainer ^b  

^a UNIVERSITY OF HAGEN   (Germany)

^b UNIVERSITY OF REGENSBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINOACYL TRANSFER RNA; CHAPERONE; COLD SHOCK PROTEIN; GENE PRODUCT; OUTER MEMBRANE PROTEIN; PROTEINASE; PROTEOME; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE; ARCHAEAL PROTEIN; BACTERIAL PROTEIN; TRANSFER RNA;

ACCURACY; ARCHAEBACTERIUM; ARTICLE; BACTERIAL GENOME; BACTERIUM; CELL FUNCTION; CELL GROWTH; CODON USAGE; CONTROLLED STUDY; EFFECTOME; ENERGY YIELD; ENVIRONMENTAL FACTOR; GENETIC CODE; GENETIC TRAIT; GLUCONEOGENESIS; GLYCOLYSIS; MOLECULAR EVOLUTION; NONHUMAN; OXIDATIVE STRESS; PROTEIN DEGRADATION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STABILITY; PROTEIN SYNTHESIS; RNA TRANSLATION; SPECIES HABITAT; ARCHAEAL GENOME; CODON; ECOSYSTEM; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; SPECIES DIFFERENCE; TIME;

ARCHAEA; BACTERIA (MICROORGANISMS);

ARCHAEA; ARCHAEAL PROTEINS; BACTERIA; BACTERIAL PROTEINS; CODON; ECOSYSTEM; EVOLUTION, MOLECULAR; GENOME, ARCHAEAL; GENOME, BACTERIAL; METABOLIC NETWORKS AND PATHWAYS; PROTEIN BIOSYNTHESIS; RNA, TRANSFER; SPECIES SPECIFICITY; TIME FACTORS;

EID: 78049388648     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-617     Document Type: Article

References (50)

1. Sharp PM, Li WH. The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 1987, 15(3):1281-1295. 10.1093/nar/15.3.1281, 340524, 3547335.
2. Hershberg R, Petrov DA. General rules for optimal codon choice. PLoS Genet 2009, 5(7):e1000556. 10.1371/journal.pgen.1000556, 2700274, 19593368.
3. Bennetzen JL, Hall BD. Codon selection in yeast. J Biol Chem 1982, 257(6):3026-3031.
4. Gouy M, Gautier C. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res 1982, 10(22):7055-7074. 10.1093/nar/10.22.7055, 326988, 6760125.
5. Grantham R, Gautier C, Gouy M, Mercier R, Pave A. Codon catalog usage and the genome hypothesis. Nucleic Acids Res 1980, 8(1):r49-r62. 10.1093/nar/8.1.197-c, 327256, 6986610.
6. Sharp PM, Li WH. An evolutionary perspective on synonymous codon usage in unicellular organisms. J Mol Evol 1986, 24(1-2):28-38. 10.1007/BF02099948, 3104616.
7. Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Biol 1981, 146(1):1-21. 10.1016/0022-2836(81)90363-6, 6167728.
8. Curran JF, Yarus M. Rates of aminoacyl-tRNA selection at 29 sense codons in vivo. J Mol Biol 1989, 209(1):65-77. 10.1016/0022-2836(89)90170-8, 2478714.
9. Pedersen S. Escherichia coli ribosomes translate in vivo with variable rate. EMBO J 1984, 3(12):2895-2898. 557784, 6396082.
10. Andersson SG, Kurland CG. Codon preferences in free-living microorganisms. Microbiol Rev 1990, 54(2):198-210. 372768, 2194095.
11. Sharp PM, Bailes E, Grocock RJ, Peden JF, Sockett RE. Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res 2005, 33(4):1141-1153. 10.1093/nar/gki242, 549432, 15728743.
12. Rocha EP. Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization. Genome Res 2004, 14(11):2279-2286. 10.1101/gr.2896904, 525687, 15479947.
13. Vieira-Silva S, Rocha EP. The systemic imprint of growth and its uses in ecological (meta)genomics. PLoS Genet 2010, 6(1):e1000808. 10.1371/journal.pgen.1000808, 2797632, 20090831.
14. Karlin S, Brocchieri L, Campbell A, Cyert M, Mrazek J. Genomic and proteomic comparisons between bacterial and archaeal genomes and related comparisons with the yeast and fly genomes. Proc Natl Acad Sci USA 2005, 102(20):7309-7314. 10.1073/pnas.0502314102, 1129125, 15883367.
15. Karlin S, Brocchieri L, Mrázek J, Kaiser D. Distinguishing features of d-proteobacterial genomes. Proc Natl Acad Sci USA 2006, 103(30):11352-11357. 10.1073/pnas.0604311103, 1544090, 16844781.
16. Roymondal U, Das S, Sahoo S. Predicting gene expression level from relative codon usage bias: an application to Escherichia coli genome. DNA Res 2009, 16(1):13-30. 10.1093/dnares/dsn029, 2646356, 19131380.
17. Sen A, Sur S, Bothra AK, Benson DR, Normand P, Tisa LS. The implication of life style on codon usage patterns and predicted highly expressed genes for three Frankia genomes. Antonie Van Leeuwenhoek 2008, 93(4):335-346. 10.1007/s10482-007-9211-1, 18293096.
18. Das S, Roymondal U, Sahoo S. Analyzing gene expression from relative codon usage bias in Yeast genome: a statistical significance and biological relevance. Gene 2009, 443(1-2):121-131. 10.1016/j.gene.2009.04.022, 19410638.
19. Carbone A. Computational prediction of genomic functional cores specific to different microbes. J Mol Evol 2006, 63(6):733-746. 10.1007/s00239-005-0250-9, 17103060.
20. Supek F, Skunca N, Repar J, Vlahovicek K, Smuc T. Translational selection is ubiquitous in prokaryotes. PLoS Genet 2010, 6(6):e1001004. 10.1371/journal.pgen.1001004, 2891978, 20585573.
21. Wright F. The 'effective number of codons' used in a gene. Gene 1990, 87(1):23-29. 10.1016/0378-1119(90)90491-9, 2110097.
22. Morton BR. Codon use and the rate of divergence of land plant chloroplast genes. Mol Biol Evol 1994, 11(2):231-238.
23. Freire-Picos MA, Gonzalez-Siso MI, Rodriguez-Belmonte E, Rodriguez-Torres AM, Ramil E, Cerdan ME. Codon usage in Kluyveromyces lactis and in yeast cytochrome c-encoding genes. Gene 1994, 139(1):43-49. 10.1016/0378-1119(94)90521-5, 8112587.
24. Karlin S, Mrázek J. Predicted highly expressed genes of diverse prokaryotic genomes. J Bacteriol 2000, 182(18):5238-5250. 10.1128/JB.182.18.5238-5250.2000, 94675, 10960111.
25. Urrutia AO, Hurst LD. Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection. Genetics 2001, 159(3):1191-1199. 1461876, 11729162.
26. Novembre JA. Accounting for background nucleotide composition when measuring codon usage bias. Mol Biol Evol 2002, 19(8):1390-1394.
27. Carbone A, Zinovyev A, Képès F. Codon adaptation index as a measure of dominating codon bias. Bioinformatics 2003, 19(16):2005-2015. 10.1093/bioinformatics/btg272, 14594704.
28. Kloster M, Tang C. SCUMBLE: a method for systematic and accurate detection of codon usage bias by maximum likelihood estimation. Nucleic Acids Res 2008, 36(11):3819-3827. 10.1093/nar/gkn288, 2441815, 18495752.
29. Coghlan A, Wolfe KH. Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast 2000, 16(12):1131-1145. 10.1002/1097-0061(20000915)16:12<1131::AID-YEA609>3.0.CO;2-F, 10953085.
30. Supek F, Vlahovicek K. Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity. BMC Bioinformatics 2005, 6(1):182. 10.1186/1471-2105-6-182, 1199580, 16029499.
31. Merkl R. A survey of codon and amino acid frequency bias in microbial genomes focusing on translational efficiency. J Mol Evol 2003, 57:453-466. 10.1007/s00239-003-2499-1, 14708578.
32. Pruitt KD, Tatusova T, Klimke W, Maglott DR. NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res 2009, (37 Database):D32-36. 10.1093/nar/gkn721, 2686572, 18927115.
33. Makarova KS, Sorokin AV, Novichkov PS, Wolf YI, Koonin EV. Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. Biol Direct 2007, 2:33. 10.1186/1745-6150-2-33, 2222616, 18042280.
34. dos Reis M, Savva R, Wernisch L. Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res 2004, 32(17):5036-5044. 10.1093/nar/gkh834, 521650, 15448185.
35. Carbone A, Kepes F, Zinovyev A. Codon bias signatures, organization of microorganisms in codon space, and lifestyle. Mol Biol Evol 2005, 22(3):547-561. 10.1093/molbev/msi040, 15537809.
36. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25(1):25-29. 10.1038/75556, 10802651.
37. Ruepp A, Zollner A, Maier D, Albermann K, Hani J, Mokrejs M, Tetko I, Güldener U, Mannhaupt G, Münsterkötter M, et al. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res 2004, 32(18):5539-5545. 10.1093/nar/gkh894, 524302, 15486203.
38. Merkl R. SIGI: score-based identification of genomic islands. BMC Bioinformatics 2004, 5:22. 10.1186/1471-2105-5-22, 394314, 15113412.
39. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, et al. The COG database: an updated version includes Eukaryotes. BMC Bioinformatics 2003, 4(1):41. 10.1186/1471-2105-4-41, 222959, 12969510.
40. Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, et al. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res 2010, (38 Database):D190-195. 10.1093/nar/gkp951, 2808932, 19900971.
41. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 2010, (38 Database):D355-360. 10.1093/nar/gkp896, 2808910, 19880382.
42. Galagan JE, Nusbaum C, Roy A, Endrizzi MG, Macdonald P, FitzHugh W, Calvo S, Engels R, Smirnov S, Atnoor D, et al. The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity. Genome Res 2002, 12(4):532-542. 10.1101/gr.223902, 187521, 11932238.
43. Koch AL. Microbial physiology and ecology of slow growth. Microbiol Mol Biol Rev 1997, 61(3):305-318. 232613, 9293184.
44. Woese CR, Olsen GJ, Ibba M, Soll D. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev 2000, 64(1):202-236. 10.1128/MMBR.64.1.202-236.2000, 98992, 10704480.
45. Brüggemann H, Bäumer S, Fricke WF, Wiezer A, Liesegang H, Decker I, Herzberg C, Martinez-Arias R, Merkl R, Henne A, et al. The genome sequence of Clostridium tetani, the causative agent of tetanus disease. Proc Natl Acad Sci USA 2003, 100(3):1316-1321. 10.1073/pnas.0335853100, 298770, 12552129.
46. Altschul SF. Amino acid substitution matrices from an information theoretic perspective. J Mol Biol 1991, 219(3):555-565. 10.1016/0022-2836(91)90193-A, 2051488.
47. Henikoff S, Henikoff JG. Automated assembly of protein blocks for database searching. Nucleic Acids Res 1991, 19(23):6565-6572. 10.1093/nar/19.23.6565, 329220, 1754394.
48. Waack S, Keller O, Asper R, Brodag T, Damm C, Fricke W, Surovcik K, Meinicke P, Merkl R. Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics 2006, 7:142. 10.1186/1471-2105-7-142, 1489950, 16542435.
49. Hiraoka Y, Kawamata K, Haraguchi T, Chikashige Y. Codon usage bias is correlated with gene expression levels in the fission yeast Schizosaccharomyces pombe. Genes Cells 2009, 14(4):499-509. 10.1111/j.1365-2443.2009.01284.x, 19335619.
50. UniProt Interface. , http://www.uniprot.org/jobs