Computational prediction of genomic functional cores specific to different microbes

Journal of Molecular Evolution

Volumn 63, Issue 6, 2006, Pages 733-746

  Carbone, Alessandra ^a  

^a SORBONNE UNIVERSITÉ   (France)

Author keywords

Codon Adaptation Index; Codon bias; Evolution; Genomic core; Minimal gene sets

Indexed keywords

ARTICLE; CODON; COMPUTER ANALYSIS; ENVIRONMENT; FUNCTIONAL GENOMICS; GENE EXPRESSION; LIFESTYLE; MICROORGANISM; NONHUMAN; ORTHOLOGY; PREDICTION; RNA TRANSLATION; STRESS; UBIQUITINATION;

BACILLUS SUBTILIS; CODON; COMPUTATIONAL BIOLOGY; ESCHERICHIA COLI; EVOLUTION; GAMMAPROTEOBACTERIA; GENOME, BACTERIAL; SYNECHOCYSTIS;

BACTERIA (MICROORGANISMS);

EID: 33845362592     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-005-0250-9     Document Type: Article

References (55)

1. Mushegian AR, Koonin EV (1996) A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci USA 93:10268-10273
2. Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage AR, Sutton G, Kelley JM, Fritchman RD, et al. (1995) The minimal gene complement of Mycoplasma genitalium. Science 270:397-403
3. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty DA, Merrick JM, et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496-512
4. Makarova KS, Aravind L, Galperin MY, Grishin NV, Tatusov RL, Wolf YI, Koonin EV (2003) Comparative genomics of the archaea (euryarchaeota): Evolution of conserved protein families, the stable core, and the variable shell. Genome Res 9:608-628
5. Nesbø CL, Boucher Y, Doolittle WF (2001) Defining the core of non-transferable prokaryotic genes: The euryarchaeal core. Mol Evol 53:340-350
6. Harris JK, Kelley JT, Spiegelman GB, Pace NR (2003) The genetic core of the universal ancestor. Genome Res 13:407-412
7. Brown JR, Douady CJ, Italia MJ, Marshall WE, Stanhope MJ (2001) Universal trees based on large combined protein sequence data sets. Nat Genet 28:281-285
8. Koonin EV (2003) Comparative genomics, minimal gene sets and the last common ancestor. Nat Rev Microbiol 1:127-136
9. Charlebois RL, Doolittle WF (2004) Computing prokaryotic gene ubiquity: Rescuing the core from extinction. Genome Res 14:2469-2477
10. Itaya M (1995) An estimation of the minimal genome size required for life. FEBS Lett 362:257-260
11. Kobayashi K, Ehrlich SD, Albertini A, Amati G, Anderson KK, Arnaud M, Asai K, Ashikaga S, Aymerich S, Bessieres P, et al. (2003) Essential Bacillus subtilis genes. Proc Natl Acad Sci USA 100:4678-4683
12. Hutchison CA, Peterson Gill SN, Cline RT, White O, Fraser CM, Smith HO, Venter JC (1999) Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286:2165-2169
13. Glass JI, Assad-Garcia N, Alperovich N, Yooseph S, Lewis MR, Maruf M, Hutchison III CA, Smith HO, Venter JC (2006) Essential genes of a minimal bacterium. Proc Natl Acad Sci USA 103:425-430
14. Akerley BJ, Rubin EJ, Novick VL, Amaya K, Judson N, Mekalanos JJ (2002) A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae. Proc Natl Acad Sci USA 99:966-971
15. Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, et al. (2003) Experimental determination and system level analysis of essential genes in Escherichia coli MG 1655. J Bacteriol 185:5673-5684
16. Hashimoto M, Ichimura T, Mizoguchi H, Tanaka K, Fujimitsuk, Keyamura K, Ote T, Yamakava T, Yamazaki Y, Mori H, Katayama MS, Kato T (2005) Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome. Mol Microbiol 55:137
17. Salama NR, et al. (2004) Global transposon mutagenesis and essential gene analysis of Helicobacter pylori. J Bacteriol 186:7926-7935
18. Ji Y, et al. (2001) Identification of critical staphylococcal genes using conditional phenotypes generated by antisense RNA. Science 293:2266-2269
19. Forsyth RA, et al. (2002) A genome-wide strategy for the identification of essential genes in Staphylococcus aureus. Mol Microbiol 43:1387-1400
20. Thanassi JA, et al. (2002) Identification of 113 conserved essential genes using a high-throughput gene disruption system in Streptococcus pneumoniae. Nucleic Acids Res 30:3152-3162
21. Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, Andre B, Bangham R, Benito R, Boeke JD, Bussey H, et al. (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285:901-906
22. Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B, et al. (2002) Functional of the Saccharomyces cerevisiae genome. Nature 418:387-391
23. Kamath RS, Fraser AG, Dong Y, Poulin G, Durbin R, Gotta M, Kanapin A, Le Bot N, Moreno S, Sohrmann M, et al. (2003) Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421:231-237
24. Nishi K, Dabbs ER, Schnier J (1985) DNA sequence and complementation analysis of a mutation in the rplX gene from Escherichia coli leading to loss of ribosomal protein L24. J Bacteriol 163:890-894
25. Gerdes SY, Scholle MD, D'Souza M, Bernal MV, Baev A, Farrell M, Kurnasov OV, Daugherty MD, Mseeh F, Polanuger BM (2002) From genetic footprinting to Antimicrobial drug targets: Examples in cofactor biosynthetic pathways. J Bacteriol 184:4555-4572
26. Grantham R, Gautier C, Gouy M, Mercier R, Pave A (1980) Codon catalog usage and the genome hypothesis. Nucleic Acids Res 8:r49-r62
27. Sharp PM, Li W-H (1987) The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acid Research 15:1281-1295
28. Carbone A, Zinovyev F, Képés F (2003) Codon Adaptation Index as a measure of dominating codon bias. Bioinformatics 19:2005-2015
29. Carbone A, Madden R (2005) Insights on the evolution of metabolic networks of unicellular translationally biased organisms from transcriptomic data and sequence analysis. J Mol Evol 61:456-469
30. Carbone A, Képés F, Zinovyev A (2004) Codon bias signatures, organisation of microorganisms in codon space and lifestyle. Mol Biol Evol 22:547-561
31. Fang G, Rocha E, Danchin A (2005) How essential are nonessential genes? Mol Biol Evol 22:2147-2156
32. Gygi SP, Rochon Y, Franza BR, Aebersold R (1999) Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 19:1720-1730
33. Daubin V, Gouy M, Perriuere G (2002) A phylogenomic approach to bacterial phylogeny: Evidence of a core of genes sharing a common history. Genome Res 12:1080-1090
34. Lerat E, Daubin V, Moran NA (2003) From gene trees to organismal phylogeny in prokaryotes: The case of the γ-proteobacteria. PLoS Biol 1:E19
35. Kreil PD, Ouzounis CA (2001) Identification of thermophilic species by the amino-acids composition deduced from their genomes. Nucleic Acids Res 29:1608-1615
36. Lynn DJ, Singer GA, Hickey DA (2002) Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res 30:4272-4277
37. Tekaia F, Yeramian E, Dujon B (2002) Amino acid composition of genomes, lifestyles of organisms, and evolutionary trends: A global picture with correspondence analysis. Gene 297:51-60
38. Sharp PM, Bailes E, Grocock RJ, Peden JF, Sockett RE (2005) Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res 33:1141-1153
39. Venter JC, Levy S, Stockwell T, Remington K, Halpern A (2003) A massive parallelism, randomness and genomic advances. Nature Genetics 33:219-227
40. Zimmer C (2003) Genomics. Tinker, tailor: Can Venter stitch together a genome from scratch? Science 299:1006-1007
41. Smith HO, Hutchison CA III, Pfannkoch C, Venter C (2003) Generating a synthetic genome by whole genome assembly: AX174 bacteriophage from synthetic oligonucleotides. Proc Natl Acad Sci USA 100:15440-15445
42. Rocha EP, Matic I, Taddei F (2002) Over-representation of repeats in stress response genes: A strategy to increase versatility under stressful conditions? Nucleic Acids Res 30:1886-1894
43. Koonin EV (2000) How many genes can make a cell: The minimal-gene-set concept. Annu Rev Genomics Hum Genet 1:99-116
44. Galagan JE, Nusbaum C, Roy A, Endrizzi MG, Macdonald P, FitzHugh W, Calvo S, Engels R, Smirnov S, Atnoor D, et al. (2002) The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res 12:532-542
45. Cohen GN, Barbe V, Flament D, Galperin M, Heilig R, Lecompte O, Poch O, Prieur D, Querellou J, Ripp R, et al. (2003) An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi. Mol Microbiol 47:1495-1512
46. Silva PJ, van den Ban EC, Wassink H, de Haaker HCB , Robb FT, Hagen WR (2000) Enzymes of hydrogen metabolism in Pyrococcus furiosus. Eur J Biochem 267:6541-6551
47. Schut GJ, Zhou J, Adams MW (2001) DNA microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus: Evidence for a new type of sulfur-reducing enzyme complex. J Bacteriol 183:7027-7036
48. Ward DE, Kengen SW, Van der Oost J, De Vos WM (2000) Purification and characterization of the alanine aminotransferase from the hyperthermophilic Archaeon Pyrococcus furiosus and its role in alanine production. J Bacteriol 182:2559-2566
49. Ajdić D, McShan WM, McLaughlin RE, Savic G, Chang J, Carson MB, Primeaux C, Tian R, Kenton S, Jia H, et al. (2002) Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen. Proc Natl Acad Sci USA 99:14434-14439
50. Illades-Aguiar B, Setlow P (1994) Studies of the processing of the protease which initiates degradation of small, acid-soluble proteins during germination of spores of Bacillus species. J Bacteriol 176:2788-2795
51. Gil R, Sabater-Muoz B, Latorre A, Silva FJ, Moya A (2002) Extreme genome reduction in Buchnera spp.: Toward the minimal genome needed for symbiotic life. Proc Natl Acad Sci USA 99:4454-4458
52. Akman L, Yamashita A, Watanabe H, Oshima K, Shiba T, Hattori M, Aksoy S (2002) Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia. Nature Genet 32:402-407
53. van Ham RCHJ , Kamerbeek J, Palacios C, Rausell C, Abascal F, Bastolla U, Fernández JM, Jiménez L, Postigo M, Silva FJ, Tamames J, Viguera E, Latorre A, Valencia A, Morán F, Moya A (2003) Reductive genome evolution in Buchnera aphidicola. Proc Natl Acad Sci USA 100:581-586
54. Zientz E, Dandekar T, Gross R (2004) Metabolic interdependence of obligate intracellular bacteria and their insect hosts. Microbiol Mol Biol Rev 68:745-770
55. Koonin EV, Mushegian AR, Galperin MY, Walker DR (1997) Comparison of archaeal and bacterial genomes: Computer analysis of protein sequences predicts novel functions and suggests a chimeric origin of the archaea. Mol Microbiol 25:619-637