Theoretical methods for identifying important functional genes in bacterial genomes

Research in Microbiology

Volumn 161, Issue 1, 2010, Pages 1-8

  Gao, Junxiang ^b   Chen, Ling Ling ^a,c  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^b BEIJING UNIVERSITY OF POSTS AND TELECOMMUNICATIONS   (China)

^c SHANDONG UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

Essential genes (EGs); Highly expressed genes (HEGs); Horizontally transferred genes (HTGs); Hypothetical genes; Pathogenic bacteria

Indexed keywords

ARTICLE; BACTERIAL GENETICS; BACTERIAL GENOME; COMPUTER MODEL; COMPUTER PREDICTION; COMPUTER PROGRAM; ESSENTIAL GENE; GENE EXPRESSION; GENE FUNCTION; GENETIC IDENTIFICATION; HORIZONTAL GENE TRANSFER; MATHEMATICAL ANALYSIS; NONHUMAN; PRIORITY JOURNAL; THEORETICAL MODEL;

BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION; GENE TRANSFER, HORIZONTAL; GENES, BACTERIAL; GENES, ESSENTIAL; GENOME, BACTERIAL;

BACTERIA (MICROORGANISMS);

EID: 74649083536     PISSN: 09232508     EISSN: 17697123     Source Type: Journal    
DOI: 10.1016/j.resmic.2009.10.007     Document Type: Article

References (81)

1. Bernardini G., Arena S., Braconi D., Scaloni A., and Santucci A. Novel identification of expressed genes and functional classification of hypothetical proteins from Neisseria meningitidis serogroup A. Proteomics 7 (2007) 3342-3347
2. Bernstein J.A., Khodursky A.B., Lin P.H., Lin-Chao S., and Cohen S.N. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 9697-9702
3. Blum G., Ott M., Lischewski A., Ritter A., Imrich H., Tschape H., et al. Excision of large DNA regions termed pathogenicity islands from tRNA-specific loci in the chromosome of an Escherichia coli wild-type pathogen. Infect. Immun. 62 (1994) 606-614
4. Bork P. Powers and pitfalls in sequence analysis: the 70% hurdle. Genome Res. 10 (2000) 398-400
5. Carbone A., Zinovyev A., and Képès F. Codon adaptation index as a measure of dominating codon bias. Bioinformatics 19 (2003) 2005-2015
6. Chen L.L. Identification of genomic islands in six plant pathogens. Gene 374 (2006) 134-141
7. Chen L.L., Ma B.G., and Gao N. Reannotation of hypothetical ORFs in plant pathogen Erwinia carotovora subsp. atroseptica SCRI1043. FEBS J. 275 (2008) 198-206
8. Chiarugi D., Degano P., and Marangoni R. A computational approach to the functional screening of genomes. PLoS Comput. Biol. 3 (2007) 1801-1806
9. Collyn F., Guy L., Marceau M., Simonet M., and Roten C.A. Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics. Bioinformatics 22 (2006) 1072-1079
10. Fleischmann R.D., Adams M.D., White O., Clayton R.A., Kirkness E.F., Kerlavage A.R., et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269 (1995) 496-512
11. Fraser C.M., Gocayne J.D., White O., Adams M.D., Clayton R.A., Fleischmann R.D., et al. The minimal gene complement of Mycoplasma genitalium. Science 270 (1995) 397-403
12. Freire-Picos M.A., González-Siso M.I., Rodríguez-Belmonte E., Rodríguez-Torres A.M., Ramil E., and Cerdán M.E. Codon usage in Kluyveromyces lactis and in yeast cytochrome c-encoding genes. Gene 139 (1994) 43-49
13. Frenkel Z.M., and Trifonov E.N. From protein sequence space to elementary protein modules. Gene 408 (2008) 64-71
14. Fu Q.S., Li F., and Chen L.L. Gene expression analysis of six GC-rich Gram-negative phytopathogens. Biochem. Biophys. Res. Commun. 332 (2005) 380-387
15. Garcia-Vallvé S., Romeu A., and Palau J. Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res. 10 (2000) 1719-1725
16. Gil R., Sabater-Muñoz B., Latorre A., Silva F.J., and Moya A. Extreme genome reduction in Buchnera spp.: toward the minimal genome needed for symbiotic life. Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 4454-4458
17. Gil R., Silva F.J., Peretó J., and Moya A. Determination of the core of a minimal bacterial gene set. Microbiol. Mol. Biol. Rev. 68 (2004) 518-537
18. Gouy M., and Gautier C. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 10 (1982) 7055-7074
19. Gribskov M., Devereux J., and Burgess R.R. The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression. Nucleic Acids Res. 12 (1984) 539-549
20. Grigoriev A. Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res. 26 (1998) 2286-2290
21. Grote A., Hiller K., Scheer M., Munch R., Nortemann B., Hempel D.C., et al. JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Res. 33 (2005) W526-W531
22. Gustafson A.M., Snitkin E.S., Parker S.C., DeLisi C., and Kasif S. Towards the identification of essential genes using targeted genome sequencing and comparative analysis. BMC Genomics 7 (2006) 265
23. Guy L. Identification and characterization of pathogenicity and other genomic islands using base composition analyses. Future Microbiol. 1 (2006) 309-316
24. Gygi S.P., Rochon Y., Franza B.R., and Aebersold R. Correlation between protein and mRNA abundance in yeast. Mol. Cell Biol. 19 (1999) 1720-1730
25. Hacker J., and Kaper J.B. Pathogenicity islands and the evolution of microbes. Annu. Rev. Microbiol. 54 (2000) 641-679
26. Hentschel U., and Hacker J. Pathogenicity islands: the tip of the iceberg. Microbes Infect. 3 (2001) 545-548
27. Hentschel U., Steinert M., and Hacker J. Common molecular mechanisms of symbiosis and pathogenesis. Trends Microbiol. 8 (2000) 226-231
28. Hooper S.D., and Berg O.G. Detection of genes with atypical nucleotide sequence in microbial genomes. J. Mol. Evol. 54 (2002) 365-375
29. Hsiao W., Wan I., Jones S.J., and Brinkman F.S.L. IslandPath: aiding detection of genomic islands in prokaryotes. Bioinformatics 19 (2003) 418-420
30. Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 2 (1985) 13-34
31. Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J. Mol. Biol. 151 (1981) 389-409
32. Karlin S., Barnett M.J., Campbell A.M., Fisher R.F., and Mrázek J. Predicting gene expression levels from codon biases in alpha-proteobacterial genomes. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 7313-7318
33. Karlin S., Brocchieri L., Mrázek J., and Kaiser D. Distinguishing features of delta-proteobacterial genomes. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 11352-11357
34. Karlin S., and Mrázek J. Predicted highly expressed genes of diverse prokaryotic genomes. J. Bacteriol. 182 (2000) 5238-5250
35. Karlin S., Mrázek J., and Campbell A.M. Codon usages in different gene classes of the Escherichia coli genome. Mol. Microbiol. 29 (1998) 1341-1355
36. Karlin S., Mrázek J., Campbell A., and Kaiser D. Characterizations of highly expressed genes of four fast-growing bacteria. J. Bacteriol. 183 (2001) 5025-5040
37. Karlin S., Theriot J., and Mrázek J. Comparative analysis of gene expression among low G + C gram-positive genomes. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 6182-6187
38. Kolker E., Makarova K.S., Shabalina S., Picone A.F., Purvine S., Holzman T., et al. Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae. Nucleic Acids Res. 32 (2004) 2353-2361
39. Koonin E.V. How many genes can make a cell: the minimal-gene-set concept. Annu. Rev. Genomics Hum. Genet. 1 (2000) 99-116
40. Lan R., and Reeves P.R. Gene transfer is a major factor in bacterial evolution. Mol. Biol. Evol. 13 (1996) 47-55
41. Lio P., and Vannucci M. Finding pathogenicity islands and gene transfer events in genome data. Bioinformatics 16 (2000) 932-940
42. Ma J., Campbell A., and Karlin S. Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures. J. Bacteriol. 184 (2002) 5733-5745
43. Mantri Y., and Williams K.P. Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities. Nucleic Acids Res. 32 (2004) D55-D58
44. McLachlan A.D., Staden R., and Boswell D.R. A method for measuring the non-random bias of a codon usage table. Nucleic Acids Res. 12 (1984) 9567-9575
45. Merkl R. A survey of codon and amino acid frequency bias in microbial genomes focusing on translational efficiency. J. Mol. Evol. 57 (2003) 453-466
46. Merkl R. SIGI: score-based identification of genomic islands. BMC Bioinformatics 5 (2004) 22
47. Mrázek J., Bhaya D., Grossman A.R., and Karlin S. Highly expressed and alien genes of the Synechocystis genome. Nucleic Acids Res. 29 (2001) 1590-1601
48. Mrázek J., Spoorman A.M., and Karlin S. Genomic comparisons among gamma-proteobacteria. Environ. Microbiol. 8 (2006) 273-288
49. Mushegian A. The minimal genome concept. Curr. Opin. Genet. Dev. 9 (1999) 709-714
50. Mushegian A.R., and Koonin E.V. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. Natl. Acad. Sci. U.S.A. 93 (1996) 10268-10273
51. Nielsen P., and Krogh A. Large-scale prokaryotic gene prediction and comparison to genome annotation. Bioinformatics 21 (2005) 4322-4329
52. Ochman H., Lawrence J.G., and Groisman E.A. Lateral gene transfer and the nature of bacterial innovation. Nature 405 (2000) 299-304
53. Ou H.Y., Chen L.L., Lonnen J., Chaudhuri R.R., Thani A.B., Smith R., et al. A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria. Nucleic Acids Res. 34 (2006) e3
54. Podell S., and Gaasterland T. DarkHorse: a method for genome-wide prediction of horizontal gene transfer. Genome Biol. 8 (2007) R16
55. Ponting C.P. Issues in predicting protein function from sequence. Brief. Bioinformatics 2 (2001) 19-29
56. Pucci M.J. Use of genomics to select antibacterial targets. Biochem. Pharmacol. 71 (2006) 1066-1072
57. Ragan M.A., Harlow T.J., and Beiko R.G. Do different surrogate methods detect lateral genetic transfer events of different relative ages?. Trends Microbiol. 14 (2006) 4-8
58. Schmidt H., and Hensel M. Pathogenicity islands in bacterial pathogenesis. Clin. Microbiol. Rev. 17 (2004) 14-56
59. Sharp P.M., Bailes E., Grocock R.J., Peden J.F., and Sockett R.E. Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res. 33 (2005) 1141-1153
60. Sharp P.M., Cowe E., Higgins D.G., Shields D.C., Wolfe K.H., and Wright F. Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity. Nucleic Acids Res. 16 (1988) 8207-8211
61. Sharp P.M., and Li W.H. The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15 (1987) 1281-1295
62. Sharp P.M., Stenico M., Peden J.F., and Lloyd A.T. Codon usage: mutational bias, translational selection, or both?. Biochem. Soc. Trans. 21 (1993) 835-841
63. Strong M., Mallick P., Pellegrini M., Thompson M.J., and Eisenberg D. Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach. Genome Biol. 4 (2003) R59
64. Supek F., and Vlahovicek K. Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity. BMC Bioinformatics 6 (2005) 182
65. Tatusov R.L., Galperin M.Y., Natale D.A., and Koonin E.V. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28 (2000) 33-36
66. Tomita M. Whole-cell simulation: a grand challenge of the 21st century. Trends Biotechnol. 19 (2001) 205-210
67. Tu Q., and Ding D. Detecting pathogenicity islands and anomalous gene clusters by iterative discriminant analysis. FEMS Microbiol. Lett. 221 (2003) 269-275
68. van Passel M.W.J., Bart A., Waaijer R.J.A., Luyf A.C.M., van Kampen A.H.C., and van der Ende A. An in vitro strategy for the selective isolation of anomalous DNA from prokaryotic genomes. Nucleic Acids Res. 32 (2004) e114
69. Velculescu V.E., Zhang L., Zhou W., Vogelstein J., Basrai M.A., Bassett Jr. D.E., et al. Characterization of the yeast transcriptome. Cell 88 (1997) 243-251
70. Vernikos G.S., and Parkhill J. Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics 22 (2006) 2196-2203
71. Watson J.D., Laskowski R.A., and Thornton J.M. Predicting protein function from sequence and structural data. Curr. Opin. Struct. Biol. 15 (2005) 275-284
72. Willenbrock H., Friis C., Juncker A.S., and Ussery D.W. An environmental signature for 323 microbial genomes based on codon adaptation indices. Genome Biol. 7 (2006) R114
73. Willenbrock H., and Ussery D.W. Prediction of highly expressed genes in microbes based on chromatin accessibility. BMC Mol. Biol. 8 (2007) 11
74. Wright F. The 'effective number of codons' used in a gene. Gene 87 (1990) 23-29
75. Wu G., Nie L., and Zhang W. Predicted highly expressed genes in Nocardia farcinica and the implication for its primary metabolism and nocardial virulence. Antonie Van Leeuwenhoek 89 (2006) 135-146
76. Xu K., and Ma B.G. Comparative analysis of predicted gene expression among deep-sea genomes. Gene 397 (2007) 136-142
77. Yoon S.H., Hur C.G., Kang H.Y., Kim Y.H., Oh T.K., and Kim J.F. A computational approach for identifying pathogenicity islands in prokaryotic genomes. BMC Bioinformatics 6 (2005) 184
78. Yoon S.H., Park Y.K., Lee S., Choi D., Oh T.K., Hur C.G., et al. Towards pathogenomics: a web-based resource for pathogenicity islands. Nucleic Acids Res. 35 (2007) D395-D400
79. Zhang C.T., Wang J., and Zhang R. A novel method to calculate the G + C content of genomic DNA sequences. J. Biomol. Struct. Dyn. 19 (2001) 333-341
80. Zhang C.T., and Zhang R. Genomic islands in Rhodopseudomonas palustris. Nat. Biotechnol. 22 (2004) 1078-1079
81. Zhang R., and Zhang C.T. A systematic method to identify genomic islands and its applications in analyzing the genomes of Corynebacterium glutamicum and Vibrio vulnificus CMCP6 chromosome I. Bioinformatics 20 (2004) 612-622