Large-scale comparative genomic ranking of taxonomically restricted genes (TRGs) in bacterial and archaeal genomes

PLoS ONE

Volumn 2, Issue 3, 2007, Pages

  Wilson, Gareth A ^a   Fell, Edward J ^b   Lilley, Andrew K ^a   Field, Dawn ^a  

^a CENTRE FOR ECOLOGY AND HYDROLOGY   (United Kingdom)

^b University of Bath   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL PROTEIN; BACTERIAL PROTEIN; TAXONOMICALLY RESTRICTED GENE; UNCLASSIFIED DRUG; PROTEOME;

ARTICLE; BACTERIAL GENETICS; BACTERIAL GENOME; CONTROLLED STUDY; GC RICH SEQUENCE; MICROBIAL COMMUNITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PROTEIN FUNCTION; QUALITY INDEX FOR PREDICTED PROTEINS; SCORING SYSTEM; SEQUENCE HOMOLOGY; TAXONOMIC RANK; TAXONOMY; ARCHAEAL GENOME; ARCHAEBACTERIUM; BACTERIUM; CLASSIFICATION; COMPARATIVE GENOMIC HYBRIDIZATION; ESCHERICHIA COLI K 12; GENETICS; METHODOLOGY; STANDARD;

ARCHAEA; BACTERIA (MICROORGANISMS);

ARCHAEA; ARCHAEAL PROTEINS; BACTERIA; BACTERIAL PROTEINS; COMPARATIVE GENOMIC HYBRIDIZATION; ESCHERICHIA COLI K12; GENOME, ARCHAEAL; GENOME, BACTERIAL; PROTEOME;

EID: 36849068613     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0000324     Document Type: Article

References (52)

1. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4: 41.
2. Charlebois RL, Doolittle WF (2004) Computing prokaryotic gene ubiquity: rescuing the core from extinction. Genome Res 14: 2469-2477.
3. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, et al. (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311: 1283-1287.
4. Wilson GA, Bertrand N, Patel Y, Hughes JB, Feil EJ, et al. (2005) Orphans as taxonomically restricted and ecologically important genes. Microbiology 151: 2499-2501.
5. Daubin V, Ochman H (2004) Bacterial Genomes as new gene homes: The genealogy of ORFans in E-coli. Genome Research 14: 1036-1042.
6. Skovgaard M, Jensen LJ, Brunak S, Ussery D, Krogh A (2001) On the total number of genes and their length distribution in complete microbial genomes. Trends in Genetics 17: 425-428.
7. Kawarabayasi Y, Hino Y, Horikawa H, Yamazaki S, Haikawa Y, et al. (1999) Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. DNA Res 6: 83-101, 145-152.
8. Fukuchi S, Nishikawa K (2004) Estimation of the number of authentic orphan genes in bacterial genomes. DNA Res 11: 219-231, 311-313.
9. Ussery DW, Hallin PF (2004) Genome Update: annotation quality in sequenced microbial genomes. Microbiology 150: 2015-2017.
10. Siew N, Fischer D (2003) Twenty thousand ORFan microbial protein families for the biologist? Structure 11: 7-9.
11. Martiny JBH, Field D (2005) Ecological Perspectives on our complete genome collection. Ecology Letters 8: 1334-1345.
12. Alimi JP, Poirot O, Lopez F, Claverie JM (2000) Reverse transcriptase-polymerase chain reaction validation of 25 "orphan" genes from Escherichia coli K-12 MG1655. Genome Research 10: 959-966.
13. Kolker E, Makarova KS, Shabalina S, Picone AF, Purvine S, et al. (2004) Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae. Nucleic Acids Res 32: 2353-2361.
14. Shmuely H, Dinitz E, Dahan I, Eichler J, Fischer D, et al. (2004) Poorly conserved ORFs in the genome of the archaea Halobacterium sp NRC-1 correspond to expressed proteins. Bioinformatics 20: 1248-1253.
15. Ruby EG, Urbanowski M, Campbell J, Dunn A, Faini M, et al. (2005) Complete genome sequence of Vibrio fischeri: a symbiotic bacterium with pathogenic congeners. Proc Natl Acad Sci U S A 102: 3004-3009.
16. Waldor MK, Mekalanos JJ (1996) Lysogenic conversion by a filamentous phage encoding cholera toxin. Science 272: 1910-1914.
17. Manning PA (1997) The tcp gene cluster of Vibrio cholerae. Gene 192: 63-70.
18. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, et al. (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A 102: 13950-13955.
19. Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R (2005) The microbial pan-genome. Curr Opin Genet Dev 15: 589-594.
20. Kosuge T, Abe T, Okido T, Tanaka N, Hirahata M, et al. (2006) Exploration and Grading of Possible Genes from 183 Bacterial Strains by a Common Protocol to Identification of New Genes: Gene Trek in Prokaryote Space (GTPS). DNA Res 13: 13.
21. Altschul SF, Boguski MS, Gish W, Wootton JC (1994) Issues in searching molecular sequence databases. Nat Genet 6: 119-129.
22. Navarre WW, Porwollik S, Wang Y, McClelland M, Rosen H, et al. (2006) Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella. Science 313: 236-238.
23. Akashi H, Gojobori T (2002) Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc Natl Acad Sci U S A 99: 3695-3700.
24. Heizer EM Jr, Raiford DW, Raymer ML, Doom TE, Miller RV, et al. (2006) Amino acid cost and codon-usage biases in 6 prokaryotic genomes: a whole-genome analysis. Mol Biol Evol 23: 1670-1680.
25. Zheng Y, Anton BP, Roberts RJ, Kasif S (2005) Phylogenetic detection of conserved gene clusters in microbial genomes. BMC Bioinformatics 6: 243.
26. Yin Y, Fischer D (2006) On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer. BMC Evol Biol 6: 63.
27. Alm EJ, Huang KH, Price MN, Koche RP, Keller K, et al. (2005) The MicrobesOnline Web site for comparative genomics. Genome Res 15: 1015-1022.
28. Gutierrez-Rios RM, Rosenblueth DA, Loza JA, Huerta AM, Glasner JD, et al. (2003) Regulatory network of Escherichia coli: consistency between literature knowledge and microarray profiles. Genome Res 13: 2435-2443.
29. Kang Y, Weber KD, Qiu Y, Kiley PJ, Blattner FR (2005) Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function. J Bacteriol 187: 1135-1160.
30. Courcelle J, Khodursky A, Peter B, Brown PO, Hanawalt PC (2001) Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli. Genetics 158: 41-64.
31. Khodursky AB, Peter BJ, Cozzarelli NR, Botstein D, Brown PO, et al. (2000) DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. Proc Natl Acad Sci U S A 97: 12170-12175.
32. Corbin RW, Paliy O, Yang F, Shabanowitz J, Platt M, et al. (2003) Toward a protein profile of Escherichia coli: comparison to its transcription profile. Proc Natl Acad Sci U S A 100: 9232-9237.
33. Gevaert K, Van Damme J, Goethals M, Thomas GR, Hoorelbeke B, et al. (2002) Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins. Mol Cell Proteomics 1: 896-903.
34. Taoka M, Yamauchi Y, Shinkawa T, Kaji H, Motohashi W, et al. (2004) Only a small subset of the horizontally transferred chromosomal genes in Escherichia coli are translated into proteins. Mol Cell Proteomics 3: 780-787.
35. Roberts RJ (2004) Identifying protein function-a call for community action. PLoS Biol 2: E42.
36. Roberts RJ, Karp P, Kasif S, Linn S, Buckley MR (2005) An Experimental Approach to Genome Annotation. Critical Issues Colloquia Report, American Society of Microbiology.
37. Galperin MY, Koonin EV (2004) 'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res 32: 5452-5463. Print 2004.
38. Nei M (2005) Selectionism and neutralism in molecular evolution. Mol Biol Evol 22: 2318-2342.
39. Hurst LD, Feil EJ, Rocha EP (2006) Protein evolution: causes of trends in amino-acid gain and loss. Nature 442: E11-12; discussion E12.
40. Petrov DA, Hartl DL (1999) Patterns of nucleotide substitution in Drosophila and mammalian genomes. Proc Natl Acad Sci U S A 96: 1475-1479.
41. Ochman H (2003) Neutral mutations and neutral substitutions in bacterial genomes. Mol Biol Evol 20: 2091-2096.
42. Foerstner KU, von Mering C, Hooper SD, Bork P (2005) Environments shape the nucleotide composition of genomes. EMBO Rep 6: 1208-1213.
43. Wernegreen JJ (2002) Genome evolution in bacterial endosymbionts of insects. Nature Review Genetics 3: 850-861.
44. Galperin MY, Kolker E (2006) New metrics for comparative genomics. Curr Opin Biotechnol 17: 440-447.
45. Amiri H, Davids W, Andersson SG (2003) Birth and death of orphan genes in Rickettsia. Mol Biol Evol 20: 1575-1587.
46. von Mering C, L JJ, Kuhn M, Chaffron S, Doerks T, et al. (2006) STRING 7 - recent developments in the integration and prediction of protein interactions. Nucleic Acids Res 10: 10.
47. Romine MF, Elias DA, Monroe ME, Auberry K, Fang R, et al. (2004) Validation of Shewanella oneidensis MR-1 small proteins by AMT tag-based proteome analysis. Omics 8: 239-254.
48. Kolker E, Picone AF, Galperin MY, Romine MF, Higdon R, et al. (2005) Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. Proc Natl Acad Sci U S A 102: 2099-2104.
49. Field D, Garrity GM, Gray T, Morrison N, Selengut JD, et al. (2007) Towards a richer description of our complete collection of genomes and metagenomes: the "Minimal Information about a Genome Sequence". Nature Biotechnology (in review).
50. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
51. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27: 4636-4641.
52. Misra RV, Horler RS, Reindl W, Goryanin II, Thomas GH (2005) EchoBASE: an integrated post-genomic database for Escherichia coli. Nucleic Acids Res 33: D329-333.