Persistence drives gene clustering in bacterial genomes

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Fang, Gang ^a   Rocha, Eduardo P C ^a,b   Danchin, Antoine ^a  

^a INSTITUT PASTEUR   (France)

^b SORBONNE UNIVERSITÉ   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENETICS; BACTERIAL GENOME; GENE CLUSTER; GENE DELETION; GENE INSERTION; GENETIC ALGORITHM; GENETIC TRANSCRIPTION; NONHUMAN; OPERON; SIMULATION; ALGORITHM; BACTERIAL GENE; BACTERIUM; BIOLOGICAL MODEL; BIOLOGY; DNA REPLICATION; GENE EXPRESSION REGULATION; GENE ORDER; GENETIC DATABASE; GENETIC VARIABILITY; GENETICS; GROWTH, DEVELOPMENT AND AGING; MOLECULAR EVOLUTION; MULTIGENE FAMILY; PHYLOGENY; STATISTICS;

BACTERIA (MICROORGANISMS);

BACTERIAL DNA;

ALGORITHMS; BACTERIA; CHROMOSOMES, BACTERIAL; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA REPLICATION; DNA, BACTERIAL; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, BACTERIAL; GENE ORDER; GENES, BACTERIAL; GENOME, BACTERIAL; MODELS, GENETIC; MULTIGENE FAMILY; OPERON; PHYLOGENY; VARIATION (GENETICS);

EID: 39549098697     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-4     Document Type: Article

References (52)

1. Krawiec S Riley M Organization of the bacterial chromosome Microbiol Rev 1990, 54(4):502-539. 372791 2087223
2. Huynen MA Bork P Measuring genome evolution Proc Natl Acad Sci U S A 1998, 95(11):5849-5856. 34486 9600883 10.1073/pnas.95.11.5849
3. Tamames J Evolution of gene order conservation in prokaryotes Genome Biol 2001 2 6 RESEARCH0020 33396 11423009 10.1186/ gb-2001-2-6-research0020
4. Rocha EP Inference and analysis of the relative stability of bacterial chromosomes Mol Biol Evol 2006, 23(3):513-522. 10.1093/molbev/msj052 16280545
5. Bentley SD Parkhill J Comparative genomic structure of prokaryotes Annu Rev Genet 2004, 38:771-792. 10.1146/annurev.genet.38.072902.094318 15568993
6. Mira A Klasson L Andersson SG Microbial genome evolution: Sources of variability Curr Opin Microbiol 2002, 5(5):506-512. 10.1016/ S1369-5274(02)00358-2 12354559
7. Rocha EP DNA repeats lead to the accelerated loss of gene order in bacteria Trends Genet 2003, 19(11):600-603. 10.1016/j.tig.2003.09.011 14585609
8. Rocha EP Order and disorder in bacterial genomes Curr Opin Microbiol 2004, 7(5):519-527. 10.1016/j.mib.2004.08.006 15451508
9. Martin MJ Herrero J Mateos A Dopazo J Comparing bacterial genomes through conservation profiles Genome Res 2003, 13(5):991-998. 430882 12695324 10.1101/gr.678303
10. Nitschke P Guerdoux-Jamet P Chiapello H Faroux G Henaut C Henaut A Danchin A Indigo: A World-Wide-Web review of genomes and gene functions FEMS Microbiol Rev 1998, 22(4):207-227. 9862121
11. Overbeek R Fonstein M D'Souza M Pusch GD Maltsev N The use of gene clusters to infer functional coupling Proc Natl Acad Sci U S A 1999, 96(6):2896-2901. 15866 10077608 10.1073/pnas.96.6.2896
12. Lewis EB Pseudoallelism and gene evolution Cold Spring Harb Symp Quant Biol 1951, 16:159-174. 14942737
13. Stephens SG Possible significances of duplication in evolution Adv Genet 1951, 4:247-265. 14943679
14. Lerat E Daubin V Ochman H Moran NA Evolutionary origins of genomic repertoires in bacteria PLoS Biol 2005, 3(5):e130. 1073693 15799709 10.1371/journal.pbio.0030130
15. Lawrence JG Roth JR Selfish operons: Horizontal transfer may drive the evolution of gene clusters Genetics 1996, 143(4):1843-1860. 1207444 8844169
16. Fang G Rocha E Danchin A How essential are nonessential genes? Mol Biol Evol 2005, 22(11):2147-2156. 10.1093/molbev/msi211 16014871
17. Pal C Hurst LD Evidence against the selfish operon theory Trends Genet 2004, 20(6):232-234. 10.1016/j.tig.2004.04.001 15145575
18. Price MN Huang KH Arkin AP Alm EJ Operon formation is driven by co-regulation and not by horizontal gene transfer Genome Res 2005, 15(6):809-819. 1142471 15930492 10.1101/gr.3368805
19. Galperin MY Koonin EV Who's your neighbor? New computational approaches for functional genomics Nat Biotechnol 2000, 18(6):609-613. 10.1038/ 76443 10835597
20. Pellegrini M Marcotte EM Thompson MJ Eisenberg D Yeates TO Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles Proc Natl Acad Sci U S A 1999, 96(8):4285-4288. 16324 10200254 10.1073/pnas.96.8.4285
21. Jacob F Perrin D Sanchez C Monod J [Operon: A group of genes with the expression coordinated by an operator.] C R Hebd Seances Acad Sci 1960, 250:1727-1729. 14406329
22. Jacob F Monod J Genetic regulatory mechanisms in the synthesis of proteins J Mol Biol 1961, 3:318-356. 13718526
23. Dandekar T Snel B Huynen M Bork P Conservation of gene order: A fingerprint of proteins that physically interact Trends Biochem Sci 1998, 23(9):324-328. 10.1016/S0968-0004(98)01274-2 9787636
24. de Daruvar A Collado-Vides J Valencia A Analysis of the cellular functions of Escherichia coli operons and their conservation in Bacillus subtilis J Mol Evol 2002, 55(2):211-221. 10.1007/s00239-002-2317-1 12107597
25. Itoh T Takemoto K Mori H Gojobori T Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes Mol Biol Evol 1999, 16(3):332-346. 10331260
26. Korbel JO Jensen LJ von Mering C Bork P Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs Nat Biotechnol 2004, 22(7):911-917. 10.1038/ nbt988 15229555
27. Campillos M von Mering C Jensen LJ Bork P Identification and analysis of evolutionarily cohesive functional modules in protein networks Genome Res 2006, 16(3):374-382. 1415216 16449501 10.1101/gr.4336406
28. Che D Li G Mao F Wu H Xu Y Detecting uber-operons in prokaryotic genomes Nucleic Acids Res 2006, 34(8):2418-2427. 1458513 16682449 10.1093/nar/ gkl294
29. Lathe WC 3rd Snel B Bork P Gene context conservation of a higher order than operons Trends Biochem Sci 2000, 25(10):474-479. 10.1016/ S0968-0004(00)01663-7 11050428
30. Rogozin IB Makarova KS Murvai J Czabarka E Wolf YI Tatusov RL Szekely LA Koonin EV Connected gene neighborhoods in prokaryotic genomes Nucleic Acids Res 2002, 30(10):2212-2223. 115289 12000841 10.1093/nar/30.10.2212
31. Hashimoto M Ichimura T Mizoguchi H Tanaka K Fujimitsu K Keyamura K Ote T Yamakawa T Yamazaki Y Mori H Katayama T Kato J Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome Mol Microbiol 2005, 55(1):137-149. 10.1111/j.1365-2958.2004.04386.x 15612923
32. Huynen M Snel B Lathe W 3rd Bork P Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences Genome Res 2000, 10(8):1204-1210. 310926 10958638 10.1101/gr.10.8.1204
33. Wolf YI Rogozin IB Kondrashov AS Koonin EV Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context Genome Res 2001, 11(3):356-372. 10.1101/ gr.GR-1619R 11230160
34. Gerdes SY Scholle MD Campbell JW Balazsi G Ravasz E Daugherty MD Somera AL Kyrpides NC Anderson I Gelfand MS Bhattacharya A Kapatral V D'Souza M Baev MV Grechkin Y Mseeh F Fonstein MY Overbeek R Barabasi AL Oltvai ZN Osterman AL Experimental determination and system level analysis of essential genes in Escherichia coli MG1655 J Bacteriol 2003, 185(19):5673-5684. 193955 13129938 10.1128/JB.185.19.5673-5684.2003
35. Kobayashi K Ehrlich SD Albertini A Amati G Andersen KK Arnaud M Asai K Ashikaga S Aymerich S Bessieres P Boland F Brignell SC Bron S Bunai K Chapuis J Christiansen LC Danchin A Debarbouille M Dervyn E Deuerling E Devine K Devine SK Dreesen O Errington J Fillinger S Foster SJ Fujita Y Galizzi A Gardan R Eschevins C Fukushima T Haga K Harwood CR Hecker M Hosoya D Hullo MF Kakeshita H Karamata D Kasahara Y Kawamura F Koga K Koski P Kuwana R Imamura D Ishimaru M Ishikawa S Ishio I Le Coq D Masson A Mauel C Meima R Mellado RP Moir A Moriya S Nagakawa E Nanamiya H Nakai S Nygaard P Ogura M Ohanan T O'Reilly M O'Rourke M Pragai Z Pooley HM Rapoport G Rawlins JP Rivas LA Rivolta C Sadaie A Sadaie Y Sarvas M Sato T Saxild HH Scanlan E Schumann W Seegers JF Sekiguchi J Sekowska A Seror SJ Simon M Stragier P Studer R Takamatsu H Tanaka T Takeuchi M Thomaides HB Vagner V van Dijl JM Watabe K Wipat A Yamamoto H Yamamoto M Yamamoto Y Yamane K Yata K Yoshida K Yoshikawa H Zuber U Ogasawara N Essential Bacillus subtilis genes Proc Natl Acad Sci U S A 2003, 100(8):4678-4683. 153615 12682299 10.1073/pnas.0730515100
36. Koonin EV Galperin MY Sequence-Evolution-Function: Computational Approaches in Comparative Genomics. Norwell, Massachusetts 02061 USA, Kluwer Academic Publishers 2003
37. Nilsson AI Koskiniemi S Eriksson S Kugelberg E Hinton JC Andersson DI Bacterial genome size reduction by experimental evolution Proc Natl Acad Sci U S A 2005, 102(34):12112-12116. 1189319 16099836 10.1073/ pnas.0503654102
38. Ochman H Jones IB Evolutionary dynamics of full genome content in Escherichia coli Embo J 2000, 19(24):6637-6643. 305890 11118198 10.1093/ emboj/19.24.6637
39. Couturier E Rocha EP Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes Mol Microbiol 2006, 59(5):1506-1518. 10.1111/ j.1365-2958.2006.05046.x 16468991
40. Butland G Peregrin-Alvarez JM Li J Yang W Yang X Canadien V Starostine A Richards D Beattie B Krogan N Davey M Parkinson J Greenblatt J Emili A Interaction network containing conserved and essential protein complexes in Escherichia coli Nature 2005, 433(7025):531-537. 10.1038/nature03239 15690043
41. Fang G Ho C Qiu Y Cubas V Yu Z Cabau C Cheung F Moszer I Danchin A Specialized microbial databases for inductive exploration of microbial genome sequences BMC Genomics 2005, 6:1-14. 549560 15698474 10.1186/ 1471-2164-6-14
42. Changeux JP Danchin A Selective stabilisation of developing synapses as a mechanism for the specification of neuronal networks Nature 1976, 264(5588):705-712. 10.1038/264705a0 189195
43. D'Haeseleer P Church GM Estimating and improving protein interaction error rates Proc IEEE Comput Syst Bioinform Conf 2004, 216-223. 16448015
44. Mitra K Schaffitzel C Shaikh T Tama F Jenni S Brooks CL 3rd Ban N Frank J Structure of the E. coli protein-conducting channel bound to a translating ribosome Nature 2005, 438(7066):318-324. 1351281 16292303 10.1038/nature04133
45. International Nucleotide Sequence Database Collaboration http://www.ebi.ac.uk/genomes/
46. Tatusov RL Koonin EV Lipman DJ A genomic perspective on protein families Science 1997, 278(5338):631-637. 10.1126/science.278.5338.631 9381173
47. Zar JH Biostatistical analysis Upper Saddle River, NJ 07458, Prentice-Hall International Limited 1996
48. Jammalamadaka SR SenGupta A In Topics in Circular Statistics Singapore, World Scientific Publishing 2001
49. Ermolaeva MD Khalak HG White O Smith HO Salzberg SL Prediction of transcription terminators in bacterial genomes J Mol Biol 2000, 301(1):27-33. 10.1006/jmbi.2000.3836 10926490
50. Salgado H Moreno-Hagelsieb G Smith TF Collado-Vides J Operons in Escherichia coli: Genomic analyses and predictions Proc Natl Acad Sci U S A 2000, 97(12):6652-6657. 18690 10823905 10.1073/pnas.110147297
51. Salgado H Gama-Castro S Peralta-Gil M Diaz-Peredo E Sanchez-Solano F Santos-Zavaleta A Martinez-Flores I Jimenez-Jacinto V Bonavides-Martinez C Segura-Salazar J Martinez-Antonio A Collado-Vides J RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions Nucleic Acids Res 2006, 34: Database issue D394-7. 1347518 16381895 10.1093/nar/gkj156
52. Mclust http://www.stat.washington.edu/mclust