Causes of insertion sequences abundance in prokaryotic genomes

Molecular Biology and Evolution

Volumn 24, Issue 4, 2007, Pages 969-981

  Touchon, Marie ^a,b   Rocha, Eduardo P C ^a,b  

^a INSTITUT PASTEUR   (France)

^b SORBONNE UNIVERSITÉ   (France)

Author keywords

Genome dynamics; Genome size; Growth; Transposable elements; Virulence

Indexed keywords

ACTINOBACTERIA; ALPHAPROTEOBACTERIA; ARCHAEBACTERIUM; ARTICLE; BETAPROTEOBACTERIA; CONTROLLED STUDY; DELTAPROTEOBACTERIA; DNA TRANSPOSITION; EPSILONPROTEOBACTERIA; FIRMICUTES; GAMMAPROTEOBACTERIA; GENE INSERTION SEQUENCE; GENE REPLICATION; GENE SEQUENCE; GENE TRANSFER; GENOME; GENOME SIZE; MOLECULAR EVOLUTION; MOLLICUTES; NONHUMAN; PATHOGENICITY; PREDICTOR VARIABLE; PROKARYOTE; SPIROCHETE;

COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; DNA TRANSPOSABLE ELEMENTS; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENOME, ARCHAEAL; GENOME, BACTERIAL; HUMANS; MUTAGENESIS, INSERTIONAL; PROKARYOTIC CELLS; RNA, RIBOSOMAL, 16S; SELECTION (GENETICS);

PROKARYOTA;

EID: 34047240364     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msm014     Document Type: Article

References (79)

1. Alokam S, Liu SL, Said K, Sanderson KE. 2002. Inversions over the terminus region in Salmonella and Escherichia coli: IS200s as the sites of homologous recombination inverting the chromosome of Salmonella enterica serovar typhi. J Bacteriol. 184:6190-6197.
2. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H. 2006. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol. 2:0008.
3. Baquero F. 2004. From pieces to patterns: evolutionary engineering in bacterial pathogens. Nat Rev Microbiol. 2:510-518.
4. Bentley SD, Parkhill J. 2004. Comparative genomic structure of prokaryotes. Annu Rev Genet. 38:771-791.
5. Blot M. 1994. Transposable elements and adaptation of host bacteria. Genetica. 93:5-12.
6. Bonnard G, Vincent F, Otten L. 1989. Sequence and distribution of IS866, a novel T region-associated insertion sequence from Agrobacterium tumefaciens. Plasmid. 22:70-81.
7. Boutoille D, Corvec S, Caroff N, Giraudeau C, Espaze E, Caillon J, Plesiat P, Reynaud A. 2004. Detection of an IS21 insertion sequence in the mexR gene of Pseudomonas aeruginosa increasing beta-lactam resistance. FEMS Microbiol Lett. 230:143-146.
8. Buchrieser C, Glaser P, Rusniok C, Nedjari H, D'Hauteville H, Kunst F, Sansonetti P, Parsot C. 2000. The virulence plasmid pWR100 and the repertoire of proteins secreted by the type III secretion apparatus of Shigella flexneri. Mol Microbiol. 38:760-771.
9. Canchaya C, Fournous G, Brussow H. 2004. The impact of prophages on bacterial chromosomes. Mol Microbiol. 53:9-18.
10. Capy P, Gasperi G, Biémont C, Bazin C. 2000. Stress and transposable elements: co-evolution of useful parasites? Heredity. 85:101-106.
11. Casjens S. 1998. The diverse and dynamic structure of bacterial genomes. Annu Rev Genet. 32:339-377.
12. Casjens S. 2003. Prophages and bacterial genomics: what have we learned so far? Mol Microbiol. 49:277-300.
13. Chain PS, Carniel E, Larimer FW, et al. 2004. Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc Natl Acad Sci USA. 101:13826-13831.
14. Chao L, Vargas C, Spear BB, Cox EC. 1983. Transposable elements as mutator genes in evolution. Nature. 303:633-635.
15. Charlesworth B, Charlesworth D. 1983. The population dynamics of transposable elements. Genet Res. 42:1-27.
16. Condit R, Stewart FM, Levin BR. 1988. The population biology of bacterial transposons: a priori conditions for maintenance as parasitic DNA. Am Nat. 132:129-147.
17. Cordaux R, Udit S, Batzer MA, Feschotte C. 2006. Birth of a chimeric primate gene by capture of the transposase gene from a mobile element. Proc Natl Acad Sci USA. 103:8101-8106.
18. Daniels SB, Peterson KR, Strausbaugh LD, Kidwell MG, Chovnick A. 1990. Evidence for horizontal transmission of the P transposable element between Drosophila species. Genetics. 124:339-355.
19. Deng W, Burland V, Plunkett G 3rd, et al. 2002. Genome sequence of Yersinia pestis KIM. J Bacteriol. 184:4601-4611.
20. Doolittle WF, Sapienza C. 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature. 284:601-603.
21. Draper GC, Gober JW. 2002. Bacterial chromosome segregation. Annu Rev Microbiol. 56:567-597.
22. Dufresne A, Garczarek L, Partensky F. 2005. Accelerated evolution associated with genome reduction in a free-living prokaryote. Genome Biol. 6:R14.
23. Fang G, Rocha EPC, Danchin A. 2005. How essential are nonessential genes? Mol Biol Evol. 22:2147-2156.
24. Finlay BB, Falkow S. 1997. Common themes in microbial pathogenicity revisited. Microbiol Mol Biol Rev. 61:136-169.
25. Frost LS, Leplae R, Summers AO, Toussaint A. 2005. Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol. 3:722-732.
26. Garcia-Vallve S, Guzman E, Montero MA, Romeu A. 2003. HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Res. 31:187-189.
27. Gray YHM. 2000. It takes two transposons to tango. Trends Genet. 16:461-468.
28. Gueguen E, Rousseau P, Duval-Valentin G, Chandler M. 2006. Truncated forms of IS911 transposase downregulate transposition. Mol Microbiol. 62:1102-1116.
29. Hall BG. 1999. Transposable elements as activators of cryptic genes in E. coli. Genetica. 107:181-187.
30. Hallet B, Rezsohazy R, Mahillon J, Delcour J. 1994. IS231A insertion specificity: consensus sequence and DNA bending at the target site. Mol Microbiol. 14:131-139.
31. Han CG, Shiga Y, Tobe T, Sasakawa C, Ohtsubo E. 2001. Structural and functional characterization of IS679 and IS66-family elements. J Bacteriol. 183:4296-4304.
32. Hartl DL, Sawyer SA. 1988. Why do unrelated insertion sequences occur together in the genome of Escherichia coli? Genetics. 118:537-541.
33. Istock CA, Duncan KE, Ferguson N, Zhou X. 1992. Sexuality in a natural population of bacteria-Bacillus subtilis challenges the clonal paradigm. Mol Ecol. 1:95-103.
34. Jin Q, Yuan Z, Xu J, et al. 2002. Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res. 30:4432-4441.
35. Kidwell MG, Lisch DR. 2001. Transposable elements, parasitic DNA and genome evolution. Evolution. 55:1-24.
36. Kobayashi K, Ehrlich SD, Albertini A, et al. 2003. Essential Bacillus subtilis genes. Proc Natl Acad Sci USA. 100:4678-4683.
37. Kolsto A-B. 1997. Dynamic bacterial genome organization. Mol Microbiol. 24:241-248.
38. Koonin EV. 2003. Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat Rev Microbiol. 1:127-136.
39. Kothapalli S, Nair S, Alokam S, Pang T, Khakhria R, Woodward D, Johnson W, Stocker BA, Sanderson KE, Liu SL. 2005. Diversity of genome structure in Salmonella enterica serovar Typhi populations. J Bacteriol. 187:2638-2650.
40. Kunst F, Ogasawara N, Moszer I, et al. 1997. The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature. 390:249-256.
41. Kunze ZM, Wall S, Appelberg R, Silva MT, Portaels F, McFadden JJ. 1991. IS901, a new member of a widespread class of atypical insertion sequences, is associated with pathogenicity in Mycobacterium avium. Mol Microbiol. 5:2265-2272.
42. Lander ES, Linton LM, Birren B, et al. 2001. Initial sequencing and analysis of the human genome. Nature. 409:860-921.
43. Lawrence JG, Hendrix RW, Casjens S. 2001. Where are the pseudogenes in bacterial genomes? Trends Microbiol. 9:535-540.
44. Lawrence JG, Ochman H, Hartl DL. 1992. The evolution of insertion sequences within enteric bacteria. Genetics. 131:9-20.
45. Lichter A, Manulis S, Valinsky L, Karniol B, Barash I. 1996. IS1327, a new insertion-like element in the pathogenicity-associated plasmid of Erwinia herbicola pv. gypsophilae. Mol Plant Microbe Interact. 9:98-104.
46. Machida C, Machida Y. 1989. Regulation of IS1 transposition by the insA gene product. J Mol Biol. 208:567-574.
47. Machida Y, Sakurai M, Kiyokawa S, Ubasawa A, Suzuki Y, Ikeda JE. 1984. Nucleotide sequence of the insertion sequence found in the T-DNA region of mutant Ti plasmid pTiA66 and distribution of its homologues in octopine Ti plasmid. Proc Natl Acad Sci USA. 81:7495-7499.
48. Mahillon J, Chandler M. 1998. Insertion sequences. Microbiol Mol Biol Rev. 62:725-774.
49. Mira A, Ochman H, Moran NA. 2001. Deletional bias and the evolution of bacterial genomes. Trends Genet. 17:589-596.
50. Mira A, Pushker R, Rodriguez-Valera F. 2006. The Neolithic revolution of bacterial genomes. Trends Microbiol. 14:200-206.
51. Moran NA, Plague GR. 2004. Genomic changes following host restriction in bacteria. Curr Opin Genet Dev. 14:627-633.
52. Moszer I, Rocha EPC, Danchin A. 1999. Codon usage and lateral gene transfer in Bacillus subtilis. Curr Opin Microbiol. 2:524-528.
53. Naas T, Blot M, Fitch WM, Arber W. 1995. Dynamics of IS-related genetic rearrangements in resting Escherichia coli K-12. Mol Biol Evol. 12:198-207.
54. Nagai T, Phan Tran LS, Inatsu Y, Itoh Y. 2000. A new IS4 family insertion sequence, IS4Bsu1, responsible for genetic instability of poly-gamma-glutamic acid production in Bacillus subtilis. J Bacteriol. 182:2387-2392.
55. Nagy Z, Chandler M. 2004. Regulation of transposition in bacteria. Res Microbiol. 155:387-398.
56. Nuzhdin SV. 1999. Sure facts, speculations, and open questions about the evolution of transposable element copy number. Genetica. 107:129-137.
57. Orgel LE, Crick FHC. 1980. Selfish DNA: the ultimate parasite. Nature. 284:604-607.
58. Papadopoulos D, Schneider D, Meier-Eiss J, Arber W, Lenski RE, Blot M. 1999. Genomic evolution during a 10,000-generation experiment with bacteria. Proc Natl Acad Sci USA. 96:3807-3812.
59. Parkhill J, Sebaihia M, Preston A, et al. 2003. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat Genet. 35:32-40.
60. Parkhill J, Wren BW, Thomson NR, et al. 2001. Genome sequence of Yersinia pestis, the causative agent of plague. Nature. 413:523-527.
61. Petrov DA, Aminetzach YT, Davis JC, Bensasson D, Hirsh AE. 2003. Size matters: non-LTR retrotransposable elements and ectopic recombination in Drosophila. Mol Biol Evol. 20:880-892.
62. Redder P, Garrett RA. 2006. Mutations and rearrangements in the genome of Sulfolobus solfataricus P2. J Bacteriol. 188:4198-4206.
63. Rocha EPC. 2003a. An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: from duplications to genome reduction. Genome Res. 13:1123-1132.
64. Rocha EPC. 2003b. DNA repeats lead to the accelerated loss of gene order in Bacteria. Trends Genet. 19:600-604.
65. Rocha EPC. 2004. Order and disorder in bacterial genomes. Curr Opin Microbiol. 7:519-527.
66. Rocha EPC. 2006. Inference and analysis of the relative stability of bacterial chromosomes. Mol Biol Evol. 23:513-522.
67. Schmid-Appert M, Zoller K, Traber H, Vuilleumier S, Leisinger T. 1997. Association of newly discovered IS elements with the dichloromethane utilization genes of methylotrophic bacteria. Microbiology. 143:2557-2567.
68. Schmidt HA, Strimmer K, Vingron M, von Haeseler A. 2002. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics. 18:502-504.
69. Schneider D, Lenski RE. 2004. Dynamics of insertion sequence elements during experimental evolution of bacteria. Res Microbiol. 155:319-327.
70. Shapiro JA. 1999a. Genome system architecture and natural genetic engineering in evolution. Ann N Y Acad Sci. 870:23-35.
71. Shapiro JA. 1999b. Transposable elements as the key to a 21st century view of evolution. Genetica. 107:171-179.
72. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. 2006. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 34:D32-D36.
73. Syvanen M. 1998. Insertion sequences and their evolutionary role. In: Weinstock GM, editor. Bacterial genomes. New York: Chapman & Hall. p. 213-220.
74. Volff JN. 2006. Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes. Bioessays. 28:913-922.
75. Wagner A. 2006. Periodic extinctions of transposable elements in bacterial lineages: evidence from intragenomic variation in multiple genomes. Mol Biol Evol. 23:723-733.
76. Wei J, Goldberg MB, Burland V, et al. 2003. Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect Immun. 71:2775-2786.
77. Weinbauer MG. 2004. Ecology of prokaryotic viruses. FEMS Microbiol Rev. 28:127-181.
78. Yang F, Yang J, Zhang X, et al. 2005. Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res. 33:6445-6458.
79. Zerbib D, Prentki P, Gamas P, Freund E, Galas DJ, Chandler M. 1990. Functional organization of the ends of IS1: specific binding site for an IS 1-encoded protein. Mol Microbiol. 4:1477-1486.