HOW DOES THE HORIZONTAL GENE TRANSFER IN BACTERIA OCCUR AND THAN IS IT TIED UP
Sergey V Shestakov
Ecological Genetics ›› 2007, Vol. 5 ›› Issue (2) : 12 -24.
HOW DOES THE HORIZONTAL GENE TRANSFER IN BACTERIA OCCUR AND THAN IS IT TIED UP
Horizontal gene transfer as well as mutations, ge- nomic reorganization and gene loss is one of major driving forces of speciation and evolution of bacteria. A notion of definition of "species genome" is presented. The role of various types of mobile elements in distant gene transfer is considered. The nature of barriers for suc- cessful gene transfer on the level of molecular, cell and population processes is uncovered. A special attention is paid to the contribution of different systems of recombination. Hypothesis on the decisive role of horizontal gene transfer in genetic and ecological diversification of bacteria is discussed.
| [1] |
Заварзин Г. А. Составляет ли эволюция смысл биологии/Заварзин Г. А.//Вестник РАН. -2006. -Т. 76, N6. -С. 522-543. |
| [2] |
Ильина Т. С. Суперинтегроны бактерий -источники новых генов с адаптивными функциями/Ильина Т. С.//Генетика. -2006. -Т. 42, N 11. -С. 1536-1546. |
| [3] |
Калакуцкий Л. В. Обращение с микроорганизмами: правила писаные и неписаные/Калакуцкий Л. В.//Вестник РФФИ. -2005. -N 2. -С. 35-60. |
| [4] |
Крылов В. М. Роль горизонтального переноса генов бактериофагами в возникновении патогенных бактерий/Крылов В. М.//Генетика. -2003. -Т. 39, N 5. -C. 595-620. |
| [5] |
Миндлин С. З. Происхождение, эволюция и миграция генов лекарственной устойчивости/Миндлин С. З., Петрова М. А., Басс И. А., Горленко Ж. М.//Генетика. -2006. -Т. 42, N 11. -С. 1495-1511. |
| [6] |
Прозоров А. А. Горизонтальный перенос генов у бактерий: лабораторное моделирование, природные популяции, данные геномики/Прозоров А. А.//Микробиология. -1999. -Т. 68, N 5. -С. 632-646. |
| [7] |
Шестаков С. В. Геномика патогенных бактерий/Шестаков С. В.//Вестник РАМН. -2001. -N 10. -С. 18-25. |
| [8] |
Шестаков С. В. О ранних этапах биологической эволюции с позиций геномики/Шестаков С. В.//Палеонтол. журнал. -2003. -N 6. -С. 50-57. |
| [9] |
Bapteste E. Phylogenetic reconstruction and lateral gene transfer/Bapteste E., Boucher Y., Leigh J., Doolittle W. F.//Trends Microbiol. -2004. -Vol. 12, N 9. -P. 406-411. |
| [10] |
Berg O. Evolution of microbial genomes: sequence acquisition and loss/Berg O., Kurland C. G.//Mol. Biol. Evol. -2002. -Vol. 19. -P. 2265-2276. |
| [11] |
Bordenstein S. R. Mobile DNA in obligate intracellular bacteria/Bordenstein S. R., Reznikoff W. S.//Nature Rev. Microbiol. -2005. -Vol. 3. -P. 688-699. |
| [12] |
Boucher Y. Microbial genomes: dealing with diversity/Boucher Y., Nesbo C. L., Doolittle W. F.//Current Opin. Microbiol. -2001. -Vol. 4 -P. 285-289. |
| [13] |
Brown J. R. Ancient horizontal gene transfer/Brown J. R.//Nature Rev. Genet. -2003. -Vol. 4. -P. 121 -132. |
| [14] |
Burris V. Conjugative transposons: the tip of the iceberg/Burris V., Pavlovich G., Decaris B., Guedon G.//Mol. Microbiol. -2002. -Vol. 46, N 3. -P. 601-610. |
| [15] |
Canchaya C. Phage as agents of lateral gene transfer/Canchaya C., Fomous G., Chibani-Chennoufi S. [et al.]//Current Opin. Microbiol. -2003. -Vol. 6. -P. 417-424. |
| [16] |
Chen I. DNA uptake during natural transformation/Chen I., Dubnau D.//Nature Rev. Microbiol. -2004. -Vol. 2. -P. 241-249. |
| [17] |
Chiley P. M. Distribution of the ArdA family of antirestrictiongeneonconjugative plasmids/Chiley P.M., Wilkins B. M.//Microbiology. -1995. -Vol. 141. -P. 2157-2164. |
| [18] |
Clewell D. B. Enterococcal plasmid transfer: sex pheromones, transfer origins, relaxases, and the Staphylococcus aureus issue/Clewell D. B., Francia M. V., Flannagan S. E., An F. Y.//Plasmid. -2002. -Vol. 48. -P. 2002. |
| [19] |
Daubin V. Phylogenetics and cohesion of bacterial genomes/Daubin V., Moran N. A., Ochman H.//Science. -2003. -Vol. 301. -P. 829-832. |
| [20] |
Daubin V., Legat E., Perriere G. The source of laterally transferredgenesinbacterialgenomes//GenomeBiol.-2003. -Vol. 4. -P. R57. |
| [21] |
Dionisio F. Plasmids spread very fast in heterogeneous bacterial communities/Dionisio F., Matic J., Radman M., Rodrigues O. R.//Genetics. -2002. -Vol. 162. -P. 1525-1532. |
| [22] |
Dobrindt U. Genomic islands in pathogenic and environmental microorganisms./Dobrindt U., Hochhut B., Hentschel U., Hacker J.//Nature Rev. Microbiol. -2004. -Vol. 2. -P. 414-424. |
| [23] |
Doolittle W. F. Lateral genomics/Doolittle W. F.//Trends Cell Biol. -1999. -N 9. -P. M5-M9. |
| [24] |
Feil E. J. Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenic consequences/Feil E. J., Holmes E. C., Bessen d. E. et al.//Proc. Natl. Acad. Sci. USA. -2001. -Vol. 98, N 1. -P. 182-187. |
| [25] |
Field D. Databases and software for the comparative genomic study of collection of genomes/Field D., Feil E., Wilson G.//Microbiology. -2005. -Vol. 151. -P. 2125-2132. |
| [26] |
Frost L. S. Mobile genetic elements: the agents of open source evolution/Frost L. S., Leplae R., Summers A. O., Toussiant A.//Nature Rev. Microbiol. -2005. -Vol. 3. -P. 722-732. |
| [27] |
Funchain P. Amplification of mutator cells in a population as a result of horizontal transfer/Funchain P., Yeumg A., Stewart J. et al.//J. Bacteriol. -2001. -Vol. 183. -P. 3737-3741. |
| [28] |
Gevers D. Re-evaluating prokaryotic species/Gevers D., Cohan F. M., Lawrence J. G. et al.//Nature Rev. Microbiol. -2005. -Vol. 3. -P. 733-739. |
| [29] |
Gogarten J. P. Prokaryotic evolution in light of gene transfer/Gogarten J. P., Doolitle W. F., Lawrence J. G.//Molec. Biol. Evol. -2002. Vol. 19, N 12. -P. 2226-2338. |
| [30] |
Gogarten J. P. Gorizontal gene transfer, genome innovation and evolution/Gogarten J. P., Townsend J. T.//Nature Rev. Microbiol. -2005. -Vol. 3. -P. 679-687. |
| [31] |
Gophna U. Weighted genome trees: refinements and application/Gophna U., Doolittle W. F., Charlebois R. L.//J. Bacteriol. -2005. -Vol. 187, N 4. -P. 1305-1316. |
| [32] |
Eisen J. A. Horizontal gene transfer among microbial genomes: new insights from complete genome analysis/Eisen J. A.//Current Opin. Genet. Dev. -2000. -Vol. 10. -P. 606-611. |
| [33] |
Grohmann E. Conjugative plasmid transfer in gram-positive bacteria/Grohmann E., Math G.,Espinosa M.//Microbiol. Biol. Rev. -2003. -Vol. 67. -P. 277-301. |
| [34] |
Hacker J. Pathogenecity islands and the evolution of microbes/Hacker J., Kaper J. B.//Annu Rev. Microbiol. -2000 -Vol. 54. -P. 641-679. |
| [35] |
Hacker J. Ecological fitness, genomic islands and bacterial pathogenecity/Hacker J., Corniel E.//EMBO Reports. -2001. -Vol. 2, N 5. -P. 376-381. |
| [36] |
Hanage W. P. Fuzzy species among recombinogenic bacteria/Hanage W. P., Fraser C., Spratt B. G.//BMC Biology. -2005. -Vol. 3. -P. 1-7. |
| [37] |
Holmes J. A. The gene cassette metagenome is a basic resource for bacterial genome evolution/Holmes J. A., Gilling M. R., Nield B. S.//Environ.Microbiol. -2003. -Vol. 5, N 5. -P. 383-394. |
| [38] |
Huson D. H. Phylogenetic trees based on gene content./Huson D. H., Steel M.//Bioinformatics. -2004. -Vol. 20. -P. 2044-2049. |
| [39] |
Ikeda H. Illigitimate recombination mediated by doublestrand breaks and end-joining in Escherichia coli/Ikeda H., Shiraishi K., Ogata Y.//Advan. Biophys. -2004. -Vol. 38. -P. 3-20. |
| [40] |
Jain R. Horizontal gene transfer among genomes: the complexity hypothesis/Jain R., Rivera M. C.,Lake J. A.//Proc. Natl. Acad. Sci. USA. 1999. -Vol. 96. -P. 3801-3806. |
| [41] |
Jain R. Horizontal gene transfer accelerates genome innovation and evolution/Jain R., Rivera M. C.,Moore J. E., Lake J. A.//Mol. Biol. Evol. -2003. -Vol. 20. -P. 1598-1602. |
| [42] |
Jeltsch A. Maintenance of species identity and controlling speciation of bacteria: a new function for restriction/modification systems/Jeltsch A.//Gene. -2003. -Vol. 317. -P. 13-16. |
| [43] |
Kobayashi I. Behaviour of restriction-modification systems as selfish mobile elements and their impact on genome evolution/Kobayashi I.//Nucleic Acids Res. -2001. -Vol. 29. -P. 3742-3756. |
| [44] |
Koonin E. V. Horizontal gene transfer in prokaryotes. Quantification and classification/Koonin E. V., Makarova K. S., Arvind L.//Annu. Rev. Microbiol. -2001. -Vol. 55. -P. 709-742. |
| [45] |
Kunin V. The balance of driving forces during genome evolution in prokaryotes/Kunin V., Ouzounis C. A.//Genome Res. -2003. Vol. 13. -P. 1589-1594. |
| [46] |
Kurland C. G. What tangled web: barriers to rampant horizontal gene transfer/Kurland C. G.//BioEssays. -2005. -Vol. 27. -P. 741 -747. |
| [47] |
Kurland C. G. Horizontal gene transfer: a critical view/Kurland C. G., Canback B., Berg J. G.//Proc. Natl. Acad. Sci. USA. -2003. -Vol. 100, N 17. -P. 9658-9662. |
| [48] |
Lan R. Intraspecies variation in bacterial genomes: the need for a species genome concept/Lan R., Reeves P. R.//Trends Microbiol. -2000. -Vol. 8. -P. 396-401. |
| [49] |
Lawrence J.G. Genetransfer in bacteria: speciation with out species/Lawrence J.G.//Theor. Popul. Biol. -2002.-Vol. 61. -P. 449-460. |
| [50] |
Lawrence J. G. Amelioration of bacterial genomes: rates of change and exchange/Lawrence J. G., Ochman H.//J. Mol. Evol. -1997. -Vol. 44. -P. 383-397. |
| [51] |
Lindell D. Transfer of photosynthesis genes to and from Prochlorococcus viruses/Lindell D., Sullivan M. B., Johnson Z. I. [et al.]//Proc. Natl. Acad. Sci. USA. -2004. -Vol. 101. -P. 11013-11018. |
| [52] |
Lorenz M. G. Bacterial gene transfer by natural genetic transformation in the invironment/Lorenz M. G., Wackernagel W.//Microbiol. Rev. -1994. -Vol. 58. -P. 563-602. |
| [53] |
Majewski J. Barriers to genetic exchange between bacterialspecies: Streptococcus pneumoniae transformation/Majewski J., Zawadski P., Plickerill P. [et al.]//J. Bacteriol. -2000. -Vol. 182. -P. 1016-1023. |
| [54] |
Mann N. H. Phages in marine cyanobacterial picophytoplancton/Mann N. H.//FEMS Microbiol. Rev. -2003. -Vol. 27, N 1. -P. 17-34. |
| [55] |
Martin W. Mosaic bacterial chromosome: a challenge en route to a tree of genomes/Martin W.//BioEssays. -1999. -Vol. 21. -P. 99 -104. |
| [56] |
Matic I. Horizontal transfer of mismatch repair genes and the variable speed of bacterial evolution/Matic I., Tenaillon O., Lecointre G. [et al.]//In: Horizontal Gene Transfer. -2002. -Academ. Press. P. 147-155. |
| [57] |
McAdams H. H. The evolution of genetic regulatory systems in bacteria/McAdams H. H., Srinivasan B. S., Arkin A. P.//Nature Rev. Genet. -2004. -Vol. 5. -P. 169-178. |
| [58] |
Meier P. Mechanisms of homology-facilitated illegitimate recombination for foreign DNA acquisition in transformable Pseudomonas stutzeri/Meier P., Wackernagel W.//Mol. Microbiol. -2003.-Vol. 48.-P. 1107-1118. |
| [59] |
Moran N. A. Microbial minimalism: genome reduction in bacterial pathogens/Moran N. A.//Cell. -2002. -Vol. 108. -P. 583 -586. |
| [60] |
Nakamura Y. Biased biological functions of horizontally transferred genes in prokaryotic genomes/Nakamura Y., Itoh T., Matsuda H., Gojobori T.//Nature Genet. -2004. -Vol. 36, N 7. -P. 760-766. |
| [61] |
Ochman H. Lateral gene transfer and the nature of bacterial innovation/Ochman H., Lawrence J. C., Groisman A. E.//nature. -2000. -Vol. 405. -P. 299 -304. |
| [62] |
Olendzenski L. Horizontal gene transfer: a new taxonomic principle?/Olendzenski L., Zhaxybayeva O., Gogarten J. P.//Horizontal Gene Transfer. -2002. -Acad. Press. -P. 427-435. |
| [63] |
Piel J. Evidence for a symbiosis island involved in horizontal acquisition of pederin biosynthetic capabilities by the bacterial symbiont of Paederus beetles/Piel J., Hofer Y., Hui D.//J. Bacteriol. -2004. -Vol. 186. -P. 1280-1286. |
| [64] |
Prudhomme M. Homologous recombination at the border: insertion-deletion and the trapping of foreign DNA in Streptococcus pneumoniae/Prudhomme M., Libante V., Claverys J. P.//Proc. Natl. Acad. Sci. USA. -2002. -Vol. 99. P. 2100-2105. |
| [65] |
Rayssiguer C. The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants/Rayssiguer C.,Thaler D. C., Radman M.//Nature. -1989. -Vol. 342. -P. 396-401. |
| [66] |
Riesenfeld C. S. Metagenomics: genomic analysis of microbial communities/Riesenfeld C. S., Schloss P. D., Handelsman J.//Ann. Rev. Genet. -2004. -Vol. 38. -P. 525-552. |
| [67] |
Rowe-Magnus D. A. Integrons: natural tools for bacterial genome evolution/Rowe-Magnus D. A., Mazel D.//Current Opin. Microbiol. -2001. -Vol. 4. -P. 565-569. |
| [68] |
Schmidt H. Pathogenicity islands in bacterial pathogenesis/Schmidt H., Hensel M.//Clin. Microbiol. Rev. -2004. -Vol. 17. -P. 14-56. |
| [69] |
Schneider D. Dynamics of insertion sequence elements during experimental evolution of bacteria/Schneider D., Lenski R. E.//Research Microbiol. -2004. -Vol. 155. -P. 319-327. |
| [70] |
Sorensen S. J. Studyingplasmid horizontal transfer in situ: a critical review/Sorensen S. J., Bailey M., Hansen L. [et al.]//Nature Rev. Microbiol. -2005. -Vol. 5. -P. 700-710. |
| [71] |
Thomas C. M. Mechanisms of, and barriers to, horizontal gene transfer between bacteria/Thomas C. M., Nielsen K. M.//Nature Rev. Microbiol. -2005. -Vol. 3. -P. 711-721. |
| [72] |
Top E. M. The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds/Top E. M., Springael D.//Current Opin. Biotech. -2003. -Vol. 14. -P. 262-269. |
| [73] |
Townsend J. P. Horizontal acquisition of divergent chromosomal DNA in bacteria: effects of mutator phenotypes/Townsend J. P., Nielsen K. M., Fisher D. S. [et al.]//Genetics. -2003. -Vol. 164. -P. 13-21. |
| [74] |
Velkov V. V. How environmental factors regulate mutagenesis and gene transfer in microorganisms/Velkov V. V.//J. Biosci. -1999. -Vol. 24. -P 529-559. |
| [75] |
Vulic M. Molecular keys to speciation: DNA polymorphism and control of exchange to enterobacteria/Vulic M., Dionisio F., Tazddei F., Radman M.//Proc. Natl. Acad. Sci. USA. -1997. -Vol. 94. -P. 9763-9769. |
| [76] |
Wilson G. A. Orphans as taxonomically restricted and ecologically important genes/Wilson G. A., Bertrand N., Patel Y.//Microbiology. -2005. -Vol. 151. -P. 2499-2501. |
| [77] |
Woese C. R. Interpreting the universal phylogenic tree/Woese C. R.//Proc. Natl. Acad. Sci. US. -2000. -Vol. 97. -P. 8392-8396. |
| [78] |
Zhaxybayeva O. Genome mosaicism and organismal lineages/Zhaxybayeva O., Lapierre P., Gogarten J. P.//Trends Genet. -2004. -Vol. 20, N 5. -P. 254-260. |
Shestakov S.V.
/
| 〈 |
|
〉 |