DNA Repeats in Bacterial Genome and Intracellular Activity of Homologous Recombinase

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Abstract


In present work distribution of perfect direct and inverted repeats in a set of bacterial genomes was analysed. Complementary cumulative distribution functions of repeat frequency for 36 bacterial strains are nonrandom and have certain characteristic features. Inverse relation of direct repeats frequency to recombinogenic activity is shown for reference E. сoli К-12 strain and P. aeruginosa strain with hyperrecombinogenic RecA protein. In general, direct repeat frequency is higher in nonpathogenic strains than that in pathogens. 

About the authors

Andrey V Ilatovsky

B.P. Konstantinov Nuclear Physics Institute, Gatchina, Leningrad Oblast, RF

Email: Andrey-soap@yandex.ru; andreyi@omrb.pnpi.spb.ru

Vladislav A Lanzov

B.P. Konstantinov Nuclear Physics Institute, Gatchina, Leningrad Oblast, RF

Email: dashach066@mail.ru

References

  1. Бабынин Э., 2007. Молекулярный механизм гомологичной рекомбинации в мейозе: происхождение и биологическое значение//Цитология. Т. 49. С. 182-193.
  2. Смирнов Г., 2007. Почему редуцируются бактериальные геномы?//Молекулярная генетика, биофизика и медицина сегодня/под ред. В. А. Ланцова. СПб.: Изд. ПИЯФ РАН. С. 34-60.
  3. Akman L., Yamashita A., Watanabe H. et al., 2002. Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia//Nat. Genet. Vol. 32. P. 402-407.
  4. Auman A., Breezee J., Gosink J. et al., 2006. Psychromonas ingrahamii sp. nov., a novel gas vacuolate, psychrophilic bacterium isolated from Arctic polar sea ice//Int. J. Syst. Evol. Microbiol. Vol. 56. P. 1001-1007.
  5. Baitin D., Zaitsev E., Lanzov V., 2003. Hyper-recombinogenic RecA protein from Pseudomonas aeruginosa with enhanced activity of its primary DNA binding site//J. Mol. Biol. Vol. 328. P. 1-7.
  6. Baitin D., Bakhlanova I., Chervyakova D. et al., 2008. Two RecA protein types that mediate different modes of hyperrecombination//J. Bacteriol. Vol. 190. P. 3036-3045.
  7. Bakhlanova I., Ogawa T., Lanzov V., 2001. Recombinogenic activity of chimeric recA genes (Pseudomonas aeruginosa/Escherichia coli): A search for RecA protein regions responsible for this activity//Genetics. Vol. 159. P. 7-15.
  8. Benson D., Karsch-Mizrachi I., Lipman D. et al., 2007. Genbank//Nucleic Acids Res. Vol. 35. P. D21-D25.
  9. Berg O., Kurland C., 2002. Evolution of microbial genomes: Sequence acquisition and loss//Mol. Biol. Evol. Vol. 19. P. 2265-2276.
  10. Buchet A., Nasser W., Eichler K., Mandrand-Berthelot M., 1999. Positive co-regulation of the Escherichia coli carnitine pathway cai and fix operons by CRP and the CaiF activator//Mol. Microbiol. Vol. 34. P. 562-575.
  11. Cox M., 2002. The nonmutagenic repair of broken replication forks via recombination//Mutat. Res. Vol. 510. P. 107-120.
  12. Dorer M., Fero J., Salama N., 2010. DNA damage triggers genetic exchange in Helicobacter pylori//PLoS Pathog. Vol. 6. P. e1001026.
  13. Eitner G., Adler B., Lanzov V., Hofemeister J., 1992. Interspecies recA protein substitution in Escherichia coli and Proteus mirabilis//Mol. Gen. Genet. Vol. 185. P. 481-486.
  14. Kawano M., Kanaya S., Oshima T. et al., 2002. Distribution of repetitive sequences on the leading and lagging strands of the Escherichia coli genome: Comparative study of long direct repeat (LDR) sequences//DNA Res. Vol. 9. P. 1-10.
  15. Kowalczykowski S., 2000. Initiation of genetic recombination and recombination-dependent replication//Trends Biochem. Sci. Vol. 25. P. 156-165.
  16. Krawiec S., Riley M., 1990. Organization of the bacterial chromosome//Microbiol. Rev. Vol. 54. P. 502-539.
  17. Lanzov V., Bakhlanova I., Clark A., 2003. Conjugational hyperrecombination achieved by derepressing the LexA regulon, altering the properties of RecA protein and inactivating mismatch repair in Escherichia coli K-12//Genetics. Vol. 163. P. 1243-1254.
  18. Mahillon J., Chandler M., 1998. Insertion sequences//Microbiol. Mol. Biol. Rev. Vol. 62. P. 725-774.
  19. McGinnis S., Madden T., 2004. BLAST: at the core of a powerful and diverse set of sequence analysis tools//Nucleic Acids Res. Vol. 32. P. W20-W25.
  20. Mertens K., Lantsheer L., Ennis D., Samuel J., 2008. Constitutive SOS expression and damage-inducible AddAB-mediated recombinational repair systems for Coxiella burnetii as potential adaptations for survival within macrophages//Mol. Microbiol. Vol. 69. P. 1411-1426
  21. Moreau P., 1987. Effects of overproduction of singlestranded DNA-binding protein on RecA protein-dependent processes in Escherichia coli//J. Mol. Biol. Vol. 194. P. 621-634.
  22. Ogawa T., Shinohara A., Ogawa 22. H., Tomizawa J., 1992. Functional structures of the RecA protein found by chimera analysis//J. Mol. Biol. Vol. 226. P. 651-660.
  23. Petrillo M., Silvestro G., Nocera P. et al., 2006. Stemloop structures in prokaryotic genomes//BMC Genomics. Vol. 7. P. 170.
  24. Riley M., Staley J., Danchin A. et al., 2008. Genomics of an extreme psychrophile, Psychromonas ingrahamii//BMC Genomics. Vol. 9. P. 210.
  25. Rocha E., 2003. An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: From duplications to genome reduction//Genome Res. Vol. 13. P. 1123-1132.
  26. Sassanfar M., Roberts J., 1990. Nature of the SOSinducing signal in Escherichia coli: The involvement of DNA replication//J. Mol. Biol. Vol. 212. P. 79-96.
  27. Story R., Weber I., Steitz T., 1992. The structure of the E. coli recA protein monomer and polymer//Nature. Vol. 355. P. 318-325.
  28. Toh H., Weiss B., Perkin S. et al., 2006. Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host//Genome Res. Vol. 16. P. 149-156.
  29. Tolstorukov M., Virnik K., Adhya S., Zhurkin V., 2005. A-tract clusters may facilitate DNA packaging in bacterial nucleoid//Nucleic Acids Res. Vol. 33. P. 3907-3918.
  30. West S., 2003. Molecular views of recombination proteins and their control//Nat. Rev. Mol. Cell Biol. Vol. 4. P. 435-445.
  31. Wu D., Daugherty S., Aken S. et al., 2006. Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters//PLoS Biol. Vol. 4. P. e188.
  32. 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. Vol. 33. P. 6445-6458.

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Copyright (c) 2011 Ilatovsky A.V., Lanzov V.A.

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