The role of mobile genetic elements in evolution of cyanobacteria

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Abstract


Possible pathways of cyanobacterial evolution are discussed on the basis of in silico analysis of fully sequenced genomes of 45 species/strains of cyanobacteria. The information on quantity and functions of different mobile elements (IS, MITE elements and group II introns) was reviewed. Positive correlation between whole genome sizes and number of genes, encoding transposases has been revealed. It is suggested that transpositions play significant role in genome rearrangements taking part in gene regulation and adaptation processes determining the directions of microevolution processes in cyanobacterial populations.

About the authors

Lidia E Mikheeva

M.V. Lomonosov Moscow State University , Moscow, RF

Email: shestakovgen@ mail.ru 119 234, Russia, Moscow, Leninskie Gory, etc. 1, p. 12, MSU

Elena A Karbysheva

M.V. Lomonosov Moscow State University , Moscow, RF

Email: shestakovgen@mail.ru 119 234, Russia, Moscow, Leninskie Gory, etc. 1, p. 12, MSU

Sergey V Shestakov

M. V. Lomonosov Moscow State University, Moscow, RF

Email: shestakovgen@mail.ru 119 234, Russia, Moscow, Leninskie Gory, etc. 1, p. 12, MSU

References

  1. Евгеньев М. Б., 2007. Мобильные элементы и эволюция генома // Молек. биол. Т. 41, № 2. С. 234-245.
  2. Заварзин Г. А., 2010. Начальные этапы эволюции биосферы // Вестник РАН. Т. 80, № 12. С. 1085-1098.
  3. Марков А. В., Захаров И. А., 2009. Эволюция генных порядков в геномах цианобактерий // Генетика. Т. 45, № 8. С. 1036-1047.
  4. Михеева Л. Е., Карбышева Е. А., Шестаков С. В., 2008. О природе протяженных нуклеотидных повторов в геномах прокариот // Вестник МГУ. Cер.16. Биология. № 1. С. 14-22.
  5. Шестаков С. В., 2007. Как происходит и чем лимитируется горизонтальный перенос генов у бактерий // Экологическая генетика. Т. 5, № 2. С. 12-24.
  6. Шестаков С. В., 2011. Геномная коэволюция цианофагов и цианобактерий // Труды XIX Международной конференции «Новые информационные технологии в медицине, биологии и экологии». С. 23-25.
  7. Axmann I., Kensche P., Vogel J. et al., 2005. Identification of cyanobacterial non-coding RNAs by comparative genome analysis // Genome Biology. Vol. 6, N 9. P. R73.
  8. Aziz R. K., Breitbart M., Edwards R. A., 2010. Transposases are the most abundant, most ubiquitous genes in nature // Nucleic Acids Research. Vol. 38, No. 13. P. 4207-4217.
  9. Bhaya D., Vaulot D., Amin P. et al., 2000. Isolation of regulated genes of the cyanobacterium Synechocystis sp. strain PCC 6803 by differential display // J. Bacteriol. Vol. 182. P. 5692-5699.
  10. Bothe H., Tripp J., Zehr J. P., 2010. Unicellular cyanobacteria with a new mode of life: the lack of photosynthetic oxygen evolution allows nitrogen fixation to proceed // Arch. Microbiol. Vol. 192. P. 783-790.
  11. Bratlie M. S., Johansen J., Sherman B. T. et al., 2010. Gene duplications in prokaryotes can be associated with environmental adaptation // BMC Genomics. Vol. 11. P. 588-605.
  12. Coleman M. L., Sullivan M. B., Martiny A. C. et al., 2006. Genomic islands and the ecology and evolution of Proclorococcus // Science. Vol. 311, N 5768. P. 1768-1770.
  13. Dufresne A., Garczarek L., Partensky F., 2005. Accelerated evolution associated with genome reduction in a free-living prokaryote // Genome Biology. Vol. 6. P. R14.
  14. Elhai J., Kato M., Cousins S. et al., 2008. Very small mobile repeated elements in cyanobacterial genomes // Genome Res. Vol. 18. P. 1484-1499.
  15. Fujisawa T., Narikawa R., Okamoto S. et al., 2010. Genomic structure of an economically important cyanobacterium, Arthrospira (Spirulina) platensis NIES-39 // DNA Research. Vol. 17, N 2. P. 85-103.
  16. Frangeul L., Quillardet P., Castets A-M. et al., 2008. Highly plastic genome of Microcystis aeruginosa PCC 7806, a ubiquitous toxic freshwater cyanobacterium // BMC Genomics. Vol. 9. P. 274.
  17. Frost L. S., Leplae R., Summers A. O., Toussaint A., 2005. Mobil elements: the agents of open source of evolution // Nat. Rev. Microbiol. Vol. 3. P. 722-732.
  18. Hewson I., Poretsky R. S., Beinart R. A. et al., 2009. In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii // ISME Journal. Vol. 3. P. 618-631.
  19. Ikeuchi M., Tabata S., 2001. Synechocystis sp. PCC 6803 - a useful tool in the study of the genetic of cyanobacteria // Photosynt. Res. Vol. 70. P. 73-83.
  20. Ilyina T. S., 2010. Miniature repetitive mobile elements of bacteria: structural organization and properties // Molec. Genet., Microbiol., Virol. Vol. 25, N. 4. P. 139-147.
  21. Jiang Q., Qin S., Wu Q., 2010. Genome-wide comparative analysis of metacaspases in unicellular and filamentous cyanobacteria // BMC Genomics. Vol. 11. P. 198.
  22. Kaneko T., Nakajama N., Okamoto S. et al., 2007. Complete genomic structure of the bloom-forming toxic cyanobacterium Microcystis aeruginosa NIES-843 // DNA Research. Vol. 14. P. 247-256.
  23. Lin S., Haas S., Zemojtel T. et al., 2011. Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators // Gene. Vol. 473, N 2. P. 139-149.
  24. Luque I., Andújar A., Jia L. et al., 2006. Regulated expression of glutamyl-tRNA synthetase is directed by a mobile genetic element in the cyanobacterium Tolypothrix sp. PCC 7601 // Mol. Microbiol. Vol. 60. P. 1276-1288.
  25. Mes T. H., Doeleman M., 2006. Positive selection on transposase genes of insertion sequences in the Crocosphaera watsonii genome // J. Bacteriol. Vol. 188, N. 20. P. 7176-7185.
  26. Mohr G., Ghanem E., Lambowitz A. M., 2010. Mechanisms used for genomic proliferation by thermophilic group II introns // PLoS Biology. Vol. 8, N6. E1000391.
  27. Nunvar J., Huckova T., Licha I., 2010. Identification and characterization of repetitive extragenic palindromes (REP)-associated tyrosine transposases: implications for REP evolution and dynamics in bacterial genomes // BMC Genomics. Vol. 11. P. 44.
  28. Okamoto S., Ikeuchi M., Ohmori M., 1999. Experimental analysis of recently transposed insertion segments in the cyanobacterium Synechocystis sp. PCC 6803 // DNA Res. Vol. 6. P. 265-273.
  29. Ran L., Larsson J., Vigil-Stenmant et al,. 2010. Genome erosion in a nitrogen-fixing vertically transmitted endosymbiotic multicellular cyanobacterium // PloS One. Vol. 5, N7. e11486.
  30. Rocap G., Distel D. L., Waterbury J. B., Chisholm S. W., 2002. Resolution of Prochlorococcus and Synechococcus ecotypes by using16S-23S ribosomal DNA internal transcribed spacer sequences // Applied. Environmental Microbiol. Vol. 68. N. 3. P. 1180-1191.
  31. Shi T., Falkowski P. G., 2008. Genome evolution in cyanobacteria: the stable core and variable shell // Proc. Natl. Acad. Sci. USA. Vol. 105. P. 2510-2515.
  32. Stucken K., John U., Cembella A. et al., 2010. The smallest known genomes of multicellular and toxic cyanobacteria: comparison, minimal gene sets for linked traits and the evolutionary implications // PLoS ONE. Vol. 5, N. 2. e9235.
  33. Swingley W. D., Chen M., Cheung P. C. et al., 2008. Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina // Proc. Natl. Acad. Sci. Vol. 105, N. 6. P. 2005-2010.
  34. Tobes R., Pareia E., 2006. Bacterial repetitive extragenic palindromic sequences are DNA targets for insertion sequence elements // BMC Genomics. Vol. 7. P. 62.
  35. Tomitani A., Knoll A., Cavanangh C. M., Oto T., 2006. The evolutionary diversification of cyanobacteria: molecular phylogenic and paleontological perspectives // Proc. Natl. Acad. Sci. USA. Vol. 103. P. 5442-5447.
  36. Touchon M., Rocha P. C., 2007. Causes of insertion sequences abundane in prokaryotic genomes // Mol. Biol. Evol. Vol. 24, N 4. P. 969-981.
  37. Tripp H. J., Bench S. R., Turk K. A. et al., 2010. Metabolic streamlining in an open-ocean nitrogen-fixing cyanobacterium // Nature. Vol. 464, N. 7285. P. 90-94.
  38. Welsh E. A., Liberton M., Stockel J. et al., 2008. The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycle // Proc. Natl. Acad. Sci. Vol. 105, N. 39. P. 15094-15099.
  39. Wilmotte A., Herdman M., 2001. Phylogenetic relationships among the cyanobacteria based on 16S rRNA sequences // Bergey's Manual of Systematic Bacteriology/ Ed. D. R. Boone, R. W. Castenholz. New York: Springer. Vol. 1. P. 487-493.
  40. Wolk C. P, Lechno-Yossef S, Jäger K. M., 2010. The insertion sequences of Anabaena sp. strain PCC 7120 and their effects on its open reading frames // J. Bacteriol. Vol. 192, N. 20. P. 5289-5303.
  41. Zehr J. P., Bench S. R., Mondragon E. A. et al., 2007. Low genomic diversity in tropical oceanic N2-fixing cyanobacteria // Proc. Natl. Acad. Sci. Vol. 104, N. 45. P. 17807-17812.
  42. Zehr J. P, Bench S. R, Carter B. J et al., 2008. Globally distributed uncultured oceanic N2-fixing cyanobacteria lack oxygenic photosystem II // Science. Vol. 322. P. 1110-1112.
  43. Zhaxybayeva O., Gogarten P. J., Charlebois R. L. et al., 2006. Phylogenetic analysis of cyanobacterial genomes:quantification of horizontal gene transfer events // Genome Res. Vol. 16. P. 1099-1108.
  44. Zhou F., Olman V., Xu Y., 2008a. Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea // BMC Genomics. Vol. 9. P. 36.
  45. Zhou F., Tran T., Xu Y., 2008b. Nezha, a novel active miniature inverted repeat transposable element in cyanobacteria // Biochem. Biophys. Res. Commun. Vol. 365. P. 790-794.

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Copyright (c) 2011 Mikheeva L.E., Karbysheva E.A., Shestakov S.V.

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