The role of mobile genetic elements in the evolution of cyanobacteria

Russian Journal of Genetics: Applied Research

Volumn 3, Issue 2, 2013, Pages 91-101

  Mikheeva, L E ^a   Karbysheva, E A ^a   Shestakov, S V ^a,b  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

^b VAVILOV INSTITUTE OF GENERAL GENETICS   (Russian Federation)

Author keywords

cyanobacteria; evolution; genome rearrangements; genomes; mobile genetic elements; transposases

Indexed keywords

TRANSPOSASE;

ARTICLE; BACTERIAL STRAIN; COMPUTER MODEL; CYANOBACTERIUM; DNA TRANSPOSITION; EVOLUTIONARY ADAPTATION; GENE REARRANGEMENT; GENE SEQUENCE; GENOME SIZE; NONHUMAN; PRIORITY JOURNAL; SIGNAL TRANSDUCTION;

CYANOBACTERIA;

EID: 84879429313     PISSN: 20790597     EISSN: 20790600     Source Type: Journal    
DOI: 10.1134/S2079059713020032     Document Type: Article

References (45)

1. Axmann, I., Kensche, P., Vogel, J., et al., Identification of Cyanobacterial Non-Coding RNAs by Comparative Genome Analysis, Genome Biology, 2005, vol. 6, no. 9, p. R73.
2. Aziz, R. K., Breitbart, M., and Edwards, R. A., Transposases Are the Most Abundant, Most Ubiquitous Genes in Nature, Nucleic Acids Res., 2010, vol. 38, no. 13, pp. 4207-4217.
3. Bhaya, D., Vaulot, D., Amin, P., et al., Isolation of Regulated Genes of the Cyanobacterium Synechocystis sp. Strain PCC 6803 by Differential Display, J. Bacteriol., 2000, vol. 182, pp. 5692-5699.
4. Bothe, H., Tripp, J., and Zehr, J. P., Unicellular Cyanobacteria with a New Mode of Life: the Lack of Photosynthetic Oxygen Evolution Allows Nitrogen Fixation to Proceed, Arch. Microbiol., 2010, vol. 192, pp. 783-790.
5. Bratlie, M. S., Johansen, J., Sherman, B. T., et al., Gene Duplications in Prokaryotes Can Be Associated with Environmental Adaptation, BMC Genomics, 2010, vol. 11, pp. 588-605.
6. Coleman, M. L., Sullivan, M. B., Martiny, A. C., et al., Genomic Islands and the Ecology and Evolution of Proclorococcus, Science, 2006, vol. 311, no. 5768, pp. 1768-1770.
7. Dufresne, A., Garczarek, L., and Partensky, F., Accelerated Evolution Associated with Genome Reduction in a Free-Living Prokaryote, Genome Biol., 2005, vol. 6, p. R14.
8. Elhai, J., Kato, M., Cousins, S., et al., Very Small Mobile Repeated Elements in Cyanobacterial Genomes, Genome Res., 2008, vol. 18, pp. 1484-1499.
9. Evgen'ev, M. B., Mobile Elements and Genome Evolution, Mol. Biol. (Moscow), 2007, vol. 41, no. 2, pp. 203-213.
10. Frangeul, L., Quillardet, P., Castets, A.-M., et al., Highly Plastic Genome of Microcystis aeruginosa PCC 7806, a Ubiquitous Toxic Freshwater Cyanobacterium, BMC Genomics, 2008, vol. 9, p. 274.
11. Frost, L. S., Leplae, R., Summers, A. O., and Toussaint, A., Mobil Elements: the Agents of Open Source of Evolution, Nat. Rev. Microbiol., 2005, vol. 3, pp. 722-732.
12. Fujisawa, T., Narikawa, R., Okamoto, S., et al., Genomic Structure of an Economically Important Cyanobacterium, Arthrospira (Spirulina) platensis NIES-39, DNA Research, 2010, vol. 17, no. 2, pp. 85-103.
13. Hewson, I., Poretsky, R. S., Beinart, R. A., et al., In Situ Transcriptomic Analysis of the Globally Important Keystone N2-Fixing Taxon Crocosphaera watsonii, ISME J., 2009, vol. 3, pp. 618-631.
14. Ikeuchi, M. and Tabata, S., Synechocystis sp. PCC 6803-A Useful Tool in the Study of the Genetic of Cyanobacteria, Photosynth. Res., 2001, vol. 70, pp. 73-83.
15. Ilyina, T. S., Miniature Repetitive Mobile Elements of Bacteria: Structural Organization and Properties, Mol. Genet. Microbiol. Virol., 2010, vol. 25, no. 4, pp. 139-147.
16. Jiang, Q., Qin, S., and Wu, Q., Genome-Wide Comparative Analysis of Metacaspases in Unicellular and Filamentous Cyanobacteria, BMC Genomics, 2010, vol. 11, p. 198.
17. Kaneko, T., Nakajama, N., Okamoto, S., et al., Complete Genomic Structure of the Bloom-Forming Toxic Cyanobacterium Microcystis aeruginosa NIES-843, DNA Research, 2007, vol. 14, pp. 247-256.
18. Lin, S., Haas, S., Zemojtel, T., et al., Genome-Wide Comparison of Cyanobacterial Transposable Elements, Potential Genetic Diversity Indicators, Gene, 2011, vol. 473, no. 2, pp. 139-149.
19. Luque, I., Andújar, A., Jia, L., et al., Regulated Expression of Glutamyl-tRNA Synthetase Is Directed by a Mobile Genetic Element in the Cyanobacterium Tolypotrix sp. PCC 7601, Mol. Microbiol., 2006, vol. 60, pp. 1276-1288.
20. Markov, A. V. and Zakharov, I. A., Evolution of Gene Orders in Genomes of Cyanobacteria, Russ. J. Genet., 2009, vol. 45, no. 8, pp. 906-916.
21. Mes, T. H. and Doeleman, M., Positive Selection on Transposase Genes of Insertion Sequences in the Crocosphaera watsonii Genome, J. Bacteriol., 2006, vol. 188, no. 20, pp. 7176-7185.
22. Mikheeva, L. E., Karbysheva, E. A., and Shestakov, S. V., On the Nature of Lengthy Nucleotide Repeated Sequences in Genomes of Prokaryotic Organisms, Mosc. Univ. Biol. Bull., 2008, no. 1, pp. 12-20.
23. Mohr, G., Ghanem, E., and Lambowitz, A. M., Mechanisms Used for Genomic Proliferation by Thermophilic Group II Introns, PLoS Biol., 2010, vol. 8, no. 6, p. E1000391.
24. Nunvar, J., Huckova, T., and Licha, I., Identification and Characterization of Repetitive Extragenic Palindromes (REP)-Associated Tyrosine Transposases: Implications for REP Evolution and Dynamics in Bacterial Genomes, BMC Genomics, 2010, vol. 11, p. 44.
25. Okamoto, S., Ikeuchi, M., and Ohmori, M., Experimental Analysis of Recently Transposed Insertion Segments in the Cyanobacterium Synechocystis sp. PCC 6803, DNA Res., 1999, vol. 6, pp. 265-273.
26. Ran, L., Larsson, J., Vigil-Stenmant, et al., Genome Erosion in a Nitrogen-Fixing Vertically Transmitted Endosymbiotic Multicellular Cyanobacterium, PloS One, 2010, vol. 5, no. 7, p. e11486.
27. Rocap, G., Distel, D. L., Waterbury, J. B., and Chisholm, S. W., Resolution of Prochlorococcus and Synechococcus Ecotypes by Using 16S-23S Ribosomal DNA Internal Transcribed Spacer Sequences, Appl. Environ. Microbiol., 2002, vol. 68, no. 3, pp. 1180-1191.
28. Shestakov, S. V., How Horizontal Gene Transfer in Bacteria Proceeds and How It Is Limited, Ekol. Genet., 2007, vol. 5, no. 2, pp. 12-24.
29. Shestakov, S. V., Genomic Coevolution of Cyanophages and Cyanobacteria, in Trudy XIX Mezhdunarodnoi konferentsii "Novye informatsionnye tekhnologii v meditsine, biologii i ekologii" (Proceedings of the XIX International Conference "New Information Technologies in Medicine, Biology, and Ecology"), 2011, pp. 23-25.
30. Shi, T. and Falkowski, P. G., Genome Evolution in Cyanobacteria: The Stable Core and Variable Shell, Proc. Natl. Acad. Sci. U. S. A., 2008, vol. 105, pp. 2510-2515.
31. Stucken, K., John, U., Cembella, A., et al., The Smallest Known Genomes of Multicellular and Toxic Cyanobacteria: Comparison, Minimal Gene Sets for Linked Traits and the Evolutionary Implications, PLoS ONE, 2010, vol. 5, no. 2, p. E9235.
32. Swingley, W. D., Chen, M., Cheung, P. C., et al., Niche Adaptation and Genome Expansion in the Chlorophyll d-Producing Cyanobacterium Acaryochloris marina, Proc. Natl. Acad. Sci. U. S. A., 2008, vol. 105, no. 6, pp. 2005-2010.
33. Tobes, R. and Pareia, E., Bacterial Repetitive Extragenic Palindromic Sequences Are DNA Targets for Insertion Sequence Elements, BMC Genomics, 2006, vol. 7, p. 62.
34. Tomitani, A., Knoll, A., Cavanangh, C. M., and Oto, T., The Evolutionary Diversification of Cyanobacteria: Molecular Phylogenic and Paleontological Perspectives, Proc. Natl. Acad. Sci. USA, 2006, vol. 103, pp. 5442-5447.
35. Touchon, M. and Rocha, P. C., Causes of Insertion Sequences Abundance in Prokaryotic Genomes, Mol. Biol. Evol., 2007, vol. 24, no. 4, pp. 969-981.
36. Tripp, H. J., Bench, S. R., Turk, K. A., et al., Metabolic Streamlining in an Open-Ocean Nitrogen-Fixing Cyanobacterium, Nature, 2010, vol. 464, no. 7285, pp. 90-94.
37. Welsh, E. A., Liberton, M., Stockel, J., et al., The Genome of Cyanothece 51142, a Unicellular Diazotrophic Cyanobacterium Important in the Marine Nitrogen Cycle, Proc. Natl. Acad. Sci. U. S. A., 2008, vol. 105, no. 39, pp. 15094-15099.
38. Wilmotte, A. and Herdman, M., Phylogenetic Relationships among the Cyanobacteria Based on 16S rRNA Sequences, in Bergey's Manual of Systematic Bacteriology, Boone, D. R. and Castenholz, R. W., Eds., New York: Springer, 2001, vol. 1, pp. 487-493.
39. Wolk, C. P., Lechno-Yossef, S., and Jager, K. M., The Insertion Sequences of Anabaena sp. Strain PCC 7120 and Their Effects on Its Open Reading Frames, J. Bacteriol., 2010, vol. 192, no. 20, pp. 5289-5303.
40. Zavarzin, G. A., Initial Stages of the Evolution of the Biosphere, Vestnik Ross. Akad. Nauk, 2010, vol. 80, no. 12, pp. 1085-1098.
41. Zehr, J. P., Bench, S. R., Mondragon, E. A., et al., Low Genomic Diversity in Tropical Oceanic N2-Fixing Cyanobacteria, Proc. Natl. Acad. Sci. U. S. A., 2007, vol. 104, no. 45, pp. 17807-17812.
42. Zehr, J. P., Bench, S. R., Carter, B. J., et al., Globally Distributed Uncultured Oceanic N2-Fixing Cyanobacteria Lack Oxygenic Photosystem II, Science, 2008, vol. 322, pp. 1110-1112.
43. Zhaxybayeva, O., Gogarten, P. J., Charlebois, R. L., et al., Phylogenetic Analysis of Cyanobacterial Genomes: Quantification of Horizontal Gene Transfer Events, Genome Res., 2006, vol. 16, pp. 1099-1108.
44. Zhou, F., Olman, V., and Xu, Y., Insertion Sequences Show Diverse Recent Activities in Cyanobacteria and Archaea, BMC Genomics, 2008a, vol. 9, p. 36.
45. Zhou, F., Tran, T., and Xu, Y., Nezha, a Novel Active Miniature Inverted Repeat Transposable Element in Cyanobacteria, Biochem. Biophys. Res. Commun., 2008b, vol. 365, pp. 790-794.