Evidence on the Presence of $tRNA^{fMet}$ Group I Intron in the Marine Cyanobacterium Synechococcus elongatus

  • Muralitharan, Gangatharan (Department of Microbiology, National Faculty for Marine Cyanobacteria, Bharathidasan University) ;
  • Thajuddin, Nooruddin (Department of Microbiology, National Faculty for Marine Cyanobacteria, Bharathidasan University)
  • Published : 2008.01.31

Abstract

Self-splicing group I introns in tRNA anticodon loops have been found in diverse groups of bacteria. In this work, we identified $tRNA^{fMet}$ group I introns in six strains of marine Synechococcus elongatus. Introns with sizes around 280 bp were consistently obtained in all the strains tested. In a phylogenetic analysis using the nucleotide sequence determined in this study with other cyanobacterial $tRNA^{fMet}$ and $tRNA^{Leu}$ intron sequences, the Synechococcus sequence was grouped together with the sequences from other unicellular cyanobacterial strains. Interestingly, the phylogenetic tree inferred from the intronic sequences clearly separates the different tRNA introns, suggesting that each family has its own evolutionary history.

Keywords

References

  1. Agrawal, M. K., S. K. Ghosh, D. Bagchi, J. Weckesser, M. Erhard, and S. N. Bagchi. 2006. Occurrence of microcystincontaining toxic water blooms in India. J. Microbiol. Biotechnol. 16: 212-218
  2. Alberte, R. S., A. M. Wood, T. A. Kursar, and R. R. L. Guillard. 1984. Novel phycoerythrins in marine Synechococcus spp.: Characterization, and evolutionary and ecological implications. Plant Physiol. 75: 732-739 https://doi.org/10.1104/pp.75.3.732
  3. Biniszkiewicz, D., E. Cesnaviciene, and D. A. Shub. 1994. Selfsplicing group I intron in cyanobacterial initiator methionine tRNA: Evidence for lateral transfer of introns in bacteria. EMBO J. 13: 4629-4635
  4. Bonocora, R. P. and D. A. Shub. 2001. A novel group I intronencoded endonuclease specific for the anticodon region of $tRNA^{fMet}$ genes. Mol. Microbiol. 39: 1299-1306 https://doi.org/10.1111/j.1365-2958.2001.02318.x
  5. Carr, N. G. and N. H. Mann. 1994. The oceanic cyanobacterial picoplankton, pp. 27-48. In D. A. Bryant (ed.), The Molecular Biology of Cyanobacteria. Kluwer Academic Publishers, Boston
  6. Delwiche, C. F., M. Kuhsel, and J. D. Palmer. 1995. Phylogenetic analysis of tufA sequences indicates a cyanobacterial origin of all plastids. Mol. Phylogenet. Evol. 4: 110-128 https://doi.org/10.1006/mpev.1995.1012
  7. Ecarot-Charrier, B. and R. J. Cedergren. 1976. The preliminary sequence of tRNAfMet from Anacystis nidulans compared with other initiator tRNAs. FEBS Lett. 63: 287-290 https://doi.org/10.1016/0014-5793(76)80113-5
  8. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791 https://doi.org/10.2307/2408678
  9. Kana, T. M., N. L. Feiwel, and L. C. Flynn. 1992. Nitrogen starvation in marine Synechococcus strains: Clonal differences in phycobiliprotein breakdown and energy coupling. Mar. Ecol. Prog. Ser. 88: 75-82 https://doi.org/10.3354/meps088075
  10. Kana, T. M. and P. M. Glibert. 1987. Effect of irradiances up to 2,000 mE $m^{-2}s^{-1}$ on marine Synechococcus WH7803. II. Photosynthetic responses and mechanisms. Deep Sea Res. 34: 497-516 https://doi.org/10.1016/0198-0149(87)90002-1
  11. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111-120 https://doi.org/10.1007/BF01731581
  12. Koksharova, O. A. and C. P. Wolk. 2002. Genetic tools for cyanobacteria. Appl. Microbiol. Biotechnol. 58: 123-137 https://doi.org/10.1007/s00253-001-0864-9
  13. Kramer, J. G. and I. Morris. 1990. Growth regulation in irradiance limited marine Synechococcus sp. WJ7803. Arch. Microbiol. 154: 286-293 https://doi.org/10.1007/BF00248969
  14. Kuhsel, M. G., R. Strickland, and J. D. Palmer. 1990. An ancient group I intron shared by eubacteria and chloroplasts. Science 250: 1570-1573 https://doi.org/10.1126/science.2125748
  15. Kumar, S., K. Tamura, and M. Nei. 2004. MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5: 150-163 https://doi.org/10.1093/bib/5.2.150
  16. Neilan, B. A. 1995. Identification and phylogenetic analysis of toxigenic cyanobacteria by multiplex randomly amplified polymorphic DNA PCR. Appl. Environ. Microbiol. 61: 2286-2291
  17. Ong, L. J. and A. N. Glazer. 1987. R-Phycocyanin II, a new phycocyanin occurring in marine Synechococcus species: Identification of the terminal energy acceptor bilin in phycocyanins. J. Biol. Chem. 262: 6323-6327
  18. Paquin, B., S. D. Kathe, S. A. Nierzwicki-Bauer, and D. A. Shub. 1997. Origin and evolution of group I introns in cyanobacterial tRNA genes. J. Bacteriol. 179: 6798-6806 https://doi.org/10.1128/jb.179.21.6798-6806.1997
  19. Reinhold-Hurek, B. and D. A. Shub. 1992. Self-splicing introns in tRNA genes of widely divergent bacteria. Nature 357: 173- 176 https://doi.org/10.1038/357173a0
  20. Rippka, R., J. Deruelles, J. B. Waterbury, M. Herdmann, and Y. Stanier. 1979. Generic assignments, strain histories and properties of pure cultures of cyanobacteria. J. Gen. Microbiol. 111: 1-61 https://doi.org/10.1099/00221287-111-1-1
  21. Rudi, K. and K. S. Jakobson. 1999. Complex evolutionary patterns of $tRNA^{Leu}$ (UAA) group I introns in cyanobacterial radiation. J. Bacteriol. 181: 3445-3451
  22. Rudi, K. and K. S. Jakobson. 1997. Cyanobacterial $tRNA^{Leu}$ (UAA) group I introns have polyphyletic origin. FEMS Microbiol. Lett. 156: 293-298 https://doi.org/10.1111/j.1574-6968.1997.tb12743.x
  23. Saitou, N. and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425
  24. Thajuddin, N. and G. Subramanian. 1992. Survey of cyanobacterial flora of the southern east coast of India. Botanica Marina 35: 305-311 https://doi.org/10.1515/botm.1992.35.4.305
  25. Thompson, J. D., D. G. Higgins, and T. J. Gilson. 1994. Clustal W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680 https://doi.org/10.1093/nar/22.22.4673
  26. Waterbury, J. B. and R. Rippka. 1989. Subsection I. Order Chroococcales. Wettstein 1924, emend. Rippka et al., 1979, pp. 1728-1746. In J. T. Staley, M. P. Bryant, N. Pfennig, J. G. Holt (eds.), Bergey's Manual of Systematic Bacteriology. Williams and Wilkins, Baltimore
  27. Waterbury, J. B., S. W. Watson, F. W. Valois, and D. G. Franks. 1986. Biological and ecological characterization of the marine unicellular cyanobacterium Synechococcus. Can. Bull. Fish. Aquat. Sci. 214: 71-120
  28. Waterbury, J. B., J. M. Willey, D. G. Franks, F. W. Valois, and S. W. Watson. 1985. A cyanobacterium capable of swimming motility. Science 230: 71-120 https://doi.org/10.1126/science.2412295
  29. Willey, J. M. and J. B. Waterbury. 1989. Chemotaxis toward nitrogenous compounds by swimming strains of marine Synechococcus spp. Appl. Environ. Microbiol. 55: 1888-1894
  30. Willey, J. M., J. B. Waterbury, and E. P. Greenberg. 1987. Sodium-coupled motility in a swimming cyanobacterium. J. Bacteriol. 169: 3429-3434 https://doi.org/10.1128/jb.169.8.3429-3434.1987
  31. Wood, A. M. 1985. Adaptation of the photosynthetic apparatus of marine ultraphytoplankton to natural light fields. Nature (London) 316: 253-255 https://doi.org/10.1038/316253a0
  32. Yong, A. C., D. K. Park, H. S. Kim, A. S. Chung, and H. M. Oh. 2004. K:Fe ratio as an indicator of cyanobacterial bloom in a eutrophic lake. J. Microbiol. Biotechnol. 14: 290-296