Korean Journal of Microbiology (미생물학회지)

The Microbiological Society of Korea (한국미생물학회)
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Characterization of Phylogenetic Incongruence among Protein Coding Genes of Vibrio Strains Pathogenic to Humans

인체 병원성 비브리오 균주간 유전자 계통의 불일치성 분석

  • Received : 2013.12.13
  • Accepted : 2013.12.27
  • Published : 2013.12.31
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Abstract

Lateral gene transfer (LGT) of genes from other bacteria into Vibrio cholerae is expectable because of the pronounced natural competence of the bacterium. In this study, quantitative aspects of LGT among the three species of Vibrio pathogenic to humans were characterized. Genome sequences of V. cholerae N16961, V. parahaemolyticus RIMD2210633, V. vulnificus CMCP6, and Escherichia coli K12 substrain MG1655 were analyzed to determine orthologous quartets of protein coding genes present in all four genomes. Phylogenetic analyses on the quartets were conducted to resolve vertical versus lateral patterns of gene polymorphisms based on congruence versus incongruence of phylogenetic trees. About 70% of the quartets could be resolved as either cohesive topology (75%) or LGT tree topologies (25%). The amount of LGT genes in Vibrio spp. appeared to be abnormally high for a genus and comparable to those of families. Patched distributions of LGT from different donors were observed on a chromosome. In the small chromosome of V. cholerae, physical linkages among LGT loci spanned half the length of the chromosome. Either accumulative selection for the donor alleles in LGT or presence of large-scale LGT events was hypothesized. These findings warrant further studies on the nature of donor-specificity of LGT alleles and its influence on evolution of Vibrio virulence to humans.

Vibrio cholerae균은 자연적으로 외부 유전자를 받아들이는 능력이 있으므로, 종간 수평적 유전자 전달 작용(LGT)을 받을 것으로 예상된다. 본 연구는 인체에 질병을 일으키는 3종의 비브리오균 사이에서 일어나는 LGT 현상의 정량적 측면들을 분석하였다. V. cholerae N16961, V. parahaemolyticus RIMD2210633, V. vulnificus CMCP6, Escherichia coli K12 substrain MG1655의 유전체 염기서열을 분석하여 4개의 유전체에 모두 존재하는 단백질 발현 유전자들의 4개 일조를 결정하였다. 각 조의 4개 유전자의 계통수를 작성하는 분석을 통하여, 다른 조들 간의 계통성의 일치성과 불일치성을 결정하고, 수직적 계통성과 수평적 계통성을 구분하였다. 약 70%의 조에서 계통수가 확정될 수 있었으며, 그 중 75%는 서로 일치하는 계통성을 보였고, 25%는 LGT 계통수를 보였다. 이 결과에 따르면, 비브리오균의 LGT는 다른 세균 분류균의 속보다는 과단위에서 발생하는 빈도의 LGT계통수를 보였다. 염색체별로 관찰하였을 때, 유전자 제공자별로 LGT가 집중되는 현상이 일부 관찰되었고, V. cholerae 균주의 작은 염색체에서는 염색체의 약 절반 길이에 해당하는 부분에서 제공자별 LGT 위치들이 집중되는 현상을 보였다. 이런 결과는 유전자 제공자에 따라 선택성이 반복적으로 작용하거나, 대규모의 LGT가 있다는 가설을 수립하게 하였으며, 유전자 제공자별로 LGT 유전형질이 선택성을 띄게 되는 원인과 그 현상이 비브리오균의 진화에 미치는 영향에 대한 연구의 필요성을 제시하였다.

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References

  1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402. https://doi.org/10.1093/nar/25.17.3389
  2. Antonova, E.S. and Hammer, B.K. 2011. Quorum-sensing autoinducer molecules produced by members of a multispecies biofilm promote horizontal gene transfer to Vibrio cholerae. FEMS Microbiol. Lett. 322, 68-76. https://doi.org/10.1111/j.1574-6968.2011.02328.x
  3. Baumann, P., Furniss, A.L., and Lee, J.V. 1984. Genus I. Vibrio. In Krieg, N.R. and Holt, J.G. (eds.), Bergey's Manual of Systematic Bacteriology, Vol. 1, pp. 518-538. Williams & Wilkins, Baltimore, M.D., USA.
  4. Boucher, Y., Cordero, O.X., Takemura, A., Hunt, D.E., Schliep, K., Bapteste, E., Lopez, P., Tarr, C.L., and Polz, M.F. 2011. Local mobile gene pools rapidly cross species boundaries to create endemicity within global Vibrio cholerae populations. MBio 2, e00335-10.
  5. Chun, J., Grim, C.J., Hasan, N.A., Lee, J.H., Choi, S.Y., Haley, B.J., Taviani, E., Jeon, Y.S., Kim, D.W., Brettin, T.S., and et al. 2009. Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae. Proc. Natl. Acad. Sci. USA 106, 15442-15447. https://doi.org/10.1073/pnas.0907787106
  6. Clarke, G.D., Beiko, R.G., Ragan, M.A., and Charlebois, R.L. 2002. Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. J. Bacteriol. 184, 2072-2080. https://doi.org/10.1128/JB.184.8.2072-2080.2002
  7. Daubin, V., Moran, N.A., and Ochman, H. 2003. Phylogenetics and the cohesion of bacterial genomes. Science 301, 829-832. https://doi.org/10.1126/science.1086568
  8. Dikow, R.B. and Smith, W.L. 2013. Genome-level homology and phylogeny of Vibrionaceae (Gammaproteobacteria: Vibrionales) with three new complete genome sequences. BMC Microbiol. 13, 80. https://doi.org/10.1186/1471-2180-13-80
  9. Doolittle, W.F. 2012. Population genomics: how bacterial species form and why they don't exist. Curr. Biol. 22, R451-453. https://doi.org/10.1016/j.cub.2012.04.034
  10. Doolittle, W.F. and Zhaxybayeva, O. 2009. On the origin of prokaryotic species. Genome Res. 19, 744-756. https://doi.org/10.1101/gr.086645.108
  11. Feil, E.J., Holmes, E.C., Bessen, D.E., Chan, M.S., Day, N.P., Enright, M.C., Goldstein, R., Hood, D.W., Kalia, A., Moore, C.E., and et al. 2001. Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences. Proc. Natl. Acad. Sci. USA 98, 182-187. https://doi.org/10.1073/pnas.98.1.182
  12. Jammalamadaka, S.R. and SenGupta, A. 2001. Topics in Circular Statistics. World Scientific Publishing Co., Singapore.
  13. Kahlke, T., Goesmann, A., Hjerde, E., Willassen, N.P., and Haugen, P. 2012. Unique core genomes of the bacterial family Vibrionaceae:insights into niche adaptation and speciation. BMC Genomics 13, 179. https://doi.org/10.1186/1471-2164-13-179
  14. Lo Scrudato, M. and Blokesch, M. 2013. A transcriptional regulator linking quorum sensing and chitin induction to render Vibrio cholerae naturally transformable. Nucleic Acids Res. 41, 3644-3658. https://doi.org/10.1093/nar/gkt041
  15. Meibom, K.L., Blokesch, M., Dolganov, N.A., Wu, C.Y., and Schoolnik, G.K. 2005. Chitin induces natural competence in Vibrio cholerae. Science 310, 1824-1827. https://doi.org/10.1126/science.1120096
  16. Ochman, H., Lawrence, J.G., and Groisman, E.A. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299-304. https://doi.org/10.1038/35012500
  17. Papke, R.T. and Gogarten, J.P. 2012. Ecology. How bacterial lineages emerge. Science 336, 45-46. https://doi.org/10.1126/science.1219241
  18. Rowe-Magnus, D.A., Guerout, A.M., Biskri, L., Bouige, P., and Mazel, D. 2003. Comparative analysis of superintegrons: engineering extensive genetic diversity in the Vibrionaceae. Genome Res. 13, 428-442. https://doi.org/10.1101/gr.617103
  19. Schmidt, H.A., Strimmer, K., Vingron, M., and von Haeseler, A. 2002. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18, 502-504. https://doi.org/10.1093/bioinformatics/18.3.502
  20. Seitz, P. and Blokesch, M. 2013. DNA-uptake machinery of naturally competent Vibrio cholerae. Proc. Natl. Acad. Sci. USA 110, 17987-17992. https://doi.org/10.1073/pnas.1315647110
  21. Shapiro, B.J., Friedman, J., Cordero, O.X., Preheim, S.P., Timberlake, S.C., Szabo, G., Polz, M.F., and Alm, E.J. 2012. Population genomics of early events in the ecological differentiation of bacteria. Science 336, 48-51. https://doi.org/10.1126/science.1218198
  22. Strimmer, K. and von Haeseler, A. 1997. Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proc. Natl. Acad. Sci. USA 94, 6815-6819. https://doi.org/10.1073/pnas.94.13.6815
  23. Tatusov, R.L., Galperin, M.Y., Natale, D.A., and Koonin, E.V. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28, 33-36. https://doi.org/10.1093/nar/28.1.33