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Identification of Recombination and Positively Selected Genes in Brucella

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Abstract

Brucella is a facultative intracellular bacterium belongs to the class alpha proteobacteria. It causes zoonotic disease brucellosis to wide range of animals. Brucella species are highly conserved in nucleotide level. Here, we employed a comparative genomics approach to examine the role of homologous recombination and positive selection in the evolution of Brucella. For the analysis, we have selected 19 complete genomes from 8 species of Brucella. Among the 1599 core genome predicted, 24 genes were showing signals of recombination but no significant breakpoint was found. The analysis revealed that recombination events are less frequent and the impact of recombination occurred is negligible on the evolution of Brucella. This leads to the view that Brucella is clonally evolved. On other hand, 56 genes (3.5 % of core genome) were showing signals of positive selection. Results suggest that natural selection plays an important role in the evolution of Brucella. Some of the genes that are responsible for the pathogenesis of Brucella were found positively selected, presumably due to their role in avoidance of the host immune system.

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References

  1. Orsi RH, Sun Q, Wiedmann M (2008) Genome-wide analyses reveal lineage specific contributions of positive selection and recombination to the evolution of Listeria monocytogenes. BMC Evol Biol 8:23. doi:10.1186/1471-2148-8-233

    Article  Google Scholar 

  2. Petersen L, Bollback JP, Dimmic M, Hubisz M, Nielsen R (2007) Genes under positive selection in Escherichia coli. Genome Res 17:1336–1343. doi:10.1101/gr.6254707

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  3. Lefebure T, Stanhope MJ (2007) Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol 8:R71. doi:10.1186/gb-2007-8-5-r71

    Article  PubMed Central  PubMed  Google Scholar 

  4. Yang Z, Wong WS, Nielsen R (2005) Bayes empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol 22:1107–1118. doi:10.1093/molbev/msi097

    Article  CAS  PubMed  Google Scholar 

  5. O’Callaghan D, Whatmore AM (2011) Brucella genomics as we enter the multi-genome era. Brief Funct Genomics 10:334–341. doi:10.1093/bfgp/elr026

    Article  PubMed  Google Scholar 

  6. Franco MP, Mulder M, Gilman RH, Smits HL (2007) Human brucellosis. Lancet Infect Dis 7:775–786. doi:10.1016/S1473-3099(07)70286-4

    Article  CAS  PubMed  Google Scholar 

  7. Xiang Z, Zheng W, He Y (2006) BBP: Brucella genome annotation with literature mining and curation. BMC Bioinformatics 7:347. doi:10.1186/1471-2105-7-347

    Article  PubMed Central  PubMed  Google Scholar 

  8. Su F, Ou HY, Tao F, Tang H, Xu P (2013) PSP: rapid identification of orthologous coding genes under positive selection across multiple closely related prokaryotic genomes. BMC Genom 14:924. doi:10.1186/1471-2164-14-924

    Article  Google Scholar 

  9. Didelot X, Falush D (2007) Inference of bacterial microevolution using multilocus sequence data. Genetics 175:1251–1266. doi:10.1534/genetics.106.063305

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  10. Darling AE, Mau B, Perna NT (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5:e11147. doi:10.1371/journal.pone.0011147

    Article  PubMed Central  PubMed  Google Scholar 

  11. Gelman A, Rubin DB (1992) Inference from iterative simulation using multiple sequences. Stat Sci 7:457–472. doi:10.2307/2246093

    Article  Google Scholar 

  12. Halling SM, Peterson-Burch BD, Bricker BJ, Zuerner RL, Qing Z, Li LL, Kapur V, Alt DP, Olsen SC (2005) Completion of the genome sequence of Brucella abortus and comparison to the highly similar genomes of Brucella melitensis and Brucella suis. J Bacteriol 187:2715–2726. doi:10.1128/JB.187.8.2715-2726.2005

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  13. Sankarasubramanian J, Vishnu US, Sridhar J, Gunasekaran P, Rajendhran J (2015) Pan-Genome of Brucella Species. Indian J Microbiol 55:88–101. doi:10.1007/s12088-014-0486-4

    Article  CAS  Google Scholar 

  14. Foster JT, Beckstrom-Sternberg SM, Pearson T, Beckstrom-Sternberg JS, Chain PS, Roberto FF, Hnath J, Brettin T, Keim P (2009) Whole-genome-based phylogeny and divergence of the genus Brucella. J Bacteriol 191:2864–2870. doi:10.1128/JB.01581-08

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  15. Tibayrenc M, Ayala FJ (2012) Reproductive clonality of pathogens: a perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa. Proc Natl Acad Sci USA 109:E3305–E3313. doi:10.1073/pnas.1212452109

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  16. Dos Vultos T, Mestre O, Rauzier J, Golec M, Rastogi N, Rasolofo V, Tonjum T, Sola C, Matic I, Gicquel B (2008) Evolution and diversity of clonal bacteria: the paradigm of Mycobacterium tuberculosis. PLoS ONE 3:e1538. doi:10.1371/journal.pone.0001538

    Article  PubMed Central  PubMed  Google Scholar 

  17. Baker S, Hanage WP, Holt KE (2010) Navigating the future of bacterial molecular epidemiology. Curr Opin Microbiol 13:640–645. doi:10.1016/j.mib.2010.08.002

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  18. Feil EJ, Cooper JE, Grundmann H, Robinson DA, Enright MC, Berendt T, Peacock SJ, Smith JM, Murphy M, Spratt BG, Moore CE, Day NPJ (2003) How clonal is Staphylococcus aureus. J Bacteriol 185:3307–3316. doi:10.1128/JB.185.11.3307-3316.2003

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  19. Kennemann L, Didelot X, Aebischer T, Kuhn S, Drescher B, Droege M, Reinhardtf R, Correag P, Meyerc TF, Josenhansa C, Falushh D, Suerbaum S (2011) Helicobacter pylori genome evolution during human infection. Proc Natl Acad Sci USA 108:5033–5038. doi:10.1073/pnas.1018444108

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  20. Silva C, Vinuesa P, Eguiarte LE, Souza V, Martinez-Romero E (2005) Evolutionary genetics and biogeographic structure of Rhizobium gallicum sensu lato, a widely distributed bacterial symbiont of diverse legumes. Mol Ecol 14:4033–4050. doi:10.1111/j.1365-294X.2005.02721.x

    Article  CAS  PubMed  Google Scholar 

  21. Arvand M, Feil EJ, Giladi M, Boulouis HJ, Viezens J (2007) Multi-locus sequence typing of Bartonella henselae isolates from three continents reveals hypervirulent and feline-associated clones. PLoS ONE 2:e1346. doi:10.1371/journal.pone.0001346

    Article  PubMed Central  PubMed  Google Scholar 

  22. Kim KM, Kim KW, Sung S, Kim H (2011) A genome-wide identification of genes potentially associated with host specificity of Brucella species. J Microbiol 49:768–775. doi:10.1007/s12275-011-1084-3

    Article  PubMed  Google Scholar 

  23. Valderas MW, Alcantara RB, Baumgartner JE, Bellaire BH, Robertson GT, Ng WL, Richardson JM, Winkler ME, Roop RM (2005) Role of HdeA in acid resistance and virulence in Brucella abortus 2308. Vet Microbiol 107:307–312. doi:10.1016/j.vetmic.2005.01.018

    Article  CAS  PubMed  Google Scholar 

  24. Sangari FJ, Seoane A, Rodríguez MC, Aguero J, Lobo JMG (2007) Characterization of the urease operon of Brucella abortus and assessment of its role in virulence of the bacterium. Infect Immun 75:774–780. doi:10.1128/IAI.01244-06

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  25. Hornback ML, Roop RM (2006) The Brucella abortus xthA-1 gene product participates in base excision repair and resistance to oxidative killing but is not required for wild-type virulence in the mouse model. J Bacteriol 188:1295–1300. doi:10.1128/JB.188.4.1295-1300.2006

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  26. Delrue RM, Lestrate P, Tibor A, Letesson JJ, De Bolle X (2004) Brucella pathogenesis, genes identified from random large-scale screens. FEMS Microbiol Lett 231:1–12. doi:10.1016/S0378-1097(03)00963-7

    Article  CAS  PubMed  Google Scholar 

  27. Kim JA, Mayfield J (2000) Identification of Brucella abortus OxyR and its role in control of catalase expression. J Bacteriol 182:5631–5633. doi:10.1128/JB.182.19.5631-5633.2000

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  28. Tsolis RM, Seshadri R, Santos RL, Sangari FJ, Lobo JMG, de Jong MF, Ren Q, Myers G, Brinkac LM, Nelson WC, Deboy RT, Angiuoli S, Khouri H, Dimitrov G, Robinson JR, Mulligan S, Walker RL, Elzer PE, Hassan KA, Paulsen IT (2009) Genome degradation in Brucella ovis corresponds with narrowing of its host range and tissue tropism. PLoS ONE 4:e5519. doi:10.1371/journal.pone.0005519

    Article  PubMed Central  PubMed  Google Scholar 

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Acknowledgments

This work was supported by the Department of Biotechnology, New Delhi through DBT-Network Project on Brucellosis. The UGC-CAS, CEGS, NRCBS, DBT-IPLS, DST-PURSE Programs of School of Biological Sciences, Madurai Kamaraj University is gratefully acknowledged.

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Authors and Affiliations

  1. Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India

    Udayakumar S. Vishnu, Jagadesan Sankarasubramanian, Jayavel Sridhar, Paramasamy Gunasekaran & Jeyaprakash Rajendhran

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  1. Udayakumar S. Vishnu
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  2. Jagadesan Sankarasubramanian
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  3. Jayavel Sridhar
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  4. Paramasamy Gunasekaran
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  5. Jeyaprakash Rajendhran
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Correspondence to Jeyaprakash Rajendhran.

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Vishnu, U.S., Sankarasubramanian, J., Sridhar, J. et al. Identification of Recombination and Positively Selected Genes in Brucella . Indian J Microbiol 55, 384–391 (2015). https://doi.org/10.1007/s12088-015-0545-5

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