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Complete genome sequence of Halomonas ventosae virulent halovirus QHHSV-1

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Abstract

A virulent halovirus QHHSV-1 which lyses Halomonas ventosae QH52-2 originating from the Qiaohou salt mine in Yunnan, Southwest China was characterized. The complete genome of QHHSV-1 is composed of a circular double-stranded DNA of 37,270 base pairs in length, with 66.8% G+C content and 69 putative open reading frames (ORFs), which were classified into five functional groups, including morphogenesis, replication/regulation, packaging, lysis and lysogeny. A putative Cro repressor gene and an integrase gene were found in the genome, showing that QHHSV-1 may utilize a lambda-like repression system under unfavorable conditions. QHHSV-1 is the first report of the whole genome sequence of the virulent Halomonas phage belonging to the family Siphoviridae.

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References

  1. Porter K, Russ BE, Dyall-Smith ML (2007) Virus-host interactions in salt lakes. Curr Opin Microbiol 10:418–424

    Article  CAS  PubMed  Google Scholar 

  2. Adriaenssens EM, Zyl LJV, Cowan DA et al (2016) Metaviromics of Namib Desert Salt Pans: a novel lineage of Haloarchaeal Salterproviruses and a rich source of ssDNA viruses. Viruses 8:14

    Article  PubMed Central  Google Scholar 

  3. Oren A (2002) Diversity of halophilic microorganisms: environments, phylogeny, physiology, and applications. J Ind Microbiol Biotechnol 28:56–63

    Article  CAS  PubMed  Google Scholar 

  4. Atanasova NS, Bamford DH, Oksanen HM (2016) Virus–host interplay in high salt environments. Environ Microbiol Rep 8:431–444

    Article  CAS  PubMed  Google Scholar 

  5. Pedrós-Alió C, Calderón-Paz JI, Maclean MH et al (2000) The microbial food web along salinity gradients. FEMS Microbiol Ecol 32:143–155

    Article  PubMed  Google Scholar 

  6. Boujelben I, Yarza P, Almansa C et al (2012) Virioplankton community structure in Tunisian solar salterns. Appl Environ Microbiol 78:7429–7437

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Atanasova NS, Oksanen HM, Bamford DH (2015) Haloviruses of archaea, bacteria, and eukaryotes. Curr Opin Microbiol 25:40–48

    Article  PubMed  Google Scholar 

  8. Fu CQ, Bai M, Wang YX et al (2017) Advances in bacteriophages isolated from hypersaline environments. Microbiol China 44(4):920−928

    Google Scholar 

  9. Vreeland RH, Litchfield CD, Martin EL et al (1980) Halomonas elongata, a new genus and species of extremely salt-tolerant bacteria. Int J Syst Bacteriol 30:485–495

    Article  CAS  Google Scholar 

  10. Lim J-M, Yoon JH, Lee J-C et al (2004) Halomonas koreensis sp. nov., a novel moderately halophilic bacterium isolated from a solar saltern in Korea. Int J Syst Evol Microbiol 54:2037–2042

    Article  CAS  PubMed  Google Scholar 

  11. Mobberley JM, Authement RN, Segall AM et al (2008) The temperate marine phage phihap-1 of Halomonas aquamarina possesses a linear plasmid-like prophage genome. J Virol 82:6618–6630

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Wang YX, Xiao W, Dong MH et al (2014) Halomonas qiaohouensis, sp. nov. isolated from salt mine soil in southwest China. Antonie van Leeuwenhoek 106:253–260

    Article  CAS  PubMed  Google Scholar 

  13. Fu CQ, Zhao Q, Li ZY et al (2016) A novel Halomonas ventosae-specific virulent halovirus isolated from the Qiaohou salt mine in Yunnan, southwest China. Extremophiles 20:101–110

    Article  CAS  PubMed  Google Scholar 

  14. Chevreux B, Pfisterer T, Drescher B et al (2004) Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 14:1147–1159

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Besemer J, Lomsadze A, Borodovsky M (2001) GenemarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 29:2607–2618

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Stephen FA, Thomas LM, Alejandro AS et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  Google Scholar 

  17. Marchler-Bauer A, Derbyshire MK, Gonzales NR et al (2015) CDD: NCBI’s conserved domain database. Nucleic Acids Res 43(Database issue):D222–D226

    Article  CAS  PubMed  Google Scholar 

  18. Bjellqvist B, Hughes GJ, Pasquali C et al (1993) The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis 14:1023–1031

    Article  CAS  PubMed  Google Scholar 

  19. Laslett D, Canback B (2004) ARAGORN, a program for the detection of transfer RNA and transfer-messenger RNA genes in nucleotide sequences. Nucleic Acids Res 32:11–16

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Becker B, de la Fuente N, Gassel M et al (1997) Head morphogenesis genes of the Bacillus subtilis bacteriophage SPP1. J MolBiol 268:822–839

    Article  CAS  Google Scholar 

  21. Duda RL, Martincic K, Hendrix RW (1995) Genetic basis of bacteriophage HK97 prohead assembly. J Mol Biol 247:636–647

    CAS  PubMed  Google Scholar 

  22. Abuladze NK, Gingery M, Tsai J et al (1994) Tail length determination in bacteriophage T4. Virology 199:301–310

    Article  CAS  PubMed  Google Scholar 

  23. Pedersen M, Ostergaard S, Bresciani J et al (2000) Mutational analysis of two structural genes of the temperate lactococcal bacteriophage TP901-1 involved in tail length determination and baseplate assembly. Virology 276:315–328

    Article  CAS  PubMed  Google Scholar 

  24. Cardarelli L, Lam R, Tuite A et al (2010) The crystal structure of bacteriophage HK97 gp6: defining a large family of head–tail connector proteins. J Mol Biol 395:754–768

    Article  CAS  PubMed  Google Scholar 

  25. Ackermann HW, DuBow MS (1987) Viruses of prokaryotes. CRC Press, Boca Raton

    Google Scholar 

  26. Ryder L, Sharples GJ, Lloyd RG (1996) Recombination-dependent growth in exonuclease-depleted recBCsbcBC strains of Escherichia coli K-12. Genetics 143:1101–1114

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Mehr IJ, Long CD, Serkin CD et al (2000) A homologue of the recombination-dependent growth gene, Rdgc, is involved in Gonococcalpilin antigenic variation. Genetics 154:523–532

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Sharples GJ, Chan SN, Mahdi AA et al (1995) Processing of intermediates in recombination and DNA repair: identification of a new endonuclease that specifically cleaves Holliday junctions. EMBO J 13:6133–6142

    Google Scholar 

  29. Mahdi AA, Sharples GJ, Mandal TN et al (1996) Holliday junction resolvases encoded by homologous rusA genes in Escherichia coli K-12 and phage 82. J Mol Biol 257:561–573

    Article  CAS  PubMed  Google Scholar 

  30. Waite-Rees PA, Keating CJ, Moran LS et al (1991) Characterization and expression of the Escherichia coli Mrr restriction system. J Bacteriol 173:5207–5219

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. King G, Murray NE (1994) Restriction enzymes in cells, not eppendorfs. Trends Microbiol 2:465–469

    Article  CAS  PubMed  Google Scholar 

  32. Bazinet C, King J (1985) The DNA translocating vertex of dsDNA bacteriophage. Annu Rev Microbiol 39:109–129

    Article  CAS  PubMed  Google Scholar 

  33. Rao VB (2008) The bacteriophage DNA packaging motor. Annu Rev Genet 42:647–681

    Article  CAS  PubMed  Google Scholar 

  34. Baxevanis AD (2005) In: Baxevanis AD, Ouellette BFF (eds) Bioinformatics. Wiley, Hoboken, pp 295–324

  35. Claverie J-M, Notredame C (2007) Bioinformatics for dummies. Wiley Publishing Inc, Indianapolis

    Google Scholar 

  36. Krupovic M, Forterre P, Bamford DH (2010) Comparative analysis of the mosaic genomes of tailed archaeal viruses and proviruses suggests common themes for virion architecture and assembly with tailed viruses of bacteria. J Mol Biol 397:144–160

    Article  CAS  PubMed  Google Scholar 

  37. Pietilä MK, Laurinmäki P, Russell DA et al (2013) Insights into head-tailed viruses infecting extremely halophilic archaea. J Virol 87:3248–3260

    Article  PubMed  PubMed Central  Google Scholar 

  38. Garcia DL, Dillard JP (2006) AmiC functions as an N-acetylmuramyl-l-alanine amidase necessary for cell separation and can promote autolysis in Neisseria gonorrhoeae. J Bacteriol 188:7211–7221

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Fattah KR, Mizutani S, Fattah FJ et al (2000) A comparative study of the immunity region of lambdoid phages including Shiga-toxin-converting phages: molecular basis for cross immunity. Genes Genet Syst 75:223–232

    Article  CAS  PubMed  Google Scholar 

  40. Ptashne M (2004) A genetic switch: phage lambda revisited. Cold Spring Harbor Laboratory Press, Cold Spring Harbor

    Google Scholar 

  41. Lehours P, Vale FF, Bjursell MK et al (2011) Genome sequencing reveals a phage in Helicobacter pylori. Mbio 2:1867–1877

    Article  Google Scholar 

  42. Mei Y, He C, Huang Y et al (2015) Salinity regulation of the interaction of halovirus SNJ1 with its host and alteration of the halovirus replication strategy to adapt to the variable ecosystem. PLoS One 10:537–542

    Google Scholar 

  43. Aalto AP, Bitto D, Ravantti JJ et al (2012) Snapshot of virus evolution in hypersaline environments from the characterization of a membrane-containing salisaeta icosahedral phage 1. Proc Natl Acad Sci USA 109:7079–7084

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Casjens SR, Gilcrease EB, Huang WM et al (2004) The pKO2 linear plasmid prophage of Klebsiella oxytoca. J Bacteriol 186:1818–1832

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Ravin V, Ravin N, Casjens S et al (2000) Genomic sequence and analysis of the atypical temperate bacteriophage N15. J Mol Biol 299:53–73

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was funded by grants from the National Natural Science Foundation of China (31660042, 31200138, 31660001 and 31660089), the National Infrastructure of Natural Resources for Science and Technology Program of China (NIMR-2016-8) and the Yunnan Provincial Sciences and Technology Department (2014FB104, 2009CD012) and the Yunnan University (2009C14Q).

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Authors and Affiliations

  1. Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, Yunnan, People’s Republic of China

    Chaoqun Fu, Qin Zhao, Zhiying Li, Yongxia Wang, Yonghong Lai, Wei Xiao & Xiaolong Cui

  2. State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, People’s Republic of China

    Chaoqun Fu, Wei Xiao & Xiaolong Cui

  3. Yunnan Engineering Laboratory of Soil Fertility and Pollution Remediation, Yunnan Agricultural University, Kunming, 650201, Yunnan, People’s Republic of China

    Shiying Zhang

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  1. Chaoqun Fu
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Correspondence to Wei Xiao or Xiaolong Cui.

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Fu, C., Zhao, Q., Li, Z. et al. Complete genome sequence of Halomonas ventosae virulent halovirus QHHSV-1. Arch Virol 162, 3215–3219 (2017). https://doi.org/10.1007/s00705-017-3415-0

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  • DOI: https://doi.org/10.1007/s00705-017-3415-0

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