Skip to main content
SpringerLink
Log in

Characterization and complete genome sequence analysis of phage GP4, a novel lytic Bcep22-like podovirus

  • Brief Report
  • Published:
Archives of Virology Aims and scope Submit manuscript

Abstract

We isolated a novel lytic phage of Ralstonia solanacearum, GP4. The GP4 phage has a latent period of ~ 2 h at its optimal multiplicity of infection and is stable at temperatures ranging from 40–70 °C. GP4 lysed 16 strains of R. solanacearum belonging to phylotype IV. High-throughput sequencing revealed that GP4 has a linear dsDNA genome that consists of 61,129 bp, contains 83 open reading frames, and encodes a tRNA for cysteine. The GP4 genome has low similarity to other phage sequences in the GenBank database. Phylogenetic analysis indicated that GP4 can be taxonomically classified as a member of the Bcep22-like subfamily of the family Podoviridae.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

References

  1. Hayward AC (1991) Biology and epidemiology of bacterial wilt caused by pseudomonas solanacearum. Ann Rev Phytopathol 29:65–87

    Article  CAS  Google Scholar 

  2. Peeters N, Guidot A, Vailleau F, Valls M (2013) Ralstonia solanacearum, a widespread bacterial plant pathogen in the post-genomic era. Mol Plant Pathol 14:651

    Article  CAS  PubMed  Google Scholar 

  3. Yu Q, Alvarez AM, Moore PH, Zee F, Kim MS (2003) Molecular diversity of Ralstonia solanacearum isolated from ginger in Hawaii. Phytopathology 93:1124

    Article  CAS  PubMed  Google Scholar 

  4. Elsas JD, Van Kastelein P, Vries PM, De Van Overbeek LS (2001) Effects of ecological factors on the survival and physiology of Ralstonia solanacearum bv. 2 in irrigation water. Can J Microbiol 47:842

    Article  PubMed  Google Scholar 

  5. Grey BE, Steck TR (2001) The viable but nonculturable state of Ralstonia solanacearum may be involved in long-term survival and plant infection. Appl Environ Microbiol 67:3866–3872

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Cruz AP, Ferreira V, Pianzzola MJ, Siri MI, Coll NS, Valls M (2014) A novel, sensitive method to evaluate potato germplasm for bacterial wilt resistance using a luminescent Ralstonia solanacearum reporter strain. Mol Plant Microb Interact 27:277–285

    Article  CAS  Google Scholar 

  7. Mcgarvey JA, Denny TP, Schell MA (1999) Spatial-temporal and quantitative analysis of growth and EPS I production by Ralstonia solanacearum in resistant and susceptible tomato cultivars. Phytopathology 89:1233

    Article  CAS  PubMed  Google Scholar 

  8. Rose S, Parker M, Punja ZK (2003) Efficacy of biological and chemical treatments for control of fusarium root and stem rot on greenhouse cucumber. Plant Dis 87:1462–1470

    Article  CAS  PubMed  Google Scholar 

  9. Su J, Sun H, Liu J, Guo Z, Fan G, Gu G, Wang G (2017) Complete genome sequence of a novel lytic bacteriophage isolated from Ralstonia solanacearum. Arch Virol 33:1–5

    CAS  Google Scholar 

  10. Akiko F, Mariko F, Ryosuke H, Takeru K, Makoto F, Takashi Y (2011) Biocontrol of Ralstonia solanacearum by treatment with lytic bacteriophages. Appl Environ Microbiol 77:4155

    Article  CAS  Google Scholar 

  11. Weiling F, Terri F, Oren M, Curtin JJ, Lehman SM, Donlan RM (2010) Bacteriophage cocktail for the prevention of biofilm formation by Pseudomonas aeruginosa on catheters in an in vitro model system. Antimicrob Agents Chemother 54:397–404

    Article  CAS  Google Scholar 

  12. Rossitto M, Fiscarelli EV, Rosati P (2018) Challenges and promises for planning future clinical research into bacteriophage therapy against Pseudomonas aeruginosa in cystic fibrosis. An argumentative review. Front Microbiol 9:775–790

    PubMed  Google Scholar 

  13. Birge EA (1981) Bacterial and bacteriophage genetics: An Introduction. Microbiology Series, Springer, New York

    Book  Google Scholar 

  14. Merabishvili M, Vandenheuvel D, Kropinski AM, Mast J, De VD, Verbeken G, Noben JP, Lavigne R, Vaneechoutte M, Pirnay JP (2014) Characterization of newly isolated lytic bacteriophages active against Acinetobacter baumannii. PLos One 9:e104853

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Chen M, Xu J, Yao H, Lu C, Zhang W (2016) Isolation, genome sequencing and functional analysis of two T7-like coliphages of avian pathogenic Escherichia coli. Gene 582:47–58

    Article  CAS  PubMed  Google Scholar 

  16. Fegan M, Prior P, Allen C, Prior P, Hayward AC (2005) How complex is the Ralstonia solanacearum species complex? Bact Wilt Dis Ralstonia Solanacearum Spec Complex 1:449–461

    Google Scholar 

  17. Mirzaei MK, Nilsson AS (2015) Isolation of phages for phage therapy: a comparison of spot tests and efficiency of plating analyses for determination of host range and efficacy. PLos One 10:e0118557

    Article  CAS  Google Scholar 

  18. Lu S, Le S, Tan Y, Zhu J, Li M, Rao X, Zou L, Li S, Wang J, Jin X (2013) Genomic and proteomic analyses of the terminally redundant genome of the Pseudomonas aeruginosa phage PaP1: establishment of genus PaP1-like phages. PLoS One 8:e62933

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Zhang X, Kang H, Li Y, Liu X, Yang Y, Li S, Pei G, Sun Q, Shu P, Mi Z (2015) Conserved termini and adjacent variable region of Twortlikevirus Staphylococcus phages. Virol Sin 30:433–440

    Article  CAS  PubMed  Google Scholar 

  20. Iida S, Streiff MB, Bickle TA, Arber W (1987) Two DNA antirestriction systems of bacteriophage P1, darA, and darB: characterization of darA- phages. Virology 157:156–166

    Article  CAS  PubMed  Google Scholar 

  21. Zhang Q, Xing S, Sun Q, Pei G, Cheng S, Liu Y, An X, Zhang X, Qu Y, Tong Y (2017) Characterization and complete genome sequence analysis of a novel virulent Siphoviridae phage against Staphylococcus aureus isolated from bovine mastitis in Xinjiang, China. Virus Genes 53:1–13

    Article  Google Scholar 

  22. Chen Y, Sun E, Song J, Yang L, Wu B (2018) Complete genome sequence of a novel T7-like bacteriophage from a pasteurella multocida capsular type A isolate. Curr Microbiol 75:574–579

    Article  CAS  PubMed  Google Scholar 

  23. Hall SD, Kolodner RD (1994) Homologous pairing and strand exchange promoted by the Escherichia coli RecT protein. Proc Natl Acad Sci USA 91:3205

    Article  CAS  PubMed  Google Scholar 

  24. Gill JJ, Summer EJ, Russell WK, Cologna SM, Carlile TM, Fuller AC, Kate K, Mebane LM, Parkinson BN, David S (2011) Genomes and characterization of phages Bcep22 and BcepIL02, founders of a novel phage type in Burkholderia cenocepacia. J Bacteriol 193:5300

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Casjens SR (2008) Diversity among the tailed-bacteriophages that infect the Enterobacteriaceae. Research in Microbiology 159:340–348

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Berry J, Summer EJ, Struck DK, Young R (2010) The final step in the phage infection cycle: the Rz and Rz1 lysis proteins link the inner and outer membranes. Mol Microbiol 70:341–351

    Article  CAS  Google Scholar 

  27. Gan HM, Sieo CC, Tang SGH, Omar AR, Yin WH (2013) The complete genome sequence of EC1-UPM, a novel N4-like bacteriophage that infects Escherichia coli O78:K80. Virol J 10:308

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 60:137–151

    Google Scholar 

Download references

Acknowledgements

Yigang Tong, Hui Liu, Taoxing Shi and Zhiqiang Mi conceived and designed the experiments and critically evaluated the manuscript. Hang Fan conducted sequence analyses. Ronghuan Wang conducted sequence analyses, biological characterization experiments and wrote the manuscript. Yu Cong isolated and identified the phage and conducted biological characterization experiments. All authors read and approved the final manuscript.

Funding

This research was supported by a grant from the National Key Research and Development Program of China (2015AA020108, 2016YFC1202705, AWS16J020 and AWS15J006), the National Natural Science Foundation of China (81572045, 81672001, and 81621005), and the State Key Laboratory of Pathogen and Biosecurity (SKLPBS1518).

Author information

Author notes

  1. Ronghuan Wang and Yu Cong have contributed equally to this work and should be regarded as co-first authors.

Authors and Affiliations

  1. School of Public Health, Lanzhou University, Lanzhou, 730000, China

    Ronghuan Wang & Hui Liu

  2. Feijielake Biotechnology Co., Ltd, Nanjing, 211100, China

    Yu Cong

  3. State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China

    Zhiqiang Mi, Hang Fan & Yigang Tong

  4. Academy of Military Medical Sciences, Beijing, 100085, China

    Taoxing Shi

  5. College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China

    Yigang Tong

Authors
  1. Ronghuan Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yu Cong
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Zhiqiang Mi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hang Fan
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Taoxing Shi
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Hui Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Yigang Tong
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Taoxing Shi, Hui Liu or Yigang Tong.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Handling Editor: Chan-Shing Lin.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wang, R., Cong, Y., Mi, Z. et al. Characterization and complete genome sequence analysis of phage GP4, a novel lytic Bcep22-like podovirus. Arch Virol 164, 2339–2343 (2019). https://doi.org/10.1007/s00705-019-04309-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-019-04309-7

Search

Navigation