Archives of Virology

, Volume 164, Issue 10, pp 2637–2640 | Cite as

Raoultella bacteriophage RP180, a new member of the genus Kagunavirus, subfamily Guernseyvirinae

  • Mikhail V. Fofanov
  • Vera V. MorozovaEmail author
  • Yuliya N. Kozlova
  • Artem Yu. Tikunov
  • Igor V. Babkin
  • Yuliya E. Poletaeva
  • Elena I. Ryabchikova
  • Nina V. TikunovaEmail author
Annotated Sequence Record


A novel lytic Raoultella phage, RP180, was isolated and characterized. The RP180 genome has 44,851 base pairs and contains 65 putative genes, 35 of them encoding proteins whose functions were predicted based on sequence similarity to known proteins. The RP180 genome possesses a gene synteny typical of members of the subfamily Guernseyvirinae. Phylogenetic analysis of the RP180 genome and similar phage genomes revealed that phage RP180 is the first member of the genus Kagunavirus, subfamily Guernseyvirinae, that is specific for Raoultella sp. The genome of RP180 encodes a putative protein with similarity to CRISPR-like Cas4 nucleases, which belong to the pfam12705/PDDEXK_1 family. Cas4-like proteins of this family have been shown to interfere with the bacterial host type II-C CRISPR-Cas system.



This study was funded by RFBR Project No. 18-29-08015; Collection EMTC of ICBFM is supported by Russian State-Funded Budget Project ICBFM SB RAS # AAAA-A17-117020210027-9.

Compliance with ethical standards

Conflict of interest

There are no conflicts of interest.

Ethical approval

This article does not involve studies with human participants or animals.

Supplementary material

705_2019_4349_MOESM1_ESM.pdf (112 kb)
Supplementary material 1 (PDF 112 kb)
705_2019_4349_MOESM2_ESM.pdf (246 kb)
Supplementary material 2 (PDF 246 kb)
705_2019_4349_MOESM3_ESM.pdf (202 kb)
Supplementary material 3 (PDF 202 kb)


  1. 1.
    Drancourt M, Bollet C, Carta A, Rousselier P (2001) Phylogenetic analyses of Klebsiella species delineate Klebsiella and Raoultella gen. nov., with description of Raoultella ornithinolytica comb. nov., Raoultella terrigena comb. nov. and Raoultella planticola comb. nov. Int J Syst Evol Microbiol 51(3):925–932Google Scholar
  2. 2.
    Ershadi A, Weiss E, Verduzco E et al (2014) Emerging pathogen: a case and review of Raoultella planticola. Infection 42(6):1043–1046Google Scholar
  3. 3.
    Fager C, Yurteri-Kaplan L (2018) Urinary tract infection with rare pathogen Raoultella planticola: a post-operative case and review. Urol Case Rep 22:76–79Google Scholar
  4. 4.
    Mehmood H, Pervin N, Ul Haq MI et al (2018) A rare case of Raoultella planticola urinary tract infection in a patient with immunoglobulin A nephropathy. J Investig Med High Impact Case Rep 6:1–3Google Scholar
  5. 5.
    Hajjar R, Schwenter F, Sebajang H et al (2018) Community-acquired infection to Raoultella ornithinolytica presenting as appendicitis and shock in a healthy individual. J Surg Case Rep 5:1–3Google Scholar
  6. 6.
    Chen DQ, Song JL, Tang HX et al (2014) Extensively drug-resistant Raoultella planticola carrying multiple resistance genes including blaNDM-1. JMM Case Rep 1(3):3–5Google Scholar
  7. 7.
    Morozova V, Kozlova Y, Shedko E et al (2016) Lytic bacteriophage PM16 specific for Proteus mirabilis: a novel member of the genus Phikmvvirus. Arch Virol 161(9):2457–2472Google Scholar
  8. 8.
    Okonechnikov K, Golosova O, Fursov M et al (2012) Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28(8):1166–1167Google Scholar
  9. 9.
    Lu G, Moriyama EN (2004) Vector NTI, a balanced all-in-one sequence analysis suite. Brief Bioinform 5(4):378–388Google Scholar
  10. 10.
    Lowe TM, Chan PP (2012) tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucl Acids Res 44:54–57Google Scholar
  11. 11.
    Liu B, Zheng D, Jin Q et al (2019) VFDB 2019: a comparative pathogenomic platform with an interactive web interface. Nucl Acids Res 47(D1):D687–D692Google Scholar
  12. 12.
    Katoh K, Rozewicki J, Yamada KD (2017) MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform 18:1–7Google Scholar
  13. 13.
    Grant JR, Stothard P (2008) The CGView server: a comparative genomics tool for circular genomes. Nucl Acids Res 36:181–184Google Scholar
  14. 14.
    Phillips JL, Gnanakaran S (2015) BioEdit: an important software for molecular biology. Proteins Struct Funct Bioinform 83(1):46–65Google Scholar
  15. 15.
    Guindon S, Dufayard J, Lefort V et al (2010) New algorithms and methods to estimate maximim-likelihood phylogenies assessing the performance of PhyML 3.0. Syst Biol 59(3):1–37Google Scholar
  16. 16.
    Ackermann H-W (2009) Phage classification and characterization. In: Clokie MR, Kropinski AM (eds) Bacteriophages methods protocol, vol 1. ISOL character interaction. Humana Press, New York, pp 127–140Google Scholar
  17. 17.
    Anany H, Switt AIM, De Lappe N et al (2015) A proposed new bacteriophage subfamily: Jerseyvirinae. Arch Virol 160(4):1021–1033Google Scholar
  18. 18.
    Hooton SPT, Connerton IF (2015) Campylobacter jejuni acquire new host-derived CRISPR spacers when in association with bacteriophages harboring a CRISPR-like Cas4 protein. Front Microbiol 5:1–9Google Scholar
  19. 19.
    Hooton SPT, Brathwaite KJ, Connerton IF (2016) The bacteriophage carrier state of Campylobacter jejuni features changes in host non-coding RNAs and the acquisition of new host-derived CRISPR spacer sequences. Front Microbiol 7:1–8Google Scholar
  20. 20.
    Hudaiberdiev S, Shmakov S, Wolf YI et al (2017) Phylogenomics of Cas4 family nucleases. BMC Evol Biol 17(1):1–14Google Scholar
  21. 21.
    Retamales J, Vasquez I, Santos L et al (2016) Complete genome sequences of lytic bacteriophages of Xanthomonas arboricola pv. juglandis. Genome Announc 4(3):3–4Google Scholar
  22. 22.
    Li E, Wei X, Ma Y et al (2016) Isolation and characterization of a bacteriophage phiEap-2 infecting multidrug resistant Enterobacter aerogenes. Sci Rep 6(1):1–9Google Scholar
  23. 23.
    Denyes JM, Krell PJ, Manderville RA et al (2014) The genome and proteome of Serratia bacteriophage η which forms unstable lysogens. Virol J 11(1):1–8Google Scholar

Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Institute of Chemical Biology and Fundamental Medicine SB RASNovosibirskRussia
  2. 2.Novosibirsk State UniversityNovosibirskRussia

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