Raoultella bacteriophage RP180, a new member of the genus Kagunavirus, subfamily Guernseyvirinae
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.
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Conflict of interest
There are no conflicts of interest.
This article does not involve studies with human participants or animals.
- 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.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.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.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.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.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.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.Okonechnikov K, Golosova O, Fursov M et al (2012) Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28(8):1166–1167Google Scholar
- 9.Lu G, Moriyama EN (2004) Vector NTI, a balanced all-in-one sequence analysis suite. Brief Bioinform 5(4):378–388Google Scholar
- 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.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.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.Grant JR, Stothard P (2008) The CGView server: a comparative genomics tool for circular genomes. Nucl Acids Res 36:181–184Google Scholar
- 14.Phillips JL, Gnanakaran S (2015) BioEdit: an important software for molecular biology. Proteins Struct Funct Bioinform 83(1):46–65Google Scholar
- 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.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.Anany H, Switt AIM, De Lappe N et al (2015) A proposed new bacteriophage subfamily: Jerseyvirinae. Arch Virol 160(4):1021–1033Google Scholar
- 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.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.Hudaiberdiev S, Shmakov S, Wolf YI et al (2017) Phylogenomics of Cas4 family nucleases. BMC Evol Biol 17(1):1–14Google Scholar
- 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.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.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