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Genomic analysis of a novel active prophage of Hafnia paralvei

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Abstract

Little is known about the prophages in Hafniaceae bacteria. A novel Hafnia phage, yong2, was induced from Hafnia paralvei by treatment with mitomycin C. The phage has an elliptical head with dimensions of approximately 45 × 38 nm and a long noncontractile tail of approximately 157 × 4 nm. The complete genome of Hafnia phage yong2 is a 39,546-bp double-stranded DNA with a G+C content of 49.9%, containing 59 open reading frames (ORFs) and having at least one fixed terminus (GGGGCAGCGACA). In phylogenetic analysis, Hafnia phage yong2 clustered with four predicted Hafnia prophages and one predicted Enterobacteriaceae prophage. These prophages and members of the family Drexlerviridae together formed two distinct subclades nested within a clade, suggesting the existence of a novel class of prophages with conserved sequences and a unique evolutionary status not yet studied before in Hafniaceae and Enterobacteriaceae bacteria.

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Acknowledgements

We are grateful for high-quality technical support provided by Pingping Zhan of the Electron Microscopy Laboratory of Ningbo University.

Funding

This study was funded by the National Key Research and Development program (2018YFA0903000) and the Open Fund of Key Laboratory of Marine Biogenetic Resources of State Oceanic Administration (HY201602), and sponsored by the K. C. Wong Magna Fund of Ningbo University.

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Authors and Affiliations

  1. Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China

    Lingting Pan, Dengfeng Li, Wencai Liu, Weinan Qin & Lihua Xu

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

    Lingting Pan, Wei Lin & Yigang Tong

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  1. Lingting Pan
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  2. Dengfeng Li
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Contributions

Dengfeng Li, Lingting Pan, and Yigang Tong designed the research. Lingting Pan, Dengfeng Li, Wei Lin, Yigang Tong, Wencai Liu, Weinan Qin, and Lihua Xu performed the research. Lingting Pan and Dengfeng Li analyzed data and wrote the paper. All authors have read and agreed to the published version of the manuscript.

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Correspondence to Dengfeng Li or Yigang Tong.

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705_2022_5498_MOESM1_ESM.tif

Supplementary Fig. S1 Proteomic tree based on genome-wide similarities determined by tBLASTx for 114 members of the class Caudoviricetes, Hafnia phage yong2, five predicted prophages related to Hafnia phage yong2, and the nine Hafnia phages introduced in the second paragraph. The red star indicates Hafnia phage yong2. The blue stars indicate the nine Hafnia phages. The green stars indicate the five predicted prophages related to Hafnia phage yong2 (TIF 56514 KB)

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Pan, L., Li, D., Lin, W. et al. Genomic analysis of a novel active prophage of Hafnia paralvei. Arch Virol 167, 2027–2034 (2022). https://doi.org/10.1007/s00705-022-05498-4

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