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Pan L, Li D, Lin W, Liu W, Qin W, Xu L, Tong Y. Genomic analysis of a novel active prophage of Hafnia paralvei. Arch Virol 2022; 167:2027-2034. [PMID: 35752683 DOI: 10.1007/s00705-022-05498-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 04/20/2022] [Indexed: 11/30/2022]
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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Affiliation(s)
- Lingting Pan
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Dengfeng Li
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Wei Lin
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Wencai Liu
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Weinan Qin
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Lihua Xu
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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Pan L, Li D, Sun Z, Lin W, Hong B, Qin W, Xu L, Liu W, Zhou Q, Wang F, Cai R, Qian M, Tong Y. First Characterization of a Hafnia Phage Reveals Extraordinarily Large Burst Size and Unusual Plaque Polymorphism. Front Microbiol 2022; 12:754331. [PMID: 35211099 PMCID: PMC8861465 DOI: 10.3389/fmicb.2021.754331] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/20/2021] [Indexed: 01/25/2023] Open
Abstract
A unique lytic phage infecting Hafnia paralvei was isolated and identified. Hafnia phage Ca belongs to the family Autographiviridae, possessing an icosahedral head with a diameter of 55 nm and a short non-contractile tail. Unusually, the burst size of Hafnia phage Ca of 10,292 ± 1,097 plaque-forming units (PFUs)/cell is much larger than other dsDNA phages reported before. Compared to the genome of the related phage, Hafnia phage Ca genome contains extra genes including DNA mimic ocr, dGTP triphosphohydrolase inhibitor, endonuclease, endonuclease VII, and HNH homing endonuclease gene. Extraordinarily, the phage developed different sizes of plaques when a single plaque was picked out and inoculated on a double-layer Luria broth agar plate with its host. Furthermore, varied packaging tightness for the tails of Hafnia phage Ca was observed (tail length: 4.35–45.92 nm). Most of the tails appeared to be like a cone with appendages, some were dot-like, bun-like, table tennis racket handle-like, and ponytail-like. Although the complete genome of Hafnia phage Ca is 40,286 bp, an incomplete genome with a deletion of a 397-bp fragment, containing one ORF predicted as HNH homing endonuclease gene (HEG), was also found by high throughput sequencing. Most of the genome of the virus particles in large plaques is complete (>98%), while most of the genome of the virus particles in small plaques is incomplete (>98%), and the abundance of both of them in medium-sized plaques is similar (complete, 40%; incomplete, 60%). In an experiment to see if the phage could be protective to brocade carps intramuscularly injected with H. paralvei LY-23 and phage Ca, the protection rate of Hafnia phage Ca to brocade carp (Cyprinus aka Koi) against H. paralvei was 33.38% (0.01 < p < 0.05). This study highlights some new insights into the peculiar biological and genomic characteristics of phage.
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Affiliation(s)
- Lingting Pan
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Dengfeng Li
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Zhitong Sun
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Wei Lin
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Binxin Hong
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Weinan Qin
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Lihua Xu
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Wencai Liu
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Qin Zhou
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Fei Wang
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Ruqian Cai
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Minhua Qian
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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Induction and Genomic Analysis of a Lysogenic Phage of Hafnia paralvei. Curr Microbiol 2022; 79:50. [PMID: 34982243 DOI: 10.1007/s00284-021-02698-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/25/2021] [Indexed: 11/03/2022]
Abstract
Hafnia paralvei is a bacterium that can cause zoonoses. No research has been reported on H. paralvei prophage. In this study, a Hafnia phage yong1 was induced from pathogenic H. paralvei LY-23 by mitomycin C. The phage showed a Myoviridae-like morphology having a hexagonal head of approximately 65 nm in diameter and a contractile tail of approximately 95 nm in length and 17 nm in width. Its genome was sequenced by using the Illumina Miseq platform. The complete genome of Hafnia phage yong1 is 43,329 bp with a G + C content of 47.65%. BLASTn analysis revealed that Hafnia phage yong1 had the highest sequence similarity with the predicted prophages of Enterobacter chengduensis strain WCHECl-C4 = WCHECh050004 recovered from a human blood sample and Escherichia coli strain L103-2 recovered from a goose farm in China. Hafnia phage yong1 contains a tRNA gene and 76 predicted open reading frames, 33 of which were annotated. Gene strings similar to the bacteriophage λ cro-cI-rexA-rexB operon conferring Imm and Rex to lysogenic cells were found in Hafnia phage yong1 genome. Hafnia phage yong1 is the first Myoviridae-like phage found to contain such contiguous genes. Hafnia phage yong1 formed an independent branch between two families, Chaseviridae and Drexlerviridae, in the Proteomic tree.
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Draft Genome Sequence of Hafnia paralvei Strain GTA-HAF03. GENOME ANNOUNCEMENTS 2015; 3:3/1/e01592-14. [PMID: 25700416 PMCID: PMC4335340 DOI: 10.1128/genomea.01592-14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Hafnia paralvei is a Gram-negative member of the Enterobacteriaceae family, closely related to the opportunistic pathogen Hafnia alvei. We report here the first draft genome sequence of H. paralvei, from the beef trim isolate GTA-HAF03, consisting of a 5.0-Mbp assembly encoding 4,382 proteins and 90 predicted RNAs.
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Savini V, Argentieri AV, Marrollo R, Carretto E, Fazii P, D’Antonio D, Huys G. The Italian Hafnia alvei strain LMG 27376 is Hafnia paralvei. Vet Microbiol 2013; 167:742-3. [DOI: 10.1016/j.vetmic.2013.07.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 07/24/2013] [Accepted: 07/26/2013] [Indexed: 10/26/2022]
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