1
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Kaminski PA. [A family of bacteriophages uses an expanded genetic alphabet]. Med Sci (Paris) 2022; 38:374-380. [PMID: 35485898 DOI: 10.1051/medsci/2022041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Bacteriophage genomes are the richest source of modified nucleobases of any life form. Of these, 2,6-diaminopurine (2-aminoadénine) that pairs with thymine by forming three hydrogen bonds is the only one violating Watson and Crick's base pairing. 2,6-diaminopurine (2-aminoadénine), initially found in the cyanophage S-2L, is more widespread than expected and has also been detected in bacteriophage infecting Gram-negative and Gram-positive bacteria. The biosynthetic pathway for aminoadenine containing DNA as well as the exclusion of adenine are now elucidated. This example of a natural deviation from the DNA canonical nucleotides represents only one of the possibilities explored by nature and provides a proof of concept for the synthetic biology of non-canonical nucleic acids.
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Affiliation(s)
- Pierre-Alexandre Kaminski
- Institut Pasteur, Université de Paris, CNRS UMR2001, Biologie des bactéries pathogènes à Gram-positif, F-75015, Paris, France
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2
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Barman RK, Chakrabarti AK, Dutta S. Screening of Potential Vibrio cholerae Bacteriophages for Cholera Therapy: A Comparative Genomic Approach. Front Microbiol 2022; 13:803933. [PMID: 35422793 PMCID: PMC9002330 DOI: 10.3389/fmicb.2022.803933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Cholera continues to be a major burden for developing nations, especially where sanitation, quality of water supply, and hospitalization have remained an issue. Recently, growing antimicrobial-resistant strains of Vibrio cholerae underscores alternative therapeutic strategies for cholera. Bacteriophage therapy is considered one of the best alternatives for antibiotic treatment. For the identification of potential therapeutic phages for cholera, we have introduced a comprehensive comparative analysis of whole-genome sequences of 86 Vibrio cholerae phages. We have witnessed extensive variation in genome size (ranging from 33 to 148 kbp), GC (G + C) content (varies from 34.5 to 50.8%), and the number of proteins (ranging from 15 to 232). We have identified nine clusters and three singletons using BLASTn, confirmed by nucleotide dot plot and sequence identity. A high degree of sequence and functional similarities in both the genomic and proteomic levels have been observed within the clusters. Evolutionary analysis confirms that phages are conserved within the clusters but diverse between the clusters. For each therapeutic phage, the top 2 closest phages have been identified using a system biology approach and proposed as potential therapeutic phages for cholera. This method can be applied for the classification of the newly isolated Vibrio cholerae phage. Furthermore, this systematic approach might be useful as a model for screening potential therapeutic phages for other bacterial diseases.
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Affiliation(s)
- Ranjan Kumar Barman
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Alok Kumar Chakrabarti
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
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3
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In Silico Approach Gives Insights into Ig-like Fold Containing Proteins in Vibrio parahaemolyticus: A Focus on the Fibrillar Adhesins. Toxins (Basel) 2022; 14:toxins14020133. [PMID: 35202160 PMCID: PMC8877628 DOI: 10.3390/toxins14020133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/06/2022] [Accepted: 02/08/2022] [Indexed: 12/10/2022] Open
Abstract
Immunoglobulin-like (Ig-like) fold domains are abundant on the surface of bacteria, where they are required for cell-to-cell recognition, adhesion, biofilm formation, and conjugative transfer. Fibrillar adhesins are proteins with Ig-like fold(s) that have filamentous structures at the cell surface, being thinner and more flexible than pili. While the roles of fibrillar adhesins have been proposed in bacteria overall, their characterization in Vibrio parahaemolyticus has not been established and, therefore, understanding about fibrillar adhesins remain limited in V. parahaemolyticus. This in silico analysis can aid in the systematic identification of Ig-like-folded and fibrillar adhesin-like proteins in V. parahaemolyticus, opening new avenues for disease prevention by interfering in microbial interaction between V. parahaemolyticus and the host.
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4
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Kaminski PA. Mechanisms supporting aminoadenine-based viral DNA genomes. Cell Mol Life Sci 2021; 79:51. [PMID: 34910247 PMCID: PMC11072226 DOI: 10.1007/s00018-021-04055-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/17/2021] [Accepted: 11/21/2021] [Indexed: 10/19/2022]
Abstract
Bacteriophage genomes are the richest source of modified nucleobases of any life form. Of these, 2,6 diaminopurine, which pairs with thymine by forming three hydrogen bonds violates Watson and Crick's base pairing. 2,6 diaminopurine initially found in the cyanophage S-2L is more widespread than expected and has also been detected in phage infecting Gram-negative and Gram-positive bacteria. The biosynthetic pathway for aminoadenine containing DNA as well as the exclusion of adenine are now elucidated. This example of a natural deviation from the genetic code represents only one of the possibilities explored by nature and provides a proof of concept for the synthetic biology of non-canonical nucleic acids.
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Affiliation(s)
- P A Kaminski
- Biologie des Bactéries Pathogènes à Gram-Positif, Institut Pasteur, CNRS-UMR 2001, Paris, France.
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5
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Czernecki D, Hu H, Romoli F, Delarue M. Structural dynamics and determinants of 2-aminoadenine specificity in DNA polymerase DpoZ of vibriophage ϕVC8. Nucleic Acids Res 2021; 49:11974-11985. [PMID: 34751404 PMCID: PMC8599892 DOI: 10.1093/nar/gkab955] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 11/12/2022] Open
Abstract
All genetic information in cellular life is stored in DNA copolymers composed of four basic building blocks (ATGC-DNA). In contrast, a group of bacteriophages belonging to families Siphoviridae and Podoviridae has abandoned the usage of one of them, adenine (A), replacing it with 2-aminoadenine (Z). The resulting ZTGC-DNA is more stable than its ATGC-DNA counterpart, owing to the additional hydrogen bond present in the 2-aminoadenine:thymine (Z:T) base pair, while the additional amino group also confers resistance to the host endonucleases. Recently, two classes of replicative proteins found in ZTGC-DNA-containing phages were characterized and one of them, DpoZ from DNA polymerase A (PolA) family, was shown to possess significant Z-vs-A specificity. Here, we present the crystallographic structure of the apo form of DpoZ of vibriophage ϕVC8, composed of the 3′-5′ exonuclease and polymerase domains. We captured the enzyme in two conformations that involve the tip of the thumb subdomain and the exonuclease domain. We highlight insertions and mutations characteristic of ϕVC8 DpoZ and its close homologues. Through mutagenesis and functional assays we suggest that the preference of ϕVC8 DpoZ towards Z relies on a polymerase backtracking process, more efficient when the nascent base pair is A:T than when it is Z:T.
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Affiliation(s)
- Dariusz Czernecki
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, 75015 Paris, France.,Sorbonne Université, Collège Doctoral, ED 515, 75005 Paris, France
| | - Haidai Hu
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, 75015 Paris, France
| | - Filippo Romoli
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, 75015 Paris, France
| | - Marc Delarue
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, 75015 Paris, France
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6
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Genome and Ecology of a Novel Alteromonas Podovirus, ZP6, Representing a New Viral Genus, Mareflavirus. Microbiol Spectr 2021; 9:e0046321. [PMID: 34643440 PMCID: PMC8515928 DOI: 10.1128/spectrum.00463-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Alteromonas is a ubiquitous, abundant, copiotrophic and phytoplankton-associated marine member of the Gammaproteobacteria with a range extending from tropical waters to polar regions and including hadal zones. Here, we describe a novel Alteromonas phage, ZP6, that was isolated from surface coastal waters of Qingdao, China. ZP6 contains a linear, double-stranded, 38,080-bp DNA molecule with 50.1% G+C content and 47 putative open reading frames (ORFs). Three auxiliary metabolic genes were identified, encoding metal-dependent phosphohydrolase, diaminopurine synthetase, and nucleotide pyrophosphohydrolase. The first two ORFs facilitate the replacement of adenine (A) by diaminopurine (Z) in phage genomes and help phages to evade attack from host restriction enzymes. The nucleotide pyrophosphohydrolase enables the host cells to stop programmed cell death and improves the survival rate of the host in a nutrient-depleted environment. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analysis revealed that ZP6 is most closely related to Enhodamvirus but with low similarity (shared genes, <30%, and average nucleotide sequence identity, <65%); it is distinct from other bacteriophages. Together, these results suggest that ZP6 could represent a novel viral genus, here named Mareflavirus. Combining its ability to infect Alteromonas, its harboring of a diaminopurine genome-biosynthetic system, and its representativeness of an understudied viral group, ZP6 could be an important and novel model system for marine virus research. IMPORTANCEAlteromonas is an important symbiotic bacterium of phytoplankton, but research on its bacteriophages is still at an elementary level. Our isolation and genome characterization of a novel Alteromonas podovirus, ZP6, identified a new viral genus of podovirus, namely, Mareflavirus. The ZP6 genome, with a diaminopurine genome-biosynthetic system, is different from those of other isolated Alteromonas phages and will bring new impetus to the development of virus classification and provide important insights into novel viral sequences from metagenomic data sets.
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Czernecki D, Bonhomme F, Kaminski PA, Delarue M. Characterization of a triad of genes in cyanophage S-2L sufficient to replace adenine by 2-aminoadenine in bacterial DNA. Nat Commun 2021; 12:4710. [PMID: 34354070 PMCID: PMC8342488 DOI: 10.1038/s41467-021-25064-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/21/2021] [Indexed: 11/09/2022] Open
Abstract
Cyanophage S-2L is known to profoundly alter the biophysical properties of its DNA by replacing all adenines (A) with 2-aminoadenines (Z), which still pair with thymines but with a triple hydrogen bond. It was recently demonstrated that a homologue of adenylosuccinate synthetase (PurZ) and a dATP triphosphohydrolase (DatZ) are two important pieces of the metabolism of 2-aminoadenine, participating in the synthesis of ZTGC-DNA. Here, we determine that S-2L PurZ can use either dATP or ATP as a source of energy, thereby also depleting the pool of nucleotides in dATP. Furthermore, we identify a conserved gene (mazZ) located between purZ and datZ genes in S-2L and related phage genomes. We show that it encodes a (d)GTP-specific diphosphohydrolase, thereby providing the substrate of PurZ in the 2-aminoadenine synthesis pathway. High-resolution crystal structures of S-2L PurZ and MazZ with their respective substrates provide a rationale for their specificities. The Z-cluster made of these three genes - datZ, mazZ and purZ - was expressed in E. coli, resulting in a successful incorporation of 2-aminoadenine in the bacterial chromosomal and plasmidic DNA. This work opens the possibility to study synthetic organisms containing ZTGC-DNA.
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Affiliation(s)
- Dariusz Czernecki
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, Paris, France
- Sorbonne Université, Collège Doctoral, ED 515, Paris, France
| | - Frédéric Bonhomme
- Unit of Epigenetic Chemical Biology, CNRS UMR 3523, 25-28 rue du Docteur Roux, Institut Pasteur, Paris, France
| | - Pierre-Alexandre Kaminski
- Unit of Biology of Pathogenic Gram-Positive Bacteria, CNRS UMR 2001, 25-28 rue du Docteur Roux, Institut Pasteur, Paris, France
| | - Marc Delarue
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, Paris, France.
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Sleiman D, Garcia PS, Lagune M, Loc'h J, Haouz A, Taib N, Röthlisberger P, Gribaldo S, Marlière P, Kaminski PA. A third purine biosynthetic pathway encoded by aminoadenine-based viral DNA genomes. Science 2021; 372:516-520. [PMID: 33926955 DOI: 10.1126/science.abe6494] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 03/25/2021] [Indexed: 01/06/2023]
Abstract
Cells have two purine pathways that synthesize adenine and guanine ribonucleotides from phosphoribose via inosylate. A chemical hybrid between adenine and guanine, 2-aminoadenine (Z), replaces adenine in the DNA of the cyanobacterial virus S-2L. We show that S-2L and Vibrio phage PhiVC8 encode a third purine pathway catalyzed by PurZ, a distant paralog of succinoadenylate synthase (PurA), the enzyme condensing aspartate and inosylate in the adenine pathway. PurZ condenses aspartate with deoxyguanylate into dSMP (N6-succino-2-amino-2'-deoxyadenylate), which undergoes defumarylation and phosphorylation to give dZTP (2-amino-2'-deoxyadenosine-5'-triphosphate), a substrate for the phage DNA polymerase. Crystallography and phylogenetics analyses indicate a close relationship between phage PurZ and archaeal PurA enzymes. Our work elucidates the biocatalytic innovation that remodeled a DNA building block beyond canonical molecular biology.
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Affiliation(s)
- Dona Sleiman
- Biology of Gram-Positive Pathogens, Institut Pasteur, CNRS-UMR 2001, Paris, France
| | - Pierre Simon Garcia
- Evolutionary Biology of the Microbial Cell, Institut Pasteur, CNRS-UMR 2001, Paris, France.,Stress Adaptation and Metabolism, Institut Pasteur, CNRS-UMR 2001, Paris, France
| | - Marion Lagune
- Biology of Gram-Positive Pathogens, Institut Pasteur, CNRS-UMR 2001, Paris, France
| | - Jerome Loc'h
- Structural Dynamics of Macromolecules, Institut Pasteur, CNRS-UMR 3528, Paris, France
| | - Ahmed Haouz
- Crystallography Platform, C2RT, Institut Pasteur, CNRS-UMR 3528, Paris, France
| | - Najwa Taib
- Evolutionary Biology of the Microbial Cell, Institut Pasteur, CNRS-UMR 2001, Paris, France.,Hub Bioinformatics and Biostatistics, Institut Pasteur, Paris, France
| | - Pascal Röthlisberger
- Bioorganic Chemistry of Nucleic Acids, Institut Pasteur, CNRS-UMR 3523, Paris, France
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell, Institut Pasteur, CNRS-UMR 2001, Paris, France
| | - Philippe Marlière
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
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9
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How cyanophage S-2L rejects adenine and incorporates 2-aminoadenine to saturate hydrogen bonding in its DNA. Nat Commun 2021; 12:2420. [PMID: 33893297 PMCID: PMC8065100 DOI: 10.1038/s41467-021-22626-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 03/16/2021] [Indexed: 02/02/2023] Open
Abstract
Bacteriophages have long been known to use modified bases in their DNA to prevent cleavage by the host's restriction endonucleases. Among them, cyanophage S-2L is unique because its genome has all its adenines (A) systematically replaced by 2-aminoadenines (Z). Here, we identify a member of the PrimPol family as the sole possible polymerase of S-2L and we find it can incorporate both A and Z in front of a T. Its crystal structure at 1.5 Å resolution confirms that there is no structural element in the active site that could lead to the rejection of A in front of T. To resolve this contradiction, we show that a nearby gene is a triphosphohydolase specific of dATP (DatZ), that leaves intact all other dNTPs, including dZTP. This explains the absence of A in S-2L genome. Crystal structures of DatZ with various ligands, including one at sub-angstrom resolution, allow to describe its mechanism as a typical two-metal-ion mechanism and to set the stage for its engineering.
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Botelho C, Dzevela Kong J, Ali Ber Lucien M, Shuai Z, Wang H. A mathematical model for Vibrio-phage interactions. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:2688-2712. [PMID: 33892567 DOI: 10.3934/mbe.2021137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A cholera model has been formulated to incorporate the interaction of bacteria and phage. It is shown that there may exist three equilibria: one disease free and two endemic equilibria. Threshold parameters have been derived to characterize stability of these equilibria. Sensitivity analysis and disease control strategies have been employed to characterize the impact of bacteria-phage interaction on cholera dynamics.
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Affiliation(s)
- Christopher Botelho
- Department of Mathematics, University of Central Florida, Orlando, Florida, 32816, USA
| | - Jude Dzevela Kong
- Department of Mathematics and Statistics, York University, Toronto, Ontario, M3J 1P3, Canada
- The Canadian Center for Disease Modelling, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Mentor Ali Ber Lucien
- Laboratoire National de Santé Publique, Ministère de la Santé Publique et de la Population d'Haiti, Port-au-Prince, HT6120, Haiti
| | - Zhisheng Shuai
- Department of Mathematics, University of Central Florida, Orlando, Florida, 32816, USA
| | - Hao Wang
- Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, Alberta, T6G 2G1, Canada
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Characterization and Genomic Analysis of ValSw3-3, a New Siphoviridae Bacteriophage Infecting Vibrio alginolyticus. J Virol 2020; 94:JVI.00066-20. [PMID: 32132234 PMCID: PMC7199398 DOI: 10.1128/jvi.00066-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/25/2020] [Indexed: 02/08/2023] Open
Abstract
A novel lytic bacteriophage, ValSw3-3, which efficiently infects pathogenic strains of Vibrio alginolyticus, was isolated from sewage water and characterized by microbiological and in silico genomic analyses. Transmission electron microscopy indicated that ValSw3-3 has the morphology of siphoviruses. This phage can infect four species in the Vibrio genus and has a latent period of 15 min and a burst size of 95 ± 2 PFU/infected bacterium. Genome sequencing results show that ValSw3-3 has a 39,846-bp double-stranded DNA genome with a GC content of 43.1%. The similarity between the genome sequences of ValSw3-3 and those of other phages recorded in the GenBank database was below 50% (42%), suggesting that ValSw3-3 significantly differs from previously reported phages at the DNA level. Multiple genome comparisons and phylogenetic analysis based on the major capsid protein revealed that phage ValSw3-3 is grouped in a clade with five other phages, including Listonella phage phiHSIC (GenBank accession no. NC_006953.1), Vibrio phage P23 (MK097141.1), Vibrio phage pYD8-B (NC_021561.1), Vibrio phage 2E1 (KX507045.1), and Vibrio phage 12G5 (HQ632860.1), and is distinct from all known genera within the Siphoviridae family that have been ratified by the International Committee on Taxonomy of Viruses (ICTV). An in silico proteomic comparison of diverse phages from the Siphoviridae family supported this clustering result and suggested that ValSw3-3, phiHSIC, P23, pYD8-B, 2E1, and 12G5 should be classified as a novel genus cluster of Siphoviridae A subsequent analysis of core genes also revealed the common genes shared within this new cluster. Overall, these results provide a characterization of Vibrio phage ValSw3-3 and support our proposal of a new viral genus within the family Siphoviridae IMPORTANCE Phage therapy has been considered a potential alternative to antibiotic therapy in treating bacterial infections. For controlling the vibriosis-causing pathogen Vibrio alginolyticus, well-documented phage candidates are still lacking. Here, we characterize a novel lytic Vibrio phage, ValSw3-3, based on its morphology, host range and infectivity, growth characteristics, stability under various conditions, and genomic features. Our results show that ValSw3-3 could be a potent candidate for phage therapy to treat V. alginolyticus infections due to its stronger infectivity and better pH and thermal stability than those of previously reported Vibrio phages. Moreover, genome sequence alignments, phylogenetic analysis, in silico proteomic comparison, and core gene analysis all support that this novel phage, ValSw3-3, and five unclassified phages form a clade distant from those of other known genera ratified by the ICTV. Thus, we propose a new viral genus within the Siphoviridae family to accommodate this clade, with ValSw3-3 as a representative member.
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12
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Decewicz P, Golec P, Szymczak M, Radlinska M, Dziewit L. Identification and Characterization of the First Virulent Phages, Including a Novel Jumbo Virus, Infecting Ochrobactrum spp. Int J Mol Sci 2020; 21:ijms21062096. [PMID: 32197547 PMCID: PMC7139368 DOI: 10.3390/ijms21062096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/14/2020] [Accepted: 03/16/2020] [Indexed: 12/26/2022] Open
Abstract
The Ochrobactrum genus consists of an extensive repertoire of biotechnologically valuable bacterial strains but also opportunistic pathogens. In our previous study, a novel strain, Ochrobactrum sp. POC9, which enhances biogas production in wastewater treatment plants (WWTPs) was identified and thoroughly characterized. Despite an insightful analysis of that bacterium, its susceptibility to bacteriophages present in WWTPs has not been evaluated. Using raw sewage sample from WWTP and applying the enrichment method, two virulent phages, vB_OspM_OC and vB_OspP_OH, which infect the POC9 strain, were isolated. These are the first virulent phages infecting Ochrobactrum spp. identified so far. Both phages were subjected to thorough functional and genomic analyses, which allowed classification of the vB_OspM_OC virus as a novel jumbo phage, with a genome size of over 227 kb. This phage encodes DNA methyltransferase, which mimics the specificity of cell cycle regulated CcrM methylase, a component of the epigenetic regulatory circuits in Alphaproteobacteria. In this study, an analysis of the overall diversity of Ochrobactrum-specific (pro)phages retrieved from databases and extracted in silico from bacterial genomes was also performed. Complex genome mining allowed us to build similarity networks to compare 281 Ochrobactrum-specific viruses. Analyses of the obtained networks revealed a high diversity of Ochrobactrum phages and their dissimilarity to the viruses infecting other bacteria.
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Affiliation(s)
- Przemyslaw Decewicz
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (P.D.); (M.R.)
| | - Piotr Golec
- Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (P.G.); (M.S.)
| | - Mateusz Szymczak
- Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (P.G.); (M.S.)
| | - Monika Radlinska
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (P.D.); (M.R.)
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (P.D.); (M.R.)
- Correspondence: ; Tel.: +48-225-541-406
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Ina-Salwany MY, Al-Saari N, Mohamad A, Mursidi FA, Mohd-Aris A, Amal MNA, Kasai H, Mino S, Sawabe T, Zamri-Saad M. Vibriosis in Fish: A Review on Disease Development and Prevention. JOURNAL OF AQUATIC ANIMAL HEALTH 2019; 31:3-22. [PMID: 30246889 DOI: 10.1002/aah.10045] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/16/2018] [Indexed: 05/19/2023]
Abstract
Current growth in aquaculture production is parallel with the increasing number of disease outbreaks, which negatively affect the production, profitability, and sustainability of the global aquaculture industry. Vibriosis is among the most common diseases leading to massive mortality of cultured shrimp, fish, and shellfish in Asia. High incidence of vibriosis can occur in hatchery and grow-out facilities, but juveniles are more susceptible to the disease. Various factors, particularly the source of fish, environmental factors (including water quality and farm management), and the virulence factors of Vibrio, influence the occurrence of the disease. Affected fish show weariness, with necrosis of skin and appendages, leading to body malformation, slow growth, internal organ liquefaction, blindness, muscle opacity, and mortality. A combination of control measures, particularly a disease-free source of fish, biosecurity of the farm, improved water quality, and other preventive measures (e.g., vaccination) might be able to control the infection. Although some control measures are expensive and less practical, vaccination is effective, relatively cheap, and easily implemented. In this review, the latest knowledge on the pathogenesis and control of vibriosis, including vaccination, is discussed.
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Affiliation(s)
- M Y Ina-Salwany
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Nurhidayu Al-Saari
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- International Institute for Halal Research and Training, International Islamic University Malaysia, KICT Building, Level 3, 53100, Gombak, Selangor, Malaysia
| | - Aslah Mohamad
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Fathin-Amirah Mursidi
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Aslizah Mohd-Aris
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Department of Biology, School of Biology, Universiti Teknologi MARA, Kampus Kuala Pilah, 72000, Kuala Pilah, Negeri Sembilan, Malaysia
| | - M N A Amal
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Hisae Kasai
- Laboratory of Fish Pathology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, 041-8611, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, 041-8611, Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, 041-8611, Japan
| | - M Zamri-Saad
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Department of Veterinary Laboratory Diagnosis, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
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14
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Guardiola-Avila I, Martínez-Vázquez V, Requena-Castro R, Juárez-Rendón K, Aguilera-Arreola M, Rivera G, Bocanegra-García V. Isolation and identification ofVibriospecies in the Rio Bravo/Grande and water bodies from Reynosa, Tamaulipas. Lett Appl Microbiol 2018; 67:190-196. [DOI: 10.1111/lam.13009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/11/2018] [Accepted: 05/12/2018] [Indexed: 02/02/2023]
Affiliation(s)
- I. Guardiola-Avila
- CONACyT Research Fellow; Centro de Biotecnología Genómica; Instituto Politécnico Nacional; Reynosa Tamaulipas México
| | - V. Martínez-Vázquez
- Centro de Biotecnología Genómica; Instituto Politécnico Nacional; Reynosa Tamaulipas México
| | - R. Requena-Castro
- Centro de Biotecnología Genómica; Instituto Politécnico Nacional; Reynosa Tamaulipas México
| | - K. Juárez-Rendón
- CONACyT Research Fellow; Centro de Biotecnología Genómica; Instituto Politécnico Nacional; Reynosa Tamaulipas México
| | - M.G. Aguilera-Arreola
- Escuela Nacional de Ciencias Biológicas; Instituto Politécnico Nacional; Ciudad de México; Mexico City México
| | - G. Rivera
- Centro de Biotecnología Genómica; Instituto Politécnico Nacional; Reynosa Tamaulipas México
| | - V. Bocanegra-García
- Centro de Biotecnología Genómica; Instituto Politécnico Nacional; Reynosa Tamaulipas México
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15
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Cholera: an overview with reference to the Yemen epidemic. Front Med 2018; 13:213-228. [DOI: 10.1007/s11684-018-0631-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 12/18/2017] [Indexed: 12/12/2022]
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