An overview on Vibrio temperate phages: Integration mechanisms, pathogenicity, and lysogeny regulation

Zaatout, Nawel; Ouchene, Rima; Bouaziz, Amira

doi:10.1016/j.micpath.2022.105490

Cited by 11 publications

(11 citation statements)

References 116 publications

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“…The literature has described co‐infections between two or more prophages with different zot‐type genes. In these cases, one of the Zot can serve as a phage assembly protein, while other variants of Zot can have a role in virulence (Ma et al, 2022; Nawel et al, 2022). The analysis of the tripartite network showed that different types of prophages, carrying different Zot types, were associated with the same species of Vibrio .…”

Section: Discussionmentioning

confidence: 99%

“…Zot protein is an enterotoxin that increases the permeability of the small intestine, disassembling the intercellular tight junctions (Di Pierro et al, 2001). zot ‐like genes have been found in different prophages present in several Vibrio species, which may also play a role in phage assembly (Castillo et al, 2018; Mauritzen et al, 2020; Nawel et al, 2022). There are different types of prophages carrying Zot in Vibrios , but there are also different types of Zot (Ma et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

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Prophages carrying Zot toxins on different Vibrio genomes: A comprehensive assessment using multilayer networks

Soto,

Alegría,

Sepúlveda

et al. 2024

Environmental Microbiology

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Vibrios, a group of bacteria that are among the most abundant in marine environments, include several species such as Vibrio cholerae and Vibrio parahaemolyticus, which can be pathogenic to humans. Some species of Vibrio contain prophages within their genomes. These prophages can carry genes that code for toxins, such as the zonula occludens toxin (Zot), which contribute to bacterial virulence. Understanding the association between different Vibrio species, prophages and Zot genes can provide insights into their ecological interactions. In this study, we evaluated 4619 Vibrio genomes from 127 species to detect the presence of prophages carrying the Zot toxin. We found 2030 potential prophages with zot‐like genes in 43 Vibrio species, showing a non‐random association within a primarily modular interaction network. Some prophages, such as CTX or Vf33, were associated with specific species. In contrast, prophages phiVCY and VfO3K6 were found in 28 and 20 Vibrio species, respectively. We also identified six clusters of Zot‐like sequences in prophages, with the ZOT2 cluster being the most frequent, present in 34 Vibrio species. This analysis helps to understand the distribution patterns of zot‐containing prophages across Vibrio genomes and the potential routes of Zot‐like toxin dissemination.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Prophages carrying Zot toxins on different Vibrio genomes: A comprehensive assessment using multilayer networks

Soto,

Alegría,

Sepúlveda

et al. 2024

Environmental Microbiology

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“…Bacterial genes may integrate into the prophage genome during replication and result in a longer genome or lose redundant genes from the prophage in order to facilitate its own replication, which results in the intermingling of host and prophage gene fragments and then changes the genome size of prophages from host species. This biodiversity in prophage genomes increases the host population-level diversity and drives the continuous host evolution (Nawel et al, 2022 ). It is rational that similar ecological functions can be mirrored by the Acetobacter -specific prophages, and the rich diversity and broad diffusivity of Acetobacter prophage populations drive the genetic plasticity of Acetobacter .…”

Section: Discussionmentioning

confidence: 99%

Comprehensive deciphering prophages in genus Acetobacter on the ecology, genomic features, toxin–antitoxin system, and linkage with CRISPR-Cas system

Qian

Liang

et al. 2022

Front. Microbiol.

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Acetobacter is the predominant microbe in vinegar production, particularly in those natural fermentations that are achieved by complex microbial communities. Co-evolution of prophages with Acetobacter, including integration, release, and dissemination, heavily affects the genome stability and production performance of industrial strains. However, little has been discussed yet about prophages in Acetobacter. Here, prophage prediction analysis using 148 available genomes from 34 Acetobacter species was carried out. In addition, the type II toxin–antitoxin systems (TAs) and CRISPR-Cas systems encoded by prophages or the chromosome were analyzed. Totally, 12,000 prophage fragments were found, of which 350 putatively active prophages were identified in 86.5% of the selected genomes. Most of the active prophages (83.4%) belonged to the order Caudovirales dominated by the families Siphoviridae and Myroviridae prophages (71.4%). Notably, Acetobacter strains survived in complex environments that frequently carried multiple prophages compared with that in restricted habits. Acetobacter prophages showed high genome diversity and horizontal gene transfer across different bacterial species by genomic feature characterization, average nucleotide identity (ANI), and gene structure visualization analyses. About 31.14% of prophages carry type II TAS, suggesting its important role in addiction, bacterial defense, and growth-associated bioprocesses to prophages and hosts. Intriguingly, the genes coding for Cse1, Cse2, Cse3, Cse4, and Cas5e involved in type I-E and Csy4 involved in type I-F CRISPR arrays were firstly found in two prophages. Type II-C CRISPR-Cas system existed only in Acetobacter aceti, while the other Acetobacter species harbored the intact or eroded type I CRISPR-Cas systems. Totally, the results of this study provide fundamental clues for future studies on the role of prophages in the cell physiology and environmental behavior of Acetobacter.

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“…Lytic phages infect a bacterial host, replicate, and then trigger cell lysis to release the mature phage progeny, killing the host in the process (Weinbauer, 2004) (Figure 1, black arrows). Temperate phages, in contrast, undergo a second mode of infection termed ‘lysogeny’ wherein the viral DNA becomes stably integrated into the host genome and replicates as part of the bacterial chromosome (Brady et al, 2021; Nawel et al, 2022) (Figure 1, blue arrows). Phage induction under these conditions occurs spontaneously at very low frequency or in response to environmental stressors and cues such as DNA damage (Howard‐Varona et al, 2017) and provides a pathway for escape when conditions become unfavorable.…”

Section: An Adversarial Arms Racementioning

confidence: 99%

Everything OLD is new again: How structural, functional, and bioinformatic advances have redefined a neglected nuclease family

Dot,

Thomason,

Chappie

2023

Molecular Microbiology

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Overcoming lysogenization defect (OLD) proteins are a conserved family of ATP‐powered nucleases that function in anti‐phage defense. Recent bioinformatic, genetic, and crystallographic studies have yielded new insights into the structure, function, and evolution of these enzymes. Here we review these developments and propose a new classification scheme to categorize OLD homologs that relies on gene neighborhoods, biochemical properties, domain organization, and catalytic machinery. This taxonomy reveals important similarities and differences between family members and provides a blueprint to contextualize future in vivo and in vitro findings. We also detail how OLD nucleases are related to PARIS and Septu anti‐phage defense systems and discuss important mechanistic questions that remain unanswered.

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An overview on Vibrio temperate phages: Integration mechanisms, pathogenicity, and lysogeny regulation

Cited by 11 publications

References 116 publications

Prophages carrying Zot toxins on different Vibrio genomes: A comprehensive assessment using multilayer networks

Prophages carrying Zot toxins on different Vibrio genomes: A comprehensive assessment using multilayer networks

Comprehensive deciphering prophages in genus Acetobacter on the ecology, genomic features, toxin–antitoxin system, and linkage with CRISPR-Cas system

Everything OLD is new again: How structural, functional, and bioinformatic advances have redefined a neglected nuclease family

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