Mutation-induced infections of phage-plasmids

Shan, Xiaoyu; Szabo, Rachel E.; Cordero, Otto X.

doi:10.1038/s41467-023-37512-x

Cited by 9 publications

(10 citation statements)

References 57 publications

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“…In contrast, genes in plasmids and P-Ps can be at a higher copy number than the chromosome (and that of the integrated prophages) during a long period of time, which provides opportunity to evolve faster 68 . Polyploidy of a P-P was recently shown to facilitate the rapid spread of mutated alleles in a population 69 . Life cycles and fitness costs of plasmids and phages are very different.…”

Section: Discussionmentioning

confidence: 99%

Phage-plasmids promote recombination and emergence of phages and plasmids

Pfeifer,

Rocha

2024

Nat Commun

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Phages and plasmids are regarded as distinct types of mobile genetic elements that drive bacterial evolution by horizontal gene transfer. However, the distinction between both types is blurred by the existence of elements known as prophage-plasmids or phage-plasmids, which transfer horizontally between cells as viruses and vertically within cellular lineages as plasmids. Here, we study gene flow between the three types of elements. We show that the gene repertoire of phage-plasmids overlaps with those of phages and plasmids. By tracking recent recombination events, we find that phage-plasmids exchange genes more frequently with plasmids than with phages, and that direct gene exchange between plasmids and phages is less frequent in comparison. The results suggest that phage-plasmids can mediate gene flow between plasmids and phages, including exchange of mobile element core functions, defense systems, and antibiotic resistance. Moreover, a combination of gene transfer and gene inactivation may result in the conversion of elements. For example, gene loss turns P1-like phage-plasmids into integrative prophages or into plasmids (that are no longer phages). Remarkably, some of the latter have acquired conjugation-related functions to became mobilisable by conjugation. Thus, our work indicates that phage-plasmids can play a key role in the transfer of genes across mobile elements within their hosts, and can act as intermediates in the conversion of one type of element into another.

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Section: Discussionmentioning

confidence: 99%

Phage-plasmids promote recombination and emergence of phages and plasmids

Pfeifer,

Rocha

2024

Nat Commun

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“…Since few PPs are culturable, most knowledge surrounding PPs comes from the in-depth characterization of one PP, bacteriophage P1 22,24,27,28,38,39 . Given the absence of widely agreed-upon criteria for defining a PP, we used the key genomic and lifestyle features of P1 as a benchmark against which to evaluate Carjivirus communis as a candidate PP.…”

Section: Resultsmentioning

confidence: 99%

Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle

Schmidtke,

Hickey,

Liachko

et al. 2024

Preprint

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The prototypic crAssphage (Carjivirus communis) is one of the most abundant, prevalent, and persistent gut bacteriophages, yet it remains uncultured and its lifestyle uncharacterized. For the last decade, crAssphage has escaped plaque-dependent culturing efforts, leading us to investigate alternative lifestyles that might explain its widespread success. Through genomic analyses and culturing, we find that crAssphage uses a phage-plasmid lifestyle to persist extrachromosomally. Plasmid-related genes are more highly expressed than those implicated in phage maintenance. Leveraging this finding, we use a plaque-free culturing approach to measure crAssphage replication in culture with Phocaeicola vulgatus, Phocaeicola dorei, and Bacteroides stercoris, revealing a broad host range. We demonstrate that crAssphage persists with its hosts in culture without causing major cell lysis events or integrating into host chromosomes. The ability to switch between phage and plasmid lifestyles within a wide range of hosts contributes to the prolific nature of crAssphage in the human gut microbiome.

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“…Nonetheless, the identification of PluMu in different serovars and countries, as in this and other studies [9,10], indicates that active A. pleuropneumoniae lytic phage may be found in future studies. Alternative approaches such as the use of constitutively lytic phage-plasmids for therapeutic use may also be possible in the future [39].…”

Section: Discussionmentioning

confidence: 99%

PluMu - a Mu-like bacteriophage infectingActinobacillus pleuropneumoniae

Julia Bartsch,

Crespo,

Wang

et al. 2024

Preprint

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Actinobacillus pleuropneumoniaeis the causative agent of pleuropneumonia, an economically important lung disease of pigs. In draft genomes of two Cypriot clinicalA. pleuropneumoniaeisolates (MIDG3457 and MIDG3459), we previously identified single genomic regions with homology to Mu-like bacteriophage and presented preliminary evidence of active phage. Here, updated Phastest genomic analysis identified two loci in both MIDG3457 and MIDG3459 that were predicted to encode proteins with high homology to, and whose organization was characteristic of, Mu-like phages. Phylogenetically, the closest matches were withMannheimiaVb andGlaesserellaSuMu phages. Phastest scored the loci as ′complete′, indicating they produced active phage. PCR amplification of the Mu-like phagecandtailgenes from DNase-treated polyethylene glycol 8000 (PEG)-precipitated supernatants of MIDG3457 and MIDG3459 (grown in either Brain Heart Infusion-NAD or Grace′s Insect Medium-NAD broth) indicated the presence of intact virions. The phages from MIDG3457 and MIDG3459 were named PluMu 3457-1, 3457-2, and PluMu 3459-1 and PluMu 3459-2, respectively. Transmission electron microscopy (TEM) of PEG-precipitated supernatants of broth-grown MIDG3459 identified virions with icosahedral heads and tails, consistent with other Mu-like phages. We conclude that MIDG3459 produces an active Mu-like phage.

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Mutation-induced infections of phage-plasmids

Cited by 9 publications

References 57 publications

Phage-plasmids promote recombination and emergence of phages and plasmids

Phage-plasmids promote recombination and emergence of phages and plasmids

Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle

PluMu - a Mu-like bacteriophage infectingActinobacillus pleuropneumoniae

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