The phage defence island of a multidrug resistant plasmid uses both BREX and type IV restriction for complementary protection from viruses

Picton, David M; Luyten, Yvette A.; Morgan, Richard D.; Nelson, Andrew; Smith, Darren; Dryden, David T. F.; Hinton, Jay C. D.; Blower, Tim R.

doi:10.1093/nar/gkab906

Cited by 58 publications

(107 citation statements)

References 63 publications

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“…Such MGE-encoded defenses may also be multilayered. For example, E. coli plasmids encoding both BREX and type IV restriction systems have recently been shown to provide complementary protection from phages [59]. This does not exclude the possibility that cells select for multiple systems of defense, but does suggest that to understand their frequency in cells one must also account for the infectivity of MGEs.…”

Section: Why Are There So Many Defense Systems In Each Genome?mentioning

confidence: 99%

Microbial defenses against mobile genetic elements and viruses: Who defends whom from what?

2022

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Prokaryotes have numerous mobile genetic elements (MGEs) that mediate horizontal gene transfer (HGT) between cells. These elements can be costly, even deadly, and cells use numerous defense systems to filter, control, or inactivate them. Recent studies have shown that prophages, conjugative elements, their parasites (phage satellites and mobilizable elements), and other poorly described MGEs encode defense systems homologous to those of bacteria. These constitute a significant fraction of the repertoire of cellular defense genes. As components of MGEs, these defense systems have presumably evolved to provide them, not the cell, adaptive functions. While the interests of the host and MGEs are aligned when they face a common threat such as an infection by a virulent phage, defensive functions carried by MGEs might also play more selfish roles to fend off other antagonistic MGEs or to ensure their maintenance in the cell. MGEs are eventually lost from the surviving host genomes by mutational processes and their defense systems can be co-opted when they provide an advantage to the cell. The abundance of defense systems in MGEs thus sheds new light on the role, effect, and fate of the so-called “cellular defense systems,” whereby they are not only merely microbial defensive weapons in a 2-partner arms race, but also tools of intragenomic conflict between multiple genetic elements with divergent interests that shape cell fate and gene flow at the population level.

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Section: Why Are There So Many Defense Systems In Each Genome?mentioning

confidence: 99%

Microbial defenses against mobile genetic elements and viruses: Who defends whom from what?

2022

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“…Escherichia plasmids had much fewer Rep_1 genes than the population in general, but they were otherwise fairly representative of the population (Supplemental Table 8). Escherichia is a common gut bacterium 74 , and thus likely present in sewage, lending credence to its prediction as a host. E. coli had by far the most varied range of backbone domains.…”

Section: Resultsmentioning

confidence: 80%

“…It made sense we found phage protection functions on our Acinetobacter plasmids, as plasmidencoded phage defense systems is a known strategy for combating phage infection 76,77 . We also found cell wall metabolism functions.…”

Section: Sewage Acinetobacter Plasmidsmentioning

confidence: 97%

Global distribution and diversity of prevalent sewage water plasmidomes

Teudt

Otani

Aarestrup

2022

Preprint

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Sewage water from around the world contains an abundance of short plasmids, a number of which harbor antimicrobial resistance genes (ARGs). The global dynamics of plasmid-derived antimicrobial resistance and functions is only starting to be unveiled. Here, we utilized a previously created dataset of 159,332 assumed small plasmids from 24 different globally collected sewage samples. We investigated the detailed phylogeny as well as the interplay between their protein domains, ARGs, and predicted bacterial host genera to help understand the global sewage plasmidome dynamics. A total of 58,429 circular elements carried genes encoding for plasmid-related features, and MASH distance analyses showed a very high degree of diversity. A single very diverse cluster of 520 predicted Acinetobacter plasmids was predominant among the European sewage water. Based on functional domain network analysis, we identified three groups of plasmids, mainly replication and mobilization domains. However, these backbone domains were not exclusive to any given group. Acinetobacter was the dominant host genus among theta-replicating plasmids at these size ranges. They contained a reservoir of the macrolide resistance gene pair msr(E) and mph(E). Macrolide resistance genes were the most common resistance genes in sewage plasmidomes and found in the largest number of unique plasmids. While msr(E) and mph(E) were limited to Acinetobacter, erm(B) was disseminated among a range of Firmicutes plasmids, including Staphylococcus and Streptococcus, highlighting a potential reservoir of antibiotics resistance for these pathogens from around the globe.

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“…Plasmids can influence phage-bacteria dynamics by transmitting traits vertically and horizontally in bacterial populations [16][17][18] . For example, TraT can block both foreign plasmids and phage invasion 16,19,20 .…”

Section: Background (4901 Words)mentioning

confidence: 99%

Urinary F plasmids reduce permissivity to coliphage infection

Hernandez

Putonti

Wolfe

2022

Preprint

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The microbial community of the urinary tract (urinary microbiota or urobiota) has been associated with human health. Bacteriophages (phages) and plasmids present in the urinary tract, like in other niches, may shape urinary bacteria dynamics. While urinary E. coli, often associated with urinary tract infection (UTI), and their phages have been catalogued for the urobiome, the dynamics of their interactions have yet to be explored. In this study, we characterized urinary E. coli F plasmids and their ability to decrease permissivity to E. coli phage (coliphage) infection. Putative F plasmids were present in 47 of 67 urinary E. coli isolates, and most of these plasmids carry genes that encode for toxin-antitoxin (TA) modules, antibiotic resistance, and/or virulence. Two urinary E. coli F plasmids, from urinary microbiota (UMB) 0928 and 1284, were conjugated into E. coli K-12 strains; plasmids included genes for antibiotic resistance and virulence. These plasmids, pU0928 and pU1284, decreased permissivity to coliphage infection by the laboratory phage P1vir and the urinary phages Greed and Lust. Furthermore, pU0928 could be maintained in E. coli K-12 for up to ten days in the absence of antibiotic resistance selection; this included maintenance of the antibiotic resistance phenotype and decreased permissivity to phage. Finally, we discuss how F plasmids present in urinary E. coli could play a role in coliphage dynamics and maintenance of antibiotic resistance in urinary E. coli.

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The phage defence island of a multidrug resistant plasmid uses both BREX and type IV restriction for complementary protection from viruses

Cited by 58 publications

References 63 publications

Microbial defenses against mobile genetic elements and viruses: Who defends whom from what?

Microbial defenses against mobile genetic elements and viruses: Who defends whom from what?

Global distribution and diversity of prevalent sewage water plasmidomes

Urinary F plasmids reduce permissivity to coliphage infection

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