The defense island repertoire of the Escherichia coli pan-genome

Hochhauser, Dina; Millman, Adi; Sorek, Rotem

doi:10.1371/journal.pgen.1010694

Cited by 48 publications

(34 citation statements)

References 58 publications

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“…Finally, we identified a third defence-hotspot encoded between LptG and a GTPase. We note that the protein annotated as GTPase is homologous to YjiA, a protein that, together with YjiO, defines the boundaries of a defence island in Escherichia coli 17 . Unlike E. coli , we did not find YjiO homologues in S. marcescens strains (Figure 1c and Table S2).…”

Section: Resultsmentioning

confidence: 99%

Multi-conflict islands are a widespread trend withinSerratiaspp

Cummins,

Garrett,

Blower

et al. 2024

Preprint

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Bacteria carry numerous anti-phage systems in 'defence islands' or hotspots. Recent studies have delineated the content and boundaries of these islands in various species, revealing instances of islands that encode additional factors, including antibiotic resistance, stress genes, Type VI Secretion System (T6SS)-dependent effectors, and virulence factors. Our study identifies three defence islands in the Serratia genus with a mixed cargo of anti-phage systems, virulence factors and different types of anti-bacterial modules, revealing a widespread trend of co-accumulation that extends beyond T6SS-dependent effectors to colicins and contact-dependent inhibition systems. We report the identification of four distinct anti-phage system/subtypes, including a previously unreported Toll/IL-1 receptor (TIR)-domain-containing system with population-wide immunity, and two loci co-opting a predicted T6SS-related protein for phage defence. This study enhances our understanding of the protein domains that can be co-opted for phage defence and of the diverse combinations in which known anti-phage proteins can be assembled, resulting in a highly diversified anti-phage arsenal.

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Section: Resultsmentioning

confidence: 99%

Multi-conflict islands are a widespread trend withinSerratiaspp

Cummins,

Garrett,

Blower

et al. 2024

Preprint

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“…The 590 high-quality bacterial genome assemblies were subjected to a prophage sequence search using PHASTER (35). A total of 2595 prophage-like sequences were detected in nearly all genomes analyzed, except for P. syringae pv.…”

Section: Resultsmentioning

confidence: 99%

“…For other plant-associated bacteria specifically, this number has been shown to be as high as 10 mechanisms for some Ralstonia and Xanthomonas isolates (34). In sharp contrast to other bacterial species (35,36), and even other Pseudomonads, CRISPR-Cas does not appear to be an important phage defense strategy in the P. syringae species complex (37,38). Instead, we demonstrated that P. syringae relies on other defense mechanisms, such as restriction enzymes and abortive infection strategies, to cope with phage predation.…”

Section: Discussionmentioning

confidence: 99%

Evidence for the key roles of thePseudomonas syringaemobilome in shaping biotic interactions

Holtappels,

Rickus,

Morgan

et al. 2024

Preprint

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The mobilome, defined as the collection of mobile genetic elements within a bacterial genome, plays a critical role in the adaptation of bacteria to abiotic and biotic drivers. In particular, prophages have been reported to contribute to bacterial resistance to virulent bacteriophages, the competitive interaction of bacterial hosts within microbial communities, and in pathogenicity and virulence. It is therefore critical to better understand the role of prophages in distributing genes and functions within and among bacterial species to predict how bacteria adapt to their biotic environment.Pseudomonas syringaeoffers an ideal study system to ask these questions both because of its broad range of lifestyles (spanning from environmental growth to plant pathogens) and its high intraspecies diversity. To examine the role of the mobilome in this species complex, we compared 590 genomes available from public databases and annotated the defense mechanisms, effectors, and prophages in the genomes. We found that this species complex has an elaborate phage pandefensome consisting of 139 defense mechanisms. Host-associatedP. syringaeisolates were found to have both elaborate phage defensomes and effectoromes. Assessing taxonomical signatures of the observed prophages uncovered broad differences in the types and numbers of genes encoded by different phage families, emphasizing how the evolutionary advantages conferred to hosts will depend on the prophage composition and offering insight to how these genes might disperse within a community. Our study highlights the intimate association of phage families with their hosts and uncovers their key role in shaping ecology for this widespread species complex.Significance statementThe bacterial accessory genome, including the mobilome and prophages, plays a critical role in shaping bacterial adaptation to abiotic and biotic drivers. These prophages are widespread across bacterial taxa and likely maintained because of their evolutionary advantage. Our ability to predict how a bacterial population will evolve over time requires a better understanding of where key functional traits arrive. To address this question, we assessed prophage-encoded phage defenses and effector acrossPseudomonas syringae. We show that prophages carrying these genes belong to specific phage taxa with differences in the types of genes encoded. This emphasizes the evolutionary advantage of these prophages, offering a framework to uncover how these genes disperse within microbial communities and their role in pathogen evolution.

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“…PPs are prolific agents of horizontal gene transfer, including implications in the spread of antibiotic resistance 39,85 . The spread of genetic content between bacteria within the gut may have dramatic effects on human health in terms of increased bacterial virulence, persistence, and antibiotic resistance 85,86 . Due to their higher levels of accessory genes and larger genomes there is more room for genome plasticity and genetic exchange without disrupting essential gene functions in PPs.…”

Section: Discussionmentioning

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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The defense island repertoire of the Escherichia coli pan-genome

Cited by 48 publications

References 58 publications

Multi-conflict islands are a widespread trend withinSerratiaspp

Multi-conflict islands are a widespread trend withinSerratiaspp

Evidence for the key roles of thePseudomonas syringaemobilome in shaping biotic interactions

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

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