Prophage-encoded hotspots of bacterial immune systems

Rousset, François; Dowding, Julien; Bernheim, Aude; Rocha, Eduardo P. C.; Bikard, David

doi:10.1101/2021.01.21.427644

Cited by 22 publications

(41 citation statements)

References 77 publications

(87 reference statements)

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“…This suggests frequent gene exchanges with other mobile genetic elements and is consistent with the observation above that the elements tend to be scattered across the genome. This is also consistent with the proposal that the cos site, between the integrase and psu, is associated with rapid diversification of the defense systems carried by P4-like elements [9]. d is the only specific P4 gene that has clear homologs in the ogr genes of P2-like phages, but sequence similarity is very low [3].…”

Section: Discussionsupporting

confidence: 89%

“…Most gene families observed between consecutive core components are located between the integrase and psu or between sid and alpA (Fig 2A, numbers below organization diagram). The first region corresponds to the previously described hotspot of phage defense systems [9], and includes the cos site in P4. The region between e and a has two frequent gene families.…”

Section: Genomic Characterization Of the P4-like Satellite Familymentioning

confidence: 99%

“…Additionally, a study of prophage domestication identified 28 elements with a homolog of sid [21], and a recent study identified more than 5000 homologs of psu in ca. 20000 E. coli genomes [9]. These studies raised key questions.…”

Section: Introductionmentioning

confidence: 99%

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To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites

Sousa

Rocha

2021

Preprint

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Bacteriophages (phages) are bacterial parasites that can themselves be parasitized by phage satellites. The molecular mechanisms used by satellites to hijack phages are sometimes understood in great detail, but the origins, abundance, distribution, and composition of these elements are poorly known. Here, we show that P4-like elements are present in more than 10% of the genomes of Enterobacterales, and in almost half of those of Escherichia coli, sometimes in multiple distinct copies. We identified over 1000 P4-like elements with very conserved genetic organization of the core genome and a few hotspots with highly variable genes. These elements are never found in plasmids and have very little homology to known phages, suggesting an independent evolutionary origin. Instead, they are scattered across chromosomes, possibly because their integrases are often exchanged with other elements. The rooted phylogenies of hijacking functions are correlated and suggest longstanding co-evolution. They also reveal broad host ranges in P4-like elements, since almost identical elements can be found in distinct bacterial genuses. Our results show that P4-like phage satellites constitute a very distinct, widespread and ancient family of mobile genetic elements. They pave the way for studying the molecular evolution of antagonistic interactions between phages and their satellites.

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Section: Discussionsupporting

confidence: 89%

Section: Genomic Characterization Of the P4-like Satellite Familymentioning

confidence: 99%

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To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites

Sousa

Rocha

2021

Preprint

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“…"Morons" can be very different even among the closely related strains and a recent study of P2 and P4 like prophages uncovered an unprecedented variety of the compact defense systems in the specific hotspot loci of their genomes [182]. In addition to the known antiviral systems, multiple gene clusters that carry predicted defense domains (~TIR, SIR2, Nuclease, ATPase) or domains of unknown function were reported in these hotspots.…”

Section: Prophage Mediated Defensementioning

confidence: 99%

Microbial Arsenal of Antiviral Defenses. Part II

Musharova

Severinov

2021

Biochemistry Moscow

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Bacteriophages or phages are viruses that infect bacterial cells (for the scope of this review we will also consider viruses that infect Archaea). The constant threat of phage infection is a major force that shapes evolution of microbial genomes. To withstand infection, bacteria had evolved numerous strategies to avoid recognition by phages or to directly interfere with phage propagation inside the cell. Classical molecular biology and genetic engineering had been deeply intertwined with the study of phages and host defenses. Nowadays, owing to the rise of phage therapy, broad application of CRISPR-Cas technologies, and development of bioinformatics approaches that facilitate discovery of new systems, phage biology experiences a revival. This review describes variety of strategies employed by microbes to counter phage infection. In the first part defense associated with cell surface, roles of small molecules, and innate immunity systems relying on DNA modification were discussed. The second part focuses on adaptive immunity systems, abortive infection mechanisms, defenses associated with mobile genetic elements, and novel systems discovered in recent years through metagenomic mining.

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“…Typhimurium D23580 prophage BTP1 [10], supporting the host to survive phage predation in the environment and drive niche specialisation. There are diverse anti-phage systems widely spread in bacteria [12,13], stressing the need to find phages that are capable of escaping these anti-phage mechanisms that protect African iNTS.…”

Section: Introductionmentioning

confidence: 99%

Isolation and characterisation of bacteriophages with activity against invasive non-typhoidalSalmonellacausing bloodstream infection in Malawi

Rodwell

Wenner

Pulford

et al. 2021

Preprint

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In recent years, novel lineages of invasive non-typhoidal Salmonella (iNTS) serovars Typhimurium and Enteritidis have been identified in patients with bloodstream infection in sub-Saharan Africa. Here, we isolated and characterised 32 phages capable of infecting S. Typhimurium and S. Enteritidis, from water sources in Malawi and the UK. The phages were classified in three major phylogenetic clusters that were geographically distributed. In terms of host range, Cluster 1 phages were able to infect all bacterial hosts tested, whereas Clusters 2 and 3 had a more restricted profile. Cluster 3 contained two sub-clusters, and 3.b contained the most novel isolates. This study represents the first exploration of the potential for phages to target the lineages of Salmonella that are responsible for bloodstream infections in sub-Saharan Africa.

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Prophage-encoded hotspots of bacterial immune systems

Cited by 22 publications

References 77 publications

To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites

To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites

Microbial Arsenal of Antiviral Defenses. Part II

Isolation and characterisation of bacteriophages with activity against invasive non-typhoidalSalmonellacausing bloodstream infection in Malawi

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