Identification of a new antiphage system in<i>Mycobacterium</i>phage Butters

Mohammed, Hamidu T.; Mageeney, Catherine M.; Ware, Vassie C.

doi:10.1101/2023.01.03.522681

Cited by 3 publications

(3 citation statements)

References 60 publications

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“…Indeed, we found that the 6 defense systems that were previously reported as the most prophage-encoded in all prokaryotic genomes (above 60% of the total number of systems) 16 were almost exclusively found in Proteobacteria (99% of the occurrences of these 6 systems). A handful of systems were recently discovered in Mycobacterium phages [45][46][47][48] , which are by far the most characterized and studied actinobacterial phages 49 . Only one of these systems, gp29-gp30, is currently detected by DefenseFinder, and it is exclusively found in Actinobacteria.…”

Section: Discussionmentioning

confidence: 99%

Genomic characterization of the antiviral arsenal of Actinobacteria

Georjon

Tesson

Shomar

et al. 2023

Preprint

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Phages are ubiquitous in nature, and bacteria with very different genomics, metabolisms, and lifestyles are subjected to their predation. Yet, the defense systems that allow bacteria to resist their phages have rarely been explored experimentally outside a very limited number of model organisms. Actinobacteria are a phylum of GC-rich gram-positive bacteria, which often produce an important diversity of secondary metabolites. Despite being ubiquitous in a wide range of environments, from soil to fresh and sea water but also the gut microbiome, relatively little is known about the anti-phage arsenal of Actinobacteria. In this work, we used DefenseFinder to systematically detect 131 anti-phage defense systems in 22,803 fully sequenced prokaryotic genomes, among which 2,253 Actinobacteria of more than 700 species. We show that, like other bacteria, Actinobacteria encode many diverse anti-phage systems that are often encoded on mobile genetic elements. We further demonstrate that most detected defense systems are absent or rarer in Actinobacteria than in other bacteria, while a few rare systems are enriched (notably gp29-gp30 and Wadjet). We characterize the spatial distribution of anti-phage systems on Streptomyces chromosomes and show that some defense systems (e.g. RM systems) tend to be encoded in the core region, while others (e.g. Lamassu and Wadjet) are enriched towards the extremities. Overall, our results suggest that Actinobacteria might be a source of novel anti-phage systems and provide clues to characterize mechanistic aspects of known anti-phage systems.

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Section: Discussionmentioning

confidence: 99%

Genomic characterization of the antiviral arsenal of Actinobacteria

Georjon

Tesson

Shomar

et al. 2023

Preprint

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“…The genome DNA of K4JX5 Phage was extracted using the phenol‐chloroform method as described earlier 53 . A total of 200 ng of the genomic DNA was electroporated into M. smegmatis strains and supplemented with 900 μl 7H9 medium, followed by shaking at 160 rpm at 37°C for 1 h. The cells were collected, re‐suspended with 200 μl of 7H9 medium, and then mixed with 1 ml of the wild‐type M. smegmatis strain and 5 ml of LB‐agar medium.…”

Section: Methodsmentioning

confidence: 99%

Insertion sequence transposition activates antimycobacteriophage immunity through an lsr2‐silenced lipid metabolism gene island

Li,

Wei,

Guo

et al. 2024

mLife

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Insertion sequences (ISs) exist widely in bacterial genomes, but their roles in the evolution of bacterial antiphage defense remain to be clarified. Here, we report that, under the pressure of phage infection, the IS1096 transposition of Mycobacterium smegmatis into the lsr2 gene can occur at high frequencies, which endows the mutant mycobacterium with a broad‐spectrum antiphage ability. Lsr2 functions as a negative regulator and directly silences expression of a gene island composed of 11 lipid metabolism‐related genes. The complete or partial loss of the gene island leads to a significant decrease of bacteriophage adsorption to the mycobacterium, thus defending against phage infection. Strikingly, a phage that has evolved mutations in two tail‐filament genes can re‐escape from the lsr2 inactivation‐triggered host defense. This study uncovered a new signaling pathway for activating antimycobacteriophage immunity by IS transposition and provided insight into the natural evolution of bacterial antiphage defense.

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“…Indeed, we found that the six defence systems that were previously reported as the most prophage-encoded in all prokaryotic genomes (above 60 % of the total number of systems) [19] were almost exclusively found in Proteobacteria (99 % of the occurrences of these six systems). A handful of systems were recently discovered in Mycobacterium phages [52,[55][56][57], which are by far the most characterized and studied actinobacterial phages [58]. Only one of these systems, gp29-gp30, is currently detected by DefenseFinder, it is exclusively found in Actinobacteria.…”

Section: Discovery Bias: More Systems To Discover In Actinobacteria A...mentioning

confidence: 99%

Genomic characterization of the antiviral arsenal of Actinobacteria

et al. 2023

View full text Add to dashboard Cite

Phages are ubiquitous in nature, and bacteria with very different genomics, metabolisms, and lifestyles are subjected to their predation. Yet, the defence systems that allow bacteria to resist their phages have rarely been explored experimentally outside a very limited number of model organisms. Actinobacteria (Actinomycetota) are a phylum of GC-rich Gram-positive bacteria, which often produce an important diversity of secondary metabolites. Despite being ubiquitous in a wide range of environments, from soil to fresh and sea water but also the gut microbiome, relatively little is known about the anti-phage arsenal of Actinobacteria. In this work, we used DefenseFinder to systematically detect 131 anti-phage defence systems in 22803 fully sequenced prokaryotic genomes, among which are 2253 Actinobacteria of more than 700 species. We show that, like other bacteria, Actinobacteria encode many diverse anti-phage systems that are often encoded on mobile genetic elements. We further demonstrate that most detected defence systems are absent or rarer in Actinobacteria than in other bacteria, while a few rare systems are enriched (notably gp29-gp30 and Wadjet). We characterize the spatial distribution of anti-phage systems on Streptomyces chromosomes and show that some defence systems (e.g. RM systems) tend to be encoded in the core region, while others (e.g. Lamassu and Wadjet) are enriched towards the extremities. Overall, our results suggest that Actinobacteria might be a source of novel anti-phage systems and provide clues to characterize mechanistic aspects of known anti-phage systems.

show abstract

Identification of a new antiphage system inMycobacteriumphage Butters

Cited by 3 publications

References 60 publications

Genomic characterization of the antiviral arsenal of Actinobacteria

Genomic characterization of the antiviral arsenal of Actinobacteria

Insertion sequence transposition activates antimycobacteriophage immunity through an lsr2‐silenced lipid metabolism gene island

Genomic characterization of the antiviral arsenal of Actinobacteria

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