Recurring and emerging themes in prokaryotic innate immunity

Boyle, Tori A; Hatoum-Aslan, Asma

doi:10.1016/j.mib.2023.102324

Cited by 8 publications

(3 citation statements)

References 66 publications

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“…Defence systems are often a modular combination of domains ( e.g. a sensor and an effector) ( 26–28 ). We thus investigated whether the newly identified systems had protein domains found in known systems using available data (Uniprot, ( 29 )), sensitive sequence similarity detection programs (HHPred ( 30 )), and structural similarity (AlphaFold ( 31 ) and FoldSeek ( 32 )) (Figure 2C, Figure S4).…”

Section: Resultsmentioning

confidence: 99%

Sedentary chromosomal integrons as biobanks of bacterial anti-phage defence systems

Darracq,

Littner,

Brunie

et al. 2024

Preprint

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Integrons are genetic systems that accelerate bacterial adaptation by acquiring and shuffling gene cassettes. Mobile integrons spread antibiotic resistance genes among bacteria, while the sedentary chromosomal integrons contain up to hundreds of cassettes of unknown function. Here, we show that many of these cassettes encode anti-phage defence systems. We found numerous streamlined variants of known systems, which have presumably evolved to fit the small size constraints of integron cassettes recombination and genesis. Intrigued by the rarity of known systems in the sedentary chromosomal integron of the Vibrio cholerae 7th cholera pandemic strain, we tested the presence of anti-phage functions in all its cassettes of unknown function. We found that at least 16 of the strain cassettes have an anti-phage activity in V. cholerae or E. coli. This represents 18% of the tested cassettes and almost 10% of all the integron cassettes, providing at long last a key adaptive role for a significant fraction of the sedentary integrons. Most of the newly discovered systems have little or no similarity to previously known ones and our experiments show that several mediate defence through cell lysis or growth arrest. One of these systems encodes a 64 amino acids protein, which represents the smallest known protein providing autonomous phage resistance. Given the thousands of uncharacterized integron cassette families, integrons could represent an untapped treasure trove of streamlined anti-phage systems.

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Section: Resultsmentioning

confidence: 99%

Sedentary chromosomal integrons as biobanks of bacterial anti-phage defence systems

Darracq,

Littner,

Brunie

et al. 2024

Preprint

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“…Solutions to this paradox include compensatory mutations improving the fitness of plasmid-carrying bacteria 8 – 10 and high conjugation rates 11 . On the other hand, bacteria have developed defense mechanisms to counteract invasion by parasitic DNAs, some of them able to limit plasmid diffusion 12 – 14 .…”

Section: Introductionmentioning

confidence: 99%

An antiplasmid system drives antibiotic resistance gene integration in carbapenemase-producing Escherichia coli lineages

Zongo,

Cabanel,

Royer

et al. 2024

Nat Commun

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Plasmids carrying antibiotic resistance genes (ARG) are the main mechanism of resistance dissemination in Enterobacterales. However, the fitness-resistance trade-off may result in their elimination. Chromosomal integration of ARGs preserves resistance advantage while relieving the selective pressure for keeping costly plasmids. In some bacterial lineages, such as carbapenemase producing sequence type ST38 Escherichia coli, most ARGs are chromosomally integrated. Here we reproduce by experimental evolution the mobilisation of the carbapenemase blaOXA-48 gene from the pOXA-48 plasmid into the chromosome. We demonstrate that this integration depends on a plasmid-induced fitness cost, a mobile genetic structure embedding the ARG and a novel antiplasmid system ApsAB actively involved in pOXA-48 destabilization. We show that ApsAB targets high and low-copy number plasmids. ApsAB combines a nuclease/helicase protein and a novel type of Argonaute-like protein. It belongs to a family of defense systems broadly distributed among bacteria, which might have a strong ecological impact on plasmid diffusion.

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“…Regardless, the identification of this novel pathway to combat the viral invasion has made something clear, in case some had remained sceptical: plants have more than RNAi in their antiviral arsenal. Considering the recent explosion in the number of identified antiphage defence systems in bacteria (Boyle & Hatoum-Aslan, 2023), it is inevitable that we now impatiently wonder if a similar revolution in plant-virus interactions will soon be coming our way. During the Arabidopsis thaliana (Arabidopsis)-AMV interaction, the viral RNA genome can get m 6 A methylated by an unknown host methyltransferase.…”

mentioning

confidence: 99%

More than annealing: RNAi is not alone in the fight against plant viruses

Lozano‐Durán

2023

The EMBO Journal

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Cellular organisms have evolved different strategies to defend themselves against the invasion by viruses. In plants, RNA interference (RNAi) or RNA silencing, which is triggered by virus‐derived double‐stranded (ds)RNA, is considered the main antiviral defence mechanism. Martínez‐Pérez et al have now uncovered an additional plant antiviral pathway, termed by the authors “m6A‐YTHDF axis,” which relies on the modification and subsequent recognition of the viral RNA.

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Recurring and emerging themes in prokaryotic innate immunity

Cited by 8 publications

References 66 publications

Sedentary chromosomal integrons as biobanks of bacterial anti-phage defence systems

Sedentary chromosomal integrons as biobanks of bacterial anti-phage defence systems

An antiplasmid system drives antibiotic resistance gene integration in carbapenemase-producing Escherichia coli lineages

More than annealing: RNAi is not alone in the fight against plant viruses

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