Trends in Genetics, Год журнала: 2024, Номер 40(11), С. 950 - 968
Опубликована: Авг. 31, 2024
Язык: Английский
Nature, Год журнала: 2024, Номер 626(7998), С. 271 - 279
Опубликована: Фев. 7, 2024
Язык: Английский
Процитировано
52
Cell Host & Microbe, Год журнала: 2024, Номер 32(4), С. 557 - 572.e6
Опубликована: Фев. 22, 2024
Bacterial defense against phage predation involves diverse systems acting individually and concurrently, yet their interactions remain poorly understood. We investigated >100 in 42,925 bacterial genomes identified numerous instances of non-random co-occurrence negative association. For several pairs significantly co-occurring Escherichia coli strains, we demonstrate synergistic anti-phage activity. Notably, Zorya II synergizes with Druantia III ietAS systems, while tmn exhibits synergy Gabija, Septu I, PrrC. co-opts the sensory switch ATPase domain, enhancing Some system that are negatively associated E. show co-occur other taxa, demonstrating immune repertoires largely shaped by selection for resistance host-specific phages rather than epistasis. Collectively, these findings compatibility between allowing bacteria to adopt flexible strategies defense.
Язык: Английский
Процитировано
39
Cell, Год журнала: 2024, Номер 187(1), С. 17 - 43
Опубликована: Янв. 1, 2024
Язык: Английский
Процитировано
35
Nature Reviews Genetics, Год журнала: 2024, Номер 25(4), С. 237 - 254
Опубликована: Янв. 30, 2024
Язык: Английский
Процитировано
33
Nature Microbiology, Год журнала: 2024, Номер 9(11), С. 2847 - 2861
Опубликована: Окт. 31, 2024
Язык: Английский
Процитировано
21
Nature, Год журнала: 2024, Номер 631(8022), С. 850 - 856
Опубликована: Июль 17, 2024
Язык: Английский
Процитировано
18
Trends in Microbiology, Год журнала: 2024, Номер 32(12), С. 1212 - 1228
Опубликована: Июнь 5, 2024
The biological interplay between phages and bacteria has driven the evolution of phage anti-defence systems (ADSs), which evade bacterial defence mechanisms. These ADSs bind inhibit host proteins, add covalent modifications deactivate degrade or sequester signalling molecules utilised by systems, synthesise restore essential depleted defences, to avoid recognition. Overall, 145 have been characterised date. counteract 27 152 different families, we hypothesise that many more are yet be discovered. We discuss high-throughput approaches (computational experimental) indispensable for discovering new limitations these approaches. A comprehensive characterisation is critical understanding phage–host developing clinical applications, such as treatment multidrug-resistant infections.
Язык: Английский
Процитировано
17
Microbiome, Год журнала: 2025, Номер 13(1)
Опубликована: Янв. 31, 2025
The prokaryotic antiviral defense systems are crucial for mediating prokaryote-virus interactions that influence microbiome functioning and evolutionary dynamics. Despite the prevalence significance of systems, their responses to abiotic stress ecological consequences remain poorly understood in soil ecosystems. We established microcosm with varying concentrations hexavalent chromium (Cr(VI)) investigate adaptive modifications under stress. Utilizing hybrid metagenomic assembly long-read short-read sequencing, we discovered were more diverse prevalent heavily polluted soils, which was corroborated by meta-analyses public datasets from various heavy metal-contaminated sites. As Cr(VI) concentration increased, prokaryotes favoring mutualism gradually supplanted those incurring high costs. Additionally, as enriched exhibited synchronization microbial metal resistance genes. Furthermore, proportion carried mobile genetic elements (MGEs), including plasmids viruses, increased approximately 43% 39%, respectively, rising Cr concentrations. This trend is conducive strengthening dissemination sharing resources within communities. Overall, our study reveals modification ecosystems stress, well positive contributions establishing evolution resistance. These findings advance understanding adaptation stressful environments may inspire novel approaches manipulation bioremediation. Video Abstract.
Язык: Английский
Процитировано
3
Nature, Год журнала: 2023, Номер 623(7987), С. 601 - 607
Опубликована: Окт. 18, 2023
Many bacteria use CRISPR-Cas systems to combat mobile genetic elements, such as bacteriophages and plasmids
Язык: Английский
Процитировано
39
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown
Опубликована: Янв. 26, 2024
In recent years, a vast number of novel antiphage defense mechanisms were uncovered. To facilitate the exploration mechanistic, ecological, and evolutionary aspects related to systems, we released DefenseFinder in 2021 (Tesson et al., 2022). is bioinformatic program designed for systematic identification known mechanisms. The initial release v1.0.0 included 60 systems. Over past three systems incorporated into has grown 152. increasing makes it challenge enter field interpretation detections difficult. Moreover, rapid development sequence-based predictions structures offers possibilities analysis should be easily available. overcome these challenges, present hub resources on including: 1) an updated version with web-service search function, 2) community-curated repository knowledge 3) precomputed databases, which include annotations done RefSeq genomes structure generated by AlphaFold. These pages can freely accessed users as starting point their journey better understand given system. We anticipate that will foster use bioinformatics study serve community researchers who This resource available at: https://defensefinder.mdmlab.fr.
Язык: Английский
Процитировано
15