A Vibrio cholerae anti-phage system depletes nicotinamide adenine dinucleotide to restrict virulent bacteriophages DOI Creative Commons

Yishak A. Woldetsadik,

David W. Lazinski,

Andrew Camilli

et al.

mBio, Journal Year: 2024, Volume and Issue: 15(11)

Published: Oct. 8, 2024

ABSTRACT Bacteria and their predatory viruses (bacteriophages or phages) are in a perpetual molecular arms race. This has led to the evolution of numerous phage defensive systems bacteria that still being discovered, as well ways interference circumvention on part phages. Here, we identify unique battle between classical biotype Vibrio cholerae virulent phages ICP1, ICP2, ICP3. We show strains resist almost all isolates these due 25-kb genomic island harboring several putative anti-phage systems. observed one systems, Nezha, encoding SIR2 - like helicase proteins, inhibited replication three Bacterial SIR2-like enzymes degrade essential metabolic coenzyme nicotinamide adenine dinucleotide (NAD + ), thereby preventing invading phage. In support this mechanism, identified isolate, ICP1_2001, which circumvents Nezha by two NAD regeneration enzymes. By restoring pool, hypothesize system antagonizes without directly interacting with its proteins should be able antagonize other deplete . IMPORTANCE race, evolving an extensive arsenal mechanisms overcome study identifies previously uncharacterized facet race -depleting called potent against Remarkably, encodes regenerate counter effects Nezha. Without genes detrimental Our provides new insight into co-evolutionary dynamics informs microbial ecology therapy fields.

Language: Английский

Plasmid targeting and destruction by the DdmDE bacterial defence system DOI
Jack P. K. Bravo, Delisa Ramos, Rodrigo Fregoso Ocampo

et al.

Nature, Journal Year: 2024, Volume and Issue: 630(8018), P. 961 - 967

Published: May 13, 2024

Language: Английский

Citations

14
Incomplete lytic cycle of a widespread Bacteroides bacteriophage leads to the formation of defective viral particles DOI Creative Commons
Sol Vendrell-Fernández, Beatriz Beamud,

Yasmina Abou Haydar

et al.

PLoS Biology, Journal Year: 2025, Volume and Issue: 23(3), P. e3002787 - e3002787

Published: March 31, 2025

Advances in metagenomics have led to the identification of new intestinal temperate bacteriophages. However, their experimental characterization remains challenging due a limited understanding lysogenic-lytic cycle and common lack plaque formation vitro. In this study, we investigated hankyphage, widespread transposable phage prominent Bacteroides symbionts. Hankyphages spontaneously produced virions laboratory conditions even absence inducer, but did not show any evidence infectivity. To increase virion production raise chances observing infection events, identified master repressor hankyphage lytic cycle, RepC HP , whose silencing amplified gene expression, enhanced replicative transposition production. attempts infect or lysogenize host cells with different capsular types remained unsuccessful. Transmission electron microscopy capsid DNA sequencing revealed an abnormal morphology incomplete packaging suggesting that it cannot complete its assembly for reasons are yet be identified. Still, metavirome phylogenetic analyses were suggestive horizontal transmission. We could also detect activity diversity-generating retroelements (DGRs) mutagenize tail fiber, likely contribute broad range. This study sheds light on life abundant bacteriophage highlights important gaps our factors required completion cycle. Elucidating puzzle will critical gain better biology ecological role.

Language: Английский

Citations

1
Going viral: The role of mobile genetic elements in bacterial immunity DOI
Beatriz Beamud, Fabienne Benz,

David Bikard

et al.

Cell Host & Microbe, Journal Year: 2024, Volume and Issue: 32(6), P. 804 - 819

Published: June 1, 2024

Language: Английский

Citations

8
Hachiman is a genome integrity sensor DOI Creative Commons
Owen T. Tuck, Benjamin A. Adler, Emily Armbruster

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 29, 2024

Hachiman is a broad-spectrum antiphage defense system of unknown function. We show here that comprises heterodimeric nuclease-helicase complex, HamAB. HamA, previously protein function, the effector nuclease. HamB sensor helicase. constrains HamA activity during surveillance intact dsDNA. When HamAB complex detects DNA damage, helicase liberates unleashing nuclease activity. activation degrades all in cell, creating ‘phantom’ cells devoid both phage and host DNA. demonstrate absence by treatment with DNA-damaging agents, suggesting responds to aberrant states. Phylogenetic similarities between eukaryotic enzymes suggest this bacterial immune has been repurposed for diverse functions across domains life.

Language: Английский

Citations

7
Cyanophage Lysis of the Cyanobacterium Nodularia spumigena Affects the Variability and Fitness of the Host‐Associated Microbiome DOI Open Access
Sigitas Šulčius, Gediminas Alzbutas,

Valiantsin Lukashevich

et al.

Environmental Microbiology, Journal Year: 2025, Volume and Issue: 27(4)

Published: March 28, 2025

ABSTRACT Cyanobacteria are intricately linked with its microbiome through multiple metabolic interactions. We assessed how these interactions might be affected by cyanophage infection and lysis in cyanobacterium Nodularia spumigena . The genome‐scale models analysis of putative revealed a bidirectional cross‐feeding potential within the N. microbiome, heterotrophic bacteria exhibiting greater level trophic dependency on cyanobacterium. Our results indicate that microbes associated rely supply various amino acids, reduced carbon compounds protein synthesis cofactors released cyanobacterial host. observed compositional changes were multiplicity increased increasing initial viral load. Higher mortality led to decreased variability relative abundances bacteria, suggesting an indirect restriction their niche space. Lysis resulted substantial decline estimated absolute indicating fitness co‐occurring absence Altogether, we demonstrate gradual increase pressure photosynthetic host propagates microbial community, disrupting cooperative nature connectivity microbiome.

Language: Английский

Citations

0
Antimicrobial Resistance in Coagulase Negative Staphylococci: Genome Analysis and Role of Horizontal Gene Transfer DOI
Tansu Dündar, Fatma Köksal Çakırlar

Research in Microbiology, Journal Year: 2025, Volume and Issue: unknown, P. 104298 - 104298

Published: April 1, 2025

Language: Английский

Citations

0
Mystique, a broad host range Acinetobacter phage, reveals the impact of culturing conditions on phage isolation and infectivity DOI Creative Commons
Ellinor Alseth, Carli Roush, Iris Irby

et al.

PLoS Pathogens, Journal Year: 2025, Volume and Issue: 21(4), P. e1012986 - e1012986

Published: April 10, 2025

With the global rise of antimicrobial resistance, phage therapy is increasingly re-gaining traction as a strategy to treat bacterial infections. For be successful however, we first need isolate appropriate candidate phages for both clinical and experimental research . Acinetobacter baumannii an opportunistic pathogen known its ability rapidly evolve resistance antibiotics, making it prime target therapy. Yet isolation may hampered by A. ’s switch between capsular states. Here, report discovery structural characterisation novel lytic phage, Mystique. This was initially isolated against wild-type AB5075: commonly used model strain. When screening Mystique on 103 highly diverse isolates , found that has broad host range, being able infect 85.4% all tested strains when lawns – range expanded 91.3% in liquid culture. variation solid culturing conditions infectivity also observed several other our collection were assumed unable AB5075, some capsule negative mutants seemed resistant proved susceptible assayed liquid. highlights how differences can drastically impact infectivity, with important consequences efforts. Finally, species multi-species applicability further research.

Language: Английский

Citations

0
Interpretable machine learning reveals a diverse arsenal of anti-defenses in bacterial viruses DOI Open Access
Anna Lopatina, Mariusz Ferenc, Nina Bartlau

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 14, 2024

Antagonistic interactions with viruses are an important driver of the ecology and evolution bacteria, associating genetic signatures to these is fundamental importance predict viral infection success. Recent studies have highlighted that bacteria possess a large, rapidly changing arsenal defense genes can neutralize at least some matching anti-defenses. However, broadly applicable approach for discovering underpinnings such missing since typically used methods as comparative genomics limited by rampant horizontal gene transfer poor annotation bacterial genes. Here we show allow overcome defenses be systematically identified using interpretable machine-learning even when diverse bacteria-virus data. To verify predictions, experimentally characterized eight previously unknown anti-defense proteins in specific Vibrio showed they counteract wide range immune systems, including AbiH, AbiU, Septu, DRT, CBASS, Retron. The power our computational identification inhibit non-homologous which Retron AbiH. We suggest prediction based on experimental offers promising avenue unravel mechanisms co-evolution between their viruses.

Language: Английский

Citations

2
DefenseFinder update advances prokaryotic antiviral system research DOI Creative Commons
Sishuo Wang

Peer Community In Genomics, Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 12, 2024

A recommendation of: F. Tesson, R. Planel, A. Egorov, H. Georjon, Vaysset, B. Brancotte, Néron, E. Mordret, Bernheim, G. Atkinson, J. Cury Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice, Wiki and Databases https://doi.org/10.1101/2024.01.25.577194

Language: Английский

Citations

1
Analyses of Xenorhabdus griffiniae genomes reveal two distinct sub-species that display intra-species variation due to prophages DOI Creative Commons
Jennifer K. Heppert, Ryan Musumba Awori, Mengyi Cao

et al.

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Nov. 15, 2024

Abstract Background Nematodes of the genus Steinernema and their Xenorhabdus bacterial symbionts are lethal entomopathogens that useful in biocontrol insect pests, as sources diverse natural products, research models for mutualism parasitism. play a central role all aspects lifecycle, deeper understanding genomes therefore has potential to spur advances each these applications. Results Here, we report comparative genomics analysis griffiniae , including symbiont hermaphroditum nematodes, which genetic genomic tools being developed. We sequenced assembled circularized three strains: HGB2511, ID10 TH1. then determined relationships other delineated species via phylogenomic analyses, concluding HGB2511 while TH1 is novel species. These additions existing X. landscape further allowed identification two subspecies within clade. Consistent with analysed encode wide array antimicrobials virulence-related proteins. Comparative creation pangenome, revealed large amount intraspecies variation contained mobilome attributable prophage loci. In addition, CRISPR arrays, secondary metabolite toxin genes varied among strains Conclusions Our findings suggest phage-related drive diversity closely related symbionts, may underlie some traits most associated lifestyle survival entomopathogenic nematodes bacteria: virulence competition. This study establishes broad knowledge base exploration not only between nematode hosts but also molecular mechanisms lifestyle.

Language: Английский

Citations

1