A novel strategy to protect prokaryotic cells from virus infection DOI Creative Commons
Yoshizumi Ishino

Engineering Microbiology, Journal Year: 2024, Volume and Issue: 4(2), P. 100153 - 100153

Published: May 29, 2024

The recent discovery of the CRISPR-Cas-mediated acquired immunity system highlights fact that our knowledge phage/virus defense mechanisms encoded in bacterial and archaeal genomes is far from complete. Indeed, new prokaryotic immune systems are now continually being discovered. A report described a novel glycosylase recognizes α-glycosyl-hydroxymethyl cytosin (α-Glu-hmC), modified base observed T4 phage genome, where it produces an abasic site, thereby inhibiting propagation.

Language: Английский

Integrons are anti-phage defence libraries in Vibrio parahaemolyticus DOI
Landon J. Getz,

Sam R Fairburn,

Yundan Liu

et al.

Nature Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 27, 2025

Language: Английский

Citations

1
Natural, modified and conjugated carbohydrates in nucleic acids DOI Creative Commons
Debashis Dhara, Laurence A. Mulard, Marcel Hollenstein

et al.

Chemical Society Reviews, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

The deep interconnection between nucleic acids and carbohydrates has prompted numerous synthetic campaigns to understand acid etiology, develop orthogonal genetic systems, improve the properties of therapeutic oligonucleotides.

Language: Английский

Citations

1
Gamma-Mobile-Trio systems are mobile elements rich in bacterial defensive and offensive tools DOI
Tridib Mahata,

Katarzyna Kanarek,

Moran G. Goren

et al.

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(12), P. 3268 - 3283

Published: Oct. 23, 2024

Language: Английский

Citations

5
Nucleic acid recognition during prokaryotic immunity DOI Creative Commons
Christian F. Baca, Luciano A. Marraffini

Molecular Cell, Journal Year: 2025, Volume and Issue: 85(2), P. 309 - 322

Published: Jan. 1, 2025

Language: Английский

Citations

0
Metagenomic selections reveal diverse antiphage defenses in human and environmental microbiomes DOI Creative Commons

Luis Rodriguez-Rodriguez,

James A. Pfister,

Liam Schuck

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

To prevent phage infection, bacteria have developed an arsenal of antiphage defense systems. Using functional metagenomic selections, we identified new examples these systems from human fecal, oral, and grassland soil microbiomes. Our selections in Escherichia coli revealed over 200 putative defenses 14 diverse bacterial phyla, highlighting the broad phylogenetic interoperability Many were unrecognizable based on sequence or predicted structure, so could only be via assays. In mechanistic studies, show that some encode nucleases degrade covalently modified DNA, but which accommodate chemical modifications. We also identify outer membrane proteins adsorption a set previously unknown with profiles modalities. Most acted against at least two phages, indicating broadly acting are widely distributed among non-model bacteria.

Language: Английский

Citations

0
A phage-encoded counter-defense inhibits an NAD-degrading anti-phage defense system DOI Creative Commons
Christian L. Loyo, Alan D. Grossman

PLoS Genetics, Journal Year: 2025, Volume and Issue: 21(4), P. e1011551 - e1011551

Published: April 2, 2025

Bacteria contain a diverse array of genes that provide defense against predation by phages. Anti-phage are frequently located on mobile genetic elements and spread through horizontal gene transfer. Despite the many anti-phage systems have been identified, less is known about how phages overcome defenses employed bacteria. The integrative conjugative element ICE Bs1 in Bacillus subtilis contains gene, spbK , confers temperate phage SPβ an abortive infection mechanism. Using biochemical analyses, we found SpbK NADase activated binding to portal protein YonE. presence YonE stimulates activity TIR domain causes cell death. We also SPβ-like Φ3T has counter-defense prevents SpbK-mediated enables produce viable progeny, even cells expressing . made SPβ-Φ3T hybrid were resistant identified single ( phi3T_120, now called nip for inhibitor from phage) was both necessary sufficient block defense. Nip binds (NADase) inhibits activity. Our results insight into bacterial immunity inhibiting enzymatic protein.

Language: Английский

Citations

0
Advancing RNA phage biology through meta-omics DOI Creative Commons
Jens Hör

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(8)

Published: April 22, 2025

Abstract Bacteriophages with RNA genomes are among the simplest biological entities on Earth. Since their discovery in 1960s, they have been used as important models to understand principal processes of life, including translation and genetic code. While phages were generally thought rare oddities nature, meta-omics methods rapidly changing this simplistic view by studying diverse biomes unprecedented resolution. Metatranscriptomics dramatically expanded number known from tens thousands, revealed widespread abundance, discovered several new families potential largely unknown hosts, biology, environmental impact. At same time, (meta)genomic analyses bacterial hosts discovering an arsenal defense systems bacteria employ protect themselves predation, whose functions immunity against we only beginning understand. Here, I review how approaches advancing field phage biology a focus might fight them.

Language: Английский

Citations

0
GMT systems define a new class of mobile elements rich in bacterial defensive and offensive tools DOI Creative Commons
Tridib Mahata,

Katarzyna Kanarek,

Moran G. Goren

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: March 28, 2023

Abstract Conflicts between bacteria and their rivals led to an evolutionary arms race the development of bacterial immune systems. Although diverse immunity mechanisms were recently identified, many remain unknown, dissemination within is poorly understood. Here, we describe a widespread genetic element, defined by presence Gamma-Mobile-Trio (GMT) proteins, that serves as survival kit. We show GMT-containing genomic islands are active mobile elements with cargo comprising various anti-phage defense systems, in addition antibacterial type VI secretion system (T6SS) effectors antibiotic resistance genes. identify four new systems encoded GMT islands. A thorough investigation one reveals it triggered phage capsid protein induce cell dormancy. Our findings underscore need broaden concept ‘defense islands’ include also offensive tools, such T6SS effectors, they share same defensive tools for dissemination.

Language: Английский

Citations

6
Pipolins are bimodular platforms that maintain a reservoir of defense systems exchangeable with various bacterial genetic mobile elements DOI Creative Commons

Víctor Mateo-Cáceres,

Modesto Redrejo‐Rodríguez

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 26, 2024

Abstract Defense genes gather in diverse types of genomic islands bacteria and provide immunity against viruses other genetic mobile elements. Here, we disclose pipolins, previously found bacterial phyla encoding a primer-independent PolB, as new category widespread defense islands. The analysis the occurrence structure pipolins revealed that they are commonly integrative elements flanked by direct repeats Gammaproteobacteria genomes, mainly Escherichia, Vibrio or Aeromonas, often taking up known integration hotspots. Remarkably, integrase dynamics correlates with alternative spots enables lifestyles, from to mobilizable plasmid such members genera Limosilactobacillus, Pseudosulfitobacter Staphylococcus. Pipolins harbor minimal core large cargo module enriched for factors. In addition, weighted gene repertoire relatedness many these factors actively exchanged These findings indicate and, potentially islands, act orthogonal reservoirs genes, transferable immune autonomous MGEs, suggesting complementary exchange mechanisms populations.

Language: Английский

Citations

1
Pipolins are bimodular platforms that maintain a reservoir of defense systems exchangeable with various bacterial genetic mobile elements DOI Creative Commons

Víctor Mateo-Cáceres,

Modesto Redrejo‐Rodríguez

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

Published: May 22, 2024

ABSTRACT Defense genes gather in diverse types of genomic islands bacteria and provide immunity against viruses other genetic mobile elements. Here, we disclose pipolins, previously found bacterial phyla encoding a primer-independent PolB, as new category widespread defense islands. The analysis the occurrence structure pipolins revealed that they are commonly integrative elements flanked by direct repeats Gammaproteobacteria genomes, mainly Escherichia , Vibrio or Aeromonas often taking up known integration hotspots. Remarkably, integrase dynamics correlates with alternative spots enables lifestyles, from to mobilizable plasmid such members genera Limosilactobacillus Pseudosulfitobacter Staphylococcus . Pipolins harbor minimal core large cargo module enriched for factors. In addition, weighted gene repertoire relatedness many these factors actively exchanged These findings indicate and, potentially islands, act orthogonal reservoirs genes, transferable immune autonomous MGEs, suggesting complementary exchange mechanisms populations.

Language: Английский

Citations

0