Autoregulation ensures vertical transmission of the linear prophage GIL01 DOI Creative Commons
Anja Pavlin,

Nadine Fornelos,

Maja Beck‐Popovic

et al.

Communications Biology, Journal Year: 2024, Volume and Issue: 7(1)

Published: Oct. 25, 2024

Betatectiviruses are prophages consisting of linear extrachromosomal genomes without obvious plasmid modules. It remains unclear how betatectiviruses maintained in low-copy numbers host cells and they vertically transmitted. Phage GIL01 is a model betatectivirus that infects the mosquito pathogen Bacillus thuringiensis serovar israelensis. Previous studies identified two closely spaced promoters, P1 P2, responsible for expression genes required prophage replication switch from lysogenic to lytic cycle. Here, we report GIL01-encoded 58-amino acid long gp1 protein forms large nucleoprotein complex represses its transcription strong promoter P2. Notably, ectopic resulted loss exponential cultures immunized against infection with GIL01, indicating plays repressive role phage This finding consistent mutations committing cycle show maintenance this variant bacterial population contingent on accumulation deletions P1-P2 region. The fact conserved across most sequenced suggests regulatory mechanism controls widespread among these bacteriophages.

Language: Английский

Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans DOI
Fabienne Benz, Sarah Camara-Wilpert, Jakob Russel

et al.

Cell Host & Microbe, Journal Year: 2024, Volume and Issue: 32(6), P. 875 - 886.e9

Published: May 15, 2024

Language: Английский

Citations

19
Interactions and evolutionary relationships among bacterial mobile genetic elements DOI
Andrew S. Lang, Alison Buchan, Vincent Burrus

et al.

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

Published: March 11, 2025

Language: Английский

Citations

1
Dispersal, habitat filtering, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography DOI Creative Commons
Anneliek M. ter Horst, Jane D. Fudyma,

Jacqueline L. Sones

et al.

The ISME Journal, Journal Year: 2023, Volume and Issue: 17(11), P. 2079 - 2089

Published: Sept. 21, 2023

Wetlands store 20-30% of the world's soil carbon, and identifying microbial controls on these carbon reserves is essential to predicting feedbacks climate change. Although viral infections likely play important roles in wetland ecosystem dynamics, we lack a basic understanding ecology. Here 63 size-fraction metagenomes (viromes) paired total were generated from three time points 2021 at seven fresh- saltwater wetlands California Bodega Marine Reserve. We recovered 12,826 population genomic sequences (vOTUs), only 4.4% which detected same field site two years prior, indicating small degree stability or recurrence. Viral communities differed most significantly among sites also structured by habitat (plant community composition salinity). Read mapping new version our reference database, PIGEONv2.0 (515,763 vOTUs), revealed 196 vOTUs present over large geographic distances, often reflecting shared characteristics. Wetland vOTU microdiversity was lower locally than globally within between points, greater divergence with increasing spatiotemporal distance. Viruses tended have broad predicted host ranges via CRISPR spacer linkages metagenome-assembled genomes, increased SNP frequencies CRISPR-targeted major tail protein genes suggest potential eco-evolutionary dynamics response both immune targeting changes cell receptors involved attachment. Together, results highlight importance dispersal, environmental selection, as drivers local global biogeography.

Language: Английский

Citations

15
Does Phage Therapy Need a Pan-Phage? DOI Creative Commons
Petros Bozidis,

Eleftheria Markou,

Athanasia Gouni

et al.

Pathogens, Journal Year: 2024, Volume and Issue: 13(6), P. 522 - 522

Published: June 20, 2024

The emergence of multidrug-resistant bacteria is undoubtedly one the most serious global health threats. One response to this threat that has been gaining momentum over past decade 'phage therapy'. According this, lytic bacteriophages are used for treatment bacterial infections, either alone or in combination with antimicrobial agents. However, ensure efficacy and broad applicability phage therapy, several challenges must be overcome. These encompass development methods strategies host range manipulation bypass resistance mechanisms developed by pathogenic bacteria, as case since advent antibiotics. As our knowledge understanding interactions between phages their hosts evolves, key issue define each application. In article, we discuss factors affect how determines classification into different categories action. For group, recent representative examples provided, together suggestions on groups can combat certain types infections. available methodologies expansion, through sequential adaptation a new pathogen genetic engineering techniques, also reviewed.

Language: Английский

Citations

5
Metabolic remodeling of microorganisms by obligate intracellular parasites alters mutualistic community composition DOI Creative Commons

Ave T. Bisesi,

Ross P. Carlson,

Lachlan Cotner

et al.

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

Published: Feb. 2, 2025

ABSTRACT Bacteria carry many types of obligate intracellular parasites, including plasmids and bacteriophage. During infection, these parasites redirect resources away from bacterial processes toward parasite production. Because parasite-induced metabolic changes influence host traits such as growth rate, nutrient uptake, waste excretion, parasitic infection should alter how microbes contribute to important community ecosystem functions. Yet there are few empirical tests shapes metabolically-mediated interactions between non-host species. Here, we integrated a genome-scale modeling approach with an in vitro cross-feeding system investigate the consequences two Escherichia coli : conjugative plasmid F128 filamentous phage M13. We examined impact on bacteria multispecies composed E. , Salmonella enterica, Methylobacterium extorquens . Modeling predicted that have for rate secretion reuptake carbon byproducts. These theoretical results aligned broadly experiments, where found changed excretion profile inducing net externalization lactate. also parasite-driven metabolism increased density species composition were generalizable across some genotypes. Our work emphasizes infected by different metabolisms than uninfected cells demonstrates shifts can significant microbial structure function. IMPORTANCE The shape function communities variety ways, killing their hosts or transferring genetic material. This study uses combination flux balance analysis consisting enterica M13, change contributions via remodeling. Flux suggests demand processes, leading identities concentrations compounds externalize into environment. finding is supported experimental results, which additionally show induce production findings extend our understanding bacteriophage communities.

Language: Английский

Citations

0
Structural basis for cooperative ssDNA binding by bacteriophage protein filament P12 DOI Creative Commons

Lothar Träger,

Morris Degen, Joana Pereira

et al.

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(5)

Published: Feb. 11, 2025

Protein-primed DNA replication is a unique mechanism, bioorthogonal to other known modes. It relies on specialised single-stranded (ssDNA)-binding proteins (SSBs) stabilise ssDNA intermediates by unknown mechanisms. Here, we present the structural and biochemical characterisation of P12, an SSB from bacteriophage PRD1. High-resolution cryo-electron microscopy reveals that P12 forms unique, cooperative filament along ssDNA. Each protomer binds phosphate backbone 6 nucleotides in sequence-independent manner, protecting nuclease degradation. Filament formation driven intrinsically disordered C-terminal tail, facilitating binding. We identify residues essential for interaction link ssDNA-binding ability toxicity host cells. Bioinformatic analyses place fold as distinct branch within OB-like family. This work offers new insights into protein-primed lays foundation biotechnological applications.

Language: Английский

Citations

0
Completing the BASEL phage collection to unlock hidden diversity for systematic exploration of phage–host interactions DOI Creative Commons
Dorentina Humolli,

Damien Piel,

Enea Maffei

et al.

PLoS Biology, Journal Year: 2025, Volume and Issue: 23(4), P. e3003063 - e3003063

Published: April 7, 2025

Research on bacteriophages, the viruses infecting bacteria, has fueled development of modern molecular biology and inspired their therapeutic application to combat bacterial multidrug resistance. However, most work so far focused a few model phages which impedes direct applications these findings in clinics suggests that vast potential powerful remained untapped. We have therefore recently composed BASEL collection Escherichia coli (BActeriophage SElection for your Laboratory), made relevant diversity E. K-12 laboratory strain accessible community. These are widely used, but assorted limited by host. now genetically overcome two major limitations K-12, its lack O-antigen glycans presence resident immunity. Restoring expression resulted isolation diverse additional viral groups like Kagunavirus , Nonanavirus Gordonclarkvirinae Gamaleyavirus while eliminating all known antiviral defenses additionally enabled us isolate Wifcevirus genus. Even though some appear be common nature, no from any them had previously been isolated using strains, they thus largely understudied. Overall, 37 new phage isolates added complete collection. were deeply characterized genomically phenotypically with regard host receptors, sensitivity defense systems, range. results highlighted dominant roles barrier recognition restriction-modification systems anticipate completed will propel research phage–host interactions mechanisms, deepening our understanding ecology fostering innovations biotechnology antimicrobial therapy.

Language: Английский

Citations

0
Phage therapy for Klebsiella pneumoniae: Understanding bacteria–phage interactions for therapeutic innovations DOI Creative Commons
Julie Le Bris, Nathalie Chen,

Adeline Supandy

et al.

PLoS Pathogens, Journal Year: 2025, Volume and Issue: 21(4), P. e1012971 - e1012971

Published: April 8, 2025

Klebsiella pneumoniae (KP) is a Gram-negative bacterium that commonly resides in the human gastrointestinal tract and can also act as an opportunistic pathogen cause extra-intestinal infections. KP poses global health threat because it causes both hospital- community-acquired infections immune-competent immunocompromised hosts. These be multidrug-resistant and/or hypervirulent, making difficult to treat deadly. In absence of effective treatments for recalcitrant infections, bacteriophage (phage) therapy gaining attention promising alternative. this review, we evaluate epidemiology epitope diversity, discuss interactions between KP-targeting phages their bacterial hosts from eco-evolutionary perspective, summarize recent efforts phage treating We novel approaches, including genetic engineering machine learning, initial steps toward developing precision medicine approach emerging dangerous pathogen.

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
Mobile Integrons Encode Phage Defense Systems DOI Creative Commons
Nicolas Kieffer, Alberto Hipólito, Laura Ortiz-Miravalles

et al.

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

Published: July 2, 2024

Abstract Integrons are bacterial genetic elements that capture, stockpile and modulate the expression of genes encoded in integron cassettes. Mobile (MI) borne on plasmids, acting as a vehicle for hundreds antimicrobial resistance among key pathogens. These also carry g ene c assettes u nknown function ( gcu s) whose role adaptive value remains unexplored. Here we show s encode phage systems, many which novel. B acteriophage r esistance i ntegron (BRiCs) can be combined mixed with cassettes to produce multiphage or drug/phage-resistance. The fitness costs BRiCs variable, dependent context, modulated by changing order array. Hence, MIs act highly mobile, low-cost defense islands. Figure Summary Novel systems identified Integrons. We confronted unknown from mobile integrons against panel phage. characterized 13 Bacteriophage Resistance Cassettes confirmed their Klebsiella pneumoniae Pseudomonas aeruginosa . Combined other cassettes, multi-phage/antibiotic resistance. Additionally, cost reduced an

Language: Английский

Citations

2