Bacteriophages and microbial interactions

Structural basis of QueC-family protein function in qatABCD anti-phage defense

This study determines the structural basis of QueC-family protein function in the qatABCD anti-phage defense system, showing their role in targeting protein substrates for N-terminal modification.

Antiviral reverse transcriptase-primase synthesizes protein-templated DNA

This study shows DRT7, a reverse transcriptase-primase, generates protein-templated DNA to provide broad-spectrum antiviral immunity through abortive infection.

Enabling the prediction of phage receptor specificity from genome data

The paper predicts phage receptor specificity from genome data using large-scale genetic screens and machine learning, achieving high accuracy for E. coli phages.

Characterization of six environmental coli-phages isolated in Astana, Kazakhstan, during the School of Molecular and Theoretical Biology

The paper isolates and characterizes six new E. coli-infecting phages from Kazakhstan, expanding a phage collection and demonstrating phage research in high school education.

Systematic mapping of insertion-tolerant regions enables capsid engineering of the RNA phage PP7

The paper identifies insertion-tolerant regions in RNA phages MS2 and PP7, enabling capsid engineering of PP7 with enhanced in vivo clearance.

Structure of a novel contractile injection system in Salmonella enterica subsp. salamae

The paper reports the structure of a novel contractile injection system in Salmonella enterica subsp. salamae and identifies a new CIS cluster.

Dynamic co-existence of bacteriophages and their hosts in the Arabidopsis thaliana phyllosphere

This study tracks bacteriophage and bacterial community dynamics in Arabidopsis thaliana phyllosphere across growth stages, finding bacterial communities are more dynamic than their phages.

Widespread Genomic Islands in Giant Viruses Shape Genome Plasticity and Mosaicism

This study identifies genomic islands in giant viruses, showing they drive genome plasticity, mosaicism, and host adaptation through gene exchange with bacteria.

Divergent successional patterns and infection dynamics in virion and transcriptionally active soil viral communities following phosphorus amendment and wet-up

This study tracks viral succession and infection dynamics in soil viral communities after rewetting and phosphorus amendment, showing distinct responses in virion and transcriptionally active viral populations.

Dormant Bacteria's Fatal Attraction to RNA Bacteriophages

The paper shows RNA phages are eliminated in dormant bacteria via ROS-mediated damage, but survival depends on genomic redundancy through co-infection.

The Joint Action of Bacteriophage and Antibiotics in the Treatment of Staphylococcus aureus infections in Galleria mellonella

This study shows that combining bacteriophage and antibiotics improves clearance of Staphylococcus aureus infections in Galleria mellonella, even when antibiotics are resistant, but treatment timing and pharmacodynamics are critical.

Structural features of E. coli Stx bacteriophage phi24B revealed with cryo-electron microscopy

The paper uses cryo-electron microscopy and proteomics to reveal the structural features of the E. coli Stx bacteriophage phi24B, including its icosahedral capsid and tail assembly.

Multiple adsorptions Shape Collective T-Even Phage Lysis Dynamics: Insights From an Individual-Based Model

The paper develops an individual-based model to simulate T-even phage lysis dynamics under varying multiplicity of infection, showing how spatial dynamics and secondary adsorption thresholds influence phage-host interactions.

Competing forms of protein-protein association and DNA binding exhibited by BrxC from the BREX phage restriction system

This study investigates the structural and functional properties of BrxC, a conserved AAA+ ATPase in the BREX phage restriction system, revealing its role in mediating competing protein associations and DNA binding that regulate host methylation and phage restriction.

A novel phage satellite class induces prophage excision in Mycolicibacterium aichiense

The paper isolates and characterizes EPIPs, a novel phage satellite class in Mycolicibacterium aichiense, which induce prophage excision through unique gene content and structural features.

Who Infects Whom? Exploiting Bacterial Minicells for Targeted Virome Enrichment and Phage-Host Interaction Analysis through an Integrated Metagenomic Approach

This paper develops a method to identify phage-host interactions using bacterial minicells, revealing a distinct E. coli-specific virome and novel phage species.

Quorum sensing and capsule expression enable subpopulation evasion of phage killing in Escherichia coli ST131: Implications for targeted therapy

This study identifies mechanisms by which E. coli ST131 evades phage killing through quorum sensing and capsule expression, and develops a phage therapy strategy to overcome these defenses in urine-based conditions.

Screening metatranscriptomes for ultrastable RNA secondary structures reveals hidden bacteriophages and novel capsid nanomaterials

cDNA-guided functional selection uncovers selective defense systems against RNA phages

This paper uses a cDNA-based functional selection strategy to identify RNA phage defense systems in Pseudomonas aeruginosa, uncovering new defense mechanisms and characterizing ZwsA as an RNA endonuclease.

Genetic Analysis of F1 Cluster Phages that Infect Mycobacterium smegmatis Identifies Two Distinct Holin-Like Proteins that Regulate the Host Lysis Event

This study identifies two holin-like proteins in F1 cluster phages that regulate lysis of Mycobacterium smegmatis, showing their distinct roles and interactions in the lysis process.

Nucleoid-associated proteins sense phage-induced genome damage to elicit abortive infection

This study identifies a novel bacterial defense mechanism where nucleoid-associated proteins detect phage-induced genome damage by relocating to the cytoplasm and activating immune effectors.

Dissecting the genetic determinants of bacterial DNA degradation by bacteriophage T5

This study identifies essential genes in bacteriophage T5 that drive host DNA degradation during infection, revealing key roles for A1 and A2 in chromosomal DNA digestion.

Subcellular reorganization upon phage infection reveals stepwise assembly of viral particles from membrane-associated precursors

This study uses electron cryo tomography to reveal the stepwise assembly of SPP1 phage particles from membrane-associated precursors within a viral DNA compartment in infected bacteria.

Cenote-Taker 3 for Fast and Accurate Virus Discovery and Annotation of the Virome

Cenote-Taker 3 is a tool for virus discovery and annotation in genomic data, outperforming existing tools in speed and accuracy.

DefensePredictor: A Machine Learning Model to Discover Novel Prokaryotic Immune Systems

DefensePredictor combines ESM2 protein language model embeddings with genomic context features in a gradient boosting classifier to identify prokaryotic anti-phage defense genes, validating 45 previously unknown Escherichia coli systems.

Synergy and antagonism in a genome-scale model of metabolic hijacking by bacteriophage

The paper integrates AMGs and phage assembly into a genome-scale metabolic model to predict their impact on host metabolism and phage production, revealing synergistic and antagonistic effects.

Phages communicate across species to shape microbial ecosystems

This study shows that bacteriophages use cross-species communication via AimP peptides and AimR receptors to influence lysogeny and prophage induction in mixed microbial cultures.

Arbitrium phages can manipulate each other's lysis - lysogeny decisions

The paper shows that Arbitrium phages from different species can influence each other's lysis-lysogeny decisions through peptide-based communication, leading to fitness advantages and coevolution.

The repertoire of resistance mutations selected by a Pseudomonas aeruginosa type IV pilus-targeting lytic bacteriophage

This paper identifies resistance mutations in Pseudomonas aeruginosa exposed to a T4P-targeting phage, showing some mutations allow recovery of pilus function after phage removal.

Bacteriophage utilize pseudolysogeny to target non-replicating bacteria and CRISPR-resistant phages eliminate recalcitrant implant infections

This study shows lytic phages can infect non-replicating bacteria through pseudolysogeny and CRISPR-resistant phages can eliminate persistent Pseudomonas infections in mice.