Joseph Bondy‐Denomy

A tripartite mechanism licenses RNA polymerase import into the phage nucleus

This study identifies a tripartite mechanism involving Imp7 and Imp1 that licenses RNA polymerase import into the phage nucleus, showing that nuclear compartment assembly precedes transcriptional and replicative programs.

A phiKMV ligase-dependent DNA repair mechanism that mitigates DNA-targeting nucleases

The paper identifies a DNA repair mechanism in phages that allows them to resist CRISPR-Cas and R-M systems by repairing nuclease-induced breaks via a ligase-dependent process.

Bacteriophage genome-wide transposon mutagenesis

This study develops a phage transposon sequencing (TnSeq) platform to identify essential genes in bacteriophages, finding ~110 fitness-conferring genes in a jumbo phage model.

CBASS limits bacteriophage production while maintaining cell viability in Pseudomonas aeruginosa

The paper shows that CBASS effector CapV limits phage production without reducing cell viability in Pseudomonas aeruginosa by interfering with phage capsid assembly.

Intracellular barriers and receptor masking limit success of a Pseudomonas aeruginosa clinical phage family

The paper identifies surface receptor masking and internal defenses as barriers to phage therapy in Pseudomonas aeruginosa clinical isolates and presents strategies to overcome these barriers through phage engineering.

Balancing of immune activation and suppression during phage infection

The paper shows how phages evade bacterial immune systems by using allelic variation and an anti-defense hotspot, revealing a similarity to a human protein.

Chemical inhibition of a bacterial immune system

This study identifies chemical inhibitors that block a bacterial immune system, enhancing phage therapy efficacy against resistant strains.

Multigenerational Proteolytic Inactivation of Restriction Upon Subtle Genomic Hypomethylation

This study shows that Pseudomonas aeruginosa inactivates its type I R-M system via proteolysis at high temperatures, leading to prolonged genomic hypomethylation and a memory effect lasting over 60 generations.

Gabija restricts phages that antagonize a conserved host DNA repair complex

The paper identifies how Gabija, a bacterial anti-phage system, discriminates self from non-self DNA by targeting phages that antagonize the host RecBCD complex.

AcrIF11 is a potent CRISPR-specific ADP-ribosyltransferase encoded by phage and plasmid

This study characterizes AcrIF11, an ADP-ribosyltransferase that inhibits CRISPR-Cas systems with high potency and specificity, and shows its reversibility through macrodomain enzymes.

END nucleases: Antiphage defense systems targeting multiple hypermodified phage genomes

The paper identifies ENDPaCF1, a novel defense system in Pseudomonas aeruginosa, which targets hypermodified phage DNA through an endonuclease domain fused to an inactive Endonuclease III, revealing its role in antiphage immunity.

Exploring the diversity of anti-defense systems across prokaryotes, phages, and mobile genetic elements

The paper develops AntiDefenseFinder to detect anti-defense systems in prokaryotes, phages, and MGEs, identifying 47,981 systems and revealing their distribution and evolutionary dynamics.

Core Defense Hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems

The paper identifies two highly conserved core defense hotspots in Pseudomonas aeruginosa containing numerous anti-phage systems, including a newly discovered system called Shango.

Next-generation interaction proteomics for quantitative Jumbophage-bacteria interaction mapping

This study uses co-fractionation mass spectrometry to map host-pathogen and pathogen-pathogen interactions in jumbophages infecting Pseudomonas aeruginosa, revealing over 6000 interactions and novel viral components.

Lack of Cas13a inhibition by anti-CRISPR proteins from Leptotrichia prophages

The paper challenges the validity of AcrVIA1-7 as type VI-A CRISPR anti-CRISPR proteins due to inconsistencies in bioinformatics and experimental results.

A minimal CRISPR-Cas3 system for genome engineering

This paper develops a minimal CRISPR-Cas3 system for efficient genome engineering, enabling large deletions in bacterial genomes.