J. Bondy-Denomy

Conserved jumbo phage factors required for protein import into a phage nucleus

The paper identifies conserved phage factors required for protein import into a phage nucleus and characterizes their interactions and roles in selectivity.

Defining the constituents and functions of a lipid-based jumbo phage compartment

The paper identifies a lipid-based compartment in early phage infection that protects phage DNA and supports early transcription and translation.

Single phage proteins sequester TIR- and cGAS-generated signaling molecules

This study identifies Tad1 and Tad2 as phage proteins that sequester cyclic nucleotides produced by TIR and cGAS systems to inhibit anti-phage immunity.

Anti-CRISPR proteins trigger a burst of CRISPR-Cas9 expression that enhances phage defense

The paper shows anti-CRISPR proteins in S. pyogenes reduce Cas9 autorepression, leading to increased CRISPR-Cas expression and enhanced phage defense.

Diverse viral cas genes antagonize CRISPR immunity

The paper identifies novel anti-CRISPR genes in Listeria isolates that antagonize diverse CRISPR-Cas systems, revealing evolutionary mechanisms of Acrs through cas gene co-option.

Phage anti-CBASS protein simultaneously sequesters cyclic trinucleotides and dinucleotides

This paper identifies Acb2 as a phage-encoded protein that sequesters multiple cyclic dinucleotides and trinucleotides, inhibiting CBASS immunity.

Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system in Clostridioides difficile

This study identifies AcrIB2, an anti-CRISPR protein from a C. difficile phage that inhibits the type I-B CRISPR-Cas system, showing that a partial cas operon is sufficient for interference.

Activation of programmed cell death and counter-defense functions of phage accessory genes

The paper identifies and characterizes phage accessory genes (AGs) that activate host antiviral immunity, including programmed cell death, and explores their evolutionary implications.

Anti-CRISPR protein mediated degradation of Cas9 in human cells

This study shows AcrIIA1 induces degradation of SpyCas9 and SauCas9 in human cells, suggesting a mechanism to modulate Cas9 activity for safer gene editing.

Translation-dependent downregulation of Cas12a mRNA by an anti-CRISPR protein

This study shows that AcrVA2 inhibits Cas12a mRNA translation, reducing its anti-phage activity and enabling specific inhibition of Cas12a orthologs.

A family of novel immune systems targets early infection of nucleus-forming jumbo phages

This study identifies a novel immune system, Juk, in Pseudomonas aeruginosa that targets jumbo phages by inhibiting early phage transcription, DNA replication, and nucleus assembly.

The {varphi}PA3 Phage Nucleus is Enclosed by a Self-Assembling, 2D Crystalline Lattice

The paper shows that the Phage Nucleus of {phi}PA3 forms a self-assembling, 2D crystalline lattice with adaptable inter-tetramer contacts and functional channels.

Bacteriophages antagonize cGAS-like immunity in bacteria

The paper identifies a phage-encoded antagonist of the bacterial CBASS immunity system, showing it is necessary for phage replication and demonstrating CBASS functions as a natural anti-phage immune system.

CRISPR-Cas12a targeting of ssDNA plays no detectable role in immunity

This study shows that CRISPR-Cas12a's ssDNA cleavage activities do not contribute to bacterial immunity, as they do not affect cell viability or provide protection against ssDNA invaders.

RNA targeting with CRISPR-Cas13a facilitates bacteriophage genome engineering

This paper develops a CRISPR-Cas13a-based method to edit bacteriophage genomes, enabling precise gene modifications and functional studies of phage genes.

F-type Pyocins are Diverse Non-Contractile Phage Tail-Like Weapons for Killing Pseudomonas aeruginosa

This paper investigates F-type pyocins, showing they are diverse, potent bacteriocins with distinct killing specificities and potential as anti-bacterial therapeutics.

Mobile element warfare via CRISPR and anti-CRISPR in Pseudomonas aeruginosa

This study identifies seven new anti-CRISPR proteins and characterizes their mechanisms against Type I-C CRISPR-Cas systems in Pseudomonas aeruginosa, revealing co-evolutionary dynamics between MGEs.

Distinct subcellular localization of a Type I CRISPR complex and the Cas3 nuclease in bacteria

The paper investigates the subcellular localization of a Type I CRISPR complex and Cas3 nuclease in Pseudomonas aeruginosa, revealing PAM-dependent nucleoid surveillance and spatiotemporal regulation.

Discovery of multiple anti-CRISPRs uncovers anti-defense gene clustering in mobile genetic elements

The paper identifies 11 new anti-CRISPR genes in Enterobacteriaceae and Pseudomonas, revealing their clustering with other anti-defense genes in genomic regions called 'anti-defense islands'.

Vast diversity of anti-CRISPR proteins predicted with a machine-learning approach

The paper predicts 2,500 novel anti-CRISPR protein families using a machine learning approach and validates one candidate's anti-CRISPR activity.

Listeria phages induce Cas9 degradation to protect lysogenic genomes

This study identifies AcrIIA1 as a phage-encoded protein that inhibits Cas9 in Listeria monocytogenes by promoting its degradation, protecting lysogenic genomes.

CRISPR-Cas immunity repressed by a biofilm-activating pathway in Pseudomonas aeruginosa

The paper identifies a regulatory pathway that represses CRISPR-Cas immunity in Pseudomonas aeruginosa, showing that biofilm activators inhibit CRISPR-Cas activity.

Cryptic inoviruses are pervasive in bacteria and archaea across Earth's biomes

The paper identifies 10,295 inovirus-like genomes across diverse ecosystems, revealing their widespread presence and complex interactions with bacterial and archaeal hosts.

Temperature-responsive competitive inhibition of CRISPR-Cas9

This study shows AcrIIA2 and AcrIIA2b inhibit Cas9 DNA binding through structural occlusion, with temperature-dependent effects due to structural and environmental differences.

A nucleus-like compartment shields bacteriophage DNA from CRISPR-Cas and restriction nucleases

This study identifies a nucleus-like compartment in a jumbo phage that protects its DNA from CRISPR-Cas and restriction nucleases, but leaves its mRNA vulnerable to Cas13a.

Bacteriophage cooperation suppresses CRISPR-Cas3 and Cas9 immunity

The paper shows that phages cooperate by sharing anti-CRISPR proteins to suppress bacterial CRISPR-Cas immunity, enabling successful infection when individual phages fail to replicate.

Bacteria defend against phages through type IV pilus glycosylation

This study shows that glycosylation of type IV pili in Pseudomonas aeruginosa protects against phage infection by masking binding sites, and identifies phage tail proteins that enable infection of glycosylated pili.

Disabling Cas9 by an anti-CRISPR DNA mimic

This study shows that AcrIIA4 inhibits Cas9 by binding to Cas9-sgRNA complexes, reducing off-target edits while allowing on-target gene editing in human cells.