Chemical inhibition of cell surface modification sensitizes bacteria to phage infection

RSC Chemical Biology, Год журнала: 2024, Номер unknown

Опубликована: Янв. 1, 2024

Many bacteriophages that infect Gram-positive bacteria rely on the bacterial cell surface polymer wall teichoic acid (WTA) as a receptor. However, some modulate their with d-alanine residues, which can disrupt phage adsorption. The prevalence and significance of WTA alanylation an anti-phage defense is unknown. A chemical inhibitor d-alanylation could be employed to efficiently screen phage-host combinations for those exhibit alanylation-dependent infections. Since incorporation residues into requires activity d-alanine:alanyl carrier protein ligase (DltA), DltA was this tool. Herein, we found probe inhibiting impeded enhanced infectivity many phages against

Язык: Английский

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Systematic, high-throughput characterization of bacteriophage gene essentiality on diverse hosts

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Окт. 11, 2024

Understanding core and conditional gene essentiality is crucial for decoding genotype-phenotype relationships in organisms. We present PhageMaP, a high-throughput method to create genome-scale phage knockout libraries systematically assessing bacteriophages. Using we generate maps across hundreds of genes the model T7 non-model Bas63, on diverse hosts. These provide fundamental insights into genome organization, function, host-specific essentiality. By applying PhageMaP collection anti-phage defense systems, uncover that either inhibit or activate eight defenses offer novel mechanistic hypotheses. Furthermore, engineer synthetic phages with enhanced infectivity by modular transfer PhageMaP-discovered inhibitor from Bas63 T7. generalizable, as it leverages homologous recombination, universal cellular process, locus-specific barcoding. This versatile tool advances bacteriophage functional genomics accelerates rational design therapy.

Язык: Английский

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Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Окт. 22, 2024

Abstract The phyllosphere microbiome can positively or negatively impact plant health and growth, but we currently lack the tools to control composition. Contributing a growing collection of bacteriophages (phages) targeting bacteria living in wheat phyllosphere, here isolate sequence eight novel phages common Erwinia Pseudomonas strains, including two jumbo phages. We characterize genomic, phylogenetic, morphological traits from these argue for establishing four viral genera. also search genomes anti-defense systems investigate DNA modifications using Nanopore sequencing. In phage Rembedalsseter find evidence 13 motif-associated single-stranded breaks. A bioinformatics revealed that 60 related are enriched same motif, suggesting nicks may be widely distributed this family Finally, Sequence Read Archive similar public metagenomes. close hits jumbo-phage Kaldavass wide variety plant, food, wastewater metagenomes near-perfect hit Spanish spinach sample, illustrating how interconnected geographically distant be.

Язык: Английский

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

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Авг. 26, 2024

Abstract Phage-encoded anti-CRISPR (Acr) proteins inhibit CRISPR-Cas systems to allow phage replication and lysogeny maintenance. Most of the Acrs characterized date are stable stoichiometric inhibitors, while enzymatic have been biochemically, little is known about their potency, specificity, reversibility. Here, we examine AcrIF11, a widespread plasmid-encoded ADP-ribosyltransferase (ART) that inhibits Type I-F system. We present an NMR structure AcrIF11 homolog reveals chemical shift perturbations consistent with NAD (cofactor) binding. In experiments model both lytic MGE/lysogen stability under high targeting pressure, highly potent inhibitor more robust Cas protein level fluctuations than inhibitors. Furthermore, demonstrate remarkably specific, predominantly ADP-ribosylating Csy1 when expressed in P. aeruginosa . Given reversible nature ADP-ribosylation, hypothesized ADPr eraser enzymes (macrodomains) could remove from Csy1, potential limitation PTM-based CRISPR inhibition. diverse macrodomains can indeed modification lysate. Together, these connect vitro observations AcrIF11’s activity its specific effects vivo , clarifying advantages drawbacks evolutionary arms race between phages bacteria.

Язык: Английский

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«The LAMP-CRISPR-Cas13a technique for detecting CBASS-mechanism of phage resistance in bacteria»

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 20, 2024

ABSTRACT Antimicrobial resistance (AMR) is an important threat to public health that has led the development of innovative alternative treatments for bacterial infections, such as phage therapy. However, one greatest disadvantages therapy generation phage-resistant mutants via defence mechanisms, which are mainly contained in genomic islands (GIs) and controlled by quorum sensing (QS) network. In this study, 309 pathogenic (PAIs) harbouring a total 22.1 % proteins related anti-phage (APD) were detected genome 48 K. pneumoniae strains. Several type I II CBASS systems also strains, but only 2 located PAIs. We constructed knockout strain, not expressing cyclase gene from system present PAIs, study regulatory role QS gene. As abortive infection (Abi) system, regulating cell viability was assessed. The strain confirmed targeting LAMP-CRISPR-Cas13a technique specifically gene, same protocol used detect main these systems, i.e. APECO1. findings demonstrate network systems. Finally, first work biotechnological application rapid-technique (<2 hours) optimizing detecting predicting potential inefficacy therapeutic thus improving patient prognosis.

Язык: Английский

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