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Bacterial peptide deformylase inhibitors induce prophages in competitors

https://doi.org/10.1101/2025.06.06.656871

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Genetic characterization of polypeptide deformylase, a distinctive enzyme of eubacterial translation.

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Structure-function relationships within the peptide deformylase family. Evidence for a conserved architecture of the active site involving three conserved motifs and a metal ion 1 1Edited by F. E. Cohen

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Prophages encode phage-defense systems with cognate self-immunity

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Chapter 8 Methods for In Silico Prediction of Microbial Polyketide and Nonribosomal Peptide Biosynthetic Pathways from DNA Sequence Data

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Solution Structure of B. subtilis Acyl Carrier Protein

inferredcites →https://doi.org/10.1021/bi992245yopenalex-snapshot

Actinonin, a Naturally Occurring Antibacterial Agent, Is a Potent Deformylase Inhibitor

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The bacterial toxin colibactin triggers prophage induction

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Small protein modules dictate prophage fates during polylysogeny

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TAC–TIC, a high-throughput genetics method to identify triggers or blockers of bacterial toxin–antitoxin systems

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Systematic analysis of prophage elements in actinobacterial genomes reveals a remarkable phylogenetic diversity

inferredcites →https://doi.org/10.1038/sdata.2018.114openalex-snapshot

Viruses of the Nahant Collection, characterization of 251 marine Vibrionaceae viruses

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A unique peptide deformylase platform to rationally design and challenge novel active compounds

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Not always an innocent bystander: the impact of stabilised phosphopantetheine moieties when studying nonribosomal peptide biosynthesis

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INfrastructure for a PHAge REference Database: Identification of Large-Scale Biases in the Current Collection of Cultured Phage Genomes

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Jalview Version 2—a multiple sequence alignment editor and analysis workbench

inferredcites →https://doi.org/10.1093/bioinformatics/bts565openalex-snapshot

CD-HIT: accelerated for clustering the next-generation sequencing data

inferredcites →https://doi.org/10.1093/bioinformatics/btt086openalex-snapshot

QUAST: quality assessment tool for genome assemblies

inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

inferredcites →https://doi.org/10.1093/bioinformatics/btu153openalex-snapshot

Prokka: rapid prokaryotic genome annotation

inferredcites →https://doi.org/10.1093/bioinformatics/btx440openalex-snapshot

VICTOR: genome-based phylogeny and classification of prokaryotic viruses

inferredcites →https://doi.org/10.1093/ismejo/wrae202openalex-snapshot

Tailless and filamentous prophages are predominant in marine Vibrio

inferredcites →https://doi.org/10.1093/molbev/msaf311openalex-snapshot

Unraveling the Prevalence and Multifaceted Roles of Accessory Peptide Deformylases in Bacterial Adaptation and Resistance

inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

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antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation

inferredcites →https://doi.org/10.1093/nar/gkae268openalex-snapshot

Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool

inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot

MUSCLE: multiple sequence alignment with high accuracy and high throughput

inferredcites →https://doi.org/10.1093/nar/gks1243openalex-snapshot

CDD: conserved domains and protein three-dimensional structure

inferredcites →https://doi.org/10.1093/nar/gkv1012openalex-snapshot

Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM)

inferredcites →https://doi.org/10.1093/nar/gkw1129openalex-snapshot

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

inferredcites →https://doi.org/10.1093/nar/gkx320openalex-snapshot

PRISM 3: expanded prediction of natural product chemical structures from microbial genomes

inferredcites →https://doi.org/10.1099/mgen.0.000685openalex-snapshot

Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification

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Public good exploitation in natural bacterioplankton communities

inferredcites →https://doi.org/10.1126/science.1219385openalex-snapshot

Ecological Populations of Bacteria Act as Socially Cohesive Units of Antibiotic Production and Resistance

inferredcites →https://doi.org/10.1128/aac.44.7.1825-1831.2000openalex-snapshot

Peptide Deformylase in Staphylococcus aureus : Resistance to Inhibition Is Mediated by Mutations in the Formyltransferase Gene

inferredcites →https://doi.org/10.1128/aac.45.2.563-570.2001openalex-snapshot

Antibiotic Activity and Characterization of BB-3497, a Novel Peptide Deformylase Inhibitor

inferredcites →https://doi.org/10.1128/aac.45.4.1058-1064.2001openalex-snapshot

Peptide Deformylase as an Antibacterial Drug Target: Target Validation and Resistance Development

inferredcites →https://doi.org/10.1128/aem.00950-09openalex-snapshot

Acyl-Homoserine Lactones Can Induce Virus Production in Lysogenic Bacteria: an Alternative Paradigm for Prophage Induction

inferredcites →https://doi.org/10.1128/aem.02147-06openalex-snapshot

Construction of a Vibrio splendidus Mutant Lacking the Metalloprotease Gene vsm by Use of a Novel Counterselectable Suicide Vector

inferredcites →https://doi.org/10.1128/am.14.4.649-653.1966openalex-snapshot

Production of a Pyrrole Antibiotic by a Marine Bacterium

inferredcites →https://doi.org/10.1128/jb.00843-12openalex-snapshot

The Bacteriophage HK97 gp15 Moron Element Encodes a Novel Superinfection Exclusion Protein

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Efficiency of induction of prophage lambda mutants as a function of recA alleles

inferredcites →https://doi.org/10.1128/mbio.00552-15openalex-snapshot

Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations

inferredcites →https://doi.org/10.1128/mmbr.48.1.60-93.1984openalex-snapshot

Mutagenesis and inducible responses to deoxyribonucleic acid damage in Escherichia coli

inferredcites →https://doi.org/10.1128/msystems.00326-22openalex-snapshot

Mining of Thousands of Prokaryotic Genomes Reveals High Abundance of Prophages with a Strictly Narrow Host Range

inferredcites →https://doi.org/10.1186/1471-2105-11-119openalex-snapshot

Prodigal: prokaryotic gene recognition and translation initiation site identification

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De novo assembly of bacterial transcriptomes from RNA-seq data

inferredcites →https://doi.org/10.1186/s13059-016-0997-xopenalex-snapshot

Mash: fast genome and metagenome distance estimation using MinHash

inferredcites →https://doi.org/10.1186/s40168-020-00867-0openalex-snapshot

VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

inferredcites →https://doi.org/10.1186/s40168-020-00990-yopenalex-snapshot

VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

inferredcites →https://doi.org/10.1186/s40168-023-01541-xopenalex-snapshot

Chromosome folding and prophage activation reveal specific genomic architecture for intestinal bacteria

inferredcites →https://doi.org/10.1371/journal.pcbi.1005595openalex-snapshot

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

inferredcites →https://doi.org/10.1371/journal.pcbi.1007732openalex-snapshot

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

inferredcites →https://doi.org/10.1371/journal.pone.0009490openalex-snapshot

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

inferredcites →https://doi.org/10.2210/pdb8v1x/pdbopenalex-snapshot

Crystal structure of polyketide synthase (PKS) thioreductase domain from Streptomyces coelicolor

inferredcites →https://doi.org/10.3390/v12111268openalex-snapshot

VIRIDIC—A Novel Tool to Calculate the Intergenomic Similarities of Prokaryote-Infecting Viruses

inferredcites →https://doi.org/10.3390/v15041007openalex-snapshot

VirClust—A Tool for Hierarchical Clustering, Core Protein Detection and Annotation of (Prokaryotic) Viruses

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1093/molbev/msaf311openalex-snapshot

Unraveling the Prevalence and Multifaceted Roles of Accessory Peptide Deformylases in Bacterial Adaptation and Resistance

inferred← citeshttps://doi.org/10.1101/2025.06.07.658423openalex-snapshot

Identification and biosynthesis of xildivaline, a novel and widespread peptide deformylase inhibitor from Gammaproteobacteria

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