Biology subjects

Lamberioux, M.

Publications and source records attributed to Lamberioux, M..

4 recordsLinked to original sources

bioRxiv2026

Coupling metabolic enhancement to plasmid spread enables programmable antimicrobial control

The rise of multidrug-resistant pathogens underscores the need for precise antimicrobial strategies that extend beyond conventional antibiotics. Conjugation-based approaches offer a powerful yet underexploited means of delivering targeted genetic interventions directly within microbial communities. In this work, we combined selective killing modules with rationally optimized conjugative vectors to target antibiotic-resistant pathogens and clinically relevant antimicrobial resistance plasmids. First, we engineered and validated toxin-intein modules, programmable cassettes that restrict toxic activity to highly specific regulatory contexts. Specifically, we developed and validated modules targeting Shigella spp., Salmonella enterica, and bacteria carrying the resistance plasmid pOXA-48, demonstrating a tunable system capable of selective activity at both the species and strain levels. To identify the most effective delivery platform, we compared mobilizable and conjugative systems and found that, in vitro, conjugative plasmids consistently outperformed mobilizable ones by approximately one order of magnitude. To further optimize delivery, we streamlined the broad-host-range plasmid RP4 and enhanced its functionality by incorporating either the metabolic fos locus, which confers a fitness advantage to cells carrying the delivery vehicle; a type IV pilus operon that promotes mating-pair stabilization and enables efficient conjugation in liquid environments; or both features combined. Using these engineered RP4 derivatives, we integrated the toxin-intein module targeting pOXA-48 and evaluated its performance in complex microbial communities. In this setting, the RP4 variant carrying both the fos locus and the type IV pilus operon effectively blocked the spread of pOXA-48. Together, this work advances the use of conjugative plasmids as robust and programmable platforms to combat antibiotic resistance and enable microbiome engineering. Beyond introducing highly specific antimicrobial modules and a new generation of optimized conjugative vectors, our results identify ecological competitiveness and plasmid transfer dynamics as critical determinants of the success of such interventions.

microbiology↗

bioRxiv2025

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

Xenorhabdus strains, Gram-negative bacteria pathogenic to insects and symbionts to nematodes of the genus Steinernema are prolific producers of various natural products. Here we describe the xisABCDE biosynthesis gene cluster from Xenorhabdus hominickii responsible for the production of xildivalines. These non-ribosomal peptide and polyketide hybrids act as peptide deformylase inhibitor (PDI) and occur also in other Gammaproteobacteria, especially Vibrio. Their structure and biosynthesis were fully elucidated despite their instability, highlighting a rare trans-methylation of their N-terminus. Subsequently, the structure of the responsible methyltransferase XisE and the peptide deformylase XisD, serving as resistance mechanism, were elucidated by X-ray crystallography, allowing insights into the function and the mode of action of this novel class of PDIs.

microbiology↗

bioRxiv2025

Unraveling the prevalence and multifaceted roles of accessory peptide deformylases in bacterial adaptation and resistance

Peptide deformylases (PDFs) are enzymes that are essential for bacterial viability and attractive targets for antibiotic development. Yet, despite their conserved function, many bacteria encode multiple PDFs, a genomic feature whose prevalence and implications remain largely unexplored. Here, we reveal that nearly half of all bacterial genomes carry more than one PDF gene, frequently embedded within mobile genetic elements such as plasmids and integrons. In Vibrio cholerae, the accessory PDF (Def2VCH) confers reduced susceptibility to actinonin (ACT), the most studied PDF inhibitor, while still supporting bacterial growth in absence of the canonical PDF copies (Def1VCH). Crystallographic analysis shows that this reduced susceptibility stems from an arginine-to-tyrosine substitution that probably reduces ACT binding. Strikingly, this resistance signature is shared by integron-encoded PDFs, and transfer of an integron-encoded PDF cassette from Pseudoxanthomonas into a susceptible V. cholerae is sufficient to abolish ACT susceptibility. These findings expose a cryptic reservoir of resistance within the bacterial mobilome and highlight a challenge to the therapeutic potential of PDF-targeting antibiotics: resistance may not only emerge, but is already encoded, mobile, and ready to spread.

microbiology↗

bioRxiv2025

Replication coordination marks the domestication of large extrachromosomal replicons in bacteria

Bacterial genomes often include extrachromosomal replicons (ERs), ranging from small plasmids to nearly chromosome-sized elements, that foster genome plasticity and adaptation. Despite their prevalence, the mechanisms underlying ER domestication and their long-term adaptation within bacterial hosts remain largely unexplored. By analyzing over 40,000 complete bacterial genomes, we identified two main ER categories: small ERs with diverse GC content and large ERs ([≥]10% the size of the main chromosome) that closely match the GC content of the chromosome. Across multiple phyla, marker frequency analyses showed that large ERs maintain a 1:1 copy number with the chromosome. Another key finding of this study is that large ERs terminate replication in synchrony with the chromosome. Hi-C contact maps revealed consistent ori-ori interactions between chromosomes and ERs. In large ERs, inter-replichore and ter-ter interactions, along with the recruitment of key chromosomal segregation motifs, suggest the co-option of chromosome-associated replication and segregation machineries. Together, our findings indicate that as ERs become larger, they become increasingly reliant on chromosome-driven processes for stable inheritance, potentially explaining why they do not exceed the size of the chromosome.

microbiology↗