Biology subjects

Renault, T. T.

Publications and source records attributed to Renault, T. T..

4 recordsLinked to original sources

bioRxiv2025

The Hok bacterial toxin: diversity, toxicity, distribution and genomic localization

The hok/Sok type I toxin-antitoxin system is encoded in chromosomes and plasmids of multiple Gram-negative bacteria. Current knowledge about hok/Sok regulation, toxicity and function originates mostly from the system present in the R1 plasmid, alongside a handful of homologs. The recent expansion of bacterial genome sequences calls for an updated analysis of hok/Sok diversity and distribution. Here, we used protein and DNA sequences as well as RNA structure to search for Hok homologs. Hok was detected in almost 80% of the available Enterobacteriaceae genomes and, more rarely, in three other bacterial families. Similarity, clustering analysis of thousands of Hok homologs unveiled high Hok sequence variability and uncovered clusters of novel homologs. Experimental validation of representative sequences revealed their toxicity, regardless of their localization. After scanning dedicated databases, we observed an enrichment of the hok sequences in prophages and large conjugative plasmids. Finally, we identified horizontal gene transfer events across genera, predominantly mediated by plasmids. Our findings yield a comprehensive and curated catalog of annotated sequences, detailing genomic localization, toxic activity and distribution across diverse bacterial genomes.

bioinformatics↗

bioRxiv2024

Bacterial motility depends on a critical flagellum length and energy-optimised assembly

The flagellum is the most complex macromolecular structure known in bacteria and comprised of around two dozen distinct proteins. The main building block of the long, external flagellar filament, flagellin, is secreted through the flagellar type-III secretion system at a remarkable rate of several tens of thousands amino acids per second, significantly surpassing the rates achieved by other pore-based protein secretion systems. The evolutionary implications and potential benefits of this high secretion rate for flagellum assembly and function, however, have remained elusive. In this study, we provide both experimental and theoretical evidence that the flagellar secretion rate has been evolutionarily optimized to facilitate rapid and efficient construction of a functional flagellum. By synchronizing flagellar assembly, we found that a minimal filament length of 2.5 {micro}m was required for swimming motility. Biophysical modelling revealed that this minimal filament length threshold resulted from an elasto-hydrodynamic instability of the whole swimming cell, dependent on the filament length. Furthermore, we developed a stepwise filament labeling method combined with electron microscopy visualization to validate predicted flagellin secretion rates of up to 10,000 amino acids per second. A biophysical model of flagellum growth demonstrates that the observed high flagellin secretion rate efficiently balances filament elongation and energy consumption, thereby enabling motility in the shortest amount of time. Taken together, these insights underscore the evolutionary pressures that have shaped the development and optimization of the flagellum and type-III secretion system, illuminating the intricate interplay between functionality and efficiency in assembly of large macromolecular structures. Significance statementOur study demonstrates how protein secretion of the bacterial flagellum is finely tuned to optimize filament assembly rate and flagellum function while minimizing energy consumption. By measuring flagellar filament lengths and bacterial swimming after initiation of flag-ellum assembly, we were able to establish the minimal filament length necessary for swimming motility, which we rationalized physically as resulting from an elasto-hydrodynamic instability of the swimming cell. Our bio-physical model of flagellum growth further illustrates how the physiological flagellin secretion rate is optimized to maximize filament elongation while conserving energy. These findings illuminate the evolutionary pressures that have shaped the function of the bacterial flagellum and type-III secretion system, driving improvements in bacterial motility and overall fitness.

microbiology↗

bioRxiv2022

Tetracenomycin X sequesters peptidyl-tRNA during translation of QK motifs

With antibiotic-resistant bacteria threatening our ability to treat common infections, new lead compounds with distinct target binding sites and limited cross-resistance are urgently needed. Natural products that inhibit the bacterial ribosome - a target for more than half of the antibiotics in use today - are a promising source of such leads and have the potential to be developed into potent drugs through structure-guided design. However, because the mechanisms of action of many of these compounds are not well understood, they are often poor candidates for a structure-based approach. Here, we use inverse toeprinting coupled to next-generation sequencing to show that the aromatic polyketide tetracenomycin X (TcmX) primarily inhibits the formation of a peptide bond between an incoming aminoacyl-tRNA and a terminal Gln-Lys (QK) motif in the nascent polypeptide. Using cryogenic electron microscopy, we reveal that translation inhibition at QK motifs occurs via an unusual mechanism involving sequestration of the 3 adenosine of peptidyl-tRNALys in the drug-occupied nascent polypeptide exit tunnel of the ribosome. Our study provides mechanistic insights into the mode of action of TcmX on the bacterial ribosome and suggests a path forward for the development of novel antibiotics based on a common aromatic polyketide scaffold.

molecular biology↗

bioRxiv2020

Controlling membrane barrier during bacterial type-III protein secretion

Type-III secretion systems (T3SSs) of the bacterial flagellum and the evolutionarily related injectisome are capable of translocating proteins with a remarkable speed of several thousand amino acids per second. Here, we investigated how T3SSs are able to transport proteins at such a high rate while preventing the leakage of small molecules. Our mutational and evolutionary analyses demonstrate that an ensemble of conserved methionine residues at the cytoplasmic side of the T3SS channel create a deformable gasket (M-gasket) around fast-moving substrates undergoing export. The unique physicochemical features of the M-gasket are crucial to preserve the membrane barrier, to accommodate local conformational changes during active secretion, and to maintain stability of the secretion pore in cooperation with a plug domain (R-plug) and a network of salt-bridges. The conservation of the M-gasket, R-plug, and salt-bridge network suggests a universal mechanism by which the membrane integrity is maintained during high-speed protein translocation in all T3SSs.

microbiology↗