Biology subjects

Vincent, M. S.

Publications and source records attributed to Vincent, M. S..

6 recordsLinked to original sources

bioRxiv2026

Periplasmic detoxification of urate hydroperoxide underpins E. coli survival in the inflamed gut

Uric acid, the final product of purine metabolism in humans, accumulates in blood and tissues at relatively high concentrations1 as humans lack the enzyme uricase2,3. Under inflammatory conditions, uric acid can be oxidised to yield reactive intermediates4. In activated neutrophils, myeloperoxidase (MPO) catalyses the oxidation of uric acid by hydrogen peroxide, leading to the formation of urate hydroperoxide (UH)5,6. While recent studies have shown that UH is toxic to bacteria lacking peroxiredoxins7, its precise mechanism of toxicity and the existence of dedicated bacterial defence systems remain unknown. Here, we identify HiuH as a periplasmic enzyme, conserved across E. coli strains, that specifically degrades UH. Our findings reveal that UH selectively induces the expression of hiuH and that HiuH efficiently detoxifies UH both in vitro and in bacterial cells. HiuH cooperates with MsrP, a periplasmic methionine sulfoxide reductase that repairs UH-induced protein-bound methionine oxidation. This combined defence offering both direct detoxification and damage repair, is essential for bacterial survival under UH stress, and confers a competitive fitness advantage in a DSS-induced mouse model of colitis. Although UH is chemically transient, our work shows that it imposes durable biological consequences and a sufficient fitness cost in the in vivo niches occupied by E. coli to favour the evolution of a dedicated detoxification pathway beyond general oxidative-stress responses, defining a key adaptation to periods of gut inflammation.

microbiology↗

bioRxiv2021

Dynamic proton-dependent motors power Type IX secretion and gliding adhesin movement in Flavobacterium

Motile bacteria usually rely on external apparatus like flagella for swimming or pili for twitching. By contrast, gliding bacteria do not rely on obvious surface appendages to move on solid surfaces. Flavobacterium johnsoniae and other bacteria in the Bacteroidetes phylum use adhesins whose movement on the cell surface supports motility. In F. johnsoniae, secretion and helicoidal motion of the main adhesin SprB are intimately linked and depend on the type IX secretion system (T9SS). Both processes necessitate the proton motive force (PMF), which is thought to fuel a molecular motor that comprises the GldL and GldM cytoplasmic membrane proteins. Here we show that F. johnsoniae gliding motility is powered by the pH gradient component of the PMF. We further delineate the interaction network between the GldLM transmembrane helices (TMH) and show that conserved glutamate residues in GldL TMH are essential for gliding motility, although having distinct roles in SprB secretion and motion. We then demonstrate that the PMF and GldL trigger conformational changes in the GldM periplasmic domain. We finally show that multiple GldLM complexes are distributed in the membrane suggesting that a network of motors may be present to move SprB along a helical path on the cell surface. Altogether, our results provide evidence that GldL and GldM assemble dynamic membrane channels that use the proton gradient to power both T9SS-dependent secretion of SprB and its motion at the cell surface.

microbiology↗

bioRxiv2021

Cellular heterogeneity in DNA alkylation repair as a trade-off between cell survival and genetic plasticity

DNA repair mechanisms fulfil a dual role, as they are essential for cell survival and genome maintenance. Here, we studied how cells regulate the interplay between DNA repair and mutation. We focused on the Escherichia coli adaptive response that increases resistance to DNA alkylation damage. Combination of single-molecule imaging and microfluidic-based single-cell microscopy showed that noise in the gene activation timing of the master regulator Ada is accurately propagated to generate a distinct subpopulation of cells in which all proteins of the adaptive response are absent. Although lack of these proteins causes extreme sensitivity to alkylation stress, cellular heterogeneity in DNA alkylation repair provides a functional benefit by increasing the evolvability of the whole population. We demonstrated this by monitoring the dynamics of nascent mutations during alkylation stress as well as the frequency of fixed mutations that are generated by the distinct subpopulations of the adaptive response. This highlighted that evolvability is a trade-off between mutability and cell survival. Stochastic modulation of DNA repair capacity by the adaptive response solves this trade-off through the generation of a viable hypermutable subpopulation of cells that acts as a source of genetic diversity in a clonal population.

microbiology↗

bioRxiv2018

A conserved motif of Porphyromonas Type IX secretion effectors C-terminal secretion signal specifies interactions with the PorKLMN core complex

The Type IX secretion system (T9SS) is a versatile protein transport apparatus restricted to the Bacteroidetes phylum. This multiprotein complex enables secretion of a wide range of effectors, such as protein toxins, filamentous adhesins, enzymes or S-layer subunits. Once translocated in the periplasm through the Sec pathway, recognition and secretion of these cargo proteins rely on a conserved C-terminal domain referred as CTD. However, the precise route followed by the CTD substrates from the periplasm to the cell exterior is yet to be determined. Here we define the interaction network of five different CTDs from the oral pathogen Porphyromonas gingivalis with the PorKLMN T9SS trans-envelope complex. We show that these five CTDs interact with the inner membrane-anchored PorM and the PorN periplasmic proteins. We further determine the contribution of the PorM IgG-like periplasmic domains and CTD conserved motifs for PorM-CTD complex formation. These results showed that all five CTDs interact with the core complex in a similar manner, suggesting a conserved mechanism of substrate selection in the periplasm. Our results thus establish a first model of the path followed by the CTD substrates through the T9SS.

microbiology↗

bioRxiv2017

QuickRNASeq: Guide For Pipeline Implementation And For Interactive Results Visualization

i.Summary/AbstractSequencing of transcribed RNA molecules (RNA-seq) has been used wildly for studying cell transcriptomes in bulk or at the single-cell level (1, 2, 3) and is becoming the de facto technology for investigating gene expression level changes in various biological conditions, on the time course, and under drug treatments. Furthermore, RNA-Seq data helped identify fusion genes that are related to certain cancers (4). Differential gene expression before and after drug treatments provides insights to mechanism of action, pharmacodynamics of the drugs, and safety concerns (5). Because each RNA-seq run generates tens to hundreds of millions of short reads with size ranging from 50bp-200bp, a tool that deciphers these short reads to an integrated and digestible analysis report is in high demand. QuickRNASeq (6) is an application for large-scale RNA-seq data analysis and real-time interactive visualization of complex data sets. This application automates the use of several of the best open-source tools to efficiently generate user friendly, easy to share, and ready to publish report. Figure 1 illustrates some of the interactive plots produced by QuickRNASeq. The visualization features of the application have been further improved since its first publication in early 2016. The original QuickRNASeq publication (6) provided details of background, software selection, and implementation. Here, we outline the steps required to implement QuickRNASeq in users own environment, as well as demonstrate some basic yet powerful utilities of the advanced interactive visualization modules in the report.\n\nO_FIG O_LINKSMALLFIG WIDTH=188 HEIGHT=200 SRC=\"FIGDIR/small/125856_fig1.gif\" ALT=\"Figure 1\">\nView larger version (59K):\norg.highwire.dtl.DTLVardef@1f6fb70org.highwire.dtl.DTLVardef@1f5a748org.highwire.dtl.DTLVardef@b990fborg.highwire.dtl.DTLVardef@dd5336_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 1C_FLOATNO Interactive plots from QuickRNASeq report. Figures (a, b, c) can be retrieved by clicking on the pointing hands as shown in figure Id. On any of these interactive plots, mouse over each sample displays associated sample QC metrics, (a) Read mapping summary in the expanded display mode, (b) SNP concordance matrix of 48 samples from 5 donors. Samples from the same donor should be highly concordant, (c) Gene expression chart, which shows the number of genes past various expression thresholds, (d) Center portion of the QuickRNASeq report, (e) Parallel plot linking multiple QC measures for the same samples plus table of multi-dimensional QC measures.\n\nC_FIG

bioinformatics↗

bioRxiv2017

Identification of drug eQTL interactions from repeat transcriptional and environmental measurements in a lupus clinical trial

BackgroundCytokines are critical to human disease and are attractive therapeutic targets given their widespread influence on gene regulation and transcription. Defining the downstream regulatory mechanisms influenced by cytokines is central to defining drug and disease mechanisms. One promising strategy is to use interactions between expression quantitative trait loci (eQTLs) and cytokine levels to define target genes and mechanisms.\n\nResultsIn a clinical trial for anti-IL-6 in patients with systemic lupus erythematosus we measured interferon (IFN) status, anti-IL-6 drug exposure and genome-wide gene expression at three time points (379 samples from 157 individuals). First, we show that repeat transcriptomic measurements increases the number of cis eQTLs identified compared to using a single time point by 64%. Then, after identifying 4,818 cis-eQTLs, we observed a statistically significant enrichment of in vivo eQTL interactions with IFN status (p<0.001 by permutation) and anti-IL-6 drug exposure (p<0.001). We observed 210 and 72 interactions for IFN and anti-IL-6 respectively (FDR<20%). Anti-IL-6 interactions have not yet been described while 99 of the IFN interactions are novel. Finally, we found transcription factor binding motifs interrupted by eQTL interaction SNPs, pointing to key regulatory mediators of these environmental stimuli and therefore potential therapeutic targets for autoimmune diseases. In particular, genes with IFN interactions are enriched for ISRE binding site motifs, while those with anti-IL-6 interactions are enriched for IRF4 motifs.\n\nConclusionThis study highlights the potential to exploit clinical trial data to discover in vivo eQTL interactions with therapeutically relevant environmental variables.

genomics↗