Biology subjects

Levesque, R. C.

Publications and source records attributed to Levesque, R. C..

8 recordsLinked to original sources

bioRxiv2025

Pectobacterium sinaloense sp. nov., a novel phytopathogenic species isolated from potato plants in Mexico

As part of a broader effort to survey and characterize the diversity of pectolytic bacteria affecting potato crops in Mexico, phytopathogenic strains were isolated from soft rot symptoms in potato plants in Sinaloa. Among them, an atypical Pectobacterium-like strain, LFLA-215T, could not be confidently assigned to any known species through biochemical or molecular methods. To clarify its taxonomic position and explore its genomic and functional features, whole-genome sequencing and comparative analyses were conducted, accompanied by biochemical, morphological and pathogenicity evaluations. The strain LFLA-215T is Gram-stain-negative, with peritrichous flagella, catalase-positive, and oxidase-negative. Phylogenetic analyses based on the 16S rRNA operon, dnaJ, and 923 core genes, confirmed that strain LFLA-215T belongs to the genus Pectobacterium. However, genomic similarity values with other Pectobacterium species, ranging from 87.73-93.53% (ANIb), 87.63-93.46% (ANIu), and 34.0-52.1% (isDDH), fell below species delineation thresholds. Pectobacterium colocasium LJ1T showed the closest relationship to LFLA-215T, whereas Pectobacterium parmentieri RNS 08-42-1AT was the most distantly related. Although LFLA-215T fulfilled Kochs postulates and demonstrated pathogenicity in potato plants, its virulence on tubers was comparatively lower than that of other known Pectobacterium strains, which could be related to the size and the reduction of the total number of genes when analyzed its complete genome reported here. Taken all together, our findings support the classification of strain LFLA-215T as a novel species within the genus Pectobacterium, for which the name Pectobacterium sinaloense sp. nov. is proposed, with LFLA-215T designated as the type strain.

microbiology↗

bioRxiv2025

PqsE is conserved and functionally relevant in Pseudomonas aeruginosa

The bacterium Pseudomonas aeruginosa is an opportunistic pathogen responsible for several acute and chronic infections. It produces a diverse array of virulence and survival determinants, many of which are tightly regulated by three interlinked quorum sensing (QS) systems named las, rhl and pqs. RhlR, the transcriptional regulator of the rhl system, activates multiple virulence genes upon binding to its cognate autoinducer signal. Meanwhile, the pqs system relies on 4-hydroxy-2-alkylquinolines (HAQs) as signaling molecules to induce the transcriptional regulator MvfR (PqsR). MvfR then activates the transcription of the pqsABCDE operon, encoding enzymes for HAQ biosynthesis. The final gene in this operon encodes PqsE, a multifunctional protein unique to P. aeruginosa. Beyond its thioesterase activity in HAQ biosynthesis, PqsE stabilizes RhlR, facilitating its regulation of target genes, some of which are implicated in virulence. Because of its role in pathogenicity, PqsE is regarded as a promising therapeutic target for combating P. aeruginosa infections. While the role of PqsE towards the RhlR regulon is increasingly understood in prototypical P. aeruginosa strains such as PA14 and PAO1, its broader relevance as an anti-virulence target remains underexplored. Here, we confirm that PqsE is functionally relevant across a panel of twelve genetically diverse P. aeruginosa strains using metabolite quantification and phenotypic assays. Significant strain-to-strain variations further highlight the importance of studying QS regulation among diverse isolates. Moreover, this study underscores PqsE as a key QS regulator with a conserved role in coordinating virulence determinant production and social behaviors across diverse P. aeruginosa populations. IMPORTANCEPseudomonas aeruginosa is a versatile opportunistic pathogen, naturally tolerant and readily acquiring resistance to multiple antibiotics. Consequently, the World Health Organization identified this bacterium as a high priority pathogen for researching and developing new antimicrobial strategies. P. aeruginosa utilizes quorum sensing, a cell-to-cell communication system, to regulate the expression of several of its virulence factors. Here, we confirm that the PqsE protein is conserved and that its function in quorum sensing, especially towards the RhlR regulator, is maintained across a panel of twelve genetically diverse P. aeruginosa strains. Since PqsE is conserved and unique to this bacterium, it could serve as an ideal target for anti-virulence therapies, offering new alternatives to combat antimicrobial resistance.

microbiology↗

bioRxiv2025

PDP-Miner: an AI/ML tool to detect prophage tail proteins with depolymerase domains across thousands of bacterial genomes

MotivationAntibiotic resistance is predicted to become the leading cause of human mortality by 2050. Despite this, no other major antibiotic class has been approved for medical use since 1987. Nevertheless, phage tail proteins offer a promising alternative, given their depolymerase activity toward outer membrane polysaccharides. Several pathogenic bacteria harbor prophages, thus making these prophages molecular target already known. ResultsWe therefore developed a wrapper for an existing machine learning-based phage depolymerase prediction tool (Depolymerase-Predictor), called PDP-Miner, which annotates phage tail proteins ab initio, detects depolymerase activity within this candidate protein subset, and then performs post-hoc validation by annotating protein domains thereby allowing the user to investigate for protein domains indicative of depolymerase activity. This tool allowed identification of 10 high confidence phage depolymerase gene candidates across all 1,294 Pseudomonas genomes available on the International Pseudomonas Consortium Database and could likely help detecting other candidates across other genome databases as well. Availability and ImplementationSource code is freely available for download at http:///www.github.com/jeffgauthier/pdpminer. Implemented in Bash, supported on native Linux or WSL and supports submitting subtasks to a SLURM workload queue. Requires Miniconda3 to install dependencies. This software is free and open source under the GNU General Public License v3.0. Contactjeff.gauthier.1@ulaval.ca; rclevesq@ibis.ulaval.ca Supplementary information[add Supp. Mat. URL here when available]

bioinformatics↗

bioRxiv2023

Dynamic gene expression analysis reveals distinct severity phases of immune and cellular dysregulation in COVID-19

BackgroundCOVID-19 patients experience dynamic changes in immune and cellular function over time with potential clinical implications. However, there is insufficient research investigating, on a gene expression level, the mechanisms that become activated or suppressed over time as patients deteriorate or recover, which can inform use of repurposed and novel drugs as therapies. ObjectiveTo investigate longitudinal changes in gene expression profiles throughout the COVID-19 disease timeline. MethodsThree-hundred whole blood samples from 128 adult patients were collected during hospitalization from COVID-19, with up to five samples per patient. Transcriptome sequencing (RNA-Seq), differential gene expression analysis and pathway enrichment was performed. Drug-gene set enrichment analysis was used to identify FDA-approved medications that could inhibit critical genes and proteins at each disease phase. Prognostic gene-expression signatures were generated using machine learning to distinguish 3 disease stages. ResultsSamples were longitudinally grouped by clinical criteria and gene expression into six disease phases: Mild, Moderate, Severe, Critical, Recovery, and Discharge. Distinct mechanisms with differing trajectories during COVID-19 hospitalization were apparent. Antiviral responses peaked early in COVID-19, while heme metabolism pathways became active much later during disease. Adaptive immune dysfunction, inflammation, and metabolic derangements were most pronounced during phases with higher disease severity, while hemostatic abnormalities were elevated early and persisted throughout the disease course. Drug-gene set enrichment analysis predicted repurposed medications for potential use, including platelet inhibitors in early disease, antidiabetic medications for patients with increased disease severity, and dasatinib throughout the disease course. Disease phases could be categorized using specific gene signatures for prognosis and treatment selection. Disease phases were also highly correlated to previously developed sepsis endotypes, indicating that severity and disease timing were significant contributors to heterogeneity observed in sepsis and COVID-19. ConclusionsHigher temporal resolution of longitudinal mechanisms in COVID-19 revealed multiple immune and cellular changes that were activated at different phases of COVID-19. Understanding how a patients gene expression profile changes over time can permit more accurate risk stratification of patients and provide time-dependent personalized treatments with repurposed medications. This creates an opportunity for timely intervention before patients transition to a more severe phase, potentially accelerating patients to recovery.

immunology↗

bioRxiv2022

Mutational spectra analysis reveals bacterial niche and transmission routes

As observed in cancers, individual mutagens and defects in DNA repair create distinctive mutational signatures that combine to form context-specific spectra within cells. We reasoned that similar processes must occur in bacterial lineages, potentially allowing decomposition analysis to identify disrupted DNA repair processes and niche-specific mutagen exposure. Here we reconstructed mutational spectra for 84 clades from 31 diverse bacterial species, assigned signatures to specific DNA repair pathways using hypermutator lineages, and, by comparing mutational spectra of clades from different environmental and biological locations, extracted reproducible niche-associated mutational signatures. We show that mutational spectra can predict general and specific bacterial niches and therefore reveal the site of infection and types of transmission routes for established and emergent human bacterial pathogens. One sentence summaryVariable mutagen exposure and DNA repair drive differential mutational spectra between bacteria and enable niche inference

microbiology↗

bioRxiv2021

Combined use of Oxford Nanopore and Illumina sequencing yields insights into soybean structural variation biology

BackgroundStructural variant (SV) discovery based on short reads is challenging due to their complex signatures and tendency to occur in repeated regions. The increasing availability of long-read technologies has greatly facilitated SV discovery, however these technologies remain too costly to apply routinely to population-level studies. Here, we combined short-read and long-read sequencing technologies to provide a comprehensive population-scale assessment of structural variation in a panel of Canadian soybean cultivars. ResultsWe used Oxford Nanopore sequencing data ([~]12X mean coverage) for 17 samples to both benchmark SV calls made from the Illumina data and predict SVs that were subsequently genotyped in a population of 102 samples using Illumina data. Benchmarking results show that variants discovered using Oxford Nanopore can be accurately genotyped from the Illumina data. We first use the genotyped SVs for population structure analysis and show that results are comparable to those based on single-nucleotide variants. We observe that the population frequency and distribution within the genome of SVs are constrained by the location of genes. Gene Ontology and PFAM domain enrichment analyses also confirm previous reports that genes harboring high-frequency SVs are enriched for functions in defense response. Finally, we discover polymorphic transposable elements from the SVs and report evidence of the recent activity of a Stowaway MITE. ConclusionsOur results demonstrate that long-read and short-read sequencing technologies can be efficiently combined to enhance SV analysis in large populations, providing a reusable framework for their study in a wider range of samples and non-model species.

genomics↗

bioRxiv2019

A megaplasmid family responsible for dissemination of multidrug resistance in Pseudomonas

Multidrug resistance (MDR) represents a global threat to health. Although plasmids can play an important role in the dissemination of MDR, they have not been commonly linked to the emergence of antimicrobial resistance in the pathogen Pseudomonas aeruginosa. We used whole genome sequencing to characterize a collection of P. aeruginosa clinical isolates from a hospital in Thailand. Using long-read sequence data we obtained complete sequences of two closely related megaplasmids (>420 kb) carrying large arrays of antibiotic resistance genes located in discrete, complex and dynamic resistance regions, and revealing evidence of extensive duplication and recombination events. A comprehensive pangenomic and phylogenomic analysis indicated that 1) these large plasmids comprise a family present in different members of the Pseudomonas genus and associated with multiple sources (geographical, clinical or environmental); 2) the megaplasmids encode diverse niche-adaptive accessory traits, including multidrug resistance; 3) the pangenome of the megaplasmid family is highly flexible and diverse, comprising a substantial core genome (average of 48% of plasmid genes), but with individual members carrying large numbers of unique genes. The history of the megaplasmid family, inferred from our analysis of the available database, suggests that members carrying multiple resistance genes date back to at least the 1970s.\n\nFundingThis work was supported by the International Pseudomonas Genomics Consortium, funded by Cystic Fibrosis Canada [RCL]; and the Secretaria de Educacion, Ciencia, Tecnologia e Innovacion (SECTEI), Mexico [AC].

microbiology↗

bioRxiv2018

Novel anionic cecropins from the spruce budworm feature a poly-L-aspartic acid C-terminus

Cecropins form a family of amphipathic -helical cationic peptides with broad-spectrum antibacterial properties and potent anticancer activity. The emergence of bacteria and cancer cells showing resistance to cationic antimicrobial peptides (CAMPs) has fostered a search for new, more selective and more effective alternatives to CAMPs. With this goal in mind, we looked for cecropin homologs in the genome and transcriptome of the spruce budworm, Choristoneura fumiferana. Not only did we find paralogs of the conventional cationic cecropins (Cfcec+), our screening also led to the identification of previously uncharacterized anionic cecropins (Cfcec-), featuring a poly-L-aspartic acid C-terminus. Comparative peptide analysis indicated that the C-terminal helix of Cfcec- is amphipathic, unlike that of Cfcec+, which is hydrophobic. Interestingly, molecular dynamics simulations pointed to the lower conformational flexibility of Cfcec- peptides, relative to that of Cfcec+. Phylogenetic analysis suggests that the evolution of distinct Cfcec+ and Cfcec- peptides may have resulted from an ancient duplication event within the Lepidoptera. Our analyses also indicated that Cfcec- shares characteristics with entericidins, which are involved in bacterial programmed cell death, lunasin, a peptide of plant origins with antimitotic effects, and APC15, a subunit of the anaphase-promoting complex. Finally, we found that both anionic and cationic cecropins contain a BH3-like motif (G-[KQR]-[HKQNR]-[IV]-[KQR]) that could interact with Bcl-2, a protein involved in apoptosis; this observation is congruent with previous reports indicating that cecropins induce apoptosis. Altogether, our observations suggest that cecropins may provide templates for the development of new anticancer drugs. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=70 SRC="FIGDIR/small/307702v2_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@ba988dorg.highwire.dtl.DTLVardef@757d76org.highwire.dtl.DTLVardef@18009b5org.highwire.dtl.DTLVardef@fd71d3_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIGenes encoding novel anionic cecropins (Cfcec-), featuring a C-terminal poly-L-aspartic acid, were found in the genome of the spruce budworm, Choristoneura fumiferana. C_LIO_LIDivergence between Cfcec+ and Cfcec- could be the result of an ancient duplication event within the Lepidoptera. C_LIO_LIThere is an apparent relationship between motifs observed in cecropin peptides and apoptosis. C_LIO_LIAnionic cecropins from the spruce budworm display characteristics suggesting they could have anticancer activity C_LI

bioinformatics↗