Biology subjects

Venturi, V.

Publications and source records attributed to Venturi, V..

10 recordsLinked to original sources

bioRxiv2026

A switch-rheostat circuit governs quorum sensing homeostasis in a phytopathogen

Pseudomonas fuscovaginae, a wide-host-range plant pathogen of several cereal and grass species, possesses two canonical N-acyl homoserine (AHL)-based quorum sensing (QS) systems called PfsI/R and PfvI/R, both of which are inactive under laboratory conditions but active in planta. The pfsI-pfsR intergenic region encodes for RsaM, a putative protein that has since been hypothesized to act as a repressor switch of this QS circuit. In the present study, we demonstrate that the stringent repression exerted on the PfsI/R system depends entirely on the divergent promoter/intergenic pfsR-rsaM region rather than RsaM itself. Remarkably, this regulatory switch element stringently represses the expression of both the pfsR and rsaM genes. We further show for the first time that RsaM is endogenously expressed and functions as a negative regulator modulating the PfsI/R circuit instead of preventing its activation. Taken together, our results evidence a unique two-tiered/hierarchical repression of a QS system, provided by a master repressor switch and a repressor modulator. ImportancePseudomonas fuscovaginae is a globally occurring plant pathogen that employs AHL QS to regulate virulence. In this bacterium, QS signaling circuits display a rather unusual feature: the lack of activation at high cell densities under standard laboratory conditions. A hypothetical regulator named RsaM was previously linked to this phenomenon as a repressor switch acting on the PfsI/R AHL QS system in the absence of an unknown signal or stimulus. In this study, we show that a regulatory element within the pfsR-rsaM intergenic region acts as the primary switch of the PfsI/R QS system, independently of RsaM. Conversely, RsaM functions as a post-activation modulator that fine-tunes the QS response. This study advances our understanding of the regulatory configurations of unconventional QS systems by revealing a two-tier control mechanism in which a master regulatory switch governs circuit activation, while the previously uncharacterized protein RsaM controls signaling output once the system is engaged.

microbiology↗

bioRxiv2026

The Distribution and Diversity of LuxI/LuxR Quorum Sensing Systems in Proteobacteria (Pseudomonadota)

In Pseudomonadota (formerly Proteobacteria), the N-acyl homoserine lactone (AHL) quorum sensing (QS) system involves LuxI/LuxR modules, where LuxI synthesizes AHLs and LuxR-AHL regulates target gene expression. Despite extensive characterization in many bacterial species, the distribution, genomic organization, and taxonomic comprehensiveness of LuxI/R systems remains unexplored at scale. In this study, we present the first large-scale, genome-wide assessment of LuxI/R QS systems across over 30,000 publicly available genomes at chromosome-level and manually curated spanning 938 genera. Using pfam-based domain annotation, we mapped the distribution, occurrence, and copy number of LuxI/R homologs. LuxI/R systems were identified in [~]32% of surveyed genera, with notable enrichment in symbiotic and plant-associated taxa such as Rhizobium, Burkholderia, and Pseudomonas, and remarkable conservation in pathogenic taxa such as Yersinia, Aeromonas, and Acinetobacter. Conversely, entire genera, including Escherichia, Salmonella, and Klebsiella, among others, lacked LuxI/R systems across all sequenced strains, suggesting evolutionary loss, niche-specific signaling strategies, or reliance on alternative currently unknown communication systems. Our results also revealed genera with multiple, non-redundant and taxonomically not-related LuxI/R pairs per genome, indicating modular architectures and unpredictable events of horizontal gene transfer events and genetic arrangements. This study delineates the complex distribution and conservation patterns of LuxI/R circuits, providing a resource for future studies into AHL-mediated QS regulation, and microbial community interactions across diverse environments. HighlightsO_LILuxI/LuxR quorum-sensing systems show an uneven distribution across Pseudomonadota (formerly Proteobacteria) and evolved through expansion, conservation, and loss, reflecting diverse ecological strategies C_LIO_LIAmong [~]31,815 high-quality Proteobacterial genomes, 6,400 (20.1%), corresponding to C_LIO_LI[~]303 genera ([~]32%), encoded at least one complete LuxI/LuxR pair. C_LIO_LIMultiple, highly variable LuxI/R copies, up to seven per genome, reveal extensive horizontal gene transfer and mosaic evolutionary histories, especially in rhizobial and plant-associated taxa. C_LIO_LIPhylogenetic analyses distinguish genera with conserved QS architectures from those with fragmented, lineage-independent LuxI/R repertoires, possibly highlighting diverse ecological pressures shaping QS. C_LI

microbiology↗

bioRxiv2026

RsaM is not a switch but a built-in modulator of quorum sensing in Pseudomonas fuscovaginae

Pseudomonas fuscovaginae, a wide host-range plant pathogen of several cereal and grass species, possesses two canonical N-acyl homoserine (AHL)-based quorum sensing (QS) systems called PfsI/R and PfvI/R, both of which are inactive under laboratory conditions but active in planta. A Tn5 mutant insertion in the pfsI and pfsR intergenic region was previously reported to trigger the PfsI/R system. This region contains coding sequences for RsaM, a putative protein that has since been hypothesized to play a central role in imposing repression on the PfsI/R system. Putative rsaM genes/RsaM proteins negatively controlling AHL QS systems have also been reported in several other bacterial species. In the present study, we report for the first time the endogenous expression of an RsaM family protein and determine its position within the PfsI/R regulatory circuit. We found that RsaM is not produced in the wild-type P. fuscovaginae and does not play a role in keeping the PfsI/R system in a quiescent state. The expression of RsaM is instead triggered upon targeted mutations in the pfsR-rsaM intergenic region, which concomitantly activate the transcription of both the pfsI and pfsR genes. Moreover, we demonstrated that RsaM attenuates the PfsI/R circuit upon its activation. Taken together, our results evidenced that RsaM does not function as a repressor switch of the PfsI/R system, but behaves as a built-in modulator that prevents overactivation of this circuit once it is triggered. ImportancePseudomonas fuscovaginae is a globally occurring plant pathogen that employs AHL QS to regulate virulence. In this bacterium, QS signalling circuits display a rather unusual feature; the lack of activation at high cell densities under standard laboratory conditions. A hypothetical regulator named RsaM was previously linked to this phenomenon as a possible repressor switch acting on the PfsI/R AHL QS system in the absence of an unknown signal or stimulus. In this study, we demonstrated that the expression of RsaM and activation of the PfsI/R system both depend on the disruption of the rsaM and pfsR divergent intergenic region, and that RsaM functions as a negative modulator of this circuit, rather than as its master repressor. This study unveils the functional position of a novel protein regulator and broadens our understanding of regulatory configurations governing QS circuits.

microbiology↗

bioRxiv2025

Bacterial community studies and novel Bradyrhizobium and Rhizobium strains from drought-tolerant legumes grown in Namibia

AimsAnalysis of the microbiota associated with root nodules of five species of drought-tolerant legumes grown in Namibia. These legumes were Lablab purpureus, Vigna radiata, Vigna unguiculata, Macrotyloma uniflorum, and Vigna aconitifolia. Methods16S rRNA gene amplicon sequencing analysis and isolation of rhizobial and non-rhizobial bacterial strains from root nodules was performed. Plant growth-promoting traits were assessed on some isolates and the genomes of four rhizobial strains were sequenced. ResultsThe microbiota analysis revealed Bradyrhizobium as the most prevalent genus in the root nodules, while most of the non-rhizobial community included members of Bacillus genus. In addition, a strain of Variovorax paradoxus was also isolated from V. unguiculata, representing the first documented isolation and characterization report in Namibia. In vitro phenotypic characterization of the non-rhizobial nodule endophytes indicated that they possessed several plant growth-promoting traits. The four rhizobial strains isolated were taxonomically affiliated to the genera Bradyrhizobium and Rhizobium. Genome sequencing revealed that these strains possibly belong to novel species since they share only a limited similarity (dDDH values<70%) to already known species. Impact StatementThis study demonstrated that drought-tolerant legume species harbour microbial diversity from Namibian soil, which allowed us to increase our knowledge on plant-associated bacteria and their possible use in sustainable farming systems, as potential bioinoculants for crop production and for soil revitalization. Utilizing locally isolated bacterial strains as microbial bioinoculants maximizes their compatibility with the local conditions increasing the potential for positive effects on plant health and ecosystem functioning.

microbiology↗

bioRxiv2025

The Genetic Basis of Bacterial Adaptation to Hosts

Microbes colonize and interact with diverse multicellular hosts using specialized genes, many of which remain unidentified. Better understanding of host-associated gene functions is a key aspect of microbial ecology. We utilized a large-scale comparative genomics approach to identify and characterize host-associated functions by comparing 72,079 high-quality bacterial genomes from host and non-host environments using five enrichment tests for high accuracy. We uncovered over 3,000 protein domains, 16,000 AlphaFold protein clusters, and 1,500 operons enriched in host-associated bacteria. Additionally, we identified proteins and domains that are enriched in animal- or plant-associated bacteria. These include new functions such as mercury detoxification in hosts and animals in particular, and numerous proteins and domains of unknown function. We validated our results by genetically disrupting five poorly annotated host-associated genes in plant-associated bacteria, resulting in a substantial reduction in rice root colonization. One of the new colonization factors strongly affected bacterial motility and resistance of oxidative stress. Our findings, presented in a new database, GOTHAM DB, reveal the genetic basis of bacterial host association, including new functions underlying host-microbe interactions, and advance our understanding of microbial evolution.

microbiology↗

bioRxiv2025

Single-cell multiomics reveals the distinct properties of neonatal and adult recent thymic emigrants

Following thymic egress, CD8+ T cells must undergo a post-thymic maturation process to transition from a recent thymic emigrant (RTE) to a mature naive T cell. Since the neonatal T cell pool is comprised of significantly more RTEs, the prevailing notion is that neonatal CD8+ T cells behave differently than their adult counterparts simply because they have undergone less post-thymic maturation. To test this theory, we leveraged a fate mapping mouse model and paired single cell transcriptome and TCR sequencing to compare neonatal and adult CD8+ RTEs that have undergone the same amount of post-thymic maturation. Interestingly, we found that neonatal and adult CD8+ RTEs exhibit distinct phenotypes, gene expression profiles, TCR usage, and functions. These data suggest that neonatal CD8+ T cells are not simply immature adult CD8+ T cells and that age-related changes in CD8+ T cell functions in early life cannot be attributed solely to differences in the amount of post-thymic maturation.

immunology↗

bioRxiv2020

Isolation and characterization of Pseudomonas chlororaphis strain ST9 and its potential as a bioinoculant for agriculture

The development of biotechnologies based on beneficial microorganisms for improving soil fertility and crop yields could help addressing many current agriculture challenges, such as food security, climate change, pests control, soil depletion while decreasing the use of chemical fertilizers and pesticides. Plant Growth Promoting (PGP) microbes can be used as probiotics in order to increase plant tolerance/resistance to abiotic/biotic stresses and in this context strains belonging to the Pseudomonas chlororaphis group have shown to have potential as PGP candidates. In this work a new P. chlororaphis isolate is reported and tested for (i) in vitro PGP features, (ii) whole genome sequence analysis, and (iii) its effects on root microbiome, plant growth and on the expression of different plant genes in greenhouse experiments. The potential use of this P. chlororaphis strain as a plant probiotic is discussed.

microbiology↗

bioRxiv2017

Molecularly barcoded Zika virus libraries to probe in vivo evolutionary dynamics

Defining the complex dynamics of Zika virus (ZIKV) infection in pregnancy and during transmission between vertebrate hosts and mosquito vectors is critical for a thorough understanding of viral transmission, pathogenesis, immune evasion, and potential reservoir establishment. Within-host viral diversity in ZIKV infection is low, which makes it difficult to evaluate infection dynamics. To overcome this biological hurdle, we constructed a molecularly barcoded ZIKV. This virus stock consists of a \"synthetic swarm\" whose members are genetically identical except for a run of eight consecutive degenerate codons, which creates approximately 64,000 theoretical nucleotide combinations that all encode the same amino acids. Deep sequencing this region of the ZIKV genome enables counting of individual barcode clonotypes to quantify the number and relative proportions of viral lineages present within a host. Here we used these molecularly barcoded ZIKV variants to study the dynamics of ZIKV infection in pregnant and non-pregnant macaques as well as during mosquito infection/transmission. The barcoded virus had no discernible fitness defects in vivo, and the proportions of individual barcoded virus templates remained stable throughout the duration of acute plasma viremia. ZIKV RNA also was detected in maternal plasma from a pregnant animal infected with barcoded virus for 64 days. The complexity of the virus population declined precipitously 8 days following infection of the dam, consistent with the timing of typical resolution of ZIKV in non-pregnant macaques, and remained low for the subsequent duration of viremia. Our approach showed that synthetic swarm viruses can be used to probe the composition of ZIKV populations over time in vivo to understand vertical transmission, persistent reservoirs, bottlenecks, and evolutionary dynamics.\n\nAuthor summaryUnderstanding the complex dynamics of Zika virus (ZIKV) infection during pregnancy and during transmission to and from vertebrate host and mosquito vector is critical for a thorough understanding of viral transmission, pathogenesis, immune evasion, and reservoir establishment. We sought to develop a virus model system for use in nonhuman primates and mosquitoes that allows for the genetic discrimination of molecularly cloned viruses. This \"synthetic swarm\" of viruses incorporates a molecular barcode that allows for tracking and monitoring individual viral lineages during infection. Here we infected rhesus macaques with this virus to study the dynamics of ZIKV infection in nonhuman primates as well as during mosquito infection/transmission. We found that the proportions of individual barcoded viruses remained relatively stable during acute infection in pregnant and nonpregnant animals. However, in a pregnant animal, the complexity of the virus population declined precipitously 8 days following infection, consistent with the timing of typical resolution of ZIKV in non-pregnant macaques, and remained low for the subsequent duration of viremia.

microbiology↗

bioRxiv2017

The spent culture supernatant of Pseudomonas syringae contains azelaic acid

Pseudomonas syringae pv. actinidiae (PSA) is an emerging kiwifruit bacterial pathogen which since 2008 has caused considerable losses. No quorum sensing (QS) signaling molecule has yet been reported from PSA and the aim of this study was to identify possible intercellular signals produced by PSA. A metabolome analysis resulted in the identification of 83 putative compounds, one of them was the nine carbon saturated dicarboxylic acid azelaic acid which for several reasons was decided to further study. Firstly azelaic acid, which is a straight chained nine-carbon (C9) saturated dicarboxylic acid, has been reported in plants as mobile signal that primes systemic defenses. Secondly its structure, which is associated with fatty acid biosynthesis, is similar to other known bacterial QS signals like the Diffusible Signal Facor (DSF). Analytical and structural studies by NMR spectroscopy confirmed that in the PSA spent supernatant azelaic acid was present. Quantification studies further revealed that 20 {micro}g/L of azelaic acid was present and was also found in spent supernatants of several other P. syringae pathovars. An RNAseq transcriptome study however did not reveal whether azelaic acid behaved as a QS molecule. This is the first report of the possible natural biosynthesis of azelaic acid by bacteria.

microbiology↗

bioRxiv2017

Impact Of Sequencing Depth And Read Length On Single Cell RNA Sequencing Data: Lessons From T Cells

Single cell RNA sequencing (scRNA-seq) has shown great potential in measuring the gene expression profiles of heterogeneous cell populations. In immunology, scRNA-seq allowed the characterisation of transcript sequence diversity of functionally relevant sub-populations of T cells, and notably the identification of the full length T cell receptor (TCR{beta}), which defines the specificity against cognate antigens. Several factors, such as RNA library capture, cell quality, and sequencing output have been suggested to affect the quality of scRNA-seq data, but these factors have not been systematically examined.\n\nWe studied the effect of read length and sequencing depth on the quality of gene expression profiles, cell type identification, and TCR{beta} reconstruction, utilising 1,305 publically available scRNA-seq datasets, and simulation-based analyses. Gene expression was characterised by an increased number of unique genes identified with short read lengths (<50 bp), but these featured higher technical variability compared to profiles from longer reads. TCR{beta} were detected in 1,027 cells (79%), with a success rate between 81% and 100% for datasets with at least 250,000 (PE) reads of length >50 bp.\n\nSufficient read length and sequencing depth can control technical noise to enable accurate identification of TCR{beta} and gene expression profiles from scRNA-seq data of T cells.

bioinformatics↗