Biology subjects

van Kessel, J.

Publications and source records attributed to van Kessel, J..

8 recordsLinked to original sources

bioRxiv2026

Catabolite Activator Protein and quorum sensing cross-control group behaviors in Vibrio campbellii

Vibrio species adapt to different niches by sensing and responding to environmental signals such as nutrients, host cues, and quorum sensing autoinducers. Vibrio campbellii uses the master quorum sensing transcription factor LuxR to control expression of hundreds of genes at high cell density. Furthermore, many gamma-proteobacteria use the global transcription factor Catabolite Activator Protein (CAP) to control numerous physiologically relevant pathways, many of which are also modulated by quorum sensing, such as competence, biofilm formation, and carbon metabolism. However, the extent to which these two global transcription factors overlap to co-regulate gene expression and bacterial behaviors is understudied. In this work, we used ChIP-seq and RNA-seq to determine the individual and combined regulons of CAP and LuxR in V. campbellii. We found that CAP and LuxR co-occupied 11 promoters to synergistically or antagonistically co-regulate genes involved with metabolism, respiration, and virulence. It was previously proposed that CAP and LuxR both bound the bioluminescence (luxCDABE) promoter to co-regulate these genes, and our RNA-seq data showed that these were indeed the most strongly co-regulated genes. However, our ChIP-seq data revealed that only LuxR bound the luxCDABE promoter in vivo. This pattern of co-regulation--where both CAP and LuxR strongly impact transcription but only LuxR binds the promoter--was the most common mechanism observed. Our model for bioluminescence regulation is that CAP indirectly activates luxCDABE expression through the regulation of an intermediate factor. This study established new connections between the global gene regulatory networks underpinning nutrient sensing and population sensing. ImportanceVibrio bacteria (vibrios) colonize and infect diverse marine hosts including corals, fish, oysters, and shrimp, and can also cause life-threatening human infections, all of which are rising annually due to increasing ocean temperatures. To develop effective treatments against Vibrio infections, it is critical to understand the global gene regulation mechanisms vibrios use that enable pathogenic lifestyles. Signal transduction systems in bacteria are well-characterized; however, how vibrios coordinate global gene expression changes in response to multiple environmental inputs is understudied. Here, we determined how the aquaculture pathogen Vibrio campbellii regulates global gene expression in response to bacterial population signals and nutrient availability signals. Our findings help contextualize how vibrios respond to their fluctuating environments in nature.

microbiology↗

bioRxiv2026

Signaling input from the polar flagellum uncouples quorum sensing from cell-density regulation in Vibrio species

Quorum sensing (QS) is traditionally recognized as a signaling mechanism that monitors cell density to coordinate bacterial group behaviors. Although the architecture of many QS pathways and their dependence on cell density are well established, the impact from other physiological cues on QS response is largely unclear. We demonstrate here that flagellar integrity profoundly influences QS responses across multiple Vibrio species. Systematic disruption of flagellar components in Vibrio cholerae revealed that loss of the hook cap protein FlgD induces QS sRNAs Qrr1-4 production independent of cell density and the canonical QS regulator LuxO. This bypass mechanism also overrides normal cell density-dependent regulation of several QS-controlled phenotypes. Notably, {Delta}flgD mutation restores intestinal colonization of {Delta}luxO mutants in an infant mouse model, indicating that flagellar defects reshape V. cholerae QS during infection. This bypass mechanism is evolutionarily conserved as {Delta}flgD mutation induced LuxO-independent qrr expression in multiple Vibrio species. The FlrBC two-component system, essential for flagellar gene expression, is required for the activation of qrr expression in {Delta}flgD mutants. FlgD specifically interacts with the FlrB histidine kinase but not the FlrC response regulator, and a hyperactive FlrC variant is sufficient to drive qrr expression even in cells with FlgD. These findings suggest that not only FlrBC senses cytoplasmic FlgD levels to monitor flagellar completeness to direct flagellar gene expression, this signaling system also functions as a link to bypass the canonical cell-density control of QS by integrating cellular structural information to coordinate group behaviors.

microbiology↗

bioRxiv2026

Vibrio campbellii encodes a distinct set of type III secretion system effectors that mediate cytotoxicity in eukaryotic host models

Type III secretion systems (T3SS) are common virulence factors that facilitate the injection of anti-eukaryotic effector toxins that damage and kill target host cells. The sequence and function of the structural and regulatory proteins of these systems are conserved across Gram-negative pathogens, including Pseudomonas, Yersinia, and Salmonella. However, the identity and function of effector proteins are not conserved and are unknown in several relevant human and animal pathogens. Here, we used comparative genomics to identify and characterize the effectors encoded by Vibrio campbellii BB120, a crustacean and fish pathogen. We showed that most sequenced Vibrio strains belonging to the Harveyi clade, including V. campbellii, encode a full set of structural and regulatory genes corresponding to the T3SS1 of V. parahaemolyticus; the exception is V. natriegens. Transcriptomic and proteomic analyses identified four V. campbellii effectors that are secreted by the T3SS. Among these, two effectors are encoded outside the T3SS island, and all effector genes were co-regulated by both the master T3SS regulator ExsA and by the master quorum sensing regulator LuxR. Three effectors - VopS, CopA, and VIBHAR_06684 - exhibited toxic activity in yeast cells or bone marrow-derived macrophages, and the toxicity phenotypes were dependent on a functional T3SS. VopS and CopA are conserved among the queried species of the Harveyi clade. VIBHAR_06684 or VIBHAR_05674 did not show conservation among the queried species. These findings demonstrate that T3SSs in bacteria from the same clade have conserved structural secretion apparatuses but exhibit variance in effector repertoires. We postulate that the functions of effectors differ between species to impart roles in host specificity. Author SummaryPathogenic Vibrio bacteria employ many virulence factors to cause disease in marine animals, including biofilms, proteases, and the secretion of toxins. Here, we identify four secreted toxins encoded by V. campbellii that are toxic to eukaryotic cells. These toxins are secreted by the type III secretion system, a needle-like apparatus used by many bacteria to inject toxins into host cells. The toxins identified in this study are regulated by quorum sensing, a method bacteria use to communicate and control virulence genes required for pathogenesis. The results of this study indicate that different Vibrio species employ distinct sets of toxins that possibly facilitate their interaction with a host.

microbiology↗

bioRxiv2024

Quorum Sensing Regulates Virulence Factors in the Coral Pathogen Vibrio coralliilyticus

The bacterial pathogen Vibrio coralliilyticus (Vcor) causes disease in coral species worldwide. The mechanisms of Vcor coral colonization, coral microbiome interactions, and virulence factor production are understudied. In other model Vibrio species, virulence factors like biofilm formation, toxin secretion, and protease production are controlled through a density-dependent communication system called quorum sensing (QS). Comparative genomics indicated that V. coralliilyticus genomes share high sequence identity for most of the QS signaling and regulatory components identified in other Vibrio species. Here, we identify an active QS signaling pathway in two V. coralliilyticus strains with distinct infection etiologies: type strain BAA-450 and coral isolate OCN008. The inter-species AI-2 autoinducer signaling pathway in both strains controls expression of the master QS transcription factor VcpR to regulate >300 genes, including protease production, biofilm formation, and two conserved type VI secretion systems (T6SSs). Activation of T6SS1 by QS results in secretion of effectors and enables interbacterial competition and killing of prey bacteria. We conclude that the QS system in V. coralliilyticus is functional and controls expression of genes involved in relevant bacterial behaviors that may influence coral infection. IMPORTANCEVibrio coralliilyticus infects many marine organisms, including multiple species of corals, and is a primary causative agent of tissue loss diseases and bacterial-induced bleaching. Here we investigate a common cell-cell communication mechanism called quorum sensing, which is known to be intimately connected to virulence in other Vibrio species. Our genetic and chemical studies of V. coralliilyticus quorum sensing uncovered an active pathway that directly regulates key virulence factors: proteases, biofilms, and secretion systems. These findings connect bacterial signaling in communities to infection of corals, which may lead to novel treatments and earlier diagnoses of coral diseases in reefs.

microbiology↗

bioRxiv2024

Ligand binding determines proteolytic stability of Vibrio LuxR/HapR quorum sensing transcription factors

In Vibrio species, quorum sensing signaling culminates in the production of the master transcription factor SmcR that regulates group behavior genes in a density-dependent manner. Previously, we identified a small molecule thiophenesulfonamide inhibitor called PTSP that targets the SmcR family of proteins and blocks activity in vivo. Here, we used structure-function analyses to identify eight PTSP-interacting residues in the ligand binding pocket that are required for PTSP inhibition of Vibrio vulnificus SmcR. Binding of PTSP to SmcR drives allosteric unfolding of the N-terminal DNA-binding domain and, in this state, SmcR is degraded by the ClpAP protease. SmcR degradation controls the timing of the phenotypic switch between high and low cell density, and strains expressing degradation-resistant smcR alleles are impervious to changes in cell density state. These studies implicate ligand binding as a mediator of SmcR protein stability and function, which dictates the timing of quorum sensing gene expression in three Vibrio pathogens. Significance StatementSmcR family proteins were discovered in the 1990s as central regulators of quorum sensing gene expression and later discovered to be conserved in all studied Vibrio species. SmcR homologs regulate a wide range of genes involved in pathogenesis, including but not limited to genes involved in biofilm production and toxin secretion. As archetypal members of the broad class of TetR-type transcription factors, each SmcR type protein has a predicted ligand binding pocket. However, no ligand has been identified for these proteins that control their function as regulators. Here, we used SmcR-specific chemical inhibitors to determine that ligand binding drives proteolytic degradation in vivo, the first demonstration of SmcR function connected to ligand binding for this historical protein family.

microbiology↗

bioRxiv2023

A simple mechanism for integration of quorum sensing and cAMP signalling in V. cholerae

Many bacteria use quorum sensing to control changes in lifestyle. The process is regulated by microbially derived "autoinducer" signalling molecules, that accumulate in the local environment. Individual cells sense autoinducer abundance, to infer population density, and alter their behaviour accordingly. In Vibrio cholerae, quorum sensing signals are transduced by phosphorelay to the transcription factor LuxO. Unphosphorylated LuxO permits expression of HapR, which alters global gene expression patterns. In this work, we have mapped the genome-wide distribution of LuxO and HapR in V. cholerae. Whilst LuxO has a small regulon, HapR targets 32 loci. Many HapR targets coincide with sites for the cAMP receptor protein (CRP) that regulates the transcriptional response to carbon starvation. This overlap, also evident in other Vibrio species, results from similarities in the DNA sequence bound by each factor. At shared sites, HapR and CRP simultaneously contact the double helix and binding is stabilised by direct interaction of the two factors. Importantly, this involves a CRP surface that usually contacts RNA polymerase to stimulate transcription. As a result, HapR can block transcription activation by CRP. Thus, by interacting at shared sites, HapR and CRP integrate information from quorum sensing and cAMP signalling to control gene expression. This likely allows V. cholerae to regulate subsets of genes during the transition between aquatic environments and the human host.

microbiology↗

bioRxiv2021

The polar flagellar transcriptional regulatory network in Vibrio campbellii deviates from canonical Vibrio species

Vibrio campbellii is a Gram-negative bacterium that is free-living and ubiquitous in marine environments, and it is a pathogen of fish and shellfish. Swimming motility via a single polar flagellum is a critical virulence factor in V. campbellii pathogenesis, and disruption of the flagellar motor significantly decreases host mortality. To examine V. campbellii flagellar gene regulation, we identified homologs of flagellar and chemotaxis genes conserved in other members of the Vibrionaceae and determined the transcriptional profile of these loci using differential RNA-seq. We systematically deleted all 63 predicted flagellar and chemotaxis genes in V. campbellii and examined their effects on motility and flagellum production. We specifically focused on the core flagellar regulators of the flagellar regulatory hierarchy established in other Vibrios: RpoN ({sigma}54), FlrA, FlrC, and FliA. Our results show that V. campbellii transcription of flagellar and chemotaxis genes is governed by a multi-tiered regulatory hierarchy similar to other motile Vibrio species but with two critical differences: the {sigma}54-dependent regulator FlrA is dispensable for motility, and Class II gene expression is independent of {sigma}54 regulation. Our genetic and phenotypic dissection of the V. campbellii flagellar regulatory network highlights the differences that have evolved in flagellar regulation across the Vibrionaceae.

microbiology↗

bioRxiv2019

Diversity in natural transformation frequencies and regulation across Vibrio species

In marine Vibrio species, chitin-induced natural transformation enables bacteria to take up DNA from the external environment and integrate it into their genome via homologous recombination. Expression of the master competence regulator TfoX bypasses the need for chitin induction and drives expression of the genes required for competence in several Vibrio species. Here, we show that TfoX expression in two Vibrio campbellii strains, DS40M4 and NBRC 15631, enables high frequencies of natural transformation. Conversely, transformation was not achieved in the model quorum-sensing strain V. campbellii BB120 (previously classified as Vibrio harveyi). Surprisingly, we find that quorum sensing is not required for transformation in V. campbellii DS40M4. This result is in contrast to Vibrio cholerae that requires the quorum-sensing regulator HapR to activate the competence regulator QstR. However, similar to V. cholerae, QstR is necessary for transformation in DS40M4. To investigate the difference in transformation frequencies between BB120 and DS40M4, we used previously studied V. cholerae competence genes to inform a comparative genomics analysis coupled with transcriptomics. BB120 encodes homologs of all known competence genes, but most of these genes were not induced by ectopic expression of TfoX, which likely accounts for the non-functional natural transformation in this strain. Comparison of transformation frequencies among Vibrio species indicates a wide disparity among even closely related strains, with Vibrio vulnificus having the lowest functional transformation frequency. We show that ectopic expression of both TfoX and QstR is sufficient to produce a significant increase in transformation frequency in Vibrio vulnificus.\n\nSignificanceNaturally transformable or competent bacteria are able to take up DNA from their environment, a key method of horizontal gene transfer for acquisition of new DNA sequences. Our research shows that Vibrio species that inhabit marine environments exhibit a wide diversity in natural transformation capability ranging from non-transformable to high transformation rates in which 10% of cells measurably incorporate new DNA. We show that the role of regulatory systems controlling the expression of competence genes (e.g., quorum sensing) is conserved among closely related species but differs throughout the genus. Expression of two key transcription factors, TfoX and QstR, are necessary and sufficient to stimulate high levels of transformation in Vibrio campbellii and recover low rates of transformation in Vibrio vulnificus.

microbiology↗