Biology subjects

Salomon, D.

Publications and source records attributed to Salomon, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Pantoea agglomerans T6SS effectors reside in hotspots with combinatorial offensive and defensive arsenals

Gram-negative bacteria deploy type VI secretion systems (T6SSs) to mediate interbacterial competition. Although numerous T6SS effectors have been identified, their pan-genomic repertoires and evolutionary dynamics remain poorly understood. Here, we combine proteomics and comparative genomics to map the T6SS effector landscape across Pantoea agglomerans, a diverse species that includes pathogenic and beneficial strains. We uncover an extensive pan-genomic arsenal in which most effectors are encoded outside the main T6SS gene cluster, within highly dynamic hotspots distributed across the chromosome and megaplasmids. Analysis of these hotspots reveals multilayered, combinatorial arrangements of shuffled genetic cargo. Remarkably, these loci act as versatile "genomic armories" that co-localize offensive antibacterial weapons with protective anti-phage defense systems. By investigating uncharacterized genes within these variable regions, we discovered and validated a novel T6SS effector and a previously unknown anti-phage defense system, named Juno. Collectively, our findings demonstrate that bacterial warfare arsenals are highly modular and reside in dynamic genomic hubs that alternate or combine interbacterial aggression with viral defense. This evolutionary association reveals a functional blurring between offensive and defensive strategies within the bacterial accessory genome. Our findings further highlight orphan effector-associated variable regions as promising leads in the search for unrecognized bacterial conflict and defense systems.

microbiology↗

bioRxiv2026

A-to-I mRNA editing recodes CqsA and affects T6SS-mediated killing in Vibrio

Adenosine-to-inosine (A-to-I) RNA editing alters genetic information post-transcriptionally, yet its ecological and evolutionary significance in bacteria remains largely unexplored. Here, we show that endogenous RNA editing has functional consequences in bacteria. Using Vibrio alginolyticus as a model, we identified 38 editing events--the highest number reported for any bacterium to date. Editing frequencies varied across growth phases and occurred within a shorter conserved sequence motif than observed in other bacteria, suggesting species-specific determinants. The mRNA of the quorum-sensing (QS) autoinducer synthase cqsA was the most extensively edited, with 70-90% of transcripts modified. Phylogenetic and experimental analyses revealed that cqsA editing is evolutionarily conserved across diverse Vibrio species, including human pathogens. Protein mass spectrometry showed that editing replaces a tyrosine with a cysteine residue at position 193 of endogenously expressed CqsA without altering its expression or the canonical downstream QS signaling pathway. However, we found that endogenous editing of cqsA alters the expression of a subset of genes and is required for efficient type VI secretion system (T6SS)-mediated interbacterial killing. Together, these findings suggest that CqsA has additional roles beyond its canonical QS function and that RNA editing can modulate bacterial physiology. SignificanceBacteria are haploid organisms having a single copy of each gene. A-to-I RNA editing can change genetic information at the RNA level, creating protein isoforms in bacteria, but its functional impact remains unclear. Here we show that a marine Vibrio species has at least 38 edited RNAs--the highest number reported in any bacterium. We further show that editing of the quorum-sensing synthase cqsA is widespread across Vibrio species and recodes CqsA protein sequence without affecting canonical quorum sensing. Instead, editing alters expression of a focused gene set, including the type VI secretion system component hcp1, and is required for efficient T6SS-mediated interbacterial killing. Our findings uncover a conserved, quorum-sensing-independent role for CqsA in bacterial competition.

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↗

bioRxiv2026

Choice of host model and manipulated transcription regulator dictates T6SS effector-mediated toxicity

Type VI secretion system (T6SS), a toxic effector-delivery apparatus primarily studied for its antibacterial properties, has recently emerged as a widespread anti-eukaryotic determinant, particularly in members of the genus Vibrio. Although various anti-eukaryotic effectors have been described, it remains unknown whether effectors target distinct hosts in a similar manner. Moreover, it is unclear whether the entire effector arsenal encoded within a single genome is co-regulated under different conditions and by different regulators. Here, we employ the anti-eukaryotic T6SS3 of Vibrio proteolyticus to address these knowledge gaps. By monitoring toxicity during infection of oyster hemocytes and comparing the results with previous infections of murine macrophages, we find that the effector Tie1 plays a role only in intoxicating murine cells, whereas Tie2 intoxicates both cell models. Furthermore, we show that artificial induction of T6SS3 via deletion of the negative regulator hns1 fails to induce the orphan effector Tie3, whereas overexpression of a T6SS3-specific activator, Ats3, induces all three known effectors. Ats3 overexpression further reveals that Tie3, not only Tie2, participates in hemocyte intoxication. Collectively, these findings indicate that analyses of T6SS-mediated infections must factor in the possibility of partial effector repertoire activation even when the main gene cluster is fully induced, and that the contribution of anti-eukaryotic T6SS effectors to intoxication is host-dependent.

microbiology↗

bioRxiv2026

Aeromonas adhesins facilitate kin and non-kin attachment to enable T6SS-mediated antagonism in liquid

Bacterial ability to deploy the type VI secretion system (T6SS) against rivals requires prolonged cell-cell interactions. Such interactions are facilitated on solid surfaces but are assumed to be absent in liquid, leading to the conventional dismissal of T6SS-mediated competition in liquid environments. Here, we find that Aeromonas jandaei employs its T6SS to eliminate diverse bacterial competitors in liquid media. Using a workflow that monitors interbacterial competition via prey luminescence, we demonstrate that auto-aggregation and co-aggregation, facilitated by distinct adhesins, enable kin and non-kin recognition and intoxication in a T6SS-dependent manner. Furthermore, we show that another marine bacterium, Vibrio coralliilyticus, employs T6SS to intoxicate rivals in liquid media. Collectively, our results indicate that T6SS-mediated competition in liquid is more common in marine bacteria than previously anticipated, and can be facilitated by diverse molecular mechanisms that govern cell aggregation.

microbiology↗

bioRxiv2025

Phage-encoded homing endonucleases attenuate bacterial immunity

The arms race between bacteria and bacteriophages (phages) gave rise to multiple layers of antagonistic mechanisms, many of which remain unexplored. Here, we investigated the anti-phage defense system GAPS4 and showed that it is a non-selective DNase triggered by sensing DNA breaks. We further demonstrated that this activation mechanism renders GAPS4 a double-edged sword, sensitizing bacteria to various forms of antibacterial antagonism. Using comparative genomics, we found that phage-encoded homing endonucleases, long considered selfish mobile genetic elements, enhance phage fitness by attenuating GAPS4-mediated immunity. Our findings shed light on the evolutionary advantage provided by these ubiquitous mobile elements to their host phages, and on the intricate evolutionary cross-talk between bacteria and their predators.

microbiology↗

bioRxiv2025

Assessing toxicity and competitive fitness of vibrios isolated from coastal waters in Israel

Several species of aquatic bacteria belonging to the genus Vibrio are emerging pathogens of humans and marine animals. Vibrio-associated infections have been shown to correlate with the increase in the oceans surface water temperatures. A slow yet steady increase in vibrios isolated from clinical settings in Israel over the past decade led us to investigate the pathogenic potential of vibrios in Israels coastal waters. We isolated and sequenced the genomes of 23 vibrios from the Mediterranean and the Red Sea. Analysis of these genomes revealed the presence of diverse toxin secretion systems and toxins, as well as mobile genetic elements known to facilitate the dissemination of fitness-enhancing determinants. Moreover, we showed that at least 10 of these isolates can induce cell death in bone marrow-derived macrophages and that at least 12 isolates can intoxicate a rival Vibrio strain in interbacterial competition. Lastly, we determined the susceptibility profiles of these isolates to common antibiotics used to treat Vibrio infections and found widespread resistance to azithromycin. Taken together, our results reveal pathogenic potential within the Vibrio population of Israels coastal waters and underline the need for continued environmental monitoring of emerging pathogens. ImportanceThe oceans surface water temperatures have increased in past decades due to climate change. This increase correlates with the spread of vibrios, a genus of aquatic bacteria, many of which are pathogens of humans and marine animals. Since Vibrio-associated illnesses are rising in Israel, we set out to investigate the Vibrio population in Israels coastal environments and monitor their pathogenic potential. We found diverse repertoires of predicted toxins, the ability to kill mammalian immune cells, and traits that enhance bacterial fitness, such as antibacterial toxicity and resistance to antibiotics commonly used to treat Vibrio infections. These findings indicate that pathogenic traits are circulating within the environmental Vibrio population in Israels coastal waters and suggest that continued monitoring is essential to identify emerging pathogenic strains.

microbiology↗

bioRxiv2024

WHIX is a T6SS secretion domain found in polymorphic double-edged sword effectors

Gram-negative bacteria employ the type VI secretion system (T6SS) to deliver toxic effectors into neighboring cells and outcompete rivals. Although many effectors have been identified, their secretion mechanism often remains unknown. Here, we describe WHIX, a domain that is sufficient to mediate the secretion of effectors via the T6SS. Remarkably, we find WHIX in T6SS effectors that contain a single toxic domain, as well as in effectors that contain two distinct toxic domains fused to either side of WHIX. We demonstrate that the latter, which we name double-edged sword effectors, require two cognate immunity proteins to antagonize their toxicity. Furthermore, we show that WHIX can be used as a chassis for T6SS-mediated secretion of multiple domains. Our findings reveal a new class of polymorphic T6SS cargo effectors with a unique secretion domain that can deploy two toxic domains in one shot, possibly reducing recipients ability to defend themselves.

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

Bile acids activate the antibacterial T6SS1 in the gut pathogen Vibrio parahaemolyticus

The marine bacterium Vibrio parahaemolyticus is a major cause of seafood-borne gastroenteritis in humans and of acute hepatopancreatic necrosis disease in shrimp. Bile acids, produced by the host and modified into secondary bile acids by commensal bacteria in the gastrointestinal tract, induce the virulence factors leading to disease in humans and shrimp. Here, we show that secondary bile acids also activate this pathogens type VI secretion system 1 (T6SS1), a toxin-delivery apparatus mediating interbacterial competition. This finding implies that Vibrio parahaemolyticus exploits secondary bile acids to activate its virulence factors and identify the presence of commensal bacteria that it needs to outcompete in order to colonize the host. ImportanceBacterial pathogens often manipulate their host and cause disease by secreting toxic proteins. However, to successfully colonize a host, they must also remove commensal bacteria that reside in it and may compete with them over resources. Here, we find that the same host-derived molecules that activate the secreted virulence toxins in a gut bacterial pathogen, Vibrio parahaemolyticus, also activate an antibacterial toxin delivery system that targets such commensal bacteria. These findings suggest that a pathogen can use one cue to launch a coordinated, trans-kingdom attack that enables it to colonize a host.

microbiology↗

bioRxiv2024

A T6SS in the coral pathogen Vibrio coralliilyticus secretes an arsenal of anti-eukaryotic effectors and contributes to virulence

Vibrio coralliilyticus (Vcor) is a pathogen of coral and shellfish, leading to devastating economic and ecological consequences worldwide. Although rising ocean temperatures correlate with increased Vcor pathogenicity, the specific molecular mechanisms and determinants contributing to virulence remain poorly understood. Here, we systematically analyzed the type VI secretion system (T6SS), a contact-dependent toxin delivery apparatus, in Vcor. We identified two omnipresent T6SSs that are activated at temperatures in which Vcor becomes virulent; T6SS1 is an antibacterial system mediating interbacterial competition, whereas T6SS2 mediates anti-eukaryotic toxicity and contributes to mortality during infection of an aquatic model organism, Artemia salina. Using comparative proteomics, we identified the T6SS1 and T6SS2 toxin arsenals of three Vcor strains with distinct disease etiologies. Remarkably, T6SS2 secretes at least nine novel anti-eukaryotic toxins comprising core and accessory repertoires. We propose that T6SSs differently contribute to Vcors virulence: T6SS2 plays a direct role by targeting the host, while T6SS1 plays an indirect role by eliminating competitors. Author SummaryCoral reefs are diverse ecosystems providing habitats for various fish, invertebrates, and microorganisms. Climate change, leading to rising ocean water temperatures, correlates with coral bleaching and mass mortality events. An implicated causal agent of coral disease outbreaks is the marine bacterium Vibrio coralliilyticus. Here, we found that two toxin injection systems present in all Vibrio coralliilyticus strains are regulated by temperature; we revealed the toxins that they secrete and their function in competition against rival bacteria and in the intoxication of an animal host. Our findings implicate these systems as previously unappreciated contributors to Vibrio coralliilyticus virulence, illuminating possible targets to treat or prevent coral infection.

microbiology↗

bioRxiv2023

An N-terminal delivery domain defines a new class of polymorphic T6SS effectors in Enterobacterales

The type VI secretion system (T6SS), a widespread protein delivery apparatus, plays a role in bacterial competition by delivering toxic effectors into neighboring cells. Identifying new T6SS effectors and deciphering the mechanism that governs their secretion remain major challenges. Here, we report two orphan, antibacterial T6SS effectors in the pathogen Pantoea agglomerans (Pa). These effectors share an N-terminal domain, PIX, that defines a widespread class of polymorphic T6SS effectors in Enterobacterales. We show that the PIX domain is necessary and sufficient for T6SS-mediated effector secretion and that PIX binds to a specialized Pa VgrG protein, outside of its C-terminal toxic domain. Our findings underline the importance of identifying and characterizing new delivery domains in polymorphic toxin classes as a tool to reveal novel effectors and shed light on effector delivery mechanisms.

microbiology↗

bioRxiv2023

A widespread bacterial mobile genetic element encodes weapons against phages, bacteria, and eukaryotes

Conflicts between bacteria and their rivals led to an evolutionary arms race and the development of bacterial immune systems. Although diverse immunity mechanisms were recently identified, many remain unknown, and their dissemination within bacteria is poorly understood. Here, we describe a widespread genetic element, defined by the presence of the Gamma-Mobile-Trio (GMT) proteins, that serves as a bacterial survival kit. We show that GMT-containing genomic islands are active mobile elements with cargo comprising various anti-phage defense systems, in addition to antibacterial type VI secretion system (T6SS) effectors and antibiotic resistance genes. We identify four new anti-phage defense systems encoded within GMT islands. A thorough investigation of one system reveals that it is triggered by a phage capsid protein to induce cell dormancy. Our findings underscore the need to broaden the concept of defense islands to include also antibacterial offensive tools, such as T6SS effectors, as they share the same mobile elements as defensive tools for dissemination.

microbiology↗

bioRxiv2023

A Vibrio T6SS-mediated lethality in a marine animal model

Bacteria belonging to the genus Vibrio include many known and emerging pathogens. Horizontal gene transfer of pathogenicity islands is a major contributor to the emergence of new pathogenic Vibrio strains. In the current report, we use the brine shrimp Artemia salina as a model to show that the marine bacterium Vibrio proteolyticus uses a mobile type VI secretion system, T6SS3, to intoxicate eukaryotic hosts. Two T6SS3 effectors, which were previously shown to induce inflammasome-mediated pyroptotic cell death in mammalian phagocytic cells, contribute to this toxicity. Furthermore, we find a novel, widespread T6SS3 effector that also contributes to the lethality mediated by this system against Artemia salina. Therefore, our results reveal a T6SS that is shared among diverse vibrios and mediates host lethality, indicating that it can lead to the emergence of new pathogenic strains.

microbiology↗

bioRxiv2022

Vibrio parahaemolyticus T6SS2 effector repertoires

All strains of the marine bacterium Vibrio parahaemolyticus harbor a type VI secretion system (T6SS) named T6SS2, suggesting that this system plays an important role in the life cycle of this emerging pathogen. Although T6SS2 was recently shown to play a role in interbacterial competition, its effector repertoire remains unknown. Here, we employed proteomics to investigate the T6SS2 secretome of two V. parahaemolyticus strains, and we identified several antibacterial effectors encoded outside of the main T6SS2 gene cluster. We revealed two T6SS2-secreted proteins that are conserved in this species, indicating that they constitute the core secretome of T6SS2; other identified effectors are found only in subsets of strains, suggesting that they comprise an accessory effector arsenal of T6SS2. Remarkably, a conserved Rhs repeat-containing effector serves as a quality control checkpoint and is required for T6SS2 activity. Our results reveal the effector repertoire of a conserved T6SS, some of which have no known activity and have not been previously associated with T6SSs.

microbiology↗

bioRxiv2022

A new class of polymorphic T6SS effectors and tethers

Bacteria use the type VI secretion system (T6SS) to deliver toxic effectors into bacterial or eukaryotic cells during interbacterial competition, host colonization, or when resisting predation. The identity of many effectors remains unknown. Here, we identify RIX, a new domain that defines a class of polymorphic T6SS cargo effectors. RIX, which is widespread in the Vibrionaceae family, is located at N-termini of proteins containing diverse antibacterial and anti-eukaryotic toxin domains. We demonstrate that RIX-containing proteins are delivered via T6SS into neighboring cells, and that RIX is necessary and sufficient for secretion. We show that RIX-containing proteins can also act as tethers, enabling the T6SS-mediated delivery of other cargo effectors by a previously undescribed mechanism. RIX-containing proteins significantly enlarge the repertoire of known T6SS effectors, especially those with anti-eukaryotic activities. Our findings also suggest that T6SSs may play a major, currently underappreciated, role in interactions between vibrios and eukaryotes.

microbiology↗

bioRxiv2022

Post-phagocytosis activation of NLRP3 inflammasome by two novel T6SS effectors

The type VI secretion system (T6SS) is used by bacteria to deliver toxic effectors directly into target cells. Most T6SSs mediate antibacterial activities, whereas the potential anti-eukaryotic role of T6SS remains understudied. Here, we found a Vibrio T6SS that delivers two novel effectors into mammalian host immune cells. We showed that these effectors induce a pyroptotic cell death in a phagocytosis-dependent manner; we identified the NLRP3 inflammasome as being the underlying mechanism leading to the T6SS-induced pyroptosis. Moreover, we identified a compensatory T6SS-induced pathway that is activated upon inhibition of the canonical pyroptosis pathway. Genetic analyses revealed possible horizontal spread of this T6SS and its anti-eukaryotic effectors into emerging pathogens in the marine environment. Our findings reveal novel T6SS effectors that activate the host inflammasome and possibly contribute to virulence and to the emergence of bacterial pathogens.

immunology↗

bioRxiv2022

Multiple T6SSs, mobile auxiliary modules, and effectors revealed in a systematic analysis of the Vibrio parahaemolyticus pan-genome

Type VI secretion systems (T6SSs) play a major role in interbacterial competition and in bacterial interactions with eukaryotic cells. The distribution of T6SSs and the effectors they secrete vary between strains of the same bacterial species. Therefore, a pan-genome investigation is required to better understand the T6SS potential of a bacterial species of interest. Here, we performed a comprehensive, systematic analysis of T6SS gene clusters and auxiliary modules found in the pan-genome of Vibrio parahaemolyticus, an emerging pathogen widespread in marine environments. We identified four different T6SS gene clusters within genomes of this species; two systems appear to be ancient and widespread, whereas the other two systems are rare and appear to have been more recently acquired via horizontal gene transfer. In addition, we identified diverse T6SS auxiliary modules containing putative effectors with either known or predicted toxin domains. Many auxiliary modules are possibly horizontally shared between V. parahaemolyticus genomes, since they are flanked by DNA mobility genes. We further investigated a DUF4225-containing protein encoded on an Hcp auxiliary module, and we showed that it is an antibacterial T6SS effector that exerts its toxicity in the bacterial periplasm, leading to cell lysis. Computational analyses of DUF4225 revealed a widespread toxin domain associated with various toxin delivery systems. Taken together, our findings reveal a diverse repertoire of T6SSs and auxiliary modules in the V. parahaemolyticus pan-genome, as well as novel T6SS effectors and toxin domains that can play a major role in the interactions of this species with other cells. ImportanceGram-negative bacteria employ toxin delivery systems to mediate their interactions with neighboring cells. Vibrio parahaemolyticus, an emerging pathogen of humans and marine animals, was shown to deploy antibacterial toxins into competing bacteria via the type VI secretion system (T6SS). Here, we analyzed 1,727 V. parahaemolyticus genomes and revealed the pan-genome T6SS repertoire of this species, including the T6SS gene clusters, horizontally shared auxiliary modules, and toxins. We also identified a role for a previously uncharacterized domain, DUF4225, as a widespread antibacterial toxin associated with diverse toxin delivery systems.

microbiology↗