Biology subjects

Fridman, C. M.

Publications and source records attributed to Fridman, C. M..

10 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

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

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↗

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↗

bioRxiv2022

The MIX domain is required for T6SS-mediated effector secretion

ABTRACTGram-negative bacteria often employ the type VI secretion system (T6SS) to deliver diverse cocktails of antibacterial effectors into rival bacteria. In many cases, even when the identity of the delivered effectors is known, their toxic activity and mechanism of secretion are not. Here, we investigate VPA1263, a Vibrio parahaemolyticus T6SS effector that belongs to a widespread class of polymorphic effectors containing a MIX domain. We reveal a C-terminal DNase toxin domain belonging to the HNH nuclease superfamily, and we show that it mediates the antibacterial toxicity of this effector during bacterial competition. Furthermore, we demonstrate that the VPA1263 MIX domain is necessary for T6SS-mediated secretion and intoxication of recipient bacteria. These results are the first indication of a functional role for MIX domains in T6SS secretion. IMPORTANCESpecialized protein delivery systems are used during bacterial competition to deploy cocktails of toxins that target conserved cellular components. Although numerous toxins have been revealed, the activity of many remains unknown. In this study, we investigated such a toxin from the pathogen Vibrio parahaemolyticus. Our findings indicated that the toxin employs a DNase domain to intoxicate competitors. We also showed that a domain used as a marker for secreted toxins is required for secretion of the toxin via a type VI secretion system.

microbiology↗

bioRxiv2021

A dynamic antibacterial T6SS in Pantoea agglomerans pv. betae delivers a lysozyme-like effector to antagonize competitors

The type VI secretion system (T6SS) is deployed by numerous Gram-negative bacteria to deliver toxic effectors into neighboring cells. The genome of Pantoea agglomerans pv. betae (Pab) phytopathogenic bacteria contains a gene cluster (T6SS1) predicted to encode a complete T6SS. Using secretion and competition assays, we found that T6SS1 in Pab is a functional antibacterial system that allows this pathogen to outcompete rival plant-associated bacteria found in its natural environment. Computational analysis of the T6SS1 gene cluster revealed that antibacterial effector and immunity proteins are encoded within three dynamic genomic islands that harbor arrays of orphan immunity genes or toxin and immunity cassettes. Functional analysis demonstrated that the specialized antibacterial effector VgrG contains a C-terminal catalytically active glucosaminidase domain that is used to degrade prey peptidoglycan. Moreover, we confirmed that a bicistronic unit at the end of the T6SS1 cluster encodes a novel antibacterial T6SS effector and immunity pair. Together, these results demonstrate that Pab T6SS1 is an antibacterial system delivering a lysozyme-like effector to eliminate competitors, and indicate that this bacterium contains novel T6SS effectors. Significance StatementIn this work, we describe the identification of a Pantoea agglomerans T6SS as an antibacterial determinant used by this phytopathogen to outcompete bacterial rivals. Furthermore, we provide an in-depth analysis of the T6SS gene cluster and the putative effector and immunity genes that comprise it, and we propose explanations for its dynamic evolution and effector diversification in Pantoea strains. Lastly, we experimentally validate two predicted effector and immunity pairs, and we demonstrate that one is a potent lysozyme-like toxin.

microbiology↗