Biology subjects

Bar Yaacov, D.

Publications and source records attributed to Bar Yaacov, D..

3 recordsLinked to original sources

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

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↗

bioRxiv2025

The tRNA epitranscriptomic landscape and RNA modification enzymes in Vibrio cholerae

Transfer RNAs (tRNAs) are central to protein synthesis, ensuring precise decoding of the genetic code by delivering aminoacids to the ribosome. Among all RNA species, tRNAs are the most heavily and diversely modified, with modifications playing critical roles in stability, folding, and function. Here, we present a comprehensive, isodecoder-level map of tRNA modifications in the human pathogen Vibrio cholerae. This map was generated by chemical-based sequencing methods, comparing wild-type and deletion strains. By assigning specific tRNA modifications to their cognate enzymes, we defined a comprehensive modification landscape in Vibrio cholerae and confirmed species-specific features, such as the presence of a functional TrmK enzyme, largely restricted to Gram-positive bacteria. Additionally, we detected a modification at U55 that occurs independently of TruB. To assess the biological significance of these modifications, we evaluated fitness under both standard conditions and subinhibitory antibiotic stress, and examined how modifications in the anticodon stem-loop region influence codon decoding efficiency and accuracy. Based on a comparative analysis of E. coli and V. cholerae, we discuss how species-specific differences in tRNA isodecoder gene repertoires may influence the functional impact and biological importance of tRNA modifications. This work provides the first experimentally validated, genome-wide map of tRNA modifications in V. cholerae, serving as a reference for future research into RNA modifications, translation regulation, and pathogen biology. Author summaryThis study charts the first genome-wide map of transfer RNA (tRNA) modifications in the cholera pathogen, Vibrio cholerae, revealing how chemical marks on tRNAs shape translation and stress responses. Using complementary chemical sequencing methods and a panel of targeted gene deletions, we assigned specific modifications to their enzymes across individual tRNA isodecoders. This integrative approach validates conserved features (e.g., {Psi}55 and T54), and specific ones, such as an active TrmK that installs m{superscript 1}A22 despite being considered largely restricted to Gram-positive bacteria, and uncovers enzyme interplay among dihydrouridine synthases. By testing mutant strains in standard and sub-inhibitory antibiotic conditions, we show that several modifications are dispensable for basal growth but become critical under proteotoxic stress, influencing fitness and translation accuracy, including stop-codon readthrough. Codon-specific reporter assays further demonstrate that modifications at wobble position 34 and at position 37 modulate decoding of distinct codon families, linking epitranscriptomic changes to gene expression programs. Comparative analysis with Escherichia coli suggests that species-specific tRNA isodecoder repertoires tune the functional impact of modifications. Our map provides an additional reference for studying RNA modification biology in pathogens and how it contributes to stress adaptation and virulence.

microbiology↗