The tRNA epitranscriptomic landscape and RNA modification enzymes in Vibrio cholerae

Abstract

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.