Are Bacterial Processes Dependent on Global Ribosome Pausing Affected by tRNA Modification Defects?

Valérie de Crécy-Lagard; Zeynep Barahoglu; Yifeng Yuan; Grégory Boël; Jill Babor; Jo Marie Bacusmo; Peter C Dedon; Peiying Ho; Katherine R Hummels; Daniel Kearns

doi:10.1016/j.jmb.2025.169107

Are Bacterial Processes Dependent on Global Ribosome Pausing Affected by tRNA Modification Defects?

J Mol Biol. 2025 Apr 9:169107. doi: 10.1016/j.jmb.2025.169107. Online ahead of print.

Authors

Affiliations

¹ Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32611, USA. Electronic address: vcrecy@ufl.edu.
² Institut Pasteur, Université Paris Cité, Epitranscriptomic and Translational Responses to Anti-bacterial Stress, 75015 Paris, France; Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, F-75005 Paris, France. Electronic address: zeynep.baharoglu@pasteur.fr.
³ Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA. Electronic address: yuanyifeng@ufl.edu.
⁴ Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, F-75005 Paris, France. Electronic address: boel@ibpc.fr.
⁵ Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA. Electronic address: Baborj1@mskcc.org.
⁶ Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA. Electronic address: jmbacusbo@ufl.edu.
⁷ Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance IRG, Singapore 138602 Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: pcdedon@mit.edu.
⁸ Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance IRG, Singapore 138602 Singapore.
⁹ Department of Biology, Indiana University, Bloomington, IN 47405, USA. Electronic address: Katherine.Hummels@uga.edu.
¹⁰ Department of Biology, Indiana University, Bloomington, IN 47405, USA. Electronic address: dbkearns@indiana.edu.

PMID: 40210524
DOI: 10.1016/j.jmb.2025.169107

Abstract

By integrating a literature review with transcriptomic, proteomic, and phenotypic data from two model bacteria, Escherichia coli and Vibrio cholerae, we put forward the hypothesis that defects in tRNA modification broadly impact processes that are evolutionarily tuned to be sensitive to translation speed. These include the translation of regulatory proteins associated with motility, iron homeostasis, and leader peptide-driven attenuation mechanisms. Some of these translation speed-dependent processes are influenced by the absence of a single modification, while others are affected by the absence of multiple modifications. Although further experiments are needed to clarify the mechanisms involved in each case, this work provides a foundational framework to guide future research.

Keywords: Escherichia coli; iron homeostasis; leader peptide; motility; tRNA modification.