Date of Award

Spring 2026

Language

English

Embargo Period

5-10-2027

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

College/School/Department

Department of Biological Sciences

Program

Biology

First Advisor

Thomas Begley

Committee Members

Marlene Belfort, Gabriele Fuchs, Alex Valm, Jia Sheng

Keywords

E. coli, MnmA, MnmH, Bioinformatics, Gaussian Mixture Model, Codon Analysis, Epitranscriptomics

Subject Categories

Bacteriology | Bioinformatics | Cell Biology | Computational Biology | Microbial Physiology | Molecular Genetics | Systems Biology

Abstract

tRNA wobble uridine (U34) modifications shape gene expression by influencing translational efficiency and decoding fidelity. In Escherichia coli, the mnm enzyme network installs chemically distinct U34 modifications, including MnmA-dependent 2-thiouridine (s²U) and the downstream MnmH-catalyzed 2-selenouridine (se²U), yet the combined contribution of both pathways to cellular regulation remains unclear. Here, we show that disruption of either MnmA or MnmH drives widespread transcriptional and translational dysregulation, revealing a central role for wobble uridine remodeling in gene-expression control. Both ∆mnmA and ∆mnmH cells exhibit uncoupling between mRNA abundance and protein output, with disproportionate disruption of key regulatory networks. In ∆mnmA cells, loss of s2U-linked chemistry disrupts regulatory nodes including RpoS, OxyR, and FliA, whereas the loss of MnmH alters coordination between regulatory programs and coincides with enhanced motility phenotypes. Genome-wide codon-usage analysis indicates that the translational dysregulation is structured rather than random: genes segregate into codon-defined clusters, and key regulators (rpoS, oxyR, and fliA) map to clusters enriched for modification-dependent codons. Together, our findings establish wobble uridine modification as a determinant of codon-dependent translational control that governs cellular adaptation in E. coli.  By revealing that a disruption to the MnmA–MnmH wobble-U remodeling selectively rewires translation of codon-defined gene programs and lifestyle outputs, our work identifies tRNA-modification enzymes as actionable targets for antimicrobial strategies to destabilize bacterial proteome allocation rather than inhibiting a single pathway.

License

This work is licensed under the University at Albany Standard Author Agreement.

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Available for download on Monday, May 10, 2027

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