Epitranscriptomic writer regulation of gene expression in Escherichia coli

The epitranscriptome is composed of enzyme catalyzed RNA modifications that can regulate tRNA, mRNA, and rRNA structure and function. RNA modifications can play key roles in regulating gene expression by controlling the when and how much of translation of specific transcripts. The SelU catalyzed tRNA wobble uridine (U) modification, occurs on tRNA lysine, glutamic acid, and glutamine. We have shown that E. coli deficient in selU gene are more sensitive to the antibiotic chloramphenicol (CAM) than their wild type counterparts. CAM works by inhibiting protein synthesis by binding to the ribosome and preventing peptide chain formation. We hypothesize that SelU translationally regulates stress response proteins in E. coli. We have used E. coli genome wide codon analytics to identify genes over-using codons decoded by specific tRNAs for lysine, glutamic acid, and glutamine. These gene lists were analyzed using the Search Tool for the Retrieval of Interacting Genes (STRING) database to identify protein networks and pathways enriched in our codon biased genes. We have determined that genes linked to the ribosome overuse both lysine codons (AAA and AAG) while genes linked to biofilm formation and flagellar assembly use contrasting glutamine codons (CAA and CAG respectively). Our studies suggest that SelU translationally regulates the production of ribosomal proteins and those used in biofilm formation and flagellar assembly. Future codon analytic studies will probe complex codon usage patterns. In addition, E. coli polysome profiles will be run to identify transcripts whose translation is perturbed under CAM exposure conditions, in a SelU dependent manner.