Poster abstracts
Poster number 114 submitted by Chathuri Pathirage
Codon and tRNA coevolution in Lactobaccilales impact on translation speed and accuracy
Chathuri Pathirage (Department of Chemistry, University of Michigan), Christopher D. Katanski (Department of Biochemistry and Molecular Biology, University of Chicago), Tyler J. Smith (Department of Chemistry, University of Michigan), Yichen Hou (Department of Biochemistry and Molecular Biology, University of Chicago), Kristin S. Koutmou (Department of Chemistry, University of Michigan), Tao Pan (Department of Biochemistry and Molecular Biology, University of Chicago)
Abstract:
Codon usage bias is widely observed in the genomes of different species, families and at the gene level within genomes. Coevolution of tRNA abundances and corresponding codon usage is supported by their positive correlation in natural selection. Here, we investigated the evolutionary divergence of Leu codon usage in four families of Lactobacillales order in correlation to their tRNA abundances and modifications. The families Carnobacteriaceae (C), Enterococcaceae (EF), Lactobacillaceae (L), and Streptococcaceae (SP) contain A/T rich genomes (~65%) and display an overall preference for UUA codon, while also exhibiting family-specific codon selectivity. Concurrently, the families show variation in the sequences, abundances and modifications in tRNAs. tRNA-seq of the oral microbiome revealed that tRNAGAGLeu, which recognizes CUC codon in EF is modified to Inosine (I) at wobble 34 in Streptococcus pyogenes of SP family. Using an E. coli reconstituted in vitro translation system, we demonstrate that I34 expands the Leu decoding ability to less-abundant codons, CUC and CUU in SP. Despite the overall high representation of UUA, certain genes in SP family such as those involved in glycolysis pathways have selectivity towards CUU and UUG. tRNA-seq of both oral and stool microbiomes showed an overall increase in ratio for tRNALeuCAA/UAA in S. pyogenes compared to Enterococcus faecalis, suggesting codon usage expansion to UUG in SP could be due to differences in corresponding tRNA abundances. Also, changes in variable loop sequences as observed between EF and SP tRNAUAALeu and tRNACAALeu may affect the overall tRNA stability and interactions. In vitro translation assays show that the changes in the variable loop of tRNALeu isodecoders lead to differences in translational efficiency, with SP tRNAUAALeu displaying a 10-fold decrease in rate compared to EF. This further supports the codon expansion to UUG, in SP. Overall, this work demonstrates how specific properties of tRNAs influence codon divergence leading to translation efficiency and optimality within families in Lactobacillales order.
Keywords: codon usage bias, tRNA coevolution, tRNA modifications