Termination efficiency of stop codons depends on the first 3’ flanking (+4) base in bacteria and eukaryotes. In both Escherichia coli and Saccharomyces cerevisiae, termination read-through is reduced in the presence of +4U; however, the molecular mechanism underlying +4U function is poorly understood. Here, we perform comparative genomics analysis on 25 bacterial species (covering Actinobacteria, Bacteriodetes, Cyanobacteria, Deinococcus-Thermus, Firmicutes, Proteobacteria and Spirochaetae) with bioinformatics approaches to examine the influence of +4U in bacterial translation termination by contrasting between highly and lowly expressed genes (HEGs and LEGs). We estimated gene expression using the recently formulated Index of Translation Elongation, ITE, and identified stop codon near-cognate tRNAs from well annotated genomes. We show that +4U was consistently over-represented in UAA-ending HEGs relative to LEGs. The result is consistent with the interpretation that +4U enhances termination mainly for UAA. Usage of +4U decreases in GC-rich species where most stop codons are UGA and UAG, with few UAA-ending genes, which is expected if UAA usage in HEGs drives up +4U usage. In highly expressed genes, +4U usage increases significantly with abundance of UAA nc_tRNAs (near-cognate tRNAs which decode codons differing from UAA by a single nucleotide), particularly those with a mismatch at the first stop codon site. UAA is always the preferred stop codon in highly expressed genes, and our results suggest that UAAU is the most efficient translation termination signal in bacteria.
- Received July 17, 2016.
- Accepted November 5, 2016.
- Copyright © 2016, The Genetics Society of America