The Role of +4U as an Extended Translation Termination Signal in Bacteria.

Yulong Wei,Xuhua Xia

doi:10.1534/genetics.116.193961

Abstract

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 highly- and lowly-expressed genes (HEGs and LEGs, respectively). We estimated gene expression using the recently formulated Index of Translation Elongation, ITE, and identified stop codon near-cognate transfer RNAs (tRNAs) from well-annotated genomes. We show that +4U was consistently overrepresented 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 HEGs, +4U usage increases significantly with abundance of UAA nc_tRNAs (near-cognate tRNAs that 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 HEGs, and our results suggest that UAAU is the most efficient translation termination signal in bacteria.

Highlights

Termination efficiency of stop codons depends on the first 39 flanking (+4) base in bacteria and eukaryotes
highly-expressed genes (HEGs) and LEGS differ in the relationship between +4U and stop codons
+4U is strongly overrepresented in all stop codons in E. coli, especially for UAA-ending and UGA-ending HEGs (Figure 2)

Summary

Introduction

Termination efficiency of stop codons depends on the first 39 flanking (+4) base in bacteria and eukaryotes. Termination efficiency of stop codons depends on the first 39-flanking (+4) base in bacterial species such as E. coli and Salmonella typhimurium (Bossi and Ruth 1980; Miller and Albertini 1983; Tate et al 1995; Poole et al 1998) and in eukaryotes (Manuvakhova et al 2000; Jungreis et al 2011). The inefficiency of translation termination associated with +4C, especially in UGA-ending genes, is well-documented in both bacteria (Brown and Tate 1994; Poole et al 1995; Tate et al 1999) and eukaryotes (Manuvakhova et al 2000; Namy et al 2001; Jungreis et al 2011; Dabrowski et al 2015; Beznoskova et al 2016). The finding that +4U reduces termination read-through is consistent with the observation that this base is overrepresented in E. coli, especially in UAA-ending genes (Brown et al 1990; Poole et al 1995; Tate et al 1996)

Methods

Results

Conclusion