Coevolution between Stop Codon Usage and Release Factors in Bacterial Species

Abstract

Three stop codons in bacteria represent different translation termination signals, and their usage is expected to depend on their differences in translation termination efficiency, mutation bias, and relative abundance of release factors (RF1 decoding UAA and UAG, and RF2 decoding UAA and UGA). In 14 bacterial species (covering Proteobacteria, Firmicutes, Cyanobacteria, Actinobacteria and Spirochetes) with cellular RF1 and RF2 quantified, UAA is consistently over-represented in highly expressed genes (HEGs) relative to lowly expressed genes (LEGs), whereas UGA usage is the opposite even in species where RF2 is far more abundant than RF1. UGA usage relative to UAG increases significantly with PRF2 [=RF2/(RF1 + RF2)] as expected from adaptation between stop codons and their decoders. PRF2 is > 0.5 over a wide range of AT content (measured by PAT3 as the proportion of AT at third codon sites), but decreases rapidly toward zero at the high range of PAT3. This explains why bacterial lineages with high PAT3 often have UGA reassigned because of low RF2. There is no indication that UAG is a minor stop codon in bacteria as claimed in a recent publication. The claim is invalid because of the failure to apply the two key criteria in identifying a minor codon: (1) it is least preferred by HEGs (or most preferred by LEGs) and (2) it corresponds to the least abundant decoder. Our results suggest a more plausible explanation for why UAA usage increases, and UGA usage decreases, with PAT3, but UAG usage remains low over the entire PAT3 range.

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

“…, +4U overrepresented in all stop codons in HEGs relative to LEGs ( Table 2 ), and all seven species belonging to Cyanobacteria and Bacilli share the B. subtilis pattern, with strong overrepresentation of +4U in UAA-ending HEGs relative UAA-ending LEGs, but no clear pattern involving UAG and UGA codons ( Table 2 ). Species with the E. coli pattern generally have far more RF2 than RF1, whereas those with the B. subtilis pattern have more RF1 than RF2 ( Wei et al 2016 ). It is likely that +4U increases termination efficiency for RF2 decoding UAA and UGA, whereas RF1 may benefit from +4U only in decoding UAA.…”

“…DIFFERENT stop codons have different termination efficiency, and replacing UGA with UAA reduces termination read-through of human genes expressed in Escherichia coli ( Meng et al 1995 ; Cesar Sanchez et al 1998 ). The discrepancies in termination efficiency among stop codons in bacteria are largely attributed to: (1) the competition between near-cognate transfer RNAs (tRNAs) (nc_tRNAs) and class I release factors (RF1 and RF2) in decoding stop codons ( Nakamura et al 1996 ; Tate et al 1999 ; Blanchet et al 2014 ), mediated by the relative abundance of RF1 and RF2 ( Korkmaz et al 2014 ; Wei et al 2016 ), and (2) nucleotide sites downstream of stop codons interacting with 18S ribosomal RNA (rRNA) and modulating the structural stability of binding sites for RF1 and RF2 ( Namy et al 2001 ) or interacting directly with release factors based on inferences from cross-linking experiments in both bacterial ( Poole et al 1998 ) and eukaryotic species ( Bulygin et al 2002 ).…”

Understanding the Genetic Code

“…These three codons are recognized by release factors (RFs): RF1 (which recognizes UAA and UAG), RF2 (which recognizes UAA and UGA), and RF3 (which functions to recycle RF1 and RF2 in Escherichia coli). These release factors may have coevolved with the stop codons (47)(48)(49). Thus, in most organismal phyla, UAA is used more frequently than UAG or UGA (44).…”

Refining the Ambush Hypothesis: Evidence That GC- and AT-Rich Bacteria Employ Different Frameshift Defence Strategies

“…2016 ). TAA and TAG are often preferred and TGA avoided in highly expressed genes ( Wei et al. 2016 ) while replacing TGA abolishes termination readthrough ( Meng et al.…”

“…While TGA is the weakest of the stops (and prone to read-through) ( Meng et al. 1995 ; Wei et al. 2016 ), TGA and TAA are unique in the specificity of release factors (RFs) decoding the stop codons: RF2 decodes both TAA and TGA ( Kisselev 2002 ).…”