Coevolution between Stop Codon Usage and Release Factors in Bacterial Species

Molecular Biology and Evolution, Aug 2016

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.

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Coevolution between Stop Codon Usage and Release Factors in Bacterial Species

Advance Access publication June Coevolution between Stop Codon Usage and Release Factors in Bacterial Species Yulong Wei 1 Juan Wang 1 Xuhua Xia 0 1 0 Ottawa Institute of Systems Biology , Ottawa, ON , Canada 1 Department of Biology, University of Ottawa , Ottawa, ON , Canada 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 overrepresented 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 [¼RF2/(RF1 þ 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. translation termination; release factors; stop codon; RF1; RF2; prfA; prfB; gene expression Introduction Most bacterial lineages share genetic code 11 with three stop codons, UAA, UAG, and UGA, which are decoded by two release factors (RF1 and RF2), with RF1 decoding UAA and UAG and RF2 decoding UAA and UGA (Scolnick et al. 1968; Milman et al. 1969; Scolnick and Caskey 1969) . In Escherichia coli, RF2 is consistently more abundant then RF1, which is associated with UGA used much more frequently than UAG. This association between the frequency of stop codon and its decoder concentration is consistent with codon–anticodon adaptation documented in bacteria (Ikemura 1981, 1992; Gouy and Gautier 1982; Xia 1998; Stoletzki and Eyre-Walker 2007; Higgs and Ran 2008; Palidwor et al. 2010; Ran and Higgs 2012) , eukaryotes (Chavancy et al. 1979) such as yeast (Sharp and Li 1986; Sharp et al. 1986; Xia 1998; Akashi 2003) and fruit flies (Moriyama and Hartl 1993; Akashi 1994, 1997; Moriyama and Powell 1997) , viruses (Sharp et al. 1984; van Weringh et al. 2011; Chithambaram et al. 2014a, 2014b; Prabhakaran et al. 2014, 2015) , and mitochondria (Xia 2005, 2008; Xia et al. 2007; Carullo and Xia 2008; Jia and Higgs 2008) . Because different stop codons may manifest as different signals to the cellular translation termination machinery, both experimental and bioinformatic approaches have been taken to characterize translation termination efficiency in association with their decoders. The experimental studies on translation termination have focused mainly on E. coli (and occasionally in the yeast, Saccharomyces cerevisiae) and addressed two questions: (1) which tRNA species tend to misread a stop codon as a near-cognate sense codon and (2) which release factor tends to misread near-cognate sense codons as stop codons. All three stop codons can be misread by tRNAs, and UGA appears to be the leakiest of the three, with a readthrough frequency of at least 10 2–10 3 in Salmonella typhimurium (Roth 1970) and E. coli (Sambrook et al. 1967; Strigini and Brickman 1973) . UAA and UAG can also be leaky in bacteria (Davies et al. 1966; Ryden and Isaksson 1984) , although their misreading has not been reported as frequently as UGA. Natural UAG readthrough frequency is mostly within the range of 1.1 10 4–7 10 3, depending on the nature of the downstream nucleotides (Bossi and Ruth 1980; Bossi 1983; Miller and Albertini 1983; Ryden and Isaksson 1984) . The readthrough of UAA seems to occur at frequencies from 9 10 4 to < 1 10 5 (Ryden and Isaksson 1984). Overall, the available experimental data suggest that in bacteria species, particularly in E. coli, readthrough is most frequent for UGA, less for UAG, and least for UAA (Strigini and Brickman 1973; Geller and Rich 1980; Parker 1989; Jorgensen et al. 1993; Meng et al. 1995; Cesar Sanchez et al. 1998; Tate et al. 1999) . 0 1 6 Translation termination error rate depends not only on readthrough by tRNA, but also on the efficiency and relative concentration of RF1 and RF2 (Korkmaz et al. 2014) . Increasing RF2 concentration decreased both UGA readthrough and frameshift (...truncated)


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Yulong Wei, Juan Wang, Xuhua Xia. Coevolution between Stop Codon Usage and Release Factors in Bacterial Species, Molecular Biology and Evolution, 2016, pp. 2357-2367, 33/9, DOI: 10.1093/molbev/msw107