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)