Recoding suppression of stop codons using the unusual amino acids
Pyrrolysine and Selenocysteine
of recoding which appears to occur in Methanosarcina, is the "suppression" of the stop codon, UAG,
by insertion of Pyrrolysine. This was first noted in the Methylamine
methyltransferases which are important in the production of methane by archaeal
methanogens. (Paul, et al., 2000) identified an in-frame amber codon (TAG) in
the trimethylamine methyltransferase genes of both M. barkeri and M. thermophila.
However, at least in the case of M. barkeri,
abundant quantities of the full-length protein could be obtained and it
appeared that the TAG codon was read as Lys. This later proved to be the unusual amino acid
pyrrolysine. Several IS copies in these archaeal methanogens carry TAG codons
which are presumably "suppressed" by decoding as pyrrolysine.
In this framework, other stop
codons are known to be suppressed by decoding as selenocysteine (Zhang, et al.,
2005); (Prat, et al., 2012); (Schimmel
& Beebe, 2004); (Srinivasan, et al., 2002). To our knowledge a single IS from the IS3
family, ISDvu3 from Desulfovibrio vulgaris, includes a
selenocysteine inserted at a stop codon in its orfB frame (M.Land personal
communication). Undoubtedly additional examples will be identified in the
of these amino acids involves the presence of specific types of secondary
structures in the mRNA (Fig 1.33.3).
- Paul L, Ferguson DJ, Jr. & Krzycki JA (2000) The
trimethylamine methyltransferase gene and multiple dimethylamine
methyltransferase genes of Methanosarcina barkeri contain in-frame and
read-through amber codons. J Bacteriol 182: 2520-2529.
- Prat L, Heinemann IU, Aerni HR, Rinehart J, O'Donoghue
P & Soll D (2012) Carbon source-dependent expansion of the genetic code in
bacteria. Proc Natl Acad Sci U S A 109: 21070-21075.
- Schimmel P & Beebe K (2004) Molecular biology:
genetic code seizes pyrrolysine. Nature 431: 257-258.
- Srinivasan G, James CM & Krzycki JA (2002)
Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized
tRNA. Science 296: 1459-1462.
Y, Baranov PV, Atkins JF & Gladyshev VN (2005) Pyrrolysine and
selenocysteine use dissimilar decoding strategies. J Biol Chem 280: