Pyrrolysine

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Pyrrolysine

Pyrrolysine is a naturally occurring, genetically coded amino acid

Amino acid

In chemistry, an amino acid is a molecule containing both amine and carboxyl functional groups. These molecules are particularly important in biochemistry, where this term refers to alpha-amino acids with the general formula H2NCHRCOOH, where R is an organic substituent....
used by some methanogenic archaea

Archaea

The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon . Archaea, like bacteria, are prokaryotic....
in enzymes that are part of their methane

Methane

Methane is a chemical compound with the molecular formula . It is the simplest alkane, and the principal component of natural gas. Methane's bond angles are 109.5 degrees....
-producing metabolism.

This lysine

Lysine

Lysine is an a-amino acid with the chemical formula HO2CCH4NH2. This amino acid is an essential amino acid, which means that humans cannot synthesize it....
derivative is encoded by the UAG codon (normally the 'amber' stop codon

Stop codon

In the genetic code, a stop codon is a nucleotide triplet within messenger RNA that signals a termination of translation. Proteins are unique sequences of amino acids, and most codons in messenger RNA correspond to the addition of an amino acid to a growing protein chain — stop codons signal the termination of this process, releasing t...
), possibly modified by the presence of a specific downstream sequence, named PYLIS, which forms a stem-loop

Stem-loop

Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same molecule, usually palindrome in nucleotide sequence, base-pair to form a double helix that ends in an unpaired loop....
in the mRNA, forcing the incorporation of pyrrolysine instead of terminating translation

Translation

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Encyclopedia

Pyrrolysine is a naturally occurring, genetically coded amino acid

Amino acid

Archaea

Methane

Lysine

Stop codon

Stem-loop

Translation

Translation is the hermeneutics of the Meaning of a text and the subsequent production of an Dynamic and formal equivalence text, likewise called a "translation," that communicates the same message in another language....
. It is also of interest to note that UAG appears to be used much less often than other stop codons and whenever it is found in an open reading frame

Open reading frame

An open reading frame is a portion of an organism's genome which contains a sequence of base pair that could potentially translation a protein....
it is always followed by one or more of the other two stop codons shortly after.

Near a methyltransferase gene cluster of Methanosarcina
Methanosarcina

Methanosarcina are the only known Anaerobic organism methanogens to produce methane using all three known metabolic pathways for methanogenesis....
barkeri is the pylT gene, which encodes an unusual transfer RNA

Transfer RNA

Transfer RNA is a small RNA that transfers a specific active amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation ....
(tRNA) with a CUA anticodon. The adjacent pylS gene encodes a class II aminoacyl-tRNA synthetase that charges the pylT-derived tRNA with pyrrolysine. The operon containing pylT and pylS are also found in the genomes of other sequenced members of the Methanosarcinaceae family. Homologs

Homology (biology)

In evolutionary biology, homology refers to any similarity between characteristics that is due to their common descent. The word homologous derives from the ancient Greek ??????e??, 'to agree'....
of pylS and pylT are found in a Gram-positive

Gram-positive

Gram-positive Bacteria are those that are stained dark blue or violet by Gram staining. This is in contrast to Gram-negative bacteria, which cannot retain the crystal violet stain, instead taking up the counterstain and appearing red or pink....
bacterium, Desulfitobacterium hafniense, although the function of these putative genes in this organism is unknown. It was initially shown that pylT encoded tRNA (CUA) can be charged with lysine by PylS. Recently, it has been shown that the tRNA(CUA) can be charged with lysine in vitro by the concerted action of the M. barkeri Class I and Class II Lysyl-tRNA synthetases. Charging a tRNA(CUA) with lysine was originally hypothesized to be the first step in translating UAG amber codons as pyrrolysine in certain methanogen

Methanogen

Methanogens are archaea that produce methane as a metabolic byproduct in anoxic conditions. They are common in wetlands, where they are responsible for marsh gas, and in the guts of animals such as ruminants and humans, where they are responsible for the methane content of flatulence....
s. The current model based on in vitro and in vivo data favors direct charging of pyrrolysine on to the tRNA(CUA) by the protein product of the pylS gene. This makes pyrrolysine the 22nd genetically encoded natural amino acid. The mechanism of encoding makes it the 21st natural directly encoded amino acid.

The joint nomenclature committee of the IUPAC/IUBMB has officially recommended the three-letter symbol Pyl and the one-letter symbol O for pyrrolysine.

Pyrrolysine

See also

External links