For decades, biology textbooks taught that all life builds its proteins from a standard set of 20 amino acids. The discovery of pyrrolysine, however, added a 22nd genetically encoded amino acid, revealing that the code of life had rare and specialized exceptions. Pyrrolysine is a rare amino acid found in some microbes. It possesses a unique structure and is incorporated into proteins through a specialized mechanism, allowing it to perform a specific function that the common amino acids cannot.
The Chemical Architecture of Pyrrolysine
All standard amino acids share a common backbone: a central carbon atom bonded to an amino group, a carboxyl group, and a hydrogen atom. What distinguishes one amino acid from another is its variable side chain, or R-group. Pyrrolysine follows this fundamental plan but possesses a large and complex R-group that sets it apart.
The side chain of pyrrolysine is a derivative of the common amino acid, lysine. Lysine has a side chain consisting of a four-carbon chain ending with an amino group. In pyrrolysine, this terminal amino group is connected to a specialized ring structure, which fundamentally alters the side chain’s properties.
This appended structure is a (4-methyl)pyrroline-5-carboxylate ring. This five-membered ring contains one nitrogen atom and four carbon atoms, with a methyl group attached. The linkage between this ring and the lysine portion occurs via an amide bond, forming a stable architecture.
While lysine’s side chain is a flexible chain, pyrrolysine’s is dominated by the rigid pyrroline ring. This structure gives the side chain a positive charge at neutral pH, similar to lysine, but its bulky nature provides distinct chemical functionalities.
Genetic Encoding and Protein Incorporation
Incorporating pyrrolysine into a protein requires expanding the genetic code. In most organisms, the mRNA sequence UAG is a stop codon that terminates protein synthesis. However, in organisms that use pyrrolysine, the UAG codon is repurposed to signal for its insertion.
This reassignment requires two specialized components. The first is a unique transfer RNA, tRNA^Pyl, which recognizes the UAG codon. The second is the enzyme pyrrolysyl-tRNA synthetase (PylRS), which specifically recognizes both pyrrolysine and tRNA^Pyl.
The PylRS enzyme attaches a molecule of pyrrolysine to its corresponding tRNA^Pyl. This charged tRNA is then ready for protein synthesis. This PylRS/tRNA^Pyl pair works as an independent system, ensuring pyrrolysine is inserted only at the designated UAG codon.
When the ribosome encounters a UAG codon during translation, the charged tRNA^Pyl binds to it. The ribosome then accepts the pyrrolysine and adds it to the growing polypeptide chain. This mechanism allows for the precise incorporation of this 22nd amino acid.
Biological Role in Methane Metabolism
Pyrrolysine’s primary purpose is to facilitate methane production, or methanogenesis. It is found in the active sites of methyltransferase enzymes, which are responsible for transferring methyl groups from substrates like methylamine.
Within the enzyme’s active site, the pyrrolysine residue performs a task other amino acids cannot handle as efficiently. Its pyrroline ring structure is directly involved in binding and transferring the methyl group. The ring acts as a scaffold, positioning the substrate correctly for the chemical reaction.
Standard amino acids lack the structure to perform this methyl transfer efficiently. Pyrrolysine is a highly tailored molecular solution that gives the microbes using it a metabolic advantage in their environmental niches.
Discovery and Natural Occurrence
Pyrrolysine was first identified in 2002 by researchers studying the archaeon Methanosarcina barkeri. This organism is a methanogen, a type of microbe that thrives in anaerobic environments like marine sediments and the digestive tracts of animals. Scientists investigating an enzyme involved in methane production encountered an amino acid that was not one of the standard 20.
Further analysis revealed its unique structure and the genetic system for its incorporation. The discovery challenged the long-standing assumption that the genetic code was limited to 20 amino acids, demonstrating it could be more flexible.
The natural occurrence of pyrrolysine is extremely limited. It has been found only in a small number of methanogenic archaea and in at least one species of bacterium. This rarity explains why it remained undiscovered for so long.