Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach.

Area of Science:

• Biochemistry
• Genomics
• Molecular Biology

Background:

• Selenocysteine and pyrrolysine are the 21st and 22nd amino acids, encoded by stop codons.
• Previous tRNA gene prediction studies suggested no unknown amino acid, but were inconclusive due to potential atypical tRNA structures.
• A protein-level investigation is needed for independent insight into novel amino acids.

Purpose of the Study:

• To systematically search for a potential 23rd genetically encoded amino acid in prokaryotic genomes.
• To independently validate findings from tRNA gene prediction studies.
• To identify novel selenoproteins and other readthrough proteins.

Main Methods:

• Computational prediction of proteins containing stop-codon-encoded amino acids from 191 prokaryotic genomes.
• Analysis based on conservation patterns of primary amino acid sequences.
• Verification of known selenoproteins and pyrrolysine proteins.

Main Results:

• No candidate for a 23rd amino acid encoded by stop codons was detected.
• The prediction method successfully identified known selenoproteins and pyrrolysine proteins.
• One novel selenoprotein was identified.

Conclusions:

• The findings suggest that a widespread 23rd amino acid encoded by stop codons does not exist.
• The phylogenetic distribution of any potential novel amino acid is likely very limited.
• The developed method can be applied to explore new readthrough events in expanding genomic databases.