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

Background: Selenocysteine and pyrrolysine are the 21st and 22nd amino acids, which are genetically encoded by stop codons. Since a number of microbial genomes have been completely sequenced to date, it is tempting to ask whether the 23rd amino acid is left undiscovered in these genomes. Recently, a computational study addressed this question and reported that no tRNA gene for unknown amino acid was found in genome sequences available. However, performance of the tRNA prediction program on an unknown tRNA family, which may have atypical sequence and structure, is unclear, thereby rendering their result inconclusive. A protein-level study will provide independent insight into the novel amino acid. Results: Assuming that the 23rd amino acid is also encoded by a stop codon, we systematically predicted proteins that contain stop-codon-encoded amino acids from 191 prokaryotic genomes. Since our prediction method relies only on the conservation patterns of primary sequences, it also provide...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Masashi Fujita, Hisaaki Mihara, Susumu Goto, Nobuyoshi Esaki, Minoru Kanehisa
• Keywords: 23rd Amino Acid, Amino Acids, BMCBI 2007, Stop Codon