title: Identifying the ligated amino acid of archaeal tRNAs based on positions outside the anticodon.
abstract: Proper recognition of tRNAs by their aminoacyl-tRNA synthetase is essential for translation accuracy. Following evidence that the enzymes can recognize the correct tRNA even when anticodon information is masked, we search for additional nucleotide positions within the tRNA molecule that potentially contain information for amino acid identification. Analyzing 3936 sequences of tRNA genes from 86 archaeal species, we show that the tRNAs' cognate amino acids can be identified by the information embedded in the tRNAs' nucleotide positions without relying on the anticodon information. We present a small set of six to 10 informative positions along the tRNA, which allow for amino acid identification accuracy of 90.6% to 97.4%, respectively. We inspected tRNAs for each of the 20 amino acid types for such informative positions and found that tRNA genes for some amino acids are distinguishable from others by as few as one or two positions. The informative nucleotide positions are in agreement with nucleotide positions that were experimentally shown to affect the loaded amino acid identity. Interestingly, the knowledge gained from the tRNA genes of one archaeal phylum does not extrapolate well to another phylum. Furthermore, each species has a unique ensemble of nucleotides in the informative tRNA positions, and the similarity between the sets of positions of two distinct species reflects their evolutionary distance. Hence, we term this set of informative positions a "tRNA cipher." It is tempting to suggest that the diverging code identified here might also serve the aminoacyl tRNA synthetase in the task of tRNA recognition.
authors: Department of Statistics and Operations Research, The Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Ramat-Aviv 69978, Israel.
authors: Tal
authors: T
authors: Galili
authors: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
authors: Hila
authors: H
authors: Gingold
authors: Department of Statistics and Operations Research, The Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Ramat-Aviv 69978, Israel.
authors: Shaul
authors: S
authors: Shaul
authors: Department of Statistics and Operations Research, The Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Ramat-Aviv 69978, Israel The Edmond J. Safra Center for Bioinformatics and The Sagol School for Neuroscience, Tel Aviv University, Ramat-Aviv 69978, Israel.
authors: Yoav
authors: Y
authors: Benjamini
mesh_terms: D000596:Amino Acids / Q000235:genetics; D000926:Anticodon / Q000235:genetics*; D001105:Archaea / Q000235:genetics*; D019143:Evolution, Molecular; D005815:Genetic Code; D019642:RNA, Archaeal / Q000235:genetics*; D012343:RNA, Transfer / Q000235:genetics*
chemical_list: D000596:Amino Acids; D000926:Anticodon; D019642:RNA, Archaeal; D012343:RNA, Transfer
keywords: RNA code; discriminate positions; evolution; second genetic code