title: Comparative study of translation termination sites and release factors (RF1 and RF2) in procaryotes.
abstract: Translation termination is catalyzed by release factors that recognize stop codons. However, previous works have shown that in some bacteria, the termination process also involves bases around stop codons. Recently, Ito et al. analyzed release factors and identified the amino acids therein that recognize stop codons. However, the amino acids that recognize bases around stop codons remain unclear. To identify the candidate amino acids that recognize the bases around stop codons, we aligned the protein sequences of the release factors of various bacteria and searched for amino acids that were conserved specifically in the sequence of bacteria that seemed to regulate translation termination by bases around stop codons. As a result, species having several highly conserved residues in RF1 and RF2 showed positive correlations between their codon usage bias and conservation of the bases around the stop codons. In addition, some of the residues were located very close to the SPF motif, which deciphers stop codons. These results suggest that these conserved amino acids enable the release factors to recognize the bases around the stop codons.
authors.affiliation: Institute for Advanced Bioscience, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-8520, Japan.
authors.forename: Y
authors.initials: Y
authors.lastname: Ozawa
authors.forename: R
authors.initials: R
authors.lastname: Saito
authors.forename: T
authors.initials: T
authors.lastname: Washio
authors.forename: M
authors.initials: M
authors.lastname: Tomita
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D018388:Codon, Terminator; D017124:Conserved Sequence; D008969:Molecular Sequence Data; D010443:Peptide Chain Termination, Translational; D010454:Peptide Termination Factors / Q000235:genetics*; D011387:Prokaryotic Cells / Q000502:physiology*; D014176:Protein Biosynthesis; D013045:Species Specificity
chemical_list: D000596:Amino Acids; D018388:Codon, Terminator; D010454:Peptide Termination Factors; C041460:peptide chain termination release factor 2