Eukaryote-specific motif of ribosomal protein S15 neighbors A site codon during elongation and termination of translation

• Published in: Biochimie 2010-07, Vol.92 (7), p.820-825
• Main Authors: Khairulina, Julia, Graifer, Dmitri, Bulygin, Konstantin, Ven'yaminova, Aliya, Frolova, Ludmila, Karpova, Galina
• Format: Article
• Language: English
• Subjects: Amino Acid Motifs; Amino Acid Sequence; Animals; Archaea; Codon - genetics; Codon - metabolism; Cyanogen Bromide - metabolism; Decoding site; Eubacteria; Eukaryota; Eukaryotic ribosomal protein S15; Eukaryotic ribosome; Humans; Models, Molecular; Molecular Sequence Data; mRNA analogues; Oligopeptides - chemistry; Oligopeptides - metabolism; Peptide Fragments - chemistry; Peptide Fragments - metabolism; Photoaffinity cross-linking; Protein Biosynthesis; Protein Conformation; Ribosomal Proteins - chemistry; Ribosomal Proteins - metabolism; RNA, Messenger - genetics; RNA, Messenger - metabolism; Sequence Homology, Amino Acid; Species Specificity
• ISSN: 0300-9084; 1638-6183
• DOI: 10.1016/j.biochi.2010.02.031

The eukaryotic ribosomal protein S15 is a key component of the decoding site in contrast to its prokaryotic counterpart, S19p, which is located away from the mRNA binding track on the ribosome. Here, we determined the oligopeptide of S15 neighboring the A site mRNA codon on the human 80S ribosome with the use of mRNA analogues bearing perfluorophenyl azide-modified nucleotides in the sense or stop codon targeted to the 80S ribosomal A site. The protein was cross-linked to mRNA analogues in specific ribosomal complexes that were obtained in the presence of eRF1 in the experiments with mRNAs bearing stop codon. Digestion of modified S15 with various specific proteolytic agents followed by identification of the resulting modified oligopeptides showed that cross-link was in C-terminal fragment in positions 131–145, most probably, in decapeptide 131-PGIGATHSSR-140. The position of cross-linking site on the S15 protein did not depend on the nature of the A site-bound codon (sense or stop codon) and on the presence of polypeptide chain release factor eRF1 in the ribosomal complexes with mRNA analogues bearing a stop codon. The results indicate an involvement of the mentioned decapeptide in the formation of the ribosomal decoding site during elongation and termination of translation. Alignment of amino acid sequences of eukaryotic S15 and its prokaryotic counterpart, S19p from eubacteria and archaea, revealed that decapeptide PGIGATHSSR in positions 131–140 is strongly conserved in eukaryotes and has minor variations in archaea but has no homology with any sequence in C-terminal part of eubacterial S19p, which suggests involvement of the decapeptide in the translation process in a eukaryote-specific manner.