Molecular contacts of ribose-phosphate backbone of mRNA with human ribosome

• Published in: Biochimica et biophysica acta 2015-08, Vol.1849 (8), p.930-939
• Main Authors: Sharifulin, Dmitri E., Grosheva, Anastasia S., Bartuli, Yulia S., Malygin, Alexey A., Meschaninova, Maria I., Ven'yaminova, Aliya G., Stahl, Joachim, Graifer, Dmitri M., Karpova, Galina G.
• Format: Article
• Language: English
• Subjects: Anticodon - chemistry; Base Sequence; Binding Sites - drug effects; Codon - chemistry; Codon - metabolism; Cross-Linking Reagents - chemistry; Hepacivirus - genetics; Human ribosome; Humans; KH domain; Mammalian ribosomal protein uS19; Mammalian ribosomal protein uS3; Models, Molecular; Molecular Sequence Data; mRNA binding site; Nucleic Acid Conformation; Ribosemonophosphates - chemistry; Ribosemonophosphates - metabolism; Ribosomal Proteins - chemistry; Ribosomal Proteins - metabolism; Ribosomes - chemistry; Ribosomes - metabolism; RNA, Messenger - chemistry; RNA, Messenger - metabolism; RNA, Transfer - chemistry; RNA, Transfer - metabolism; RNA, Viral - chemistry; RNA, Viral - metabolism; Site-directed cross-linking; Transcription Initiation Site
• ISSN: 1874-9399; 0006-3002; 1876-4320
• DOI: 10.1016/j.bbagrm.2015.06.001

In this work, intimate contacts of riboses of mRNA stretch from nucleotides in positions +3 to +12 with respect to the first nucleotide of the P site codon were studied using cross-linking of short mRNA analogs with oxidized 3′-terminal riboses bound to human ribosomes in the complexes stabilized by codon–anticodon interactions and in the binary complexes. It was shown that in all types of complexes cross-links of the mRNA analogs to ribosomal protein (rp) uS3 occur and the yield of these cross-links does not depend on the presence of tRNA and on sequences of the mRNA analogs. Site of the mRNA analogs cross-linking in rp uS3 was mapped to the peptide in positions 55–64 that is located away from the mRNA binding site. Additionally, in complexes with P site-bound tRNA, riboses of mRNA nucleotides in positions +4 to +7 cross-linked to the C-terminal tail of rp uS19 displaying a contact specific to the decoding site of the mammalian ribosome, and tRNA bound at the A site completely blocked this cross-linking. Remarkably, rps uS3 and uS19 were also able to cross-link to the fragment of HCV IRES containing unstructured 3′-terminal part restricted by the AUGC tetraplet with oxidized 3′-terminal ribose. However, no cross-linking to rp uS3 was observed in the 48S preinitiation complex assembled in reticulocyte lysate with this HCV IRES derivative. The results obtained show an ability of rp uS3 to interact with single-stranded RNAs. Possible roles of rp uS3 region 55–64 in the functioning of ribosomes are discussed. •Short unstructured RNAs can interact with rp uS3 in 40S and 80S ribosomal complexes.•RNAs interact with rp uS3 via a KH domain peptide away from the mRNA binding site.•Rp uS3 becomes inaccessible in the 48S complex assembled in a reticulocyte lysate.•KH domain peptide is likely connected with 18S rRNA h16 during translation initiation.•Riboses of mRNA codon at the ribosomal decoding site contact the C-tail of rp uS19.