P-site Pairing Subtleties Revealed by the Effects of Different tRNAs on Programmed Translational Bypassing where Anticodon Re-pairing to mRNA is Separated from Dissociation

• Published in: Journal of molecular biology Vol. 345; no. 1; pp. 39 - 49
• Main Authors: Bucklin, Douglas J., Wills, Norma M., Gesteland, Raymond F., Atkins, John F.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 07-01-2005
• Subjects: Anticodon - genetics; Anticodon - metabolism; Arginine - genetics; Base Sequence; Codon - genetics; Codon - metabolism; codon:anticodon interaction; Cytosine - metabolism; DNA, Bacterial - genetics; DNA, Bacterial - metabolism; frameshifting; Guanine - metabolism; Inosine - genetics; Nucleic Acid Conformation; Nucleoside Q - genetics; Nucleoside Q - metabolism; P-site; Phage T4; Protein Biosynthesis; ribosome; Ribosomes - metabolism; RNA, Messenger - genetics; RNA, Messenger - metabolism; RNA, Transfer - genetics; RNA, Transfer - metabolism; Serine - genetics; translational bypassing; Valine - genetics; frameshifting; ribosome; cmo 5U; translational bypassing; codon:anticodon interaction; P-site
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2004.10.037

Programmed ribosomal bypassing occurs in decoding phage T4 gene
60 mRNA. Half the ribosomes bypass a 50 nucleotide gap between codons 46 and 47. Peptidyl-tRNA dissociates from the “take-off” GGA, codon 46, and re-pairs to mRNA at a matched GGA “landing site” codon directly 5′ of codon 47 where translation resumes. The system described here allows the contribution of peptidyl-tRNA re-pairing to be measured independently of dissociation. The matched GGA codons have been replaced by 62 other matched codons, giving a wide range of bypassing efficiencies. Codons with G or C in either or both of the first two codon positions yielded high levels of bypassing. The results are compared with those from a complementary study of non-programmed bypassing, where the combined effects of peptidyl-tRNA dissociation and reassociation were measured. The wild-type, GGA, matched codons are the most efficient in their gene
60 context in contrast to the relatively low value in the non-programmed bypassing study.