Abstract
Translating ribosomes can skip over stretches of messenger RNA and resume protein chain elongation after a "bypassed" region. We have previously shown that limitation for isoleucyl-tRNA can initiate a ribosome bypass when an AUA codon is in the ribosomal A-site. We have now generalized this effect to other "hungry" codons calling for four different limiting aminoacyl-tRNA species, suggesting that a pause at any A-site will have this effect. We have assessed bypassing in a large family of reporters with nearly every different triplet in the "takeoff site", i.e. the P-site on the 5′ side of the hungry codon, and an identical "landing site" codon 16 nucleotides downstream. The different takeoff sites vary over a factor of 50 in bypassing proficiency. At least part of this variation appears to reflect stability of the codon::anticodon interaction at the takeoff site, as indicated by the following: (a) the bypassing proficiency of different tRNAs shows a rough correlation with the frequency of A::U as opposed to G::C pairs in the codon::anticodon association; (b) specific tRNAs bypass more frequently from codons ending in U than from their synonym ending in C; (c) an arginine tRNA with Inosine in the wobble position which reads CGU, CGC, and CGA bypasses much more frequently from the last codon than the first two synonyms.
Original language | English (US) |
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Pages (from-to) | 713-724 |
Number of pages | 12 |
Journal | Journal of Molecular Biology |
Volume | 342 |
Issue number | 3 |
DOIs | |
State | Published - Sep 17 2004 |
Externally published | Yes |
Keywords
- A-site
- bypassing
- hungry codon
- P-site
- ribosome
ASJC Scopus subject areas
- Structural Biology
- Molecular Biology