Effects of the nucleotide 3′ to an amber codon on ribosomal selection rates of suppressor tRNA and release factor-1

Abstract

Rates of ribosomal selection of both release factor 1 (RF1) and a suppressor tRNA (Su7C33) were studied at an amber codon at which the 3′ neighbor was permuted. Rates of RF1 selection vary 2.6-fold among contexts. The 3′ neighbor-dependent variation of RF1 action correlates very strongly with the non-random frequencies of 3′ neighbors at UAG terminators ( r = 0·97), which argues that the rate of RF1 selection is an important determinant 3′ neighbor choice at termination codons. The data are consistent with a model for RF1 selection in which RF1 makes a specific contact(s) to the 3′ neighbor and that this interaction is most favorable to uridylic acid. Measured rates of Su7C33 selection vary fivefold among 3′ contexts. We also develop a method to calculate rates of selection for other suppressors, based on the assumption that rates of RF1 selection at each 3′ context can be generalized to other sites that have the same 3′ neighbor. Rates for various suppressors appear to vary from two- to fivefold depending on the 3′ neighbor. Generally, the rate of selection of suppressors at different contexts correlates with the stacking strength of the 3′ neighbor as measured in vitro. The two- to fivefold range of 3′ neighbor effects on rate of aminoacyl-tRNA selection is greater than that previously observed within sets of codons read by the same tRNA. It is suggested that the choice of codons to achieve favorable contexts may be more important than the choice of a common codon at some message sites.