Improvement of reading frame maintenance is a common function for several tRNA modifications

Abstract

Transfer RNAs from all organisms contain many modi®ed nucleosides. Their vastly different chemical structures, their presence in different tRNAs, their occurrence in different locations in tRNA and their in¯uence on different reactions in which tRNA participates suggest that each modi®ed nucleoside may have its own speci®c function. However, since the frequency of frameshifting in several different mutants [mnmA, mnmE, tgt, truA (hisT), trmD, miaA, miaB and miaE] defective in tRNA modi®cation was higher compared with the corresponding wild-type controls, these modi®cations have a common function: they all improve reading frame maintenance. Frameshifting occurs by peptidyl-tRNA slippage, which is in¯uenced by the hypomodi®ed tRNA in two ways: (i) a hypomodi®ed tRNA in the ternary complex may decrease the rate by which the complex is recruited to the A-site and thereby increasing peptidyl-tRNA slippage; or (ii) a hypomodi®ed peptidyl-tRNA may be more prone to slip than its fully modi®ed counterpart. We propose that the improvement of reading frame maintenance has been and is the major selective factor for the emergence of new modi®ed nucleosides. Keywords: frameshift/modi®ed nucleoside/tRNA/ translation IntroductionThe capacity of the translation apparatus has evolved to read long messages and thereby to make sophisticated proteins required for life as we see it today. Although the translation apparatus has the ability to decode faithfully, errors occur with frequencies of 10 ±3 ±10 ±4 per codon (Kurland et al., 1996). Most missense errors are not harmful to proteins, since many amino acids can be substituted without affecting the stability or the activity of the protein. In sharp contrast to the missense errors, almost all of the frameshift errors are detrimental to the synthesis of a functional protein, since following such a shift in frame the amino acid sequence becomes completely different and eventually the ribosome usually encounters a stop codon. This results in a truncated, usually unstable or inactive, peptide. Clearly, during evolution, features of the translation apparatus that are pivotal for reading frame maintenance have evolved. To understand the mechanism by which the ribosome traverses the mRNA in a faithful manner, one has to unravel the features of the translation apparatus that are important for maintaining the correct reading frame.There are several examples of how frameshift errors occur by peptidyl-tRNA slippage induced by a pause occurring in the A-site (reviewed in Farabaugh, 1997;Farabaugh and Bjo Èrk, 1999; see also Figure 1). The length of the pause in the A-site, the ®tness of the tRNA in the P-site and the mRNA sequence determine the frequency of slippage by the peptidyl-tRNA and thus the frequency of frameshift. Changes in the tRNA structure, such as that induced by a de®ciency of a modi®ed nucleoside, may therefore affect reading frame maintenance. Modi®ed nucleosides are derivatives of the four major nucleosides U, C, A and G, and at present 81 different modi®ed nucleosides have ...

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