Decoding and Recoding of mRNA Sequences by the Ribosome

Abstract

Faithful translation of messenger RNA (mRNA) into protein is essential to maintain protein homeostasis in the cell. Spontaneous translation errors are very rare due to stringent selection of cognate aminoacyl transfer RNAs (tRNAs) and the tight control of the mRNA reading frame by the ribosome. Recoding events, such as stop codon readthrough, frameshifting, and translational bypassing, reprogram the ribosome to make intentional mistakes and produce alternative proteins from the same mRNA. The hallmark of recoding is the change of ribosome dynamics. The signals for recoding are built into the mRNA, but their reading depends on the genetic makeup of the cell, resulting in cell-specific changes in expression programs. In this review, I discuss the mechanisms of canonical decoding and tRNA–mRNA translocation; describe alternative pathways leading to recoding; and identify the links among mRNA signals, ribosome dynamics, and recoding.

A structural and functional analysis of opal stop codon translational readthrough during Chikungunya virus replication

“…It seems unlikely that such a low frequency of TR would be compatible with the rapid and efficient characteristics of alphavirus replication, as this would result in only 1 polymerase molecule for every 100 000 translation events. Having said that, the fact that alphaviruses contain opal stop codons in preference to the other two stop codons, and the predominance of a C directly 3′ to the stop codon, correlates with the fact that an opal codon followed by a C is the most efficient context for TR [30]. Our data show that the presence of an opal stop codon has no detrimental effect on genome replication in any cells tested – human, murine or mosquito.…”

“…Misreading of a stop codon (TR) is estimated to occur spontaneously approximately 10 −5 times per codon [30]. It seems unlikely that such a low frequency of TR would be compatible with the rapid and efficient characteristics of alphavirus replication, as this would result in only 1 polymerase molecule for every 100 000 translation events.…”

Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers

“… Cognate tRNAs allow for local rearrangements of rRNA bases, inducing 30S domain closure, subsequent hydrolysis of GTP, and tRNA accommodation into the A site . Most near- and noncognate pAA-tRNAs are unable to form WC interactions in the rigid decoding center and 30S domain closure does not occur, encouraging dissociation from the ribosome. ,− While a subset of near-cognate pAA-tRNAs can form nonstandard base pairs that may sample WC-like conformations, GTPase activation and accommodation is generally slower, promoting dissociation before peptidyl transfer. ,,− Overall, these initial proofreading steps closely monitor the WC geometry of N36•N′1 and N35•N′2 via the minor groove. To facilitate these conserved WC interactions, N36 and N35 are almost never modified in any organism. , …”

Interferon-Stimulated Genes that Target Retrovirus Translation

“…Normally, this occurs very infrequently. The spontaneous readthrough frequency for human RNA sequences is usually rather low, in the range of 0.001% per stop codon, but can be enhanced by several factors, including the codon context [ 131 ].…”