PolyA tracks, polybasic peptides, poly-translational hurdles

Abstract

The abundance of messenger RNA (mRNA) is one of the major determinants of protein synthesis. As such, factors that influence mRNA stability often contribute to gene regulation. Polyadenylation of the 3' end of mRNA transcripts, the poly(A) tail, has long been recognized as one of these regulatory elements given its influence on translation efficiency and mRNA stability. Unwanted translation of the poly(A) tail signals to the cell an aberrant polyadenylation event or the lack of stop codons, which makes this sequence an important element in translation fidelity and mRNA surveillance response. Consequently, investigations into the effects of the poly(A) tail lead to the discoveries that poly-lysine as well as other polybasic peptide sequences and, to a much greater extent, polyA mRNA sequences within the open reading frame influence mRNA stability and translational efficiency. Conservation and evolutionary selection of codon usage in polyA track sequences across multiple organisms suggests a biological significance for coding polyA tracks in the regulation of gene expression. Here, we discuss the cellular responses and consequences of coding polyA track translation and synthesis of polybasic peptides. This article is categorized under: Translation > Translation Mechanisms Translation > Translation Regulation RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms.

Keywords: RNA biology; mRNA turnover; translation; translational control.

Figure 1. Normal and aberrant translation

(a) Scheme of translation of normal mRNA with 5’ cap (m⁷GpppG), 3’ poly(A) tail, 3’ and 5’ untranslated regions (UTR), and open reading frame (ORF) indicated. Translation proceeds in three phases; initiation, elongation, and termination. (b) In the absence of an in-frame stop codon, the ribosome continues elongation into the poly(A) tail. This activates nonstop decay and the recruitment of the GTPase Ski7 in Saccharomyces cerevisiae. In other eukaryotes, Dom34 and Hbs1 are recruited. (c) Peptide or mRNA induced stalls (indicated by gray box on mRNA scheme) during the elongation cycle activate the no-go mRNA decay pathway. The rescue factors Dom34 and Hbs1 are recruited to recycle the ribosome in this pathway as well. Both nonstop decay and no-go decay result in endonucleolytic cleavage and degradation of the mRNA and ubiquitylation and degradation of the nascent peptide. (d) Table of factors involved in ribosome stall induction, ribosome release, and nascent protein degradation discussed in text (if different than human gene nomenclature, yeast homologs are indicated).

Figure 2. Coding polyA tracks induce translational frameshifting and ribosome stalling

Translation of polyA tracks in coding sequences of mRNAs can result in two possible outcomes – frameshifting and ribosome stalling. Frameshifting on polyA tracks (depicted by change in the ORF and protein color) does not require mRNA structure elements seen in programmed frameshifting in viruses. Ribosome stalling (indicated by gray box on mRNA scheme) results in activation of NGD mechanisms with reduction in protein levels (illustrated by released ribosomes) but synthesis of the full length protein in correct frame.

Figure 3. Potential outcomes of programmed ribosome frameshifting on coding polyA tracks

(a) Ribosomes that frameshift on a polyA track or other recoding element will continue elongation until reaching a stop codon in the new frame (protein sequence from non-zero frame indicated by red line). Encountering a premature termination codon will initiate the mRNA surveillance pathway, nonsense mediated decay to degrade both the mRNA and nascent peptide. If the premature termination codon occurs before the last exon junction complex (EJC), degradation by NMD is stimulated. Ubiquitination of the frameshifted nascent protein is indicated (*). (b) If the frameshift happens in the last exon, the transcript may evade NMD and instead synthesize a nascent peptide with an alternative C-terminus coded by the non-zero frame (indicated by UAA*) after the polyA track and either truncated (top) or extended (bottom) depending on the position of the out of frame termination codon.

Figure 4. Model of effects of synonymous mutations within coding polyA tracks

(a) Scheme of translation of mRNA with polyA track indicated by the grey segment in the open reading frame. The translation efficiency of mRNAs with a polyA track are sensitive to synonymous mutations. (b) Mutations that increase the number of adenosine residues, Lys AAG to AAA, will increase stalling and frameshifting on the polyA track, leading to reduced WT protein expression from the mRNA and greater frequency of production of alternative C-terminus proteins. (c) The opposite mutation, Lys AAA to AAG, will increase WT protein expression and decrease frequency of alternative C-terminus protein production by decreasing the frequency of stalling and frameshifting on the polyA tracks.