Translational control by lysine-encoding A-rich sequences

Abstract

Regulation of gene expression involves a wide array of cellular mechanisms that control the abundance of the RNA or protein products of that gene. Here we describe a gene-regulatory mechanism that is based on poly(A) tracks that stall the translation apparatus. We show that creating longer or shorter runs of adenosine nucleotides, without changes in the amino acid sequence, alters the protein output and the stability of mRNA. Sometimes these changes result in the production of an alternative “frame-shifted” protein product. These observations are corroborated using reporter constructs and in the context of recombinant gene sequences. Approximately two percent of genes in the human genome may be subject to this uncharacterized, yet fundamental form of gene regulation. The potential pool of regulated genes encodes many proteins involved in nucleic acid binding. We hypothesize that the genes we identify are part of a large network whose expression is fine-tuned by poly(A)-tracks, and we provide a mechanism through which synonymous mutations may influence gene expression in pathological states.

Increased ribosome density associated to positively charged residues is evident in ribosome profiling experiments performed in the absence of translation inhibitors

“…Ribosome sliding occurs on mRNAs regions that are rich in homopolymeric-A stretches and leads to mRNA degradation, frameshifts and alterations in protein output. 25,26 Since Homopolymeric-A stretches can be associated with translation of lysine residues, consequently ribosome sliding might be related to its charge. However, it is important to note that homopolymeric-A stretches do not necessarily code only for lysines.…”

PATACSDB—the database of polyA translational attenuators in coding sequences

“…In concordance with our experimental data from the controlled expression of reporter sequences or natural gene expression profiles we have designed a 12A-1 pattern, that is pattern of twelve adenines in coding region allowing for one mismatch. Based on our experiments, this is a minimal pattern that should result in reduction of expression by roughly 30%, a magnitude that can potentially have a measurable biological impact in human cells (Arthur et al, 2015). We have extrapolated this pattern to other organisms, because without further experimental work we have no way to define the minimal polyA pattern in other organisms.…”

“…In the previous studies Arthur et al, 2015) we focused mainly on polyA tracks from human and yeast genomes, using the NCBI (Pruitt et al, 2014) database and SGD (Cherry et al, 1998) as data sources, respectively. Overall there is a good agreement between our previous analysis and this study for high eukaryotes, while we see some discrepancies for lower eukaryotes such as yeast.…”

“…Over the years, we have got to know that certain sequence features can trigger ribosome stalling. These are damaged bases (Cruz-Vera et al, 2004), stable stem-loop structures (Doma & Parker, 2006), rare codons (Letzring, Dean & Grayhack, 2010), mRNAs lacking stop codons (so called non-stop mRNAs) (Dimitrova et al, 2009), runs of codons that encode consecutive basic aminoacids (Kuroha et al, 2010;Brandman et al, 2012), or finally, runs of adenines encoding poly-lysine tracks Arthur et al, 2015).…”

“…We have recently shown that polyA tracks trigger a response in a different manner than runs of basic aminoacids (Arthur et al, 2015). In addition to stalling, they occasionally lead to ribosome sliding on mRNA transcript which results in production of additional frameshifted product next to the known and well annotated gene protein product.…”