Inverted translational control of eukaryotic gene expression by ribosome collisions

Abstract

The canonical model of eukaryotic translation posits that ef cient translation initiation increases protein expression and mRNA stability. Contrary to this dogma, we show that increasing initiation rate can decrease both protein expression and stability of certain mRNAs in the budding yeast, S. cerevisiae. These mRNAs contain a stretch of poly-basic residues that cause ribosome stalling. Using computational modeling, we predict that the observed decrease in gene expression at high initiation rates occurs when ribosome collisions at stalls stimulate abortive termination of the leading ribosome and cause endonucleolytic mRNA cleavage. We test our prediction by identifying critical roles for the collision-associated quality control factors, Asc1 and Hel2 (RACK1 and ZNF598 in humans, respectively). Remarkably, hundreds of S. cerevisiae mRNAs that contain ribosome-stall sequences also exhibit lower translation ef ciency. We propose that these mRNAs have undergone evolutionary selection for inef cient initiation to escape collision-stimulated reduction in gene expression.

Rqc1 and other yeast proteins containing highly positively charged sequences are not targets of the RQC complex

“…If the presence of polybasic sequences represents an important obstacle to translation, we expect to find signatures of poor translatability in proteins that contain them. For example, endogenous genes containing stall sequences have a slower or less efficient translation initiation; this is thought to be an adaptation to avoid ribosome collision during elongation [32]. Therefore, we asked whether the polybasic and the ICP data sets would be significantly different from the rest of the yeast genes in experimental measurements that reflect translation activity.…”

“…Different studies have shown that the existence of stalling features in endogenous sequences seems to be accompanied by other unique characteristics, such as low initiation efficiency [31,32] and/or the positioning of the stall sequence at the beginning of the transcript [33]. These adaptations are thought to result in fewer ribosomes per transcript, which would avoid ribosome collisions at the stalling-prone segments, thus preventing RQC activation.…”

Construction of High-Quality Rice Ribosome Footprint Library

“…To monitor gene expression, series of methodologies have been well developed from small-scale ones such as Northern blotting ( Krumlauf, 1994 ), qRT-PCR ( Nolan et al, 2006 ) and Western blotting ( Burnette, 2011 ), to genome-wide ones such as microarray analysis ( Slonim and Yanai, 2009 ), transcriptome ( Zhang et al, 2018b ) and protein sequencing ( Timp and Timp, 2020 ). In contrast, the methodology that can directly evaluate mRNA translation is still greatly limited, though the crucial roles of translation regulation in gene expression have been well documented ( Istomine et al, 2016 ; Merchante et al, 2017 ; Zhang et al, 2018c ; Moissoglu et al, 2019 ; Park and Subramaniam, 2019 ).…”

A Nascent Peptide Code for Translational Control of mRNA Stability in Human Cells

“…Additionally, the protein coding region has been recently recognized as a critical determinant of eukaryotic mRNA stability (2,3). The role of the coding sequence in mRNA stability is best understood in the budding yeast S. cerevisiae where poorly translated codons and nascent peptide motifs with positively charged residues can destabilize mRNAs (4)(5)(6)(7). Poorly translated codons have also been implicated in regulation of mRNA stability in several other organisms (8)(9)(10)(11).…”