Readthrough errors purge deleterious cryptic sequences, facilitating the birth of coding sequences

Abstract

De novo protein-coding innovations sometimes emerge from ancestrally non-coding DNA, despite the expectation that translating random sequences is overwhelmingly likely to be deleterious. The "preadapting selection" hypothesis claims that emergence is facilitated by prior, low-level translation of noncoding sequences via molecular errors. It predicts that selection on polypeptides translated only in error is strong enough to matter, and is strongest when erroneous expression is high. To test this hypothesis, we examined non-coding sequences located downstream of stop codons (i.e. those potentially translated by readthrough errors) in Saccharomyces cerevisiae genes. We identified a class of "fragile" proteins under strong selection to reduce readthrough, which are unlikely substrates for co-option.Among the remainder, sequences showing evidence of readthrough translation, as assessed by ribosome profiling, encoded C-terminal extensions with higher intrinsic structural disorder, supporting the pre-adapting selection hypothesis. The cryptic sequences beyond the stop codon, rather than spillover effects from the regular C-termini, are primarily responsible for the higher disorder. Results are robust to controlling for the fact that stronger selection also reduces the length of C-terminal extensions. These findings indicate that selection acts on 3′ UTRs in S. cerevisiae to purge potentially deleterious variants of cryptic polypeptides, acting more strongly in genes that experience more readthrough errors.

Random peptides rich in small and disorder-promoting amino acids are less likely to be harmful

“…However, if driven in part by selection, it is possibly not just on GC content, but also on peptides from non-coding regions translated by error (Rajon and Masel 2011;Wilson and Masel 2011). Selection on translation errors is for example strong enough to shape non-coding sequences beyond stop codons in Saccharomyces cerevisiae (Kosinski and Masel 2020).…”

“…Selection on translation errors is for example strong enough to shape non-coding sequences beyond stop codons in Saccharomyces cerevisiae (Kosinski and Masel 2020).…”

Why is the average collateral effect of synonymous mutations so similar across alternative reading frames?

“…More generally, if partially frameshifted sequences are tolerated they constitute new protein sequence space. All of these mechanisms bear some similarity to another process highlighted recently, where stochastic stop codon read-through allows some sequences after stop codons to contribute to protein novelty (Kosinski and Masel 2020).…”

Alternative reading frames are an underappreciated source of protein sequence novelty

“…A fourth possible mechanism is stop codon readthrough, either at the ends of genes (L. J. Kosinski and Masel 2020) or following premature truncation (Feng et al 2022), leading to the translation of out-of-frame sequences. Other hypotheses have also been proposed.…”

“…The non-coding sequences which are the raw materials of gene birth often have unusual sequence properties which may predispose them towards gene formation (Wilson et al 2017;Schmitz, Ullrich, and Bornberg-Bauer 2018;Vakirlis et al 2018;Willis and Masel 2018; L. J. Kosinski and Masel 2020;L. Kosinski et al 2022).…”