Stop-codon read-through arises largely from molecular errors and is generally nonadaptive

Abstract

Stop-codon read-through refers to the phenomenon that a ribosome goes past the stop codon and continues translating into the otherwise untranslated region (UTR) of a transcript. Recent ribosome-profiling experiments in eukaryotes uncovered widespread stop-codon read-through that also varies among tissues, prompting the adaptive hypothesis that stop-codon read-through is an important, regulated mechanism for generating proteome diversity. Here we propose and test a competing hypothesis that stop-codon read-through arises mostly from molecular errors and is largely nonadaptive. The error hypothesis makes distinct predictions about the probability of read-through, frequency of sequence motifs for read-through, and conservation of the read-through region, each of which is supported by genome-scale data from yeasts and fruit flies. Thus, except for the few cases with demonstrated functions, stop-codon read-through is generally nonadaptive. This finding, along with other molecular errors recently quantified, reveals a much less precise or orderly cellular life than is commonly thought.

Translational readthrough goes unseen by natural selection

“…This is in accordance with other studies that find continuous TR 265 to be heterogeneously present [26]. 266 Recently, TR has been suggested to be non-adaptive as its presence appear 267 stochastic [27]. However, biological heterogeneity and stochastic processes is raw 268 material for novel adaptations [28].…”

“…the 26 error rate during DNA replication, which leads to heritable variation. Phenotypic 27 mutations have been suggested to act as intermediate stepping stones for traits not yet 28 encoded on the DNA level [4]. In the context of two correlated point mutations, which 29 are jointly required for the formation of stabilising interactions in a protein, this has 30 lead to the formulation of "the look-ahead effect" [4].…”

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

“…For example, Drosophila melanogaster has been shown to have significant functional ("programmed") readthrough (Jungreis, et al 2011). However, pervasive programmed readthrough seems to be phylogenetically restricted to Pancrustaceae (Jungreis, et al 2016), and does not occur in our focal species of S. cerevisiae (Jungreis, et al 2016;Li and Zhang 2019). We can therefore assume that ribohits to 3' UTR sequences indicate translational errors, rather than alternative already-functional protein products.…”

“…We also sometimes assess or review other analyses of disorder at the level of individual amino acids in isolation, in terms of disorder propensity (Theillet, et al 2013), relative solvent accessibility (RSA) (Tien, et al 2013), or simply proportion of hydrophobic amino acids (where e.g. G, A, V, I, L, M, F, Y, and W are considered hydrophobic (Li and Zhang 2019)).…”

“…It is therefore straightforward to count ribosome profiling hits ("ribohits") beyond the stop codon as a direct measure of readthrough. This is better than using protein abundance as an indirect measure of opportunities for readthrough, because highly abundant proteins tend to have lower readthrough rates per translation event (Bonetti, et al 1995;Li and Zhang 2019). Our ability to directly quantify the amount of erroneous translation using ribohits makes stop codon readthrough a perfect test case for assessing whether pre-adapting selection can ever occur.…”