Evidence of evolutionary selection for co-translational folding

Abstract

Recent experiments and simulations have demonstrated that proteins can fold on the ribosome. However, the extent and generality of fitness effects resulting from co-translational folding remain open questions. Here we report a genome-wide analysis that uncovers evidence of evolutionary selection for co-translational folding. We describe a robust statistical approach to identify loci within genes that are both significantly enriched in slowly translated codons and evolutionarily conserved. Surprisingly, we find that domain boundaries can explain only a small fraction of these conserved loci. Instead, we propose that regions enriched in slowly translated codons are associated with co-translational folding intermediates, which may be smaller than a single domain. We show that the intermediates predicted by a native-centric model of co-translational folding account for the majority of these loci across more than 500 E. coli proteins. By making a direct connection to protein folding, this analysis provides strong evidence that many synonymous substitutions have been selected to optimize translation rates at specific locations within genes. More generally, our results indicate that kinetics, and not just thermodynamics, can significantly alter the efficiency of self-assembly in a biological context. INTRODUCTIONMany proteins can begin folding to their native states before their synthesis is complete [1,2]. As much as one-third of a bacterial proteome is believed to fold cotranslationally [3], with an even higher percentage likely in more slowly translated eukaryotic proteomes. Numerous experiments on both natural and engineered aminoacid sequences have shown that folding during synthesis can have profound effects: compared to denatured and refolded chains, co-translationally folded proteins may be less prone to misfolding [4][5][6][7][8][9][10][11], aggregation [12] and degradation [13], or they may preferentially adopt alternate stable structures [14][15][16]. Because the timescales for protein synthesis and folding are often similar [17,18], it is clear that the rate of translation can be used to tune the self-assembly of peptide chains in vivo [19,20]. To this point, however, there exists little evidence that evolution has selected specifically for efficient co-translational folding kinetics across any substantial fraction of an organism's proteome.In this work, we provide evidence that evolutionary selection has tuned protein-translation rates to optimize co-translational folding pathways. Our approach is motivated by the hypothesis that pauses during protein synthesis may be beneficial for promoting the formation of native structure. By increasing the separation between the timescales for folding and translation, such pauses may promote the assembly of on-pathway intermediates, which, in turn, template the growth of further native structure. Many experimental and computational studies have shown that protein-folding naturally proceeds in a step-wise manner via structurally distinct intermediates [21,22], and that...

Accessibility of the Shine–Dalgarno sequence dictates N-terminal codon bias inE. coli

“…For example, codons that are under-represented in highly expressed genes tend to be translated more slowly and with slightly less accuracy (Bulmer, 1991;Eyre-Walker and Bulmer, 1993;Sharp and Li, 1987), suggesting that essential genes have been optimized for translational efficiency. Even within a gene, rare codons often appear in conserved clusters (Chaney and Clark, 2015;Chaney et al, 2017;Clarke and Clark, 2010;Jacobs and Shakhnovich, 2017), indicating that, in some cases, rare codons might also be under positive selection.…”