Robustness by intrinsically disordered C-termini and translational readthrough

Abstract

During protein synthesis genetic instructions are passed from DNA via mRNA to the ribosome to assemble a protein chain. Occasionally, stop codons in the mRNA are bypassed and translation continues into the untranslated region (3'-UTR). This process, called translational readthrough (TR), yields a protein chain that becomes longer than would be predicted from the DNA sequence alone. Protein sequences vary in propensity for translational errors, which may yield evolutionary constraints by limiting evolutionary paths. Here we investigated TR in Saccharomyces cerevisiae by analysing ribosome profiling data. We clustered proteins as either prone or non-prone to TR, and conducted comparative analyses. We find that a relatively high frequency (5%) of genes undergo TR, including ribosomal subunit proteins. Our main finding is that proteins undergoing TR are highly expressed and have intrinsically disordered C-termini. We suggest that highly expressed proteins may compensate for the deleterious effects of TR by having intrinsically disordered C-termini, which may provide conformational flexibility but without distorting native function. Moreover, we discuss whether minimizing deleterious effects of TR is also enabling exploration of the phenotypic landscape of protein isoforms.

Figure 1.

Density distributions of characteristics in sets (A–E). (A) mRNA stability (as minimum free energy) for each of the sets. The mRNA is more unstable the closer to 0. (B) Translational efficiency of the proteins in each set. (C) Gene expression (Transcript per million) for proteins in each set (log transformed). (D) Gene length (log transformed) for CDS in each set. (E) Frequency of optimal codon amongst sets. Ratio goes from 0 to 1, where 0 is non-optimized and 1 is fully optimized. Correlation plots of TR rate against different variables (A–E). TR rate is always depicted on the Y-axis and the other variable on the X-axis. a: TR rate versus mRNA stability. b: TR rate versus Translational Efficiency. c: TR rate versus gene expression. d: TR rate versus gene (CDS) length. e: TR rate versus codon usage (calculated according to Cai, see Materials and Methods).

Figure 2.

Ratio of disordered residues of full protein sequences. The -axis displays density of sequences and the X-axes display ratio of disordered residues. The colours display what set the proteins belong too. (A) The leaky set (red) is mostly overlapping with the semi-leaky set (blue), but also overlapping with the non-leaky set (green). (B) The leaky and semi-leaky sets are clustered as one (purple), whereas non-leaky is maintained unaltered (green). The leaky and semi-leaky sets have a significantly higher proportion of disordered residues (Mann Whitney test, p-value 0.005, U-value 966).

Figure 3.

Ratio of disordered residues of last 30 amino acids of protein sequences in sets. The Y-axis displays density of sequences and the X-axis displays ratio of disordered residues. Leaky and semi-leaky sets are clustered as one (purple), whereas non-leaky is maintained unaltered (green). Many proteins of both error prone and non-leaky set have intrinsically disordered C-termini, but the C-termini of error-prone proteins are more disordered.