Origin of a folded protein from an intrinsically disordered ancestral peptide

Contemporary proteins can be traced back to a basic set of a few thousand domain prototypes. The origin of these domain prototypes, however, remains poorly understood. We have proposed that they arose from an ancestral set of peptides, which acted as cofactors of RNA-mediated catalysis and replication. Their ability to fold was an emergent property of peptide-RNA coevolution. The ribosome is the main survivor of this primordial RNA world and offers an excellent model system for retracing the steps that led to the folded proteins of today. We have retraced this emancipation from the RNA scaffold computationally and experimentally, by investigating the plausible ancestor in ribosomal proteins for a cytosolic protein fold, the tetratricopeptide repeat (TPR). The repeat units of the fold are helical hairpins. These αα-hairpins in all known TPR-containing proteins can be detected using a single sequence profile, underscoring their homologous origin. More importantly, the αα-hairpin has been discovered to occur in multiple seemingly unrelated protein folds. Through the sequence and structure comparison of the TPR αα-hairpins to all proteins of known structure, we detected several potential homologs in non-repetitive proteins, including one from a ribosomal protein S20 (RPS20). Subsequently, by amplifying an αα-hairpin from a RPS20, which is unstructured in the absence of the cognate ribosomal RNA, we explored whether an intrinsically disordered peptide could form a folded protein through an increase in complexity afforded by repetition. Simple repetition was not sufficient in our case, but the repeat protein was so close to a folded structure that only two point mutations per repeat were necessary to allow it to fold reliably. The mutations needed for this transition did not appear to affect negatively the interaction with the RNA scaffold and were neutral for survival and growth in the parent organism, raising the possibility that they could have been among the variants sampled multiply in the course of evolution. TPRs could thus have plausibly arisen by amplification from an ancestral, RNA-dependent helical hairpin, as proposed by our theory.