Large-Scale Analyses of Site-Specific Evolutionary Rates across Eukaryote Proteomes Reveal Confounding Interactions between Intrinsic Disorder, Secondary Structure, and Functional Domains

Abstract

Various structural and functional constraints govern the evolution of protein sequences. As a result, the relative rates of amino acid replacement among sites within a protein can vary significantly. Previous large-scale work on Metazoan (Animal) protein sequence alignments indicated that amino acid replacement rates are partially driven by a complex interaction among three factors: intrinsic disorder propensity; secondary structure; and functional domain involvement. Here, we use sequence-based predictors to evaluate the effects of these factors on site-specific sequence evolutionary rates within four eukaryotic lineages: Metazoans; Plants; Saccharomycete Fungi; and Alveolate Protists. Our results show broad, consistent trends across all four Eukaryote groups. In all four lineages, there is a significant increase in amino acid replacement rates when comparing: (i) disordered vs. ordered sites; (ii) random coil sites vs. sites in secondary structures; and (iii) inter-domain linker sites vs. sites in functional domains. Additionally, within Metazoans, Plants, and Saccharomycetes, there is a strong confounding interaction between intrinsic disorder and secondary structure—alignment sites exhibiting both high disorder propensity and involvement in secondary structures have very low average rates of sequence evolution. Analysis of gene ontology (GO) terms revealed that in all four lineages, a high fraction of sequences containing these conserved, disordered-structured sites are involved in nucleic acid binding. We also observe notable differences in the statistical trends of Alveolates, where intrinsically disordered sites are more variable than in other Eukaryotes and the statistical interactions between disorder and other factors are less pronounced.

Proteome-wide signatures of function in highly diverged intrinsically disordered regions

“…Our evolutionary analysis addresses challenges in assigning function to highly diverged intrinsically disordered regions whose presence is conserved in orthologs. Although there are examples of slowly evolving disordered regions (Ahrens et al, 2016; Ahrens et al, 2018; Brown et al, 2002), these reflect a minority of IDRs, and pose less of a challenge for standard protein sequence analysis methods. Because we take the evolutionary rate of IDRs into account in our analysis, we do not identify constrained molecular features for these slowly evolving IDRs, as they would not be significantly different in our simulated IDRs.…”

Intrinsic disorder in protein domains contributes to both organism complexity and clade-specific functions

“…IDPs play important roles in various biological processes [1][2][3] and they usually have special evolutionary features 1,2 . For example, genes encoding IDPs tend to be evolutionarily young 49 ; the disordered regions in IDPs tend to have higher amino acid replacement rates 50 and biased amino acid composition affected by the GC content 51 . In general, these disordered regions in proteins are usually the linking regions between different protein domains 20,51 .…”

In Silico Study of Rett Syndrome Treatment-Related Genes, MECP2, CDKL5, and FOXG1, by Evolutionary Classification and Disordered Region Assessment

“…This module can be present as short linear motifs (SLiMs) or intrinsically disordered domains (IDDs) [26,38]. These regions commonly have secondary structures that may be important for binding and, hence, slowing their evolutionary rates [36,39]. IDDs were observed in the MBD—which was predicted to be partly disordered—and in the TRD and NID of MeCP2; it is in accordance with previous reports that structured regions are found only in the MBD, while other regions are extensively disordered [17,18,40].…”