Human long intrinsically disordered protein regions are frequent targets of positive selection

Abstract

Intrinsically disordered regions occur frequently in proteins and are characterized by a lack of a well-defined three-dimensional structure. Although these regions do not show a higher order of structural organization, they are known to be functionally important. Disordered regions are rapidly evolving, largely attributed to relaxed purifying selection and an increased role of genetic drift. It has also been suggested that positive selection might contribute to their rapid diversification. However, for our own species, it is currently unknown whether positive selection has played a role during the evolution of these protein regions. Here, we address this question by investigating the evolutionary pattern of more than 6600 human proteins with intrinsically disordered regions and their ordered counterparts. Our comparative approach with data from more than 90 mammalian genomes uses a priori knowledge of disordered protein regions, and we show that this increases the power to detect positive selection by an order of magnitude. We can confirm that human intrinsically disordered regions evolve more rapidly, not only within humans but also across the entire mammalian phylogeny. They have, however, experienced substantial evolutionary constraint, hinting at their fundamental functional importance. We find compelling evidence that disordered protein regions are frequent targets of positive selection and estimate that the relative rate of adaptive substitutions differs fourfold between disordered and ordered protein regions in humans. Our results suggest that disordered protein regions are important targets of genetic innovation and that the contribution of positive selection in these regions is more pronounced than in other protein parts.

Figure 1.

Histograms of paired differences in ω (ω = d_N/d_S) and d_S values in proteins with disordered and ordered protein regions. Shown are the pairwise differences in disordered minus ordered protein regions (Δω and Δd_S) of the same protein. Substitution rates for nonsynonymous (d_N) and synonymous (d_S) sites are obtained from a one-ratio model. ω values are significantly different for ordered and disordered regions (Wilcoxon signed-rank test, paired, P < 2.2 × 10⁻¹⁶); the difference d_S has a greater P-value (P < 4 × 10⁻⁴).

Figure 2.

Estimates of sequence evolution in a nearly neutral model. Distributions of ω = d_N/d_S values (left panel) and the proportion of the neutrally evolved sites (right panel) for ordered (blue), disordered (green), and ordered and disordered protein regions jointly analyzed (orange).

Figure 3.

Three-dimensional features of positively selected sites in the disordered region of human interleukin 21. (A) Cartoon of the NMR structure of human interleukin 21 (PDB Code: 2OQP) including its disordered region indicating B-factor scores from the molecular dynamics analysis. Three residues have been identified as positively selected in a PAML branch-site test (Ser81, Gly85, and Arg91) in the disordered region. (B) Molecular dynamics analysis; shown are the B-factors of all residues. Here, B-factors reflect the fluctuation of single amino acids (C_α atom) about their average positions during the MD simulation. The predicted disordered region by MobiDB is indicated in green as well as the three identified residues under positive selection (S81, G85, and R91).

Figure 4.

Evidence for differences in the selective effects in disordered and ordered protein regions in humans. (A) Nucleotide diversity at synonymous sites (π_S, left panel) and the ratio of nucleotide diversity at nonsynonymous sites over synonymous sites (π_N/π_S, right panel) for ordered, disordered, and jointly obtained protein regions in humans. (B) The distribution of fitness effects of nonsynonymous mutations estimated separately for ordered and disordered protein regions, as well as when jointly estimated. Error bars represent the standard error. N_es denotes the effective population size (N_e) scaled strength of selection (s). (C) Estimates of the role of positive selection for the analyzed protein set. The proportion of nonsynonymous substitutions that can be attributed to positive selection (α) and the adaptive divergence relative to the synonymous divergence (ω_a) estimated separately for ordered and disordered protein regions, as well as when jointly estimated. All pairwise comparisons are significantly different (Wilcoxon signed-rank test, paired, P < 3 × 10⁻¹²).