Intrinsically disordered segments affect protein half-life in the cell and during evolution

Abstract

Precise control of protein turnover is essential for cellular homeostasis. The ubiquitin-proteasome system is well established as a major regulator of protein degradation, but an understanding of how inherent structural features influence the lifetimes of proteins is lacking. We report that yeast, mouse, and human proteins with terminal or internal intrinsically disordered segments have significantly shorter half-lives than proteins without these features. The lengths of the disordered segments that affect protein half-life are compatible with the structure of the proteasome. Divergence in terminal and internal disordered segments in yeast proteins originating from gene duplication leads to significantly altered half-life. Many paralogs that are affected by such changes participate in signaling, where altered protein half-life will directly impact cellular processes and function. Thus, natural variation in the length and position of disordered segments may affect protein half-life and could serve as an underappreciated source of genetic variation with important phenotypic consequences.

Graphical abstract

Figure 1

The Effects of Terminal Disordered Segments on Protein Half-Life (A) A total of 3,273 yeast proteins were grouped based on the length of the disordered segment at the N terminus. Long (dark red) and short (light red) terminal disordered segments were defined as stretches of >30 and ≤30 disordered residues. (B–D) Boxplots of protein half-life distributions. Proteins were classified based on the length of the disordered segment at the N terminus (B) or the C terminus (C) and the presence of N-terminal disordered or structured segments (D, long N-terminal structured regions [dark gray] were defined as >30 structured residues). (E) Boxplots of the distributions of N-terminal disorder length for different half-life groups, indicated with schematic exponential degradation curves (from short half-life [dark green] to long half-life [light green]). Central boxplot notches mark the median and the 95% confidence interval. Colored boxes represent the 50% of data points above (×0.75) and below (×0.25) the median (×0.50). Vertical lines (whiskers) connected to the boxes by the horizontal dashed lines represent the largest and the smallest nonoutlier data points. Outliers are not shown to improve visualization. p values reported are from Mann-Whitney U (B–D) and Kruskal-Wallis (E) tests. p values, the number of data points (n), and differences between the half-life medians of the compared groups $\left(\Delta \tilde{\text{H}}\right)$ are shown to the right. See also Figures S1 and S3 and Table S1.

Figure 2

The Effects of Internal Disordered Segments on Protein Half-Life (A) Boxplots of protein half-life distributions for different groups of yeast proteins that contain (dark red) or lack (light red) an internal disordered segment (defined as a continuous stretch of ≥40 disordered residues), subclassified based on (B and D) the length of N-terminal disorder (as in Figure 1: long, >30 residues or short, ≤ 30 residues) and (C) the number of internal disordered segments (from zero, top, to three or more, bottom). Each protein is present in only one category per panel. See Figure 1 for further information. See also Figures S2 and S3 and Tables S1 and S4.

Figure 3

The Effects of Disordered Segments on Protein Turnover in Mouse and Human Boxplots of the distributions of half-life values in Mus musculus (A–C), and relative degradation rates in Homo sapiens (D–F), for proteins with long and short N-terminal, C-terminal, and internal disordered segments. Note that the scale for protein half-life is in hours for mouse, rather than minutes as in yeast. Values are reversed for the human data: proteins with a short half-life have a high relative degradation rate. See Figure 1 for further information. See also Table S5.

Figure 4

Divergence in Disordered Segments during Evolution Can Impact Protein Half-Life (A) Schematic depiction of how the half-life of paralogs could be altered by changes in N-terminal and/or internal disordered segments during evolution. The dark and light green degradation curves denote a short and long half-life. This schematic is not intended to cover all possible scenarios for divergence of disordered segments between paralogs. (B) Distributions of half-life differences (ΔH) in pairs of yeast paralogs, grouped according to the difference in the length of their N-terminal disordered segments. Top: one paralog has a short and the other paralog a long disordered N terminus (SL). Bottom: both paralogs have short (both ≤30 residues; SS) or both have long (both >30 residues; LL) disordered N termini. (C) Distribution of half-life differences (ΔH) in paralog pairs, grouped according to the difference in the number of internal disordered regions (ΔI). Top: pairs where one of the two paralogs has a higher number of internal disordered segments (ΔI ≥ 1). Bottom: pairs with identical numbers of internal disordered segment (ΔI = 0). Each paralog pair is arranged so that ΔL = L₁ − L₂ (B) and ΔI = I₁ − I₂ (C) are always positive (i.e., L₁ ≥ L₂ and I₁ ≥ I₂). This order is used for the ΔH calculation (that is, the half-life of the paralog with the shortest N-terminal disorder, or the smallest number of internal disordered segments, will be subtracted from the half-life of the other one; ΔH = H₁ − H₂). As a result, ΔH will be negative for pairs where an increase in N-terminal or internal disorder coincides with a shorter half-life (Experimental Procedures). For ΔI = 0 (C, bottom), two ΔH distributions were obtained by ordering the paralogs within a pair according to the total length of all internal disordered segments (increasing and decreasing to simulate gain and loss of internal disorder length during evolution; Table S6A). See Figure 1 for further information. See also Figure S4 and Table S6.

Figure 5

Concept Describing the General Relationship between the Presence of Long Terminal or Internal Disordered Segments and Protein Half-Life Disordered segments influence protein half-life by permitting efficient initiation of degradation by the proteasome. Ubiquitination and other factors contributing to substrate targeting to the proteasome are not depicted.