Abstract
Theoretical calculations suggest that, in addition to translational error-induced protein misfolding, a non-negligible fraction of misfolded proteins are error free.
We propose that the anticorrelation between the expression level of a protein and its rate of sequence evolution be explained by an overarching protein-misfolding-avoidance hypothesis that includes selection against both error-induced and error-free protein misfolding, and verify this model by a molecular-level evolutionary simulation.
We provide strong empirical evidence for the protein-misfolding-avoidance hypothesis, including a positive correlation between protein expression level and stability, enrichment of misfolding-minimizing codons and amino acids in highly expressed genes, and stronger evolutionary conservation of residues in which nonsynonymous changes are more likely to increase protein misfolding.
The rate of protein sequence evolution has long been of central interest to molecular evolutionists. Different proteins of the same species evolve at vastly different rates, which is commonly explained by a variation in functional constraint among different proteins (Kimura and Ohta, 1974). However, it is unclear how to quantify the functional constraint of a protein from the knowledge of its function. In the past decade, various types of genomic data from model organisms have been examined to look for the determinants of the rate of protein sequence evolution. The most unexpected discovery was a very strong anticorrelation between the expression level and evolutionary rate of a protein (E–R anticorrelation) (Pal et al, 2001). The prevailing explanation of the E–R anticorrelation is the translational robustness hypothesis (Drummond et al, 2005). This hypothesis posits that mistranslation induces protein misfolding, which is toxic to cells (Figure 1). Consequently, highly expressed proteins are under stronger pressures to be translationally robust and thus are more constrained in sequence evolution. However, the impact of the other source of misfolded proteins, translational error-free proteins (Figure 1), has not been evaluated. By theoretical calculation, computer simulation, and empirical data analysis, we examined the role of selection against both error-induced and error-free protein misfolding in creating the E–R correlation.
Our theoretical calculations suggested that a non-negligible fraction of misfolded proteins are error free. We estimated that when a protein is not very stable, on average ∼20% of misfolded molecules are error free. However, when a protein is very stable, this fraction reduces to ∼5%, which is probably a result of natural selection against protein misfolding.
We conducted a molecular-level evolutionary simulation (Figure 2A) using three different schemes: error-induced misfolding only, error-free misfolding only, and both types of misfolding. As expected, results from the first simulation are similar to those from a previous study that considers only error-induced misfolding (Drummond and Wilke, 2008). Interestingly, the second and third simulations can also generate the same patterns, including a positive correlation between the protein expression level and the unfolding energy (ΔG) of the error-free protein (Figure 2B), a negative correlation between the expression level and the fraction of protein molecules that misfold after being mistranslated (Figure 2C), a negative correlation between ΔG and the evolutionary rate (Figure 2D), and a negative correlation between the expression level and the evolutionary rate (i.e., the E–R anticorrelation) (Figure 2E). Furthermore, we found that selection against protein misfolding is more effective in reducing error-free misfolding than error-induced misfolding.
Based on these results, we propose that an overarching protein-misfolding-avoidance hypothesis that includes both sources of misfolding is superior to the prevailing translational robustness hypothesis, which considers only error-induced misfolding. We tested three key predictions of the protein-misfolding-avoidance hypotheses using yeast data. First, we showed that, consistent with our prediction, a positive correlation exists between the protein expression level and stability, which is measured by the unfolding energy or melting temperature. In addition, protein expression level is negatively correlated with protein aggregation propensity. Second, we found that codons minimizing protein misfolding are used more frequently in highly expressed proteins than in lowly expressed ones. Third, we showed that, within the same protein, amino acid residues in which random nonsynonymous mutations are more likely to increase protein misfolding are evolutionarily more conserved.
Together, these results provide unambiguous evidence that avoidance of both error-induced and error-free protein misfolding is a major source of the E–R anticorrelation and that protein stability and mistranslation have important roles in protein evolution.
What determines the rate of protein evolution is a fundamental question in biology. Recent genomic studies revealed a surprisingly strong anticorrelation between the expression level of a protein and its rate of sequence evolution. This observation is currently explained by the translational robustness hypothesis in which the toxicity of translational error-induced protein misfolding selects for higher translational robustness of more abundant proteins, which constrains sequence evolution. However, the impact of error-free protein misfolding has not been evaluated. We estimate that a non-negligible fraction of misfolded proteins are error free and demonstrate by a molecular-level evolutionary simulation that selection against protein misfolding results in a greater reduction of error-free misfolding than error-induced misfolding. Thus, an overarching protein-misfolding-avoidance hypothesis that includes both sources of misfolding is superior to the translational robustness hypothesis. We show that misfolding-minimizing amino acids are preferentially used in highly abundant yeast proteins and that these residues are evolutionarily more conserved than other residues of the same proteins. These findings provide unambiguous support to the role of protein-misfolding-avoidance in determining the rate of protein sequence evolution.
Collapse