TY - JOUR T1 - Site-Specific Amino-Acid Preferences are Mostly Conserved in Two Closely Related Protein Homologs JF - bioRxiv DO - 10.1101/018457 SP - 018457 AU - Michael B. Doud AU - Orr Ashenberg AU - Jesse D. Bloom Y1 - 2015/01/01 UR - http://biorxiv.org/content/early/2015/04/23/018457.abstract N2 - Evolution drives changes in a protein’s sequence over time. The extent to which these changes in sequence affect the underlying preferences for each amino acid at each site is an important question with implications for comparative sequence-analysis methods such as molecular phylogenetics. To quantify the extent that site-specific amino-acid preferences change during evolution, we performed deep mutational scanning on two homologs of human influenza nucleoprotein with 94% amino-acid identity. We found that only a small fraction of sites (14 out of 497) exhibited changes in their amino-acid preferences that exceeded the noise in our experiments. Given the limited change in amino-acid preferences between these close homologs, we tested whether our measurements could be used to build site-specific substitution models that describe the evolution of nucleoproteins from more diverse influenza viruses. We found that site-specific evolutionary models informed by our experiments greatly outperformed non-site-specific alternatives in fitting the phylogenies of nucleoproteins from human, swine, equine, and avian influenza. Combining the experimental data from both nucleoprotein homologs improved phylogenetic fit, in part because measurements in multiple genetic contexts better captured the evolutionary average of the amino-acid preferences for sites with changing preferences. Overall, our results show that site-specific amino-acid preferences are sufficiently conserved during evolution that measuring mutational effects in one protein provides information that can improve quantitative evolutionary modeling of nearby homologs.Author Summary Every site in a protein has inherent preferences for particular amino-acids, meaning that some mutations are better tolerated than others. These preferences result from constraints on protein structure and function, and it is hotly debated how much these preferences change as the protein’s sequence evolves. Only if these preferences are substantially conserved during evolution can we measure them in one protein and extrapolate the results to related proteins. To investigate this issue, we measured the site-specific amino-acid preferences of a pair of homologous proteins from two human influenza strains separated by 30 years of evolution. We found that the amino-acid preferences are conserved for most sites in the homologs. We then used these amino-acid preferences to build site-specific models describing the evolution of homologs from more diverse influenza viruses. These models outperformed traditional non-site-specific models, suggesting that preferences are likely conserved across even longer periods of evolution than those examined in our experiments. Our results show that amino-acid preferences are mostly conserved in closely related proteins, and therefore suggest that site-independent but site-specific evolutionary models are likely to represent substantial improvements over non-site-specific ones. ER -