Interplay of structural and regulatory evolution in functional evolution of glycolytic enzymes
Authors: Mohammad Siddiq 1,2; Hannah Kania 1,2; Nick Brown 3; Patricia Wittkopp 1,2
Affiliations: 1) Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI; 2) Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI; 3) College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI
Keywords: Experimental evolution
Genes often have multiple functions, and some of these functions change over time while others remain conserved. How do different factors constrain or enable the evolution of a gene's functions at the molecular level? One way of addressing this question is by concurrently studying the structural and regulatory evolution of a gene because what a gene product (e.g, protein) does and can do is determined by when, how, and in what form that product exists. Here, we investigate how gene structure and regulation have coevolved and shaped functional conservation and diversification of the three GAPDH genes in Saccharomyces yeast. The GAPDHs—named TDH1, TDH2, and TDH3 in S. cerevisiae-- catalyze the sixth step of glycolysis, are among the most highly expressed proteins in yeast, and last shared a common ancestor >100 million years ago despite their high sequence similarity to each other (~90% sequence identity). Yet, the presence of three GAPDH enzymes is not necessary for glycolysis; numerous fungi outside of the Saccharomyces clade have only GAPDH. Here, we explore the extent to which the genes have functionally diverged from each other. We first use controlled perturbations of the genes individually and combinatorically to assess their effects on enzymatic activity and growth rate and find that paralogous pairs vary in their level of functional redundancy. We find that changes in gene expression mediated through cis- regulatory sequences are sufficient to explain most of the functional divergence between paralogs with respect to their effects on growth rate. However, we also find that at least one of the paralogs is post-transcriptionally regulated such that its localization extends beyond the cytoplasm—the canonical domain of glycolytic enzymes—to the nucleus and also outside of the cell. Our ongoing work aims to resolve whether the paralogs are differentially distributed in the cells and characterize how protein coding changes affect functions in the different locales, where the roles of these canonical housekeeping genes remain largely unknown. Collectively, the results from this work will both highlight how coupling experimental and evolutionary frameworks can reveal new molecular functions of a gene and provide mechanistic insight into the ways those diverse functions have coevolved through changes in gene structure and regulation.