Abstract
Sequence divergence of orthologous proteins enables adaptation to environmental stresses and promotes evolution of novel functions. Limits on evolution imposed by constraints on sequence and structure were explored using a model TIM barrel protein, indole-3-glycerol phosphate synthase (IGPS). Fitness effects of point mutations in three phylogenetically divergent IGPS proteins during adaptation to temperature stress were probed by auxotrophic complementation of yeast with prokaryotic, thermophilic IGPS. Analysis of beneficial mutations pointed to an unexpected, long-range allosteric pathway towards the active site of the protein. Significant correlations between the fitness landscapes of distant orthologues implicate both sequence and structure as primary forces in defining the TIM barrel fitness landscape and suggest that fitness landscapes can be translocated in sequence space. Exploration of fitness landscapes in the context of a protein fold provides a strategy for elucidating the sequence-structure-fitness relationships in other common motifs.
Highlights
Follow this and additional works at: https://escholarship.umassmed.edu/bioinformatics_pubs Part of the Biochemistry Commons, Bioinformatics Commons, Computational Biology Commons, Molecular Biology Commons, and the Structural Biology Commons
We chose three phylogenetically divergent indole-3-glycerol phosphate synthase (IGPS) orthologues from a thermophilic archeaon, S. solfataricus (SsIGPS), and two thermophilic bacteria, T. maritima (TmIGPS) and T. thermophilus (TtIGPS), Table 1
We have explored the fitness landscapes of three orthologous TIM barrel proteins from archaea and bacteria to answer two important questions at the intersection of biophysics and evolutionary biology: (1) what are the salient sequence and structural correlates of a TIM barrel fitness landscape, and (2) are the fitness landscapes of phylogenetically divergent orthologous proteins correlated with each other and, if so, what is the basis of the correlation?
Summary
Follow this and additional works at: https://escholarship.umassmed.edu/bioinformatics_pubs Part of the Biochemistry Commons, Bioinformatics Commons, Computational Biology Commons, Molecular Biology Commons, and the Structural Biology Commons. Limits on evolution imposed by constraints on sequence and structure were explored using a model TIM barrel protein, indole-3-glycerol phosphate synthase (IGPS). Mutational scans showed that site-specific amino-acid preferences and, presumably, fitness landscapes are nearly identical in homologues of influenza virus nucleoprotein with 94% identity[14]. To date, it remains unclear whether the fitness landscapes remain similar in homologous proteins with a strongly divergent evolutionary history. We perform a mutational scan of three orthologous TIM barrel fold proteins, indole-3-glycerol phosphate synthase (IGPS), to experimentally determine the fitness landscapes of proteins sharing the same fold and function, but with ancient divergences and low sequence identity. Relative fitness of the mutants, which depends on IGPS activity, was determined by the abundance of the mutant DNA sequence relative to wildtype (WT) over time[20]
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