The genotype-phenotype landscape of an allosteric protein.

Drew S Tack,Peter D Tonner,Sasha F Levy,Olga Vasilyeva,Nathan D Olson,David Ross,Nina Alperovich,Eugenia F Romantseva,Abe Pressman

doi:10.15252/msb.202010179

Abstract

Allostery is a fundamental biophysical mechanism that underlies cellular sensing, signaling, and metabolism. Yet a quantitative understanding of allosteric genotype‐phenotype relationships remains elusive. Here, we report the large‐scale measurement of the genotype‐phenotype landscape for an allosteric protein: the lac repressor from Escherichia coli, LacI. Using a method that combines long‐read and short‐read DNA sequencing, we quantitatively measure the dose‐response curves for nearly 105 variants of the LacI genetic sensor. The resulting data provide a quantitative map of the effect of amino acid substitutions on LacI allostery and reveal systematic sequence‐structure‐function relationships. We find that in many cases, allosteric phenotypes can be quantitatively predicted with additive or neural‐network models, but unpredictable changes also occur. For example, we were surprised to discover a new band‐stop phenotype that challenges conventional models of allostery and that emerges from combinations of nearly silent amino acid substitutions.

Highlights

Described fitness landscape approaches have enabled the phenotypic characterization of 104 to genotypes simultaneously[7,8,9,10,11,12]
Our findings suggest that a surprising diversity of useful and potentially novel allosteric phenotypes exist with genotypes that are discoverable only via large-scale landscape measurements
For the goal of an improved understanding of allostery, our results reveal the dual nature of the problem: First, the deep neural network model (DNN) model and the mapping of single-substitution effects demonstrate that largescale measurements and analysis can overcome the challenges inherent to the structural complexity of allosteric function

Summary

Introduction

Described fitness landscape approaches have enabled the phenotypic characterization of 104 to genotypes simultaneously[7,8,9,10,11,12]. Measurements at this scale facilitate the exploration of genotypes with widely distributed mutations, making them ideal for probing complex biological mechanisms like allostery. To quantitatively characterize the sense-and-response phenotypes inherent to allostery, a measurement must encompass the full dose-response curve that describes biomolecular activity as a function of ligand concentration. We report the large-scale measurement of the genotype-phenotype landscape for an allosteric protein: the lac repressor from Escherichia coli, LacI. We were surprised to discover a new band-stop phenotype that challenges conventional models of allostery and that emerges from combinations of nearly silent amino acid substitutions

Methods

Results

Conclusion