Genotype networks, innovation, and robustness in sulfur metabolism

TL;DR

This study explores the structure and properties of metabolic genotype networks in sulfur metabolism, revealing how network connectivity influences the potential for metabolic innovation and robustness in evolving organisms.

Contribution

It provides a detailed analysis of the genotype network topology in sulfur metabolism and links network features to the capacity for phenotypic innovation.

Findings

Genotype networks form large connected components.

Distance in genotype space correlates with super-essential reactions.

Genotype neighborhoods contain diverse novel phenotypes.

Abstract

Metabolic networks are complex systems that comprise hundreds of chemical reactions which synthesize biomass molecules from chemicals in an organism's environment. The metabolic network of any one organism is encoded by a metabolic genotype, defined by a set of enzyme-coding genes whose products catalyze the network's reactions. Each metabolic genotype has a metabolic phenotype, such as the ability to synthesize biomass on a spectrum of different sources of chemical elements and energy. We here focus on sulfur metabolism, which is attractive to study the evolution of metabolic networks, because it involves many fewer reactions than carbon metabolism. Specifically, we study properties of the space of all possible metabolic genotypes, and analyze properties of random metabolic genotypes that are viable on different numbers of sulfur sources. We show that metabolic genotypes with the same phenotype form large connected genotype networks that extend far through metabolic genotype space. How far they reach through this space is a linear function of the number of super-essential reactions in such networks, the number of reactions that occur in all networks with the same phenotype. We show that different neighborhoods of any genotype network harbor very different novel phenotypes, metabolic innovations that can sustain life on novel sulfur sources. We also analyze the ability of evolving populations of metabolic networks to explore novel metabolic phenotypes. This ability is facilitated by the existence of genotype networks, because different neighborhoods of these networks contain very different novel phenotypes. In contrast to macromolecules, where phenotypic robustness may facilitate phenotypic innovation, we show that here the ability to access novel phenotypes does not monotonically increase with robustness.