Unraveling the complexity of flux regulation: A new method demonstrated for nutrient starvation in <i>Saccharomyces cerevisiae</i>

TLDR

Metabolic fluxes can be regulated by gene expression or by metabolic mechanisms, with local step regulation and its impact on overall pathway flux being the two key aspects. The authors developed a regulation‑analysis framework to dissect local flux control across all pathway steps and applied it to yeast glycolytic and fermentative enzymes during nutrient starvation. The method quantitatively separates regulation into hierarchical changes in Vmax and metabolic interactions, and introduces a nuanced leader‑follower‑conservative enzyme classification. The analysis revealed that flux regulation spans from fully hierarchical to purely metabolic, falsifying conventional paradigms and demonstrating that a leader‑follower‑conservative scheme can be experimentally tested.

Abstract

An important question is to what extent metabolic fluxes are regulated by gene expression or by metabolic regulation. There are two distinct aspects to this question: (i) the local regulation of the fluxes through the individual steps in the pathway and (ii) the influence of such local regulation on the pathway's flux. We developed regulation analysis so as to address the former aspect for all steps in a pathway. We demonstrate the method for the issue of how Saccharomyces cerevisiae regulates the fluxes through its individual glycolytic and fermentative enzymes when confronted with nutrient starvation. Regulation was dissected quantitatively into (i) changes in maximum enzyme activity (Vmax, called hierarchical regulation) and (ii) changes in the interaction of the enzyme with the rest of metabolism (called metabolic regulation). Within a single pathway, the regulation of the fluxes through individual steps varied from fully hierarchical to exclusively metabolic. Existing paradigms of flux regulation (such as single- and multisite modulation and exclusively metabolic regulation) were tested for a complete pathway and falsified for a major pathway in an important model organism. We propose a subtler mechanism of flux regulation, with different roles for different enzymes, i.e., "leader," "follower," or "conservative," the latter attempting to hold back the change in flux. This study makes this subtlety, so typical for biological systems, tractable experimentally and invites reformulation of the questions concerning the drives and constraints governing metabolic flux regulation.