Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase

Metabolic networks are interconnected and influence diverse cellular processes. The protein-metabolite interactions that mediate these networks are frequently low affinity and challenging to systematically discover. We developed mass spectrometry integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS) to identify such interactions. Analysis of 33 enzymes from human carbohydrate metabolism identified 830 protein-metabolite interactions, including known regulators, substrates, and products as well as previously unreported interactions. We functionally validated a subset of interactions, including the isoform-specific inhibition of lactate dehydrogenase by long-chain acyl-coenzyme A. Cell treatment with fatty acids caused a loss of pyruvate-lactate interconversion dependent on lactate dehydrogenase isoform expression. These protein-metabolite interactions may contribute to the dynamic, tissue-specific metabolic flexibility that enables growth and survival in an ever-changing nutrient environment.

Automated summary

Metabolic networks play a crucial role in various cellular processes. Discovering low-affinity protein-metabolite interactions that govern these networks is challenging. A new method, called mass spectrometry integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS), was developed to identify such interactions. In a study involving enzymes from human carbohydrate metabolism, 830 protein-metabolite interactions were discovered, including both known and unknown interactions. Some of these interactions were functionally validated, revealing the isoform-specific inhibition of lactate dehydrogenase by long-chain acyl-coenzyme A. The findings suggest that these protein-metabolite interactions contribute to the adaptive metabolic flexibility in different tissues.