Respiromics – An integrative analysis linking mitochondrial bioenergetics to molecular signatures

Highlights

• Integrative analysis of respiration and quantitative proteomics of liver mitochondria in response to high-fat diets.

• Evidence for mitochondrial pyruvate transport as important regulator of mitochondrial energy turnover.

• High-confidence prediction of stress and disease-related networks facilitating lipid oxidation.

• Evidence that nutritional stress impacts nuclear, but not mitochondrial, regulation of respiratory complex I.

Abstract

Objective

Energy metabolism is challenged upon nutrient stress, eventually leading to a variety of metabolic diseases that represent a major global health burden.

Methods

Here, we combine quantitative mitochondrial respirometry (Seahorse technology) and proteomics (LC-MS/MS-based total protein approach) to understand how molecular changes translate to changes in mitochondrial energy transduction during diet-induced obesity (DIO) in the liver.

Results

The integrative analysis reveals that significantly increased palmitoyl-carnitine respiration is supported by an array of proteins enriching lipid metabolism pathways. Upstream of the respiratory chain, the increased capacity for ATP synthesis during DIO associates strongest to mitochondrial uptake of pyruvate, which is routed towards carboxylation. At the respiratory chain, robust increases of complex I are uncovered by cumulative analysis of single subunit concentrations. Specifically, nuclear-encoded accessory subunits, but not mitochondrial-encoded or core units, appear to be permissive for enhanced lipid oxidation.

Conclusion

Our integrative analysis, that we dubbed “respiromics”, represents an effective tool to link molecular changes to functional mechanisms in liver energy metabolism, and, more generally, can be applied for mitochondrial analysis in a variety of metabolic and mitochondrial disease models.