Defining the ATPome reveals cross-optimization of metabolic pathways

Neal K. Bennett, Mai K. Nguyen, Maxwell A. Darch, Hiroki J. Nakaoka, Derek Cousineau, Johanna Hoeve, Thomas G. Graeber, Markus Schuelke, Emin Maltepe, Martin Kampmann, Bryce A. Mendelsohn, Jean L. Nakamura and Ken Nakamura ()
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Neal K. Bennett: Gladstone Institute of Neurological Disease
Mai K. Nguyen: Gladstone Institute of Neurological Disease
Maxwell A. Darch: Gladstone Institute of Neurological Disease
Hiroki J. Nakaoka: University of California
Derek Cousineau: Gladstone Institute of Neurological Disease
Johanna Hoeve: UCLA Metabolomics Center, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California
Thomas G. Graeber: UCLA Metabolomics Center, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California
Markus Schuelke: NeuroCure Clinical Research Center, Charité–Universitätsmedizin Berlin
Emin Maltepe: University of California
Martin Kampmann: University of California
Bryce A. Mendelsohn: Gladstone Institute of Neurological Disease
Jean L. Nakamura: University of California
Ken Nakamura: Gladstone Institute of Neurological Disease

Nature Communications, 2020, vol. 11, issue 1, 1-16

Abstract: Abstract Disrupted energy metabolism drives cell dysfunction and disease, but approaches to increase or preserve ATP are lacking. To generate a comprehensive metabolic map of genes and pathways that regulate cellular ATP—the ATPome—we conducted a genome-wide CRISPR interference/activation screen integrated with an ATP biosensor. We show that ATP level is modulated by distinct mechanisms that promote energy production or inhibit consumption. In our system HK2 is the greatest ATP consumer, indicating energy failure may not be a general deficiency in producing ATP, but rather failure to recoup the ATP cost of glycolysis and diversion of glucose metabolites to the pentose phosphate pathway. We identify systems-level reciprocal inhibition between the HIF1 pathway and mitochondria; glycolysis-promoting enzymes inhibit respiration even when there is no glycolytic ATP production, and vice versa. Consequently, suppressing alternative metabolism modes paradoxically increases energy levels under substrate restriction. This work reveals mechanisms of metabolic control, and identifies therapeutic targets to correct energy failure.

Date: 2020
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DOI: 10.1038/s41467-020-18084-6

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