Defining the ATPome reveals cross-optimization of metabolic pathways

Nat Commun. 2020 Aug 28;11(1):4319. doi: 10.1038/s41467-020-18084-6.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphate / genetics
  • Adenosine Triphosphate / metabolism*
  • CRISPR-Cas Systems
  • Cell Line
  • Energy Metabolism
  • Female
  • Fibroblasts
  • Gene Expression Regulation
  • Gene Knockdown Techniques
  • Glucose / metabolism
  • Glycolysis / physiology
  • Hexokinase / genetics
  • Hexokinase / metabolism
  • Humans
  • K562 Cells
  • Metabolic Networks and Pathways / genetics*
  • Metabolic Networks and Pathways / physiology*
  • Metabolomics
  • Mitochondria / metabolism
  • Pentose Phosphate Pathway
  • Point Mutation


  • Adenosine Triphosphate
  • Hexokinase
  • Glucose

Associated data

  • figshare/10.6084/m9.figshare.12678938