title: Systems-level analysis of mechanisms regulating yeast metabolic flux.
abstract: Cellular metabolic fluxes are determined by enzyme activities and metabolite abundances. Biochemical approaches reveal the impact of specific substrates or regulators on enzyme kinetics but do not capture the extent to which metabolite and enzyme concentrations vary across physiological states and, therefore, how cellular reactions are regulated. We measured enzyme and metabolite concentrations and metabolic fluxes across 25 steady-state yeast cultures. We then assessed the extent to which flux can be explained by a Michaelis-Menten relationship between enzyme, substrate, product, and potential regulator concentrations. This revealed three previously unrecognized instances of cross-pathway regulation, which we biochemically verified. One of these involved inhibition of pyruvate kinase by citrate, which accumulated and thereby curtailed glycolytic outflow in nitrogen-limited yeast. Overall, substrate concentrations were the strongest driver of the net rates of cellular metabolic reactions, with metabolite concentrations collectively having more than double the physiological impact of enzymes.
authors: Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
authors: Sean R
authors: SR
authors: Hackett
authors: Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
authors: Vito R T
authors: VR
authors: Zanotelli
authors: Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA. Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.
authors: Wenxin
authors: W
authors: Xu
authors: Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
authors: Jonathan
authors: J
authors: Goya
authors: Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
authors: Junyoung O
authors: JO
authors: Park
authors: Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.
authors: David H
authors: DH
authors: Perlman
authors: Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA. Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
authors: Patrick A
authors: PA
authors: Gibney
authors: Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA. Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
authors: David
authors: D
authors: Botstein
authors: Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA. Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA. Center for Statistics and Machine Learning, Princeton University, Princeton, NJ 08544, USA.
authors: John D
authors: JD
authors: Storey
authors: Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA. Department of Chemistry, Princeton University, Princeton, NJ 08544, USA. joshr@genomics.princeton.edu.
authors: Joshua D
authors: JD
authors: Rabinowitz
mesh_terms: D000494:Allosteric Regulation; D002951:Citrates / Q000378:metabolism; D006019:Glycolysis; D007700:Kinetics; D053858:Metabolic Networks and Pathways; D009584:Nitrogen / Q000172:deficiency; D011770:Pyruvate Kinase / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000201:enzymology*; D029701:Saccharomyces cerevisiae Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism*
chemical_list: D002951:Citrates; D029701:Saccharomyces cerevisiae Proteins; D011770:Pyruvate Kinase; D009584:Nitrogen