title: The multifarious short-term regulation of ammonium assimilation of Escherichia coli: dissection using an in silico replica.
abstract: Ammonium assimilation in Escherichia coli is regulated through multiple mechanisms (metabolic, signal transduction leading to covalent modification, transcription, and translation), which (in-)directly affect the activities of its two ammonium-assimilating enzymes, i.e. glutamine synthetase (GS) and glutamate dehydrogenase (GDH). Much is known about the kinetic properties of the components of the regulatory network that these enzymes are part of, but the ways in which, and the extents to which the network leads to subtle and quasi-intelligent regulation are unappreciated. To determine whether our present knowledge of the interactions between and the kinetic properties of the components of this network is complete - to the extent that when integrated in a kinetic model it suffices to calculate observed physiological behaviour - we now construct a kinetic model of this network, based on all of the kinetic data on the components that is available in the literature. We use this model to analyse regulation of ammonium assimilation at various carbon statuses for cells that have adapted to low and high ammonium concentrations. We show how a sudden increase in ammonium availability brings about a rapid redirection of the ammonium assimilation flux from GS/glutamate synthase (GOGAT) to GDH. The extent of redistribution depends on the nitrogen and carbon status of the cell. We develop a method to quantify the relative importance of the various regulators in the network. We find the importance is shared among regulators. We confirm that the adenylylation state of GS is the major regulator but that a total of 40% of the regulation is mediated by ADP (22%), glutamate (10%), glutamine (7%) and ATP (1%). The total steady-state ammonium assimilation flux is remarkably robust against changes in the ammonium concentration, but the fluxes through GS and GDH are completely nonrobust. Gene expression of GOGAT above a threshold value makes expression of GS under ammonium-limited conditions, and of GDH under glucose-limited conditions, sufficient for ammonium assimilation.
authors.affiliation: Molecular Cell Physiology, Institute of Molecular Cell Biology, CRBCS, Vrije Universiteit, Amsterdam, the Netherlands.
authors.forename: Frank J
authors.initials: FJ
authors.lastname: Bruggeman
authors.forename: Fred C
authors.initials: FC
authors.lastname: Boogerd
authors.forename: Hans V
authors.initials: HV
authors.lastname: Westerhoff
mesh_terms: D000244:Adenosine Diphosphate / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000378:metabolism; D000641:Ammonia / Q000378:metabolism*; D019295:Computational Biology; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D005947:Glucose / Q000378:metabolism; D005969:Glutamate Dehydrogenase / Q000378:metabolism; D005970:Glutamate Synthase / Q000378:metabolism; D005973:Glutamine / Q000378:metabolism; D007700:Kinetics; D008954:Models, Biological; D009154:Mutation / Q000235:genetics; D009713:Nucleotidyltransferases / Q000378:metabolism; D051922:PII Nitrogen Regulatory Proteins; D015203:Reproducibility of Results; D012984:Software; D013997:Time Factors
chemical_list: D051922:PII Nitrogen Regulatory Proteins; D005973:Glutamine; D000244:Adenosine Diphosphate; D000641:Ammonia; D000255:Adenosine Triphosphate; D005970:Glutamate Synthase; D005969:Glutamate Dehydrogenase; D009713:Nucleotidyltransferases; C020658:glutamine-synthetase adenylyltransferase; C022515:regulatory protein uridylyltransferase; D005947:Glucose