title: Tracing regulatory routes in metabolism using generalised supply-demand analysis.
abstract: BACKGROUND
  Generalised supply-demand analysis is a conceptual framework that views metabolism as a molecular economy. Metabolic pathways are partitioned into so-called supply and demand blocks that produce and consume a particular intermediate metabolite. By studying the response of these reaction blocks to perturbations in the concentration of the linking metabolite, different regulatory routes of interaction between the metabolite and its supply and demand blocks can be identified and their contribution quantified. These responses are mediated not only through direct substrate/product interactions, but also through allosteric effects. Here we subject previously published kinetic models of pyruvate metabolism in Lactococcus lactis and aspartate-derived amino acid synthesis in Arabidopsis thaliana to generalised supply-demand analysis.
  
  
  RESULTS
  Multiple routes of regulation are brought about by different mechanisms in each model, leading to behavioural and regulatory patterns that are generally difficult to predict from simple inspection of the reaction networks depicting the models. In the pyruvate model the moiety-conserved cycles of ATP/ADP and NADH/NAD(+) allow otherwise independent metabolic branches to communicate. This causes the flux of one ATP-producing reaction block to increase in response to an increasing ATP/ADP ratio, while an NADH-consuming block flux decreases in response to an increasing NADH/NAD(+) ratio for certain ratio value ranges. In the aspartate model, aspartate semialdehyde can inhibit its supply block directly or by increasing the concentration of two amino acids (Lys and Thr) that occur as intermediates in demand blocks and act as allosteric inhibitors of isoenzymes in the supply block. These different routes of interaction from aspartate semialdehyde are each seen to contribute differently to the regulation of the aspartate semialdehyde supply block.
  
  
  CONCLUSIONS
  Indirect routes of regulation between a metabolic intermediate and a reaction block that either produces or consumes this intermediate can play a much larger regulatory role than routes mediated through direct interactions. These indirect routes of regulation can also result in counter-intuitive metabolic behaviour. Performing generalised supply-demand analysis on two previously published models demonstrated the utility of this method as an entry point in the analysis of metabolic behaviour and the potential for obtaining novel results from previously analysed models by using new approaches.
authors.affiliation: Laboratory for Molecular Systems Biology, Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa. carldc@sun.ac.za.
authors.forename: Carl D
authors.initials: CD
authors.lastname: Christensen
authors.affiliation: Laboratory for Molecular Systems Biology, Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa. jhsh@sun.ac.za.|Centre for Studies in Complexity, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa. jhsh@sun.ac.za.
authors.forename: Jan-Hendrik S
authors.initials: JH
authors.lastname: Hofmeyr
authors.affiliation: Laboratory for Molecular Systems Biology, Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa. jr@sun.ac.za.
authors.forename: Johann M
authors.initials: JM
authors.lastname: Rohwer
mesh_terms: D000596:Amino Acids / Q000096:biosynthesis; D017360:Arabidopsis / Q000378:metabolism*; D013294:Lactococcus lactis / Q000378:metabolism*; D053858:Metabolic Networks and Pathways / Q000502:physiology*; D008954:Models, Biological; D019289:Pyruvic Acid / Q000378:metabolism; D049490:Systems Biology / Q000379:methods*
chemical_list: D000596:Amino Acids; D019289:Pyruvic Acid