title: Why in vivo may not equal in vitro - new effectors revealed by measurement of enzymatic activities under the same in vivo-like assay conditions.
abstract: Does the understanding of the dynamics of biochemical networks in vivo, in terms of the properties of their components determined in vitro, require the latter to be determined all under the same conditions? An in vivo-like assay medium for enzyme activity determination was designed based on the concentrations of the major ionic constituents of the Escherichia coli cytosol: K(+), Na(+), Mg(2+), phosphate, glutamate, sulfate and Cl(-). The maximum capacities (V(max)) of the extracted enzymes of two pathways were determined using both this in vivo-like assay medium and the assay medium specific for each enzyme. The enzyme activities differed between the two assay conditions. Most of the differences could be attributed to unsuspected, pleiotropic effects of K(+) and phosphate. K(+) activated some enzymes (aldolase, enolase and glutamate dehydrogenase) and inhibited others (phosphoglucose isomerase, phosphofructokinase, triosephosphate isomerase, glyceraldehyde 3-phosphate dehydrogenase, phosphoglycerate kinase, phosphoglycerate mutase), whereas phosphate inhibited all glycolytic enzymes and glutamine synthetase but only activated glutamine 2-oxoglutarate amidotransferase. Neither a high glutamate concentration, nor macromolecular crowding affected the glycolytic or nitrogen assimilation enzymes, other than through the product inhibition of glutamate dehydrogenase by glutamate. This strategy of assessing all pathway enzymes kinetically under the same conditions may be necessary to avoid inadvertent differences between in vivo and in vitro biochemistry. It may also serve to reveal otherwise unnoticed pleiotropic regulation, such as that demonstrated in the present study by K(+) and phosphate.
authors.affiliation: Section of Molecular Cell Physiology, Netherlands Institute for Systems Biology, VU University Amsterdam, The Netherlands.
authors.forename: Rodolfo
authors.initials: R
authors.lastname: García-Contreras
authors.forename: Paul
authors.initials: P
authors.lastname: Vos
authors.forename: Hans V
authors.initials: HV
authors.lastname: Westerhoff
authors.forename: Fred C
authors.initials: FC
authors.lastname: Boogerd
mesh_terms: D001681:Biological Assay; D002244:Carbon / Q000378:metabolism*; D003600:Cytosol / Q000201:enzymology*; D005634:Fructose-Bisphosphate Aldolase / Q000378:metabolism; D005956:Glucose-6-Phosphate Isomerase / Q000378:metabolism; D005986:Glyceraldehyde 3-Phosphate / Q000378:metabolism; D005987:Glyceraldehyde-3-Phosphate Dehydrogenases / Q000378:metabolism; D006019:Glycolysis / Q000502:physiology*; D006801:Humans; D066298:In Vitro Techniques; D009584:Nitrogen / Q000378:metabolism*; D010710:Phosphates / Q000378:metabolism*; D010732:Phosphofructokinase-1 / Q000378:metabolism; D010735:Phosphoglycerate Kinase / Q000378:metabolism; D010736:Phosphoglycerate Mutase / Q000378:metabolism; D010751:Phosphopyruvate Hydratase / Q000378:metabolism; D011188:Potassium / Q000378:metabolism*; D011770:Pyruvate Kinase / Q000378:metabolism; D014305:Triose-Phosphate Isomerase / Q000378:metabolism
chemical_list: D010710:Phosphates; D005986:Glyceraldehyde 3-Phosphate; D002244:Carbon; D005987:Glyceraldehyde-3-Phosphate Dehydrogenases; D010732:Phosphofructokinase-1; D011770:Pyruvate Kinase; D010735:Phosphoglycerate Kinase; D005634:Fructose-Bisphosphate Aldolase; D010751:Phosphopyruvate Hydratase; D014305:Triose-Phosphate Isomerase; D005956:Glucose-6-Phosphate Isomerase; D010736:Phosphoglycerate Mutase; D009584:Nitrogen; D011188:Potassium