Denise
You can't really conclude that steps in a pathway beyond a certain
metabolite have no flux control just because adding the metabolite
increases the flux, so you can't conclude that steps before the metabolite
must have most of the control: it depends on the relative elasticities of
the groups of reactions before and after your metabolite to the
concentration of that metabolite.
If you choose to use gene expression to measure control coefficients, you
need to be aware that the numbers you get refer to the effect of the gene
manipulation on the flux with a long relaxation time, and this is not
neccessarily the same as the effect of the enzyme on the flux with a short
relaxation time. So if the gene expression causes secondary unidentified
changes in the system (such as consequential changes in the expression of
other genes) these changes appear with gene manipulation but not with
direct inhibition of the enzyme or from elasticities. Which type of flux
control coefficient you want to know is a matter of choice, but they may
differ.
To avoid gene manipulation you can either inhibit your pet enzyme and see
what happens, or do the analysis by measuring elasticities and solving the
relevant equations.
I think you can't make a metabolite a parameter without altering the nature
of the pathway under investigation: it is now (at least) two pathways, one
leading to your clamped metabolite and the other leading away from it. But
you can solve the control around your metabolite by measuring the relative
changes in the fluxes in these pathways when you raise the metabolite
slightly, since the flux changes are related to the elasticity ratios and
the control coefficients.
Martin Brand
Martin D. Brand
Department of Biochemistry, University of Cambridge
Tennis Court Road, Cambridge CB2 1QW UK
phone: +44 1223 333648, fax: +44 1223 333345
Internet: http://www.bio.cam.ac.uk/dept/biochem/brand/
