Unraveling the complexity of flux regulation new insights through the quantitative description of regulatory processes

new insights through the quantitative description of regulatory processes Sergio Rossell This thesis has been reviewed by: prof. dr. Abbreviations and symbols 2PG 2-phosphoglycerate 3PG 3-phosphoglycerate AA aminoacids synthesis pathways ACE acetaldehyde ADH alcohol dehydrogenase –E.C. 1.1.1.1 ALD fluctose bisphosphate aldolase –E.C. 4.1.2.13 BPG 1,3-bisphosphoglycerate C J ei flux control coefficient of enzyme i C xj ei concentration control coefficient of enzyme i on metabolite x j DHAP dihydroxyacetonephosphate ε vi xj elasticity of the rate v i for the metabolite x j ENO enolase –E.C. 2.7.1.40 EtOH ethanol F6P fructose-6-phosphate F16P fructose-1,6-bisphosphate Γ mass-actio ratio G6P glucose-6-phosphate GAP glyceraldehyde-3-phosphate GAPDH glyceraldehyde-3-phosphate dehydrogenase –E.C.1.2.1.12 GLC glucose GLCi intracellular glucose GLT glucose transporter HK hexokinase –E.C. 2.7.1.1 J steady-state flux k cat catalytic constant of an enzyme k deg first order kinetic constant of the rate of protein degradation K Eq equilibrium constant K m Michaelis-Menten constant ii Abbreviations and symbols k trans first order kinetic constant of the rate of translation P reaction of pathway product v P J xi partitioned response coefficient for the metabolite x i PEP phosphoenolpyruvate PDC pyruvate decarboxylase –E. PPP pentose phosphate pathway PYR pyruvate ρ dd,protein degradation/dilution regulation coefficient for a protein ρ dd,Vmax degradation/dilution regulation coefficient for V max ρ h hierarchical regulation coefficient ρ m metabolic regualtion coefficient ρ mRN A,f lux transcriptional regulation coefficient for an enzyme flux ρ mRN A,protein transcriptional regulation coefficient for a protein ρ mRN A,Vmax transcriptional regulation coefficient for V max ρ P T,V max posttranslational regulation coefficient for V max ρ trans,Vmax translational regulation coeffcient for V max ρ trans,protein translational regulation coefficient for a protein R j i response coefficent of the variable or parameter i on the variable j S reaction or pathway substrate SD standard deviation SEM standard error of the mean SC storage carbohydrates –glycogen and trehalose TPI triose-phosphate isomerase –E.C. 5.3.1.1. v enzyme rate v trans rate of translation v deg rate of protein degradation v dil rate of protein dilution due to growth Summary This thesis is concerned with the study of the regulatory processes involved in the adaptation of metabolic systems to environmental and genetic changes. The study of regulation is an endeavor unique to biology. It addresses systems of a complexity that is unparalleled in the inanimate realm. More importantly, these systems are adaptive: living cells modulate their system properties in response to environmental changes. These modulations …