Robustness in Glyoxylate Bypass Regulation

The glyoxylate bypass allows Escherichia coli to grow on carbon sources with only two carbons by bypassing the loss of carbons as CO2 in the tricarboxylic acid cycle. The flux toward this bypass is regulated by the phosphorylation of the enzyme isocitrate dehydrogenase (IDH) by a bifunctional kinase–phosphatase called IDHKP. In this system, IDH activity has been found to be remarkably robust with respect to wide variations in the total IDH protein concentration. Here, we examine possible mechanisms to explain this robustness. Explanations in which IDHKP works simultaneously as a first-order kinase and as a zero-order phosphatase with a single IDH binding site are found to be inconsistent with robustness. Instead, we suggest a robust mechanism where both substrates bind the bifunctional enzyme to form a ternary complex.

[1]  D. Koshland,et al.  Compensatory phosphorylation of isocitrate dehydrogenase. A mechanism for adaptation to the intracellular environment. , 1985, The Journal of biological chemistry.

[2]  G. Nimmo,et al.  The regulatory properties of isocitrate dehydrogenase kinase and isocitrate dehydrogenase phosphatase from Escherichia coli ML308 and the roles of these activities in the control of isocitrate dehydrogenase. , 1984, European journal of biochemistry.

[3]  Uri Alon,et al.  Sensitivity and Robustness in Chemical Reaction Networks , 2009, SIAM J. Appl. Math..

[4]  J. Doyle,et al.  Robust perfect adaptation in bacterial chemotaxis through integral feedback control. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[5]  U. Alon,et al.  Robustness in bacterial chemotaxis , 2022 .

[6]  Mark Goulian,et al.  Continuous Control in Bacterial Regulatory Circuits , 2004, Journal of bacteriology.

[7]  P. Bennett,et al.  Regulation of isocitrate dehydrogenase activity in Escherichia coli on adaptation to acetate. , 1971, Journal of general microbiology.

[8]  Mark Goulian,et al.  High stimulus unmasks positive feedback in an autoregulated bacterial signaling circuit , 2008, Proceedings of the National Academy of Sciences.

[9]  A. Levchenko,et al.  Models of eukaryotic gradient sensing: application to chemotaxis of amoebae and neutrophils. , 2001, Biophysical journal.

[10]  Katherine C. Chen,et al.  Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. , 2003, Current opinion in cell biology.

[11]  N. Barkai,et al.  Scaling of the BMP activation gradient in Xenopus embryos , 2008, Nature.

[12]  D. Laporte,et al.  Isocitrate dehydrogenase kinase/phosphatase. , 1989, Biochimie.

[13]  D. Koshland,et al.  A protein with kinase and phosphatase activities involved in regulation of tricarboxylic acid cycle , 1982, Nature.

[14]  R. Chollet,et al.  Regulation of pyruvate, orthophosphate dikinase by ADP-/Pi-dependent reversible phosphorylation in C3 and C4 plants , 2003 .

[15]  N. Barkai,et al.  Variability and robustness in biomolecular systems. , 2007, Molecular cell.

[16]  L. Segel,et al.  On the validity of the steady state assumption of enzyme kinetics. , 1988, Bulletin of mathematical biology.

[17]  H. Reeves,et al.  Phosphorylation of Isocitrate dehydrogenase of Escherichia coli. , 1979, Science.

[18]  M. Goulian,et al.  Robustness and the cycle of phosphorylation and dephosphorylation in a two-component regulatory system , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[19]  Naama Barkai,et al.  Self-enhanced ligand degradation underlies robustness of morphogen gradients. , 2003, Developmental cell.

[20]  D E Koshland,et al.  The branch point effect. Ultrasensitivity and subsensitivity to metabolic control. , 1984, The Journal of biological chemistry.

[21]  H. G. Nimmo,et al.  Isolation of active and inactive forms of isocitrate dehydrogenase from Escherichia coli ML 308. , 1984, European journal of biochemistry.

[22]  D. Koshland,et al.  Amplification and adaptation in regulatory and sensory systems. , 1982, Science.

[23]  Andrea Ciliberto,et al.  Antagonism and bistability in protein interaction networks. , 2008, Journal of theoretical biology.

[24]  D. Koshland,et al.  An amplified sensitivity arising from covalent modification in biological systems. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[25]  Stephen P. Miller,et al.  Isocitrate Dehydrogenase Kinase/Phosphatase , 1996, The Journal of Biological Chemistry.

[26]  M. Savageau,et al.  Parameter Sensitivity as a Criterion for Evaluating and Comparing the Performance of Biochemical Systems , 1971, Nature.

[27]  S. Leibler,et al.  Robustness in simple biochemical networks , 1997, Nature.

[28]  D. Koshland,et al.  Ultrasensitivity in biochemical systems controlled by covalent modification. Interplay between zero-order and multistep effects. , 1984, The Journal of biological chemistry.

[29]  D. Fell Understanding the Control of Metabolism , 1996 .

[30]  D. Koshland,et al.  Phosphorylation of isocitrate dehydrogenase as a demonstration of enhanced sensitivity in covalent regulation , 1983, Nature.

[31]  L. Segel,et al.  Extending the quasi-steady state approximation by changing variables. , 1996, Bulletin of mathematical biology.

[32]  Ned S. Wingreen,et al.  Precise adaptation in bacterial chemotaxis through “assistance neighborhoods” , 2006, Proceedings of the National Academy of Sciences.

[33]  N. Barkai,et al.  Robustness of the BMP morphogen gradient in Drosophila embryonic patterning , 2022 .

[34]  Jörg Raisch,et al.  Subnetwork analysis reveals dynamic features of complex (bio)chemical networks , 2007, Proceedings of the National Academy of Sciences.

[35]  L. Hood,et al.  Reverse Engineering of Biological Complexity , 2007 .

[36]  Uri Alon,et al.  Input–output robustness in simple bacterial signaling systems , 2007, Proceedings of the National Academy of Sciences.