Effects of sequestration on signal transduction cascades

The building blocks of most signal transduction pathways are pairs of enzymes, such as kinases and phosphatases, that control the activity of protein targets by covalent modification. It has previously been shown [Goldbeter A & Koshland DE (1981) Proc Natl Acad Sci USA78, 6840–6844] that these systems can be highly sensitive to changes in stimuli if their catalysing enzymes are saturated with their target protein substrates. This mechanism, termed zero‐order ultrasensitivity, may set thresholds that filter out subthreshold stimuli. Experimental data on protein abundance suggest that the enzymes and their target proteins are present in comparable concentrations. Under these conditions a large fraction of the target protein may be sequestrated by the enzymes. This causes a reduction in ultrasensitivity so that the proposed mechanism is unlikely to account for ultrasensitivity under the conditions present in most in vivo signalling cascades. Furthermore, we show that sequestration changes the dynamics of a covalent modification cycle and may account for signal termination and a sign‐sensitive delay. Finally, we analyse the effect of sequestration on the dynamics of a complex signal transduction cascade: the mitogen‐activated protein kinase (MAPK) cascade with negative feedback. We show that sequestration limits ultrasensitivity in this cascade and may thereby abolish the potential for oscillations induced by negative feedback.

[1]  James E. Ferrell,et al.  The JNK Cascade as a Biochemical Switch in Mammalian Cells Ultrasensitive and All-or-None Responses , 2003, Current Biology.

[2]  Jan Lankelma,et al.  Principles behind the multifarious control of signal transduction , 2004, The FEBS journal.

[3]  S. Mangan,et al.  The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. , 2003, Journal of molecular biology.

[4]  B N Kholodenko,et al.  Spatial gradients of cellular phospho‐proteins , 1999, FEBS letters.

[5]  E. Wimmer,et al.  MAP Kinase Phosphatase As a Locus of Flexibility in a Mitogen-Activated Protein Kinase Signaling Network , 2022 .

[6]  Thomas Höfer,et al.  Allosteric regulation of the transcription factor NFAT1 by multiple phosphorylation sites: a mathematical analysis. , 2003, Journal of molecular biology.

[7]  H. Sauro,et al.  Quantitative analysis of signaling networks. , 2004, Progress in biophysics and molecular biology.

[8]  A. Cornish-Bowden,et al.  Characteristics necessary for an interconvertible enzyme cascade to generate a highly sensitive response to an effector. , 1989, The Biochemical journal.

[9]  B. Wright,et al.  Cellular concentrations of enzymes and their substrates. , 1990, Journal of theoretical biology.

[10]  Tobias Meyer,et al.  An ultrasensitive Ca2+/calmodulin-dependent protein kinase II-protein phosphatase 1 switch facilitates specificity in postsynaptic calcium signaling , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[11]  C. Marshall,et al.  Specificity of receptor tyrosine kinase signaling: Transient versus sustained extracellular signal-regulated kinase activation , 1995, Cell.

[12]  Raymond J. Deshaies,et al.  Multisite Phosphorylation and the Countdown to S Phase , 2001, Cell.

[13]  Tony Pawson,et al.  Multisite phosphorylation of a CDK inhibitor sets a threshold for the onset of DNA replication , 2001, Nature.

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

[15]  J. Tavernier,et al.  Down-modulation of Type 1 Interferon Responses by Receptor Cross-competition for a Shared Jak Kinase* , 2001, The Journal of Biological Chemistry.

[16]  Prahlad T. Ram,et al.  MAP Kinase Phosphatase As a Locus of Flexibility in a Mitogen-Activated Protein Kinase Signaling Network , 2002, Science.

[17]  J. Ferrell Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs. , 1996, Trends in biochemical sciences.

[18]  James R. Johnson,et al.  Oscillations in NF-κB Signaling Control the Dynamics of Gene Expression , 2004, Science.

[19]  Chi-Ying F. Huang,et al.  Ultrasensitivity in the mitogen-activated protein kinase cascade. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[20]  D. Fell Metabolic control analysis: a survey of its theoretical and experimental development. , 1992, The Biochemical journal.

[21]  H. Westerhoff,et al.  Product dependence and bifunctionality compromise the ultrasensitivity of signal transduction cascades , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Nils Blüthgen,et al.  Ultrasensitization: Switch-Like Regulation of Cellular Signaling by Transcriptional Induction , 2005, PLoS Comput. Biol..

[23]  J. Bishop,et al.  Zero-order ultrasensitivity in the regulation of glycogen phosphorylase. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[24]  B. Kholodenko,et al.  Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades , 2004, The Journal of cell biology.

[25]  Y. Goldberg,et al.  Protein phosphatase 2A: who shall regulate the regulator? , 1999, Biochemical pharmacology.

[26]  J E Ferrell,et al.  The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. , 1998, Science.

[27]  H. Kacser,et al.  Metabolic control analysis of moiety-conserved cycles. , 1986, European journal of biochemistry.

[28]  B. Kholodenko,et al.  Modular response analysis of cellular regulatory networks. , 2002, Journal of theoretical biology.

[29]  B. Kholodenko,et al.  Quantification of information transfer via cellular signal transduction pathways , 1997, FEBS letters.

[30]  W. Kolch,et al.  Suppression of Raf-1 kinase activity and MAP kinase signalling by RKIP , 1999, Nature.

[31]  D A Fell,et al.  Covalent modification and metabolic control analysis. Modification to the theorems and their application to metabolic systems containing covalently modifiable enzymes. , 1990, European journal of biochemistry.

[32]  R Heinrich,et al.  A linear steady-state treatment of enzymatic chains. Critique of the crossover theorem and a general procedure to identify interaction sites with an effector. , 1974, European journal of biochemistry.

[33]  H. Westerhoff,et al.  Control theory of regulatory cascades. , 1991, Journal of theoretical biology.

[34]  H. Kacser,et al.  The control of flux. , 1995, Biochemical Society transactions.

[35]  A Goldbeter,et al.  A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[36]  B N Kholodenko,et al.  Why do protein kinase cascades have more than one level? , 1997, Trends in biochemical sciences.

[37]  D. Fell,et al.  Metabolic control analysis. The effects of high enzyme concentrations. , 1990, European journal of biochemistry.

[38]  H. Sauro Moiety-conserved cycles and metabolic control analysis: problems in sequestration and metabolic channelling. , 1994, Bio Systems.

[39]  B. Kholodenko,et al.  Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. , 2000, European journal of biochemistry.

[40]  Bard Ermentrout,et al.  Simulating, analyzing, and animating dynamical systems - a guide to XPPAUT for researchers and students , 2002, Software, environments, tools.

[41]  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.

[42]  D B Kell,et al.  Oscillations in NF-kappaB signaling control the dynamics of gene expression. , 2004, Science.

[43]  E. Gilles,et al.  Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors , 2002, Nature Biotechnology.