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Decision Making in Cells

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Systems Biology for Signaling Networks

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Abstract

Cellular signal transduction networks are structured in a highly complex manner that strongly suggests they have functions beyond simply passing information from the outside of the cell to the interior. Recent evidence from mathematical and systems approaches to the study of these networks indicates that these complex networks might actually process external signals in a nontrivial way, endowing the cell emergent-decision making ability. In this chapter, we will first analyze the concepts of information, information processing, and decision making from a quantitative perspective. We will then apply that analysis to the structures and functions of intracellular signal transduction networks and see that they have many features that are consistent with nontrivial decision-making systems.

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References

  • AFCS (2009) Alliance for Cellular Signaling. http://www.afcs.org. Accessed August 17 2009

  • Albert R, Chiu Y, Othmer HG (2004) Dynamic receptor team formation can explain the high signal transduction gain in Escherichia coli. Biophys J 86:2650–2659

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Alon U, Surette MG, Barkai N et al (1999) Robustness in bacterial chemotaxis. Nature 397: 168–171

    Article  CAS  PubMed  Google Scholar 

  • Angeli D, Ferrell JEJ, Sontag ED (2004) Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems. Proc Natl Acad Sci USA 101:1822–1827

    Article  CAS  PubMed  Google Scholar 

  • Bagley RJ, Glass L (1996) Counting and classifying attractors in high dimensional dynamical systems. J Theor Biol 183:269–284

    Article  CAS  PubMed  Google Scholar 

  • Bagowski CP, Ferrell JEJ (2001) Bistability in the JNK cascade. Curr Biol: CB 11:1176–82

    Article  CAS  PubMed  Google Scholar 

  • Bagowski CP, Besser J, Frey CR et al (2003) The JNK cascade as a biochemical switch in mammalian cells: ultrasensitive and all-or-none responses. Curr Biol CB 13:315–20

    Article  CAS  Google Scholar 

  • Barak R, Eisenbach M (1992) Correlation between phosphorylation of the chemotaxis protein CheY and its activity at the flagellar motor. Biochemistry 31:1821–1826

    Article  CAS  PubMed  Google Scholar 

  • Barkai N, Leibler S (1997) Robustness in simple biochemical networks. Nature 387:913–917

    Article  CAS  PubMed  Google Scholar 

  • Bhalla US, Iyengar R (1999) Emergent properties of networks of biological signaling pathways. Science 283:381–387

    Article  CAS  PubMed  Google Scholar 

  • Bhalla US, Ram PT, Iyengar R (2002) MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science 297:1018–1023

    Article  CAS  PubMed  Google Scholar 

  • Blair DF (1995) How bacteria sense and swim. Ann Rev Microbiol 49:489–522

    Article  CAS  Google Scholar 

  • Bourret RB, Stock AM (2002) Molecular information processing: lessons from bacterial chemotaxis. J Biol Chem 277:9625–9628

    Article  CAS  PubMed  Google Scholar 

  • Bourret RB, Borkovich KA, Simon MI (1991) Signal transduction pathways involving protein phosphorylation in prokaryotes. Ann Rev Biochem 60:401–441

    Article  CAS  PubMed  Google Scholar 

  • Brandman O, Meyer T (2008) Feedback loops shape cellular signals in space and time. Science 322:390–395

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Bray D (1990) Intracellular signalling as a parallel distributed process. J Theor Biol 143:215–231

    Article  CAS  PubMed  Google Scholar 

  • Bray D (1995) Protein molecules as computational elements in living cells. Nature 376:307–312

    Article  CAS  PubMed  Google Scholar 

  • Bray D (2002) Bacterial chemotaxis and the question of gain. Proc Natl Acad Sci USA 99:7–9

    Article  CAS  PubMed  Google Scholar 

  • Bray D (2003) Molecular networks: the top-down view. Science 301:1864–1865

    Article  CAS  PubMed  Google Scholar 

  • Bren A, Eisenbach M (2000) How signals are heard during bacterial chemotaxis: protein-protein interactions in sensory signal propagation. J Bacteriol 182:6865–6873

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Brondello JM, Pouysségur J, McKenzie FR (1999) Reduced MAP kinase phosphatase-1 degradation after p42/p44MAPK-dependent phosphorylation. Science 286:2514–2517

    Article  CAS  PubMed  Google Scholar 

  • Choi H, Han S, Yokota H et al (2007) Coupled positive feedbacks provoke slow induction plus fast switching in apoptosis. FEBS Lett 581:2684–2690

    Article  CAS  PubMed  Google Scholar 

  • Cinquin O, Demongeot J (2002) Roles of positive and negative feedback in biological systems. C R Biol 325:1085–1095

    Article  PubMed  Google Scholar 

  • Cotton M, Claing A (2009) G protein-coupled receptors stimulation and the control of cell migration. Cell Signal 21:1045–1053

    Article  CAS  PubMed  Google Scholar 

  • Covert M (2009) NetworkAnalyzer. http://covertlab.stanford.edu/projects/NetworkAnalyzer/bin/. Accessed August 17 2009

  • Crutchfield J, Young K (1989) Inferring statistical complexity. Phys Rev Lett 63:105–108

    Article  PubMed  Google Scholar 

  • Derrida B, Stauffer D (1986) Phase transitions in two-dimensional Kauffman Cellular Automata. Europhys Lett 2:739–745

    Article  Google Scholar 

  • Dhanasekaran N, Premkumar Reddy E (1998) Signaling by dual specificity kinases. Oncogene 17:1447–1455

    Article  CAS  PubMed  Google Scholar 

  • Feret J, Danos V, Krivine J et al (2009) Internal coarse-graining of molecular systems. Proc Natl Acad Sci USA 106:6453–6458

    Article  CAS  PubMed  Google Scholar 

  • Ferrell JEJ (1996) Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs. Trends Biochem Sci 21:460–466

    Article  CAS  PubMed  Google Scholar 

  • Ferrell JEJ (2002) Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. Curr Opin Cell Biol 14:140–148

    Article  CAS  PubMed  Google Scholar 

  • Ferrell JEJ, Machleder EM (1998) The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science 280:895–898

    Article  CAS  PubMed  Google Scholar 

  • Fisher AG (2002) Cellular identity and lineage choice. Nat Rev Immunol 2:977–82

    Article  CAS  PubMed  Google Scholar 

  • Flyvbjerg H (1988) An order parameter for networks of automata. J Phys A 21:L955–L960

    Article  Google Scholar 

  • Fukuda K, Takayasu H, Takayasu M (2000) Origin of critical behavior in ethernet Traffic!!. Phys A 287:289–301

    Article  Google Scholar 

  • Garrington TP, Johnson GL (1999) Organization and regulation of mitogen-activated protein kinase signaling pathways. Curr Opin Cell Biol 11:211–218

    Article  CAS  PubMed  Google Scholar 

  • Haneda M, Sugimoto T, Kikkawa R (1999) Mitogen-activated protein kinase phosphatase: a negative regulator of the mitogen-activated protein kinase cascade. Eur J Pharmacol 365:1–7

    Article  CAS  PubMed  Google Scholar 

  • Haykin, S. (1999) Neural networks, a comprehensive foundation. Englewood Cliffs, NJ

    Google Scholar 

  • Hazelbauer GL, Falke JJ, Parkinson JS (2008) Bacterial chemoreceptors: high-performance signaling in networked arrays. Trends Biochem Sci 33:9–19

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hehlgans S, Haase M, Cordes, N (2007) Signalling via integrins: implications for cell survival and anticancer strategies. Biochim Et Biophys acta 1775:163–80

    CAS  Google Scholar 

  • Helikar T, Konvalina J, Heidel J et al (2008) Emergent decision-making in biological signal transduction networks. Proc Natl Acad Sci USA 105:1913–1918

    Article  CAS  PubMed  Google Scholar 

  • Henson ES, Gibson SB (2006) Surviving cell death through epidermal growth factor (EGF) signal transduction pathways: implications for cancer therapy. Cell Signal 18:2089–2097

    Article  CAS  PubMed  Google Scholar 

  • Hess JF, Oosawa K, Kaplan N et al (1988) Phosphorylation of three proteins in the signaling pathway of bacterial chemotaxis. Cell 53:79–87

    Article  CAS  PubMed  Google Scholar 

  • Hogg T, Huberman B (1986) Order, complexity and disorder. Mondes Devel 54–55:175–184

    Google Scholar 

  • Huang CY, Ferrell JEJ (1996) Ultrasensitivity in the mitogen-activated protein kinase cascade. Proc Natl Acad Sci USA 93:10078–10083

    Article  CAS  PubMed  Google Scholar 

  • Huang S (2001) Genomics, complexity and drug discovery: insights from Boolean network models of cellular regulation. Pharmacogenomics 2:203–22

    Article  CAS  PubMed  Google Scholar 

  • Huveneers S, Danen EHJ (2009) Adhesion signaling – crosstalk between integrins, Src and Rho. J Cell Sci 122:1059–1069

    Article  CAS  PubMed  Google Scholar 

  • Juliano RL (1994) Integrin signals and tumor growth control. Princess Takamatsu Symp 24:118–24

    CAS  PubMed  Google Scholar 

  • Juliano RL (2002) Signal transduction by cell adhesion receptors and the cytoskeleton: functions of integrins, cadherins, selectins, and immunoglobulin-superfamily members. Ann Rev Pharmacol Toxicol 42:283–323

    Article  CAS  Google Scholar 

  • Kauffman S (1969) Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol 22:437–467

    Article  CAS  PubMed  Google Scholar 

  • Kauffman, S. (1993) The origins of order. Oxford University Press, Oxford

    Google Scholar 

  • Kholodenko BN (2000) Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. Eur J Biochem/FEBS 267:1583–1588

    Article  CAS  Google Scholar 

  • Kirouac DC, Madlambayan GJ, Yu M, et al (2009) Cell-cell interaction networks regulate blood stem and progenitor cell fate. Mol Syst Biol 5:293

    Article  PubMed Central  PubMed  Google Scholar 

  • Konvalina J, Konfisakhar I, Heidel J et al (2006) Combinatorial fractal geometry with a biological application. Fractals 14:133–142

    Article  Google Scholar 

  • Kyriakis JM (1999) Making the connection: coupling of stress-activated ERK/MAPK (extracellular-signal-regulated kinase/mitogen-activated protein kinase) core signalling modules to extracellular stimuli and biological responses. Biochem Soc Symp 64:29–48

    CAS  PubMed  Google Scholar 

  • Langton C (1990) Computation at the edge of chaos. Phys D. Nonlinear Phenomena 42:12–37

    Article  Google Scholar 

  • Legewie S, Blüthgen N, Herzel H (2006) Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability. PLoS Comput Biol 2:e120

    Article  PubMed Central  PubMed  Google Scholar 

  • Levchenko A (2003) Dynamical and integrative cell signaling: challenges for the new biology. Biotechnol Bioeng 84:773–82

    Article  CAS  PubMed  Google Scholar 

  • Lin LL, Wartmann M, Lin AY et al (1993) cPLA2 is phosphorylated and activated by MAP kinase. Cell 72:269–278

    Article  CAS  PubMed  Google Scholar 

  • Luque B, Ferrera A (2000) Measuring mutual information in random boolean networks. Complex Syst 12:241–252

    Google Scholar 

  • Luque B, Solé R (2000) Lyapunov exponents in random boolean networks. Physica A 284:33–45

    Article  Google Scholar 

  • Lux T, Marchesi M (1999) Scaling and criticality in a stochastic multi-agent model of a financial market. Nature 397:498–500

    Article  CAS  Google Scholar 

  • Ma’ayan A, Jenkins SL, Neves S et al (2005) Formation of regulatory patterns during signal propagation in a Mammalian cellular network. Science 309:1078–1083

    Article  PubMed Central  PubMed  Google Scholar 

  • Mai Z, Liu H (2009) Boolean network-based analysis of the apoptosis network: Irreversible apoptosis and stable surviving. J Theor Biol 259:760–769

    Google Scholar 

  • Martin KH, Slack JK, Boerner SA et al (2002) Integrin connections map: to infinity and beyond. Science 296:1652–1653

    Article  CAS  PubMed  Google Scholar 

  • McCubrey JA, Steelman LS, Chappell WH, et al (2007) Roles of the Raf/MEK/ERK pathway in cell growth, malignant transformation and drug resistance. Biochimica Et Biophysica Acta 1773:1263–84

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Mitchell M, Hraber P, Crutchfield J (1993) Revisiting the edge of chaos: evolving cellular automata to perform computations. Complex Syst 7:89–130

    Google Scholar 

  • Mueller PR, Coleman TR, Dunphy WG (1995) Cell cycle regulation of a Xenopus Wee1-like kinase. Mol Biol Cell 6:119–134

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Mueller PR, Coleman TR, Kumagai A et al (1995) Myt1: a membrane-associated inhibitory kinase that phosphorylates Cdc2 on both threonine-14 and tyrosine-15. Science 270:86–90

    Article  CAS  PubMed  Google Scholar 

  • Muppidi JR, Tschopp J, Siegel RM (2004) Life and death decisions: secondary complexes and lipid rafts in TNF receptor family signal transduction. Immunity 21:461–465

    Article  CAS  PubMed  Google Scholar 

  • Nemenoff RA, Winitz S, Qian NX et al (1993) Phosphorylation and activation of a high molecular weight form of phospholipase A2 by p42 microtubule-associated protein 2 kinase and protein kinase C. J Biol Chem 268:1960–1964

    CAS  PubMed  Google Scholar 

  • Nishizuka Y (1992) Intracellular signaling by hydrolysis of phospholipids and activation of protein kinase C. Science 258:607–614

    Article  CAS  PubMed  Google Scholar 

  • NTCNP (2008) National technology centers for networks and pathways. http://ntcnp.org/about.html. Accessed August 17 2009

  • Packard N (1988). Adaptation toward the edge of chaos. In: Shlesinger MF (ed) Dynamic patterns in complex systems. World Scientific Pub Co Inc, pp 293–301, Singapore

    Google Scholar 

  • Perens B (2009) The emerging economic paradigm of open source. http://perens.com/Articles/Economic.html. Accessed August 17 2009

  • Persidis A (1998) Signal transduction as a drug-discovery platform. Nat Biotechnol 16:1082–3

    Article  CAS  PubMed  Google Scholar 

  • Rao CV, Kirby JR, Arkin AP (2004) Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis. PLoS Biol 2:E49

    Article  PubMed Central  PubMed  Google Scholar 

  • Rosales C, O’Brien V, Kornberg L, et al (1995) Signal transduction by cell adhesion receptors. Biochim Et Biophys Acta 1242:77–98

    Google Scholar 

  • Ruths DA, Nakhleh L, Iyengar MS et al (2006) Hypothesis generation in signaling networks. J comput biol 13;1546–57

    Article  CAS  PubMed  Google Scholar 

  • SaezRodriguez J, Simeoni L, Lindquist J et al (2007) A logical model provides insights into T cell receptor signaling. PloS Comput Biol 3:e163

    Article  Google Scholar 

  • Schamel WW, Dick TP (1996) Signal transduction: specificity of growth factors explained by parallel distributed processing. Med Hypotheses 47:249–55

    Article  CAS  PubMed  Google Scholar 

  • Schneider E (2009) Developers programming speed? Check. Time to Fix Bugs? Not So Fast. http://advice.cio.com/esther_schindler/enterprise_developers_programming_speed_check_time_to_fix_bugs_not_so_much. Accessed August 17 2009

  • Shannon C (1948) The mathematical theory of communication. Bell Syst Techn J 27:379–423

    Article  Google Scholar 

  • Shinomura T, Asaoka Y, Oka M et al (1991) Synergistic action of diacylglycerol and unsaturated fatty acid for protein kinase C activation: its possible implications. Proc Natl Acad Sci USA 88:5149–5153

    Article  CAS  PubMed  Google Scholar 

  • Sible JC (2003) Cell biology: thanks for the memory. Nature 426:392–393

    Google Scholar 

  • STKE (2008) Signal transduction knowledge environment. http://stke.sciencemag.org. Accessed August 17 2009

  • Stock JB, Levit MN, Wolanin PM (2002) Information processing in bacterial chemotaxis. Sci STKE 2002:PE25

    Google Scholar 

  • Sun H, Charles CH, Lau LF et al (1993) MKP-1 (3CH134), an immediate early gene product, is a dual specificity phosphatase that dephosphorylates MAP kinase in vivo. Cell 75:487–493

    Article  CAS  PubMed  Google Scholar 

  • Tsai TY, Choi YS, Ma W et al (2008) Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Science 321:126–129

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Tyson JJ, Chen KC, Novak B (2003) Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol 15:221–231

    Article  CAS  PubMed  Google Scholar 

  • Weng G, Bhalla US, Iyengar R (1999) Complexity in biological signaling systems. Science 284:92–96

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Wentian L (1991) On the relationship between complexity and entropy for Markov chains and regular languages. Complex Syst 5:381–399

    Google Scholar 

  • Wolfram, S. (1986) Theory and application of cellular automata. World Scientific Pub Co Inc, Singapore

    Google Scholar 

  • Xiong W, Ferrell JEJ (2003) A positive-feedback-based bistable ‘memory module’ that governs a cell fate decision. Nature 426:460–465

    Article  CAS  PubMed  Google Scholar 

  • Yi TM, Huang Y, Simon MI et al (2000) Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proc Natl Acad Sci USA 97:4649–4653

    Article  CAS  PubMed  Google Scholar 

  • Zonia L, Bray D (2009) Swimming patterns and dynamics of simulated Escherichia coli bacteria. J Royal Soc, Interf/Royal Soc 6:1035–1046

    Google Scholar 

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Authors and Affiliations

  1. Department of Pathology and Microbiology, University of Nebraska Medical Center, 983135 Nebraska Medical Center, Omaha, NE, 68198, USA

    Tomáš Helikar

  2. Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, 985805 Nebraska Medical Center, Omaha, NE, 68198, USA

    Naomi Kochi

  3. Department of Mathematics, University of Nebraska, 6001 Dodge Street, Omaha, NE, 68182, USA

    John Konvalina & Jim A. Rogers

Authors
  1. Tomáš Helikar
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  2. Naomi Kochi
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  3. John Konvalina
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  4. Jim A. Rogers
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Corresponding author

Correspondence to Jim A. Rogers .

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Editors and Affiliations

  1. College of Natural Science, Dept. Biological Science, Department of Molecular Science and Tech, Suwon, 442-749, Korea, Republic of (South Korea)

    Sangdun Choi

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Helikar, T., Kochi, N., Konvalina, J., Rogers, J.A. (2010). Decision Making in Cells. In: Choi, S. (eds) Systems Biology for Signaling Networks. Systems Biology. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-5797-9_12

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