G Protein–Coupled Receptor Signaling Networks from a Systems Perspective

The signal-transduction network of a mammalian cell integrates internal and external cues to initiate adaptive responses. Among the cell-surface receptors are the G protein–coupled receptors (GPCRs), which have remarkable signal-integrating capabilities. Binding of extracellular signals stabilizes intracellular-domain conformations that selectively activate intracellular proteins. Hereby, multiple signaling routes are activated simultaneously to degrees that are signal-combination dependent. Systems-biology studies indicate that signaling networks have emergent processing capabilities that go far beyond those of single proteins. Such networks are spatiotemporally organized and capable of gradual, oscillatory, all-or-none, and subpopulation-generating responses. Protein-protein interactions, generating feedback and feedforward circuitry, are generally required for these spatiotemporal phenomena. Understanding of information processing by signaling networks therefore requires network theories in addition to biochemical and biophysical concepts. Here we review some of the key signaling systems behaviors that have been discovered recurrently across signaling networks. We emphasize the role of GPCRs, so far underappreciated receptors in systems-biology research.

[1]  D. Hall,et al.  Modeling the functional effects of allosteric modulators at pharmacological receptors: an extension of the two-state model of receptor activation. , 2000, Molecular pharmacology.

[2]  Nils Blüthgen,et al.  Mechanisms Generating Ultrasensitivity, Bistability, and Oscillations in Signal Transduction , 2007 .

[3]  B. Hille,et al.  Kinetics of M1 muscarinic receptor and G protein signaling to phospholipase C in living cells , 2010 .

[4]  S. Nuber,et al.  Fluorescence/Bioluminescence Resonance Energy Transfer Techniques to Study G-Protein-Coupled Receptor Activation and Signaling , 2012, Pharmacological Reviews.

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

[6]  L. Pardo,et al.  Ligand-specific regulation of the extracellular surface of a G protein coupled receptor , 2009, Nature.

[7]  A. Szabó,et al.  Role of diffusion in ligand binding to macromolecules and cell-bound receptors. , 1982, Biophysical journal.

[8]  P. Sexton,et al.  Allosteric modulation of G protein-coupled receptors: A pharmacological perspective , 2011, Neuropharmacology.

[9]  Akihiro Kusumi,et al.  Single-molecule imaging revealed dynamic GPCR dimerization. , 2014, Current opinion in cell biology.

[10]  R. Iyengar,et al.  Hormone receptor-mediated stimulation of adenylyl cyclase systems. Nucleotide effects and analysis in terms of a simple two-state model for the basic receptor-affected enzyme. , 1980, The Journal of biological chemistry.

[11]  G. Milligan,et al.  Allosteric modulation of heterodimeric G-protein-coupled receptors. , 2007, Trends in pharmacological sciences.

[12]  I. Nemenman,et al.  Cellular noise and information transmission. , 2014, Current opinion in biotechnology.

[13]  M. Lohse,et al.  Kinetics and mechanism of G protein-coupled receptor activation. , 2014, Current opinion in cell biology.

[14]  Wei Tang,et al.  Coordinate Regulation of G Protein Signaling via Dynamic Interactions of Receptor and GAP , 2008, PLoS Comput. Biol..

[15]  Yuval Hart,et al.  Comparing Apples and Oranges: Fold-Change Detection of Multiple Simultaneous Inputs , 2013, PloS one.

[16]  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.

[17]  Uri Alon,et al.  Dynamics and variability of ERK2 response to EGF in individual living cells. , 2009, Molecular cell.

[18]  Ryan T. Strachan,et al.  Regulation of b 2 -Adrenergic Receptor Function by Conformationally Selective Single-Domain Intrabodies s , 2014 .

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

[20]  R. Lefkowitz,et al.  Differential Kinetic and Spatial Patterns of β-Arrestin and G Protein-mediated ERK Activation by the Angiotensin II Receptor* , 2004, Journal of Biological Chemistry.

[21]  P. Sorger,et al.  Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis , 2009, Nature.

[22]  Carsten Hoffmann,et al.  Sequential Inter- and Intrasubunit Rearrangements During Activation of Dimeric Metabotropic Glutamate Receptor 1 , 2012, Science Signaling.

[23]  P. Lásló,et al.  Multilineage Transcriptional Priming and Determination of Alternate Hematopoietic Cell Fates , 2006, Cell.

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

[25]  A. Oudenaarden,et al.  Cellular Decision Making and Biological Noise: From Microbes to Mammals , 2011, Cell.

[26]  Carsten Peterson,et al.  Transcriptional Dynamics of the Embryonic Stem Cell Switch , 2006, PLoS Comput. Biol..

[27]  Ravi Iyengar,et al.  Robustness of the bistable behavior of a biological signaling feedback loop. , 2001, Chaos.

[28]  F. Bruggeman,et al.  Contributions of cell growth and biochemical reactions to nongenetic variability of cells. , 2014, Biophysical journal.

[29]  I. Nemenman,et al.  Information Transduction Capacity of Noisy Biochemical Signaling Networks , 2011, Science.

[30]  R. Milo,et al.  Variability and memory of protein levels in human cells , 2006, Nature.

[31]  J. Ferrell,et al.  Ultrasensitivity part II: multisite phosphorylation, stoichiometric inhibitors, and positive feedback. , 2014, Trends in biochemical sciences.

[32]  D. Lauffenburger,et al.  Physicochemical modelling of cell signalling pathways , 2006, Nature Cell Biology.

[33]  Sanjay Jain,et al.  Bistability in a model of early B cell receptor activation and its role in tonic signaling and system tunability. , 2013, Molecular bioSystems.

[34]  J. Ferrell,et al.  Ultrasensitivity in the Regulation of Cdc25C by Cdk1. , 2011, Molecular cell.

[35]  Nils Blüthgen,et al.  Noise Management by Molecular Networks , 2009, PLoS Comput. Biol..

[36]  C. Murga,et al.  G protein-coupled receptor kinase 2 negatively regulates chemokine signaling at a level downstream from G protein subunits. , 2005, Molecular biology of the cell.

[37]  Boris N Kholodenko,et al.  MAP kinase cascade signaling and endocytic trafficking: a marriage of convenience? , 2002, Trends in cell biology.

[38]  F. Bruggeman,et al.  The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise , 2015, Molecular biology of the cell.

[39]  J. Ferrell,et al.  Ultrasensitivity part III: cascades, bistable switches, and oscillators. , 2014, Trends in biochemical sciences.

[40]  J. Changeux 50 years of allosteric interactions: the twists and turns of the models , 2013, Nature Reviews Molecular Cell Biology.

[41]  D. Morrison,et al.  MAP kinase pathways. , 2012, Cold Spring Harbor perspectives in biology.

[42]  O. Elemento,et al.  Cancer systems biology: embracing complexity to develop better anticancer therapeutic strategies , 2014, Oncogene.

[43]  Eduardo Sontag,et al.  Fold-change detection and scalar symmetry of sensory input fields , 2010, Proceedings of the National Academy of Sciences.

[44]  Leif Dehmelt,et al.  Spatial organization of intracellular communication: insights from imaging , 2010, Nature Reviews Molecular Cell Biology.

[45]  A. Hoffmann,et al.  The I (cid:1) B –NF-(cid:1) B Signaling Module: Temporal Control and Selective Gene Activation , 2022 .

[46]  A. Shukla Biasing GPCR Signaling from Inside , 2014, Science Signaling.

[47]  R. Mullins,et al.  β-Arrestin–Dependent Endocytosis of Proteinase-Activated Receptor 2 Is Required for Intracellular Targeting of Activated Erk1/2 , 2000, The Journal of cell biology.

[48]  Andreas Radbruch,et al.  Short-term memory in gene induction reveals the regulatory principle behind stochastic IL-4 expression , 2010, Molecular systems biology.

[49]  Robert J. Lefkowitz,et al.  Transduction of Receptor Signals by ß-Arrestins , 2005, Science.

[50]  N. Ip,et al.  Integration of Signals from Receptor Tyrosine Kinases and G Protein-Coupled Receptors , 2002, Neurosignals.

[51]  B. Kholodenko Cell-signalling dynamics in time and space , 2006, Nature Reviews Molecular Cell Biology.

[52]  J. Ferrell,et al.  Ultrasensitivity part I: Michaelian responses and zero-order ultrasensitivity. , 2014, Trends in biochemical sciences.

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

[54]  Xin Lin,et al.  β-Arrestin 2 is required for lysophosphatidic acid-induced NF-κB activation , 2008, Proceedings of the National Academy of Sciences.

[55]  Julie A. Pitcher,et al.  Feedback Inhibition of G Protein-coupled Receptor Kinase 2 (GRK2) Activity by Extracellular Signal-regulated Kinases* , 1999, The Journal of Biological Chemistry.

[56]  Lopamudra Giri,et al.  A G-protein subunit translocation embedded network motif underlies GPCR regulation of calcium oscillations. , 2014, Biophysical journal.

[57]  H. Kitano,et al.  A comprehensive pathway map of epidermal growth factor receptor signaling , 2005, Molecular systems biology.

[58]  Boris N Kholodenko,et al.  Complexity of receptor tyrosine kinase signal processing. , 2013, Cold Spring Harbor perspectives in biology.

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

[60]  E Bornberg-Bauer,et al.  Switching from simple to complex oscillations in calcium signaling. , 2000, Biophysical journal.

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

[62]  Ingo Roeder,et al.  Nanog Variability and Pluripotency Regulation of Embryonic Stem Cells - Insights from a Mathematical Model Analysis , 2010, PloS one.

[63]  H. Shankaran,et al.  Oscillatory dynamics of the extracellular signal-regulated kinase pathway. , 2010, Current opinion in genetics & development.

[64]  R. Lefkowitz,et al.  Beta-arrestins and cell signaling. , 2007, Annual review of physiology.

[65]  B. Palsson,et al.  Towards genome-scale signalling-network reconstructions , 2010, Nature Reviews Genetics.

[66]  J. Paulsson Summing up the noise in gene networks , 2004, Nature.

[67]  Muffy Calder,et al.  The Mammalian MAPK/ERK Pathway Exhibits Properties of a Negative Feedback Amplifier , 2010, Science Signaling.

[68]  J. Benovic,et al.  Pepducin targeting the C-X-C chemokine receptor type 4 acts as a biased agonist favoring activation of the inhibitory G protein , 2013, Proceedings of the National Academy of Sciences.

[69]  H. Hamm,et al.  Heterotrimeric G protein activation by G-protein-coupled receptors , 2008, Nature Reviews Molecular Cell Biology.

[70]  Boris N. Kholodenko,et al.  Signalling ballet in space and time , 2010, Nature Reviews Molecular Cell Biology.

[71]  H. Hamm,et al.  Conformational flexibility and structural dynamics in GPCR-mediated G protein activation: a perspective. , 2013, Journal of molecular biology.

[72]  P. Swain,et al.  Strategies for cellular decision-making , 2009, Molecular systems biology.

[73]  Zachary A. King,et al.  Constraint-based models predict metabolic and associated cellular functions , 2014, Nature Reviews Genetics.

[74]  J. Violin,et al.  Biased ligands at G-protein-coupled receptors: promise and progress. , 2014, Trends in pharmacological sciences.

[75]  F. Bruggeman,et al.  A conformation‐equilibrium model captures ligand–ligand interactions and ligand‐biased signalling by G‐protein coupled receptors , 2014, The FEBS journal.

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

[77]  Eric R. Prossnitz,et al.  Full characterization of GPCR monomer–dimer dynamic equilibrium by single molecule imaging , 2011, The Journal of cell biology.

[78]  T. Kenakin Quantifying biased β-arrestin signaling. , 2014, Handbook of experimental pharmacology.

[79]  K. Venkatesh,et al.  Optical control demonstrates switch-like PIP3 dynamics underlying the initiation of immune cell migration , 2013, Proceedings of the National Academy of Sciences.

[80]  U. Alon,et al.  The incoherent feedforward loop can provide fold-change detection in gene regulation. , 2009, Molecular cell.

[81]  Liang Qiao,et al.  Bistability and Oscillations in the Huang-Ferrell Model of MAPK Signaling , 2007, PLoS Comput. Biol..

[82]  J. Elf,et al.  Fast evaluation of fluctuations in biochemical networks with the linear noise approximation. , 2003, Genome research.

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

[84]  M. Babu,et al.  Molecular signatures of G-protein-coupled receptors , 2013, Nature.

[85]  Thomas C. Rich,et al.  Quantitative Modeling of GRK-Mediated β2AR Regulation , 2010, PLoS Comput. Biol..

[86]  R. Lefkowitz,et al.  β-Arrestins and Cell Signaling , 2007 .

[87]  Nils Blüthgen,et al.  Effects of sequestration on signal transduction cascades , 2006, The FEBS journal.

[88]  S. Ferguson Phosphorylation-independent attenuation of GPCR signalling. , 2007, Trends in pharmacological sciences.

[89]  James E. Ferrell,et al.  A positive-feedback-based bistable ‘memory module’ that governs a cell fate decision , 2007, Nature.

[90]  Z. Goldsmith,et al.  G Protein regulation of MAPK networks , 2007, Oncogene.

[91]  Eric Trinquet,et al.  Structural insights into biased G protein-coupled receptor signaling revealed by fluorescence spectroscopy , 2012, Proceedings of the National Academy of Sciences.

[92]  Nils Blüthgen,et al.  Competing docking interactions can bring about bistability in the MAPK cascade. , 2007, Biophysical journal.

[93]  A. Hoffmann,et al.  The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation. , 2002, Science.

[94]  J. Ferrell,et al.  A positive-feedback-based bistable ‘memory module’ that governs a cell fate decision , 2003, Nature.

[95]  Paolo Sassone-Corsi,et al.  The cyclic AMP pathway. , 2012, Cold Spring Harbor perspectives in biology.

[96]  Peter S. Swain,et al.  Cross-Talk between Signaling Pathways Can Generate Robust Oscillations in Calcium and cAMP , 2009, PloS one.

[97]  Nils Blüthgen,et al.  Strong negative feedback from Erk to Raf confers robustness to MAPK signalling , 2011, Molecular systems biology.

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

[99]  François Fages,et al.  Competing G protein-coupled receptor kinases balance G protein and β-arrestin signaling , 2012, Molecular systems biology.

[100]  D. Lauffenburger,et al.  Receptors: Models for Binding, Trafficking, and Signaling , 1993 .

[101]  Arthur Christopoulos,et al.  Signalling bias in new drug discovery: detection, quantification and therapeutic impact , 2012, Nature Reviews Drug Discovery.

[102]  T. Rink,et al.  Calcium oscillations , 1989, Nature.

[103]  Marco Beato,et al.  Optical measurement of mGluR1 conformational changes reveals fast activation, slow deactivation, and sensitization , 2009, Proceedings of the National Academy of Sciences.

[104]  Haluk Resat,et al.  Rapid and sustained nuclear–cytoplasmic ERK oscillations induced by epidermal growth factor , 2009, Molecular systems biology.

[105]  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.

[106]  J. Black,et al.  Operational models of pharmacological agonism , 1983, Proceedings of the Royal Society of London. Series B. Biological Sciences.

[107]  Bertram Klinger,et al.  Supplementary Materials for : Network quantification of EGFR signaling unveils potential for targeted combination therapy , 2022 .

[108]  A. Oudenaarden,et al.  Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences , 2008, Cell.

[109]  Kunhong Xiao,et al.  Multiple ligand-specific conformations of the β2-adrenergic receptor. , 2011, Nature chemical biology.

[110]  Gregory I. Mashanov,et al.  Formation and dissociation of M1 muscarinic receptor dimers seen by total internal reflection fluorescence imaging of single molecules , 2010, Proceedings of the National Academy of Sciences.

[111]  Tamara L. Kinzer-Ursem,et al.  Both Ligand- and Cell-Specific Parameters Control Ligand Agonism in a Kinetic Model of G Protein–Coupled Receptor Signaling , 2007, PLoS Comput. Biol..

[112]  Lewis C. Cantley,et al.  Cell-to-Cell Variability in PI3K Protein Level Regulates PI3K-AKT Pathway Activity in Cell Populations , 2011, Current Biology.

[113]  R. Lefkowitz,et al.  A ternary complex model explains the agonist-specific binding properties of the adenylate cyclase-coupled beta-adrenergic receptor. , 1980, The Journal of biological chemistry.

[114]  Annie Z. Tremp Malaria: Plasmodium develops in lymph nodes , 2006, Nature Reviews Microbiology.