Utilization of extracellular information before ligand-receptor binding reaches equilibrium expands and shifts the input dynamic range

Significance Many cell decisions depend on precise measurements of external ligands reversibly bound to receptors. Yeast cells orient in gradients of sex pheromone detecting differences in the amount of ligand-receptor complex. However, yeast can orient in gradients with nearly all receptors occupied. We describe a general systems-level mechanism, pre-equilibrium sensing and signaling (PRESS), which overcomes this saturation limit by shifting and expanding the input dynamic range to which cells can respond. PRESS requires that events downstream of the receptor be transient and faster than the time required for the receptor to reach equilibrium binding. Experiments and simulations show that PRESS operates in yeast and may help cells orient in gradients. Many ligand-receptor interactions are slow, suggesting that PRESS is widespread throughout eukaryotes. Cell signaling systems sense and respond to ligands that bind cell surface receptors. These systems often respond to changes in the concentration of extracellular ligand more rapidly than the ligand equilibrates with its receptor. We demonstrate, by modeling and experiment, a general “systems level” mechanism cells use to take advantage of the information present in the early signal, before receptor binding reaches a new steady state. This mechanism, pre-equilibrium sensing and signaling (PRESS), operates in signaling systems in which the kinetics of ligand-receptor binding are slower than the downstream signaling steps, and it typically involves transient activation of a downstream step. In the systems where it operates, PRESS expands and shifts the input dynamic range, allowing cells to make different responses to ligand concentrations so high as to be otherwise indistinguishable. Specifically, we show that PRESS applies to the yeast directional polarization in response to pheromone gradients. Consideration of preexisting kinetic data for ligand-receptor interactions suggests that PRESS operates in many cell signaling systems throughout biology. The same mechanism may also operate at other levels in signaling systems in which a slow activation step couples to a faster downstream step.

[1]  L. Lim,et al.  Single-Molecule Analysis of Chemotactic Signaling in Dictyostelium Cells , 2001 .

[2]  W. Marasco,et al.  Formyl peptide chemotaxis receptors on the rat neutrophil: Experimental evidence for negative cooperativity , 1985, Journal of cellular biochemistry.

[3]  Z Bajzer,et al.  Binding, internalization, and intracellular processing of proteins interacting with recycling receptors. A kinetic analysis. , 1989, The Journal of biological chemistry.

[4]  Chuan-Hsiang Huang,et al.  Eukaryotic chemotaxis: a network of signaling pathways controls motility, directional sensing, and polarity. , 2010, Annual review of biophysics.

[5]  S. T. Buckland,et al.  An Introduction to the Bootstrap. , 1994 .

[6]  R. Nuzzo,et al.  A method for filling complex polymeric microfluidic devices and arrays. , 2001, Analytical chemistry.

[7]  L. Hartwell,et al.  The C-terminus of the S. cerevisiae α-pheromone receptor mediates an adaptive response to pheromone , 1988, Cell.

[8]  Brian D. Slaughter,et al.  Symmetry breaking in the life cycle of the budding yeast. , 2009, Cold Spring Harbor perspectives in biology.

[9]  Adam C. Martin,et al.  Spatial dynamics of receptor-mediated endocytic trafficking in budding yeast revealed by using fluorescent alpha-factor derivatives. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[10]  J. Segall,et al.  Polarization of yeast cells in spatial gradients of alpha mating factor. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[11]  A. Nern,et al.  A GTP-exchange factor required for cell orientation , 1998, Nature.

[12]  Robert Tibshirani,et al.  An Introduction to the Bootstrap CHAPMAN & HALL/CRC , 1993 .

[13]  C. Pesce,et al.  Regulated cell-to-cell variation in a cell-fate decision system , 2005, Nature.

[14]  R. Yu,et al.  Single-cell quantification of molecules and rates using open-source microscope-based cytometry , 2007, Nature Methods.

[15]  R. Yu,et al.  Fus3 generates negative feedback that improves information transmission in yeast pheromone response , 2008, Nature.

[16]  E. Horwitz,et al.  Kinetic identification of a two-state glucagon receptor system in isolated hepatocytes. Interconversion of homogeneous receptors. , 1985, The Journal of biological chemistry.

[17]  Leland H. Hartwell,et al.  Courtship in S. cerevisiae: Both cell types choose mating partners by responding to the strongest pheromone signal , 1990, Cell.

[18]  L. Hartwell,et al.  Courtship in Saccharomyces cerevisiae: an early cell-cell interaction during mating , 1990, Molecular and cellular biology.

[19]  H. Kitano,et al.  A quantitative characterization of the yeast heterotrimeric G protein cycle , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[20]  M. Snyder,et al.  Bud-site selection and cell polarity in budding yeast. , 2002, Current opinion in microbiology.

[21]  K. Clark,et al.  Association of the yeast pheromone response G protein beta gamma subunits with the MAP kinase scaffold Ste5p. , 1995, Science.

[22]  I. Mellman,et al.  Purificaton of a functional mouse Fc receptor through the use of a monoclonal antibody , 1980, The Journal of experimental medicine.

[23]  Michael W. Davidson,et al.  A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum , 2013, Nature Methods.

[24]  A. Schier,et al.  Chemical Gradients and Chemotropism in Yeast , 2009 .

[25]  N. Barkai,et al.  Improved readout precision of the Bicoid morphogen gradient by early decoding , 2011, Journal of Biological Physics.

[26]  Kendall A. Smith,et al.  The interleukin 2 receptor. Functional consequences of its bimolecular structure , 1987, The Journal of experimental medicine.

[27]  Melanie I. Stefan,et al.  Ligand Depletion in vivo Modulates the Dynamic Range and Cooperativity of Signal Transduction , 2010, PloS one.

[28]  Mark H Ellisman,et al.  A FlAsH-based FRET approach to determine G protein–coupled receptor activation in living cells , 2005, Nature Methods.

[29]  Sigurd B. Angenent,et al.  On the spontaneous emergence of cell polarity , 2008, Nature.

[30]  L. Hartwell,et al.  Saccharomyces cerevisiae cells execute a default pathway to select a mate in the absence of pheromone gradients , 1995, The Journal of cell biology.

[31]  I. Herskowitz,et al.  A yeast gene (BEM1) necessary for cell polarization whose product contains two SH3 domains , 1992, Nature.

[32]  John E. Lisman,et al.  The sequence of events that underlie quantal transmission at central glutamatergic synapses , 2007, Nature Reviews Neuroscience.

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

[34]  P. Devreotes,et al.  Switching of chemoattractant receptors programs development and morphogenesis in Dictyostelium: receptor subtypes activate common responses at different agonist concentrations. , 1998, Developmental biology.

[35]  P. J. Huang,et al.  Parts-per-million of polyethylene glycol as a non-interfering blocking agent for homogeneous biosensor development. , 2013, Analytical chemistry.

[36]  R. Tibshirani,et al.  An introduction to the bootstrap , 1993 .

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

[38]  S. Basu,et al.  Spatiotemporal control of gene expression with pulse-generating networks. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[39]  T. Maiwald,et al.  Materials and Methods SOM Text Figs. S1 to S16 References Materials and Methods , 2022 .

[40]  L. Sklar,et al.  Competitive binding kinetics in ligand-receptor-competitor systems. Rate parameters for unlabeled ligands for the formyl peptide receptor. , 1985, Molecular pharmacology.

[41]  John J Tyson,et al.  Functional motifs in biochemical reaction networks. , 2010, Annual review of physical chemistry.

[42]  R. Patterson,et al.  Binding constants of IgE receptors on human blood basophils for IgE. , 1986, Immunology.

[43]  G. Westbrook,et al.  The impact of receptor desensitization on fast synaptic transmission , 1996, Trends in Neurosciences.

[44]  Leland H. Hartwell,et al.  Binding of α-factor pheromone to yeast a cells: Chemical and genetic evidence for an α-factor receptor , 1983, Cell.

[45]  S. Bergmann,et al.  Pre-Steady-State Decoding of the Bicoid Morphogen Gradient , 2007, PLoS biology.

[46]  J. Becker,et al.  A fluorescent alpha-factor analogue exhibits multiple steps on binding to its G protein coupled receptor in yeast. , 2004, Biochemistry.

[47]  L. Hartwell,et al.  Binding of alpha-factor pheromone to Saccharomyces cerevisiae a cells: dissociation constant and number of binding sites , 1986, Molecular and cellular biology.

[48]  Jacob Roll,et al.  Systems biology: model based evaluation and comparison of potential explanations for given biological data , 2009, The FEBS journal.

[49]  D C Teller,et al.  Kinetics of insulin binding to rat white fat cells at 15 degrees C. , 1986, The Journal of biological chemistry.

[50]  D. Lew,et al.  Beyond symmetry-breaking: competition and negative feedback in GTPase regulation. , 2013, Trends in cell biology.

[51]  M. Davis,et al.  Kinetics of T-cell receptor binding to peptide/I-Ek complexes: correlation of the dissociation rate with T-cell responsiveness. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[52]  Tamar Friedlander,et al.  Adaptive response and enlargement of dynamic range. , 2010, Mathematical biosciences and engineering : MBE.

[53]  L. Hartwell,et al.  Binding of alpha-factor pheromone to yeast a cells: chemical and genetic evidence for an alpha-factor receptor. , 1983, Cell.

[54]  G. Balázsi,et al.  Negative autoregulation linearizes the dose–response and suppresses the heterogeneity of gene expression , 2009, Proceedings of the National Academy of Sciences.

[55]  W. Lim,et al.  Defining Network Topologies that Can Achieve Biochemical Adaptation , 2009, Cell.

[56]  Aljoscha Nern,et al.  A Cdc24p-Far1p-Gβγ Protein Complex Required for Yeast Orientation during Mating , 1999, The Journal of cell biology.

[57]  Roger Brent,et al.  Detailed Simulations of Cell Biology with Smoldyn 2.1 , 2010, PLoS Comput. Biol..

[58]  P. Pryciak,et al.  Membrane recruitment of the kinase cascade scaffold protein Ste5 by the Gbetagamma complex underlies activation of the yeast pheromone response pathway. , 1998, Genes & development.

[59]  Daniel J. Lew,et al.  Inhibitory GEF Phosphorylation Provides Negative Feedback in the Yeast Polarity Circuit , 2014, Current Biology.

[60]  K. Clark,et al.  Pheromone Response in Yeast: Association of Bem1p with Proteins of the MAP Kinase Cascade and Actin , 1995, Science.

[61]  I. Herskowitz,et al.  The role of Far1p in linking the heterotrimeric G protein to polarity establishment proteins during yeast mating. , 1998, Science.

[62]  A. Colman-Lerner,et al.  Quantitative measurement of protein relocalization in live cells. , 2013, Biophysical journal.

[63]  Nan Hao,et al.  Dose-to-Duration Encoding and Signaling beyond Saturation in Intracellular Signaling Networks , 2008, PLoS Comput. Biol..

[64]  Amy S. Gladfelter,et al.  Scaffold-mediated symmetry breaking by Cdc42p , 2003, Nature Cell Biology.

[65]  Kay Hofmann,et al.  A positive feedback loop stabilizes the guanine‐nucleotide exchange factor Cdc24 at sites of polarization , 2002, The EMBO journal.

[66]  A Ciechanover,et al.  Kinetics of internalization and recycling of transferrin and the transferrin receptor in a human hepatoma cell line. Effect of lysosomotropic agents. , 1983, The Journal of biological chemistry.

[67]  M. Herkenham,et al.  Cannabinoid Receptor Localization in Brain: Relationship to Motor and Reward Systems , 1992, Annals of the New York Academy of Sciences.

[68]  Uri Alon,et al.  An Introduction to Systems Biology , 2006 .

[69]  J. Pringle,et al.  Genetic analysis of the bipolar pattern of bud site selection in the yeast Saccharomyces cerevisiae , 1996, Molecular and cellular biology.

[70]  G. Saari,et al.  The Saccharomyces cerevisiae BAR1 gene encodes an exported protein with homology to pepsin. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[71]  David G. Drubin,et al.  A role for the yeast actin cytoskeleton in pheromone receptor clustering and signalling , 1998, Current Biology.

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

[73]  Uri Alon,et al.  Negative auto-regulation increases the input dynamic-range of the arabinose system of Escherichia coli , 2011, BMC Systems Biology.

[74]  G. Westbrook,et al.  The time course of glutamate in the synaptic cleft. , 1992, Science.

[75]  A. Folch,et al.  Microfluidic “jets” for generating steady-state gradients of soluble molecules on open surfaces , 2006 .

[76]  R. Dengler,et al.  Control of kinetic properties of GluR2 flop AMPA‐type channels: impact of R/G nuclear editing , 2002, The European journal of neuroscience.

[77]  S. Zigmond Chemotactic response of neutrophils. , 1989, American journal of respiratory cell and molecular biology.

[78]  G. Fink,et al.  Methods in enzymology vol 194 guide to yeast genetics and molecular biology , 1991 .

[79]  Qing Nie,et al.  Robust Spatial Sensing of Mating Pheromone Gradients by Yeast Cells , 2008, PloS one.

[80]  R. Macnab,et al.  The gradient-sensing mechanism in bacterial chemotaxis. , 1972, Proceedings of the National Academy of Sciences of the United States of America.

[81]  Noa Rappaport,et al.  Disentangling signaling gradients generated by equivalent sources , 2012, Journal of biological physics.

[82]  Bruce Bowerman,et al.  Symmetry breaking in biology. , 2010, Cold Spring Harbor perspectives in biology.

[83]  Ned S Wingreen,et al.  Responding to chemical gradients: bacterial chemotaxis. , 2012, Current opinion in cell biology.

[84]  K. Yamada,et al.  The interaction of plasma fibronectin with fibroblastic cells in suspension. , 1985, The Journal of biological chemistry.

[85]  Gerald R. Fink,et al.  Guide to yeast genetics and molecular biology , 1993 .

[86]  P. Insel,et al.  Characterization of coexisting alpha 1- and beta 2-adrenergic receptors on a cloned muscle cell line, BC3H-1. , 1982, Molecular pharmacology.

[87]  K A Overholser,et al.  Rate constants for binding, dissociation, and internalization of EGF: effect of receptor occupancy and ligand concentration. , 1990, Biochemistry.

[88]  R. Cook,et al.  Mutagenesis in the C-terminal region of human interleukin 5 reveals a central patch for receptor alpha chain recognition. , 1995, Proceedings of the National Academy of Sciences of the United States of America.