A Design Principle of Group-level Decision Making in Cell Populations

Populations of cells often switch states as a group to cope with environmental changes such as nutrient availability and cell density. Although the gene circuits that underlie the switches are well understood at the level of single cells, the ways in which such circuits work in concert among many cells to support group-level switches are not fully explored. Experimental studies of microbial quorum sensing show that group-level changes in cellular states occur in either a graded or an all-or-none fashion. Here, we show through numerical simulations and mathematical analysis that these behaviors generally originate from two distinct forms of bistability. The choice of bistability is uniquely determined by a dimensionless parameter that compares the synthesis and the transport of the inducing molecules. The role of the parameter is universal, such that it not only applies to the autoinducing circuits typically found in bacteria but also to the more complex gene circuits involved in transmembrane receptor signaling. Furthermore, in gene circuits with negative feedback, the same dimensionless parameter determines the coherence of group-level transitions from quiescence to a rhythmic state. The set of biochemical parameters in bacterial quorum-sensing circuits appear to be tuned so that the cells can use either type of transition. The design principle identified here serves as the basis for the analysis and control of cellular collective decision making.

[1]  James P. Keener,et al.  Mathematical physiology , 1998 .

[2]  J. Keizer Biochemical Oscillations and Cellular Rhythms: The molecular bases of periodic and chaotic behaviour, by Albert Goldbeter , 1998 .

[3]  Tobin J Dickerson,et al.  Revisiting quorum sensing: Discovery of additional chemical and biological functions for 3-oxo-N-acylhomoserine lactones. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Andrew B Goryachev,et al.  Understanding bacterial cell-cell communication with computational modeling. , 2011, Chemical reviews.

[5]  Stephen J. Hagen,et al.  Heterogeneous Response to a Quorum-Sensing Signal in the Luminescence of Individual Vibrio fischeri , 2010, PloS one.

[6]  J. Buck,et al.  Mechanism of Rhythmic Synchronous Flashing of Fireflies , 1968, Science.

[7]  E. Greenberg,et al.  Acyl homoserine-lactone quorum-sensing signal generation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[8]  Sune Danø,et al.  Dynamical quorum sensing: Population density encoded in cellular dynamics , 2007, Proceedings of the National Academy of Sciences.

[9]  Ned S Wingreen,et al.  Active regulation of receptor ratios controls integration of quorum-sensing signals in Vibrio harveyi , 2011, Molecular systems biology.

[10]  A. Winfree The geometry of biological time , 1991 .

[11]  A. Levchenko,et al.  Diverse Sensitivity Thresholds in Dynamic Signaling Responses by Social Amoebae , 2012, Science Signaling.

[12]  Ali Khademhosseini,et al.  Microwell-mediated control of embryoid body size regulates embryonic stem cell fate via differential expression of WNT5a and WNT11 , 2009, Proceedings of the National Academy of Sciences.

[13]  C Jeffrey Brinker,et al.  Confinement-induced quorum sensing of individual Staphylococcus aureus bacteria. , 2010, Nature chemical biology.

[14]  D. Gillespie Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[15]  J. Reiser,et al.  Autoinducer-mediated regulation of rhamnolipid biosurfactant synthesis in Pseudomonas aeruginosa. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[16]  James C. W. Locke,et al.  Stochastic Pulse Regulation in Bacterial Stress Response , 2011, Science.

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

[18]  E. Greenberg,et al.  Quorum sensing in bacteria: the LuxR-LuxI family of cell density-responsive transcriptional regulators , 1994, Journal of bacteriology.

[19]  Mattias Goksör,et al.  Sustained glycolytic oscillations in individual isolated yeast cells , 2012, The FEBS journal.

[20]  Cédric Lhoussaine,et al.  Theoretical basis of the community effect in development , 2010, BMC Systems Biology.

[21]  A Goldbeter,et al.  A Model Based on Receptor Desensitization for Cyclic AMP Signaling in Dictyostelium Cells. , 1987, Biophysical journal.

[22]  K. Showalter,et al.  Dynamical Quorum Sensing and Synchronization in Large Populations of Chemical Oscillators , 2009, Science.

[23]  Lingchong You,et al.  Optimal tuning of bacterial sensing potential , 2009, Molecular systems biology.

[24]  Philip S. Stewart,et al.  Diffusion in Biofilms , 2003, Journal of bacteriology.

[25]  J. Ferrell Bistability, Bifurcations, and Waddington's Epigenetic Landscape , 2012, Current Biology.

[26]  Eugene M. Izhikevich,et al.  Dynamical Systems in Neuroscience: The Geometry of Excitability and Bursting , 2006 .

[27]  S. Molin,et al.  Methods for detecting acylated homoserine lactones produced by Gram-negative bacteria and their application in studies of AHL-production kinetics. , 2001, Journal of microbiological methods.

[28]  M. Elowitz,et al.  Modeling a synthetic multicellular clock: repressilators coupled by quorum sensing. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[29]  K. M. Lee,et al.  QscR, a modulator of quorum-sensing signal synthesis and virulence in Pseudomonas aeruginosa , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[30]  Griffin M. Weber,et al.  BioNumbers—the database of key numbers in molecular and cell biology , 2009, Nucleic Acids Res..

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

[32]  K. Kaneko,et al.  Regulative differentiation as bifurcation of interacting cell population. , 2007, Journal of theoretical biology.

[33]  A. Kornberg,et al.  Alginate, inorganic polyphosphate, GTP and ppGpp synthesis co‐regulated in Pseudomonas aeruginosa: implications for stationary phase survival and synthesis of RNA/DNA precursors , 1998, Molecular microbiology.

[34]  P. Seed,et al.  Activation of the Pseudomonas aeruginosa lasI gene by LasR and the Pseudomonas autoinducer PAI: an autoinduction regulatory hierarchy , 1995, Journal of bacteriology.

[35]  K. Kaneko,et al.  The combination of positive and negative feedback loops confers exquisite flexibility to biochemical switches , 2009, Physical biology.

[36]  D. Dubnau,et al.  Bistability in the Bacillus subtilis K‐state (competence) system requires a positive feedback loop , 2005, Molecular microbiology.

[37]  J. Collins,et al.  Programmable cells: interfacing natural and engineered gene networks. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[38]  B. Séraphin,et al.  Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion , 2001, The EMBO journal.

[39]  C. Lim,et al.  Regulated Fluctuations in Nanog Expression Mediate Cell Fate Decisions in Embryonic Stem Cells , 2009, PLoS biology.

[40]  E. Greenberg,et al.  The Vibrio fischeri quorum‐sensing systems ain and lux sequentially induce luminescence gene expression and are important for persistence in the squid host , 2003, Molecular microbiology.

[41]  A. Levchenko,et al.  Robust and sensitive control of a quorum-sensing circuit by two interlocked feedback loops , 2008, Molecular systems biology.

[42]  Rajan P Kulkarni,et al.  Tunability and Noise Dependence in Differentiation Dynamics , 2007, Science.

[43]  H. L. Martin,et al.  THE DIFFUSION OF ADENOSINE TRIPHOSPHATE THROUGH AQUEOUS SOLUTIONS. , 1964, Archives of biochemistry and biophysics.

[44]  D. Spring,et al.  Structure-activity relationships of Erwinia carotovora quorum sensing signaling molecules. , 2005, Bioorganic & medicinal chemistry letters.

[45]  Julien Tremblay,et al.  Increase in Rhamnolipid Synthesis under Iron-Limiting Conditions Influences Surface Motility and Biofilm Formation in Pseudomonas aeruginosa , 2010, Journal of bacteriology.

[46]  M. Dworkin,et al.  Solubility and diffusion coefficient of adenosine 3':5'-monophosphate. , 1977, The Journal of biological chemistry.

[47]  Stephen J. Hagen,et al.  Noise and crosstalk in two quorum-sensing inputs of Vibrio fischeri , 2011, BMC Systems Biology.

[48]  Galit Lahav,et al.  Basal Dynamics of p53 Reveal Transcriptionally Attenuated Pulses in Cycling Cells , 2010, Cell.

[49]  N. Wingreen,et al.  Negative feedback loops involving small regulatory RNAs precisely control the Vibrio harveyi quorum-sensing response. , 2010, Molecular cell.

[50]  Matthias Heinemann,et al.  The Cost of Virulence: Retarded Growth of Salmonella Typhimurium Cells Expressing Type III Secretion System 1 , 2011, PLoS pathogens.

[51]  Ned S Wingreen,et al.  Quantifying the Integration of Quorum-Sensing Signals with Single-Cell Resolution , 2009, PLoS biology.

[52]  F. Arnold,et al.  Implications of Rewiring Bacterial Quorum Sensing , 2007, Applied and Environmental Microbiology.

[53]  Satoshi Sawai,et al.  An autoregulatory circuit for long-range self-organization in Dictyostelium cell populations , 2005, Nature.

[54]  P. Gilon,et al.  Influence of cell number on the characteristics and synchrony of Ca2+ oscillations in clusters of mouse pancreatic islet cells , 1999, The Journal of physiology.

[55]  Lian-Hui Zhang,et al.  Anti‐activator QslA defines the quorum sensing threshold and response in Pseudomonas aeruginosa , 2011, Molecular microbiology.

[56]  L. Tsimring,et al.  A synchronized quorum of genetic clocks , 2009, Nature.

[57]  Matthias Heinemann,et al.  Condition-Dependent Cell Volume and Concentration of Escherichia coli to Facilitate Data Conversion for Systems Biology Modeling , 2011, PloS one.

[58]  C. Furusawa,et al.  Emergence of rules in cell society: Differentiation, hierarchy, and stability , 1998, Bulletin of mathematical biology.

[59]  Bonnie L Bassler,et al.  Chemical communication among bacteria , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[60]  Jürgen Kurths,et al.  Synchronization - A Universal Concept in Nonlinear Sciences , 2001, Cambridge Nonlinear Science Series.

[61]  K. Fujimoto,et al.  Noisy signal amplification in ultrasensitive signal transduction. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[62]  K. Tanaka,et al.  A hierarchical quorum‐sensing cascade in Pseudomonas aeruginosa links the transcriptional activators LasR and RhIR (VsmR) to expression of the stationary‐phase sigma factor RpoS , 1996, Molecular microbiology.

[63]  Tetsuya J. Kobayashi,et al.  Melanopsin-dependent photo-perturbation reveals desynchronization underlying the singularity of mammalian circadian clocks , 2007, Nature Cell Biology.

[64]  Robert E. Cohen,et al.  The Onset of Collective Behavior in Social Amoebae , 2011 .

[65]  Mark Ptashne,et al.  A Genetic Switch, Phage Lambda Revisited , 2004 .

[66]  C. Clevenger Signal transduction. , 2003, Breast disease.

[67]  A. Goryachev,et al.  Systems analysis of a quorum sensing network: design constraints imposed by the functional requirements, network topology and kinetic constants. , 2006, Bio Systems.

[68]  B. Bassler,et al.  Societal interactions in ovarian cancer metastasis: a quorum-sensing hypothesis , 2008, Clinical & Experimental Metastasis.

[69]  Kirsten Jung,et al.  Heterogeneity in quorum sensing‐regulated bioluminescence of Vibrio harveyi , 2009, Molecular microbiology.

[70]  M Welch,et al.  N‐acyl homoserine lactone binding to the CarR receptor determines quorum‐sensing specificity in Erwinia , 2000, The EMBO journal.

[71]  E. Greenberg,et al.  Diffusion of autoinducer is involved in regulation of the Vibrio fischeri luminescence system , 1985, Journal of bacteriology.

[72]  K. Woodhouse,et al.  Control of Human Embryonic Stem Cell Colony and Aggregate Size Heterogeneity Influences Differentiation Trajectories , 2008, Stem cells.

[73]  M. Cohen,et al.  Iontophoresis of cyclic AMP. , 1975, Biophysical journal.

[74]  S. Hagen,et al.  Quorum activation at a distance: spatiotemporal patterns of gene regulation from diffusion of an autoinducer signal. , 2012, Journal of the American Chemical Society.

[75]  Yoshiki Kuramoto,et al.  Chemical Oscillations, Waves, and Turbulence , 1984, Springer Series in Synergetics.

[76]  Jordi Garcia-Ojalvo,et al.  Gene circuit designs for noisy excitable dynamics. , 2011, Mathematical biosciences.

[77]  Satoshi Sawai,et al.  Collective oscillations in developing cells: Insights from simple systems , 2011, Development, growth & differentiation.

[78]  Jeffrey W. Smith,et al.  Stochastic Gene Expression in a Single Cell , .

[79]  B. Iglewski,et al.  Active Efflux and Diffusion Are Involved in Transport of Pseudomonas aeruginosa Cell-to-Cell Signals , 1999, Journal of bacteriology.

[80]  J. Gurdon,et al.  eFGF and its mode of action in the community effect during Xenopus myogenesis. , 2001, Development.

[81]  K. V. Venkatesh,et al.  Prediction by Promoter Logic in Bacterial Quorum Sensing , 2012, PLoS Comput. Biol..

[82]  Sui Huang Reprogramming cell fates: reconciling rarity with robustness , 2009, BioEssays : news and reviews in molecular, cellular and developmental biology.

[83]  K. Nealson,et al.  Autoinduction of bacterial bioluminescence in a carbon limited chemostat , 1981, Archives of Microbiology.

[84]  S. Kjelleberg,et al.  Luminescence control in the marine bacterium Vibrio fischeri: An analysis of the dynamics of lux regulation. , 2000, Journal of molecular biology.

[85]  G. Gerisch,et al.  Intracellular oscillations and release of cyclic AMP from Dictyostelium cells. , 1975, Biochemical and biophysical research communications.

[86]  Janet Rossant,et al.  The Crumbs complex couples cell density sensing to Hippo-dependent control of the TGF-β-SMAD pathway. , 2010, Developmental cell.

[87]  R. Ismagilov,et al.  Microfluidic confinement of single cells of bacteria in small volumes initiates high-density behavior of quorum sensing and growth and reveals its variability. , 2009, Angewandte Chemie.

[88]  E. P. Greenberg,et al.  Reversible Acyl-Homoserine Lactone Binding to Purified Vibrio fischeri LuxR Protein , 2004, Journal of bacteriology.

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

[90]  Leo Eberl,et al.  Inhibition of quorum sensing in Pseudomonas aeruginosa biofilm bacteria by a halogenated furanone compound. , 2002, Microbiology.

[91]  M. Thattai,et al.  Stochastic Gene Expression in Fluctuating Environments , 2004, Genetics.

[92]  K. Nealson,et al.  Cellular Control of the Synthesis and Activity of the Bacterial Luminescent System , 1970, Journal of bacteriology.

[93]  Ertugrul M. Ozbudak,et al.  Multistability in the lactose utilization network of Escherichia coli , 2004, Nature.

[94]  Philip S. Stewart,et al.  Physiological heterogeneity in biofilms , 2008, Nature Reviews Microbiology.

[95]  C. Kuttler,et al.  Dynamic regulation of N-acyl-homoserine lactone production and degradation in Pseudomonas putida IsoF. , 2010, FEMS microbiology ecology.

[96]  Sune Danø,et al.  On the mechanisms of glycolytic oscillations in yeast , 2005, The FEBS journal.

[97]  P. Liberali,et al.  Population context determines cell-to-cell variability in endocytosis and virus infection , 2009, Nature.

[98]  J. Costerton,et al.  The involvement of cell-to-cell signals in the development of a bacterial biofilm. , 1998, Science.

[99]  Y. Prokazov,et al.  Desynchronisation of Glycolytic Oscillations in Yeast Cell Populations , 2012, PloS one.

[100]  E. Greenberg,et al.  A second N-acylhomoserine lactone signal produced by Pseudomonas aeruginosa. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[101]  J. Collins,et al.  Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.

[102]  J. Keener,et al.  A mathematical model for quorum sensing in Pseudomonas aeruginosa , 2001, Bulletin of mathematical biology.

[103]  S. Kjelleberg,et al.  Do marine natural products interfere with prokaryotic AHL regulatory systems , 1997 .

[104]  J. Massagué TGF-beta signal transduction. , 1998, Annual review of biochemistry.

[105]  O. Kuipers,et al.  Bistability, epigenetics, and bet-hedging in bacteria. , 2008, Annual review of microbiology.

[106]  K. Nealson,et al.  Bacterial bioluminescence: Isolation and genetic analysis of functions from Vibrio fischeri , 1983, Cell.

[107]  Dynamical quorum sensing and synchronization in collections of excitable and oscillatory catalytic particles , 2010 .

[108]  Luhua Lai,et al.  Robustness and modular design of the Drosophila segment polarity network , 2006, Molecular systems biology.

[109]  Sano,et al.  Proportion regulation of biological cells in globally coupled nonlinear systems. , 1995, Physical review letters.

[110]  J. Costerton,et al.  Pseudomonas aeruginosa Displays Multiple Phenotypes during Development as a Biofilm , 2002, Journal of bacteriology.

[111]  R. Briandet,et al.  Evidence of Autoinduction Heterogeneity via Expression of the Agr System of Listeria monocytogenes at the Single-Cell Level , 2011, Applied and Environmental Microbiology.

[112]  B. Iglewski,et al.  Roles of Pseudomonas aeruginosa las and rhl quorum-sensing systems in control of elastase and rhamnolipid biosynthesis genes , 1997, Journal of bacteriology.

[113]  A. Novick,et al.  ENZYME INDUCTION AS AN ALL-OR-NONE PHENOMENON. , 1957, Proceedings of the National Academy of Sciences of the United States of America.

[114]  A. Goldbeter,et al.  Biochemical Oscillations And Cellular Rhythms: Contents , 1996 .

[115]  Lian-Hui Zhang,et al.  Quorum-quenching microbial infections: mechanisms and implications , 2007, Philosophical Transactions of the Royal Society B: Biological Sciences.

[116]  P. Meda,et al.  Rhamnolipids Are Virulence Factors That Promote Early Infiltration of Primary Human Airway Epithelia by Pseudomonas aeruginosa , 2006, Infection and Immunity.

[117]  E. Greenberg,et al.  Census and consensus in bacterial ecosystems: the LuxR-LuxI family of quorum-sensing transcriptional regulators. , 1996, Annual review of microbiology.

[118]  C. van Delden,et al.  Autoinducer production and quorum-sensing dependent phenotypes of Pseudomonas aeruginosa vary according to isolation site during colonization of intubated patients , 2007, BMC Microbiology.

[119]  Ivan Razinkov,et al.  Sensing array of radically coupled genetic biopixels , 2011, Nature.