Ultrasensitivity and noise propagation in a synthetic transcriptional cascade.

The precise nature of information flow through a biological network, which is governed by factors such as response sensitivities and noise propagation, greatly affects the operation of biological systems. Quantitative analysis of these properties is often difficult in naturally occurring systems but can be greatly facilitated by studying simple synthetic networks. Here, we report the construction of synthetic transcriptional cascades comprising one, two, and three repression stages. These model systems enable us to analyze sensitivity and noise propagation as a function of network complexity. We demonstrate experimentally steady-state switching behavior that becomes sharper with longer cascades. The regulatory mechanisms that confer this ultrasensitive response both attenuate and amplify phenotypical variations depending on the system's input conditions. Although noise attenuation allows the cascade to act as a low-pass filter by rejecting short-lived perturbations in input conditions, noise amplification results in loss of synchrony among a cell population. The experimental results demonstrating the above network properties correlate well with simulations of a simple mathematical model of the system.

[1]  Donald A. McQuarrie,et al.  Kinetics of Small Systems. I , 1963 .

[2]  Parag A. Pathak,et al.  Massachusetts Institute of Technology , 1964, Nature.

[3]  M. Savageau Biochemical systems analysis. II. The steady-state solutions for an n-pool system using a power-law approximation. , 1969, Journal of theoretical biology.

[4]  M. Savageau Comparison of classical and autogenous systems of regulation in inducible operons , 1974, Nature.

[5]  P. B. Chock,et al.  Superiority of interconvertible enzyme cascades in metabolite regulation: analysis of multicyclic systems. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

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

[7]  B. Bainbridge,et al.  Genetics , 1981, Experientia.

[8]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[9]  L. Hartwell,et al.  Checkpoints: controls that ensure the order of cell cycle events. , 1989, Science.

[10]  H. Sambrook Molecular cloning : a laboratory manual. Cold Spring Harbor, NY , 1989 .

[11]  Qiang Zheng,et al.  Comparison of deterministic and stochastic kinetics for nonlinear systems , 1991 .

[12]  AC Tose Cell , 1993, Cell.

[13]  W. Saenger,et al.  Structure of the Tet repressor-tetracycline complex and regulation of antibiotic resistance. , 1994, Science.

[14]  A. Mccarthy Development , 1996, Current Opinion in Neurobiology.

[15]  B. Müller-Hill The lac Operon: A Short History of a Genetic Paradigm , 1996 .

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

[17]  T. Lamb,et al.  Gain and kinetics of activation in the G-protein cascade of phototransduction. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[18]  H. Bujard,et al.  Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. , 1997, Nucleic acids research.

[19]  E. Davidson,et al.  The hardwiring of development: organization and function of genomic regulatory systems. , 1997, Development.

[20]  A. Arkin,et al.  Stochastic mechanisms in gene expression. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

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

[22]  D. Botstein,et al.  The transcriptional program of sporulation in budding yeast. , 1998, Science.

[23]  M. Gustin,et al.  MAP Kinase Pathways in the YeastSaccharomyces cerevisiae , 1998, Microbiology and Molecular Biology Reviews.

[24]  A. Arkin,et al.  Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. , 1998, Genetics.

[25]  A. Arkin,et al.  It's a noisy business! Genetic regulation at the nanomolar scale. , 1999, Trends in genetics : TIG.

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

[27]  W. Saenger,et al.  Structural basis of gene regulation by the tetracycline inducible Tet repressor–operator system , 2000, Nature Structural Biology.

[28]  M. Elowitz,et al.  A synthetic oscillatory network of transcriptional regulators , 2000, Nature.

[29]  L. Serrano,et al.  Engineering stability in gene networks by autoregulation , 2000, Nature.

[30]  Anirvan M. Sengupta,et al.  Engineering aspects of enzymatic signal transduction: photoreceptors in the retina. , 2000, Biophysical journal.

[31]  U. Alon,et al.  Ordering Genes in a Flagella Pathway by Analysis of Expression Kinetics from Living Bacteria , 2001, Science.

[32]  S. Shen-Orr,et al.  Network motifs in the transcriptional regulation network of Escherichia coli , 2002, Nature Genetics.

[33]  Ertugrul M. Ozbudak,et al.  Regulation of noise in the expression of a single gene , 2002, Nature Genetics.

[34]  Nicola J. Rinaldi,et al.  Transcriptional Regulatory Networks in Saccharomyces cerevisiae , 2002, Science.

[35]  M. Thattai,et al.  Attenuation of noise in ultrasensitive signaling cascades. , 2002, Biophysical journal.

[36]  L. Hood,et al.  A Genomic Regulatory Network for Development , 2002, Science.

[37]  P. Swain,et al.  Stochastic Gene Expression in a Single Cell , 2002, Science.

[38]  Farren J. Isaacs,et al.  Prediction and measurement of an autoregulatory genetic module , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[39]  Uri Alon,et al.  Response delays and the structure of transcription networks. , 2003, Journal of molecular biology.

[40]  Lucy Shapiro,et al.  A Bacterial Cell-Cycle Regulatory Network Operating in Time and Space , 2003, Science.

[41]  Mads Kærn,et al.  Noise in eukaryotic gene expression , 2003, Nature.

[42]  A. Ninfa,et al.  Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli , 2003, Cell.

[43]  U. Alon,et al.  Just-in-time transcription program in metabolic pathways , 2004, Nature Genetics.

[44]  R. Weiss,et al.  Optimizing genetic circuits by global sensitivity analysis. , 2004, Biophysical journal.

[45]  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.