Literature DB >> 15738412

Ultrasensitivity and noise propagation in a synthetic transcriptional cascade.

Sara Hooshangi1, Stephan Thiberge, Ron Weiss.   

Abstract

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.

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Year:  2005        PMID: 15738412      PMCID: PMC552778          DOI: 10.1073/pnas.0408507102

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  36 in total

1.  Engineering aspects of enzymatic signal transduction: photoreceptors in the retina.

Authors:  P B Detwiler; S Ramanathan; A Sengupta; B I Shraiman
Journal:  Biophys J       Date:  2000-12       Impact factor: 4.033

Review 2.  A genomic regulatory network for development.

Authors:  Eric H Davidson; Jonathan P Rast; Paola Oliveri; Andrew Ransick; Cristina Calestani; Chiou-Hwa Yuh; Takuya Minokawa; Gabriele Amore; Veronica Hinman; Cesar Arenas-Mena; Ochan Otim; C Titus Brown; Carolina B Livi; Pei Yun Lee; Roger Revilla; Alistair G Rust; Zheng jun Pan; Maria J Schilstra; Peter J C Clarke; Maria I Arnone; Lee Rowen; R Andrew Cameron; David R McClay; Leroy Hood; Hamid Bolouri
Journal:  Science       Date:  2002-03-01       Impact factor: 47.728

3.  Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria.

Authors:  S Kalir; J McClure; K Pabbaraju; C Southward; M Ronen; S Leibler; M G Surette; U Alon
Journal:  Science       Date:  2001-06-15       Impact factor: 47.728

4.  Attenuation of noise in ultrasensitive signaling cascades.

Authors:  Mukund Thattai; Alexander van Oudenaarden
Journal:  Biophys J       Date:  2002-06       Impact factor: 4.033

5.  Network motifs in the transcriptional regulation network of Escherichia coli.

Authors:  Shai S Shen-Orr; Ron Milo; Shmoolik Mangan; Uri Alon
Journal:  Nat Genet       Date:  2002-04-22       Impact factor: 38.330

6.  Regulation of noise in the expression of a single gene.

Authors:  Ertugrul M Ozbudak; Mukund Thattai; Iren Kurtser; Alan D Grossman; Alexander van Oudenaarden
Journal:  Nat Genet       Date:  2002-04-22       Impact factor: 38.330

7.  Noise in eukaryotic gene expression.

Authors:  William J Blake; Mads KAErn; Charles R Cantor; J J Collins
Journal:  Nature       Date:  2003-04-10       Impact factor: 49.962

8.  Stochastic gene expression in a single cell.

Authors:  Michael B Elowitz; Arnold J Levine; Eric D Siggia; Peter S Swain
Journal:  Science       Date:  2002-08-16       Impact factor: 47.728

9.  Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli.

Authors:  Mariette R Atkinson; Michael A Savageau; Jesse T Myers; Alexander J Ninfa
Journal:  Cell       Date:  2003-05-30       Impact factor: 41.582

10.  Transcriptional regulatory networks in Saccharomyces cerevisiae.

Authors:  Tong Ihn Lee; Nicola J Rinaldi; François Robert; Duncan T Odom; Ziv Bar-Joseph; Georg K Gerber; Nancy M Hannett; Christopher T Harbison; Craig M Thompson; Itamar Simon; Julia Zeitlinger; Ezra G Jennings; Heather L Murray; D Benjamin Gordon; Bing Ren; John J Wyrick; Jean-Bosco Tagne; Thomas L Volkert; Ernest Fraenkel; David K Gifford; Richard A Young
Journal:  Science       Date:  2002-10-25       Impact factor: 47.728

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  182 in total

1.  A combination of multisite phosphorylation and substrate sequestration produces switchlike responses.

Authors:  Xinfeng Liu; Lee Bardwell; Qing Nie
Journal:  Biophys J       Date:  2010-04-21       Impact factor: 4.033

2.  Bimodal gene expression in noncooperative regulatory systems.

Authors:  Anna Ochab-Marcinek; Marcin Tabaka
Journal:  Proc Natl Acad Sci U S A       Date:  2010-12-06       Impact factor: 11.205

Review 3.  Dynamical systems approach to endothelial heterogeneity.

Authors:  Erzsébet Ravasz Regan; William C Aird
Journal:  Circ Res       Date:  2012-06-22       Impact factor: 17.367

Review 4.  Noise in gene expression: origins, consequences, and control.

Authors:  Jonathan M Raser; Erin K O'Shea
Journal:  Science       Date:  2005-09-23       Impact factor: 47.728

5.  An optimal number of molecules for signal amplification and discrimination in a chemical cascade.

Authors:  Yoshihiro Morishita; Tetsuya J Kobayashi; Kazuyuki Aihara
Journal:  Biophys J       Date:  2006-06-23       Impact factor: 4.033

6.  Autogenous and nonautogenous control of response in a genetic network.

Authors:  Francisco M Camas; Jesús Blázquez; Juan F Poyatos
Journal:  Proc Natl Acad Sci U S A       Date:  2006-08-14       Impact factor: 11.205

7.  Ribozyme-based insulator parts buffer synthetic circuits from genetic context.

Authors:  Chunbo Lou; Brynne Stanton; Ying-Ja Chen; Brian Munsky; Christopher A Voigt
Journal:  Nat Biotechnol       Date:  2012-10-03       Impact factor: 54.908

8.  Robust, tunable genetic memory from protein sequestration combined with positive feedback.

Authors:  Tatenda Shopera; William R Henson; Andrew Ng; Young Je Lee; Kenneth Ng; Tae Seok Moon
Journal:  Nucleic Acids Res       Date:  2015-09-17       Impact factor: 16.971

Review 9.  Nature, nurture, or chance: stochastic gene expression and its consequences.

Authors:  Arjun Raj; Alexander van Oudenaarden
Journal:  Cell       Date:  2008-10-17       Impact factor: 41.582

10.  Spectral solutions to stochastic models of gene expression with bursts and regulation.

Authors:  Andrew Mugler; Aleksandra M Walczak; Chris H Wiggins
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2009-10-20
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