Literature DB >> 21135209

Bimodal gene expression in noncooperative regulatory systems.

Anna Ochab-Marcinek1, Marcin Tabaka.   

Abstract

Bimodality of gene expression, as a mechanism contributing to phenotypic diversity, enhances the survival of cells in a fluctuating environment. To date, the bimodal response of a gene regulatory system has been attributed to the cooperativity of transcription factor binding or to feedback loops. It has remained unclear whether noncooperative binding of transcription factors can give rise to bimodality in an open-loop system. We study a theoretical model of gene expression in a two-step cascade (a deterministically monostable system) in which the regulatory gene produces transcription factors that have a nonlinear effect on the activity of the target gene. We show that a unimodal distribution of transcription factors over the cell population can generate a bimodal steady-state output without cooperative transcription factor binding. We introduce a simple method of geometric construction that allows one to predict the onset of bimodality. The construction only involves the parameters of bursting of the regulatory gene and the dose-response curve of the target gene. Using this method, we show that the gene expression may switch between unimodal and bimodal as the concentration of inducers or corepressors is varied. These findings may explain the experimentally observed bimodal response of cascades consisting of a fluorescent protein reporter controlled by the tetracycline repressor. The geometric construction provides a useful tool for designing experiments and for interpretation of their results. Our findings may have important implications for understanding the strategies adopted by cell populations to survive in changing environments.

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Year:  2010        PMID: 21135209      PMCID: PMC3009792          DOI: 10.1073/pnas.1008965107

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


  52 in total

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2.  Quantification of protein half-lives in the budding yeast proteome.

Authors:  Archana Belle; Amos Tanay; Ledion Bitincka; Ron Shamir; Erin K O'Shea
Journal:  Proc Natl Acad Sci U S A       Date:  2006-08-17       Impact factor: 11.205

Review 3.  Living with noisy genes: how cells function reliably with inherent variability in gene expression.

Authors:  Narendra Maheshri; Erin K O'Shea
Journal:  Annu Rev Biophys Biomol Struct       Date:  2007

4.  Analytical distributions for stochastic gene expression.

Authors:  Vahid Shahrezaei; Peter S Swain
Journal:  Proc Natl Acad Sci U S A       Date:  2008-11-06       Impact factor: 11.205

5.  How noise statistics impact models of enzyme cycles.

Authors:  Aryeh Warmflash; David N Adamson; Aaron R Dinner
Journal:  J Chem Phys       Date:  2008-06-14       Impact factor: 3.488

6.  The effects of reversibility and noise on stochastic phosphorylation cycles and cascades.

Authors:  Clark A Miller; Daniel A Beard
Journal:  Biophys J       Date:  2008-05-30       Impact factor: 4.033

7.  Stochastic switching as a survival strategy in fluctuating environments.

Authors:  Murat Acar; Jerome T Mettetal; Alexander van Oudenaarden
Journal:  Nat Genet       Date:  2008-03-23       Impact factor: 38.330

Review 8.  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

9.  Positive receptor feedback during lineage commitment can generate ultrasensitivity to ligand and confer robustness to a bistable switch.

Authors:  Santhosh Palani; Casim A Sarkar
Journal:  Biophys J       Date:  2008-05-09       Impact factor: 4.033

10.  Noise in transcription negative feedback loops: simulation and experimental analysis.

Authors:  Yann Dublanche; Konstantinos Michalodimitrakis; Nico Kümmerer; Mathilde Foglierini; Luis Serrano
Journal:  Mol Syst Biol       Date:  2006-08-01       Impact factor: 11.429

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  20 in total

Review 1.  Single-Cell RNA Sequencing: A New Window into Cell Scale Dynamics.

Authors:  Sabyasachi Dasgupta; Gary D Bader; Sidhartha Goyal
Journal:  Biophys J       Date:  2018-07-11       Impact factor: 4.033

2.  Nonlinear signalling networks and cell-to-cell variability transform external signals into broadly distributed or bimodal responses.

Authors:  Maciej Dobrzyński; Lan K Nguyen; Marc R Birtwistle; Alexander von Kriegsheim; Alfonso Blanco Fernández; Alex Cheong; Walter Kolch; Boris N Kholodenko
Journal:  J R Soc Interface       Date:  2014-09-06       Impact factor: 4.118

3.  Gene expression noise is affected differentially by feedback in burst frequency and burst size.

Authors:  Pavol Bokes; Abhyudai Singh
Journal:  J Math Biol       Date:  2016-09-24       Impact factor: 2.259

4.  Circuit-Host Coupling Induces Multifaceted Behavioral Modulations of a Gene Switch.

Authors:  Andrew E Blanchard; Chen Liao; Ting Lu
Journal:  Biophys J       Date:  2018-02-06       Impact factor: 4.033

5.  Type of noise defines global attractors in bistable molecular regulatory systems.

Authors:  Joanna Jaruszewicz; Pawel J Zuk; Tomasz Lipniacki
Journal:  J Theor Biol       Date:  2012-10-11       Impact factor: 2.691

6.  Transcription factor levels enable metabolic diversification of single cells of environmental bacteria.

Authors:  Raúl Guantes; Ilaria Benedetti; Rafael Silva-Rocha; Víctor de Lorenzo
Journal:  ISME J       Date:  2015-12-04       Impact factor: 10.302

7.  A genetic bistable switch utilizing nonlinear protein degradation.

Authors:  Daniel Huang; William J Holtz; Michel M Maharbiz
Journal:  J Biol Eng       Date:  2012-07-09       Impact factor: 4.355

8.  Speed, sensitivity, and bistability in auto-activating signaling circuits.

Authors:  Rutger Hermsen; David W Erickson; Terence Hwa
Journal:  PLoS Comput Biol       Date:  2011-11-17       Impact factor: 4.475

9.  Cooperative binding of transcription factors promotes bimodal gene expression response.

Authors:  Pablo S Gutierrez; Diana Monteoliva; Luis Diambra
Journal:  PLoS One       Date:  2012-09-12       Impact factor: 3.240

10.  In search of noise-induced bimodality.

Authors:  Kyung Hyuk Kim; Herbert M Sauro
Journal:  BMC Biol       Date:  2012-11-07       Impact factor: 7.431

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