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Lai W, Xiong X, Wang F, Li Q, Li L, Fan C, Pei H. Nonlinear Regulation of Enzyme-Free DNA Circuitry with Ultrasensitive Switches. ACS Synth Biol 2019; 8:2106-2112. [PMID: 31461263 DOI: 10.1021/acssynbio.9b00208] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA is used to construct synthetic chemical reaction networks (CRNs), such as inorganic oscillators and gene regulatory networks. Nonlinear regulation with a simpler molecular mechanism is particularly important in large-scale CRNs with complex dynamics, such as bistability, adaptation, and oscillation of cellular functions. Here we introduce a new approach based on ultrasensitive switches as modular regulatory elements to nonlinearly regulate DNA-based CRNs. The nonlinear behavior of the systems can be finely tuned by programmable regulation of the linker length and the ligand binding sites, of which the Hill coefficients (nH) are in the range of 1.00-2.32. By integrating two different strand displacement reactions with low-order nonlinearities (nH ≈ 1.44 and 1.54), we could construct CRNs exhibiting high-order nonlinearities with Hill coefficients of up to ∼2.70. In addition, this could provide an efficient approach for designing CRNs at will with complex chemical dynamics by incorporating our design with previously developed enzyme-free DNA circuits.
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Affiliation(s)
- Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Xiewei Xiong
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Fei Wang
- School of Chemistry and Chemical Engineering and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Qian Li
- School of Chemistry and Chemical Engineering and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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Ochab-Marcinek A, Jędrak J, Tabaka M. Hill kinetics as a noise filter: the role of transcription factor autoregulation in gene cascades. Phys Chem Chem Phys 2018; 19:22580-22591. [PMID: 28809965 DOI: 10.1039/c7cp00743d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An intuition based on deterministic models of chemical kinetics is that population heterogeneity of transcription factor levels in cells is transmitted unchanged downstream to the target genes. We use a stochastic model of a two-gene cascade with a self-regulating upstream gene to show that, counter to the intuition, there is no simple mapping (bimodal to bimodal, unimodal to unimodal) between the shapes of the distributions of transcription factor numbers and target protein numbers in cells. Due to the presence of the two regulations, the system contains two nonlinear transfer functions, defined by the Hill kinetics of transcription factor binding. The transfer function of the regulator can "interfere" with the transfer function of the target, converting the bimodal input into a unimodal output or vice versa. We show that this effect can be predicted by a geometric construction. As an example application of the method, we present a case study of a system of several downstream genes of different sensitivities, controlled by a common transcription factor which also regulates its own transcription. We show that a single regulator can induce qualitatively different patterns (binary or graded) of responses to a signal in different downstream genes, depending on whether the sensitivity regions of the transfer functions of the upstream and downstream genes overlap or not. Alternatively, the same model can be interpreted as describing a single downstream gene that has different sensitivities in different cell lines due to mutations. Our model shows, therefore, a possible kinetic mechanism by which different genes can interpret the same biological signal in a different manner.
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Affiliation(s)
- Anna Ochab-Marcinek
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Jakub Jędrak
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Marcin Tabaka
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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Altszyler E, Ventura AC, Colman-Lerner A, Chernomoretz A. Ultrasensitivity in signaling cascades revisited: Linking local and global ultrasensitivity estimations. PLoS One 2017; 12:e0180083. [PMID: 28662096 PMCID: PMC5491127 DOI: 10.1371/journal.pone.0180083] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 05/23/2017] [Indexed: 01/04/2023] Open
Abstract
Ultrasensitive response motifs, capable of converting graded stimuli into binary responses, are well-conserved in signal transduction networks. Although it has been shown that a cascade arrangement of multiple ultrasensitive modules can enhance the system's ultrasensitivity, how a given combination of layers affects a cascade's ultrasensitivity remains an open question for the general case. Here, we introduce a methodology that allows us to determine the presence of sequestration effects and to quantify the relative contribution of each module to the overall cascade's ultrasensitivity. The proposed analysis framework provides a natural link between global and local ultrasensitivity descriptors and it is particularly well-suited to characterize and understand mathematical models used to study real biological systems. As a case study, we have considered three mathematical models introduced by O'Shaughnessy et al. to study a tunable synthetic MAPK cascade, and we show how our methodology can help modelers better understand alternative models.
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Affiliation(s)
- Edgar Altszyler
- Laboratorio de Inteligencia Artificial Aplicada, Universidad de Buenos Aires, Departamento de Computación - CONICET, Ciudad Universitaria, Pabellón I, Buenos Aires, C1428EHA, Argentina
| | - Alejandra C. Ventura
- IFIBYNE-UBA-CONICET and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires, C1428EHA, Argentina
| | - Alejandro Colman-Lerner
- IFIBYNE-UBA-CONICET and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires, C1428EHA, Argentina
| | - Ariel Chernomoretz
- Departamento de Física FCEN UBA - IFIBA CONICET, Ciudad Universitaria, Pabellón I, Buenos Aires, C1428EHA, Argentina
- Fundación Instituto Leloir, Av Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina
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Tsvetanova NG, Trester-Zedlitz M, Newton BW, Riordan DP, Sundaram AB, Johnson JR, Krogan NJ, von Zastrow M. G Protein-Coupled Receptor Endocytosis Confers Uniformity in Responses to Chemically Distinct Ligands. Mol Pharmacol 2016; 91:145-156. [PMID: 27879340 DOI: 10.1124/mol.116.106369] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 11/18/2016] [Indexed: 12/19/2022] Open
Abstract
The ability of chemically distinct ligands to produce different effects on the same G protein-coupled receptor (GPCR) has interesting therapeutic implications, but, if excessively propagated downstream, would introduce biologic noise compromising cognate ligand detection. We asked whether cells have the ability to limit the degree to which chemical diversity imposed at the ligand-GPCR interface is propagated to the downstream signal. We carried out an unbiased analysis of the integrated cellular response elicited by two chemically and pharmacodynamically diverse β-adrenoceptor agonists, isoproterenol and salmeterol. We show that both ligands generate an identical integrated response, and that this stereotyped output requires endocytosis. We further demonstrate that the endosomal β2-adrenergic receptor signal confers uniformity on the downstream response because it is highly sensitive and saturable. Based on these findings, we propose that GPCR signaling from endosomes functions as a biologic noise filter to enhance reliability of cognate ligand detection.
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Affiliation(s)
- Nikoleta G Tsvetanova
- Department of Psychiatry (N.G.T., M.T.-Z., M.Z.), Department of Cellular and Molecular Pharmacology (M.Z.), California Institute for Quantitative Biosciences (B.W.N., J.R.J., N.J.K.), and Lung Biology Center, Department of Medicine (A.B.S.), University of California, San Francisco, San Francisco, California; J. David Gladstone Institute, San Francisco, California (N.J.K.); and Department of Biochemistry, Stanford University, Stanford, California (D.P.R.)
| | - Michelle Trester-Zedlitz
- Department of Psychiatry (N.G.T., M.T.-Z., M.Z.), Department of Cellular and Molecular Pharmacology (M.Z.), California Institute for Quantitative Biosciences (B.W.N., J.R.J., N.J.K.), and Lung Biology Center, Department of Medicine (A.B.S.), University of California, San Francisco, San Francisco, California; J. David Gladstone Institute, San Francisco, California (N.J.K.); and Department of Biochemistry, Stanford University, Stanford, California (D.P.R.)
| | - Billy W Newton
- Department of Psychiatry (N.G.T., M.T.-Z., M.Z.), Department of Cellular and Molecular Pharmacology (M.Z.), California Institute for Quantitative Biosciences (B.W.N., J.R.J., N.J.K.), and Lung Biology Center, Department of Medicine (A.B.S.), University of California, San Francisco, San Francisco, California; J. David Gladstone Institute, San Francisco, California (N.J.K.); and Department of Biochemistry, Stanford University, Stanford, California (D.P.R.)
| | - Daniel P Riordan
- Department of Psychiatry (N.G.T., M.T.-Z., M.Z.), Department of Cellular and Molecular Pharmacology (M.Z.), California Institute for Quantitative Biosciences (B.W.N., J.R.J., N.J.K.), and Lung Biology Center, Department of Medicine (A.B.S.), University of California, San Francisco, San Francisco, California; J. David Gladstone Institute, San Francisco, California (N.J.K.); and Department of Biochemistry, Stanford University, Stanford, California (D.P.R.)
| | - Aparna B Sundaram
- Department of Psychiatry (N.G.T., M.T.-Z., M.Z.), Department of Cellular and Molecular Pharmacology (M.Z.), California Institute for Quantitative Biosciences (B.W.N., J.R.J., N.J.K.), and Lung Biology Center, Department of Medicine (A.B.S.), University of California, San Francisco, San Francisco, California; J. David Gladstone Institute, San Francisco, California (N.J.K.); and Department of Biochemistry, Stanford University, Stanford, California (D.P.R.)
| | - Jeffrey R Johnson
- Department of Psychiatry (N.G.T., M.T.-Z., M.Z.), Department of Cellular and Molecular Pharmacology (M.Z.), California Institute for Quantitative Biosciences (B.W.N., J.R.J., N.J.K.), and Lung Biology Center, Department of Medicine (A.B.S.), University of California, San Francisco, San Francisco, California; J. David Gladstone Institute, San Francisco, California (N.J.K.); and Department of Biochemistry, Stanford University, Stanford, California (D.P.R.)
| | - Nevan J Krogan
- Department of Psychiatry (N.G.T., M.T.-Z., M.Z.), Department of Cellular and Molecular Pharmacology (M.Z.), California Institute for Quantitative Biosciences (B.W.N., J.R.J., N.J.K.), and Lung Biology Center, Department of Medicine (A.B.S.), University of California, San Francisco, San Francisco, California; J. David Gladstone Institute, San Francisco, California (N.J.K.); and Department of Biochemistry, Stanford University, Stanford, California (D.P.R.)
| | - Mark von Zastrow
- Department of Psychiatry (N.G.T., M.T.-Z., M.Z.), Department of Cellular and Molecular Pharmacology (M.Z.), California Institute for Quantitative Biosciences (B.W.N., J.R.J., N.J.K.), and Lung Biology Center, Department of Medicine (A.B.S.), University of California, San Francisco, San Francisco, California; J. David Gladstone Institute, San Francisco, California (N.J.K.); and Department of Biochemistry, Stanford University, Stanford, California (D.P.R.)
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