1
|
Han CS, Kim S, Lee SE, Choi S, Kim SH, Yoon IS, Hwang YS. Cross-talk between ABA and sugar signaling is mediated by the ACGT core and CE1 element reciprocally in OsTIP3;1 promoter. JOURNAL OF PLANT PHYSIOLOGY 2018; 224-225:103-111. [PMID: 29614396 DOI: 10.1016/j.jplph.2018.03.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 05/11/2023]
Abstract
Recently, much effort has been made to determine the molecular links and cross-talk between sugar and abscisic acid (ABA) signaling pathways. ABA-inducible expression of OsTIP3;1, encoding a rice tonoplast intrinsic protein, was enhanced by sugar depletion. Such a stimulatory increase in OsTIP3;1 expression under sugar-starvation is possibly not owing to changes in endogenous ABA content. The transient expression assay indicated that the 5' flanking region of OsTIP3;1 delivered similar collaborative responsiveness to starvation and ABA, suggesting that this gene promoter could be a good molecular probe to examine the interaction between sugar and ABA signaling pathways. Targeted mutagenesis demonstrated that disruption of ACGT cores decreased the induction of OsTIP3;1 promoter activity under either starvation or ABA, whereas mutation of coupling element 1 (CE1), which is an ABI4 binding site, reversely increased it, suggesting that those two distinct cis-regulatory elements reciprocally regulate the responsiveness of this promoter to both sugar and ABA. Consistent with this result, antisense inhibition of ABI4 increased the OsTIP3;1 promoter activity. ABI4 expression was also enhanced by sugars and repressed by ABA, suggesting that reduced ABI4 binding to CE1 in the absence of sugar and presence of ABA could increase ABA-induction of the OsTIP3;1 promoter activity.
Collapse
Affiliation(s)
- Chae-Seong Han
- Department of Systems Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - Sol Kim
- Department of Systems Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - Sung-Eun Lee
- Department of Systems Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - Siyoung Choi
- Department of Systems Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - Soo-Hwan Kim
- Division of Biological Science and Technology, Yonsei University, Wonju, 220-710, Republic of Korea
| | - In Sun Yoon
- Molecular Breeding Division, Natural Institute of Agricultural Sciences, Rural Development Administration, Jeonju 55365, Republic of Korea
| | - Yong-Sic Hwang
- Department of Systems Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea.
| |
Collapse
|
2
|
Ang J, Harris E, Hussey BJ, Kil R, McMillen DR. Tuning response curves for synthetic biology. ACS Synth Biol 2013; 2:547-67. [PMID: 23905721 PMCID: PMC3805330 DOI: 10.1021/sb4000564] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Indexed: 01/07/2023]
Abstract
Synthetic biology may be viewed as an effort to establish, formalize, and develop an engineering discipline in the context of biological systems. The ability to tune the properties of individual components is central to the process of system design in all fields of engineering, and synthetic biology is no exception. A large and growing number of approaches have been developed for tuning the responses of cellular systems, and here we address specifically the issue of tuning the rate of response of a system: given a system where an input affects the rate of change of an output, how can the shape of the response curve be altered experimentally? This affects a system's dynamics as well as its steady-state properties, both of which are critical in the design of systems in synthetic biology, particularly those with multiple components. We begin by reviewing a mathematical formulation that captures a broad class of biological response curves and use this to define a standard set of varieties of tuning: vertical shifting, horizontal scaling, and the like. We then survey the experimental literature, classifying the results into our defined categories, and organizing them by regulatory level: transcriptional, post-transcriptional, and post-translational.
Collapse
Affiliation(s)
- Jordan Ang
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - Edouard Harris
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - Brendan J. Hussey
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - Richard Kil
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - David R. McMillen
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| |
Collapse
|
3
|
Murphy KF, Balázsi G, Collins JJ. Combinatorial promoter design for engineering noisy gene expression. Proc Natl Acad Sci U S A 2007; 104:12726-31. [PMID: 17652177 PMCID: PMC1931564 DOI: 10.1073/pnas.0608451104] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Understanding the behavior of basic biomolecular components as parts of larger systems is one of the goals of the developing field of synthetic biology. A multidisciplinary approach, involving mathematical and computational modeling in parallel with experimentation, is often crucial for gaining such insights and improving the efficiency of artificial gene network design. Here we used such an approach and developed a combinatorial promoter design strategy to characterize how the position and multiplicity of tetO(2) operator sites within the GAL1 promoter affect gene expression levels and gene expression noise in Saccharomyces cerevisiae. We observed stronger transcriptional repression and higher gene expression noise as a single operator site was moved closer to the TATA box, whereas for multiple operator-containing promoters, we found that the position and number of operator sites together determined the dose-response curve and gene expression noise. We developed a generic computational model that captured the experimentally observed differences for each of the promoters, and more detailed models to successively predict the behavior of multiple operator-containing promoters from single operator-containing promoters. Our results suggest that the independent binding of single repressors is not sufficient to explain the more complex behavior of the multiple operator-containing promoters. Taken together, our findings highlight the importance of joint experimental-computational efforts and some of the challenges of using a bottom-up approach based on well characterized, isolated biomolecular components for predicting the behavior of complex, synthetic gene networks, e.g., the whole can be different from the sum of its parts.
Collapse
Affiliation(s)
- Kevin F Murphy
- Department of Biomedical Engineering, Center for BioDynamics and Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA
| | | | | |
Collapse
|
4
|
Acevedo-Hernández GJ, León P, Herrera-Estrella LR. Sugar and ABA responsiveness of a minimal RBCS light-responsive unit is mediated by direct binding of ABI4. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 43:506-19. [PMID: 16098105 DOI: 10.1111/j.1365-313x.2005.02468.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Photosynthesis-associated nuclear genes (PhANGs) are able to respond to multiple environmental and developmental signals, including light, sugars and abscisic acid (ABA). PhANGs have been extensively studied at the level of transcriptional regulation and several cis-acting elements important for light responsiveness have been identified in their promoter sequences. However, the regulatory elements involved in sugar and ABA regulation of PhANGs have not been completely characterized. Using conserved modular arrangement 5 (CMA5), a previously characterized minimal light-responsive unit, we show that in Arabidopsis thaliana this unit responds not only positively to light signals, but also negatively to sugars and ABA. The latter responses were found to be impaired in the abi4 mutant, indicating that ABSCISIC ACID INSENSITIVE-4 (ABI4) is a regulator involved in sugar and ABA repression of this minimal regulatory unit. Furthermore, we report a new sequence element conserved in several rbcS promoters, herewith named S-box, which is important for the sugar and ABA responsiveness of CMA5. This sequence corresponds to a putative ABI4-binding site, which is in fact bound by the Arabidopsis ABI4 protein in vitro. The S-box is closely associated with the G-box present in CMA5, and this association is conserved in the promoters of several RBCS genes. This phylogenetically conserved promoter feature probably reflects a common regulatory mechanism and identifies a point of convergence between light- and sugar-signaling pathways.
Collapse
Affiliation(s)
- Gustavo Javier Acevedo-Hernández
- Departamento de Ingeniería Genética de Plantas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional - Unidad Irapuato, Apartado Postal 629, Irapuato, Guanajuato 36500, Mexico
| | | | | |
Collapse
|
5
|
Wang R, Zhou X, Wang X. Chemically regulated expression systems and their applications in transgenic plants. Transgenic Res 2004; 12:529-40. [PMID: 14601652 DOI: 10.1023/a:1025852307127] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
In the past 20 years, several systems have been developed to control transgene expression in plants using chemicals. The components used to construct these systems are derived from regulatory sequences mostly from non-plant organisms such as bacteria, fungi, insects and mammals. These constructs allowed transgene expression to be controlled temporally, spatially and quantitatively with the help of exogenous chemicals, without disturbing endogenous plant gene expression. Various chemically regulated transgene expression systems, their advantages/disadvantages and their potential for large-scale field application are reviewed.
Collapse
Affiliation(s)
- Renhou Wang
- Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, PR China
| | | | | |
Collapse
|
6
|
Abstract
Gene regulation by tetracyclines has become a widely-used tool to study gene functions in pro- and eukaryotes. This regulatory system originates from Gram-negative bacteria, in which it fine-tunes expression of a tetracycline-specific export protein mediating resistance against this antibiotic. This review attempts to describe briefly the selective pressures governing the evolution of tetracycline regulation, which have led to the unique regulatory properties underlying its success in manifold applications. After discussing the basic mechanisms we will present the large variety of designed alterations of activities which have contributed to the still growing tool-box of components available for adjusting the regulatory properties to study gene functions in different organisms or tissues. Finally, we provide an overview of the various experimental setups available for pro- and eukaryotes, and touch upon some highlights discovered by the use of tetracycline-dependent gene regulation.
Collapse
Affiliation(s)
- Christian Berens
- Lehrstuhl für Mikrobiologie, Friedrich-Alexander Universität Erlangen-Nürnberg, Staudtstr. 5, D-91058, Erlangen, Germany
| | | |
Collapse
|
7
|
Berens C, Hillen W. Gene regulation by tetracyclines. Constraints of resistance regulation in bacteria shape TetR for application in eukaryotes. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:3109-21. [PMID: 12869186 DOI: 10.1046/j.1432-1033.2003.03694.x] [Citation(s) in RCA: 184] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Tet repressor protein (TetR) regulates transcription of a family of tetracycline (tc) resistance determinants in Gram-negative bacteria. The resistance protein TetA, a membrane-spanning H+-[tc.M]+ antiporter, must be sensitively regulated because its expression is harmful in the absence of tc, yet it has to be expressed before the drugs' concentration reaches cytoplasmic levels inhibitory for protein synthesis. Consequently, TetR shows highly specific tetO binding to reduce basal expression and high affinity to tc to ensure sensitive induction. Tc can cross biological membranes by diffusion enabling this inducer to penetrate the majority of cells. These regulatory and pharmacological properties are the basis for application of TetR to selectively control the expression of single genes in lower and higher eukaryotes. TetR can be used for that purpose in some organisms without further modifications. In mammals and in a large variety of other organisms, however, eukaryotic transcriptional activator or repressor domains are fused to TetR to turn it into an efficient regulator. Mechanistic understanding and the ability to engineer and screen for mutants with specific properties allow tailoring of the DNA recognition specificity, the response to inducer tc and the dimerization specificity of TetR-based eukaryotic regulators. This review provides an overview of the TetR properties as they evolved in bacteria, the functional modifications necessary to transform it into a convenient, specific and efficient regulator for use in eukaryotes and how the interplay between structure--function studies in bacteria and specific requirements of particular applications in eukaryotes have made it a versatile and highly adaptable regulatory system.
Collapse
Affiliation(s)
- Christian Berens
- Lehrstuhl für Mikrobiologie, Institut für Mikrobiologie, Biochemie und Genetik, Friedrich-Alexander Universität Erlangen-Nürnberg, Germany
| | | |
Collapse
|
8
|
Frey AD, Rimann M, Bailey JE, Kallio PT, Thompson CJ, Fussenegger M. Novel pristinamycin-responsive expression systems for plant cells. Biotechnol Bioeng 2001; 74:154-63. [PMID: 11370004 DOI: 10.1002/bit.1105] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Novel gene regulation systems were designed for plant cells responsive to the streptogramin antibiotic pristinamycin. The pristinamycin-repressible plant gene regulation concept (PIPpOFF) is based on a transcriptional activator (PIT) which consists of the Pip protein, the repressor of the pristinamycin resistance operon of Streptomyces coelicolor, fused to the VP16 transactivation domain of the Herpes simplex virus. PIT mediates pristinamycin-repressible activation of a synthetic plant promoter (P(pPIR)) in tobacco cells consisting of a nine Pip-binding site-containing artificial operator (PIR3) placed upstream of a TATA-box derived from the cauliflower mosaic virus 35S promoter (P(CaMV35S)). Pristinamycin interferes with induction by negatively regulating the DNA-binding capacity of the Pip moiety of PIT. A second, streptogramin-inducible plant gene regulation system (PIPpON) was constructed by combining Pip expression with a plant-specific pristinamycin-inducible promoter (P(pPIRON)). P(pPIRON) consists of a PIR3 module cloned downstream of the strong constitutive plant promoter P(CaMV35S). As in the native Streptomyces configuration, Pip binds to its cognate sequence within P(pPIRON) in the absence of regulating antibiotic and silences the chimeric plant promoter. Upon addition of pristinamycin, Pip is released from the PIR3 operator and full P(CaMV35S)-driven expression of desired plant genes is induced. The PIPpOFF and PIPpON systems performed well in Nicotiana tabacum suspension cultures and promise to provide an attractive extension of existing plant gene regulation technology for basic plant research or biopharmaceutical manufacturing using plant tissue culture.
Collapse
Affiliation(s)
- A D Frey
- Institute of Biotechnology, Swiss Federal Institute of Technology, ETH Zurich, CH-8093 Zurich, Switzerland
| | | | | | | | | | | |
Collapse
|
9
|
Abstract
Promoters that respond to otherwise inactive chemicals will enhance the tools available for analyzing gene function in vivo and for altering defined traits of plants at will. Approaches to provide such tools have yielded plant promoters that respond to compounds activating defense genes. In addition, the transfer of regulatory elements from prokaryotes, insects, and mammals has opened new avenues to construct chemically inducible promoters that respond to signals normally not recognized by plants. This review describes results and applications of these two approaches.
Collapse
Affiliation(s)
- C. Gatz
- Pflanzenphysiologisches Institut, Georg-August-Universitat Gottingen, Untere Karspule 2, Gottingen, 37073 Germany
| |
Collapse
|
10
|
|
11
|
Abstract
An inducible expression system was developed for the protozoan parasite Trypanosoma brucei. Transgenic trypanosomes expressing the tetracycline repressor of Escherichia coli exhibited inducer (tetracycline)-dependent expression of chromosomally integrated reporter genes under the control of a procyclic acidic repetitive protein (PARP) promoter bearing a tet operator. Reporter expression could be controlled over a range of four orders of magnitude in response to tetracycline concentration, a degree of regulation that exceeds those exhibited by other eukaryotic repression-based systems. The tet repressor-controlled PARP promoter should be a valuable tool for the study of trypanosome biochemistry, pathogenicity, and cell and molecular biology.
Collapse
Affiliation(s)
- E Wirtz
- Zentrum für Molekulare Biologie, Universität Heidelberg, Germany
| | | |
Collapse
|
12
|
Affiliation(s)
- C Gatz
- Institut für Genetik, Universität Bielefeld, Germany
| |
Collapse
|