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Andres J, Blomeier T, Zurbriggen MD. Synthetic Switches and Regulatory Circuits in Plants. Plant Physiol 2019; 179:862-884. [PMID: 30692218 PMCID: PMC6393786 DOI: 10.1104/pp.18.01362] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/18/2019] [Indexed: 05/20/2023]
Abstract
Synthetic biology is an established but ever-growing interdisciplinary field of research currently revolutionizing biomedicine studies and the biotech industry. The engineering of synthetic circuitry in bacterial, yeast, and animal systems prompted considerable advances for the understanding and manipulation of genetic and metabolic networks; however, their implementation in the plant field lags behind. Here, we review theoretical-experimental approaches to the engineering of synthetic chemical- and light-regulated (optogenetic) switches for the targeted interrogation and control of cellular processes, including existing applications in the plant field. We highlight the strategies for the modular assembly of genetic parts into synthetic circuits of different complexity, ranging from Boolean logic gates and oscillatory devices up to semi- and fully synthetic open- and closed-loop molecular and cellular circuits. Finally, we explore potential applications of these approaches for the engineering of novel functionalities in plants, including understanding complex signaling networks, improving crop productivity, and the production of biopharmaceuticals.
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Affiliation(s)
- Jennifer Andres
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, 40225 Duesseldorf, Germany
| | - Tim Blomeier
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, 40225 Duesseldorf, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, 40225 Duesseldorf, Germany
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Fultz D, Slotkin RK. Exogenous Transposable Elements Circumvent Identity-Based Silencing, Permitting the Dissection of Expression-Dependent Silencing. Plant Cell 2017; 29:360-376. [PMID: 28193737 PMCID: PMC5354191 DOI: 10.1105/tpc.16.00718] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 12/19/2016] [Accepted: 02/10/2017] [Indexed: 05/09/2023]
Abstract
The propagation of epigenetic marks has received a great deal of attention, yet the initiation of epigenetic silencing of a new transgene, virus, or transposable element (TE) remains enigmatic. The overlapping and simultaneous function of multiple silencing mechanisms has obscured this area of investigation. Here, we revealed two broad mechanisms that can initiate silencing independently: identity-based and expression-dependent silencing. We found that identity-based silencing is targeted by 21- to 22-nucleotide or 24-nucleotide small interfering RNAs (siRNAs) generated from previously silenced regions of the genome. By transforming exogenous TEs into Arabidopsis thaliana, we circumvented identity-based silencing, allowing us to isolate and investigate the molecular mechanism of expression-dependent silencing. We found that several siRNA-generating mechanisms all trigger de novo expression-dependent RNA-directed DNA methylation (RdDM) through RNA Polymerase V. In addition, while full-length TEs quickly progress beyond RdDM to heterochromatin formation and the final maintenance methylation state, TE fragments stall at the RdDM phase. Lastly, we found that transformation into a mutant genotype followed by introgression into the wild type does not result in the same level of silencing as direct transformation into the wild type. This demonstrates that the plant genotype during a narrow window of time at TE insertion (or transgene transformation) is key for establishing the transgenerational extent of epigenetic silencing.
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Affiliation(s)
- Dalen Fultz
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
- Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, Ohio 43210
| | - R Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
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Paszkowski J. Controlled activation of retrotransposition for plant breeding. Curr Opin Biotechnol 2015; 32:200-206. [PMID: 25615932 DOI: 10.1016/j.copbio.2015.01.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 12/30/2014] [Accepted: 01/05/2015] [Indexed: 12/16/2022]
Abstract
Plant genomes consist to a large extent of transposable elements (TEs), predominantly retrotransposons. Their accumulation through periodic transposition bursts has shaped the structure and regulatory organization of plant genomes, often contributing to phenotypic traits. Transposon-generated phenotypes selected by humans during plant domestication have been maintained under strict selection during subsequent plant breeding. Our knowledge of the epigenetic, environmental, and developmental regulation of TE activity has advanced considerably in recent years. Here I will consider TEs as an attractive endogenous source of genetic variation that can be liberated in a controlled fashion and thus offer novel phenotypic diversity to be selected for crop improvement.
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Affiliation(s)
- Jerzy Paszkowski
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom.
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Abstract
Synthetic biology methods are routinely applied in the plant field as in other eukaryotic model systems. Several synthetic components have been developed in plants and an increasing number of studies report on the assembly into functional synthetic genetic circuits. This chapter gives an overview of the existing plant genetic networks and describes in detail the application of two systems for inducible gene expression. The ethanol-inducible system relies on the ethanol-responsive interaction of the AlcA transcriptional activator and the AlcR receptor resulting in the transcription of the gene of interest (GOI). In comparison, the translational fusion of GOI and the glucocorticoid receptor (GR) domain leads to the dexamethasone-dependent nuclear translocation of the GOI::GR protein. This chapter contains detailed protocols for the application of both systems in the model plants potato and Arabidopsis, respectively.
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Affiliation(s)
- Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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Tramontano A, Donath A, Bernhart SH, Reiche K, Böhmdorfer G, Stadler PF, Bachmair A. Deletion analysis of the 3' long terminal repeat sequence of plant retrotransposon Tto1 identifies 125 base pairs redundancy as sufficient for first strand transfer. Virology 2011; 412:75-82. [PMID: 21262516 PMCID: PMC3061985 DOI: 10.1016/j.virol.2010.12.059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 10/29/2010] [Accepted: 12/31/2010] [Indexed: 11/30/2022]
Abstract
Retroviruses and many retrotransposons are flanked by sequence repeats called long terminal repeats (LTRs). These sequences contain a promoter region, which is active in the 5′ LTR, and transcription termination signals, which are active in the LTR copy present at the 3′ end. A section in the middle of the LTR, called Redundancy region, occurs at both ends of the mRNA. Here we show that in the copia type retrotransposon Tto1, the promoter and terminator functions of the LTR can be supplied by heterologous sequences, thereby converting the LTR into a significantly shorter sub-terminal repeat. An engineered Tto1 element with 125 instead of the usual 574 base pairs repeated in the 5′ and 3′ region can still promote strand transfer during cDNA synthesis, defining a minimal Redundancy region for this element. Based on this finding, we propose a model for first strand transfer of Tto1.
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Affiliation(s)
- Andrea Tramontano
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany
| | - Alexander Donath
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center of Bioinformatics, University of Leipzig, Härtelstrasse 16–18, D-04107 Leipzig, Germany
| | - Stephan H. Bernhart
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center of Bioinformatics, University of Leipzig, Härtelstrasse 16–18, D-04107 Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria
| | - Kristin Reiche
- RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology IZI, Perlickstr. 1, D-04103 Leipzig, Germany
| | - Gudrun Böhmdorfer
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center of Bioinformatics, University of Leipzig, Härtelstrasse 16–18, D-04107 Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria
- RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology IZI, Perlickstr. 1, D-04103 Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D-04103 Leipzig, Germany
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Andreas Bachmair
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany
- Corresponding author. Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria.
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