51
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Huang D, Kosentka PZ, Liu W. Synthetic biology approaches in regulation of targeted gene expression. CURRENT OPINION IN PLANT BIOLOGY 2021; 63:102036. [PMID: 33930839 DOI: 10.1016/j.pbi.2021.102036] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 05/15/2023]
Abstract
Synthetic biology approaches are highly sought-after to facilitate the regulation of targeted gene expression in plants for functional genomics research and crop trait improvement. To date, synthetic regulation of gene expression predominantly focuses at the transcription level via engineering of synthetic promoters and transcription factors, while pioneering examples have started to emerge for synthetic regulation of gene expression at the levels of mRNA stability, translation, and protein degradation. This review discusses recent advances in plant synthetic biology for the regulation of gene expression at multiple levels, and highlights their future directions.
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Affiliation(s)
- Debao Huang
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Pawel Z Kosentka
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA.
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52
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Tagliani A. Synthetic promoters went green: MinSyns bridge the gap between tunable expression and synthetic biology in plants. Synth Biol (Oxf) 2021; 5:ysaa027. [PMID: 34557593 PMCID: PMC8454517 DOI: 10.1093/synbio/ysaa027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 11/11/2020] [Accepted: 11/16/2020] [Indexed: 11/14/2022] Open
Affiliation(s)
- Andrea Tagliani
- Department of Biosciences, Università degli Studi di Milano, 20133 Milan, Italy
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53
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Dudley QM, Cai YM, Kallam K, Debreyne H, Carrasco Lopez JA, Patron NJ. Biofoundry-assisted expression and characterization of plant proteins. Synth Biol (Oxf) 2021; 6:ysab029. [PMID: 34693026 PMCID: PMC8529701 DOI: 10.1093/synbio/ysab029] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 08/25/2021] [Accepted: 09/09/2021] [Indexed: 12/29/2022] Open
Abstract
Many goals in synthetic biology, including the elucidation and refactoring of biosynthetic pathways and the engineering of regulatory circuits and networks, require knowledge of protein function. In plants, the prevalence of large gene families means it can be particularly challenging to link specific functions to individual proteins. However, protein characterization has remained a technical bottleneck, often requiring significant effort to optimize expression and purification protocols. To leverage the ability of biofoundries to accelerate design-built-test-learn cycles, we present a workflow for automated DNA assembly and cell-free expression of plant proteins that accelerates optimization and enables rapid screening of enzyme activity. First, we developed a phytobrick-compatible Golden Gate DNA assembly toolbox containing plasmid acceptors for cell-free expression using Escherichia coli or wheat germ lysates as well as a set of N- and C-terminal tag parts for detection, purification and improved expression/folding. We next optimized automated assembly of miniaturized cell-free reactions using an acoustic liquid handling platform and then compared tag configurations to identify those that increase expression. We additionally developed a luciferase-based system for rapid quantification that requires a minimal 11-amino acid tag and demonstrate facile removal of tags following synthesis. Finally, we show that several functional assays can be performed with cell-free protein synthesis reactions without the need for protein purification. Together, the combination of automated assembly of DNA parts and cell-free expression reactions should significantly increase the throughput of experiments to test and understand plant protein function and enable the direct reuse of DNA parts in downstream plant engineering workflows.
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Affiliation(s)
- Quentin M Dudley
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk UK
| | - Yao-Min Cai
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk UK
| | - Kalyani Kallam
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk UK
| | - Hubert Debreyne
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk UK
| | | | - Nicola J Patron
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk UK
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54
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Schwope R, Magris G, Miculan M, Paparelli E, Celii M, Tocci A, Marroni F, Fornasiero A, De Paoli E, Morgante M. Open chromatin in grapevine marks candidate CREs and with other chromatin features correlates with gene expression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1631-1647. [PMID: 34219317 PMCID: PMC8518642 DOI: 10.1111/tpj.15404] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 05/14/2023]
Abstract
Vitis vinifera is an economically important crop and a useful model in which to study chromatin dynamics. In contrast to the small and relatively simple genome of Arabidopsis thaliana, grapevine contains a complex genome of 487 Mb that exhibits extensive colonization by transposable elements. We used Hi-C, ChIP-seq and ATAC-seq to measure how chromatin features correlate to the expression of 31 845 grapevine genes. ATAC-seq revealed the presence of more than 16 000 open chromatin regions, of which we characterize nearly 5000 as possible distal enhancer candidates that occur in intergenic space > 2 kb from the nearest transcription start site (TSS). A motif search identified more than 480 transcription factor (TF) binding sites in these regions, with those for TCP family proteins in greatest abundance. These open chromatin regions are typically within 15 kb from their nearest promoter, and a gene ontology analysis indicated that their nearest genes are significantly enriched for TF activity. The presence of a candidate cis-regulatory element (cCRE) > 2 kb upstream of the TSS, location in the active nuclear compartment as determined by Hi-C, and the enrichment of H3K4me3, H3K4me1 and H3K27ac at the gene are correlated with gene expression. Taken together, these results suggest that regions of intergenic open chromatin identified by ATAC-seq can be considered potential candidates for cis-regulatory regions in V. vinifera. Our findings enhance the characterization of a valuable agricultural crop, and help to clarify the understanding of unique plant biology.
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Affiliation(s)
- Rachel Schwope
- Dipartimento di Scienze AgroalimentariAmbientali e Animali (DI4A)UdineI‐33100Italy
- Istituto di Genomica ApplicataUdineI‐33100Italy
| | - Gabriele Magris
- Dipartimento di Scienze AgroalimentariAmbientali e Animali (DI4A)UdineI‐33100Italy
- Istituto di Genomica ApplicataUdineI‐33100Italy
| | - Mara Miculan
- Dipartimento di Scienze AgroalimentariAmbientali e Animali (DI4A)UdineI‐33100Italy
- Istituto di Genomica ApplicataUdineI‐33100Italy
- Present address:
Institute of Life SciencesScuola Superiore Sant'Anna PisaPisa56127Italy
| | - Eleonora Paparelli
- Dipartimento di Scienze AgroalimentariAmbientali e Animali (DI4A)UdineI‐33100Italy
- Istituto di Genomica ApplicataUdineI‐33100Italy
- Present address:
IGA Technology ServicesUdineI‐33100Italy
| | - Mirko Celii
- Dipartimento di Scienze AgroalimentariAmbientali e Animali (DI4A)UdineI‐33100Italy
- Istituto di Genomica ApplicataUdineI‐33100Italy
- Present address:
Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE)KAUSTThuwalMakkahSaudi Arabia
| | - Aldo Tocci
- Dipartimento di Scienze AgroalimentariAmbientali e Animali (DI4A)UdineI‐33100Italy
- Istituto di Genomica ApplicataUdineI‐33100Italy
- Scuola Internazionale Superiore di Studi AvanzatiTriesteFriuli‐Venezia GiuliaItaly
| | - Fabio Marroni
- Dipartimento di Scienze AgroalimentariAmbientali e Animali (DI4A)UdineI‐33100Italy
- Istituto di Genomica ApplicataUdineI‐33100Italy
| | - Alice Fornasiero
- Dipartimento di Scienze AgroalimentariAmbientali e Animali (DI4A)UdineI‐33100Italy
- Istituto di Genomica ApplicataUdineI‐33100Italy
- Present address:
Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE)KAUSTThuwalMakkahSaudi Arabia
| | - Emanuele De Paoli
- Dipartimento di Scienze AgroalimentariAmbientali e Animali (DI4A)UdineI‐33100Italy
| | - Michele Morgante
- Dipartimento di Scienze AgroalimentariAmbientali e Animali (DI4A)UdineI‐33100Italy
- Istituto di Genomica ApplicataUdineI‐33100Italy
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55
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Garagounis C, Delkis N, Papadopoulou KK. Unraveling the roles of plant specialized metabolites: using synthetic biology to design molecular biosensors. THE NEW PHYTOLOGIST 2021; 231:1338-1352. [PMID: 33997999 DOI: 10.1111/nph.17470] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/16/2021] [Indexed: 05/25/2023]
Abstract
Plants are a rich source of specialized metabolites with a broad range of bioactivities and many applications in human daily life. Over the past decades significant progress has been made in identifying many such metabolites in different plant species and in elucidating their biosynthetic pathways. However, the biological roles of plant specialized metabolites remain elusive and proposed functions lack an identified underlying molecular mechanism. Understanding the roles of specialized metabolites frequently is hampered by their dynamic production and their specific spatiotemporal accumulation within plant tissues and organs throughout a plant's life cycle. In this review, we propose the employment of strategies from the field of Synthetic Biology to construct and optimize genetically encoded biosensors that can detect individual specialized metabolites in a standardized and high-throughput manner. This will help determine the precise localization of specialized metabolites at the tissue and single-cell levels. Such information will be useful in developing complete system-level models of specialized plant metabolism, which ultimately will demonstrate how the biosynthesis of specialized metabolites is integrated with the core processes of plant growth and development.
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Affiliation(s)
- Constantine Garagounis
- Department of Biochemistry and Biotechnology, Plant and Environmental Biotechnology Laboratory, University of Thessaly, Larissa, 41500, Greece
| | - Nikolaos Delkis
- Department of Biochemistry and Biotechnology, Plant and Environmental Biotechnology Laboratory, University of Thessaly, Larissa, 41500, Greece
| | - Kalliope K Papadopoulou
- Department of Biochemistry and Biotechnology, Plant and Environmental Biotechnology Laboratory, University of Thessaly, Larissa, 41500, Greece
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56
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Cai YM, Dudley QM, Patron NJ. Measurement of Transgene Copy Number in Plants Using Droplet Digital PCR. Bio Protoc 2021; 11:e4075. [PMID: 34327272 PMCID: PMC8292117 DOI: 10.21769/bioprotoc.4075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 11/02/2022] Open
Abstract
Transgenic plants are produced both to investigate gene function and to confer desirable traits into crops. Transgene copy number is known to influence expression levels, and consequently, phenotypes. Similarly, knowledge of transgene zygosity is desirable for making quantitative assessments of phenotype and tracking the inheritance of transgenes in progeny generations. Since the first transgenic plants were produced, several methods for determining copy number have been applied, including Southern blotting, quantitative real-time PCR, and more recently, sequencing methods; however, each method has specific disadvantages, compromising throughput, accuracy, or expense. Digital PCR (dPCR) divides reactions into partitions, converting the exponential, analogue nature of PCR into a linear, digital signal that allows the frequency of occurrence of specific sequences to be accurately estimated. Confidence increases with the number of partitions; therefore, the availability of emulsion technologies that enable reactions to be divided into tens of thousands of nanodroplets allows accurate determination of copy number in what has become known as digital droplet PCR (ddPCR). ddPCR offers similar benefits of low costs and scalability as other PCR techniques but with superior accuracy and reliability. Graphic abstract: Digital PCR (dPCR) divides reactions into partitions, converting the exponential, analogue nature of PCR into a linear, digital signal that allows the frequency of transgene copy number to be accurately assessed.
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Affiliation(s)
- Yao-Min Cai
- Earlham Institute, Norwich Research Park, Colney lane, Norwich, UK
| | | | - Nicola J. Patron
- Earlham Institute, Norwich Research Park, Colney lane, Norwich, UK
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57
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Yang Y, Lee JH, Poindexter MR, Shao Y, Liu W, Lenaghan SC, Ahkami AH, Blumwald E, Stewart CN. Rational design and testing of abiotic stress-inducible synthetic promoters from poplar cis-regulatory elements. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1354-1369. [PMID: 33471413 PMCID: PMC8313130 DOI: 10.1111/pbi.13550] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 12/31/2020] [Accepted: 01/09/2021] [Indexed: 05/27/2023]
Abstract
Abiotic stress resistance traits may be especially crucial for sustainable production of bioenergy tree crops. Here, we show the performance of a set of rationally designed osmotic-related and salt stress-inducible synthetic promoters for use in hybrid poplar. De novo motif-detecting algorithms yielded 30 water-deficit (SD) and 34 salt stress (SS) candidate DNA motifs from relevant poplar transcriptomes. We selected three conserved water-deficit stress motifs (SD18, SD13 and SD9) found in 16 co-expressed gene promoters, and we discovered a well-conserved motif for salt response (SS16). We characterized several native poplar stress-inducible promoters to enable comparisons with our synthetic promoters. Fifteen synthetic promoters were designed using various SD and SS subdomains, in which heptameric repeats of five-to-eight subdomain bases were fused to a common core promoter downstream, which, in turn, drove a green fluorescent protein (GFP) gene for reporter assays. These 15 synthetic promoters were screened by transient expression assays in poplar leaf mesophyll protoplasts and agroinfiltrated Nicotiana benthamiana leaves under osmotic stress conditions. Twelve synthetic promoters were induced in transient expression assays with a GFP readout. Of these, five promoters (SD18-1, SD9-2, SS16-1, SS16-2 and SS16-3) endowed higher inducibility under osmotic stress conditions than native promoters. These five synthetic promoters were stably transformed into Arabidopsis thaliana to study inducibility in whole plants. Herein, SD18-1 and SD9-2 were induced by water-deficit stress, whereas SS16-1, SS16-2 and SS16-3 were induced by salt stress. The synthetic biology design pipeline resulted in five synthetic promoters that outperformed endogenous promoters in transgenic plants.
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Affiliation(s)
- Yongil Yang
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Jun Hyung Lee
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Magen R. Poindexter
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Yuanhua Shao
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Wusheng Liu
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Department of Horticultural ScienceNorth Carolina State UniversityRaleighNCUSA
| | - Scott C. Lenaghan
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Food ScienceUniversity of TennesseeKnoxvilleTNUSA
| | - Amir H. Ahkami
- Environmental Molecular Sciences Laboratory (EMSL)Pacific Northwest National Laboratory (PNNL)RichlandWAUSA
| | | | - Charles Neal Stewart
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
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58
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Jores T, Tonnies J, Wrightsman T, Buckler ES, Cuperus JT, Fields S, Queitsch C. Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters. NATURE PLANTS 2021; 7:842-855. [PMID: 34083762 PMCID: PMC10246763 DOI: 10.1038/s41477-021-00932-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/27/2021] [Indexed: 05/24/2023]
Abstract
Targeted engineering of plant gene expression holds great promise for ensuring food security and for producing biopharmaceuticals in plants. However, this engineering requires thorough knowledge of cis-regulatory elements to precisely control either endogenous or introduced genes. To generate this knowledge, we used a massively parallel reporter assay to measure the activity of nearly complete sets of promoters from Arabidopsis, maize and sorghum. We demonstrate that core promoter elements-notably the TATA box-as well as promoter GC content and promoter-proximal transcription factor binding sites influence promoter strength. By performing the experiments in two assay systems, leaves of the dicot tobacco and protoplasts of the monocot maize, we detect species-specific differences in the contributions of GC content and transcription factors to promoter strength. Using these observations, we built computational models to predict promoter strength in both assay systems, allowing us to design highly active promoters comparable in activity to the viral 35S minimal promoter. Our results establish a promising experimental approach to optimize native promoter elements and generate synthetic ones with desirable features.
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Affiliation(s)
- Tobias Jores
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jackson Tonnies
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Graduate Program in Biology, University of Washington, Seattle, WA, USA
| | - Travis Wrightsman
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Edward S Buckler
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
- Agricultural Research Service, United States Department of Agriculture, Ithaca, NY, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Department of Medicine, University of Washington, Seattle, WA, USA.
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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Einhaus A, Baier T, Rosenstengel M, Freudenberg RA, Kruse O. Rational Promoter Engineering Enables Robust Terpene Production in Microalgae. ACS Synth Biol 2021; 10:847-856. [PMID: 33764741 DOI: 10.1021/acssynbio.0c00632] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Microalgal biotechnology promises sustainable light-driven production of valuable bioproducts and addresses urgent demands to attain a sustainable economy. However, to unfold its full potential as a platform for biotechnology, new and powerful tools for nuclear engineering need to be established. Chlamydomonas reinhardtii, the model for microalgal synthetic biology and genetic engineering has already been used to produce various bioproducts. Nevertheless, low transgene titers, the lack of potent expression elements, and sparse comparative evaluation prevents further development of C. reinhardtii as a biotechnological host. By systematically evaluating existing expression elements combined with rational promoter engineering, we established novel synthetic expression elements, improved the standardized application of synthetic biology tools, and unveiled an existing synergism between the PSAD 5' UTR and its corresponding chloroplast targeting peptide. Promoter engineering strategies, implemented in a newly designed synthetic algal promoter, increased the production of the sesquiterpene (E)-α-bisabolene by 18-fold compared to its native version and 4-fold to commonly used expression elements. Our results improve the application of synthetic biology in microalgae and display a significant step toward establishing C. reinhardtii as a sustainable green cell-factory.
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Affiliation(s)
- Alexander Einhaus
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitaetsstrasse 27, 33615 Bielefeld, Germany
| | - Thomas Baier
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitaetsstrasse 27, 33615 Bielefeld, Germany
| | - Marian Rosenstengel
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitaetsstrasse 27, 33615 Bielefeld, Germany
| | - Robert A. Freudenberg
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitaetsstrasse 27, 33615 Bielefeld, Germany
| | - Olaf Kruse
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitaetsstrasse 27, 33615 Bielefeld, Germany
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Biosensors: A Sneak Peek into Plant Cell's Immunity. Life (Basel) 2021; 11:life11030209. [PMID: 33800034 PMCID: PMC7999283 DOI: 10.3390/life11030209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/23/2021] [Accepted: 03/03/2021] [Indexed: 12/26/2022] Open
Abstract
Biosensors are indispensable tools to understand a plant’s immunity as its spatiotemporal dimension is key in withstanding complex plant immune signaling. The diversity of genetically encoded biosensors in plants is expanding, covering new analytes with ever higher sensitivity and robustness, but their assortment is limited in some respects, such as their use in following biotic stress response, employing more than one biosensor in the same chassis, and their implementation into crops. In this review, we focused on the available biosensors that encompass these aspects. We show that in vivo imaging of calcium and reactive oxygen species is satisfactorily covered with the available genetically encoded biosensors, while on the other hand they are still underrepresented when it comes to imaging of the main three hormonal players in the immune response: salicylic acid, ethylene and jasmonic acid. Following more than one analyte in the same chassis, upon one or more conditions, has so far been possible by using the most advanced genetically encoded biosensors in plants which allow the monitoring of calcium and the two main hormonal pathways involved in plant development, auxin and cytokinin. These kinds of biosensor are also the most evolved in crops. In the last section, we examine the challenges in the use of biosensors and demonstrate some strategies to overcome them.
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Grützner R, Schubert R, Horn C, Yang C, Vogt T, Marillonnet S. Engineering Betalain Biosynthesis in Tomato for High Level Betanin Production in Fruits. FRONTIERS IN PLANT SCIENCE 2021; 12:682443. [PMID: 34177999 PMCID: PMC8220147 DOI: 10.3389/fpls.2021.682443] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/11/2021] [Indexed: 05/06/2023]
Abstract
Betalains are pigments found in plants of the Caryophyllales order, and include the red-purple betacyanins and the yellow-orange betaxanthins. The red pigment from red beets, betanin, is made from tyrosine by a biosynthetic pathway that consists of a cytochrome P450, a L-DOPA dioxygenase, and a glucosyltransferase. The entire pathway was recently reconstituted in plants that do not make betalains naturally including potato and tomato plants. The amount of betanin produced in these plants was however not as high as in red beets. It was recently shown that a plastidic arogenate dehydrogenase gene involved in biosynthesis of tyrosine in plants is duplicated in Beta vulgaris and other betalain-producing plants, and that one of the two encoded enzymes, BvADHα, has relaxed feedback inhibition by tyrosine, contributing to the high amount of betanin found in red beets. We have reconstituted the complete betanin biosynthetic pathway in tomato plants with or without a BvADHα gene, and with all genes expressed under control of a fruit-specific promoter. The plants obtained with a construct containing BvADHα produced betanin at a higher level than plants obtained with a construct lacking this gene. These results show that use of BvADHα can be useful for high level production of betalains in heterologous hosts. Unlike red beets that produce both betacyanins and betaxanthins, the transformed tomatoes produced betacyanins only, conferring a bright purple-fuschia color to the tomato juice.
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Efremova LN, Strelnikova SR, Gazizova GR, Minkina EA, Komakhin RA. A Synthetic Strong and Constitutive Promoter Derived from the Stellaria media pro-SmAMP1 and pro-SmAMP2 Promoters for Effective Transgene Expression in Plants. Genes (Basel) 2020; 11:E1407. [PMID: 33256091 PMCID: PMC7760760 DOI: 10.3390/genes11121407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/22/2020] [Accepted: 11/24/2020] [Indexed: 01/05/2023] Open
Abstract
Synthetic promoters are vital for genetic engineering-based strategies for crop improvement, but effective methodologies for their creation and systematic testing are lacking. We report here on the comparative analysis of the promoters pro-SmAMP1 and pro-SmAMP2 from Stellaria media ANTIMICROBIAL PEPTIDE1 (AMP1) and ANTIMICROBIAL PEPTIDE2 (AMP2). These promoters are more effective than the well-known Cauliflower mosaic virus 35S promoter. Although these promoters share about 94% identity, the pro-SmAMP1 promoter demonstrated stronger transient expression of a reporter gene in Agrobacterium infiltration of Nicotiana benthamiana leaves, while the pro-SmAMP2 promoter was more effective for the selection of transgenic tobacco (Nicotiana tabacum) cells when driving a selectable marker. Using the cap analysis of gene expression method, we detected no differences in the structure of the transcription start sites for either promoter in transgenic plants. For both promoters, we used fine-scale deletion analysis to identify 160 bp-long sequences that retain the unique properties of each promoter. With the use of chimeric promoters and directed mutagenesis, we demonstrated that the superiority of the pro-SmAMP1 promoter for Agrobacterium-mediated infiltration is caused by the proline-inducible ACTCAT cis-element strictly positioned relative to the TATA box in the core promoter. Surprisingly, the ACTCAT cis-element not only activated but also suppressed the efficiency of the pro-SmAMP1 promoter under proline stress. The absence of the ACTCAT cis-element and CAANNNNATC motif (negative regulator) in the pro-SmAMP2 promoter provided a more constitutive gene expression profile and better selection of transgenic cells on selective medium. We created a new synthetic promoter that enjoys high effectiveness both in transient expression and in selection of transgenic cells. Intact promoters with differing properties and high degrees of sequence identity may thus be used as a basis for the creation of new synthetic promoters for precise and coordinated gene expression.
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Affiliation(s)
- Larisa N. Efremova
- All-Russia Research Institute of Agricultural Biotechnology, Moscow 127550, Russia; (L.N.E.); (S.R.S.)
| | - Svetlana R. Strelnikova
- All-Russia Research Institute of Agricultural Biotechnology, Moscow 127550, Russia; (L.N.E.); (S.R.S.)
| | - Guzel R. Gazizova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia; (G.R.G.); (E.A.M.)
| | - Elena A. Minkina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia; (G.R.G.); (E.A.M.)
| | - Roman A. Komakhin
- All-Russia Research Institute of Agricultural Biotechnology, Moscow 127550, Russia; (L.N.E.); (S.R.S.)
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