1
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Khan MA, Herring G, Zhu JY, Oliva M, Fourie E, Johnston B, Zhang Z, Potter J, Pineda L, Pflueger J, Swain T, Pflueger C, Lloyd JPB, Secco D, Small I, Kidd BN, Lister R. CRISPRi-based circuits to control gene expression in plants. Nat Biotechnol 2024:10.1038/s41587-024-02236-w. [PMID: 38769424 DOI: 10.1038/s41587-024-02236-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 04/10/2024] [Indexed: 05/22/2024]
Abstract
The construction of synthetic gene circuits in plants has been limited by a lack of orthogonal and modular parts. Here, we implement a CRISPR (clustered regularly interspaced short palindromic repeats) interference (CRISPRi)-based reversible gene circuit platform in plants. We create a toolkit of engineered repressible promoters of different strengths and construct NOT and NOR gates in Arabidopsis thaliana protoplasts. We determine the optimal processing system to express single guide RNAs from RNA Pol II promoters to introduce NOR gate programmability for interfacing with host regulatory sequences. The performance of a NOR gate in stably transformed Arabidopsis plants demonstrates the system's programmability and reversibility in a complex multicellular organism. Furthermore, cross-species activity of CRISPRi-based logic gates is shown in Physcomitrium patens, Triticum aestivum and Brassica napus protoplasts. Layering multiple NOR gates together creates OR, NIMPLY and AND logic functions, highlighting the modularity of our system. Our CRISPRi circuits are orthogonal, compact, reversible, programmable and modular and provide a platform for sophisticated spatiotemporal control of gene expression in plants.
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Affiliation(s)
- Muhammad Adil Khan
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Gabrielle Herring
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jia Yuan Zhu
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Marina Oliva
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Elliott Fourie
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Benjamin Johnston
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Zhining Zhang
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jarred Potter
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Luke Pineda
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jahnvi Pflueger
- Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - Tessa Swain
- Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - Christian Pflueger
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - James P B Lloyd
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - David Secco
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Brendan N Kidd
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
- CSIRO Synthetic Biology Future Science Platform, Brisbane, Queensland, Australia.
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
- Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia.
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2
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Boo A, Toth T, Yu Q, Pfotenhauer A, Fields BD, Lenaghan SC, Stewart CN, Voigt CA. Synthetic microbe-to-plant communication channels. Nat Commun 2024; 15:1817. [PMID: 38418817 PMCID: PMC10901793 DOI: 10.1038/s41467-024-45897-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
Plants and microbes communicate to collaborate to stop pests, scavenge nutrients, and react to environmental change. Microbiota consisting of thousands of species interact with each other and plants using a large chemical language that is interpreted by complex regulatory networks. In this work, we develop modular interkingdom communication channels, enabling bacteria to convey environmental stimuli to plants. We introduce a "sender device" in Pseudomonas putida and Klebsiella pneumoniae, that produces the small molecule p-coumaroyl-homoserine lactone (pC-HSL) when the output of a sensor or circuit turns on. This molecule triggers a "receiver device" in the plant to activate gene expression. We validate this system in Arabidopsis thaliana and Solanum tuberosum (potato) grown hydroponically and in soil, demonstrating its modularity by swapping bacteria that process different stimuli, including IPTG, aTc and arsenic. Programmable communication channels between bacteria and plants will enable microbial sentinels to transmit information to crops and provide the building blocks for designing artificial consortia.
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Affiliation(s)
- Alice Boo
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tyler Toth
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Qiguo Yu
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Alexander Pfotenhauer
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Brandon D Fields
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Scott C Lenaghan
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - C Neal Stewart
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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3
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Pfotenhauer AC, Reuter DN, Clark M, Harbison SA, Schimel TM, Stewart CN, Lenaghan SC. Development of new binary expression systems for plant synthetic biology. PLANT CELL REPORTS 2023; 43:22. [PMID: 38150091 DOI: 10.1007/s00299-023-03100-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/10/2023] [Indexed: 12/28/2023]
Abstract
KEY MESSAGE A novel plant binary expression system was developed from the compactin biosynthetic pathway 27 of Penicillium citrinum ML-236B. The system achieved >fivefold activation of gene expression in 28 transgenic tobacco. A diverse and well-characterized genetic toolset is fundamental to achieve the overall goals of plant synthetic biology. To properly coordinate expression of a multigene pathway, this toolset should include binary systems that control gene expression at the level of transcription. In plants, few highly functional, orthogonal transcriptional regulators have been identified. Here, we describe the process of developing synthetic plant transcription factors using regulatory elements from the Penicillium citrinum ML-236B (compactin) pathway. This pathway contains several genes including mlcA and mlcC that are transcriptionally regulated in a dose-dependent manner by the activator mlcR. In Nicotiana benthamiana, we first expressed mlcR with several cognate synthetic promoters driving expression of GFP. Synthetic promoters contained operator sequences from the compactin gene cluster. Following identification of the most active synthetic promoter, the DNA-binding domain from mlcR was used to generate chimeric transcription factors containing variable activation domains, including QF from the Neurospora crassa Q-system. Activity was measured at both protein and RNA levels which correlated with an R2 value of 0.94. A synthetic transcription factor with a QF activation domain increased gene expression from its synthetic promoter up to sixfold in N. benthamiana. Two systems were characterized in transgenic tobacco plants. The QF-based plants maintained high expression in tobacco, increasing expression from the cognate synthetic promoter by fivefold. Transgenic plants and non-transgenic plants were morphologically indistinguishable. The framework of this study can easily be adopted for other putative transcription factors to continue improvement of the plant synthetic biology toolbox.
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Affiliation(s)
- Alexander C Pfotenhauer
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - D Nikki Reuter
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Mikayla Clark
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Stacee A Harbison
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Tayler M Schimel
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - C Neal Stewart
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, USA
| | - Scott C Lenaghan
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA.
- Department of Food Science, The University of Tennessee, Knoxville, Knoxville, TN, USA.
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4
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Yang EJ, Nemhauser JL. Building a pipeline to identify and engineer constitutive and repressible promoters. QUANTITATIVE PLANT BIOLOGY 2023; 4:e12. [PMID: 37901686 PMCID: PMC10600573 DOI: 10.1017/qpb.2023.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 07/24/2023] [Accepted: 09/13/2023] [Indexed: 10/31/2023]
Abstract
To support the increasingly complex circuits needed for plant synthetic biology applications, additional constitutive promoters are essential. Reusing promoter parts can lead to difficulty in cloning, increased heterogeneity between transformants, transgene silencing and trait instability. We have developed a pipeline to identify genes that have stable expression across a wide range of Arabidopsis tissues at different developmental stages and have identified a number of promoters that are well expressed in both transient (Nicotiana benthamiana) and stable (Arabidopsis) transformation assays. We have also introduced two genome-orthogonal gRNA target sites in a subset of the screened promoters, converting them into NOR logic gates. The work here establishes a pipeline to screen for additional constitutive promoters and can form the basis of constructing more complex information processing circuits in the future.
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Affiliation(s)
- Eric J.Y. Yang
- Department of Biology, University of Washington, Seattle, WA, USA
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5
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Koukara J, Papadopoulou KK. Advances in plant synthetic biology approaches to control expression of gene circuits. Biochem Biophys Res Commun 2023; 654:55-61. [PMID: 36889035 DOI: 10.1016/j.bbrc.2023.02.061] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 03/08/2023]
Abstract
The applications of synthetic biology range from creating simple circuits to monitor an organism's state to complex circuits capable of reconstructing aspects of life. The latter has the potential to be used in plant synthetic biology to address current societal issues by reforming agriculture and enhancing production of molecules of increased demand. For this reason, development of efficient tools to precisely control gene expression of circuits must be prioritized. In this review, we report the latest efforts towards characterization, standardization and assembly of genetic parts into higher-order constructs, as well as available types of inducible systems to modulate their transcription in plant systems. Subsequently, we discuss recent developments in the orthogonal control of gene expression, Boolean logic gates and synthetic genetic toggle-like switches. Finally, we conclude that by combining different means of controlling gene expression, we can create complex circuits capable of reshaping plant life.
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Affiliation(s)
- Jenny Koukara
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Kalliope K Papadopoulou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece.
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6
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Yang Y, Chaffin TA, Ahkami AH, Blumwald E, Stewart CN. Plant synthetic biology innovations for biofuels and bioproducts. Trends Biotechnol 2022; 40:1454-1468. [PMID: 36241578 DOI: 10.1016/j.tibtech.2022.09.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/26/2022] [Accepted: 09/15/2022] [Indexed: 01/21/2023]
Abstract
Plant-based biosynthesis of fuels, chemicals, and materials promotes environmental sustainability, which includes decreases in greenhouse gas emissions, water pollution, and loss of biodiversity. Advances in plant synthetic biology (synbio) should improve precision and efficacy of genetic engineering for sustainability. Applicable synbio innovations include genome editing, gene circuit design, synthetic promoter development, gene stacking technologies, and the design of environmental sensors. Moreover, recent advancements in developing spatially resolved and single-cell omics contribute to the discovery and characterization of cell-type-specific mechanisms and spatiotemporal gene regulations in distinct plant tissues for the expression of cell- and tissue-specific genes, resulting in improved bioproduction. This review highlights recent plant synbio progress and new single-cell molecular profiling towards sustainable biofuel and biomaterial production.
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Affiliation(s)
- Yongil Yang
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, USA; Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Timothy Alexander Chaffin
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, USA; Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Amir H Ahkami
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, USA
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Charles Neal Stewart
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, USA; Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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7
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Ojeda-Rivera JO, Alejo-Jacuinde G, Nájera-González HR, López-Arredondo D. Prospects of genetics and breeding for low-phosphate tolerance: an integrated approach from soil to cell. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4125-4150. [PMID: 35524816 PMCID: PMC9729153 DOI: 10.1007/s00122-022-04095-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 03/31/2022] [Indexed: 05/04/2023]
Abstract
Improving phosphorus (P) crop nutrition has emerged as a key factor toward achieving a more resilient and sustainable agriculture. P is an essential nutrient for plant development and reproduction, and phosphate (Pi)-based fertilizers represent one of the pillars that sustain food production systems. To meet the global food demand, the challenge for modern agriculture is to increase food production and improve food quality in a sustainable way by significantly optimizing Pi fertilizer use efficiency. The development of genetically improved crops with higher Pi uptake and Pi-use efficiency and higher adaptability to environments with low-Pi availability will play a crucial role toward this end. In this review, we summarize the current understanding of Pi nutrition and the regulation of Pi-starvation responses in plants, and provide new perspectives on how to harness the ample repertoire of genetic mechanisms behind these adaptive responses for crop improvement. We discuss on the potential of implementing more integrative, versatile, and effective strategies by incorporating systems biology approaches and tools such as genome editing and synthetic biology. These strategies will be invaluable for producing high-yielding crops that require reduced Pi fertilizer inputs and to develop a more sustainable global agriculture.
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Affiliation(s)
- Jonathan Odilón Ojeda-Rivera
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, USA
| | - Gerardo Alejo-Jacuinde
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, USA
| | - Héctor-Rogelio Nájera-González
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, USA
| | - Damar López-Arredondo
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, USA.
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8
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Brophy JAN, Magallon KJ, Duan L, Zhong V, Ramachandran P, Kniazev K, Dinneny JR. Synthetic genetic circuits as a means of reprogramming plant roots. Science 2022; 377:747-751. [PMID: 35951698 DOI: 10.1126/science.abo4326] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The shape of a plant's root system influences its ability to reach essential nutrients in the soil and to acquire water during drought. Progress in engineering plant roots to optimize water and nutrient acquisition has been limited by our capacity to design and build genetic programs that alter root growth in a predictable manner. We developed a collection of synthetic transcriptional regulators for plants that can be compiled to create genetic circuits. These circuits control gene expression by performing Boolean logic operations and can be used to predictably alter root structure. This work demonstrates the potential of synthetic genetic circuits to control gene expression across tissues and reprogram plant growth.
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Affiliation(s)
- Jennifer A N Brophy
- Department of Biology, Stanford University, Stanford, CA, USA.,Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Lina Duan
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Vivian Zhong
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Kiril Kniazev
- Department of Biology, Stanford University, Stanford, CA, USA
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, CA, USA
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9
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Kar S, Bordiya Y, Rodriguez N, Kim J, Gardner EC, Gollihar JD, Sung S, Ellington AD. Orthogonal control of gene expression in plants using synthetic promoters and CRISPR-based transcription factors. PLANT METHODS 2022; 18:42. [PMID: 35351174 PMCID: PMC8966344 DOI: 10.1186/s13007-022-00867-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/01/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND The construction and application of synthetic genetic circuits is frequently improved if gene expression can be orthogonally controlled, relative to the host. In plants, orthogonality can be achieved via the use of CRISPR-based transcription factors that are programmed to act on natural or synthetic promoters. The construction of complex gene circuits can require multiple, orthogonal regulatory interactions, and this in turn requires that the full programmability of CRISPR elements be adapted to non-natural and non-standard promoters that have few constraints on their design. Therefore, we have developed synthetic promoter elements in which regions upstream of the minimal 35S CaMV promoter are designed from scratch to interact via programmed gRNAs with dCas9 fusions that allow activation of gene expression. RESULTS A panel of three, mutually orthogonal promoters that can be acted on by artificial gRNAs bound by CRISPR regulators were designed. Guide RNA expression targeting these promoters was in turn controlled by either Pol III (U6) or ethylene-inducible Pol II promoters, implementing for the first time a fully artificial Orthogonal Control System (OCS). Following demonstration of the complete orthogonality of the designs, the OCS was tied to cellular metabolism by putting gRNA expression under the control of an endogenous plant signaling molecule, ethylene. The ability to form complex circuitry was demonstrated via the ethylene-driven, ratiometric expression of fluorescent proteins in single plants. CONCLUSIONS The design of synthetic promoters is highly generalizable to large tracts of sequence space, allowing Orthogonal Control Systems of increasing complexity to potentially be generated at will. The ability to tie in several different basal features of plant molecular biology (Pol II and Pol III promoters, ethylene regulation) to the OCS demonstrates multiple opportunities for engineering at the system level. Moreover, given the fungibility of the core 35S CaMV promoter elements, the derived synthetic promoters can potentially be utilized across a variety of plant species.
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Affiliation(s)
- Shaunak Kar
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA.
| | - Yogendra Bordiya
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Life Sciences Solutions Group, Thermo Fisher Scientific, Austin, TX, USA
| | - Nestor Rodriguez
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Junghyun Kim
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Elizabeth C Gardner
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Sibum Sung
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
| | - Andrew D Ellington
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA.
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10
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Han S, Jiang S, Xiong R, Shafique K, Zahid KR, Wang Y. Response and tolerance mechanism of food crops under high temperature stress: a review. BRAZ J BIOL 2022; 82:e253898. [PMID: 35107484 DOI: 10.1590/1519-6984.253898] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 11/23/2021] [Indexed: 01/15/2023] Open
Abstract
High temperature stress events are critical factors inhibiting crop yield. Meanwhile, world population is growing very rapidly and will be reached up to 9 billion by 2050. To feed increasing world population, it is challenging task to increase about 70% global food productions. Food crops have significant contribution toward global food demand and food security. However, consequences from increasing heat stress events are demolishing their abilities to survive and sustain yield when subjected to extreme high temperature stress. Therefore, there is dire need to better understand response and tolerance mechanism of food crops following exposure to heat stress. Here, we aimed to provide recent update on impact of high temperature stress on crop yield of food crops, pollination, pollinators, and novel strategies for improving tolerance of food crop under high temperature stress. Importantly, development of heat-resistant transgenic food crops can grant food security through transformation of superior genes into current germplasm, which are associated with various signaling pathways as well as epigenetic regulation in response to extreme high temperature stress.
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Affiliation(s)
- S Han
- Liupanshui Normal University, School of Biological Sciences and Technology, Liupanshui, China
| | - S Jiang
- Zhengzhou Normal University, Bioengineering Research Center, Zhengzhou, Henan, P.R. China
| | - R Xiong
- Liupanshui Normal University, School of Biological Sciences and Technology, Liupanshui, China
| | - K Shafique
- Government Sadiq College Women University, Department of Botany, Bahawalpur, Pakistan
| | - K R Zahid
- Shenzhen University, Carson International Cancer Center, College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen, Guangdong, China
| | - Y Wang
- Liupanshui Normal University, School of Biological Sciences and Technology, Liupanshui, China
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11
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Lohani N, Singh MB, Bhalla PL. Biological Parts for Engineering Abiotic Stress Tolerance in Plants. BIODESIGN RESEARCH 2022; 2022:9819314. [PMID: 37850130 PMCID: PMC10521667 DOI: 10.34133/2022/9819314] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/17/2021] [Indexed: 10/19/2023] Open
Abstract
It is vital to ramp up crop production dramatically by 2050 due to the increasing global population and demand for food. However, with the climate change projections showing that droughts and heatwaves becoming common in much of the globe, there is a severe threat of a sharp decline in crop yields. Thus, developing crop varieties with inbuilt genetic tolerance to environmental stresses is urgently needed. Selective breeding based on genetic diversity is not keeping up with the growing demand for food and feed. However, the emergence of contemporary plant genetic engineering, genome-editing, and synthetic biology offer precise tools for developing crops that can sustain productivity under stress conditions. Here, we summarize the systems biology-level understanding of regulatory pathways involved in perception, signalling, and protective processes activated in response to unfavourable environmental conditions. The potential role of noncoding RNAs in the regulation of abiotic stress responses has also been highlighted. Further, examples of imparting abiotic stress tolerance by genetic engineering are discussed. Additionally, we provide perspectives on the rational design of abiotic stress tolerance through synthetic biology and list various bioparts that can be used to design synthetic gene circuits whose stress-protective functions can be switched on/off in response to environmental cues.
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Affiliation(s)
- Neeta Lohani
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Mohan B. Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Prem L. Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
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12
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May MP, Munsky B. Exploiting Noise, Non-Linearity, and Feedback for Differential Control of Multiple Synthetic Cells with a Single Optogenetic Input. ACS Synth Biol 2021; 10:3396-3410. [PMID: 34793137 PMCID: PMC9875732 DOI: 10.1021/acssynbio.1c00341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Synthetic biology seeks to develop modular biocircuits that combine to produce complex, controllable behaviors. These designs are often subject to noisy fluctuations and uncertainties, and most modern synthetic biology design processes have focused to create robust components to mitigate the noise of gene expression and reduce the heterogeneity of single-cell responses. However, a deeper understanding of noise can achieve control goals that would otherwise be impossible. We explore how an "Optogenetic Maxwell Demon" could selectively amplify noise to control multiple cells using single-input-multiple-output (SIMO) feedback. Using data-constrained stochastic model simulations and theory, we show how an appropriately selected stochastic SIMO controller can drive multiple different cells to different user-specified configurations irrespective of initial conditions. We explore how controllability depends on cells' regulatory structures, the amount of information available to the controller, and the accuracy of the model used. Our results suggest that gene regulation noise, when combined with optogenetic feedback and non-linear biochemical auto-regulation, can achieve synergy to enable precise control of complex stochastic processes.
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Affiliation(s)
- Michael P May
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA, 80523
| | - Brian Munsky
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA, 80523,Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, USA, 80523
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13
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Wu T, Kerbler SM, Fernie AR, Zhang Y. Plant cell cultures as heterologous bio-factories for secondary metabolite production. PLANT COMMUNICATIONS 2021; 2:100235. [PMID: 34746764 PMCID: PMC8554037 DOI: 10.1016/j.xplc.2021.100235] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/27/2021] [Accepted: 08/19/2021] [Indexed: 05/06/2023]
Abstract
Synthetic biology has been developing rapidly in the last decade and is attracting increasing attention from many plant biologists. The production of high-value plant-specific secondary metabolites is, however, limited mostly to microbes. This is potentially problematic because of incorrect post-translational modification of proteins and differences in protein micro-compartmentalization, substrate availability, chaperone availability, product toxicity, and cytochrome p450 reductase enzymes. Unlike other heterologous systems, plant cells may be a promising alternative for the production of high-value metabolites. Several commercial plant suspension cell cultures from different plant species have been used successfully to produce valuable metabolites in a safe, low cost, and environmentally friendly manner. However, few metabolites are currently being biosynthesized using plant platforms, with the exception of the natural pigment anthocyanin. Both Arabidopsis thaliana and Nicotiana tabacum cell cultures can be developed by multiple gene transformations and CRISPR-Cas9 genome editing. Given that the introduction of heterologous biosynthetic pathways into Arabidopsis and N. tabacum is not widely used, the biosynthesis of foreign metabolites is currently limited; however, therein lies great potential. Here, we discuss the exemplary use of plant cell cultures and prospects for using A. thaliana and N. tabacum cell cultures to produce valuable plant-specific metabolites.
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Affiliation(s)
- Tong Wu
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Sandra M. Kerbler
- Leibniz-Institute für Gemüse- und Zierpflanzenbau, Theodor-Echtermeyer-Weg 1, 14979 Groβbeeren, Germany
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
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14
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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: 22] [Impact Index Per Article: 7.3] [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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15
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McCarthy DM, Medford JI. Quantitative and Predictive Genetic Parts for Plant Synthetic Biology. FRONTIERS IN PLANT SCIENCE 2020; 11:512526. [PMID: 33123175 PMCID: PMC7573182 DOI: 10.3389/fpls.2020.512526] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
Plant synthetic biology aims to harness the natural abilities of plants and to turn them to new purposes. A primary goal of plant synthetic biology is to produce predictable and programmable genetic circuits from simple regulatory elements and well-characterized genetic components. The number of available DNA parts for plants is increasing, and the methods for rapid quantitative characterization are being developed, but the field of plant synthetic biology is still in its early stages. We here describe methods used to describe the quantitative properties of genetic components needed for plant synthetic biology. Once the quantitative properties and transfer function of a variety of genetic parts are known, computers can select the optimal components to assemble into functional devices, such as toggle switches and positive feedback circuits. However, while the variety of circuits and traits that can be put into plants are limitless, doing synthetic biology in plants poses unique challenges. Plants are composed of differentiated cells and tissues, each representing potentially unique regulatory or developmental contexts to introduced synthetic genetic circuits. Further, plants have evolved to be highly sensitive to environmental influences, such as light or temperature, any of which can affect the quantitative function of individual parts or whole circuits. Measuring the function of plant components within the context of a plant cell and, ideally, in a living plant, will be essential to using these components in gene circuits with predictable function. Mathematical modeling will be needed to account for the variety of contexts a genetic part will experience in different plant tissues or environments. With such understanding in hand, it may be possible to redesign plant traits to serve human and environmental needs.
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16
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Lu H, Yuan G, Strauss SH, Tschaplinski TJ, Tuskan GA, Chen JG, Yang X. Reconfiguring Plant Metabolism for Biodegradable Plastic Production. BIODESIGN RESEARCH 2020; 2020:9078303. [PMID: 37849903 PMCID: PMC10530661 DOI: 10.34133/2020/9078303] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/11/2020] [Indexed: 10/19/2023] Open
Abstract
For decades, plants have been the subject of genetic engineering to synthesize novel, value-added compounds. Polyhydroxyalkanoates (PHAs), a large class of biodegradable biopolymers naturally synthesized in eubacteria, are among the novel products that have been introduced to make use of plant acetyl-CoA metabolic pathways. It was hoped that renewable PHA production would help address environmental issues associated with the accumulation of nondegradable plastic wastes. However, after three decades of effort synthesizing PHAs, and in particular the simplest form polyhydroxybutyrate (PHB), and seeking to improve their production in plants, it has proven very difficult to reach a commercially profitable rate in a normally growing plant. This seems to be due to the growth defects associated with PHA production and accumulation in plant cells. Here, we review major breakthroughs that have been made in plant-based PHA synthesis using traditional genetic engineering approaches and discuss challenges that have been encountered. Then, from the point of view of plant synthetic biology, we provide perspectives on reprograming plant acetyl-CoA pathways for PHA production, with the goal of maximizing PHA yield while minimizing growth inhibition. Specifically, we suggest genetic elements that can be considered in genetic circuit design, approaches for nuclear genome and plastome modification, and the use of multiomics and mathematical modeling in understanding and restructuring plant metabolic pathways.
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Affiliation(s)
- Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Steven H. Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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17
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Yang X, Cushman JC, Borland AM, Liu Q. Editorial: Systems Biology and Synthetic Biology in Relation to Drought Tolerance or Avoidance in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:394. [PMID: 32328077 PMCID: PMC7161431 DOI: 10.3389/fpls.2020.00394] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/18/2020] [Indexed: 05/09/2023]
Affiliation(s)
- Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Oak Ridge National Laboratory, The Center for Bioenergy Innovation, Oak Ridge, TN, United States
| | - John C. Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, United States
| | - Anne M. Borland
- School of Natural and Environmental Science, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Qingchang Liu
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, China
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18
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Bernabé-Orts JM, Quijano-Rubio A, Vazquez-Vilar M, Mancheño-Bonillo J, Moles-Casas V, Selma S, Gianoglio S, Granell A, Orzaez D. A memory switch for plant synthetic biology based on the phage ϕC31 integration system. Nucleic Acids Res 2020; 48:3379-3394. [PMID: 32083668 PMCID: PMC7102980 DOI: 10.1093/nar/gkaa104] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 02/07/2023] Open
Abstract
Synthetic biology has advanced from the setup of basic genetic devices to the design of increasingly complex gene circuits to provide organisms with new functions. While many bacterial, fungal and mammalian unicellular chassis have been extensively engineered, this progress has been delayed in plants due to the lack of reliable DNA parts and devices that enable precise control over these new synthetic functions. In particular, memory switches based on DNA site-specific recombination have been the tool of choice to build long-term and stable synthetic memory in other organisms, because they enable a shift between two alternative states registering the information at the DNA level. Here we report a memory switch for whole plants based on the bacteriophage ϕC31 site-specific integrase. The switch was built as a modular device made of standard DNA parts, designed to control the transcriptional state (on or off) of two genes of interest by alternative inversion of a central DNA regulatory element. The state of the switch can be externally operated by action of the ϕC31 integrase (Int), and its recombination directionality factor (RDF). The kinetics, memory, and reversibility of the switch were extensively characterized in Nicotiana benthamiana plants.
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Affiliation(s)
- Joan Miquel Bernabé-Orts
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Alfredo Quijano-Rubio
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Marta Vazquez-Vilar
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Javier Mancheño-Bonillo
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Victor Moles-Casas
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Sara Selma
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Silvia Gianoglio
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
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19
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Lohani N, Jain D, Singh MB, Bhalla PL. Engineering Multiple Abiotic Stress Tolerance in Canola, Brassica napus. FRONTIERS IN PLANT SCIENCE 2020; 11:3. [PMID: 32161602 PMCID: PMC7052498 DOI: 10.3389/fpls.2020.00003] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/03/2020] [Indexed: 05/22/2023]
Abstract
Impacts of climate change like global warming, drought, flooding, and other extreme events are posing severe challenges to global crop production. Contribution of Brassica napus towards the oilseed industry makes it an essential component of international trade and agroeconomics. Consequences from increasing occurrences of multiple abiotic stresses on this crop are leading to agroeconomic losses making it vital to endow B. napus crop with an ability to survive and maintain yield when faced with simultaneous exposure to multiple abiotic stresses. For an improved understanding of the stress sensing machinery, there is a need for analyzing regulatory pathways of multiple stress-responsive genes and other regulatory elements such as non-coding RNAs. However, our understanding of these pathways and their interactions in B. napus is far from complete. This review outlines the current knowledge of stress-responsive genes and their role in imparting multiple stress tolerance in B. napus. Analysis of network cross-talk through omics data mining is now making it possible to unravel the underlying complexity required for stress sensing and signaling in plants. Novel biotechnological approaches such as transgene-free genome editing and utilization of nanoparticles as gene delivery tools are also discussed. These can contribute to providing solutions for developing climate change resilient B. napus varieties with reduced regulatory limitations. The potential ability of synthetic biology to engineer and modify networks through fine-tuning of stress regulatory elements for plant responses to stress adaption is also highlighted.
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Affiliation(s)
| | | | | | - Prem L. Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
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20
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He J, Xin P, Ma X, Chu J, Wang G. Gibberellin Metabolism in Flowering Plants: An Update and Perspectives. FRONTIERS IN PLANT SCIENCE 2020; 11:532. [PMID: 32508855 PMCID: PMC7248407 DOI: 10.3389/fpls.2020.00532] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/08/2020] [Indexed: 05/09/2023]
Abstract
In plants, gibberellins (GAs) play important roles in regulating growth and development. Early studies revealed the large chemodiversity of gibberellins in plants, but only GA1, GA3, GA4, and GA7 show biological activity that controls plant development. However, the elucidation of the GA metabolic network at the molecular level has lagged far behind the chemical discovery of GAs. Recent advances in downstream GA biosynthesis (after GA12 formation) suggest that species-specific gibberellin modifications were acquired during flowering plant evolution. Here, we summarize the current knowledge of GA metabolism in flowering plants and the physiological functions of GA deactivation, with a focus on GA 13 hydroxylation. The potential applications of GA synthetic biology for plant development are also discussed.
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Affiliation(s)
- Juan He
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Peiyong Xin
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Xueting Ma
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jinfang Chu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Guodong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Guodong Wang,
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21
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Pasin F, Menzel W, Daròs J. Harnessed viruses in the age of metagenomics and synthetic biology: an update on infectious clone assembly and biotechnologies of plant viruses. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1010-1026. [PMID: 30677208 PMCID: PMC6523588 DOI: 10.1111/pbi.13084] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/09/2018] [Accepted: 01/15/2019] [Indexed: 05/12/2023]
Abstract
Recent metagenomic studies have provided an unprecedented wealth of data, which are revolutionizing our understanding of virus diversity. A redrawn landscape highlights viruses as active players in the phytobiome, and surveys have uncovered their positive roles in environmental stress tolerance of plants. Viral infectious clones are key tools for functional characterization of known and newly identified viruses. Knowledge of viruses and their components has been instrumental for the development of modern plant molecular biology and biotechnology. In this review, we provide extensive guidelines built on current synthetic biology advances that streamline infectious clone assembly, thus lessening a major technical constraint of plant virology. The focus is on generation of infectious clones in binary T-DNA vectors, which are delivered efficiently to plants by Agrobacterium. We then summarize recent applications of plant viruses and explore emerging trends in microbiology, bacterial and human virology that, once translated to plant virology, could lead to the development of virus-based gene therapies for ad hoc engineering of plant traits. The systematic characterization of plant virus roles in the phytobiome and next-generation virus-based tools will be indispensable landmarks in the synthetic biology roadmap to better crops.
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Affiliation(s)
- Fabio Pasin
- Agricultural Biotechnology Research CenterAcademia SinicaTaipeiTaiwan
| | - Wulf Menzel
- Leibniz Institute DSMZ‐German Collection of Microorganisms and Cell CulturesBraunschweigGermany
| | - José‐Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas‐Universitat Politècnica de València)ValenciaSpain
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22
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Ali S, Kim WC. A Fruitful Decade Using Synthetic Promoters in the Improvement of Transgenic Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:1433. [PMID: 31737027 PMCID: PMC6838210 DOI: 10.3389/fpls.2019.01433] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 10/16/2019] [Indexed: 05/17/2023]
Abstract
Advances in plant biotechnology provide various means to improve crop productivity and greatly contributing to sustainable agriculture. A significant advance in plant biotechnology has been the availability of novel synthetic promoters for precise spatial and temporal control of transgene expression. In this article, we review the development of various synthetic promotors and the rise of their use over the last several decades for regulating the transcription of various transgenes. Similarly, we provided a brief description of the structure and scope of synthetic promoters and the engineering of their cis-regulatory elements for different targets. Moreover, the functional characteristics of different synthetic promoters, their modes of regulating the expression of candidate genes in response to different conditions, and the resulting plant trait improvements reported in the past decade are discussed.
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23
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Hanson AD, Jez JM. Synthetic biology meets plant metabolism. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:1-2. [PMID: 29907301 DOI: 10.1016/j.plantsci.2018.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 04/06/2018] [Indexed: 05/23/2023]
Affiliation(s)
- Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, United States; Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, United States
| | - Joseph M Jez
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, United States; Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, United States.
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