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Yang Y, Chaffin TA, Shao Y, Balasubramanian VK, Markillie M, Mitchell H, Rubio‐Wilhelmi MM, Ahkami AH, Blumwald E, Neal Stewart C. Novel synthetic inducible promoters controlling gene expression during water-deficit stress with green tissue specificity in transgenic poplar. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1596-1609. [PMID: 38232002 PMCID: PMC11123411 DOI: 10.1111/pbi.14289] [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: 08/06/2023] [Revised: 11/16/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
Synthetic promoters may be designed using short cis-regulatory elements (CREs) and core promoter sequences for specific purposes. We identified novel conserved DNA motifs from the promoter sequences of leaf palisade and vascular cell type-specific expressed genes in water-deficit stressed poplar (Populus tremula × Populus alba), collected through low-input RNA-seq analysis using laser capture microdissection. Hexamerized sequences of four conserved 20-base motifs were inserted into each synthetic promoter construct. Two of these synthetic promoters (Syn2 and Syn3) induced GFP in transformed poplar mesophyll protoplasts incubated in 0.5 M mannitol solution. To identify effect of length and sequence from a valuable 20 base motif, 5' and 3' regions from a basic sequence (GTTAACTTCAGGGCCTGTGG) of Syn3 were hexamerized to generate two shorter synthetic promoters, Syn3-10b-1 (5': GTTAACTTCA) and Syn3-10b-2 (3': GGGCCTGTGG). These promoters' activities were compared with Syn3 in plants. Syn3 and Syn3-10b-1 were specifically induced in transient agroinfiltrated Nicotiana benthamiana leaves in water cessation for 3 days. In stable transgenic poplar, Syn3 presented as a constitutive promoter but had the highest activity in leaves. Syn3-10b-1 had stronger induction in green tissues under water-deficit stress conditions than mock control. Therefore, a synthetic promoter containing the 5' sequence of Syn3 endowed both tissue-specificity and water-deficit inducibility in transgenic poplar, whereas the 3' sequence did not. Consequently, we have added two new synthetic promoters to the poplar engineering toolkit: Syn3-10b-1, a green tissue-specific and water-deficit stress-induced promoter, and Syn3, a green tissue-preferential constitutive promoter.
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Affiliation(s)
- Yongil Yang
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTennesseeUSA
| | - Timothy A. Chaffin
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTennesseeUSA
| | - Yuanhua Shao
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTennesseeUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTennesseeUSA
| | | | - Meng Markillie
- Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichlandWAUSA
| | - Hugh Mitchell
- Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichlandWAUSA
| | | | - Amir H. Ahkami
- Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichlandWAUSA
| | - Eduardo Blumwald
- Department of Plant SciencesUniversity of CaliforniaDavisCaliforniaUSA
| | - C. Neal Stewart
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTennesseeUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTennesseeUSA
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2
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Shakhova ES, Karataeva TA, Markina NM, Mitiouchkina T, Palkina KA, Perfilov MM, Wood MG, Hoang TT, Hall MP, Fakhranurova LI, Alekberova AE, Malyshevskaia AK, Gorbachev DA, Bugaeva EN, Pletneva LK, Babenko VV, Boldyreva DI, Gorokhovatsky AY, Balakireva AV, Gao F, Choob VV, Encell LP, Wood KV, Yampolsky IV, Sarkisyan KS, Mishin AS. An improved pathway for autonomous bioluminescence imaging in eukaryotes. Nat Methods 2024; 21:406-410. [PMID: 38253843 PMCID: PMC10927554 DOI: 10.1038/s41592-023-02152-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 12/13/2023] [Indexed: 01/24/2024]
Abstract
The discovery of the bioluminescence pathway in the fungus Neonothopanus nambi enabled engineering of eukaryotes with self-sustained luminescence. However, the brightness of luminescence in heterologous hosts was limited by performance of the native fungal enzymes. Here we report optimized versions of the pathway that enhance bioluminescence by one to two orders of magnitude in plant, fungal and mammalian hosts, and enable longitudinal video-rate imaging.
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Affiliation(s)
- Ekaterina S Shakhova
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana A Karataeva
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nadezhda M Markina
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana Mitiouchkina
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Kseniia A Palkina
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maxim M Perfilov
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | | | | | | | - Anna E Alekberova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alena K Malyshevskaia
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A Gorbachev
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Vladislav V Babenko
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Daria I Boldyreva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Andrey Y Gorokhovatsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anastasia V Balakireva
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Feng Gao
- Synthetic Biology Group, MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Vladimir V Choob
- Planta LLC, Moscow, Russia
- Botanical Garden of Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Ilia V Yampolsky
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Light Bio Inc, Ketchum, ID, USA
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Karen S Sarkisyan
- Planta LLC, Moscow, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
- Synthetic Biology Group, MRC Laboratory of Medical Sciences, London, UK.
- Institute of Clinical Sciences, Faculty of Medicine and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.
- Light Bio Inc, Ketchum, ID, USA.
| | - Alexander S Mishin
- Planta LLC, Moscow, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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3
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Calvache C, Vazquez‐Vilar M, Moreno‐Giménez E, Orzaez D. A quantitative autonomous bioluminescence reporter system with a wide dynamic range for Plant Synthetic Biology. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:37-47. [PMID: 37882352 PMCID: PMC10754000 DOI: 10.1111/pbi.14146] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/24/2023] [Accepted: 07/24/2023] [Indexed: 10/27/2023]
Abstract
Plant Synthetic Biology aims to enhance the capacities of plants by designing and integrating synthetic gene circuits (SGCs). Quantitative reporting solutions that can produce quick, rich datasets affordably are necessary for SGC optimization. In this paper, we present a new, low-cost, and high-throughput reporter system for the quantitative measurement of gene expression in plants based on autonomous bioluminescence. This method eliminates the need for an exogenous supply of luciferase substrate by exploiting the entire Neonothopanus nambi fungal bioluminescence cyclic pathway to build a self-sustained reporter. The HispS gene, the pathway's limiting step, was set up as the reporter's transcriptional entry point as part of the new system's design, which significantly improved the output's dynamic range and brought it on par with that of the gold standard FLuc/RLuc reporter. Additionally, transient ratiometric measurements in N. benthamiana were made possible by the addition of an enhanced GFP as a normalizer. The performance of new NeoLuc/eGFP system was extensively validated with SGCs previously described, including phytohormone and optogenetic sensors. Furthermore, we employed NeoLuc/eGFP in the optimization of challenging SGCs, including new configurations for an agrochemical (copper) switch, a new blue optogenetic sensor, and a dual copper/red-light switch for tight regulation of metabolic pathways.
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Affiliation(s)
- Camilo Calvache
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValénciaValenciaSpain
| | - Marta Vazquez‐Vilar
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValénciaValenciaSpain
| | - Elena Moreno‐Giménez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValénciaValenciaSpain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValénciaValenciaSpain
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4
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De Paola C, Garcia-Carpintero V, Vazquez-Vilar M, Kaminski K, Fernandez-Del-Carmen A, Sierro N, Ivanov NV, Giuliano G, Waterhouse P, Orzaez D. Comparative analysis of the Squamosa Promoter Binding-Like (SPL) gene family in Nicotiana benthamiana and Nicotiana tabacum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111797. [PMID: 37467788 DOI: 10.1016/j.plantsci.2023.111797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
SQUAMOSA PROMOTER BINDING-LIKE (SPL) proteins constitute a large family of transcription factors known to play key roles in growth and developmental processes, including juvenile-to-adult and vegetative-to-reproductive phase transitions. This makes SPLs interesting targets for precision breeding in plants of the Nicotiana genus used as e.g. recombinant biofactories. We report the identification of 49 SPL genes in Nicotiana tabacum cv. K326 and 43 SPL genes in Nicotiana benthamiana LAB strain, which were classified into eight phylogenetic groups according to the SPL classification in Arabidopsis. Exon-intron gene structure and DNA-binding domains were highly conserved between homeologues and orthologues. Thirty of the NbSPL genes and 33 of the NtSPL genes were found to be possible targets of microRNA 156. The expression of SPL genes in leaves was analysed by RNA-seq at three different stages, revealing that genes not under miR156 control were in general constitutively expressed at high levels, whereas miR156-regulated genes showed lower expression, often developmentally regulated. We selected the N. benthamiana SPL13_1a gene as target for a CRISPR/Cas9 knock-out experiment. We show here that a full knock-out in this single gene leads to a significant delay in flowering time, a trait that could be exploited to increase biomass for recombinant protein production.
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Affiliation(s)
- Carmine De Paola
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain
| | | | - Marta Vazquez-Vilar
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain
| | | | | | - Nicolas Sierro
- PMI R&D, Philip Morris Products S.A, Neuchâtel, Switzerland
| | | | | | | | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain.
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5
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Moreno-Giménez E, Gandía M, Sáez Z, Manzanares P, Yenush L, Orzáez D, Marcos JF, Garrigues S. FungalBraid 2.0: expanding the synthetic biology toolbox for the biotechnological exploitation of filamentous fungi. Front Bioeng Biotechnol 2023; 11:1222812. [PMID: 37609115 PMCID: PMC10441238 DOI: 10.3389/fbioe.2023.1222812] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/12/2023] [Indexed: 08/24/2023] Open
Abstract
Fungal synthetic biology is a rapidly expanding field that aims to optimize the biotechnological exploitation of fungi through the generation of standard, ready-to-use genetic elements, and universal syntax and rules for contributory use by the fungal research community. Recently, an increasing number of synthetic biology toolkits have been developed and applied to filamentous fungi, which highlights the relevance of these organisms in the biotechnology field. The FungalBraid (FB) modular cloning platform enables interchangeability of DNA parts with the GoldenBraid (GB) platform, which is designed for plants, and other systems that are compatible with the standard Golden Gate cloning and syntax, and uses binary pCAMBIA-derived vectors to allow Agrobacterium tumefaciens-mediated transformation of a wide range of fungal species. In this study, we have expanded the original FB catalog by adding 27 new DNA parts that were functionally validated in vivo. Among these are the resistance selection markers for the antibiotics phleomycin and terbinafine, as well as the uridine-auxotrophic marker pyr4. We also used a normalized luciferase reporter system to validate several promoters, such as PpkiA, P7760, Pef1α, and PafpB constitutive promoters, and PglaA, PamyB, and PxlnA inducible promoters. Additionally, the recently developed dCas9-regulated GB_SynP synthetic promoter collection for orthogonal CRISPR activation (CRISPRa) in plants has been adapted in fungi through the FB system. In general, the expansion of the FB catalog is of great interest to the scientific community since it increases the number of possible modular and interchangeable DNA assemblies, exponentially increasing the possibilities of studying, developing, and exploiting filamentous fungi.
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Affiliation(s)
- Elena Moreno-Giménez
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universitat Politècnica de València (UPV), Valencia, Spain
| | - Mónica Gandía
- Preventive Medicine and Public Health, Food Science, Toxicology and Forensic Medicine Department. Faculty of Pharmacy. Universitat de València. Vicente Andrés Estellés s/n, Valencia, Spain
| | - Zara Sáez
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Paloma Manzanares
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Lynne Yenush
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universitat Politècnica de València (UPV), Valencia, Spain
| | - Diego Orzáez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universitat Politècnica de València (UPV), Valencia, Spain
| | - Jose F. Marcos
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Sandra Garrigues
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
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6
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Kocaoglan EG, Radhakrishnan D, Nakayama N. Synthetic developmental biology: molecular tools to re-design plant shoots and roots. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3864-3876. [PMID: 37155965 PMCID: PMC10826796 DOI: 10.1093/jxb/erad169] [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: 01/18/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023]
Abstract
Plant morphology and anatomy strongly influence agricultural yield. Crop domestication has strived for desirable growth and developmental traits, such as larger and more fruits and semi-dwarf architecture. Genetic engineering has accelerated rational, purpose-driven engineering of plant development, but it can be unpredictable. Developmental pathways are complex and riddled with environmental and hormonal inputs, as well as feedback and feedforward interactions, which occur at specific times and places in a growing multicellular organism. Rational modification of plant development would probably benefit from precision engineering based on synthetic biology approaches. This review outlines recently developed synthetic biology technologies for plant systems and highlights their potential for engineering plant growth and development. Streamlined and high-capacity genetic construction methods (Golden Gate DNA Assembly frameworks and toolkits) allow fast and variation-series cloning of multigene transgene constructs. This, together with a suite of gene regulation tools (e.g. cell type-specific promoters, logic gates, and multiplex regulation systems), is starting to enable developmental pathway engineering with predictable outcomes in model plant and crop species.
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Affiliation(s)
- Elif Gediz Kocaoglan
- Department of Bioengineering, Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Dhanya Radhakrishnan
- Department of Bioengineering, Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Naomi Nakayama
- Department of Bioengineering, Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
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7
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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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8
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Kallam K, Moreno-Giménez E, Mateos-Fernández R, Tansley C, Gianoglio S, Orzaez D, Patron N. Tunable control of insect pheromone biosynthesis in Nicotiana benthamiana. PLANT BIOTECHNOLOGY JOURNAL 2023. [PMID: 37032497 DOI: 10.1111/pbi.14048] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 03/14/2023] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Previous work has demonstrated that plants can be used as production platforms for molecules used in health, medicine, and agriculture. Production has been exemplified in both stable transgenic plants and using transient expression strategies. In particular, species of Nicotiana have been engineered to produce a range of useful molecules, including insect sex pheromones, which are valued for species-specific control of agricultural pests. To date, most studies have relied on strong constitutive expression of all pathway genes. However, work in microbes has demonstrated that yields can be improved by controlling and balancing gene expression. Synthetic regulatory elements that provide control over the timing and levels of gene expression are therefore useful for maximizing yields from heterologous biosynthetic pathways. In this study, we demonstrate the use of pathway engineering and synthetic genetic elements for controlling the timing and levels of production of Lepidopteran sex pheromones in Nicotiana benthamiana. We demonstrate that copper can be used as a low-cost molecule for tightly regulated inducible expression. Further, we show how construct architecture influences relative gene expression and, consequently, product yields in multigene constructs. We compare a number of synthetic orthogonal regulatory elements and demonstrate maximal yields from constructs in which expression is mediated by dCas9-based synthetic transcriptional activators. The approaches demonstrated here provide new insights into the heterologous reconstruction of metabolic pathways in plants.
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Affiliation(s)
- Kalyani Kallam
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk, UK
| | - Elena Moreno-Giménez
- Institute for Plant Molecular and Cell Biology (IBMCP), UPV-CSIC, Valencia, Spain
| | | | - Connor Tansley
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk, UK
| | - Silvia Gianoglio
- Institute for Plant Molecular and Cell Biology (IBMCP), UPV-CSIC, Valencia, Spain
| | - Diego Orzaez
- Institute for Plant Molecular and Cell Biology (IBMCP), UPV-CSIC, Valencia, Spain
| | - Nicola Patron
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk, UK
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9
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Yasmeen E, Wang J, Riaz M, Zhang L, Zuo K. Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants. PLANT COMMUNICATIONS 2023:100558. [PMID: 36760129 PMCID: PMC10363483 DOI: 10.1016/j.xplc.2023.100558] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
With the development of high-throughput biology techniques and artificial intelligence, it has become increasingly feasible to design and construct artificial biological parts, modules, circuits, and even whole systems. To overcome the limitations of native promoters in controlling gene expression, artificial promoter design aims to synthesize short, inducible, and conditionally controlled promoters to coordinate the expression of multiple genes in diverse plant metabolic and signaling pathways. Synthetic promoters are versatile and can drive gene expression accurately with smart responses; they show potential for enhancing desirable traits in crops, thereby improving crop yield, nutritional quality, and food security. This review first illustrates the importance of synthetic promoters, then introduces promoter architecture and thoroughly summarizes advances in synthetic promoter construction. Restrictions to the development of synthetic promoters and future applications of such promoters in synthetic plant biology and crop improvement are also discussed.
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Affiliation(s)
- Erum Yasmeen
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Riaz
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lida Zhang
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kaijing Zuo
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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10
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Clustered regularly interspaced short palindromic repeats tools for plant metabolic engineering: achievements and perspectives. Curr Opin Biotechnol 2023; 79:102856. [PMID: 36473330 DOI: 10.1016/j.copbio.2022.102856] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/17/2022] [Indexed: 12/09/2022]
Abstract
The plant kingdom represents the biggest source of feedstock, food, and added-value compounds. Engineering plant metabolic pathways to increase the phytochemical production or improve the nutraceutical value of crops is challenging because of the intricate interaction networks that link multiple genes, enzymatic steps, and metabolites, even when pathways are fully elucidated. The development of clustered regularly interspaced short palindromic repeats - CRISPR-associated (CRISPR-Cas) technologies has helped to overcome limitations in metabolic engineering, providing efficient and versatile tools for multigene editing. CRISPR approaches in plants were shown to have a remarkable efficiency in genome editing of different species to improve agronomic and metabolic traits. Here, we give an overview of the different achievements and perspectives of CRISPR technology in plant metabolic engineering.
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