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Chen F, Chen L, Yan Z, Xu J, Feng L, He N, Guo M, Zhao J, Chen Z, Chen H, Yao G, Liu C. Recent advances of CRISPR-based genome editing for enhancing staple crops. FRONTIERS IN PLANT SCIENCE 2024; 15:1478398. [PMID: 39376239 PMCID: PMC11456538 DOI: 10.3389/fpls.2024.1478398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Accepted: 09/03/2024] [Indexed: 10/09/2024]
Abstract
An increasing population, climate change, and diminishing natural resources present severe threats to global food security, with traditional breeding and genetic engineering methods often falling short in addressing these rapidly evolving challenges. CRISPR/Cas systems have emerged as revolutionary tools for precise genetic modifications in crops, offering significant advancements in resilience, yield, and nutritional value, particularly in staple crops like rice and maize. This review highlights the transformative potential of CRISPR/Cas technology, emphasizing recent innovations such as prime and base editing, and the development of novel CRISPR-associated proteins, which have significantly improved the specificity, efficiency, and scope of genome editing in agriculture. These advancements enable targeted genetic modifications that enhance tolerance to abiotic stresses as well as biotic stresses. Additionally, CRISPR/Cas plays a crucial role in improving crop yield and quality by enhancing photosynthetic efficiency, nutrient uptake, and resistance to lodging, while also improving taste, texture, shelf life, and nutritional content through biofortification. Despite challenges such as off-target effects, the need for more efficient delivery methods, and ethical and regulatory concerns, the review underscores the importance of CRISPR/Cas in addressing global food security and sustainability challenges. It calls for continued research and integration of CRISPR with other emerging technologies like nanotechnology, synthetic biology, and machine learning to fully realize its potential in developing resilient, productive, and sustainable agricultural systems.
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Affiliation(s)
- Feng Chen
- School of Biology and Food Engineering, Changshu Institute of Technology, Changshu, Suzhou, Jiangsu, China
| | - Lu Chen
- Pharma Technology A/S, Køge, Denmark
| | - Zhao Yan
- School of Biology and Food Engineering, Changshu Institute of Technology, Changshu, Suzhou, Jiangsu, China
| | - Jingyuan Xu
- School of Biology and Food Engineering, Changshu Institute of Technology, Changshu, Suzhou, Jiangsu, China
| | - Luoluo Feng
- School of Biology and Food Engineering, Changshu Institute of Technology, Changshu, Suzhou, Jiangsu, China
| | - Na He
- School of Biology and Food Engineering, Changshu Institute of Technology, Changshu, Suzhou, Jiangsu, China
| | - Mingli Guo
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Jiaxiong Zhao
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhijun Chen
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Huiqi Chen
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Gengzhen Yao
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Chunping Liu
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, Guangdong, China
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Ferreira SS, Antunes MS. Genetically encoded Boolean logic operators to sense and integrate phenylpropanoid metabolite levels in plants. THE NEW PHYTOLOGIST 2024; 243:674-687. [PMID: 38752334 DOI: 10.1111/nph.19823] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/30/2024] [Indexed: 06/21/2024]
Abstract
Synthetic biology has the potential to revolutionize biotechnology, public health, and agriculture. Recent studies have shown the enormous potential of plants as chassis for synthetic biology applications. However, tools to precisely manipulate metabolic pathways for bioproduction in plants are still needed. We used bacterial allosteric transcription factors (aTFs) that control gene expression in a ligand-specific manner and tested their ability to repress semi-synthetic promoters in plants. We also tested the modulation of their repression activity in response to specific plant metabolites, especially phenylpropanoid-related molecules. Using these aTFs, we also designed synthetic genetic circuits capable of computing Boolean logic operations. Three aTFs, CouR, FapR, and TtgR, achieved c. 95% repression of their respective target promoters. For TtgR, a sixfold de-repression could be triggered by inducing its ligand accumulation, showing its use as biosensor. Moreover, we designed synthetic genetic circuits that use AND, NAND, IMPLY, and NIMPLY Boolean logic operations and integrate metabolite levels as input to the circuit. We showed that biosensors can be implemented in plants to detect phenylpropanoid-related metabolites and activate a genetic circuit that follows a predefined logic, demonstrating their potential as tools for exerting control over plant metabolic pathways and facilitating the bioproduction of natural products.
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Affiliation(s)
- Savio S Ferreira
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
- BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA
| | - Mauricio S Antunes
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
- BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA
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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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Joshi J, Hanson AD. A pilot oral history of plant synthetic biology. PLANT PHYSIOLOGY 2024; 195:36-47. [PMID: 38163646 PMCID: PMC11060686 DOI: 10.1093/plphys/kiad585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/15/2023] [Indexed: 01/03/2024]
Abstract
The whole field of synthetic biology (SynBio) is only about 20 years old, and plant SynBio is younger still. Nevertheless, within that short time, SynBio in general has drawn more scientific, philosophical, government, and private-sector interest than anything in biology since the recombinant DNA revolution. Plant SynBio, in particular, is now drawing more and more interest in relation to plants' potential to help solve planetary problems such as carbon capture and storage and replacing fossil fuels and feedstocks. As plant SynBio is so young and so fast-developing, we felt it was too soon to try to analyze its history. Instead, we set out to capture the essence of plant SynBio's origins and early development through interviews with 8 of the field's founders, representing 5 countries and 3 continents. We then distilled these founders' personal recollections and reflections into this review, centering the narrative on timelines for pivotal events, articles, funding programs, and quoting from interviews. We have archived the interview recordings and documented timeline entries. This work provides a resource for future historical scholarship.
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Affiliation(s)
- Jaya Joshi
- Department of Wood Science, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, 2550 Hull Road, Gainesville, FL 32611, USA
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