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Sobrino-Mengual G, Alvarez D, Twyman RM, Gerrish C, Fraser PD, Capell T, Christou P. Activation of the native PHYTOENE SYNTHASE 1 promoter by modifying near-miss cis-acting elements induces carotenoid biosynthesis in embryogenic rice callus. PLANT CELL REPORTS 2024; 43:118. [PMID: 38632121 PMCID: PMC11024007 DOI: 10.1007/s00299-024-03199-7] [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: 02/05/2024] [Accepted: 03/13/2024] [Indexed: 04/19/2024]
Abstract
KEY MESSAGE Modification of silent latent endosperm-enabled promoters (SLEEPERs) allows the ectopic activation of non-expressed metabolic genes in rice callus Metabolic engineering in plants typically involves transgene expression or the mutation of endogenous genes. An alternative is promoter modification, where small changes in the promoter sequence allow genes to be switched on or off in particular tissues. To activate silent genes in rice endosperm, we screened native promoters for near-miss cis-acting elements that can be converted to endosperm-active regulatory motifs. We chose rice PHYTOENE SYNTHASE 1 (PSY1), encoding the enzyme responsible for the first committed step in the carotenoid biosynthesis pathway, because it is not expressed in rice endosperm. We identified six motifs within a 120-bp region, upstream of the transcriptional start site, which differed from endosperm-active elements by up to four nucleotides. We mutated four motifs to match functional elements in the endosperm-active BCH2 promoter, and this promoter was able to drive GFP expression in callus and in seeds of regenerated plants. The 4 M promoter was not sufficient to drive PSY1 expression, so we mutated the remaining two elements and used the resulting 6 M promoter to drive PSY1 expression in combination with a PDS transgene. This resulted in deep orange callus tissue indicating the accumulation of carotenoids, which was subsequently confirmed by targeted metabolomics analysis. PSY1 expression driven by the uncorrected or 4 M variants of the promoter plus a PDS transgene produced callus that lacked carotenoids. These results confirm that the adjustment of promoter elements can facilitate the ectopic activation of endogenous plant promoters in rice callus and endosperm and most likely in other tissues and plant species.
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Affiliation(s)
- Guillermo Sobrino-Mengual
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Derry Alvarez
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
- Division of Biological and Environmental Sciences and Engineering, Center for Desert Agriculture, BioActives Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Christopher Gerrish
- Department of Biological Sciences, Royal Holloway University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
| | - Paul D Fraser
- Department of Biological Sciences, Royal Holloway University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
| | - Teresa Capell
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Paul Christou
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain.
- ICREA, Catalan Institute for Research and Advanced Studies, Barcelona, Spain.
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Ho WK, Tanzi AS, Sang F, Tsoutsoura N, Shah N, Moore C, Bhosale R, Wright V, Massawe F, Mayes S. A genomic toolkit for winged bean Psophocarpus tetragonolobus. Nat Commun 2024; 15:1901. [PMID: 38429275 PMCID: PMC10907731 DOI: 10.1038/s41467-024-45048-x] [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: 02/13/2022] [Accepted: 01/12/2024] [Indexed: 03/03/2024] Open
Abstract
A sustainable supply of plant protein is critical for future generations and needs to be achieved while reducing green house gas emissions from agriculture and increasing agricultural resilience in the face of climate volatility. Agricultural diversification with more nutrient-rich and stress tolerant crops could provide the solution. However, this is often hampered by the limited availability of genomic resources and the lack of understanding of the genetic structure of breeding germplasm and the inheritance of important traits. One such crop with potential is winged bean (Psophocarpus tetragonolobus), a high seed protein tropical legume which has been termed 'the soybean for the tropics'. Here, we present a chromosome level winged bean genome assembly, an investigation of the genetic diversity of 130 worldwide accessions, together with two linked genetic maps and a trait QTL analysis (and expression studies) for regions of the genome with desirable ideotype traits for breeding, namely architecture, protein content and phytonutrients.
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Affiliation(s)
- Wai Kuan Ho
- Future Food Beacon, School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
- Crops for the Future (UK) CIC, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Alberto Stefano Tanzi
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Fei Sang
- Deep Seq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Niki Tsoutsoura
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Niraj Shah
- Digital and Technology Services, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Christopher Moore
- Deep Seq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Rahul Bhosale
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Victoria Wright
- Deep Seq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Festo Massawe
- Future Food Beacon, School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Sean Mayes
- Crops for the Future (UK) CIC, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK.
- International Centre for Research in the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502324, India.
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Li X, Cao X, Li J, Niu Q, Mo Y, Xiao L. Genome-wide characterization of C2H2 zinc-finger gene family provides insight into the mechanisms and evolution of the dehydration-rehydration responses in Physcomitrium and Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:953459. [PMID: 36262662 PMCID: PMC9574186 DOI: 10.3389/fpls.2022.953459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
Dehydration tolerance is a vital factor for land plant evolution and world agricultural production. Numerous studies enlightened that the plant-specific C2H2-type zinc-finger proteins (C2H2-ZFPs) as master regulators played pivotal roles in the abiotic stress responses of plants. However, a comprehensive understanding of the evolution of C2H2-ZFPs in terrestrial plants and its regulatory mechanism in dehydration and rehydration response remains a mystery. In this study, the genome-wide identification of C2H2-ZFP genes revealed 549 homologs in the representatives of terrestrial plant lineages from liverwort to angiosperms. Based on the characteristics of the conserved C2H2-ZF domains, four major C2H2-ZF types (M-, Z-, Q-, and D-type) were identified in the C2H2-ZFPs, with the dominants of M-type in all selected species and followed by Z-type in non-seed plants and Q-type in seed plants, respectively. Phylogenetic analyses of the identified C2H2-ZFPs supported four major groups in the land plant representatives, among which the members from the desiccation-tolerant Physcomitrium patens and the dehydration-sensitive Arabidopsis thaliana displayed different topological relationships in the phylogenies reconstructed for a single species. C2H2-ZFPs clustered in the same subclades shared similar features in their conserved domains and gene structures. Approximately, 81% of the C2H2-ZFP promoters of all 549 identified C2H2-ZFPs harbored the conserved ABA-responsive elements (ABREs) and/or dehydration-responsive elements (DREs). Comparative transcriptomic analyses showed that 50 PpZFPs and 56 AtZFPs significantly changed their transcripts abundance. Interestingly, most of the dehydration- and rehydration-responsive PpZPFs and AtZFPs had been predicted to contain the ABRE and DRE elements in their promoter regions and with over half of which phylogenetically belonging to group III. The differences in the expression patterns of C2H2-ZFPs in responses to dehydration and rehydration between P. patens and A. thaliana reflected their different strategies to adapt to dehydration. The identified candidate PpZFPs were specifically induced by moderate dehydration and reached the peak transcript abundance in severe dehydration. Our study lays the foundations for further functional investigation of C2H2-ZFPs in dehydration responses from an evolutionary perspective in land plants. The findings will provide us with genetic resources and potential targets for drought tolerance breeding in crops and beyond.
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Bublyk OM, Andreev IO, Kunakh VA. Comparative Analysis of Promoters of DREB2B Transcription Factor Genes in Deschampsia antarctica and Other Grasses. CYTOL GENET+ 2022. [DOI: 10.3103/s0095452722050048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Sultana MS, Mazarei M, Millwood RJ, Liu W, Hewezi T, Stewart CN. Functional analysis of soybean cyst nematode-inducible synthetic promoters and their regulation by biotic and abiotic stimuli in transgenic soybean ( Glycine max). FRONTIERS IN PLANT SCIENCE 2022; 13:988048. [PMID: 36160998 PMCID: PMC9501883 DOI: 10.3389/fpls.2022.988048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
We previously identified cis-regulatory motifs in the soybean (Glycine max) genome during interaction between soybean and soybean cyst nematode (SCN), Heterodera glycines. The regulatory motifs were used to develop synthetic promoters, and their inducibility in response to SCN infection was shown in transgenic soybean hairy roots. Here, we studied the functionality of two SCN-inducible synthetic promoters; 4 × M1.1 (TAAAATAAAGTTCTTTAATT) and 4 × M2.3 (ATATAATTAAGT) each fused to the -46 CaMV35S core sequence in transgenic soybean. Histochemical GUS analyses of transgenic soybean plants containing the individual synthetic promoter::GUS construct revealed that under unstressed condition, no GUS activity is present in leaves and roots. While upon nematode infection, the synthetic promoters direct GUS expression to roots predominantly in the nematode feeding structures induced by the SCN and by the root-knot nematode (RKN), Meloidogyne incognita. There were no differences in GUS activity in leaves between nematode-infected and non-infected plants. Furthermore, we examined the specificity of the synthetic promoters in response to various biotic (insect: fall armyworm, Spodoptera frugiperda; and bacteria: Pseudomonas syringe pv. glycinea, P. syringe pv. tomato, and P. marginalis) stresses. Additionally, we examined the specificity to various abiotic (dehydration, salt, cold, wounding) as well as to the signal molecules salicylic acid (SA), methyl jasmonate (MeJA), and abscisic acid (ABA) in the transgenic plants. Our wide-range analyses provide insights into the potential applications of synthetic promoter engineering for conditional expression of transgenes leading to transgenic crop development for resistance improvement in plant.
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Affiliation(s)
- Mst Shamira Sultana
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, United States
| | - Mitra Mazarei
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, United States
| | - Reginald J. Millwood
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | - C. Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, United States
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6
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Tu Z, Yu L, Wen S, Zhai X, Li W, Li H. Identification and analysis of HD-Zip genes involved in the leaf development of Liriodendron chinense using multidimensional analysis. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:874-886. [PMID: 35491433 DOI: 10.1111/plb.13431] [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: 01/30/2022] [Accepted: 04/25/2022] [Indexed: 06/14/2023]
Abstract
Homeodomain-leucine zipper (HD-Zip) proteins are plant-specific transcription factors that play important roles in different biological processes, especially leaf development. However, no studies to date have identified the HD-Zip genes in Liriodendron chinense nor characterized their functions. We identified the HD-Zip genes in L. chinense by analysing the phylogeny, chromosome location, structure, conserved motif, cis-regulatory elements, synteny, post-transcriptional regulation and expression patterns of these genes during leaf development. A total of 36 LcHD-Zip genes were identified and divided into four subfamilies (HD-Zip I to IV). Synteny analysis revealed that segmental duplication was the main force driving the expansion of LcHD-Zip genes. These 36 LcHD-Zip genes exhibited 11 different expression patterns. Pattern 1, 2, 3, 4, 6, 7, 8 and 9 genes may play important roles in leaf development, such as leaf initiation, leaf polarity establishment, leaf shape development, phytohormone-mediated leaf growth and leaf epidermal structure formation. Four HD-Zip III genes were targeted by microRNAs (miRNAs), and the miR165/166a-HD-Zip regulatory module formed regulated leaf initiation and leaf polarity establishment. Overall, LcHD-Zip genes play key roles in leaf development of L. chinense. This work provides a foundation for the functional verification of HD-Zip genes identified in this study.
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Affiliation(s)
- Z Tu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - L Yu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - S Wen
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - X Zhai
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - W Li
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - H Li
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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7
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Sultana MS, Millwood RJ, Mazarei M, Stewart CN. Proteinase inhibitors in legume herbivore defense: from natural to genetically engineered protectants. PLANT CELL REPORTS 2022; 41:293-305. [PMID: 34674016 DOI: 10.1007/s00299-021-02800-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Proteinase inhibitors (PIs) from legumes have the potential for use as protectants in response to pests and pathogens. Legumes have evolved PIs that inhibit digestive proteinases upon herbivory resulting in delayed development, deformities, and reduced fertility of herbivorous insects. Legume PIs (serine proteinase inhibitors and cysteine proteinase inhibitors) have been overexpressed in plants to confer plant protection against herbivores. Recently, the co-expression of multiple PIs in transgenic plants enhanced host defense over single PI expression, i.e., in an additive fashion. Therefore, a synthetic PI could conceivably be designed using different inhibitory domains that may provide multifunctional protection. Little attention has yet given to expanding PI gene repertoires to improve PI efficacy for targeting multiple proteinases. Also, PIs have been shown to play an important role in response to abiotic stresses. Previously published papers have presented several aspects of strategic deployment of PIs in transgenic plants, which is the focus of this review by providing a comprehensive update of the recent progress of using PIs in transgenic plants. We also emphasize broadening the potential usefulness of PIs and their future direction in research, which will likely result in a more potent defense against herbivores.
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Affiliation(s)
| | | | - Mitra Mazarei
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, USA.
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8
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Huang D, Kosentka PZ, Liu W. Synthetic biology approaches in regulation of targeted gene expression. CURRENT OPINION IN PLANT BIOLOGY 2021; 63:102036. [PMID: 33930839 DOI: 10.1016/j.pbi.2021.102036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 05/15/2023]
Abstract
Synthetic biology approaches are highly sought-after to facilitate the regulation of targeted gene expression in plants for functional genomics research and crop trait improvement. To date, synthetic regulation of gene expression predominantly focuses at the transcription level via engineering of synthetic promoters and transcription factors, while pioneering examples have started to emerge for synthetic regulation of gene expression at the levels of mRNA stability, translation, and protein degradation. This review discusses recent advances in plant synthetic biology for the regulation of gene expression at multiple levels, and highlights their future directions.
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Affiliation(s)
- Debao Huang
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Pawel Z Kosentka
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA.
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Efremova LN, Strelnikova SR, Gazizova GR, Minkina EA, Komakhin RA. A Synthetic Strong and Constitutive Promoter Derived from the Stellaria media pro-SmAMP1 and pro-SmAMP2 Promoters for Effective Transgene Expression in Plants. Genes (Basel) 2020; 11:E1407. [PMID: 33256091 PMCID: PMC7760760 DOI: 10.3390/genes11121407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/22/2020] [Accepted: 11/24/2020] [Indexed: 01/05/2023] Open
Abstract
Synthetic promoters are vital for genetic engineering-based strategies for crop improvement, but effective methodologies for their creation and systematic testing are lacking. We report here on the comparative analysis of the promoters pro-SmAMP1 and pro-SmAMP2 from Stellaria media ANTIMICROBIAL PEPTIDE1 (AMP1) and ANTIMICROBIAL PEPTIDE2 (AMP2). These promoters are more effective than the well-known Cauliflower mosaic virus 35S promoter. Although these promoters share about 94% identity, the pro-SmAMP1 promoter demonstrated stronger transient expression of a reporter gene in Agrobacterium infiltration of Nicotiana benthamiana leaves, while the pro-SmAMP2 promoter was more effective for the selection of transgenic tobacco (Nicotiana tabacum) cells when driving a selectable marker. Using the cap analysis of gene expression method, we detected no differences in the structure of the transcription start sites for either promoter in transgenic plants. For both promoters, we used fine-scale deletion analysis to identify 160 bp-long sequences that retain the unique properties of each promoter. With the use of chimeric promoters and directed mutagenesis, we demonstrated that the superiority of the pro-SmAMP1 promoter for Agrobacterium-mediated infiltration is caused by the proline-inducible ACTCAT cis-element strictly positioned relative to the TATA box in the core promoter. Surprisingly, the ACTCAT cis-element not only activated but also suppressed the efficiency of the pro-SmAMP1 promoter under proline stress. The absence of the ACTCAT cis-element and CAANNNNATC motif (negative regulator) in the pro-SmAMP2 promoter provided a more constitutive gene expression profile and better selection of transgenic cells on selective medium. We created a new synthetic promoter that enjoys high effectiveness both in transient expression and in selection of transgenic cells. Intact promoters with differing properties and high degrees of sequence identity may thus be used as a basis for the creation of new synthetic promoters for precise and coordinated gene expression.
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Affiliation(s)
- Larisa N. Efremova
- All-Russia Research Institute of Agricultural Biotechnology, Moscow 127550, Russia; (L.N.E.); (S.R.S.)
| | - Svetlana R. Strelnikova
- All-Russia Research Institute of Agricultural Biotechnology, Moscow 127550, Russia; (L.N.E.); (S.R.S.)
| | - Guzel R. Gazizova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia; (G.R.G.); (E.A.M.)
| | - Elena A. Minkina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia; (G.R.G.); (E.A.M.)
| | - Roman A. Komakhin
- All-Russia Research Institute of Agricultural Biotechnology, Moscow 127550, Russia; (L.N.E.); (S.R.S.)
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Li Q, Sapkota M, van der Knaap E. Perspectives of CRISPR/Cas-mediated cis-engineering in horticulture: unlocking the neglected potential for crop improvement. HORTICULTURE RESEARCH 2020; 7:36. [PMID: 32194972 PMCID: PMC7072075 DOI: 10.1038/s41438-020-0258-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/09/2020] [Accepted: 02/11/2020] [Indexed: 05/14/2023]
Abstract
Directed breeding of horticultural crops is essential for increasing yield, nutritional content, and consumer-valued characteristics such as shape and color of the produce. However, limited genetic diversity restricts the amount of crop improvement that can be achieved through conventional breeding approaches. Natural genetic changes in cis-regulatory regions of genes play important roles in shaping phenotypic diversity by altering their expression. Utilization of CRISPR/Cas editing in crop species can accelerate crop improvement through the introduction of genetic variation in a targeted manner. The advent of CRISPR/Cas-mediated cis-regulatory region engineering (cis-engineering) provides a more refined method for modulating gene expression and creating phenotypic diversity to benefit crop improvement. Here, we focus on the current applications of CRISPR/Cas-mediated cis-engineering in horticultural crops. We describe strategies and limitations for its use in crop improvement, including de novo cis-regulatory element (CRE) discovery, precise genome editing, and transgene-free genome editing. In addition, we discuss the challenges and prospects regarding current technologies and achievements. CRISPR/Cas-mediated cis-engineering is a critical tool for generating horticultural crops that are better able to adapt to climate change and providing food for an increasing world population.
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Affiliation(s)
- Qiang Li
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an, China
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA USA
| | - Manoj Sapkota
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA USA
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA USA
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA USA
- Department of Horticulture, University of Georgia, Athens, GA USA
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11
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Sánchez-Álvarez A, Ruíz-López N, Moreno-Pérez AJ, Martínez-Force E, Garcés R, Salas JJ. Agrobacterium-Mediated Transient Gene Expression in Developing Ricinus communis Seeds: A First Step in Making the Castor Oil Plant a Chemical Biofactory. FRONTIERS IN PLANT SCIENCE 2019; 10:1410. [PMID: 31737023 PMCID: PMC6831639 DOI: 10.3389/fpls.2019.01410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 10/11/2019] [Indexed: 06/10/2023]
Abstract
The castor oil plant represents a promising platform to produce oils with industrial applications. However, its use in biotechnology is limited by the absence of a well-established procedure to transform it, and a poor understanding of gene regulation and promoter use in this species. As such, a method has been developed to express proteins or hairpin-RNA in this plant, a method based on the direct injection of Agrobacterium into the developing endosperm of castor oil fruit, enabling different constructs and promoters to be tested. This method produces a high rate of transformation and a good proportion of viable seeds that express reporter genes for up to 20 days after infiltration (DAI). Gene expression under the control of different promoters was tested by quantitative real-time polymerase chain reaction and by directly assaying the activity of the galactouronidase reporter gene, which proved to be strongest when driven by the glycinin promoter. Constructs expressing a fatty acid elongase from Lesquerella fendleri were tested, the expression of which provoked an important increase in the lesquerolic acid in the castor oil endosperm at 5 and 10 DAI, although this fatty acid did not accumulate significantly in the final mature seeds. The nature of this response could reflect the poor availability of substrates for this enzyme. In the light of this data, the potential of this technique to test promoters and different constructs in castor oil plants and other oilseeds is discussed.
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Affiliation(s)
- Alfonso Sánchez-Álvarez
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Sevilla, Spain
| | | | - Antonio Javier Moreno-Pérez
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Sevilla, Spain
| | - Enrique Martínez-Force
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Sevilla, Spain
| | - Rafael Garcés
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Sevilla, Spain
| | - Joaquín J. Salas
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Sevilla, Spain
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Arnaiz A, Martinez M, Gonzalez-Melendi P, Grbic V, Diaz I, Santamaria ME. Plant Defenses Against Pests Driven by a Bidirectional Promoter. FRONTIERS IN PLANT SCIENCE 2019; 10:930. [PMID: 31379907 PMCID: PMC6652247 DOI: 10.3389/fpls.2019.00930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/02/2019] [Indexed: 05/06/2023]
Abstract
The plant defense responses to pests results in the synchronized change of a complex network of interconnected genes and signaling pathways. An essential part of this process is mediated by the binding of transcription factors to the specific responsive cis-elements within in the promoters of phytophagous-responsive genes. In this work, it is reported the identification and characterization of a bidirectional promoter that simultaneously co-regulate two divergent genes, At5g10300 and At5g10290, upon arthropod feeding. Computational analysis identified the presence of cis-elements within the intergenic region between two loci, mainly from the DOF but also from the AP2/ERF, Golden 2-like and bHLH families. The function of the bidirectional promoter was analyzed using two enhanced variants of the GFP and CherryFP reporter genes, in both orientations, in transient tobacco and stably transformed Arabidopsis plants. Promoter activity was tested in response to feeding of Tetranychus urticae and Pieris brassicae, as well as wounding, flagellin and chitin treatments. Using RT-qPCR assays and confocal microscopy, it was shown that all treatments resulted in the induction of both reporter genes. Furthermore, our findings revealed the asymmetric character of the promoter with stronger activity in the forward than in the reverse orientation. This study provides an example of a bidirectional promoter with a strong potential to be used in plant biotechnology in pest control that requires stacking of the defense genes.
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Affiliation(s)
- Ana Arnaiz
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
| | - Manuel Martinez
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Pablo Gonzalez-Melendi
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Vojislava Grbic
- Department of Biology, The University of Western Ontario, London, ON, Canada
| | - Isabel Diaz
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - M. Estrella Santamaria
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
- *Correspondence: M. Estrella Santamaria,
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