1
|
Owens NA, Anborgh PH, Kolotilin I. Chromatography affinity resin with photosynthetically-sourced protein A ligand. Sci Rep 2024; 14:8714. [PMID: 38622266 PMCID: PMC11018848 DOI: 10.1038/s41598-024-59266-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/09/2024] [Indexed: 04/17/2024] Open
Abstract
Green, photosynthesizing plants can be proficiently used as cost-effective, single-use, fully biodegradable bioreactors for environmentally-friendly production of a variety of valuable recombinant proteins. Being near-infinitely scalable and most energy-efficient in generating biomass, plants represent profoundly valid alternatives to conventionally used stationary fermenters. To validate this, we produced a plastome-engineered tobacco bioreactor line expressing a recombinant variant of the protein A from Staphylococcus aureus, an affinity ligand widely useful in antibody purification processes, reaching accumulation levels up to ~ 250 mg per 1 kg of fresh leaf biomass. Chromatography resin manufactured from photosynthetically-sourced recombinant protein A ligand conjugated to agarose beads demonstrated the innate pH-driven ability to bind and elute IgG-type antibodies and allowed one-step efficient purification of functional monoclonal antibodies from the supernatants of the producing hybridomas. The results of this study emphasize the versatility of plant-based recombinant protein production and illustrate its vast potential in reducing the cost of diverse biotechnological applications, particularly the downstream processing and purification of monoclonal antibodies.
Collapse
Affiliation(s)
- Nisha A Owens
- The School of Applied Science and Technology, Fanshawe College, London, ON, Canada
| | - Pieter H Anborgh
- The School of Applied Science and Technology, Fanshawe College, London, ON, Canada
| | | |
Collapse
|
2
|
Han F, Zhang X, Liu Y, Liu Y, Zhao H, Li Z. One-step creation of CMS lines using a BoCENH3-based haploid induction system in Brassica crop. Nat Plants 2024; 10:581-586. [PMID: 38499776 PMCID: PMC11035129 DOI: 10.1038/s41477-024-01643-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 02/04/2024] [Indexed: 03/20/2024]
Abstract
Heterosis utilization in a large proportion of crops depends on the use of cytoplasmic male sterility (CMS) tools, requiring the development of homozygous fertile lines and CMS lines1. Although doubled haploid (DH) technology has been developed for several crops to rapidly generate fertile lines2,3, CMS lines are generally created by multiple rounds of backcrossing, which is time consuming and expensive4. Here we describe a method for generating both homozygous fertile and CMS lines through in vivo paternal haploid induction (HI). We generated in-frame deletion and restored frameshift mutants of BoCENH3 in Brassica oleracea using the CRISPR/Cas9 system. The mutants induced paternal haploids by outcrossing. We subsequently generated HI lines with CMS cytoplasm, which enabled the generation of homozygous CMS lines in one step. The BoCENH3-based HI system provides a new DH technology to accelerate breeding in Brassica and other crops.
Collapse
Affiliation(s)
- Fengqing Han
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoli Zhang
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Yuxiang Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory for Vegetable Biology of Hunan Province, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Hunan Agricultural University, Changsha, China
| | - Yumei Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hong Zhao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
| | - Zhansheng Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
| |
Collapse
|
3
|
Ragland CJ, Shih KY, Dinneny JR. Choreographing root architecture and rhizosphere interactions through synthetic biology. Nat Commun 2024; 15:1370. [PMID: 38355570 PMCID: PMC10866969 DOI: 10.1038/s41467-024-45272-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 01/18/2024] [Indexed: 02/16/2024] Open
Abstract
Climate change is driving extreme changes to the environment, posing substantial threats to global food security and bioenergy. Given the direct role of plant roots in mediating plant-environment interactions, engineering the form and function of root systems and their associated microbiota may mitigate these effects. Synthetic genetic circuits have enabled sophisticated control of gene expression in microbial systems for years and a surge of advances has heralded the extension of this approach to multicellular plant species. Targeting these tools to affect root structure, exudation, and microbe activity on root surfaces provide multiple strategies for the advancement of climate-ready crops.
Collapse
Affiliation(s)
- Carin J Ragland
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Kevin Y Shih
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
| |
Collapse
|
4
|
Zhang X, Liu Y, Yuan G, Wang S, Wang D, Zhu T, Wu X, Ma M, Guo L, Guo H, Bhadauria V, Liu J, Peng YL. The synthetic NLR RGA5 HMA5 requires multiple interfaces within and outside the integrated domain for effector recognition. Nat Commun 2024; 15:1104. [PMID: 38321036 PMCID: PMC10847126 DOI: 10.1038/s41467-024-45380-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/19/2024] [Indexed: 02/08/2024] Open
Abstract
Some plant sensor nucleotide-binding leucine-rich repeat (NLR) receptors detect pathogen effectors through their integrated domains (IDs). Rice RGA5 sensor NLR recognizes its corresponding effectors AVR-Pia and AVR1-CO39 from the blast fungus Magnaporthe oryzae through direct binding to its heavy metal-associated (HMA) ID to trigger the RGA4 helper NLR-dependent resistance in rice. Here, we report a mutant of RGA5 named RGA5HMA5 that confers complete resistance in transgenic rice plants to the M. oryzae strains expressing the noncorresponding effector AVR-PikD. RGA5HMA5 carries three engineered interfaces, two of which lie in the HMA ID and the other in the C-terminal Lys-rich stretch tailing the ID. However, RGA5 variants having one or two of the three interfaces, including replacing all the Lys residues with Glu residues in the Lys-rich stretch, failed to activate RGA4-dependent cell death of rice protoplasts. Altogether, this work demonstrates that sensor NLRs require a concerted action of multiple surfaces within and outside the IDs to both recognize effectors and activate helper NLR-mediated resistance, and has implications in structure-guided designing of sensor NLRs.
Collapse
Affiliation(s)
- Xin Zhang
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, 100193, Beijing, China
| | - Yang Liu
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, 100193, Beijing, China
| | - Guixin Yuan
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, 100193, Beijing, China
| | - Shiwei Wang
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, 100193, Beijing, China
| | - Dongli Wang
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, 100193, Beijing, China
| | - Tongtong Zhu
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, 100193, Beijing, China
| | - Xuefeng Wu
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, 100193, Beijing, China
| | - Mengqi Ma
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, 100193, Beijing, China
| | - Liwei Guo
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, 650201, Kunming, China
| | - Hailong Guo
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China
| | - Vijai Bhadauria
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China
| | - Junfeng Liu
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China.
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, 100193, Beijing, China.
| | - You-Liang Peng
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China.
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, 100193, Beijing, China.
| |
Collapse
|
5
|
Polturak G, Misra RC, El-Demerdash A, Owen C, Steed A, McDonald HP, Wang J, Saalbach G, Martins C, Chartrain L, Wilkinson B, Nicholson P, Osbourn A. Discovery of isoflavone phytoalexins in wheat reveals an alternative route to isoflavonoid biosynthesis. Nat Commun 2023; 14:6977. [PMID: 37914713 PMCID: PMC10620232 DOI: 10.1038/s41467-023-42464-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/12/2023] [Indexed: 11/03/2023] Open
Abstract
Isoflavones are a group of phenolic compounds mostly restricted to plants of the legume family, where they mediate important interactions with plant-associated microbes, including in defense from pathogens and in nodulation. Their well-studied health promoting attributes have made them a prime target for metabolic engineering, both for bioproduction of isoflavones as high-value molecules, and in biofortification of food crops. A key gene in their biosynthesis, isoflavone synthase, was identified in legumes over two decades ago, but little is known about formation of isoflavones outside of this family. Here we identify a specialized wheat-specific isoflavone synthase, TaCYP71F53, which catalyzes a different reaction from the leguminous isoflavone synthases, thus revealing an alternative path to isoflavonoid biosynthesis and providing a non-transgenic route for engineering isoflavone production in wheat. TaCYP71F53 forms part of a biosynthetic gene cluster that produces a naringenin-derived O-methylated isoflavone, 5-hydroxy-2',4',7-trimethoxyisoflavone, triticein. Pathogen-induced production and in vitro antimicrobial activity of triticein suggest a defense-related role for this molecule in wheat. Genomic and metabolic analyses of wheat ancestral grasses further show that the triticein gene cluster was introduced into domesticated emmer wheat through natural hybridization ~9000 years ago, and encodes a pathogen-responsive metabolic pathway that is conserved in modern bread wheat varieties.
Collapse
Affiliation(s)
- Guy Polturak
- Biochemistry and Metabolism Department, John Innes Centre, Norwich, NR4 7UH, UK.
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
| | | | - Amr El-Demerdash
- Biochemistry and Metabolism Department, John Innes Centre, Norwich, NR4 7UH, UK
- Division of Organic Chemistry, Department of Chemistry, School of Sciences, Mansoura University, Mansoura, 35516, Egypt
| | - Charlotte Owen
- Biochemistry and Metabolism Department, John Innes Centre, Norwich, NR4 7UH, UK
| | - Andrew Steed
- Crop Genetics Department, John Innes Centre, Norwich, NR4 7UH, UK
| | - Hannah P McDonald
- Molecular Microbiology Department, John Innes Centre, Norwich, NR4 7UH, UK
| | - JiaoJiao Wang
- Biochemistry and Metabolism Department, John Innes Centre, Norwich, NR4 7UH, UK
- Tsinghua-Peking Joint Center for Life Sciences, and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | | | - Carlo Martins
- Proteomics Facility, John Innes Centre, Norwich, NR4 7UH, UK
| | | | - Barrie Wilkinson
- Molecular Microbiology Department, John Innes Centre, Norwich, NR4 7UH, UK
| | - Paul Nicholson
- Crop Genetics Department, John Innes Centre, Norwich, NR4 7UH, UK
| | - Anne Osbourn
- Biochemistry and Metabolism Department, John Innes Centre, Norwich, NR4 7UH, UK.
| |
Collapse
|
6
|
Liu J, Wang FZ, Li C, Li Y, Li JF. Hidden prevalence of deletion-inversion bi-alleles in CRISPR-mediated deletions of tandemly arrayed genes in plants. Nat Commun 2023; 14:6787. [PMID: 37880225 PMCID: PMC10600118 DOI: 10.1038/s41467-023-42490-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023] Open
Abstract
Tandemly arrayed genes (TAGs) with functional redundancy and chromosomal linkage constitute 14 ~ 35% in sequenced plant genomes. The multiplex CRISPR system is the tool of choice for creating targeted TAG deletions. Here, we show that up to ~80% of CRISPR-mediated TAG knockout alleles in Arabidopsis and rice are deletion-inversion (delinver) bi-alleles, which are easily misidentified as homozygous deletion alleles by routine PCR-based genotyping. This can lead to misinterpretation of experimental data and production of progenies with genetic heterogeneity in an unnoticed manner. In ~2,650 transgenic events, delinver mutation frequencies are predominantly correlated with deletion frequencies but unrelated to chromosomal locations or deletion sizes. Delinver mutations also occur frequently at genomic non-TAG loci during multiplexed CRISPR editing. Our work raises the alarm about delinver mutations as common unwanted products of targeted TAG deletions in plants and helps prevent false interpretation of plant TAG functions due to this hidden genotype issue.
Collapse
Affiliation(s)
- Jiuer Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Feng-Zhu Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Chong Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yujia Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jian-Feng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| |
Collapse
|
7
|
Kunert M, Langley C, Lucier R, Ploss K, Rodríguez López CE, Serna Guerrero DA, Rothe E, O'Connor SE, Sonawane PD. Promiscuous CYP87A enzyme activity initiates cardenolide biosynthesis in plants. Nat Plants 2023; 9:1607-1617. [PMID: 37723202 PMCID: PMC10581899 DOI: 10.1038/s41477-023-01515-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 08/16/2023] [Indexed: 09/20/2023]
Abstract
Cardenolides are specialized, steroidal metabolites produced in a wide array of plant families1,2. Cardenolides play protective roles in plants, but these molecules, including digoxin from foxglove (Digitalis spp.), are better known for treatment of congenital heart failure, atrial arrhythmia, various cancers and other chronic diseases3-9. However, it is still unknown how plants synthesize 'high-value', complex cardenolide structures from, presumably, a sterol precursor. Here we identify two cytochrome P450, family 87, subfamily A (CYP87A) enzymes that act on both cholesterol and phytosterols (campesterol and β-sitosterol) to form pregnenolone, the first committed step in cardenolide biosynthesis in the two phylogenetically distant plants Digitalis purpurea and Calotropis procera. Arabidopsis plants overexpressing these CYP87A enzymes ectopically accumulated pregnenolone, whereas silencing of CYP87A in D. purpurea leaves by RNA interference resulted in substantial reduction of pregnenolone and cardenolides. Our work uncovers the key entry point to the cardenolide pathway, and expands the toolbox for sustainable production of high-value plant steroids via synthetic biology.
Collapse
Affiliation(s)
- Maritta Kunert
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Chloe Langley
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Rosalind Lucier
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Kerstin Ploss
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Carlos E Rodríguez López
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Delia A Serna Guerrero
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Eva Rothe
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany.
| | - Prashant D Sonawane
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany.
| |
Collapse
|
8
|
Zhong Z, Liu G, Tang Z, Xiang S, Yang L, Huang L, He Y, Fan T, Liu S, Zheng X, Zhang T, Qi Y, Huang J, Zhang Y. Efficient plant genome engineering using a probiotic sourced CRISPR-Cas9 system. Nat Commun 2023; 14:6102. [PMID: 37773156 PMCID: PMC10541446 DOI: 10.1038/s41467-023-41802-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 09/19/2023] [Indexed: 10/01/2023] Open
Abstract
Among CRISPR-Cas genome editing systems, Streptococcus pyogenes Cas9 (SpCas9), sourced from a human pathogen, is the most widely used. Here, through in silico data mining, we have established an efficient plant genome engineering system using CRISPR-Cas9 from probiotic Lactobacillus rhamnosus. We have confirmed the predicted 5'-NGAAA-3' PAM via a bacterial PAM depletion assay and showcased its exceptional editing efficiency in rice, wheat, tomato, and Larix cells, surpassing LbCas12a, SpCas9-NG, and SpRY when targeting the identical sequences. In stable rice lines, LrCas9 facilitates multiplexed gene knockout through coding sequence editing and achieves gene knockdown via targeted promoter deletion, demonstrating high specificity. We have also developed LrCas9-derived cytosine and adenine base editors, expanding base editing capabilities. Finally, by harnessing LrCas9's A/T-rich PAM targeting preference, we have created efficient CRISPR interference and activation systems in plants. Together, our work establishes CRISPR-LrCas9 as an efficient and user-friendly genome engineering tool for diverse applications in crops and beyond.
Collapse
Affiliation(s)
- Zhaohui Zhong
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, 610054, Chengdu, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, 400715, Chongqing, China
| | - Guanqing Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, 225012, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, 225012, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, 225012, Yangzhou, China
| | - Zhongjie Tang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, 610054, Chengdu, China
| | - Shuyue Xiang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, 610054, Chengdu, China
| | - Liang Yang
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Sichuan, China
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, 610066, Chengdu, China
| | - Lan Huang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, 610054, Chengdu, China
| | - Yao He
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, 610054, Chengdu, China
| | - Tingting Fan
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, 610054, Chengdu, China
| | - Shishi Liu
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, 610054, Chengdu, China
| | - Xuelian Zheng
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, 610054, Chengdu, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, 400715, Chongqing, China
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, 225012, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, 225012, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, 225012, Yangzhou, China
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA.
| | - Jian Huang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, 610054, Chengdu, China.
| | - Yong Zhang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, 610054, Chengdu, China.
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, 400715, Chongqing, China.
| |
Collapse
|
9
|
Zhang Z, Zhang X, Chen Y, Jiang W, Zhang J, Wang J, Wu Y, Wang S, Yang X, Liu M, Zhang Y. Understanding the mechanism of red light-induced melatonin biosynthesis facilitates the engineering of melatonin-enriched tomatoes. Nat Commun 2023; 14:5525. [PMID: 37684283 PMCID: PMC10491657 DOI: 10.1038/s41467-023-41307-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
Melatonin is a functionally conserved broad-spectrum physiological regulator found in most biological organisms in nature. Enrichment of tomato fruit with melatonin not only enhances its agronomic traits but also provides extra health benefits. In this study, we elucidate the full melatonin biosynthesis pathway in tomato fruit by identifying biosynthesis-related genes that encode caffeic acid O-methyltransferase 2 (SlCOMT2) and N-acetyl-5-hydroxytryptamine-methyltransferases 5/7 (SlASMT5/7). We further reveal that red light supplementation significantly enhances the melatonin content in tomato fruit. This induction relies on the "serotonin-N-acetylserotonin-melatonin" biosynthesis route via the SlphyB2-SlPIF4-SlCOMT2 module. Based on the regulatory mechanism, we design a gene-editing strategy to target the binding motif of SlPIF4 in the promoter of SlCOMT2, which significantly enhances the production of melatonin in tomato fruit. Our study provides a good example of how the understanding of plant metabolic pathways responding to environmental factors can guide the engineering of health-promoting foods.
Collapse
Affiliation(s)
- Zixin Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Xin Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yuting Chen
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Wenqian Jiang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jing Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jiayu Wang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yanjun Wu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Shouchuang Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Xiao Yang
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu National Agricultural Science & Technology Center, Chengdu, 610213, China
| | - Mingchun Liu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yang Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| |
Collapse
|
10
|
Bourdon M, Lyczakowski JJ, Cresswell R, Amsbury S, Vilaplana F, Le Guen MJ, Follain N, Wightman R, Su C, Alatorre-Cobos F, Ritter M, Liszka A, Terrett OM, Yadav SR, Vatén A, Nieminen K, Eswaran G, Alonso-Serra J, Müller KH, Iuga D, Miskolczi PC, Kalmbach L, Otero S, Mähönen AP, Bhalerao R, Bulone V, Mansfield SD, Hill S, Burgert I, Beaugrand J, Benitez-Alfonso Y, Dupree R, Dupree P, Helariutta Y. Ectopic callose deposition into woody biomass modulates the nano-architecture of macrofibrils. Nat Plants 2023; 9:1530-1546. [PMID: 37666966 PMCID: PMC10505557 DOI: 10.1038/s41477-023-01459-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 06/14/2023] [Indexed: 09/06/2023]
Abstract
Plant biomass plays an increasingly important role in the circular bioeconomy, replacing non-renewable fossil resources. Genetic engineering of this lignocellulosic biomass could benefit biorefinery transformation chains by lowering economic and technological barriers to industrial processing. However, previous efforts have mostly targeted the major constituents of woody biomass: cellulose, hemicellulose and lignin. Here we report the engineering of wood structure through the introduction of callose, a polysaccharide novel to most secondary cell walls. Our multiscale analysis of genetically engineered poplar trees shows that callose deposition modulates cell wall porosity, water and lignin contents and increases the lignin-cellulose distance, ultimately resulting in substantially decreased biomass recalcitrance. We provide a model of the wood cell wall nano-architecture engineered to accommodate the hydrated callose inclusions. Ectopic polymer introduction into biomass manifests in new physico-chemical properties and offers new avenues when considering lignocellulose engineering.
Collapse
Affiliation(s)
- Matthieu Bourdon
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK.
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland.
| | - Jan J Lyczakowski
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Sam Amsbury
- Centre for Plant Science, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Plants, Photosynthesis and Soil, School of Biosciences, The University of Sheffield, Sheffield, UK
| | - Francisco Vilaplana
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, Stockholm, Sweden
- Wallenberg Wood Science Centre (WWSC), KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Nadège Follain
- Normandie Université, UNIROUEN Normandie, INSA Rouen, CNRS, PBS, Rouen, France
| | - Raymond Wightman
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Chang Su
- Wood Development Group, University of Helsinki, Helsinki, Finland
| | - Fulgencio Alatorre-Cobos
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Conacyt-Unidad de Bioquimica y Biologia Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Maximilian Ritter
- Wood Materials Science, Institute for Building Materials, ETH Zürich, Zürich, Switzerland
- Empa Wood Tec, Cellulose and Wood Materials Laboratory, Dübendorf, Switzerland
| | - Aleksandra Liszka
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Oliver M Terrett
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Shri Ram Yadav
- Wood Development Group, University of Helsinki, Helsinki, Finland
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Anne Vatén
- Wood Development Group, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- Stomatal Development and Plasticity group, University of Helsinki, Helsinki, Finland
| | - Kaisa Nieminen
- Wood Development Group, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- Production systems / Tree Breeding Department, Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Gugan Eswaran
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Juan Alonso-Serra
- Wood Development Group, University of Helsinki, Helsinki, Finland
- UMR 5667 Reproduction et Développement Des Plantes, ENS de Lyon, France
| | - Karin H Müller
- Cambridge Advanced Imaging Centre, Department of Physiology, Development and Neuroscience, Cambridge, UK
| | - Dinu Iuga
- Department of Physics, University of Warwick, Coventry, UK
| | - Pal Csaba Miskolczi
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Lothar Kalmbach
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Molecular Plant Physiology, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Sofia Otero
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Science and Technology Office of the Congress of Deputies, Madrid, Spain
| | - Ari Pekka Mähönen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Rishikesh Bhalerao
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Vincent Bulone
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, Stockholm, Sweden
- College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stefan Hill
- Scion, Te Papa Tipu Innovation Park, Rotorua, New Zealand
| | - Ingo Burgert
- Wood Materials Science, Institute for Building Materials, ETH Zürich, Zürich, Switzerland
- Empa Wood Tec, Cellulose and Wood Materials Laboratory, Dübendorf, Switzerland
| | - Johnny Beaugrand
- Biopolymères Interactions Assemblages (BIA), INRA, Nantes, France
| | - Yoselin Benitez-Alfonso
- The Centre for Plant Science, The Bragg Centre, The Astbury Centre, University of Leeds, Leeds, UK
| | - Ray Dupree
- Department of Physics, University of Warwick, Coventry, UK
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Ykä Helariutta
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK.
- Wood Development Group, University of Helsinki, Helsinki, Finland.
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
11
|
Karki U, Perez Sanchez P, Chakraborty S, Dickey B, Vargas Ulloa J, Zhang N, Xu J. Intracellular trafficking and glycosylation of hydroxyproline-O-glycosylation module in tobacco BY-2 cells is dependent on medium composition and transcriptome analysis. Sci Rep 2023; 13:13506. [PMID: 37598266 PMCID: PMC10439957 DOI: 10.1038/s41598-023-40723-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023] Open
Abstract
Expression of recombinant proteins in plant cells with a "designer" hydroxyproline (Hyp)-O-glycosylated peptide (HypGP), such as tandem repeats of a "Ser-Pro" motif, has been shown to boost the secreted protein yields. However, dramatic secretion and Hyp-O-glycosylation of HypGP-tagged proteins can only be achieved when the plant cells were grown in nitrogen-deficient SH medium. Only trace amounts of secreted fusion protein were detected in MS medium. This study aims to gain a deeper understanding of the possible mechanism underlying these results by examining the intracellular trafficking and Hyp-O-glycosylation of enhanced green fluorescent protein (EGFP) fused with a (SP)32 tag, consisting of 32 repeats of a "Ser-Pro" motif, in tobacco BY-2 cells. When cells were grown in MS medium, the (SP)32-EGFP formed protein body-like aggregate and was retained in the ER, without undergoing Hyp-O-glycosylation. In contrast, the fusion protein becomes fully Hyp-O-glycosylated, and then secreted in SH medium. Transcriptome analysis of the BY-2 cells grown in SH medium vs. MS medium revealed over 16,000 DEGs, with many upregulated DEGs associated with the microtubule-based movement, movement of subcellular component, and microtubule binding. These DEGs are presumably responsible for the enhanced ER-Golgi transport of HypGP-tagged proteins, enabling their glycosylation and secretion in SH medium.
Collapse
Affiliation(s)
- Uddhab Karki
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR, 72401, USA
- Molecular BioSciences Program, Arkansas State University, Jonesboro, AR, 72401, USA
| | - Paula Perez Sanchez
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, 72401, USA
| | - Sankalpa Chakraborty
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR, 72401, USA
- Molecular BioSciences Program, Arkansas State University, Jonesboro, AR, 72401, USA
| | - Berry Dickey
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, 72401, USA
| | | | - Ningning Zhang
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR, 72401, USA
- Molecular BioSciences Program, Arkansas State University, Jonesboro, AR, 72401, USA
| | - Jianfeng Xu
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR, 72401, USA.
- Molecular BioSciences Program, Arkansas State University, Jonesboro, AR, 72401, USA.
- College of Agriculture, Arkansas State University, Jonesboro, AR, 72401, USA.
| |
Collapse
|
12
|
Zhan X, Liu W, Nie B, Zhang F, Zhang J. Cas13d-mediated multiplex RNA targeting confers a broad-spectrum resistance against RNA viruses in potato. Commun Biol 2023; 6:855. [PMID: 37591976 PMCID: PMC10435558 DOI: 10.1038/s42003-023-05205-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 08/02/2023] [Indexed: 08/19/2023] Open
Abstract
CRISPR-Cas systems endow the bacterial and archaeal species with adaptive immune mechanisms to fend off invading phages and foreign plasmids. The class 2 type VI CRISPR/Cas effector Cas13d has been harnessed to confer the protection against RNA viruses in diverse eukaryotic species. However a vast number of different viruses can potentially infect the same host plant resulting in mixed infection, thus necessitating the generation of crops with broad-spectrum resistance to multiple viruses. Here we report the repurposing of CRISPR/Cas13d coupled with an endogenous tRNA-processing system (polycistronic tRNA-gRNA, PTG) to target the multiple potato RNA viruses. Expression of Cas13d and four different gRNAs were observed in transgenic potato lines expressing the Cas13d/PTG construct. We show that the Cas13d/PTG transgenic plants exhibit resistance to either PVY, PVS, PVX or PLRV alone or two/three viruses simultaneously by reducing viral accumulation in plant cells. In sum, our findings provide an efficient strategy for engineering crops that can simultaneously resist infection by multiple RNA viruses.
Collapse
Affiliation(s)
- Xiaohui Zhan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Wenting Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Bihua Nie
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fengjuan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, 430062, China.
| | - Jiang Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, 430062, China.
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China.
| |
Collapse
|
13
|
Nishiguchi M, Futamura N, Endo M, Mikami M, Toki S, Katahata SI, Ohmiya Y, Konagaya KI, Nanasato Y, Taniguchi T, Maruyama TE. CRISPR/Cas9-mediated disruption of CjACOS5 confers no-pollen formation on sugi trees (Cryptomeria japonica D. Don). Sci Rep 2023; 13:11779. [PMID: 37479866 PMCID: PMC10361980 DOI: 10.1038/s41598-023-38339-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 07/06/2023] [Indexed: 07/23/2023] Open
Abstract
Sugi (Cryptomeria japonica D. Don) is an economically important coniferous tree in Japan. However, abundant sugi pollen grains are dispersed and transported by the wind each spring and cause a severe pollen allergy syndrome (Japanese cedar pollinosis). The use of pollen-free sugi that cannot produce pollen has been thought as a countermeasure to Japanese cedar pollinosis. The sugi CjACOS5 gene is an ortholog of Arabidopsis ACOS5 and rice OsACOS12, which encode an acyl-CoA synthetase that is involved in the synthesis of sporopollenin in pollen walls. To generate pollen-free sugi, we mutated CjACOS5 using the CRISPR/Cas9 system. As a result of sugi transformation mediated by Agrobacterium tumefaciens harboring the CjACOS5-targeted CRISPR/Cas9 vector, 1 bp-deleted homo biallelic mutant lines were obtained. Chimeric mutant lines harboring both mutant and wild-type CjACOS5 genes were also generated. The homo biallelic mutant lines had no-pollen in male strobili, whereas chimeric mutant lines had male strobili with or without pollen grains. Our results suggest that CjACOS5 is essential for the production of pollen in sugi and that its disruption is useful for the generation of pollen-free sugi. In addition to conventional transgenic technology, genome editing technology, including CRISPR/Cas9, can confer new traits on sugi.
Collapse
Affiliation(s)
- Mitsuru Nishiguchi
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute (FFPRI), 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan.
| | - Norihiro Futamura
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute (FFPRI), 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
| | - Masaki Endo
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa, 236-0027, Japan
| | - Masafumi Mikami
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Seiichi Toki
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa, 236-0027, Japan
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan
| | - Shin-Ichiro Katahata
- Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu, 501-1193, Japan
| | - Yasunori Ohmiya
- Extension and International Cooperation Department, Forest Tree Breeding Center, Forestry and Forest Products Research Institute (FFPRI), 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Ken-Ichi Konagaya
- Forest Bio-Research Center, Forestry and Forest Products Research Institute (FFPRI), 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Yoshihiko Nanasato
- Forest Bio-Research Center, Forestry and Forest Products Research Institute (FFPRI), 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Toru Taniguchi
- Forest Bio-Research Center, Forestry and Forest Products Research Institute (FFPRI), 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Tsuyoshi Emilio Maruyama
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute (FFPRI), 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
| |
Collapse
|
14
|
Guiziou S, Maranas CJ, Chu JC, Nemhauser JL. An integrase toolbox to record gene-expression during plant development. Nat Commun 2023; 14:1844. [PMID: 37012288 PMCID: PMC10070421 DOI: 10.1038/s41467-023-37607-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/23/2023] [Indexed: 04/05/2023] Open
Abstract
There are many open questions about the mechanisms that coordinate the dynamic, multicellular behaviors required for organogenesis. Synthetic circuits that can record in vivo signaling networks have been critical in elucidating animal development. Here, we report on the transfer of this technology to plants using orthogonal serine integrases to mediate site-specific and irreversible DNA recombination visualized by switching between fluorescent reporters. When combined with promoters expressed during lateral root initiation, integrases amplify reporter signal and permanently mark all descendants. In addition, we present a suite of methods to tune the threshold for integrase switching, including: RNA/protein degradation tags, a nuclear localization signal, and a split-intein system. These tools improve the robustness of integrase-mediated switching with different promoters and the stability of switching behavior over multiple generations. Although each promoter requires tuning for optimal performance, this integrase toolbox can be used to build history-dependent circuits to decode the order of expression during organogenesis in many contexts.
Collapse
Affiliation(s)
- Sarah Guiziou
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | | | - Jonah C Chu
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | | |
Collapse
|
15
|
Chaudhary S, Ali Z, Tehseen M, Haney EF, Pantoja-Angles A, Alshehri S, Wang T, Clancy GJ, Ayach M, Hauser C, Hong PY, Hamdan SM, Hancock REW, Mahfouz M. Efficient in planta production of amidated antimicrobial peptides that are active against drug-resistant ESKAPE pathogens. Nat Commun 2023; 14:1464. [PMID: 36928189 PMCID: PMC10020429 DOI: 10.1038/s41467-023-37003-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
Antimicrobial peptides (AMPs) are promising next-generation antibiotics that can be used to combat drug-resistant pathogens. However, the high cost involved in AMP synthesis and their short plasma half-life render their clinical translation a challenge. To address these shortcomings, we report efficient production of bioactive amidated AMPs by transient expression of glycine-extended AMPs in Nicotiana benthamiana line expressing the mammalian enzyme peptidylglycine α-amidating mono-oxygenase (PAM). Cationic AMPs accumulate to substantial levels in PAM transgenic plants compare to nontransgenic N. benthamiana. Moreover, AMPs purified from plants exhibit robust killing activity against six highly virulent and antibiotic resistant ESKAPE pathogens, prevent their biofilm formation, analogous to their synthetic counterparts and synergize with antibiotics. We also perform a base case techno-economic analysis of our platform, demonstrating the potential economic advantages and scalability for industrial use. Taken together, our experimental data and techno-economic analysis demonstrate the potential use of plant chassis for large-scale production of clinical-grade AMPs.
Collapse
Affiliation(s)
- Shahid Chaudhary
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Muhammad Tehseen
- Laboratory of DNA Replication and Recombination, Division of Biological Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Evan F Haney
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Aarón Pantoja-Angles
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Salwa Alshehri
- Laboratory for Nanomedicine, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Biochemistry Department, Faculty of Science, University of Jeddah, Jeddah, 21577, Saudi Arabia
| | - Tiannyu Wang
- Water Desalination and Reuse Center, Division of Biological Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Gerard J Clancy
- Analytical Chemistry Core Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Maya Ayach
- Imaging & Characterization Core Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Charlotte Hauser
- Laboratory for Nanomedicine, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Pei-Ying Hong
- Water Desalination and Reuse Center, Division of Biological Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Samir M Hamdan
- Laboratory of DNA Replication and Recombination, Division of Biological Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Robert E W Hancock
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
| |
Collapse
|
16
|
Wang M, Zhong Z, Gallego-Bartolomé J, Li Z, Feng S, Kuo HY, Kan RL, Lam H, Richey JC, Tang L, Zhou J, Liu M, Jami-Alahmadi Y, Wohlschlegel J, Jacobsen SE. A gene silencing screen uncovers diverse tools for targeted gene repression in Arabidopsis. Nat Plants 2023; 9:460-472. [PMID: 36879017 PMCID: PMC10027610 DOI: 10.1038/s41477-023-01362-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 02/01/2023] [Indexed: 05/18/2023]
Abstract
DNA methylation has been utilized for target gene silencing in plants. However, it is not well understood whether other silencing pathways can be also used to manipulate gene expression. Here we performed a gain-of-function screen for proteins that could silence a target gene when fused to an artificial zinc finger. We uncovered many proteins that suppressed gene expression through DNA methylation, histone H3K27me3 deposition, H3K4me3 demethylation, histone deacetylation, inhibition of RNA polymerase II transcription elongation or Ser-5 dephosphorylation. These proteins also silenced many other genes with different efficacies, and a machine learning model could accurately predict the efficacy of each silencer on the basis of various chromatin features of the target loci. Furthermore, some proteins were also able to target gene silencing when used in a dCas9-SunTag system. These results provide a more comprehensive understanding of epigenetic regulatory pathways in plants and provide an armament of tools for targeted gene manipulation.
Collapse
Affiliation(s)
- Ming Wang
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Zhenhui Zhong
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Javier Gallego-Bartolomé
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, Spain
| | - Zheng Li
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
- Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California at Los Angeles, Los Angeles, CA, USA
| | - Hsuan Yu Kuo
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Ryan L Kan
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Hoiyan Lam
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - John Curtis Richey
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Linli Tang
- Department of Statistics, University of California, Riverside, CA, USA
| | - Jessica Zhou
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Mukun Liu
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California at Los Angeles, Los Angeles, CA, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, University of California at Los Angeles, Los Angeles, CA, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA.
- Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California at Los Angeles, Los Angeles, CA, USA.
- Department of Biological Chemistry, University of California at Los Angeles, Los Angeles, CA, USA.
- Howard Hughes Medical Institute (HHMI), University of California at Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
17
|
Wang N, Ryan L, Sardesai N, Wu E, Lenderts B, Lowe K, Che P, Anand A, Worden A, van Dyk D, Barone P, Svitashev S, Jones T, Gordon-Kamm W. Leaf transformation for efficient random integration and targeted genome modification in maize and sorghum. Nat Plants 2023; 9:255-270. [PMID: 36759580 PMCID: PMC9946824 DOI: 10.1038/s41477-022-01338-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/21/2022] [Indexed: 05/28/2023]
Abstract
Transformation in grass species has traditionally relied on immature embryos and has therefore been limited to a few major Poaceae crops. Other transformation explants, including leaf tissue, have been explored but with low success rates, which is one of the major factors hindering the broad application of genome editing for crop improvement. Recently, leaf transformation using morphogenic genes Wuschel2 (Wus2) and Babyboom (Bbm) has been successfully used for Cas9-mediated mutagenesis, but complex genome editing applications, requiring large numbers of regenerated plants to be screened, remain elusive. Here we demonstrate that enhanced Wus2/Bbm expression substantially improves leaf transformation in maize and sorghum, allowing the recovery of plants with Cas9-mediated gene dropouts and targeted gene insertion. Moreover, using a maize-optimized Wus2/Bbm construct, embryogenic callus and regenerated plantlets were successfully produced in eight species spanning four grass subfamilies, suggesting that this may lead to a universal family-wide method for transformation and genome editing across the Poaceae.
Collapse
Affiliation(s)
- Ning Wang
- Corteva Agriscience, Johnston, IA, USA
| | | | | | - Emily Wu
- Corteva Agriscience, Johnston, IA, USA
| | | | | | - Ping Che
- Corteva Agriscience, Johnston, IA, USA
| | - Ajith Anand
- Corteva Agriscience, Johnston, IA, USA
- MyFloraDNA, Woodland, CA, USA
| | | | | | | | | | | | | |
Collapse
|
18
|
Tsakirpaloglou N, Bueno-Mota GM, Soriano JC, Arcillas E, Arines FM, Yu SM, Stangoulis J, Trijatmiko KR, Reinke R, Tohme J, Bouis H, Slamet-Loedin IH. Proof of concept and early development stage of market-oriented high iron and zinc rice expressing dicot ferritin and rice nicotianamine synthase genes. Sci Rep 2023; 13:676. [PMID: 36635301 DOI: 10.1038/s41598-022-26854-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/21/2022] [Indexed: 01/14/2023] Open
Abstract
Micronutrient deficiencies such as iron (Fe), zinc (Zn), and vitamin A, constitute a severe global public health phenomenon. Over half of preschool children and two-thirds of nonpregnant women of reproductive age worldwide have micronutrient deficiencies. Biofortification is a cost-effective strategy that comprises a meaningful and sustainable means of addressing this issue by delivering micronutrients through staple foods to populations with limited access to diverse diets and other nutritional interventions. Here, we report on the proof-of-concept and early development stage of a collection of biofortified rice events with a high density of Fe and Zn in polished grains that have been pursued further to advance development for product release. In total, eight constructs were developed specifically expressing dicot ferritins and the rice nicotianamine synthase 2 (OsNAS2) gene under different combinations of promoters. A large-scale transformation of these constructs to Bangladesh and Philippines commercial indica cultivars and subsequent molecular screening and confined field evaluations resulted in the identification of a pool of ten events with Fe and Zn concentrations in polished grains of up to 11 μg g-1 and up to 37 μg g-1, respectively. The latter has the potential to reduce the prevalence of inadequate Zn intake for women of childbearing age in Bangladesh and in the Philippines by 30% and 50%, respectively, compared to the current prevalence. To our knowledge, this is the first potential biotechnology public-sector product that adopts the product cycle phase-gated approach, routinely applied in the private sector.
Collapse
|
19
|
Vernet A, Meynard D, Lian Q, Mieulet D, Gibert O, Bissah M, Rivallan R, Autran D, Leblanc O, Meunier AC, Frouin J, Taillebois J, Shankle K, Khanday I, Mercier R, Sundaresan V, Guiderdoni E. High-frequency synthetic apomixis in hybrid rice. Nat Commun 2022; 13:7963. [PMID: 36575169 DOI: 10.1038/s41467-022-35679-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/18/2022] [Indexed: 12/28/2022] Open
Abstract
Introducing asexual reproduction through seeds - apomixis - into crop species could revolutionize agriculture by allowing F1 hybrids with enhanced yield and stability to be clonally propagated. Engineering synthetic apomixis has proven feasible in inbred rice through the inactivation of three genes (MiMe), which results in the conversion of meiosis into mitosis in a line ectopically expressing the BABYBOOM1 (BBM1) parthenogenetic trigger in egg cells. However, only 10-30% of the seeds are clonal. Here, we show that synthetic apomixis can be achieved in an F1 hybrid of rice by inducing MiMe mutations and egg cell expression of BBM1 in a single step. We generate hybrid plants that produce more than 95% of clonal seeds across multiple generations. Clonal apomictic plants maintain the phenotype of the F1 hybrid along successive generations. Our results demonstrate that there is no barrier to almost fully penetrant synthetic apomixis in an important crop species, rendering it compatible with use in agriculture.
Collapse
|
20
|
Abstract
Chloroplast DNA (cpDNA) encodes up to 315 (typically, 120-130) genes1, including those for essential components in photosystems I and II and the large subunit of RuBisCo, which catalyses CO2 fixation in plants. Targeted mutagenesis in cpDNA will be broadly useful for studying the functions of these genes in molecular detail and for developing crops and other plants with desired traits. Unfortunately, CRISPR-Cas9 and CRISPR-derived base editors, which enable targeted genetic modifications in nuclear DNA, are not suitable for organellar DNA editing2, owing to the difficulty of delivering guide RNA into organelles. CRISPR-free, protein-only base editors (including DddA-derived cytosine base editors3-8 and zinc finger deaminases9), originally developed for mitochondrial DNA editing in mammalian cells, can be used for C-to-T, rather than A-to-G, editing in cpDNA10-12. Here we show that heritable homoplasmic A-to-G edits can be induced in cpDNA, leading to phenotypic changes, using transcription activator-like effector-linked deaminases13.
Collapse
Affiliation(s)
- Young Geun Mok
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
- GreenGene Inc., Seoul, Republic of Korea
| | - Sunghyun Hong
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
- GreenGene Inc., Seoul, Republic of Korea
| | - Su-Ji Bae
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Sung-Ik Cho
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea.
- GreenGene Inc., Seoul, Republic of Korea.
| |
Collapse
|
21
|
Kolotilin I. Plant-produced recombinant cytokines IL-37b and IL-38 modulate inflammatory response from stimulated human PBMCs. Sci Rep 2022; 12:19450. [PMID: 36376518 PMCID: PMC9663505 DOI: 10.1038/s41598-022-23828-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
Abstract
Affordable therapeutics are vitally needed for humans worldwide. Plant-based production of recombinant proteins can potentially enhance, back-up, or even substitute for the manufacturing capacity of the conventional, fermenter-based technologies. We plastome-engineered a tobacco cultivar to express high levels of two "plantakines" - recombinant human cytokines, interleukins IL-37b and IL-38, and confirmed their native conformation and folding. Assessment of their biological functionality was performed ex vivo by analyzing the effects exerted by the plantakines on levels of 11 cytokines secreted from human peripheral blood mononuclear cells (PBMCs) challenged with an inflammatory agent. Application of the plant-produced IL-37b and IL-38 in PBMCs stimulated with Lipopolysaccharide or Phytohaemagglutinin resulted in significant, and in particular cases-dose-dependent modulation of pro-inflammatory cytokines secretion, showing attenuation in two-thirds of significant level modulations observed. Plantakine treatments that increased inflammatory responses were associated with the higher dosage. Our results demonstrate feasibility of manufacturing functional recombinant human proteins using scalable, cost-effective and eco-friendly plant-based bioreactors.
Collapse
|
22
|
Casarin T, Freitas NC, Pinto RT, Breitler JC, Rodrigues LAZ, Marraccini P, Etienne H, Diniz LEC, Andrade AC, Paiva LV. Multiplex CRISPR/Cas9-mediated knockout of the phytoene desaturase gene in Coffea canephora. Sci Rep 2022; 12:17270. [PMID: 36241651 DOI: 10.1038/s41598-022-21566-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/28/2022] [Indexed: 01/06/2023] Open
Abstract
Coffea canephora (2n = 2x = 22 chromosomes) is a species with extensive genetic diversity and desirable agronomic traits for coffee breeding programs. However, obtaining a new coffee cultivar through conventional breeding techniques may require more than 30 years of crossing cycles and selection, which hampers the effort of keeping up with market demands and rapidly proposing more resilient to climate change varieties. Although, the application of modern biotechnology tools such as precision genetic engineering technologies may enable a faster cultivar development process. Therefore, we aimed to validate the CRISPR/Cas9 system to generate mutations on a selected genotype of C. canephora, the clone 14. Embryogenic calli and a multiplex binary vector containing two sgRNAs targeting different exons of the CcPDS gene were used. The sgRNAs were under the C. canephora U6 promoter regulation. The target gene encodes phytoene desaturase, an enzyme essential for photosynthesis involved in β-carotene biosynthesis. Somatic seedlings and embryos with albino, variegated and green phenotypes regenerated after Agrobacterium tumefaciens-mediated genetic transformation were analyzed by verifying the insertion of the Cas9 gene and later by sequencing the sgRNAs target regions in the genome of Robusta modified seedlings. Among them, 77% had the expected mutations, and of which, 50% of them had at least one target with a homozygous mutation. The genotype, temperature of co-cultivation with the bacteria, and light intensity used for subsequent embryo regeneration appeared to strongly influence the successful regeneration of plants with a mutated CcPDS gene in the Coffea genus.
Collapse
|
23
|
Hoelscher MP, Forner J, Calderone S, Krämer C, Taylor Z, Loiacono FV, Agrawal S, Karcher D, Moratti F, Kroop X, Bock R. Expression strategies for the efficient synthesis of antimicrobial peptides in plastids. Nat Commun 2022; 13:5856. [PMID: 36195597 DOI: 10.1038/s41467-022-33516-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 09/21/2022] [Indexed: 12/29/2022] Open
Abstract
Antimicrobial peptides (AMPs) kill microbes or inhibit their growth and are promising next-generation antibiotics. Harnessing their full potential as antimicrobial agents will require methods for cost-effective large-scale production and purification. Here, we explore the possibility to exploit the high protein synthesis capacity of the chloroplast to produce AMPs in plants. Generating a large series of 29 sets of transplastomic tobacco plants expressing nine different AMPs as fusion proteins, we show that high-level constitutive AMP expression results in deleterious plant phenotypes. However, by utilizing inducible expression and fusions to the cleavable carrier protein SUMO, the cytotoxic effects of AMPs and fused AMPs are alleviated and plants with wild-type-like phenotypes are obtained. Importantly, purified AMP fusion proteins display antimicrobial activity independently of proteolytic removal of the carrier. Our work provides expression strategies for the synthesis of toxic polypeptides in chloroplasts, and establishes transplastomic plants as efficient production platform for antimicrobial peptides.
Collapse
|
24
|
Li J, Scarano A, Gonzalez NM, D'Orso F, Yue Y, Nemeth K, Saalbach G, Hill L, de Oliveira Martins C, Moran R, Santino A, Martin C. Biofortified tomatoes provide a new route to vitamin D sufficiency. Nat Plants 2022; 8:611-616. [PMID: 35606499 PMCID: PMC9213236 DOI: 10.1038/s41477-022-01154-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 04/12/2022] [Indexed: 05/04/2023]
Abstract
Poor vitamin D status is a global health problem; insufficiency underpins higher risk of cancer, neurocognitive decline and all-cause mortality. Most foods contain little vitamin D and plants are very poor sources. We have engineered the accumulation of provitamin D3 in tomato by genome editing, modifying a duplicated section of phytosterol biosynthesis in Solanaceous plants, to provide a biofortified food with the added possibility of supplement production from waste material.
Collapse
Affiliation(s)
- Jie Li
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Aurelia Scarano
- Institute of Sciences of Food Production, C.N.R., Unit of Lecce, Lecce, Italy
| | - Nestor Mora Gonzalez
- Recombinant Biopharmaceutical Laboratory, Department of Pharmacology, Biological Sciences Faculty, University of Concepción, Concepción, Chile
| | - Fabio D'Orso
- John Innes Centre, Norwich Research Park, Norwich, UK
- CREA-Research Centre for Genomics and Bioinformatics, Rome, Italy
| | - Yajuan Yue
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | - Lionel Hill
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | - Angelo Santino
- Institute of Sciences of Food Production, C.N.R., Unit of Lecce, Lecce, Italy
| | - Cathie Martin
- John Innes Centre, Norwich Research Park, Norwich, UK.
| |
Collapse
|
25
|
Slattery SS, Giguere DJ, Stuckless EE, Shrestha A, Briere LAK, Galbraith A, Reaume S, Boyko X, Say HH, Browne TS, Frederick MI, Lant JT, Heinemann IU, O'Donoghue P, Dsouza L, Martin S, Howard P, Jedeszko C, Ali K, Styba G, Flatley M, Karas BJ, Gloor GB, Edgell DR. Phosphate-regulated expression of the SARS-CoV-2 receptor-binding domain in the diatom Phaeodactylum tricornutum for pandemic diagnostics. Sci Rep 2022; 12:7010. [PMID: 35487958 PMCID: PMC9051505 DOI: 10.1038/s41598-022-11053-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/18/2022] [Indexed: 12/22/2022] Open
Abstract
The worldwide COVID-19 pandemic caused by the SARS-CoV-2 betacoronavirus has highlighted the need for a synthetic biology approach to create reliable and scalable sources of viral antigen for uses in diagnostics, therapeutics and basic biomedical research. Here, we adapt plasmid-based systems in the eukaryotic microalgae Phaeodactylum tricornutum to develop an inducible overexpression system for SARS-CoV-2 proteins. Limiting phosphate and iron in growth media induced expression of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein from the P. tricornutum HASP1 promoter in the wild-type strain and in a histidine auxotrophic strain that alleviates the requirement for antibiotic selection of expression plasmids. The RBD was purified from whole cell extracts (algae-RBD) with yield compromised by the finding that 90-95% of expressed RBD lacked the genetically encoded C-terminal 6X-histidine tag. Constructs that lacked the TEV protease site between the RBD and C-terminal 6X-histidine tag retained the tag, increasing yield. Purified algae-RBD was found to be N-linked glycosylated by treatment with endoglycosidases, was cross-reactive with anti-RBD polyclonal antibodies, and inhibited binding of recombinant RBD purified from mammalian cell lines to the human ACE2 receptor. We also show that the algae-RBD can be used in a lateral flow assay device to detect SARS-CoV-2 specific IgG antibodies from donor serum at sensitivity equivalent to assays performed with RBD made in mammalian cell lines. Our study shows that P. tricornutum is a scalable system with minimal biocontainment requirements for the inducible production of SARS-CoV-2 or other coronavirus antigens for pandemic diagnostics.
Collapse
Affiliation(s)
- Samuel S Slattery
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Daniel J Giguere
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Emily E Stuckless
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Arina Shrestha
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Lee-Ann K Briere
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Alexa Galbraith
- Lambton College, 1457 London Rd, Sarnia, ON, N7S 6K4, Canada
| | - Stephen Reaume
- Lambton College, 1457 London Rd, Sarnia, ON, N7S 6K4, Canada
| | - Xenia Boyko
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Henry H Say
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Tyler S Browne
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Mallory I Frederick
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Jeremy T Lant
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Ilka U Heinemann
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Patrick O'Donoghue
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
- Department of Chemistry, Western University, London, ON, N6A 3K7, Canada
| | - Liann Dsouza
- Pond Technologies Inc., Markham, ON, L3R 9W7, Canada
| | - Steven Martin
- Pond Technologies Inc., Markham, ON, L3R 9W7, Canada
| | - Peter Howard
- Pond Technologies Inc., Markham, ON, L3R 9W7, Canada
| | - Christopher Jedeszko
- International Point of Care Inc., 135 The West Mall Unit 9, Toronto, ON, M9C 1C2, Canada
| | - Kinza Ali
- International Point of Care Inc., 135 The West Mall Unit 9, Toronto, ON, M9C 1C2, Canada
| | - Garth Styba
- International Point of Care Inc., 135 The West Mall Unit 9, Toronto, ON, M9C 1C2, Canada
| | - Martin Flatley
- Suncor Energy Inc., Sarnia Refinery, 1900 River Road, Sarnia, ON, N7T 7J3, Canada
| | - Bogumil J Karas
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Gregory B Gloor
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada.
| | - David R Edgell
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada.
| |
Collapse
|
26
|
Forner J, Kleinschmidt D, Meyer EH, Fischer A, Morbitzer R, Lahaye T, Schöttler MA, Bock R. Targeted introduction of heritable point mutations into the plant mitochondrial genome. Nat Plants 2022; 8:245-256. [PMID: 35301443 PMCID: PMC8940627 DOI: 10.1038/s41477-022-01108-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 02/10/2022] [Indexed: 05/05/2023]
Abstract
The development of technologies for the genetic manipulation of mitochondrial genomes remains a major challenge. Here we report a method for the targeted introduction of mutations into plant mitochondrial DNA (mtDNA) that we refer to as transcription activator-like effector nuclease (TALEN) gene-drive mutagenesis (GDM), or TALEN-GDM. The method combines TALEN-induced site-specific cleavage of the mtDNA with selection for mutations that confer resistance to the TALEN cut. Applying TALEN-GDM to the tobacco mitochondrial nad9 gene, we isolated a large set of mutants carrying single amino acid substitutions in the Nad9 protein. The mutants could be purified to homochondriomy and stably inherited their edited mtDNA in the expected maternal fashion. TALEN-GDM induces both transitions and transversions, and can access most nucleotide positions within the TALEN binding site. Our work provides an efficient method for targeted mitochondrial genome editing that produces genetically stable, homochondriomic and fertile plants with specific point mutations in their mtDNA.
Collapse
Affiliation(s)
- Joachim Forner
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Dennis Kleinschmidt
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Etienne H Meyer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
- Institut für Pflanzenphysiologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Axel Fischer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Robert Morbitzer
- ZMBP, Allgemeine Genetik, Universität Tübingen, Tübingen, Germany
| | - Thomas Lahaye
- ZMBP, Allgemeine Genetik, Universität Tübingen, Tübingen, Germany
| | - Mark A Schöttler
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany.
| |
Collapse
|
27
|
Yang R, Wu Z, Bai C, Sun Z, Wang M, Huo Y, Zhang H, Wang Y, Zhou H, Dai S, Liu W, Fu C. Overexpression of PvWOX3a in switchgrass promotes stem development and increases plant height. Hortic Res 2021; 8:252. [PMID: 34848686 PMCID: PMC8633294 DOI: 10.1038/s41438-021-00678-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 07/12/2021] [Accepted: 08/16/2021] [Indexed: 05/17/2023]
Abstract
Switchgrass (Panicum virgatum L.) is an important perennial, noninvasive, tall ornamental grass that adds color and texture to gardens and landscapes. Moreover, switchgrass has been considered a forage and bioenergy crop because of its vigorous growth, low-input requirements, and broad geography. Here, we identified PvWOX3a from switchgrass, which encodes a WUSCHEL-related homeobox transcription factor. Transgenic overexpression of PvWOX3a in switchgrass increased stem length, internode diameter, and leaf blade length and width, all of which contributed to a 95% average increase in dry weight biomass compared with control plants. Yeast one-hybrid and transient dual-luciferase assays showed that PvWOX3a can repress the expression of gibberellin 2-oxidase and cytokinin oxidase/dehydrogenase through apparently direct interaction with their promoter sequences. These results suggested that overexpression of PvWOX3a could increase gibberellin and cytokinin levels in transgenic switchgrass plants, which promotes cell division, elongation, and vascular bundle development. We also overexpressed PvWOX3a in a transgenic miR156-overexpressing switchgrass line that characteristically exhibited more tillers, thinner internodes, and narrower leaf blades. Double transgenic switchgrass plants displayed significant increases in internode length and diameter, leaf blade width, and plant height but retained a tiller number comparable to that of plants expressing miR156 alone. Ultimately, the double transgenic switchgrass plants produced 174% more dry-weight biomass and 162% more solubilized sugars on average than control plants. These findings indicated that PvWOX3a is a viable potential genetic target for engineering improved shoot architecture and biomass yield of horticulture, fodder, and biofuel crops.
Collapse
Affiliation(s)
- Ruijuan Yang
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zhenying Wu
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, Shandong, China
| | - Chen Bai
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, Shandong, China
- Shanghai Normal University, 201418, Shanghai, China
| | - Zhichao Sun
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, Shandong, China
| | - Mengqi Wang
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, Shandong, China
| | - Yuzhu Huo
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, Shandong, China
| | - Hailing Zhang
- Grass and Science Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Yamei Wang
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, Shandong, China
| | - Huapeng Zhou
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, 610064, Chengdu, China
| | - Shaojun Dai
- Shanghai Normal University, 201418, Shanghai, China
| | - Wenwen Liu
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, Shandong, China.
| | - Chunxiang Fu
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, Shandong, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
| |
Collapse
|
28
|
Huang B, Hu G, Wang K, Frasse P, Maza E, Djari A, Deng W, Pirrello J, Burlat V, Pons C, Granell A, Li Z, van der Rest B, Bouzayen M. Interaction of two MADS-box genes leads to growth phenotype divergence of all-flesh type of tomatoes. Nat Commun 2021; 12:6892. [PMID: 34824241 PMCID: PMC8616914 DOI: 10.1038/s41467-021-27117-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 11/02/2021] [Indexed: 12/19/2022] Open
Abstract
All-flesh tomato cultivars are devoid of locular gel and exhibit enhanced firmness and improved postharvest storage. Here, we show that SlMBP3 is a master regulator of locular tissue in tomato fruit and that a deletion at the gene locus underpins the All-flesh trait. Intriguingly, All-flesh varieties lack the deleterious phenotypes reported previously for SlMBP3 under-expressing lines and which preclude any potential commercial use. We resolve the causal factor for this phenotypic divergence through the discovery of a natural mutation at the SlAGL11 locus, a close homolog of SlMBP3. Misexpressing SlMBP3 impairs locular gel formation through massive transcriptomic reprogramming at initial phases of fruit development. SlMBP3 influences locule gel formation by controlling cell cycle and cell expansion genes, indicating that important components of fruit softening are determined at early pre-ripening stages. Our findings define potential breeding targets for improved texture in tomato and possibly other fleshy fruits.
Collapse
Affiliation(s)
- Baowen Huang
- grid.508721.9Université de Toulouse, INRAe/INP Toulouse, UMR990 Génomique et Biotechnologie des Fruits, Avenue de l’Agrobiopole, Castanet-Tolosan, F-31326 France ,grid.15781.3a0000 0001 0723 035XLaboratoire de Recherche en Sciences Végétales - UMR5546, Université de Toulouse, CNRS, UPS, Toulouse, INP France
| | - Guojian Hu
- grid.508721.9Université de Toulouse, INRAe/INP Toulouse, UMR990 Génomique et Biotechnologie des Fruits, Avenue de l’Agrobiopole, Castanet-Tolosan, F-31326 France ,grid.15781.3a0000 0001 0723 035XLaboratoire de Recherche en Sciences Végétales - UMR5546, Université de Toulouse, CNRS, UPS, Toulouse, INP France
| | - Keke Wang
- grid.508721.9Université de Toulouse, INRAe/INP Toulouse, UMR990 Génomique et Biotechnologie des Fruits, Avenue de l’Agrobiopole, Castanet-Tolosan, F-31326 France ,grid.15781.3a0000 0001 0723 035XLaboratoire de Recherche en Sciences Végétales - UMR5546, Université de Toulouse, CNRS, UPS, Toulouse, INP France
| | - Pierre Frasse
- grid.508721.9Université de Toulouse, INRAe/INP Toulouse, UMR990 Génomique et Biotechnologie des Fruits, Avenue de l’Agrobiopole, Castanet-Tolosan, F-31326 France ,grid.15781.3a0000 0001 0723 035XLaboratoire de Recherche en Sciences Végétales - UMR5546, Université de Toulouse, CNRS, UPS, Toulouse, INP France
| | - Elie Maza
- grid.508721.9Université de Toulouse, INRAe/INP Toulouse, UMR990 Génomique et Biotechnologie des Fruits, Avenue de l’Agrobiopole, Castanet-Tolosan, F-31326 France ,grid.15781.3a0000 0001 0723 035XLaboratoire de Recherche en Sciences Végétales - UMR5546, Université de Toulouse, CNRS, UPS, Toulouse, INP France
| | - Anis Djari
- grid.508721.9Université de Toulouse, INRAe/INP Toulouse, UMR990 Génomique et Biotechnologie des Fruits, Avenue de l’Agrobiopole, Castanet-Tolosan, F-31326 France ,grid.15781.3a0000 0001 0723 035XLaboratoire de Recherche en Sciences Végétales - UMR5546, Université de Toulouse, CNRS, UPS, Toulouse, INP France
| | - Wei Deng
- grid.190737.b0000 0001 0154 0904Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331 Chongqing, China
| | - Julien Pirrello
- grid.508721.9Université de Toulouse, INRAe/INP Toulouse, UMR990 Génomique et Biotechnologie des Fruits, Avenue de l’Agrobiopole, Castanet-Tolosan, F-31326 France ,grid.15781.3a0000 0001 0723 035XLaboratoire de Recherche en Sciences Végétales - UMR5546, Université de Toulouse, CNRS, UPS, Toulouse, INP France
| | - Vincent Burlat
- grid.15781.3a0000 0001 0723 035XLaboratoire de Recherche en Sciences Végétales - UMR5546, Université de Toulouse, CNRS, UPS, Toulouse, INP France
| | - Clara Pons
- grid.4711.30000 0001 2183 4846Instituto de Biología Molecular y Cellular de Plantas, Consejo Superior de Investigaciones Cientificas- Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Antonio Granell
- grid.4711.30000 0001 2183 4846Instituto de Biología Molecular y Cellular de Plantas, Consejo Superior de Investigaciones Cientificas- Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China. .,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, 401331, Chongqing, China.
| | - Benoît van der Rest
- Université de Toulouse, INRAe/INP Toulouse, UMR990 Génomique et Biotechnologie des Fruits, Avenue de l'Agrobiopole, Castanet-Tolosan, F-31326, France. .,Laboratoire de Recherche en Sciences Végétales - UMR5546, Université de Toulouse, CNRS, UPS, Toulouse, INP, France.
| | - Mondher Bouzayen
- Université de Toulouse, INRAe/INP Toulouse, UMR990 Génomique et Biotechnologie des Fruits, Avenue de l'Agrobiopole, Castanet-Tolosan, F-31326, France. .,Laboratoire de Recherche en Sciences Végétales - UMR5546, Université de Toulouse, CNRS, UPS, Toulouse, INP, France. .,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, 401331, Chongqing, China.
| |
Collapse
|
29
|
Achary VMM, Reddy MK. CRISPR-Cas9 mediated mutation in GRAIN WIDTH and WEIGHT2 (GW2) locus improves aleurone layer and grain nutritional quality in rice. Sci Rep 2021; 11:21941. [PMID: 34753955 PMCID: PMC8578329 DOI: 10.1038/s41598-021-00828-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 10/08/2021] [Indexed: 11/27/2022] Open
Abstract
Enhancing crop productivity and their nutritional quality are the key components and primary focus of crop improvement strategy for fulfilling future food demand and improving human health. Grain filling and endosperm development are the key determinants of grain yield and nutritional quality. GRAIN WIDTH and WEIGHT2 (GW2) gene encodes a RING-type E3 ubiquitin ligase and determines the grain weight in cereal crops. Here we report GW2 knockout (KO) mutants in Indica (var. MTU1010) through CRISPR/Cas9 genome editing. The endosperm of GW2-KO mutant seed displays a thick aleurone layer with enhanced grain protein content. Further the loss of function of OsGW2 results in improved accumulation of essential dietary minerals (Fe, Zn, K, P, Ca) in the endosperm of rice grain. Additionally, the mutants displayed an early growth vigour phenotype with an improved root and shoot architecture. The hull morphology of GW2-KO lines also showed improved, grain filling thereby promoting larger grain architecture. Together, our findings indicate that GW2 may serve as a key regulator of improved grain architecture, grain nutritional quality and an important modulator of plant morphology. The study offers a strategy for the development of improved rice cultivars with enriched nutritional quality and its possible implementation in other cereals as well.
Collapse
Affiliation(s)
- V. Mohan Murali Achary
- grid.425195.e0000 0004 0498 7682Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067 India
| | - Malireddy K. Reddy
- grid.425195.e0000 0004 0498 7682Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067 India
| |
Collapse
|
30
|
Yuan G, Lu H, Tang D, Hassan MM, Li Y, Chen JG, Tuskan GA, Yang X. Expanding the application of a UV-visible reporter for transient gene expression and stable transformation in plants. Hortic Res 2021; 8:234. [PMID: 34719678 PMCID: PMC8558336 DOI: 10.1038/s41438-021-00663-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/25/2021] [Accepted: 08/01/2021] [Indexed: 05/08/2023]
Abstract
Green fluorescent protein (GFP) has been widely used for monitoring gene expression and protein localization in diverse organisms. However, highly sensitive imaging equipment, like fluorescence microscope, is usually required for the visualization of GFP, limitings its application to fixed locations in samples. A reporter that can be visualized in real-time regardless the shape, size and location of the target samples will increase the flexibility and efficiency of research work. Here, we report the application of a GFP-like protein, called eYGFPuv, in both transient expression and stable transformation, in two herbaceous plant species (Arabidopsis and tobacco) and two woody plant species (poplar and citrus). We observed bright fluorescence under UV light in all of the four plant species without any effects on plant growth or development. eYGFPuv was shown to be effective for imaging transient expression in leaf and root tissues. With a focus on in vitro transformation, we demonstrated that the transgenic events expressing 1x eYGFPuv could be easily identified visually during the callus stage and the shoot stage, enabling early and efficient selection of transformants. Furthermore, whole-plant level visualization of eYGFPuv revealed its ubiquitous stability in transgenic plants. In addition, our transformation experiments showed that eYGFPuv can also be used to select transgenic plants without antibiotics. This work demonstrates the feasibility of utilizing 1x eYGFPuv in studies of gene expression and plant transformation in diverse plants.
Collapse
Affiliation(s)
- 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
| | - Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Dan Tang
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, 06269, USA
- National Center for Citrus Improvement, College of Horticulture, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Md Mahmudul Hassan
- 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
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh
| | - Yi Li
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, 06269, 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
| | - 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.
| | - 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.
| |
Collapse
|
31
|
Bigelyte G, Young JK, Karvelis T, Budre K, Zedaveinyte R, Djukanovic V, Van Ginkel E, Paulraj S, Gasior S, Jones S, Feigenbutz L, Clair GS, Barone P, Bohn J, Acharya A, Zastrow-Hayes G, Henkel-Heinecke S, Silanskas A, Seidel R, Siksnys V. Miniature type V-F CRISPR-Cas nucleases enable targeted DNA modification in cells. Nat Commun 2021; 12:6191. [PMID: 34702830 PMCID: PMC8548392 DOI: 10.1038/s41467-021-26469-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/28/2021] [Indexed: 12/26/2022] Open
Abstract
Class 2 CRISPR systems are exceptionally diverse, nevertheless, all share a single effector protein that contains a conserved RuvC-like nuclease domain. Interestingly, the size of these CRISPR-associated (Cas) nucleases ranges from >1000 amino acids (aa) for Cas9/Cas12a to as small as 400-600 aa for Cas12f. For in vivo genome editing applications, compact RNA-guided nucleases are desirable and would streamline cellular delivery approaches. Although miniature Cas12f effectors have been shown to cleave double-stranded DNA, targeted DNA modification in eukaryotic cells has yet to be demonstrated. Here, we biochemically characterize two miniature type V-F Cas nucleases, SpCas12f1 (497 aa) and AsCas12f1 (422 aa), and show that SpCas12f1 functions in both plant and human cells to produce targeted modifications with outcomes in plants being enhanced with short heat pulses. Our findings pave the way for the development of miniature Cas12f1-based genome editing tools.
Collapse
Affiliation(s)
- Greta Bigelyte
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Joshua K Young
- Molecular Engineering, Corteva Agriscience™, Johnston, IA, USA.
| | - Tautvydas Karvelis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
| | - Karolina Budre
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Rimante Zedaveinyte
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | | | | | | | - Stephen Gasior
- Molecular Engineering, Corteva Agriscience™, Johnston, IA, USA
| | - Spencer Jones
- Molecular Engineering, Corteva Agriscience™, Johnston, IA, USA
| | | | - Grace St Clair
- Molecular Engineering, Corteva Agriscience™, Johnston, IA, USA
| | | | - Jennifer Bohn
- Molecular Engineering, Corteva Agriscience™, Johnston, IA, USA
| | - Ananta Acharya
- Molecular Engineering, Corteva Agriscience™, Johnston, IA, USA
| | | | | | - Arunas Silanskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Ralf Seidel
- Institute of Experimental Physics, Leipzig University, Leipzig, Germany
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
| |
Collapse
|
32
|
Top O, Milferstaedt SWL, van Gessel N, Hoernstein SNW, Özdemir B, Decker EL, Reski R. Expression of a human cDNA in moss results in spliced mRNAs and fragmentary protein isoforms. Commun Biol 2021; 4:964. [PMID: 34385580 PMCID: PMC8361020 DOI: 10.1038/s42003-021-02486-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 07/26/2021] [Indexed: 12/18/2022] Open
Abstract
Production of biopharmaceuticals relies on the expression of mammalian cDNAs in host organisms. Here we show that the expression of a human cDNA in the moss Physcomitrium patens generates the expected full-length and four additional transcripts due to unexpected splicing. This mRNA splicing results in non-functional protein isoforms, cellular misallocation of the proteins and low product yields. We integrated these results together with the results of our analysis of all 32,926 protein-encoding Physcomitrella genes and their 87,533 annotated transcripts in a web application, physCO, for automatized optimization. A thus optimized cDNA results in about twelve times more protein, which correctly localizes to the ER. An analysis of codon preferences of different production hosts suggests that similar effects occur also in non-plant hosts. We anticipate that the use of our methodology will prevent so far undetected mRNA heterosplicing resulting in maximized functional protein amounts for basic biology and biotechnology.
Collapse
Affiliation(s)
- Oguz Top
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
- Plant Molecular Cell Biology, Department Biology I, LMU Biocenter, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Stella W L Milferstaedt
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Freiburg, Germany
| | - Nico van Gessel
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Bugra Özdemir
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany.
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany.
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Freiburg, Germany.
- CIBSS - Centre for Integrative Biological Signalling Studies, Freiburg, Germany.
| |
Collapse
|
33
|
Goralogia GS, Howe GT, Brunner AM, Helliwell E, Nagle MF, Ma C, Lu H, Goddard AL, Magnuson AC, Klocko AL, Strauss SH. Overexpression of SHORT VEGETATIVE PHASE-LIKE (SVL) in Populus delays onset and reduces abundance of flowering in field-grown trees. Hortic Res 2021; 8:167. [PMID: 34333535 PMCID: PMC8325693 DOI: 10.1038/s41438-021-00600-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 04/23/2021] [Accepted: 06/07/2021] [Indexed: 05/02/2023]
Abstract
The spread of transgenes and exotic germplasm from planted crops into wild or feral species is a difficult problem for public and regulatory acceptance of genetically engineered plants, particularly for wind-pollinated trees such as poplar. We report that overexpression of a poplar homolog of the floral repressor SHORT VEGETATIVE PHASE-LIKE (SVL), a homolog of the Arabidopsis MADS-box repressor SHORT VEGETATIVE PHASE (SVP), delayed the onset of flowering several years in three genotypes of field-grown transgenic poplars. Higher expression of SVL correlated with a delay in flowering onset and lower floral abundance, and did not cause morphologically obvious or statistically significant effects on leaf characteristics, tree form, or stem volume. Overexpression effects on reproductive and vegetative phenology in spring was modest and genotype-specific. Our results suggest that use of SVL and related floral repressors can be useful tools to enable a high level of containment for vegetatively propagated short-rotation woody energy or pulp crops.
Collapse
Affiliation(s)
- Greg S Goralogia
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Glenn T Howe
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Amy M Brunner
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, VA, USA
| | - Emily Helliwell
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Michael F Nagle
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Cathleen Ma
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Haiwei Lu
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Amanda L Goddard
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Anna C Magnuson
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Amy L Klocko
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, USA
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA.
| |
Collapse
|
34
|
Lobato-Gómez M, Hewitt S, Capell T, Christou P, Dhingra A, Girón-Calva PS. Transgenic and genome-edited fruits: background, constraints, benefits, and commercial opportunities. Hortic Res 2021; 8:166. [PMID: 34274949 PMCID: PMC8286259 DOI: 10.1038/s41438-021-00601-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/14/2021] [Accepted: 05/20/2021] [Indexed: 05/14/2023]
Abstract
Breeding has been used successfully for many years in the fruit industry, giving rise to most of today's commercial fruit cultivars. More recently, new molecular breeding techniques have addressed some of the constraints of conventional breeding. However, the development and commercial introduction of such novel fruits has been slow and limited with only five genetically engineered fruits currently produced as commercial varieties-virus-resistant papaya and squash were commercialized 25 years ago, whereas insect-resistant eggplant, non-browning apple, and pink-fleshed pineapple have been approved for commercialization within the last 6 years and production continues to increase every year. Advances in molecular genetics, particularly the new wave of genome editing technologies, provide opportunities to develop new fruit cultivars more rapidly. Our review, emphasizes the socioeconomic impact of current commercial fruit cultivars developed by genetic engineering and the potential impact of genome editing on the development of improved cultivars at an accelerated rate.
Collapse
Affiliation(s)
- Maria Lobato-Gómez
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio CERCA Center, Lleida, 25198, Spain
| | - Seanna Hewitt
- Department of Horticulture, Washington State University, PO Box, 646414, Pullman, WA, USA
| | - Teresa Capell
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio CERCA Center, Lleida, 25198, Spain
| | - Paul Christou
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio CERCA Center, Lleida, 25198, Spain
- ICREA, Catalan Institute for Research and Advanced Studies, 08010, Barcelona, Spain
| | - Amit Dhingra
- Department of Horticulture, Washington State University, PO Box, 646414, Pullman, WA, USA
| | - Patricia Sarai Girón-Calva
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio CERCA Center, Lleida, 25198, Spain.
| |
Collapse
|
35
|
Luo D, Xiong C, Lin A, Zhang C, Sun W, Zhang J, Yang C, Lu Y, Li H, Ye Z, He P, Wang T. SlBBX20 interacts with the COP9 signalosome subunit SlCSN5-2 to regulate anthocyanin biosynthesis by activating SlDFR expression in tomato. Hortic Res 2021; 8:163. [PMID: 34193855 PMCID: PMC8245592 DOI: 10.1038/s41438-021-00595-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/24/2021] [Accepted: 04/19/2021] [Indexed: 05/09/2023]
Abstract
Anthocyanins play vital roles in plant stress tolerance and growth regulation. Previously, we reported that the photomorphogenesis-related transcription factor SlBBX20 regulates anthocyanin accumulation in tomato. However, the underlying mechanism remains unclear. Here, we showed that SlBBX20 promotes anthocyanin biosynthesis by binding the promoter of the anthocyanin biosynthesis gene SlDFR, suggesting that SlBBX20 directly activates anthocyanin biosynthesis genes. Furthermore, we found by yeast two-hybrid screening that SlBBX20 interacts with the COP9 signalosome subunit SlCSN5-2, and the interaction was confirmed by bimolecular fluorescence complementation and coimmunoprecipitation assays. SlCSN5 gene silencing led to anthocyanin hyperaccumulation in the transgenic tomato calli and shoots, and SlCSN5-2 overexpression decreased anthocyanin accumulation, suggesting thSlCSN5-2 enhanced the ubiquitination of SlBBX20 and promoted the degradation of SlBBX20 in vivo. Consistently, silencing the SlCSN5-2 homolog in tobacco significantly increased the accumulation of the SlBBX20 protein. Since SlBBX20 is a vital regulator of photomorphogenesis, the SlBBX20-SlCSN5-2 module may represent a novel regulatory pathway in light-induced anthocyanin biosynthesis.
Collapse
Affiliation(s)
- Dan Luo
- Key Laboratory of Horticulture Plant Biology, Ministry of Education, Huazhong Agriculture University, 430070, Wuhan, China
| | - Cheng Xiong
- Key Laboratory of Horticulture Plant Biology, Ministry of Education, Huazhong Agriculture University, 430070, Wuhan, China
| | - Aihua Lin
- Key Laboratory of Horticulture Plant Biology, Ministry of Education, Huazhong Agriculture University, 430070, Wuhan, China
| | - Chunli Zhang
- Key Laboratory of Horticulture Plant Biology, Ministry of Education, Huazhong Agriculture University, 430070, Wuhan, China
| | - Wenhui Sun
- Key Laboratory of Horticulture Plant Biology, Ministry of Education, Huazhong Agriculture University, 430070, Wuhan, China
| | - Junhong Zhang
- Key Laboratory of Horticulture Plant Biology, Ministry of Education, Huazhong Agriculture University, 430070, Wuhan, China
| | - Changxian Yang
- Key Laboratory of Horticulture Plant Biology, Ministry of Education, Huazhong Agriculture University, 430070, Wuhan, China
| | - Yongen Lu
- Key Laboratory of Horticulture Plant Biology, Ministry of Education, Huazhong Agriculture University, 430070, Wuhan, China
| | - Hanxia Li
- Key Laboratory of Horticulture Plant Biology, Ministry of Education, Huazhong Agriculture University, 430070, Wuhan, China
| | - Zhibiao Ye
- Key Laboratory of Horticulture Plant Biology, Ministry of Education, Huazhong Agriculture University, 430070, Wuhan, China
| | - Ping He
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Taotao Wang
- Key Laboratory of Horticulture Plant Biology, Ministry of Education, Huazhong Agriculture University, 430070, Wuhan, China.
| |
Collapse
|
36
|
Tuo D, Yan P, Zhao G, Cui H, Zhu G, Liu Y, Yang X, Wang H, Li X, Shen W, Zhou P. An efficient papaya leaf distortion mosaic potyvirus vector for virus-induced gene silencing in papaya. Hortic Res 2021; 8:144. [PMID: 34193861 PMCID: PMC8245588 DOI: 10.1038/s41438-021-00579-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/13/2021] [Accepted: 04/19/2021] [Indexed: 05/11/2023]
Abstract
Papaya (Carica papaya L.) is regarded as an excellent model for genomic studies of tropical trees because of its short generation time and its small genome that has been sequenced. However, functional genomic studies in papaya depend on laborious genetic transformations because no rapid tools exist for this species. Here, we developed a highly efficient virus-induced gene silencing (VIGS) vector for use in papaya by modifying an artificially attenuated infectious clone of papaya leaf distortion mosaic virus (PLDMV; genus: Potyvirus), PLDMV-E, into a stable Nimble Cloning (NC)-based PLDMV vector, pPLDMV-NC, in Escherichia coli. The target fragments for gene silencing can easily be cloned into pPLDMV-NC without multiple digestion and ligation steps. Using this PLDMV VIGS system, we silenced and characterized five endogenous genes in papaya, including two common VIGS marker genes, namely, phytoene desaturase, Mg-chelatase H subunit, putative GIBBERELLIN (GA)-INSENSITIVE DWARF1A and 1B encoding GA receptors; and the cytochrome P450 gene CYP83B1, which encodes a key enzyme involved in benzylglucosinolate biosynthesis. The results demonstrate that our newly developed PLDMV VIGS vector is a rapid and convenient tool for functional genomic studies in papaya.
Collapse
Affiliation(s)
- Decai Tuo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources & Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, 571101, Haikou, China
| | - Pu Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources & Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, 571101, Haikou, China
| | - Guangyuan Zhao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101, Haikou, China
| | - Hongguang Cui
- College of Plant Protection, Hainan University, 570228, Haikou, China
| | - Guopeng Zhu
- College of Horticulture, Hainan University, 570228, Haikou, China
| | - Yang Liu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101, Haikou, China
- College of Horticulture, Hainan University, 570228, Haikou, China
| | - Xiukun Yang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101, Haikou, China
- College of Horticulture, Hainan University, 570228, Haikou, China
| | - He Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101, Haikou, China
- College of Horticulture, Hainan University, 570228, Haikou, China
| | - Xiaoying Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources & Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, 571101, Haikou, China
| | - Wentao Shen
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101, Haikou, China.
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources & Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, 571101, Haikou, China.
- College of Horticulture, Hainan University, 570228, Haikou, China.
- Hainan Key Laboratory of Tropical Microbe Resources, 571101, Haikou, China.
| | - Peng Zhou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101, Haikou, China.
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources & Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, 571101, Haikou, China.
- College of Horticulture, Hainan University, 570228, Haikou, China.
- Hainan Key Laboratory of Tropical Microbe Resources, 571101, Haikou, China.
| |
Collapse
|
37
|
Kang BC, Bae SJ, Lee S, Lee JS, Kim A, Lee H, Baek G, Seo H, Kim J, Kim JS. Chloroplast and mitochondrial DNA editing in plants. Nat Plants 2021; 7:899-905. [PMID: 34211132 PMCID: PMC8289734 DOI: 10.1038/s41477-021-00943-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/11/2021] [Indexed: 05/21/2023]
Abstract
Plant organelles including mitochondria and chloroplasts contain their own genomes, which encode many genes essential for respiration and photosynthesis, respectively. Gene editing in plant organelles, an unmet need for plant genetics and biotechnology, has been hampered by the lack of appropriate tools for targeting DNA in these organelles. In this study, we developed a Golden Gate cloning system1, composed of 16 expression plasmids (8 for the delivery of the resulting protein to mitochondria and the other 8 for delivery to chloroplasts) and 424 transcription activator-like effector subarray plasmids, to assemble DddA-derived cytosine base editor (DdCBE)2 plasmids and used the resulting DdCBEs to efficiently promote point mutagenesis in mitochondria and chloroplasts. Our DdCBEs induced base editing in lettuce or rapeseed calli at frequencies of up to 25% (mitochondria) and 38% (chloroplasts). We also showed DNA-free base editing in chloroplasts by delivering DdCBE mRNA to lettuce protoplasts to avoid off-target mutations caused by DdCBE-encoding plasmids. Furthermore, we generated lettuce calli and plantlets with edit frequencies of up to 99%, which were resistant to streptomycin or spectinomycin, by introducing a point mutation in the chloroplast 16S rRNA gene.
Collapse
Affiliation(s)
- Beum-Chang Kang
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Su-Ji Bae
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Seonghyun Lee
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Jeong Sun Lee
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Annie Kim
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Hyunji Lee
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Gayoung Baek
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Huiyun Seo
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Jihun Kim
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea.
| |
Collapse
|
38
|
Alexander A, Singh VK, Mishra A. Overexpression of differentially expressed AhCytb6 gene during plant-microbe interaction improves tolerance to N 2 deficit and salt stress in transgenic tobacco. Sci Rep 2021; 11:13435. [PMID: 34183701 PMCID: PMC8239016 DOI: 10.1038/s41598-021-92424-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 06/08/2021] [Indexed: 02/06/2023] Open
Abstract
Stenotrophomonas maltophilia has plant growth-promoting potential, and interaction with Arachis hypogaea changes host-plant physiology, biochemistry, and metabolomics, which provides tolerance under the N2 starvation conditions. About 226 suppression subtractive hybridization clones were obtained from plant-microbe interaction, of which, about 62% of gene sequences were uncharacterized, whereas 23% of sequences were involved in photosynthesis. An uncharacterized SSH clone, SM409 (full-length sequence showed resemblance with Cytb6), showed about 4-fold upregulation during the interaction was transformed to tobacco for functional validation. Overexpression of the AhCytb6 gene enhanced the seed germination efficiency and plant growth under N2 deficit and salt stress conditions compared to wild-type and vector control plants. Results confirmed that transgenic lines maintained high photosynthesis and protected plants from reactive oxygen species buildup during stress conditions. Microarray-based whole-transcript expression of host plants showed that out of 272,410 genes, 8704 and 24,409 genes were significantly (p < 0.05) differentially expressed (> 2 up or down-regulated) under N2 starvation and salt stress conditions, respectively. The differentially expressed genes belonged to different regulatory pathways. Overall, results suggested that overexpression of AhCytb6 regulates the expression of various genes to enhance plant growth under N2 deficit and abiotic stress conditions by modulating plant physiology.
Collapse
Affiliation(s)
- Ankita Alexander
- Division of Applied Phycology and Biotechnology, CSIR-Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat, 364002, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR, Ghaziabad, India
| | - Vijay K Singh
- Division of Applied Phycology and Biotechnology, CSIR-Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat, 364002, India
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Avinash Mishra
- Division of Applied Phycology and Biotechnology, CSIR-Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat, 364002, India.
- Academy of Scientific and Innovative Research (AcSIR), CSIR, Ghaziabad, India.
| |
Collapse
|
39
|
Kahn TW, Duck NB, McCarville MT, Schouten LC, Schweri K, Zaitseva J, Daum J. A Bacillus thuringiensis Cry protein controls soybean cyst nematode in transgenic soybean plants. Nat Commun 2021; 12:3380. [PMID: 34099714 PMCID: PMC8184815 DOI: 10.1038/s41467-021-23743-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 05/13/2021] [Indexed: 11/18/2022] Open
Abstract
Plant-parasitic nematodes (PPNs) are economically important pests of agricultural crops, and soybean cyst nematode (SCN) in particular is responsible for a large amount of damage to soybean. The need for new solutions for controlling SCN is becoming increasingly urgent, due to the slow decline in effectiveness of the widely used native soybean resistance derived from genetic line PI 88788. Thus, developing transgenic traits for controlling SCN is of great interest. Here, we report a Bacillus thuringiensis delta-endotoxin, Cry14Ab, that controls SCN in transgenic soybean. Experiments in C. elegans suggest the mechanism by which the protein controls nematodes involves damaging the intestine, similar to the mechanism of Cry proteins used to control insects. Plants expressing Cry14Ab show a significant reduction in cyst numbers compared to control plants 30 days after infestation. Field trials also show a reduction in SCN egg counts compared with control plants, demonstrating that this protein has excellent potential to control PPNs in soybean.
Collapse
Affiliation(s)
| | - Nicholas B Duck
- BASF, Morrisville, NC, USA
- Avertica, Research Triangle Park, NC, USA
| | | | | | | | | | | |
Collapse
|
40
|
Zhang B, Xu X, Huang R, Yang S, Li M, Guo Y. CRISPR/Cas9-mediated targeted mutation reveals a role for AN4 rather than DPL in regulating venation formation in the corolla tube of Petunia hybrida. Hortic Res 2021; 8:116. [PMID: 34059660 PMCID: PMC8166957 DOI: 10.1038/s41438-021-00555-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/25/2021] [Accepted: 04/01/2021] [Indexed: 05/11/2023]
Abstract
Venation is a common anthocyanin pattern displayed in flowers that confers important ornamental traits to plants. An anthocyanin-related R2R3-MYB transcription factor, DPL, has been proposed to regulate corolla tube venation in petunia plants. Here, however, we provide evidence redefining the role of DPL in petunia. A CRISPR/Cas9-mediated mutation of DPL resulted in the absence of the vein-associated anthocyanin pattern above the abaxial surface of the flower bud, but not corolla tube venation, thus indicating that DPL did not regulate the formation of corolla tube venation. Alternately, quantitative real-time PCR analysis demonstrated that the spatiotemporal expression pattern of another R2R3-MYB gene, AN4, coincided with the formation of corolla tube venation in petunia. Furthermore, overexpression of AN4 promoted anthocyanin accumulation by increasing the expression of anthocyanin biosynthesis genes. CRISPR/Cas9-mediated mutation of AN4 led to an absence of corolla tube venation, suggesting that this gene in fact determines this key plant trait. Taken together, the results presented here redefine the prime regulator of corolla tube venation, paving the way for further studies on the molecular mechanisms underlying the various venation patterns in petunia.
Collapse
Affiliation(s)
- Bin Zhang
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, 400716, Chongqing, China
- College of Agriculture, Guizhou University, 550025, Guiyang, Guizhou, China
| | - Xiaojing Xu
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, 400716, Chongqing, China
| | - Renwei Huang
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, 400716, Chongqing, China
- Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, College of Chemistry and Life Sciences, Chengdu Normal University, 611130, Chengdu, China
| | - Sha Yang
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, 400716, Chongqing, China
| | - Mingyang Li
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, 400716, Chongqing, China.
| | - Yulong Guo
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, 400716, Chongqing, China.
| |
Collapse
|
41
|
Mota APZ, Brasileiro ACM, Vidigal B, Oliveira TN, da Cunha Quintana Martins A, Saraiva MADP, de Araújo ACG, Togawa RC, Grossi-de-Sá MF, Guimaraes PM. Defining the combined stress response in wild Arachis. Sci Rep 2021; 11:11097. [PMID: 34045561 PMCID: PMC8160017 DOI: 10.1038/s41598-021-90607-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/11/2021] [Indexed: 02/04/2023] Open
Abstract
Nematodes and drought are major constraints in tropical agriculture and often occur simultaneously. Plant responses to these stresses are complex and require crosstalk between biotic and abiotic signaling pathways. In this study, we explored the transcriptome data of wild Arachis species subjected to drought (A-metaDEG) and the root-knot nematode Meloidogyne arenaria (B-metaDEG) via meta-analysis, to identify core-stress responsive genes to each individual and concurrent stresses in these species. Transcriptome analysis of a nematode/drought bioassay (cross-stress) showed that the set of stress responsive DEGs to concurrent stress is distinct from those resulting from overlapping A- and B-metaDEGs, indicating a specialized and unique response to combined stresses in wild Arachis. Whilst individual biotic and abiotic stresses elicit hormone-responsive genes, most notably in the jasmonic and abscisic acid pathways, combined stresses seem to trigger mainly the ethylene hormone pathway. The overexpression of a cross-stress tolerance candidate gene identified here, an endochitinase-encoding gene (AsECHI) from Arachis stenosperma, reduced up to 30% of M. incognita infection and increased post-drought recovery in Arabidopsis plants submitted to both stresses. The elucidation of the network of cross-stress responsive genes in Arachis contributes to better understanding the complex regulation of biotic and abiotic responses in plants facilitating more adequate crop breeding for combined stress tolerance.
Collapse
Affiliation(s)
- Ana Paula Zotta Mota
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.8532.c0000 0001 2200 7498Universidade Federal do Rio Grande do Sul, Porto Alegre, RS Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil ,grid.8183.20000 0001 2153 9871Present Address: CIRAD, UMR AGAP, 34398 Montpellier, France ,grid.463758.b0000 0004 0445 8705Present Address: AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Ana Cristina Miranda Brasileiro
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
| | - Bruna Vidigal
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
| | - Thais Nicolini Oliveira
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
| | - Andressa da Cunha Quintana Martins
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
| | - Mario Alfredo de Passos Saraiva
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
| | - Ana Claudia Guerra de Araújo
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
| | - Roberto C. Togawa
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
| | - Maria Fatima Grossi-de-Sá
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil ,grid.411952.a0000 0001 1882 0945Universidade Católica de Brasília (UCB)-Genomic Sciences and Biotechnology, Brasilia, DF Brazil
| | - Patricia Messenberg Guimaraes
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
| |
Collapse
|
42
|
Wang X, Tu M, Wang Y, Yin W, Zhang Y, Wu H, Gu Y, Li Z, Xi Z, Wang X. Whole-genome sequencing reveals rare off-target mutations in CRISPR/Cas9-edited grapevine. Hortic Res 2021; 8:114. [PMID: 33931634 PMCID: PMC8087786 DOI: 10.1038/s41438-021-00549-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 03/03/2021] [Accepted: 03/14/2021] [Indexed: 05/08/2023]
Abstract
The CRISPR (clustered regularly interspaced short palindromic repeats)-associated protein 9 (Cas9) system is a powerful tool for targeted genome editing, with applications that include plant biotechnology and functional genomics research. However, the specificity of Cas9 targeting is poorly investigated in many plant species, including fruit trees. To assess the off-target mutation rate in grapevine (Vitis vinifera), we performed whole-genome sequencing (WGS) of seven Cas9-edited grapevine plants in which one of two genes was targeted by CRISPR/Cas9 and three wild-type (WT) plants. In total, we identified between 202,008 and 272,397 single nucleotide polymorphisms (SNPs) and between 26,391 and 55,414 insertions/deletions (indels) in the seven Cas9-edited grapevine plants compared with the three WT plants. Subsequently, 3272 potential off-target sites were selected for further analysis. Only one off-target indel mutation was identified from the WGS data and validated by Sanger sequencing. In addition, we found 243 newly generated off-target sites caused by genetic variants between the Thompson Seedless cultivar and the grape reference genome (PN40024) but no true off-target mutations. In conclusion, we observed high specificity of CRISPR/Cas9 for genome editing of grapevine.
Collapse
Affiliation(s)
- Xianhang Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, 712100, Yangling, Shaanxi, China
- College of Enology, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Mingxing Tu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, 712100, Yangling, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Ya Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, 712100, Yangling, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Wuchen Yin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, 712100, Yangling, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Yu Zhang
- Novogene Technologies Corporation, 100000, Beijing, China
| | - Hongsong Wu
- Novogene Technologies Corporation, 100000, Beijing, China
| | - Yincong Gu
- OEbiotech Corporation, 200000, Shanghai, China
| | - Zhi Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, 712100, Yangling, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Zhumei Xi
- College of Enology, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Xiping Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, 712100, Yangling, Shaanxi, China.
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, 712100, Yangling, Shaanxi, China.
| |
Collapse
|
43
|
Zhai L, Wang X, Tang D, Qi Q, Yer H, Jiang X, Han Z, McAvoy R, Li W, Li Y. Molecular and physiological characterization of the effects of auxin-enriched rootstock on grafting. Hortic Res 2021; 8:74. [PMID: 33790234 PMCID: PMC8012700 DOI: 10.1038/s41438-021-00509-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/28/2020] [Accepted: 01/03/2021] [Indexed: 05/12/2023]
Abstract
Grafting is a highly useful technique, and its success largely depends on graft union formation. In this study, we found that root-specific expression of the auxin biosynthetic gene iaaM in tobacco, when used as rootstock, resulted in more rapid callus formation and faster graft healing. However, overexpression of the auxin-inactivating iaaL gene in rootstocks delayed graft healing. We observed increased endogenous auxin levels and auxin-responsive DR5::GUS expression in scions of WT/iaaM grafts compared with those found in WT/WT grafts, which suggested that auxin is transported upward from rootstock to scion tissues. A transcriptome analysis showed that auxin enhanced graft union formation through increases in the expression of genes involved in graft healing in both rootstock and scion tissues. We also observed that the ethylene biosynthetic gene ACS1 and the ethylene-responsive gene ERF5 were upregulated in both scions and rootstocks of the WT/iaaM grafts. Furthermore, exogenous applications of the ethylene precursor ACC to the junction of WT/WT grafts promoted graft union formation, whereas application of the ethylene biosynthesis inhibitor AVG delayed graft healing in WT/WT grafts, and the observed delay was less pronounced in the WT/iaaM grafts. These results demonstrated that elevated auxin levels in the iaaM rootstock in combination with the increased auxin levels in scions caused by upward transport/diffusion enhanced graft union formation and that ethylene was partially responsible for the effects of auxin on grafting. Our findings showed that grafting success can be enhanced by increasing the auxin levels in rootstocks using transgenic or gene-editing techniques.
Collapse
Affiliation(s)
- Longmei Zhai
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, 06269, USA
- College of Horticulture, China Agricultural University, Beijing, 100193, PR China
| | - Xiaomin Wang
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, 06269, USA
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, PR China
| | - Dan Tang
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, 06269, USA
| | - Qi Qi
- College of Horticulture, China Agricultural University, Beijing, 100193, PR China
- National Engineering Laboratory for Tree Breeding, College of Life Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, PR China
| | - Huseyin Yer
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, 06269, USA
| | - Xiangning Jiang
- National Engineering Laboratory for Tree Breeding, College of Life Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, PR China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, 100193, PR China
| | - Richard McAvoy
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, 06269, USA
| | - Wei Li
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, 06269, USA.
- College of Horticulture, China Agricultural University, Beijing, 100193, PR China.
| | - Yi Li
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, 06269, USA.
| |
Collapse
|
44
|
Chiong KT, Cody WB, Scholthof HB. RNA silencing suppressor-influenced performance of a virus vector delivering both guide RNA and Cas9 for CRISPR gene editing. Sci Rep 2021; 11:6769. [PMID: 33762584 PMCID: PMC7990971 DOI: 10.1038/s41598-021-85366-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 02/26/2021] [Indexed: 11/09/2022] Open
Abstract
We report on further development of the agroinfiltratable Tobacco mosaic virus (TMV)-based overexpression (TRBO) vector to deliver CRISPR/Cas9 components into plants. First, production of a Cas9 (HcoCas9) protein from a binary plasmid increased when co-expressed in presence of suppressors of gene silencing, such as the TMV 126-kDa replicase or the Tomato bushy stunt virus P19 protein. Such suppressor-generated elevated levels of Cas9 expression translated to efficient gene editing mediated by TRBO-G-3'gGFP expressing GFP and also a single guide RNA targeting the mgfp5 gene in the Nicotiana benthamiana GFP-expressing line 16c. Furthermore, HcoCas9 encoding RNA, a large cargo insert of 4.2 kb, was expressed from TRBO-HcoCas9 to yield Cas9 protein again at higher levels upon co-expression with P19. Likewise, co-delivery of TRBO-HcoCas9 and TRBO-G-3'gGFP in the presence of P19 also resulted in elevated levels percentages of indels (insertions and deletions). These data also revealed an age-related phenomenon in plants whereby the RNA suppressor P19 had more of an effect in older plants. Lastly, we used a single TRBO vector to express both Cas9 and a sgRNA. Taken together, we suggest that viral RNA suppressors could be used for further optimization of single viral vector delivery of CRISPR gene editing parts.
Collapse
Affiliation(s)
- Kelvin T Chiong
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Will B Cody
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA
- Department of Chemical Engineering, Shriram Center for Bioengineering and Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Herman B Scholthof
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA.
| |
Collapse
|
45
|
Sakuraba Y, Chaganzhana, Mabuchi A, Iba K, Yanagisawa S. Enhanced NRT1.1/NPF6.3 expression in shoots improves growth under nitrogen deficiency stress in Arabidopsis. Commun Biol 2021; 4:256. [PMID: 33637855 PMCID: PMC7910545 DOI: 10.1038/s42003-021-01775-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 01/24/2021] [Indexed: 01/31/2023] Open
Abstract
Identification of genes and their alleles capable of improving plant growth under low nitrogen (N) conditions is key for developing sustainable agriculture. Here, we show that a genome-wide association study using Arabidopsis thaliana accessions suggested an association between different magnitudes of N deficiency responses and diversity in NRT1.1/NPF6.3 that encodes a dual-affinity nitrate transporter involved in nitrate uptake by roots. Various analyses using accessions exhibiting reduced N deficiency responses revealed that enhanced NRT1.1 expression in shoots rather than in roots is responsible for better growth of Arabidopsis seedlings under N deficient conditions. Furthermore, polymorphisms that increased NRT1.1 promoter activity were identified in the NRT1.1 promoter sequences of the accessions analyzed. Hence, our data indicated that polymorphism-dependent activation of the NRT1.1 promoter in shoots could serve as a tool in molecular breeding programs for improving plant growth in low N environments.
Collapse
Affiliation(s)
- Yasuhito Sakuraba
- grid.26999.3d0000 0001 2151 536XPlant Functional Biotechnology, Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo Japan
| | - Chaganzhana
- grid.26999.3d0000 0001 2151 536XPlant Functional Biotechnology, Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo Japan
| | - Atsushi Mabuchi
- grid.177174.30000 0001 2242 4849Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Koh Iba
- grid.177174.30000 0001 2242 4849Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Shuichi Yanagisawa
- grid.26999.3d0000 0001 2151 536XPlant Functional Biotechnology, Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo Japan
| |
Collapse
|
46
|
Zhang M, Wang Y, Chen X, Xu F, Ding M, Ye W, Kawai Y, Toda Y, Hayashi Y, Suzuki T, Zeng H, Xiao L, Xiao X, Xu J, Guo S, Yan F, Shen Q, Xu G, Kinoshita T, Zhu Y. Plasma membrane H +-ATPase overexpression increases rice yield via simultaneous enhancement of nutrient uptake and photosynthesis. Nat Commun 2021; 12:735. [PMID: 33531490 PMCID: PMC7854686 DOI: 10.1038/s41467-021-20964-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/04/2021] [Indexed: 01/30/2023] Open
Abstract
Nitrogen (N) and carbon (C) are essential elements for plant growth and crop yield. Thus, improved N and C utilisation contributes to agricultural productivity and reduces the need for fertilisation. In the present study, we find that overexpression of a single rice gene, Oryza sativa plasma membrane (PM) H+-ATPase 1 (OSA1), facilitates ammonium absorption and assimilation in roots and enhanced light-induced stomatal opening with higher photosynthesis rate in leaves. As a result, OSA1 overexpression in rice plants causes a 33% increase in grain yield and a 46% increase in N use efficiency overall. As PM H+-ATPase is highly conserved in plants, these findings indicate that the manipulation of PM H+-ATPase could cooperatively improve N and C utilisation, potentially providing a vital tool for food security and sustainable agriculture.
Collapse
Affiliation(s)
- Maoxing Zhang
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environment Sciences, Nanjing Agricultural University, Nanjing, China
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Yin Wang
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
- Institute of Ecology, College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes of Ministry of Education, Peking University, Beijing, China
| | - Xi Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Feiyun Xu
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environment Sciences, Nanjing Agricultural University, Nanjing, China
| | - Ming Ding
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environment Sciences, Nanjing Agricultural University, Nanjing, China
| | - Wenxiu Ye
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuya Kawai
- Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yosuke Toda
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
- Japan Science and Technology Agency (JST), PRESTO, Kawaguchi, Japan
| | - Yuki Hayashi
- Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Houqing Zeng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Liang Xiao
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environment Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xin Xiao
- College of Resources and Environment, Anhui Science and Technology University, Fengyang, China
| | - Jin Xu
- College of Horticulture, Shanxi Agricultural University, Taigu, China
| | - Shiwei Guo
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environment Sciences, Nanjing Agricultural University, Nanjing, China
| | - Feng Yan
- Institute of Agronomy and Plant Breeding, Justus Liebig University, Giessen, Germany
| | - Qirong Shen
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environment Sciences, Nanjing Agricultural University, Nanjing, China
| | - Guohua Xu
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environment Sciences, Nanjing Agricultural University, Nanjing, China
| | - Toshinori Kinoshita
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan.
- Graduate School of Science, Nagoya University, Nagoya, Japan.
| | - Yiyong Zhu
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environment Sciences, Nanjing Agricultural University, Nanjing, China.
| |
Collapse
|
47
|
Song ZZ, Peng B, Gu ZX, Tang ML, Li B, Liang MX, Wang LM, Guo XT, Wang JP, Sha YF, Zhang HX. Site-directed mutagenesis identified the key active site residues of alcohol acyltransferase PpAAT1 responsible for aroma biosynthesis in peach fruits. Hortic Res 2021; 8:32. [PMID: 33518702 PMCID: PMC7847995 DOI: 10.1038/s41438-021-00461-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/24/2020] [Accepted: 11/13/2020] [Indexed: 05/10/2023]
Abstract
The aroma of peach fruit is predominantly determined by the accumulation of γ-decalactone and ester compounds. A previous study showed that the biosynthesis of these aroma compounds in peach fruit is catalyzed by PpAAT1, an alcohol acyltransferase. In this work, we investigated the key active site residues responsible for γ-decalactone and ester biosynthesis. A total of 14 candidate amino acid residues possibly involved in internal esterification and 9 candidate amino acid residues possibly involved in esterification of PpAAT1 were assessed via site-directed mutagenesis. Analyses of the in vitro enzyme activities of PpAAT1 and its site-directed mutant proteins (PpAAT1-SMs) with different amino acid residue mutations as well as the contents of γ-decalactone in transgenic tobacco leaves and peach fruits transiently expressing PpAAT1 and PpAAT1-SMs revealed that site-directed mutation of H165 in the conserved HxxxD motif led to lost enzymatic activity of PpAAT1 in both internal esterification and its reactions, whereas mutation of the key amino acid residue D376 led to the total loss of γ-decalactone biosynthesis activity of PpAAT1. Mutations of 9 and 7 other amino acid residues also dramatically affected the enzymatic activity of PpAAT1 in the internal esterification and esterification reactions, respectively. Our findings provide a biochemical foundation for the mechanical biosynthesis of γ-decalactone and ester compounds catalyzed by PpAAT1 in peach fruits, which could be used to guide the molecular breeding of new peach species with more favorable aromas for consumers.
Collapse
Affiliation(s)
- Zhi-Zhong Song
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, 264025, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), 186 Hongqizhong Road, Yantai, 264025, China
| | - Bin Peng
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, 264025, China.
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), 186 Hongqizhong Road, Yantai, 264025, China.
| | - Zi-Xia Gu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, 1 Qianhuhoucun, Nanjing, 210014, China
| | - Mei-Ling Tang
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), 186 Hongqizhong Road, Yantai, 264025, China
- Yantai Academy of Agricultural Science, 26 Gangcheng West Street, Yantai, 265500, China
| | - Bei Li
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, 264025, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), 186 Hongqizhong Road, Yantai, 264025, China
| | - Mei-Xia Liang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, 264025, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), 186 Hongqizhong Road, Yantai, 264025, China
| | - Li-Min Wang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, 264025, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), 186 Hongqizhong Road, Yantai, 264025, China
| | - Xiao-Tong Guo
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, 264025, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), 186 Hongqizhong Road, Yantai, 264025, China
| | - Jian-Ping Wang
- Yantai Academy of Agricultural Science, 26 Gangcheng West Street, Yantai, 265500, China
| | - Yu-Fen Sha
- Yantai Academy of Agricultural Science, 26 Gangcheng West Street, Yantai, 265500, China
| | - Hong-Xia Zhang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, 264025, China.
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), 186 Hongqizhong Road, Yantai, 264025, China.
| |
Collapse
|
48
|
Jiang X, Payá-Tormo L, Coroian D, García-Rubio I, Castellanos-Rueda R, Eseverri Á, López-Torrejón G, Burén S, Rubio LM. Exploiting genetic diversity and gene synthesis to identify superior nitrogenase NifH protein variants to engineer N 2-fixation in plants. Commun Biol 2021; 4:4. [PMID: 33398015 PMCID: PMC7782807 DOI: 10.1038/s42003-020-01536-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 11/25/2020] [Indexed: 01/01/2023] Open
Abstract
Engineering nitrogen fixation in eukaryotes requires high expression of functional nitrogenase structural proteins, a goal that has not yet been achieved. Here we build a knowledge-based library containing 32 nitrogenase nifH sequences from prokaryotes of diverse ecological niches and metabolic features and combine with rapid screening in tobacco to identify superior NifH variants for plant mitochondria expression. Three NifH variants outperform in tobacco mitochondria and are further tested in yeast. Hydrogenobacter thermophilus (Aquificae) NifH is isolated in large quantities from yeast mitochondria and fulfills NifH protein requirements for efficient N2 fixation, including electron transfer for substrate reduction, P-cluster maturation, and FeMo-co biosynthesis. H. thermophilus NifH expressed in tobacco leaves shows lower nitrogenase activity than that from yeast. However, transfer of [Fe4S4] clusters from NifU to NifH in vitro increases 10-fold the activity of the tobacco-isolated NifH, revealing that plant mitochondria [Fe-S] cluster availability constitutes a bottleneck to engineer plant nitrogenases.
Collapse
Affiliation(s)
- Xi Jiang
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - Lucía Payá-Tormo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - Diana Coroian
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Inés García-Rubio
- Centro Universitario de la Defensa, Ctra. de Huesca s/n, 50090, Zaragoza, Spain
| | - Rocío Castellanos-Rueda
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain
- Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland
| | - Álvaro Eseverri
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - Gema López-Torrejón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - Stefan Burén
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain.
| | - Luis Manuel Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain.
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain.
| |
Collapse
|
49
|
Hao X, Xie C, Ruan Q, Zhang X, Wu C, Han B, Qian J, Zhou W, Nützmann HW, Kai G. The transcription factor OpWRKY2 positively regulates the biosynthesis of the anticancer drug camptothecin in Ophiorrhiza pumila. Hortic Res 2021; 8:7. [PMID: 33384421 PMCID: PMC7775441 DOI: 10.1038/s41438-020-00437-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/22/2020] [Accepted: 10/17/2020] [Indexed: 05/03/2023]
Abstract
The limited bioavailability of plant-derived natural products with anticancer activity poses major challenges to the pharmaceutical industry. An example of this is camptothecin, a monoterpene indole alkaloid with potent anticancer activity that is extracted at very low concentrations from woody plants. Recently, camptothecin biosynthesis has been shown to become biotechnologically amenable in hairy-root systems of the natural producer Ophiorrhiza pumila. Here, time-course expression and metabolite analyses were performed to identify novel transcriptional regulators of camptothecin biosynthesis in O. pumila. It is shown here that camptothecin production increased over cultivation time and that the expression pattern of the WRKY transcription factor encoding gene OpWRKY2 is closely correlated with camptothecin accumulation. Overexpression of OpWRKY2 led to a more than three-fold increase in camptothecin levels. Accordingly, silencing of OpWRKY2 correlated with decreased camptothecin levels in the plant. Further detailed molecular characterization by electrophoretic mobility shift, yeast one-hybrid and dual-luciferase assays showed that OpWRKY2 directly binds and activates the central camptothecin pathway gene OpTDC. Taken together, the results of this study demonstrate that OpWRKY2 acts as a direct positive regulator of camptothecin biosynthesis. As such, a feasible strategy for the over-accumulation of camptothecin in a biotechnologically amenable system is presented.
Collapse
Affiliation(s)
- Xiaolong Hao
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, 310053, Hangzhou, China
| | - Chenhong Xie
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, 310053, Hangzhou, China
| | - Qingyan Ruan
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, 310053, Hangzhou, China
| | - Xichen Zhang
- Institute of Plant Biotechnology, School of Life Sciences, Shanghai Normal University, 200234, Shanghai, China
| | - Chao Wu
- Institute of Plant Biotechnology, School of Life Sciences, Shanghai Normal University, 200234, Shanghai, China
| | - Bing Han
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, 310053, Hangzhou, China
| | - Jun Qian
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, 310053, Hangzhou, China
| | - Wei Zhou
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, 310053, Hangzhou, China
| | - Hans-Wilhelm Nützmann
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Guoyin Kai
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, 310053, Hangzhou, China.
| |
Collapse
|
50
|
Shipman EN, Yu J, Zhou J, Albornoz K, Beckles DM. Can gene editing reduce postharvest waste and loss of fruit, vegetables, and ornamentals? Hortic Res 2021; 8:1. [PMID: 33384412 PMCID: PMC7775472 DOI: 10.1038/s41438-020-00428-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 05/22/2023]
Abstract
Postharvest waste and loss of horticultural crops exacerbates the agricultural problems facing humankind and will continue to do so in the next decade. Fruits and vegetables provide us with a vast spectrum of healthful nutrients, and along with ornamentals, enrich our lives with a wide array of pleasant sensory experiences. These commodities are, however, highly perishable. Approximately 33% of the produce that is harvested is never consumed since these products naturally have a short shelf-life, which leads to postharvest loss and waste. This loss, however, could be reduced by breeding new crops that retain desirable traits and accrue less damage over the course of long supply chains. New gene-editing tools promise the rapid and inexpensive production of new varieties of crops with enhanced traits more easily than was previously possible. Our aim in this review is to critically evaluate gene editing as a tool to modify the biological pathways that determine fruit, vegetable, and ornamental quality, especially after storage. We provide brief and accessible overviews of both the CRISPR-Cas9 method and the produce supply chain. Next, we survey the literature of the last 30 years, to catalog genes that control or regulate quality or senescence traits that are "ripe" for gene editing. Finally, we discuss barriers to implementing gene editing for postharvest, from the limitations of experimental methods to international policy. We conclude that in spite of the hurdles that remain, gene editing of produce and ornamentals will likely have a measurable impact on reducing postharvest loss and waste in the next 5-10 years.
Collapse
Affiliation(s)
- Emma N Shipman
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Plant Biology Graduate Group, University of California, Davis, CA, 95616, USA.
| | - Jingwei Yu
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Graduate Group of Horticulture & Agronomy, University of California, Davis, CA, 95616, USA.
| | - Jiaqi Zhou
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Graduate Group of Horticulture & Agronomy, University of California, Davis, CA, 95616, USA.
| | - Karin Albornoz
- Departamento de Produccion Vegetal, Universidad de Concepcion, Region del BioBio, Concepcion, Chile.
| | - Diane M Beckles
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| |
Collapse
|