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Liu L, Qu J, Wang C, Liu M, Zhang C, Zhang X, Guo C, Wu C, Yang G, Huang J, Yan K, Shu H, Zheng C, Zhang S. An efficient genetic transformation system mediated by Rhizobium rhizogenes in fruit trees based on the transgenic hairy root to shoot conversion. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38491985 DOI: 10.1111/pbi.14328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/21/2024] [Accepted: 02/25/2024] [Indexed: 03/18/2024]
Abstract
Genetic transformation is a critical tool for gene editing and genetic improvement of plants. Although many model plants and crops can be genetically manipulated, genetic transformation systems for fruit trees are either lacking or perform poorly. We used Rhizobium rhizogenes to transfer the target gene into the hairy roots of Malus domestica and Actinidia chinensis. Transgenic roots were generated within 3 weeks, with a transgenic efficiency of 78.8%. Root to shoot conversion of transgenic hairy roots was achieved within 11 weeks, with a regeneration efficiency of 3.3%. Finally, the regulatory genes involved in stem cell activity were used to improve shoot regeneration efficiency. MdWOX5 exhibited the most significant effects, as it led to an improved regeneration efficiency of 20.6% and a reduced regeneration time of 9 weeks. Phenotypes of the overexpression of RUBY system mediated red roots and overexpression of MdRGF5 mediated longer root hairs were observed within 3 weeks, suggesting that the method can be used to quickly screen genes that influence root phenotype scores through root performance, such as root colour, root hair, and lateral root. Obtaining whole plants of the RUBY system and MdRGF5 overexpression lines highlights the convenience of this technology for studying gene functions in whole plants. Overall, we developed an optimized method to improve the transformation efficiency and stability of transformants in fruit trees.
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Affiliation(s)
- Lin Liu
- College of Life Sciences, Shandong Agricultural University, Tai'an, China
- National Engineering Research Center for Apple and Technology Innovation Alliance of Apple Industry, Shandong Agricultural University, Tai'an, China
| | - Jinghua Qu
- College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Chunyan Wang
- College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Miao Liu
- College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Chunmeng Zhang
- College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Xinyue Zhang
- College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Cheng Guo
- College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Changai Wu
- College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Guodong Yang
- College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Jinguang Huang
- College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Kang Yan
- College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Huairui Shu
- National Engineering Research Center for Apple and Technology Innovation Alliance of Apple Industry, Shandong Agricultural University, Tai'an, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Chengchao Zheng
- College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Shizhong Zhang
- College of Life Sciences, Shandong Agricultural University, Tai'an, China
- National Engineering Research Center for Apple and Technology Innovation Alliance of Apple Industry, Shandong Agricultural University, Tai'an, China
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
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2
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Faist H, Ankenbrand MJ, Sickel W, Hentschel U, Keller A, Deeken R. Opportunistic Bacteria of Grapevine Crown Galls Are Equipped with the Genomic Repertoire for Opine Utilization. Genome Biol Evol 2023; 15:evad228. [PMID: 38085065 PMCID: PMC10745273 DOI: 10.1093/gbe/evad228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Young grapevines (Vitis vinifera) suffer and eventually can die from the crown gall disease caused by the plant pathogen Allorhizobium vitis (Rhizobiaceae). Virulent members of A. vitis harbor a tumor-inducing plasmid and induce formation of crown galls due to the oncogenes encoded on the transfer DNA. The expression of oncogenes in transformed host cells induces unregulated cell proliferation and metabolic and physiological changes. The crown gall produces opines uncommon to plants, which provide an important nutrient source for A. vitis harboring opine catabolism enzymes. Crown galls host a distinct bacterial community, and the mechanisms establishing a crown gall-specific bacterial community are currently unknown. Thus, we were interested in whether genes homologous to those of the tumor-inducing plasmid coexist in the genomes of the microbial species coexisting in crown galls. We isolated 8 bacterial strains from grapevine crown galls, sequenced their genomes, and tested their virulence and opine utilization ability in bioassays. In addition, the 8 genome sequences were compared with 34 published bacterial genomes, including closely related plant-associated bacteria not from crown galls. Homologous genes for virulence and opine anabolism were only present in the virulent Rhizobiaceae. In contrast, homologs of the opine catabolism genes were present in all strains including the nonvirulent members of the Rhizobiaceae and non-Rhizobiaceae. Gene neighborhood and sequence identity of the opine degradation cluster of virulent and nonvirulent strains together with the results of the opine utilization assay support the important role of opine utilization for cocolonization in crown galls, thereby shaping the crown gall community.
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Affiliation(s)
- Hanna Faist
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Tulln 3430, Austria
- Julius-von-Sachs Institute for Biological Sciences, Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg 97082, Germany
| | - Markus J Ankenbrand
- Faculty of Biology, Center for Computational and Theoretical Biology, University of Würzburg, Würzburg 97074, Germany
| | - Wiebke Sickel
- Institute of Biodiversity, Thuenen-Institute of Biodiversity, Braunschweig 38116, Germany
| | - Ute Hentschel
- RD3 Marine Ecology, RU Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24105, Germany
- Sektion Biologie, Christian-Albrechts University of Kiel, Kiel 24105, Germany
| | - Alexander Keller
- Cellular and Organismic Networks, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Rosalia Deeken
- Julius-von-Sachs Institute for Biological Sciences, Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg 97082, Germany
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Ali A, Zafar MM, Farooq Z, Ahmed SR, Ijaz A, Anwar Z, Abbas H, Tariq MS, Tariq H, Mustafa M, Bajwa MH, Shaukat F, Razzaq A, Maozhi R. Breakthrough in CRISPR/Cas system: Current and future directions and challenges. Biotechnol J 2023; 18:e2200642. [PMID: 37166088 DOI: 10.1002/biot.202200642] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023]
Abstract
Targeted genome editing (GE) technology has brought a significant revolution in fictional genomic research and given hope to plant scientists to develop desirable varieties. This technology involves inducing site-specific DNA perturbations that can be repaired through DNA repair pathways. GE products currently include CRISPR-associated nuclease DNA breaks, prime editors generated DNA flaps, single nucleotide-modifications, transposases, and recombinases. The discovery of double-strand breaks, site-specific nucleases (SSNs), and repair mechanisms paved the way for targeted GE, and the first-generation GE tools, ZFNs and TALENs, were successfully utilized in plant GE. However, CRISPR-Cas has now become the preferred tool for GE due to its speed, reliability, and cost-effectiveness. Plant functional genomics has benefited significantly from the widespread use of CRISPR technology for advancements and developments. This review highlights the progress made in CRISPR technology, including multiplex editing, base editing (BE), and prime editing (PE), as well as the challenges and potential delivery mechanisms.
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Affiliation(s)
- Ahmad Ali
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | | | - Zunaira Farooq
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Syed Riaz Ahmed
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Science (PIEAS), Nilore, Pakistan
| | - Aqsa Ijaz
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Science (PIEAS), Nilore, Pakistan
| | - Zunaira Anwar
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Science (PIEAS), Nilore, Pakistan
| | - Huma Abbas
- Department of Plant Pathology, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Sayyam Tariq
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Science (PIEAS), Nilore, Pakistan
| | - Hala Tariq
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Mahwish Mustafa
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | | | - Fiza Shaukat
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Abdul Razzaq
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Ren Maozhi
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Institute of, Urban Agriculture, Chinese Academy of Agriculture Science, Chengdu, China
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Wang L, Zhao F, Liu H, Chen H, Zhang F, Li S, Sun T, Nekrasov V, Huang S, Dong S. A modified Agrobacterium-mediated transformation for two oomycete pathogens. PLoS Pathog 2023; 19:e1011346. [PMID: 37083862 PMCID: PMC10156060 DOI: 10.1371/journal.ppat.1011346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 05/03/2023] [Accepted: 04/06/2023] [Indexed: 04/22/2023] Open
Abstract
Oomycetes are a group of filamentous microorganisms that include some of the biggest threats to food security and natural ecosystems. However, much of the molecular basis of the pathogenesis and the development in these organisms remains to be learned, largely due to shortage of efficient genetic manipulation methods. In this study, we developed modified transformation methods for two important oomycete species, Phytophthora infestans and Plasmopara viticola, that bring destructive damage in agricultural production. As part of the study, we established an improved Agrobacterium-mediated transformation (AMT) method by prokaryotic expression in Agrobacterium tumefaciens of AtVIP1 (VirE2-interacting protein 1), an Arabidopsis bZIP gene required for AMT but absent in oomycetes genomes. Using the new method, we achieved an increment in transformation efficiency in two P. infestans strains. We further obtained a positive GFP transformant of P. viticola using the modified AMT method. By combining this method with the CRISPR/Cas12a genome editing system, we successfully performed targeted mutagenesis and generated loss-of-function mutations in two P. infestans genes. We edited a MADS-box transcription factor-encoding gene and found that a homozygous mutation in MADS-box results in poor sporulation and significantly reduced virulence. Meanwhile, a single-copy avirulence effector-encoding gene Avr8 in P. infestans was targeted and the edited transformants were virulent on potato carrying the cognate resistance gene R8, suggesting that loss of Avr8 led to successful evasion of the host immune response by the pathogen. In summary, this study reports on a modified genetic transformation and genome editing system, providing a potential tool for accelerating molecular genetic studies not only in oomycetes, but also other microorganisms.
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Affiliation(s)
- Luyao Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Department of Plant Pathology and Key Laboratory of Integrated Management of Crop Disease and Pests (Ministry of Education), Nanjing Agricultural University, Nanjing, China
| | - Fei Zhao
- Department of Plant Pathology and Key Laboratory of Integrated Management of Crop Disease and Pests (Ministry of Education), Nanjing Agricultural University, Nanjing, China
| | - Haohao Liu
- Department of Plant Pathology and Key Laboratory of Integrated Management of Crop Disease and Pests (Ministry of Education), Nanjing Agricultural University, Nanjing, China
| | - Han Chen
- Department of Plant Pathology and Key Laboratory of Integrated Management of Crop Disease and Pests (Ministry of Education), Nanjing Agricultural University, Nanjing, China
| | - Fan Zhang
- Department of Plant Pathology and Key Laboratory of Integrated Management of Crop Disease and Pests (Ministry of Education), Nanjing Agricultural University, Nanjing, China
| | - Suhua Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Tongjun Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Vladimir Nekrasov
- Plant Sciences and the Bioeconomy, Rothamsted Research, Harpenden, United Kingdom
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Suomeng Dong
- Department of Plant Pathology and Key Laboratory of Integrated Management of Crop Disease and Pests (Ministry of Education), Nanjing Agricultural University, Nanjing, China
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5
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Akbarimotlagh M, Azizi A, Shams-Bakhsh M, Jafari M, Ghasemzadeh A, Palukaitis P. Critical points for the design and application of RNA silencing constructs for plant virus resistance. Adv Virus Res 2023; 115:159-203. [PMID: 37173065 DOI: 10.1016/bs.aivir.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Control of plant virus diseases is a big challenge in agriculture as is resistance in plant lines to infection by viruses. Recent progress using advanced technologies has provided fast and durable alternatives. One of the most promising techniques against plant viruses that is cost-effective and environmentally safe is RNA silencing or RNA interference (RNAi), a technology that could be used alone or along with other control methods. To achieve the goals of fast and durable resistance, the expressed and target RNAs have been examined in many studies, with regard to the variability in silencing efficiency, which is regulated by various factors such as target sequences, target accessibility, RNA secondary structures, sequence variation in matching positions, and other intrinsic characteristics of various small RNAs. Developing a comprehensive and applicable toolbox for the prediction and construction of RNAi helps researchers to achieve the acceptable performance level of silencing elements. Although the attainment of complete prediction of RNAi robustness is not possible, as it also depends on the cellular genetic background and the nature of the target sequences, some important critical points have been discerned. Thus, the efficiency and robustness of RNA silencing against viruses can be improved by considering the various parameters of the target sequence and the construct design. In this review, we provide a comprehensive treatise regarding past, present and future prospective developments toward designing and applying RNAi constructs for resistance to plant viruses.
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Affiliation(s)
- Masoud Akbarimotlagh
- Plant Pathology Department, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran, Iran
| | - Abdolbaset Azizi
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran.
| | - Masoud Shams-Bakhsh
- Plant Pathology Department, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran, Iran
| | - Majid Jafari
- Department of Plant Protection, Higher Education Complex of Saravan, Saravan, Iran
| | - Aysan Ghasemzadeh
- Plant Pathology Department, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran, Iran
| | - Peter Palukaitis
- Department of Horticulture Sciences, Seoul Women's University, Seoul, Republic of Korea.
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6
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Zhang X, Hooykaas MJG, van Heusden GP, Hooykaas PJJ. The translocated virulence protein VirD5 causes DNA damage and mutation during Agrobacterium-mediated transformation of yeast. SCIENCE ADVANCES 2022; 8:eadd3912. [PMID: 36383666 PMCID: PMC9668295 DOI: 10.1126/sciadv.add3912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
The soil bacterium Agrobacterium tumefaciens is a preferred gene vector not only for plants but also for fungi. Agrobacterium delivers a small set of virulence proteins into host cells concomitantly with transferred DNA (T-DNA) to support the transformation process. Here, we find that expression of one of these proteins, called VirD5, in yeast host cells causes replication stress and DNA damage. This can result in both genomic rearrangements and local mutations, especially small deletions. Delivery of VirD5 during cocultivation with Agrobacterium led to mutations in the yeast genome that were unlinked to the integration of T-DNA. This load of mutations can be prevented by using a virD5 mutant for genome engineering, but this leads to a lower transformation frequency.
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Tiwari M, Mishra AK, Chakrabarty D. Agrobacterium-mediated gene transfer: recent advancements and layered immunity in plants. PLANTA 2022; 256:37. [PMID: 35819629 PMCID: PMC9274631 DOI: 10.1007/s00425-022-03951-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/19/2022] [Indexed: 05/15/2023]
Abstract
Plant responds to Agrobacterium via three-layered immunity that determines its susceptibility or resistance to Agrobacterium infection. Agrobacterium tumefaciens is a soil-borne Gram-negative bacterium that causes crown gall disease in plants. The remarkable feat of interkingdom gene transfer has been extensively utilised in plant biotechnology to transform plant as well as non-host systems. In the past two decades, the molecular mode of the pathogenesis of A. tumefaciens has been extensively studied. Agrobacterium has also been utilised as a premier model to understand the defence response of plants during plant-Agrobacterium interaction. Nonetheless, the threat of Agrobacterium-mediated crown gall disease persists and is associated with a huge loss of plant vigour in agriculture. Understanding the molecular dialogues between these two interkingdom species might provide a cure for crown gall disease. Plants respond to A. tumefaciens by mounting a three-layered immune response, which is manipulated by Agrobacterium via its virulence effector proteins. Comparative studies on plant defence proteins versus the counter-defence of Agrobacterium have shed light on plant susceptibility and tolerance. It is possible to manipulate a plant's immune system to overcome the crown gall disease and increase its competence via A. tumefaciens-mediated transformation. This review summarises the recent advances in the molecular mode of Agrobacterium pathogenesis as well as the three-layered immune response of plants against Agrobacterium infection.
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Affiliation(s)
- Madhu Tiwari
- Biotechnology and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005, India
| | - Arun Kumar Mishra
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005, India
| | - Debasis Chakrabarty
- Biotechnology and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Agrobacterium expressing a type III secretion system delivers Pseudomonas effectors into plant cells to enhance transformation. Nat Commun 2022; 13:2581. [PMID: 35546550 PMCID: PMC9095702 DOI: 10.1038/s41467-022-30180-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/20/2022] [Indexed: 01/07/2023] Open
Abstract
Agrobacterium-mediated plant transformation (AMT) is the basis of modern-day plant biotechnology. One major drawback of this technology is the recalcitrance of many plant species/varieties to Agrobacterium infection, most likely caused by elicitation of plant defense responses. Here, we develop a strategy to increase AMT by engineering Agrobacterium tumefaciens to express a type III secretion system (T3SS) from Pseudomonas syringae and individually deliver the P. syringae effectors AvrPto, AvrPtoB, or HopAO1 to suppress host defense responses. Using the engineered Agrobacterium, we demonstrate increase in AMT of wheat, alfalfa and switchgrass by ~250%–400%. We also show that engineered A. tumefaciens expressing a T3SS can deliver a plant protein, histone H2A-1, to enhance AMT. This strategy is of great significance to both basic research and agricultural biotechnology for transient and stable transformation of recalcitrant plant species/varieties and to deliver proteins into plant cells in a non-transgenic manner. Agrobacterium infection can cause defense responses in many plants, which leads to transformation recalcitrance. Here, the authors express type III secretion system in Agrobacterium to deliver effector proteins into plant cells to suppress host defense responses and thus enhance transformation in some plant species.
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Singer K, Lee LY, Yuan J, Gelvin SB. Characterization of T-Circles and Their Formation Reveal Similarities to Agrobacterium T-DNA Integration Patterns. FRONTIERS IN PLANT SCIENCE 2022; 13:849930. [PMID: 35599900 PMCID: PMC9121065 DOI: 10.3389/fpls.2022.849930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/29/2022] [Indexed: 06/15/2023]
Abstract
Agrobacterium transfers T-DNA to plants where it may integrate into the genome. Non-homologous end-joining (NHEJ) has been invoked as the mechanism of T-DNA integration, but the role of various NHEJ proteins remains controversial. Genetic evidence for the role of NHEJ in T-DNA integration has yielded conflicting results. We propose to investigate the formation of T-circles as a proxy for understanding T-DNA integration. T-circles are circular double-strand T-DNA molecules, joined at their left (LB) and right (RB) border regions, formed in plants. We characterized LB-RB junction regions from hundreds of T-circles formed in Nicotiana benthamiana or Arabidopsis thaliana. These junctions resembled T-DNA/plant DNA junctions found in integrated T-DNA: Among complex T-circles composed of multiple T-DNA molecules, RB-RB/LB-LB junctions predominated over RB-LB junctions; deletions at the LB were more frequent and extensive than those at the RB; microhomology was frequently used at junction sites; and filler DNA, from the plant genome or various Agrobacterium replicons, was often present between the borders. Ku80 was not required for efficient T-circle formation, and a VirD2 ω mutation affected T-circle formation and T-DNA integration similarly. We suggest that investigating the formation of T-circles may serve as a surrogate for understanding T-DNA integration.
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DNA Double-Strand Break Repairs and Their Application in Plant DNA Integration. Genes (Basel) 2022; 13:genes13020322. [PMID: 35205367 PMCID: PMC8871565 DOI: 10.3390/genes13020322] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/07/2022] [Accepted: 02/07/2022] [Indexed: 01/25/2023] Open
Abstract
Double-strand breaks (DSBs) are considered to be one of the most harmful and mutagenic forms of DNA damage. They are highly toxic if unrepaired, and can cause genome rearrangements and even cell death. Cells employ two major pathways to repair DSBs: homologous recombination (HR) and non-homologous end-joining (NHEJ). In plants, most applications of genome modification techniques depend on the development of DSB repair pathways, such as Agrobacterium-mediated transformation (AMT) and gene targeting (GT). In this paper, we review the achieved knowledge and recent advances on the DNA DSB response and its main repair pathways; discuss how these pathways affect Agrobacterium-mediated T-DNA integration and gene targeting in plants; and describe promising strategies for producing DSBs artificially, at definite sites in the genome.
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Rehman F, Gong H, Bao Y, Zeng S, Huang H, Wang Y. CRISPR gene editing of major domestication traits accelerating breeding for Solanaceae crops improvement. PLANT MOLECULAR BIOLOGY 2022; 108:157-173. [PMID: 35032250 DOI: 10.1007/s11103-021-01229-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Domestication traits particularly fruit size and plant architecture and flowering are critical in transforming a progenitor's wild stature into a super improved plant. The latest advancements in the CRISPR system, as well as its rapid adoption, are speeding up plant breeding. Solanaceae has a varied range of important crops, with a few model crops, such as tomato and, more recently, groundcherry, serving as a foundation for developing molecular techniques, genome editing tools, and establishing standards for other crops. Domestication traits in agricultural plants are quantified and widely adopted under modern plant breeding to improve small-fruited and bushy crop species like goji berry. The molecular mechanisms of the FW2.2, FW3.2, FW11.3, FAS/CLV3, LC/WUS, SP, SP5G, and CRISPR genome editing technology have been described in detail here. Furthermore, special focus has been placed on CRISPR gene editing achievements for revolutionizing Solanaceae breeding and changing the overall crop landscape. This review seeks to provide a thorough overview of the CRISPR technique's ongoing advancements, particularly in Solanaceae, in terms of domesticated features, future prospects, and regulatory risks. We believe that this vigorous discussion will lead to a broader understanding of CRISPR gene editing as a tool for achieving key breeding goals in other Solanaceae minor crops with significant industrial value.
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Affiliation(s)
- Fazal Rehman
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Haiguang Gong
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yufei Bao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shaohua Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- GNNU-SCBG Joint Laboratory of Modern Agricultural Technology, College of Life Sciences, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Hongwen Huang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- GNNU-SCBG Joint Laboratory of Modern Agricultural Technology, College of Life Sciences, Gannan Normal University, Ganzhou, 341000, Jiangxi, China.
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.
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12
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Dey A, Nandy S. CRISPER/Cas in Plant Natural Product Research: Therapeutics as Anticancer and other Drug Candidates and Recent Patents. Recent Pat Anticancer Drug Discov 2021; 16:460-468. [PMID: 34911411 DOI: 10.2174/1574892816666210706155602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/02/2021] [Accepted: 02/15/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR- associated9 (Cas9) endonuclease system is a facile, highly efficient and selective site-directed mutagenesis tool for RNA-guided genome-editing. CRISPR/Cas9 genome-editing strategy uses designed guide-RNAs that recognizes a 3 base-pair protospacer adjacent motif (PAM) sequence in the target-DNA. CRISPR/Cas-editing tools have mainly been employed in crop plants in relation to yield and stress tolerance. However, the immense potential of this technology has not yet been fully utilized in medicinal plants in deciphering or modulating secondary metabolic pathways producing therapeutically active phytochemicals against cancer and other diseases. OBJECTIVE The present review elucidates the use of CRISPR-Cas9 as a promising genome-editing tool in plants and plant-derived natural products with anticancer and other therapeutic applications. It also includes recent patents on the therapeutic applications of CRISPR-CAS systems implicated to cancer and other human medical conditions. METHODS Popular search engines, such as PubMed, Scopus, Google Scholar, Google Patents, Medline, ScienceDirect, SpringerLink, EMBASE, Mendeley, etc., were searched in order to retrieve literature using relevant keywords viz. CRISPER/Cas, plant natural product research, anticancer, therapeutics, etc., either singly or in various combinations. RESULTS Retrieved citations and further cross-referencing among the literature have resulted in a total number of 71 publications and 3 patents are being cited in this work. Information presented in this review aims to support further biotechnological and clinical strategies to be carried using CRISPER/ Cas mediated optimization of plant natural products against cancer and an array of other human medical conditions. CONCLUSION Off late, knock-in and knock-out, point mutation, controlled tuning of gene-expression and targeted mutagenesis have enabled the versatile CRISPR/Cas-editing device to engineer medicinal plants' genomes. In addition, by combining CRISPR/Cas-editing tool with next-generation sequencing (NGS) and various tools of system biology, many medicinal plants have been engineered genetically to optimize the production of valuable bioactive compounds of industrial significance.
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Affiliation(s)
- Abhijit Dey
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, India
| | - Samapika Nandy
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, India
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Iwakawa H, Melkonian K, Schlüter T, Jeon HW, Nishihama R, Motose H, Nakagami H. Agrobacterium-Mediated Transient Transformation of Marchantia Liverworts. PLANT & CELL PHYSIOLOGY 2021; 62:1718-1727. [PMID: 34383076 DOI: 10.1093/pcp/pcab126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
Agrobacterium-mediated transient gene expression is a rapid and useful approach for characterizing functions of gene products in planta. However, the practicability of the method in the model liverwort Marchantia polymorpha has not yet been thoroughly described. Here we report a simple and robust method for Agrobacterium-mediated transient transformation of Marchantia thalli and its applicability. When thalli of M. polymorpha were co-cultured with Agrobacterium tumefaciens carrying β-glucuronidase (GUS) genes, GUS staining was observed primarily in assimilatory filaments and rhizoids. GUS activity was detected 2 days after infection and saturated 3 days after infection. We were able to transiently co-express fluorescently tagged proteins with proper localizations. Furthermore, we demonstrate that our method can be used as a novel pathosystem to study liverwort-bacteria interactions. We also provide evidence that air chambers support bacterial colonization.
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Affiliation(s)
- Hidekazu Iwakawa
- Basic Immune System of Plants, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne 50829, Germany
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Katharina Melkonian
- Basic Immune System of Plants, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne 50829, Germany
| | - Titus Schlüter
- Basic Immune System of Plants, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne 50829, Germany
| | - Hyung-Woo Jeon
- Basic Immune System of Plants, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne 50829, Germany
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Hiroyasu Motose
- Division of Bioscience, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushimanaka, Okayama 700-8530, Japan
| | - Hirofumi Nakagami
- Basic Immune System of Plants, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne 50829, Germany
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Li Y, Guo G, Xu H, He T, Zong Y, Zhang S, Faheem M, Lu R, Zhou L, Liu C. Comparative transcriptome analysis reveals compatible and recalcitrant genotypic response of barley microspore-derived embryogenic callus toward Agrobacterium infection. BMC PLANT BIOLOGY 2021; 21:579. [PMID: 34876002 PMCID: PMC8650547 DOI: 10.1186/s12870-021-03346-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/15/2021] [Indexed: 05/16/2023]
Abstract
BACKGROUND The Agrobacterium mediated transformation has been routinely used in lots of plant species as a powerful tool to deliver genes of interest into a host plant. However, the transformation of elite and commercially valuable cultivar is still limited by the genotype-dependency, and the efficiency of Agrobacterium infection efficiency is crucial for the success of transformation. RESULTS In this study, the microspore-derived embryogenic calli (MDEC) of barley elite cultivars and breeding lines were employed as unique subjects to characterize the genotypic response during Agrobacterium infection process. Our results identified compatible barley genotypes (GanPi 6 and L07, assigned as GP6-L07 group) and one recalcitrant genotype (Hong 99, assigned as H99) for the Agrobacterium strain LBA4404 infection using GUS assay. The accumulation trend of reactive oxygen species (ROS) was similar among genotypes across the time course. The results of RNA-seq depicted that the average expressional intensity of whole genomic genes was similar among barley genotypes during Agrobacterium infection. However, the numbers of differentially expressed genes (DEGs) exhibited significant expressional variation between GP6-L07 and H99 groups from 6 to 12 h post-inoculation (hpi). Gene ontology (GO) enrichment analysis revealed different regulation patterns for the predicted biological processes between the early (up-regulated DEGs overrepresented at 2 hpi) and late stages (down-regulated DEGs overrepresented from 6 to 24 hpi) of infection. KEGG analysis predicted 12 pathways during Agrobacterium infection. Among which one pathway related to pyruvate metabolism was enriched in GP6 and L07 at 6 hpi. Two pathways related to plant hormone signal transduction and DNA replication showed expressional variation between GP6-L07 and H99 at 24 hpi. It was further validated by qRT-PCR assay for seven candidate genes (Aldehyde dehydrogenase, SAUR, SAUR50, ARG7, Replication protein A, DNA helicase and DNA replication licensing factor) involved in the three pathways, which are all up-regulated in compatible while down-regulated in recalcitrant genotypes, suggesting the potential compatibility achieved at later stage for the growth of Agrobacterium infected cells. CONCLUSIONS Our findings demonstrated the similarity and difference between compatible and recalcitrant genotypes of barley MDEC upon Agrobacterium infection. Seven candidate genes involved in pyruvate metabolism, hormonal signal transduction and DNA replication were identified, which advocates the genotypic dependency during Agrobacterium infection process.
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Affiliation(s)
- Yingbo Li
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China
| | - Guimei Guo
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China
| | - Hongwei Xu
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China
| | - Ting He
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China
| | - Yingjie Zong
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China
| | - Shuwei Zhang
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China
| | | | - Ruiju Lu
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China
| | - Longhua Zhou
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China.
| | - Chenghong Liu
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China.
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Kaur M, Manchanda P, Kalia A, Ahmed FK, Nepovimova E, Kuca K, Abd-Elsalam KA. Agroinfiltration Mediated Scalable Transient Gene Expression in Genome Edited Crop Plants. Int J Mol Sci 2021; 22:10882. [PMID: 34639221 PMCID: PMC8509792 DOI: 10.3390/ijms221910882] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/23/2021] [Accepted: 10/03/2021] [Indexed: 02/07/2023] Open
Abstract
Agrobacterium-mediated transformation is one of the most commonly used genetic transformation method that involves transfer of foreign genes into target plants. Agroinfiltration, an Agrobacterium-based transient approach and the breakthrough discovery of CRISPR/Cas9 holds trending stature to perform targeted and efficient genome editing (GE). The predominant feature of agroinfiltration is the abolishment of Transfer-DNA (T-DNA) integration event to ensure fewer biosafety and regulatory issues besides showcasing the capability to perform transcription and translation efficiently, hence providing a large picture through pilot-scale experiment via transient approach. The direct delivery of recombinant agrobacteria through this approach carrying CRISPR/Cas cassette to knockout the expression of the target gene in the intercellular tissue spaces by physical or vacuum infiltration can simplify the targeted site modification. This review aims to provide information on Agrobacterium-mediated transformation and implementation of agroinfiltration with GE to widen the horizon of targeted genome editing before a stable genome editing approach. This will ease the screening of numerous functions of genes in different plant species with wider applicability in future.
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Affiliation(s)
- Maninder Kaur
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, Punjab 141004, India;
| | - Pooja Manchanda
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, Punjab 141004, India;
| | - Anu Kalia
- Electron Microscopy and Nanoscience Laboratory, Department of Soil Science, College of Agriculture, Punjab Agricultural University, Ludhiana, Punjab 141004, India;
| | - Farah K. Ahmed
- Biotechnology English Program, Faculty of Agriculture, Cairo University, Giza 12613, Egypt;
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003 Hradec Kralove, Czech Republic;
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003 Hradec Kralove, Czech Republic;
- Biomedical Research Center, University Hospital Hradec Kralove, 50005 Hradec Kralove, Czech Republic
| | - Kamel A. Abd-Elsalam
- Plant Pathology Research Institute, Agricultural Research Center (ARC), 9-Gamaa St., Giza 12619, Egypt;
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Elakhdar A, Fukuda M, Kubo T. Agrobacterium-mediated Transformation of Japonica Rice Using Mature Embryos and Regenerated Transgenic Plants. Bio Protoc 2021; 11:e4143. [PMID: 34692903 DOI: 10.21769/bioprotoc.4143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/11/2021] [Accepted: 05/16/2021] [Indexed: 11/02/2022] Open
Abstract
Identification of novel genes and their functions in rice is a critical step to improve economic traits. Agrobacterium tumefaciens-mediated transformation is a proven method in many laboratories and widely adopted for genetic engineering in rice. However, the efficiency of gene transfer by Agrobacterium in rice is low, particularly among japonica and indica varieties. In this protocol, we elucidate a rapid and highly efficient protocol to transform and regenerate transgenic rice plants through important key features of Agrobacterium transformation and standard regeneration media, especially enhancing culture conditions, timing, and growth hormones. With this protocol, transformed plantlets from the embryogenetic callus of the japonica cultivar 'Taichung 65' may be obtained within 90 days. This protocol may be used with other japonica rice varieties.
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Affiliation(s)
- Ammar Elakhdar
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan.,Field Crops Research Institute, Agricultural Research Center, Giza 12619, Egypt
| | - Masako Fukuda
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan
| | - Takahiko Kubo
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan
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17
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Rao MJ, Wang L. CRISPR/Cas9 technology for improving agronomic traits and future prospective in agriculture. PLANTA 2021; 254:68. [PMID: 34498163 DOI: 10.1007/s00425-021-03716-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
In this review, we have focused on the CRISPR/Cas9 technology for improving the agronomic traits in plants through point mutations, knockout, and single base editing, and we highlighted the recent progress in plant metabolic engineering. CRISPR/Cas9 technology has immense power to reproduce plants with desired characters and revolutionizing the field of genome engineering by erasing the barriers in targeted genome editing. Agriculture fields are using this advance genome editing tool to get the desired traits in the crops plants such as increase yield, improve product quality attributes, and enhance resistance against biotic and abiotic stresses by identifying and editing genes of interest. This review focuses on CRISPR/Cas-based gene knockout for trait improvement and single base editing to boost yield, quality, stress tolerance, and disease resistance traits in crops. Use of CRISPR/Cas9 system to facilitate crop domestication and hybrid breeding are also touched. We summarize recent developments and up-gradation of delivery mechanism (nanotechnology and virus particle-based delivery system) and progress in multiplex gene editing. We also shed lights in advances and challenges of engineering the important metabolic pathways that contain a variety of dietary metabolites and phytochemicals. In addition, we endorsed substantial technical hurdles and possible ways to overcome the unpredictability of CRISPR/Cas technology for broader application across various crop species. We speculated that by making a strong interconnection among all genomic fields will give a gigantic bunt of knowledge to develop crop expressing desired traits.
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Affiliation(s)
- Muhammad Junaid Rao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, Guangxi, 530004, People's Republic of China
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, 100 Daxue Rd., 8, Nanning, Guangxi, 530004, People's Republic of China
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Ministry of Agriculture), Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Lingqiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, Guangxi, 530004, People's Republic of China.
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, 100 Daxue Rd., 8, Nanning, Guangxi, 530004, People's Republic of China.
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Matsuoka A, Maliga P. Prospects for Reengineering Agrobacterium tumefaciens for T-DNA Delivery to Chloroplasts. PLANT PHYSIOLOGY 2021; 186:215-220. [PMID: 33620481 PMCID: PMC8154051 DOI: 10.1093/plphys/kiab081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 02/02/2021] [Indexed: 06/12/2023]
Abstract
Targeting the phiC31 phage integrase for direct export from Agrobacterium to chloroplasts reveals the feasibility of retargeting the Agrobacterium Vir proteins for T-DNA delivery to chloroplasts.
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Affiliation(s)
- Aki Matsuoka
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854, USA
| | - Pal Maliga
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854, USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA
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Ramos-Vega A, Monreal-Escalante E, Dumonteil E, Bañuelos-Hernández B, Angulo C. Plant-made vaccines against parasites: bioinspired perspectives to fight against Chagas disease. Expert Rev Vaccines 2021; 20:1373-1388. [PMID: 33612044 DOI: 10.1080/14760584.2021.1893170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Introduction: Three decades of evidence have demonstrated that plants are an affordable platform for biopharmaceutical production and delivery. For instance, several plant-made recombinant proteins have been approved for commercialization under good manufacturing practice (GMP). Thus far, plant-based vaccine prototypes have been evaluated at pre- and clinical levels. Particularly, plant-made vaccines against parasitic diseases, such as malaria, cysticercosis, and toxoplasmosis have been successfully produced and orally delivered with promising outcomes in terms of immunogenicity and protection. The experience on several approaches and technical strategies over 30 years accounts for their potential low-cost, high scalability, and easy administration.Areas covered: This platform is an open technology to fight against Chagas disease, one of the most important neglected tropical diseases worldwide.Expert opinion: This review provides a perspective for the potential use of plants as a production platform and delivery system of Trypanosoma cruzi recombinant antigens, analyzing the advantages and limitations with respect to plant-made vaccines produced for other parasitic diseases. Plant-made vaccines are envisioned to fight against Chagas disease and other neglected tropical diseases in those countries suffering endemic prevalence.
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Affiliation(s)
- Abel Ramos-Vega
- Grupo de Inmunología & Vacunología. Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR), Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz, B.c.s. C.p., México
| | - Elizabeth Monreal-Escalante
- Grupo de Inmunología & Vacunología. Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR), Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz, B.c.s. C.p., México.,CONACYT- Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR), Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz, B.c.s. C.p, México
| | - Eric Dumonteil
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, and Vector-Borne and Infectious Disease Research Center, Tulane University, New Orleans, LA, USA
| | - Bernardo Bañuelos-Hernández
- Facultad de Agronomía Y Veterinaria, Universidad de La Salle Bajio, Avenida Universidad 602, Lomas del Campestre, León Guanajuato, México
| | - Carlos Angulo
- Grupo de Inmunología & Vacunología. Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR), Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz, B.c.s. C.p., México
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20
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Nishizawa-Yokoi A, Saika H, Hara N, Lee LY, Toki S, Gelvin SB. Agrobacterium T-DNA integration in somatic cells does not require the activity of DNA polymerase θ. THE NEW PHYTOLOGIST 2021; 229:2859-2872. [PMID: 33105034 DOI: 10.1111/nph.17032] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Integration of Agrobacterium tumefaciens transferred DNA (T-DNA) into the plant genome is the last step required for stable plant genetic transformation. The mechanism of T-DNA integration remains controversial, although scientists have proposed the participation of various nonhomologous end-joining (NHEJ) pathways. Recent evidence suggests that in Arabidopsis, DNA polymerase θ (PolQ) may be a crucial enzyme involved in T-DNA integration. We conducted quantitative transformation assays of wild-type and polQ mutant Arabidopsis and rice, analyzed T-DNA/plant DNA junction sequences, and (for Arabidopsis) measured the amount of integrated T-DNA in mutant and wild-type tissue. Unexpectedly, we were able to generate stable transformants of all tested lines, although the transformation frequency of polQ mutants was c. 20% that of wild-type plants. T-DNA/plant DNA junctions from these transformed rice and Arabidopsis polQ mutants closely resembled those from wild-type plants, indicating that loss of PolQ activity does not alter the characteristics of T-DNA integration events. polQ mutant plants show growth and developmental defects, perhaps explaining previous unsuccessful attempts at their stable transformation. We suggest that either multiple redundant pathways function in T-DNA integration, and/or that integration requires some yet unknown pathway.
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Affiliation(s)
- Ayako Nishizawa-Yokoi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, 305-8634, Japan
- Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Hiroaki Saika
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, 305-8634, Japan
| | - Naho Hara
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, 305-8634, Japan
| | - Lan-Ying Lee
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907-1392, USA
| | - Seiichi Toki
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, 305-8634, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12, Maioka-cho, Yokohama, 244-0813, Japan
| | - Stanton B Gelvin
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907-1392, USA
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21
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Dey A. CRISPR/Cas genome editing to optimize pharmacologically active plant natural products. Pharmacol Res 2020; 164:105359. [PMID: 33285226 DOI: 10.1016/j.phrs.2020.105359] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/15/2020] [Accepted: 11/30/2020] [Indexed: 12/26/2022]
Abstract
Since time immemorial, human use medicinal plants as sources of food, therapy and industrial purpose. Classical biotechnology and recent next-generation sequencing (NGS) techniques have been successfully used to optimize plant-derived natural-products of biomedical significance. Earlier, protein based editing tools viz. zinc-finger nucleases (ZFNs) and transcription activator-like endonucleases (TALENs) have been popularized for transcriptional level genome manipulation. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated9 (Cas9) endonuclease system is an efficient, robust and selective site-directed mutagenesis strategy for RNA-guided genome-editing. CRISPR/Cas9 genome-editing tool employs designed guide-RNAs that identifies a 3 base-pair protospacer adjacent motif (PAM) sequence occurring downstream of the target-DNA. The present review comprehensively complies the recent literature (2010-2020) retrieved from scientific-databases on the application of CRISPR/Cas9-editing-tools as potent genome-editing strategies in medicinal-plants discussing the recent developments, challenges and future-perspectives with notes on broader applicability of the technique in plants and lower-organisms. In plants, CRISPR/Cas-editing has been implemented successfully in relation to crop-yield and stress-tolerance. However, very few medicinal plants have been edited using CRISPR/Cas genome tool owing to the lack of whole-genome and mRNA-sequences and shortfall of suitable transformation and regeneration strategies. However, recently a number of plant secondary metabolic-pathways (viz. alkaloid, terpenoid, flavonoids, phenolic, saponin etc.) have been engineered employing CRISPR/Cas-editing via knock-out, knock-in, point-mutation, fine-tuning of gene-expression and targeted-mutagenesis. This genome-editing tool further extends its applicability incorporating the tools of synthetic- and systems-biology, functional-genomics and NGS to produce genetically-engineered medicinal-crops with advanced-traits facilitating the production of pharmaceuticals and nutraceuticals.
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Affiliation(s)
- Abhijit Dey
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, India.
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F-Box Gene D5RF Is Regulated by Agrobacterium Virulence Protein VirD5 and Essential for Agrobacterium-Mediated Plant Transformation. Int J Mol Sci 2020; 21:ijms21186731. [PMID: 32937889 PMCID: PMC7555846 DOI: 10.3390/ijms21186731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/10/2020] [Accepted: 09/12/2020] [Indexed: 11/16/2022] Open
Abstract
We previously reported that the Agrobacterium virulence protein VirD5 possesses transcriptional activation activity, binds to a specific DNA element D5RE, and is required for Agrobacterium-mediated stable transformation, but not for transient transformation. However, direct evidence for a role of VirD5 in plant transcriptional regulation has been lacking. In this study, we found that the Arabidopsis gene D5RF (coding for VirD5 response F-box protein, At3G49480) is regulated by VirD5. D5RF has two alternative transcripts of 930 bp and 1594 bp that encode F-box proteins of 309 and 449 amino acids, designated as D5RF.1 and D5RF.2, respectively. D5RF.2 has a N-terminal extension of 140 amino acids compared to D5RF.1, and both of them are located in the plant cell nucleus. The promoter of the D5RF.1 contains two D5RE elements and can be activated by VirD5. The expression of D5RF is downregulated when the host plant is infected with virD5 deleted Agrobacterium. Similar to VirD5, D5RF also affects the stable but not transient transformation efficiency of Agrobacterium. Some pathogen-responsive genes are downregulated in the d5rf mutant. In conclusion, this study further confirmed Agrobacterium VirD5 as the plant transcription activator and identified Arabidopsis thalianaD5RF.1 as the first target gene of VirD5 in regulation.
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Basso MF, Arraes FBM, Grossi-de-Sa M, Moreira VJV, Alves-Ferreira M, Grossi-de-Sa MF. Insights Into Genetic and Molecular Elements for Transgenic Crop Development. FRONTIERS IN PLANT SCIENCE 2020; 11:509. [PMID: 32499796 PMCID: PMC7243915 DOI: 10.3389/fpls.2020.00509] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 04/03/2020] [Indexed: 05/21/2023]
Abstract
Climate change and the exploration of new areas of cultivation have impacted the yields of several economically important crops worldwide. Both conventional plant breeding based on planned crosses between parents with specific traits and genetic engineering to develop new biotechnological tools (NBTs) have allowed the development of elite cultivars with new features of agronomic interest. The use of these NBTs in the search for agricultural solutions has gained prominence in recent years due to their rapid generation of elite cultivars that meet the needs of crop producers, and the efficiency of these NBTs is closely related to the optimization or best use of their elements. Currently, several genetic engineering techniques are used in synthetic biotechnology to successfully improve desirable traits or remove undesirable traits in crops. However, the features, drawbacks, and advantages of each technique are still not well understood, and thus, these methods have not been fully exploited. Here, we provide a brief overview of the plant genetic engineering platforms that have been used for proof of concept and agronomic trait improvement, review the major elements and processes of synthetic biotechnology, and, finally, present the major NBTs used to improve agronomic traits in socioeconomically important crops.
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Affiliation(s)
| | - Fabrício Barbosa Monteiro Arraes
- Plant Biotechnology, Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
- Department of Molecular Biology and Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Maíra Grossi-de-Sa
- Plant Biotechnology, Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - Valdeir Junio Vaz Moreira
- Plant Biotechnology, Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
- Department of Molecular Biology and Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Maria Fatima Grossi-de-Sa
- Plant Biotechnology, Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
- Department of Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília, Brazil
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Li X, Zhu T, Tu H, Pan SQ. Agrobacterium VirE3 Uses Its Two Tandem Domains at the C-Terminus to Retain Its Companion VirE2 on the Cytoplasmic Side of the Host Plasma Membrane. FRONTIERS IN PLANT SCIENCE 2020; 11:464. [PMID: 32373148 PMCID: PMC7187210 DOI: 10.3389/fpls.2020.00464] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 03/30/2020] [Indexed: 05/30/2023]
Abstract
Agrobacterium tumefaciens is the causal agent of crown gall disease in nature; in the laboratory the bacterium is widely used for plant genetic modification. The bacterium delivers a single-stranded transferred DNA (T-DNA) and a group of crucial virulence proteins into host cells. A putative T-complex is formed inside host cells that is composed of T-DNA and virulence proteins VirD2 and VirE2, which protect the foreign DNA from degradation and guide its way into the host nucleus. However, little is known about how the T-complex is assembled inside host cells. We combined the split-GFP and split-sfCherry labeling systems to study the interaction of Agrobacterium-delivered VirE2 and VirE3 in host cells. Our results indicated that VirE2 co-localized with VirE3 on the cytoplasmic side of the host cellular membrane upon the delivery. We identified and characterized two tandem domains at the VirE3 C-terminus that interacted with VirE2 in vitro. Deletion of these two domains abolished the VirE2 accumulation on the host plasma membrane and affected the transformation. Furthermore, the two VirE2-interacting domains of VirE3 exhibited different affinities with VirE2. Collectively, this study demonstrates that the anchorage protein VirE3 uses the two tandem VirE2-interacting domains to facilitate VirE2 protection for T-DNA at the cytoplasmic side of the host cell entrance.
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Affiliation(s)
- Xiaoyang Li
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Tingting Zhu
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Haitao Tu
- School of Stomatology and Medicine, Foshan Institute of Molecular Bio-Engineering, Foshan University, Foshan, China
| | - Shen Q. Pan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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Harris MO, Pitzschke A. Plants make galls to accommodate foreigners: some are friends, most are foes. THE NEW PHYTOLOGIST 2020; 225:1852-1872. [PMID: 31774564 DOI: 10.1111/nph.16340] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 07/24/2019] [Indexed: 06/10/2023]
Abstract
At the colonization site of a foreign entity, plant cells alter their trajectory of growth and development. The resulting structure - a plant gall - accommodates various needs of the foreigner, which are phylogenetically diverse: viruses, bacteria, protozoa, oomycetes, true fungi, parasitic plants, and many types of animals, including rotifers, nematodes, insects, and mites. The plant species that make galls also are diverse. We assume gall production costs the plant. All is well if the foreigner provides a gift that makes up for the cost. Nitrogen-fixing nodule-inducing bacteria provide nutritional services. Gall wasps pollinate fig trees. Unfortunately for plants, most galls are made for foes, some of which are deeply studied pathogens and pests: Agrobacterium tumefaciens, Rhodococcus fascians, Xanthomonas citri, Pseudomonas savastanoi, Pantoea agglomerans, 'Candidatus' phytoplasma, rust fungi, Ustilago smuts, root knot and cyst nematodes, and gall midges. Galls are an understudied phenomenon in plant developmental biology. We propose gall inception for discovering unifying features of the galls that plants make for friends and foes, talk about molecules that plants and gall-inducers use to get what they want from each other, raise the question of whether plants colonized by arbuscular mycorrhizal fungi respond in a gall-like manner, and present a research agenda.
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Affiliation(s)
- Marion O Harris
- Department of Entomology, North Dakota State University, Fargo, ND, 58014, USA
| | - Andrea Pitzschke
- Department of Biosciences, Salzburg University, Hellbrunner Strasse 34, A-5020, Salzburg, Austria
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Shanmugaraj B, Rattanapisit K, Manopwisedjaroen S, Thitithanyanont A, Phoolcharoen W. Monoclonal Antibodies B38 and H4 Produced in Nicotiana benthamiana Neutralize SARS-CoV-2 in vitro. FRONTIERS IN PLANT SCIENCE 2020; 11:589995. [PMID: 33329653 PMCID: PMC7728718 DOI: 10.3389/fpls.2020.589995] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/28/2020] [Indexed: 05/20/2023]
Abstract
The ongoing coronavirus disease 2019 (COVID-19) outbreak caused by novel zoonotic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was initially reported in Wuhan city, Hubei Province of China, in late December 2019. The rapid global spread of the virus calls for the urgent development of vaccines or therapeutics for human applications to combat the coronavirus infection. Monoclonal antibodies (mAbs) have been utilized as effective therapeutics for treating various infectious diseases. In the present study, we evaluated the feasibility of plant expression system for the rapid production of recently identified therapeutically suitable human anti-SARS-CoV-2 mAbs B38 and H4. Transient co-expression of heavy-chain and light-chain sequences of both the antibodies by using plant expression geminiviral vector resulted in rapid accumulation of assembled mAbs in Nicotiana benthamiana leaves within 4 days post-infiltration. Furthermore, both the mAbs were purified from the plant crude extracts with single-step protein A affinity column chromatography. The expression level of mAb B38 and H4 was estimated to be 4 and 35 μg/g leaf fresh weight, respectively. Both plant-produced mAbs demonstrated specific binding to receptor binding domain (RBD) of SARS-CoV-2 and exhibited efficient virus neutralization activity in vitro. To the best of our knowledge, this is the first report of functional anti-SARS-CoV-2 mAbs produced in plants, which demonstrates the ability of using a plant expression system as a suitable platform for the production of effective, safe, and affordable SARS-CoV-2 mAbs to fight against the spread of this highly infectious pathogen.
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Affiliation(s)
- Balamurugan Shanmugaraj
- Research Unit for Plant-produced Pharmaceuticals, Chulalongkorn University, Bangkok, Thailand
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Kaewta Rattanapisit
- Research Unit for Plant-produced Pharmaceuticals, Chulalongkorn University, Bangkok, Thailand
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | | | | | - Waranyoo Phoolcharoen
- Research Unit for Plant-produced Pharmaceuticals, Chulalongkorn University, Bangkok, Thailand
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
- *Correspondence: Waranyoo Phoolcharoen,
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Abd-El-Khair H. Biological Control of Phyto-pathogenic Bacteria. COTTAGE INDUSTRY OF BIOCONTROL AGENTS AND THEIR APPLICATIONS 2020:299-336. [DOI: 10.1007/978-3-030-33161-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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28
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Han R, Gu C, Li R, Xu W, Wang S, Liu C, Qu C, Chen S, Liu G, Yu Q, Jiang J, Li H. Characterization and T-DNA insertion sites identification of a multiple-branches mutant br in Betula platyphylla × Betula pendula. BMC PLANT BIOLOGY 2019; 19:491. [PMID: 31718548 PMCID: PMC6852751 DOI: 10.1186/s12870-019-2098-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 10/23/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND Plant architecture, which is mostly determined by shoot branching, plays an important role in plant growth and development. Thus, it is essential to explore the regulatory molecular mechanism of branching patterns based on the economic and ecological importance. In our previous work, a multiple-branches birch mutant br was identified from 19 CINNAMOYL-COENZYME A REDUCTASE 1 (CCR1)-overexpressed transgenic lines, and the expression patterns of differentially expressed genes in br were analyzed. In this study, we further explored some other characteristics of br, including plant architecture, wood properties, photosynthetic characteristics, and IAA and Zeatin contents. Meanwhile, the T-DNA insertion sites caused by the insertion of exogenous BpCCR1 in br were identified to explain the causes of the mutation phenotypes. RESULTS The mutant br exhibited slower growth, more abundant and weaker branches, and lower wood basic density and lignin content than BpCCR1 transgenic line (OE2) and wild type (WT). Compared to WT and OE2, br had high stomatal conductance (Gs), transpiration rate (Tr), but a low non-photochemical quenching coefficient (NPQ) and chlorophyll content. In addition, br displayed an equal IAA and Zeatin content ratio of main branches' apical buds to lateral branches' apical buds and high ratio of Zeatin to IAA content. Two T-DNA insertion sites caused by the insertion of exogenous BpCCR1 in br genome were found. On one site, chromosome 2 (Chr2), no known gene was detected on the flanking sequence. The other site was on Chr5, with an insertion of 388 bp T-DNA sequence, resulting in deletion of 107 bp 5' untranslated region (UTR) and 264 bp coding sequence (CDS) on CORONATINE INSENSITIVE 1 (BpCOII). In comparison with OE2 and WT, BpCOI1 was down-regulated in br, and the sensitivity of br to Methyl Jasmonate (MeJA) was abnormal. CONCLUSIONS Plant architecture, wood properties, photosynthetic characteristics, and IAA and Zeatin contents in main and lateral branches' apical buds changed in br over the study's time period. One T-DNA insertion was identified on the first exon of BpCOI1, which resulted in the reduction of BpCOI1 expression and abnormal perception to MeJA in br. These mutation phenotypes might be associated with a partial loss of BpCOI1 in birch.
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Affiliation(s)
- Rui Han
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 China
| | - Chenrui Gu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 China
| | - Ranhong Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 China
| | - Wendi Xu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 China
| | - Shuo Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 China
| | - Chaoyi Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 China
| | - Chang Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 China
| | - Guifeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 China
| | - Qibin Yu
- Institute of Food and Agricultural Sciences, Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850 USA
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 China
| | - Huiyu Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 China
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McCarthy RR, Yu M, Eilers K, Wang Y, Lai E, Filloux A. Cyclic di-GMP inactivates T6SS and T4SS activity in Agrobacterium tumefaciens. Mol Microbiol 2019; 112:632-648. [PMID: 31102484 PMCID: PMC6771610 DOI: 10.1111/mmi.14279] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2019] [Indexed: 01/17/2023]
Abstract
The Type VI secretion system (T6SS) is a bacterial nanomachine that delivers effector proteins into prokaryotic and eukaryotic preys. This secretion system has emerged as a key player in regulating the microbial diversity in a population. In the plant pathogen Agrobacterium tumefaciens, the signalling cascades regulating the activity of this secretion system are poorly understood. Here, we outline how the universal eubacterial second messenger cyclic di-GMP impacts the production of T6SS toxins and T6SS structural components. We demonstrate that this has a significant impact on the ability of the phytopathogen to compete with other bacterial species in vitro and in planta. Our results suggest that, as opposed to other bacteria, c-di-GMP turns down the T6SS in A. tumefaciens thus impacting its ability to compete with other bacterial species within the rhizosphere. We also demonstrate that elevated levels of c-di-GMP within the cell decrease the activity of the Type IV secretion system (T4SS) and subsequently the capacity of A. tumefaciens to transform plant cells. We propose that such peculiar control reflects on c-di-GMP being a key second messenger that silences energy-costing systems during early colonization phase and biofilm formation, while low c-di-GMP levels unleash T6SS and T4SS to advance plant colonization.
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Affiliation(s)
- Ronan R. McCarthy
- MRC Centre for Molecular Bacteriology and Infection, Department of Life SciencesImperial College LondonLondonSW7 2AZUK
- Division of Biosciences, Department of Life SciencesCollege of Health and Life Sciences, Brunel University LondonUxbridgeUB8 3PHUK
| | - Manda Yu
- Institute of Plant and Microbial BiologyAcademia SinicaTaipei11529Taiwan
| | - Kira Eilers
- MRC Centre for Molecular Bacteriology and Infection, Department of Life SciencesImperial College LondonLondonSW7 2AZUK
| | - Yi‐Chieh Wang
- Institute of Plant and Microbial BiologyAcademia SinicaTaipei11529Taiwan
| | - Erh‐Min Lai
- Institute of Plant and Microbial BiologyAcademia SinicaTaipei11529Taiwan
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life SciencesImperial College LondonLondonSW7 2AZUK
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Zuniga-Soto E, Fitzpatrick DA, Doohan FM, Mullins E. Insights into the transcriptomic response of the plant engineering bacterium Ensifer adhaerens OV14 during transformation. Sci Rep 2019; 9:10344. [PMID: 31316079 PMCID: PMC6637203 DOI: 10.1038/s41598-019-44648-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 05/08/2019] [Indexed: 11/08/2022] Open
Abstract
The ability to engineer plant genomes has been primarily driven by the soil bacterium Agrobacterium tumefaciens but recently the potential of alternative rhizobia such as Rhizobium etli and Ensifer adhaerens OV14, the latter of which supports Ensifer Mediated Transformation (EMT) has been reported. Surprisingly, a knowledge deficit exists in regards to understanding the whole genome processes underway in plant transforming bacteria, irrespective of the species. To begin to address the issue, we undertook a temporal RNAseq-based profiling study of E. adhaerens OV14 in the presence/absence of Arabidopsis thaliana tissues. Following co-cultivation with root tissues, 2333 differentially expressed genes (DEGs) were noted. Meta-analysis of the RNAseq data sets identified a clear shift from plasmid-derived gene expression to chromosomal-based transcription within the early stages of bacterium-plant co-cultivation. During this time, the number of differentially expressed prokaryotic genes increased steadily out to 7 days co-cultivation, a time at which optimum rates of transformation were observed. Gene ontology evaluations indicated a role for both chromosomal and plasmid-based gene families linked specifically with quorum sensing, flagellin production and biofilm formation in the process of EMT. Transcriptional evaluation of vir genes, housed on the pCAMBIA 5105 plasmid in E. adhaerens OV14 confirmed the ability of E. adhaerens OV14 to perceive and activate its transcriptome in response to the presence of 200 µM of acetosyringone. Significantly, this is the first study to characterise the whole transcriptomic response of a plant engineering bacterium in the presence of plant tissues and provides a novel insight into prokaryotic genetic processes that support T-DNA transfer.
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Affiliation(s)
- Evelyn Zuniga-Soto
- Department of Crop Science, Teagasc Crops Research Centre, Oak Park, Carlow, Ireland
- School of Biology and Environmental Sciences, University College Dublin, Belfield, Dublin 4, Ireland
| | - David A Fitzpatrick
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland
| | - Fiona M Doohan
- School of Biology and Environmental Sciences, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ewen Mullins
- Department of Crop Science, Teagasc Crops Research Centre, Oak Park, Carlow, Ireland.
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31
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Chen K, Wang Y, Zhang R, Zhang H, Gao C. CRISPR/Cas Genome Editing and Precision Plant Breeding in Agriculture. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:667-697. [PMID: 30835493 DOI: 10.1146/annurev-arplant-050718-100049] [Citation(s) in RCA: 607] [Impact Index Per Article: 121.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Enhanced agricultural production through innovative breeding technology is urgently needed to increase access to nutritious foods worldwide. Recent advances in CRISPR/Cas genome editing enable efficient targeted modification in most crops, thus promising to accelerate crop improvement. Here, we review advances in CRISPR/Cas9 and its variants and examine their applications in plant genome editing and related manipulations. We highlight base-editing tools that enable targeted nucleotide substitutions and describe the various delivery systems, particularly DNA-free methods, that have linked genome editing with crop breeding. We summarize the applications of genome editing for trait improvement, development of techniques for fine-tuning gene regulation, strategies for breeding virus resistance, and the use of high-throughput mutant libraries. We outline future perspectives for genome editing in plant synthetic biology and domestication, advances in delivery systems, editing specificity, homology-directed repair, and gene drives. Finally, we discuss the challenges and opportunities for precision plant breeding and its bright future in agriculture.
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Affiliation(s)
- Kunling Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Yanpeng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Rui Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Huawei Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
- University of Chinese Academy of Sciences, Beijing, China 100864
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Agrobacterium-mediated horizontal gene transfer: Mechanism, biotechnological application, potential risk and forestalling strategy. Biotechnol Adv 2018; 37:259-270. [PMID: 30579929 DOI: 10.1016/j.biotechadv.2018.12.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 12/18/2018] [Accepted: 12/18/2018] [Indexed: 11/20/2022]
Abstract
The extraordinary capacity of Agrobacterium to transfer its genetic material to host cell makes it evolve from phytopathogen to a powerful transgenic vector. Agrobacterium-mediated stable transformation is widely used as the preferred method to create transgenic plants for molecular plant biology research and crop breeding. Recent years, both mechanism and application of Agrobacterium-mediated horizontal gene transfer have made significant progresses, especially Agrobacterium-mediated transient transformation was developed for plant biotechnology industry to produce recombinant proteins. Agrobacterium strains are almost used and saved not only by each of microbiology and molecular plant labs, but also by many of plant biotechnology manufacturers. Agrobacterium is able to transfer its genetic material to a broad range of hosts, including plant and non-plant hosts. As a consequence, the concern of environmental risk associated with the accidental release of genetically modified Agrobacterium arises. In this article, we outline the recent progress in the molecular mechanism of Agrobacterium-meditated gene transfer, focus on the application of Agrobacterium-mediated horizontal gene transfer, and review the potential risk associated with Agrobacterium-meditated gene transfer. Based on the comparison between the infecting process of Agrobacterium as a pathogen and the transgenic process of Agrobacterium as a transgenic vector, we realize that chemotaxis is the distinct difference between these two biological processes and thus discuss the possible role of chemotaxis in forestalling the potential risk of Agrobacterium-meditated horizontal gene transfer to non-target plant species.
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33
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Gelvin SB. The VirE-asy Way to Genetically Transform Plants. Trends Microbiol 2018; 26:973-975. [PMID: 30472994 DOI: 10.1016/j.tim.2018.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 10/12/2018] [Indexed: 11/19/2022]
Abstract
Agrobacterium transfers T-DNA and several virulence effector proteins to plant cells. It is not known how and where T-complexes containing these components are assembled. A new study suggests that T-complexes form on the plant plasma membrane, mediated by the effector protein VirE3.
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Affiliation(s)
- Stanton B Gelvin
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
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34
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Park D, Park SH, Kim YS, Choi BS, Kim JK, Kim NS, Choi IY. NGS sequencing reveals that many of the genetic variations in transgenic rice plants match the variations found in natural rice population. Genes Genomics 2018; 41:213-222. [PMID: 30406575 DOI: 10.1007/s13258-018-0754-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/15/2018] [Indexed: 11/27/2022]
Abstract
BACKGROUND As the transformation process can induce mutations in host plants, molecular characterization of the associated genomic changes is important not only for practical food safety but also for understanding the fundamental theories of genome evolution. OBJECTIVES To investigate a population-scale comparative study of the genome-wide spectrum of sequence variants in the transgenic genome with the variations present in 3000 rice varieties. RESULTS On average, we identified 19,273 SNPs (including Indels) per transgenic line in which 10,729 SNPs were at the identical locations in the three transgenic rice plants. We found that these variations were predominantly present in specific regions in chromosomes 8 and 10. Majority (88%) of the identified variations were detected at the same genomic locations as those in natural rice population, implying that the transgenic induced mutations had a tendency to be common alleles. CONCLUSION Genomic variations in transgenic rice plants frequently occurred at the same sites as the major alleles found in the natural rice population, which implies that the sequence variations occur within the limits of a biological system to ensure survival.
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Affiliation(s)
- Doori Park
- Department of Molecular Bioscience, Kangwon National University, Chuncheon, South Korea
| | - Su-Hyun Park
- Graduate School of International Agricultural Technology and Crop Biotech Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, South Korea
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Youn Shic Kim
- Graduate School of International Agricultural Technology and Crop Biotech Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, South Korea
| | | | - Ju-Kon Kim
- Graduate School of International Agricultural Technology and Crop Biotech Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, South Korea.
| | - Nam-Soo Kim
- Department of Molecular Bioscience, Kangwon National University, Chuncheon, South Korea.
- Institute of Bioscience and Biomedical Sciences, Kangwon National University, Chuncheon, South Korea.
| | - Ik-Young Choi
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea.
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35
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Sardesai N, Foulk S, Chen W, Wu H, Etchison E, Gupta M. Coexpression of octopine and succinamopine Agrobacterium virulence genes to generate high quality transgenic events in maize by reducing vector backbone integration. Transgenic Res 2018; 27:539-550. [PMID: 30293127 DOI: 10.1007/s11248-018-0097-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 09/25/2018] [Indexed: 10/28/2022]
Abstract
Agrobacterium-mediated transformation is a complex process that is widely utilized for generating transgenic plants. However, one of the major concerns of this process is the frequent presence of undesirable T-DNA vector backbone sequences in the transgenic plants. To mitigate this deficiency, a ternary strain of A. tumefaciens was modified to increase the precision of T-DNA border nicking such that the backbone transfer is minimized. This particular strain supplemented the native succinamopine VirD1/VirD2 of EHA105 with VirD1/VirD2 derived from an octopine source (pTi15955), the same source as the binary T-DNA borders tested here, residing on a ternary helper plasmid containing an extra copy of the succinamopine VirB/C/G operons and VirD1. Transformation of maize immature embryos was carried out with two different test constructs, pDAB101556 and pDAB111437, bearing the reporter YFP gene and insecticidal toxin Cry1Fa gene, respectively, contained in the VirD-supplemented and regular control ternary strains. Molecular analyses of ~ 700 transgenic events revealed a significant 2.6-fold decrease in events containing vector backbone sequences, from 35.7% with the control to 13.9% with the VirD-supplemented strain for pDAB101556 and from 24.9% with the control to 9.3% with the VirD-supplemented strain for pDAB111437, without compromising transformation efficiency. In addition, while the number of single copy events recovered was similar, there was a 24-26% increase in backbone-free events with the VirD-supplemented strain compared to the control strain. Thus, supplementing existing VirD1/VirD2 genes in Agrobacterium, to recognize diverse T-DNA borders, proved to be a useful tool to increase the number of high quality events in maize.
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Affiliation(s)
- Nagesh Sardesai
- Dow AgroSciences LLC, 9330 Zionsville Rd, Indianapolis, IN, USA.
| | - Stephen Foulk
- Dow AgroSciences LLC, 9330 Zionsville Rd, Indianapolis, IN, USA
| | - Wei Chen
- Dow AgroSciences LLC, 9330 Zionsville Rd, Indianapolis, IN, USA
| | - Huixia Wu
- Dow AgroSciences LLC, 9330 Zionsville Rd, Indianapolis, IN, USA
| | - Emily Etchison
- Dow AgroSciences LLC, 9330 Zionsville Rd, Indianapolis, IN, USA
| | - Manju Gupta
- Dow AgroSciences LLC, 9330 Zionsville Rd, Indianapolis, IN, USA
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Bertier LD, Ron M, Huo H, Bradford KJ, Britt AB, Michelmore RW. High-Resolution Analysis of the Efficiency, Heritability, and Editing Outcomes of CRISPR/Cas9-Induced Modifications of NCED4 in Lettuce ( Lactuca sativa). G3 (BETHESDA, MD.) 2018; 8:1513-1521. [PMID: 29511025 PMCID: PMC5940144 DOI: 10.1534/g3.117.300396] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 02/25/2018] [Indexed: 12/26/2022]
Abstract
CRISPR/Cas9 is a transformative tool for making targeted genetic alterations. In plants, high mutation efficiencies have been reported in primary transformants. However, many of the mutations analyzed were somatic and therefore not heritable. To provide more insights into the efficiency of creating stable homozygous mutants using CRISPR/Cas9, we targeted LsNCED4 (9-cis-EPOXYCAROTENOID DIOXYGENASE4), a gene conditioning thermoinhibition of seed germination in lettuce. Three constructs, each capable of expressing Cas9 and a single gRNA targeting different sites in LsNCED4, were stably transformed into lettuce (Lactuca sativa) cvs. Salinas and Cobham Green. Analysis of 47 primary transformants (T1) and 368 T2 plants by deep amplicon sequencing revealed that 57% of T1 plants contained events at the target site: 28% of plants had germline mutations in one allele indicative of an early editing event (mono-allelic), 8% of plants had germline mutations in both alleles indicative of two early editing events (bi-allelic), and the remaining 21% of plants had multiple low frequency mutations indicative of late events (chimeric plants). Editing efficiency was similar in both genotypes, while the different gRNAs varied in efficiency. Amplicon sequencing of 20 T1 and more than 100 T2 plants for each of the three gRNAs showed that repair outcomes were not random, but reproducible and characteristic for each gRNA. Knockouts of NCED4 resulted in large increases in the maximum temperature for seed germination, with seeds of both cultivars capable of germinating >70% at 37°. Knockouts of NCED4 provide a whole-plant selectable phenotype that has minimal pleiotropic consequences. Targeting NCED4 in a co-editing strategy could therefore be used to enrich for germline-edited events simply by germinating seeds at high temperature.
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Affiliation(s)
| | | | - Heqiang Huo
- Department of Plant Sciences, Seed Biotechnology Center
| | | | | | - Richard W Michelmore
- Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, CA 95616
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Norashikin MN, Loh SH, Aziz A, Cha TS. Metabolic engineering of fatty acid biosynthesis in Chlorella vulgaris using an endogenous omega-3 fatty acid desaturase gene with its promoter. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.02.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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38
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Shih P, Chou S, Müller C, Halkier BA, Deeken R, Lai E. Differential roles of glucosinolates and camalexin at different stages of Agrobacterium-mediated transformation. MOLECULAR PLANT PATHOLOGY 2018; 19:1956-1970. [PMID: 29498790 PMCID: PMC6638096 DOI: 10.1111/mpp.12672] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 02/14/2018] [Accepted: 02/28/2018] [Indexed: 05/16/2023]
Abstract
Agrobacterium tumefaciens is the causal agent of crown gall disease in a wide range of plants via a unique interkingdom DNA transfer from bacterial cells into the plant genome. Agrobacterium tumefaciens is capable of transferring its T-DNA into different plant parts at different developmental stages for transient and stable transformation. However, the plant genes and mechanisms involved in these transformation processes are not well understood. We used Arabidopsis thaliana Col-0 seedlings to reveal the gene expression profiles at early time points during Agrobacterium infection. Common and differentially expressed genes were found in shoots and roots. A gene ontology analysis showed that the glucosinolate (GS) biosynthesis pathway was an enriched common response. Strikingly, several genes involved in indole glucosinolate (iGS) modification and the camalexin biosynthesis pathway were up-regulated, whereas genes in aliphatic glucosinolate (aGS) biosynthesis were generally down-regulated, on Agrobacterium infection. Thus, we evaluated the impacts of GSs and camalexin during different stages of Agrobacterium-mediated transformation combining Arabidopsis mutant studies, metabolite profiling and exogenous applications of various GS hydrolysis products or camalexin. The results suggest that the iGS hydrolysis pathway plays an inhibitory role on transformation efficiency in Arabidopsis seedlings at the early infection stage. Later in the Agrobacterium infection process, the accumulation of camalexin is a key factor inhibiting tumour development on Arabidopsis inflorescence stalks. In conclusion, this study reveals the differential roles of GSs and camalexin at different stages of Agrobacterium-mediated transformation and provides new insights into crown gall disease control and improvement of plant transformation.
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Affiliation(s)
- Po‐Yuan Shih
- Institute of Plant and Microbial Biology, Academia Sinica115 TaipeiTaiwan
- Molecular and Biological Agricultural Sciences ProgramTaiwan International Graduate Program, Academia Sinica115 TaipeiTaiwan
- Graduate Institute of Biotechnology, National Chung‐Hsing University402 TaichungTaiwan
| | - Shu‐Jen Chou
- Institute of Plant and Microbial Biology, Academia Sinica115 TaipeiTaiwan
| | - Caroline Müller
- Chemical Ecology, Bielefeld University33615 BielefeldGermany
| | - Barbara Ann Halkier
- Department of Plant and Environmental Sciences, DynaMo CenterUniversity of Copenhagen1817 Frederiksberg CDenmark
| | - Rosalia Deeken
- Molecular Plant Physiology and Biophysics, Julius‐von‐Sachs‐Institute for Biological Sciences, University of Wuerzburg97082 WuerzburgGermany
| | - Erh‐Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica115 TaipeiTaiwan
- Molecular and Biological Agricultural Sciences ProgramTaiwan International Graduate Program, Academia Sinica115 TaipeiTaiwan
- Biotechnology Center, National Chung‐Hsing University402 TaichungTaiwan
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Arabidopsis RETICULON-LIKE3 (RTNLB3) and RTNLB8 Participate in Agrobacterium-Mediated Plant Transformation. Int J Mol Sci 2018; 19:ijms19020638. [PMID: 29495267 PMCID: PMC5855860 DOI: 10.3390/ijms19020638] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/21/2018] [Accepted: 02/21/2018] [Indexed: 12/05/2022] Open
Abstract
Agrobacterium tumefaciens can genetically transform various eukaryotic cells because of the presence of a resident tumor-inducing (Ti) plasmid. During infection, a defined region of the Ti plasmid, transfer DNA (T-DNA), is transferred from bacteria into plant cells and causes plant cells to abnormally synthesize auxin and cytokinin, which results in crown gall disease. T-DNA and several virulence (Vir) proteins are secreted through a type IV secretion system (T4SS) composed of T-pilus and a transmembrane protein complex. Three members of Arabidopsis reticulon-like B (RTNLB) proteins, RTNLB1, 2, and 4, interact with VirB2, the major component of T-pilus. Here, we have identified that other RTNLB proteins, RTNLB3 and 8, interact with VirB2 in vitro. Root-based A. tumefaciens transformation assays with Arabidopsis rtnlb3, or rtnlb5-10 single mutants showed that the rtnlb8 mutant was resistant to A. tumefaciens infection. In addition, rtnlb3 and rtnlb8 mutants showed reduced transient transformation efficiency in seedlings. RTNLB3- or 8 overexpression transgenic plants showed increased susceptibility to A. tumefaciens and Pseudomonas syringae infection. RTNLB1-4 and 8 transcript levels differed in roots, rosette leaves, cauline leaves, inflorescence, flowers, and siliques of wild-type plants. Taken together, RTNLB3 and 8 may participate in A. tumefaciens infection but may have different roles in plants.
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Kunkel BN, Harper CP. The roles of auxin during interactions between bacterial plant pathogens and their hosts. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:245-254. [PMID: 29272462 DOI: 10.1093/jxb/erx447] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Plant pathogens have evolved several strategies to manipulate the biology of their hosts to facilitate colonization, growth to high levels in plant tissue, and production of disease. One of the less well known of these strategies is the synthesis of plant hormones and hormone analogs, and there is growing evidence that modulation of host hormone signaling is important during pathogenesis. Several plant pathogens produce the auxin indole-3-acetic acid (IAA) and/or virulence factors that modulate host auxin signaling. Auxin is well known for being involved in many aspects of plant growth and development, but recent findings have revealed that elevated IAA levels or enhanced auxin signaling can also promote disease development in some plant-pathogen interactions. In addition to stimulating plant cell growth during infection by gall-forming bacteria, auxin and auxin signaling can antagonize plant defense responses. Auxin can also act as a microbial signaling molecule to impact the biology of some pathogens directly. In this review, we summarize recent progress towards elucidating the roles that auxin production, modification of host auxin signaling, and direct effects of auxin on pathogens play during pathogenesis, with emphasis on the impacts of auxin on interactions with bacterial pathogens.
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Affiliation(s)
- Barbara N Kunkel
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
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Hooykaas PJJ, van Heusden GPH, Niu X, Reza Roushan M, Soltani J, Zhang X, van der Zaal BJ. Agrobacterium-Mediated Transformation of Yeast and Fungi. Curr Top Microbiol Immunol 2018; 418:349-374. [PMID: 29770864 DOI: 10.1007/82_2018_90] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Two decades ago, it was discovered that the well-known plant vector Agrobacterium tumefaciens can also transform yeasts and fungi when these microorganisms are co-cultivated on a solid substrate in the presence of a phenolic inducer such as acetosyringone. It is important that the medium has a low pH (5-6) and that the temperature is kept at room temperature (20-25 °C) during co-cultivation. Nowadays, Agrobacterium-mediated transformation (AMT) is the method of choice for the transformation of many fungal species; as the method is simple, the transformation efficiencies are much higher than with other methods, and AMT leads to single-copy integration much more frequently than do other methods. Integration of T-DNA in fungi occurs by non-homologous end-joining (NHEJ), but also targeted integration of the T-DNA by homologous recombination (HR) is possible. In contrast to AMT of plants, which relies on the assistance of a number of translocated virulence (effector) proteins, none of these (VirE2, VirE3, VirD5, VirF) are necessary for AMT of yeast or fungi. This is in line with the idea that some of these proteins help to overcome plant defense. Importantly, it also showed that VirE2 is not necessary for the transport of the T-strand into the nucleus. The yeast Saccharomyces cerevisiae is a fast-growing organism with a relatively simple genome with reduced genetic redundancy. This yeast species has therefore been used to unravel basic molecular processes in eukaryotic cells as well as to elucidate the function of virulence factors of pathogenic microorganisms acting in plants or animals. Translocation of Agrobacterium virulence proteins into yeast was recently visualized in real time by confocal microscopy. In addition, the yeast 2-hybrid system, one of many tools that have been developed for use in this yeast, was used to identify plant and yeast proteins interacting with the translocated Agrobacterium virulence proteins. Dedicated mutant libraries, containing for each gene a mutant with a precise deletion, have been used to unravel the mode of action of some of the Agrobacterium virulence proteins. Yeast deletion mutant collections were also helpful in identifying host factors promoting or inhibiting AMT, including factors involved in T-DNA integration. Thus, the homologous recombination (HR) factor Rad52 was found to be essential for targeted integration of T-DNA by HR in yeast. Proteins mediating double-strand break (DSB) repair by end-joining (Ku70, Ku80, Lig4) turned out to be essential for non-homologous integration. Inactivation of any one of the genes encoding these end-joining factors in other yeasts and fungi was employed to reduce or totally eliminate non-homologous integration and promote efficient targeted integration at the homologous locus by HR. In plants, however, their inactivation did not prevent non-homologous integration, indicating that T-DNA is captured by different DNA repair pathways in plants and fungi.
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Affiliation(s)
- Paul J J Hooykaas
- Sylvius Lab, Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
| | - G Paul H van Heusden
- Sylvius Lab, Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Xiaolei Niu
- Sylvius Lab, Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - M Reza Roushan
- Sylvius Lab, Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Jalal Soltani
- Sylvius Lab, Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Xiaorong Zhang
- Sylvius Lab, Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Bert J van der Zaal
- Sylvius Lab, Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
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42
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Willig CJ, Duan K, Zhang ZJ. Transcriptome Profiling of Plant Genes in Response to Agrobacterium tumefaciens-Mediated Transformation. Curr Top Microbiol Immunol 2018; 418:319-348. [PMID: 30062593 DOI: 10.1007/82_2018_115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Agrobacterium tumefaciens is a plant pathogen that causes crown gall disease. During infection of the host plant, Agrobacterium transfers T-DNA from its Ti plasmid into the host cell, which can then be integrated into the host genome. This unique genetic transformation capability has been employed as the dominant technology for producing genetically modified plants for both basic research and biotechnological applications. Agrobacterium has been well studied as a disease-causing agent. The Agrobacterium-mediated transformation process involves early attachment of the bacterium to the host's surface, followed by transfer of T-DNA and virulence proteins into the plant cell. Throughout this process, the host plants exhibit dynamic gene expression patterns at each infection stage or in response to Agrobacterium strains with varying pathogenic capabilities. Shifting host gene expression patterns throughout the transformation process have effects on transformation frequency, host morphology, and metabolism. Thus, gene expression profiling during the Agrobacterium infection process can be an important approach to help elucidate the interaction between Agrobacterium and plants. This review highlights recent findings on host plant differential gene expression patterns in response to A. tumefaciens or related elicitor molecules.
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Affiliation(s)
| | - Kaixuan Duan
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Zhanyuan J Zhang
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA.
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43
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Wang Y, Zhang S, Huang F, Zhou X, Chen Z, Peng W, Luo M. VirD5 is required for efficient Agrobacterium infection and interacts with Arabidopsis VIP2. THE NEW PHYTOLOGIST 2018; 217:726-738. [PMID: 29084344 DOI: 10.1111/nph.14854] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/13/2017] [Indexed: 05/28/2023]
Abstract
During Agrobacterium (Agrobacterium tumefaciens) infection, the translocated virulence proteins (VirD2, VirE2, VirE3, VirF and VirD5) play crucial roles. It is thought that, through protein-protein interactions, Agrobacterium uses and abuses host plant factors and systems to facilitate its infection. Although some molecular functions have been revealed, the roles of VirD5 still need to be further elucidated. Here, plant transformation and tumorigenesis mediated by genetically modified Agrobacterium strains were performed to examine VirD5 roles. In addition, protein-protein interaction-associated molecular and biochemistry technologies were used to reveal and elucidate VirD5 interaction with Arabidopsis VirE2 interacting protein 2 (VIP2). Our results showed that deleting virD5 from Agrobacterium reduced its tumor formation ability and stable transformation efficiency but did not affect the transient transformation efficiency. We also found that VirD5 can interact with Arabidopsis VIP2. Further experiments demonstrated that VirD5 can affect VIP2 binding to cap-binding proteins (CBP20 and CBP80). The tumorigenesis efficiency for cbp80 mutant was not significantly changed, but that for cbp20, cbp20cbp80 mutants were significantly increased. This work demonstrates experimentally that VirD5 is required for efficient Agrobacterium infection and may promote this process by competitive interaction with Arabidopsis VIP2. CBP20 is involved in the Agrobacterium infection process and its effect can be synergistically enhanced by CBP80.
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Affiliation(s)
- Yafei Wang
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Basic Forestry and Proteomics Research Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shaojuan Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fei Huang
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xu Zhou
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhuo Chen
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wei Peng
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Meizhong Luo
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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44
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Beyond Agrobacterium-Mediated Transformation: Horizontal Gene Transfer from Bacteria to Eukaryotes. Curr Top Microbiol Immunol 2018; 418:443-462. [DOI: 10.1007/82_2018_82] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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45
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The Mechanism of T-DNA Integration: Some Major Unresolved Questions. Curr Top Microbiol Immunol 2018; 418:287-317. [DOI: 10.1007/82_2018_98] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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46
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Abstract
Agrobacterium strains transfer a single-strand form of T-DNA (T-strands) and Virulence (Vir) effector proteins to plant cells. Following transfer, T-strands likely form complexes with Vir and plant proteins that traffic through the cytoplasm and enter the nucleus. T-strands may subsequently randomly integrate into plant chromosomes and permanently express encoded transgenes, a process known as stable transformation. The molecular processes by which T-strands integrate into the host genome remain unknown. Although integration resembles DNA repair processes, the requirement of known DNA repair pathways for integration is controversial. The configuration and genomic position of integrated T-DNA molecules likely affect transgene expression, and control of integration is consequently important for basic research and agricultural biotechnology applications. This article reviews our current knowledge of the process of T-DNA integration and proposes ways in which this knowledge may be manipulated for genome editing and synthetic biology purposes.
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Affiliation(s)
- Stanton B Gelvin
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392, USA;
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47
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Hwang HH, Yu M, Lai EM. Agrobacterium-mediated plant transformation: biology and applications. THE ARABIDOPSIS BOOK 2017; 15:e0186. [PMID: 31068763 PMCID: PMC6501860 DOI: 10.1199/tab.0186] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Plant genetic transformation heavily relies on the bacterial pathogen Agrobacterium tumefaciens as a powerful tool to deliver genes of interest into a host plant. Inside the plant nucleus, the transferred DNA is capable of integrating into the plant genome for inheritance to the next generation (i.e. stable transformation). Alternatively, the foreign DNA can transiently remain in the nucleus without integrating into the genome but still be transcribed to produce desirable gene products (i.e. transient transformation). From the discovery of A. tumefaciens to its wide application in plant biotechnology, numerous aspects of the interaction between A. tumefaciens and plants have been elucidated. This article aims to provide a comprehensive review of the biology and the applications of Agrobacterium-mediated plant transformation, which may be useful for both microbiologists and plant biologists who desire a better understanding of plant transformation, protein expression in plants, and plant-microbe interaction.
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Affiliation(s)
- Hau-Hsuan Hwang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, 402
| | - Manda Yu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, 115
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, 115
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Dehghani J, Movafeghi A, Barzegari A, Barar J. Efficient and stable transformation of Dunaliella pseudosalina by 3 strains of Agrobacterium tumefaciens. ACTA ACUST UNITED AC 2017; 7:247-254. [PMID: 29435432 PMCID: PMC5801536 DOI: 10.15171/bi.2017.29] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/30/2017] [Accepted: 09/05/2017] [Indexed: 12/30/2022]
Abstract
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Introduction:
Several platforms including mammalian, plant and insect cells as well as bacteria, yeasts, and microalgae are available for the production of recombinant proteins. Low efficiency of delivery systems, extracellular and intracellular degradation of foreign genes during transformation, difficulties in targeting and importing into the nucleus, and finally problems in integration into nuclear genome are the most bottlenecks of classical plasmids for producing recombinant proteins. Owing to high growth rate, no common pathogen with humans, being utilized as humans’ food, and capability to perform N-glycosylation, microalgae are proposed as an ideal system for such biotechnological approaches. Here, Agrobacterium tumefaciens is introduced as an alternative tool for transformation of the microalga Dunaliella pseudosalina.
Methods: The transformation of gfp gene into the D. pseudosalina was evaluated by three strains including EHA101, GV3301 and GV3850 of A. tumefaciens. The integrating and expression of gfp gene were determined by PCR, RT-PCR, Q-PCR and SDS-PAGE analyses.
Results: The T-DNA of pCAMBIA1304 plasmid was successfully integrated into the genome of the microalgal cells. Although all of the strains were able to transform the algal cells, GV3301 possessed higher potential to transform the microalgal cells in comparison to EHA101 and GV3850 strains. Moreover, the stability of gfp gene was successfully established during a course of two months period in the microalgal genome.
Conclusion : Agrobacterium is introduced as a competent system for stable transformation of Dunaliella strains in order to produce eukaryotic recombinant proteins.
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Affiliation(s)
- Jaber Dehghani
- Department of Plant Biology, Faculty of Natural Science, University of Tabriz, 29th Bahman Blvd, Tabriz, Iran.,Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Science, Tabriz, Iran
| | - Ali Movafeghi
- Department of Plant Biology, Faculty of Natural Science, University of Tabriz, 29th Bahman Blvd, Tabriz, Iran
| | - Abolfazl Barzegari
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Science, Tabriz, Iran.,School of Advanced Biomedical Sciences, Tabriz University of Medical Science, Daneshgah street, Tabriz, Iran
| | - Jaleh Barar
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Science, Tabriz, Iran
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49
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Kadam US, Chavhan RL, Schulz B, Irudayaraj J. Single molecule Raman spectroscopic assay to detect transgene from GM plants. Anal Biochem 2017; 532:60-63. [DOI: 10.1016/j.ab.2017.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 06/03/2017] [Accepted: 06/05/2017] [Indexed: 01/01/2023]
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50
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Genetic manipulations in crops: Challenges and opportunities. Genomics 2017; 109:494-505. [PMID: 28778540 DOI: 10.1016/j.ygeno.2017.07.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 01/01/2023]
Abstract
An alarming increase in the human population necessitates doubling the world food production in the next few decades. Although a number of possible biotechnological measures are under consideration, central to these efforts is the development of transgenic crops to produce more food, and the traits with which plants could better adapt to adverse environmental conditions in a changing climate. The emergence of new tools for the introduction of foreign genes into plants has increased both our knowledge and the capacity to develop transgenic plants. In addition, a better understanding of genetic modifications has allowed us to study the impact that genetically modified crop plants may have on the environment. This article discusses different techniques routinely used to carry out genetic modifications in plants while highlighting challenges with them, which future research must address to increase acceptance of GM crops for meeting food security challenges effectively.
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