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Mitra S, Anand U, Ghorai M, Kant N, Kumar M, Radha, Jha NK, Swamy MK, Proćków J, de la Lastra JMP, Dey A. Genome editing technologies, mechanisms and improved production of therapeutic phytochemicals: Opportunities and prospects. Biotechnol Bioeng 2023; 120:82-94. [PMID: 36224758 PMCID: PMC10091730 DOI: 10.1002/bit.28260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/10/2022] [Accepted: 10/08/2022] [Indexed: 11/09/2022]
Abstract
Plants produce a large number of secondary metabolites, known as phytometabolites that may be employed as medicines, dyes, poisons, and insecticides in the field of medicine, agriculture, and industrial use, respectively. The rise of genome management approaches has promised a factual revolution in genetic engineering. Targeted genome editing in living entities permits the understanding of the biological systems very clearly, and also sanctions to address a wide-ranging objective in the direction of improving features of plant and their yields. The last few years have introduced a number of unique genome editing systems, including transcription activator-like effector nucleases, zinc finger nucleases, and miRNA-regulated clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9). Genome editing systems have helped in the transformation of metabolic engineering, allowing researchers to modify biosynthetic pathways of different secondary metabolites. Given the growing relevance of editing genomes in plant research, the exciting novel methods are briefly reviewed in this chapter. Also, this chapter highlights recent discoveries on the CRISPR-based modification of natural products in different medicinal plants.
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Affiliation(s)
- Sicon Mitra
- Department of Biotechnology, School of Engineering & TechnologySharda UniversityGreater NoidaUttar PradeshIndia
| | | | - Mimosa Ghorai
- Department of Life SciencesPresidency UniversityKolkataWest BengalIndia
| | - Nishi Kant
- Department of Chemical EngineeringIndian Institute of Technology DelhiDelhiNew DelhiIndia
| | - Manoj Kumar
- Chemical and Biochemical Processing DivisionICAR‐Central Institute for Research on Cotton TechnologyMumbaiMaharashtraIndia
| | - Radha
- School of Biological and Environmental SciencesShoolini University of Biotechnology and Management SciencesSolanHimachal PradeshIndia
| | - Niraj K. Jha
- Department of Biotechnology, School of Engineering & TechnologySharda UniversityGreater NoidaUttar PradeshIndia
- Department of Biotechnology Engineering and Food TechnologyChandigarh UniversityMohaliPunjabIndia
- Department of Biotechnology, School of Applied & Life SciencesUttaranchal UniversityDehradunUttarakhandIndia
| | - Mallappa K. Swamy
- Department of BiotechnologyEast West First Grade College of ScienceBengaluruKarnatakaIndia
| | - Jarosław Proćków
- Department of Plant Biology, Institute of Environmental BiologyWrocław University of Environmental and Life SciencesWrocławPoland
| | - José M. Pérez de la Lastra
- Biotechnology of Macromolecules Research Group, Department of Life and Earth SciencesInstituto de Productos Naturales y Agrobiología‐Consejo Superior de Investigaciones Científicas, (IPNA‐CSIC)San Cristóbal de La LagunaTenerifeSpain
| | - Abhijit Dey
- Department of Life SciencesPresidency UniversityKolkataWest BengalIndia
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McCarthy HM, Tarallo M, Mesarich CH, McDougal RL, Bradshaw RE. Targeted Gene Mutations in the Forest Pathogen Dothistroma septosporum Using CRISPR/Cas9. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11081016. [PMID: 35448744 PMCID: PMC9025729 DOI: 10.3390/plants11081016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 05/19/2023]
Abstract
Dothistroma needle blight, caused by Dothistroma septosporum, has increased in incidence and severity over the last few decades and is now one of the most important global diseases of pines. Disease resistance breeding could be accelerated by knowledge of pathogen virulence factors and their host targets. However, this is hindered due to inefficient targeted gene disruption in D. septosporum, which is required for virulence gene characterisation. Here we report the first successful application of CRISPR/Cas9 gene editing to a Dothideomycete forest pathogen, D. septosporum. Disruption of the dothistromin pathway regulator gene AflR, with a known phenotype, was performed using nonhomologous end-joining repair with an efficiency of > 90%. Transformants with a range of disruption mutations in AflR were produced. Disruption of Ds74283, a D. septosporum gene encoding a secreted cell death elicitor, was also achieved using CRISPR/Cas9, by using a specific donor DNA repair template to aid selection where the phenotype was unknown. In this case, 100% of screened transformants were identified as disruptants. In establishing CRISPR/Cas9 as a tool for gene editing in D. septosporum, our research could fast track the functional characterisation of candidate virulence factors in D. septosporum and helps set the foundation for development of this technology in other forest pathogens.
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Affiliation(s)
- Hannah M. McCarthy
- BioProtection Aotearoa, School of Natural Sciences, Massey University, Palmerston North 4472, New Zealand; (M.T.); (R.E.B.)
- Correspondence:
| | - Mariana Tarallo
- BioProtection Aotearoa, School of Natural Sciences, Massey University, Palmerston North 4472, New Zealand; (M.T.); (R.E.B.)
| | - Carl H. Mesarich
- BioProtection Aotearoa, School of Agriculture and Environment, Massey University, Palmerston North 4472, New Zealand;
| | - Rebecca L. McDougal
- Scion, New Zealand Forest Research Institute Ltd., Rotorua 3010, New Zealand;
| | - Rosie E. Bradshaw
- BioProtection Aotearoa, School of Natural Sciences, Massey University, Palmerston North 4472, New Zealand; (M.T.); (R.E.B.)
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Kozieł E, Otulak-Kozieł K, Bujarski JJ. Plant Cell Wall as a Key Player During Resistant and Susceptible Plant-Virus Interactions. Front Microbiol 2021; 12:656809. [PMID: 33776985 PMCID: PMC7994255 DOI: 10.3389/fmicb.2021.656809] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 02/19/2021] [Indexed: 01/06/2023] Open
Abstract
The cell wall is a complex and integral part of the plant cell. As a structural element it sustains the shape of the cell and mediates contact among internal and external factors. We have been aware of its involvement in both abiotic (like drought or frost) and biotic stresses (like bacteria or fungi) for some time. In contrast to bacterial and fungal pathogens, viruses are not mechanical destructors of host cell walls, but relatively little is known about remodeling of the plant cell wall in response to viral biotic stress. New research results indicate that the cell wall represents a crucial active component during the plant’s response to different viral infections. Apparently, cell wall genes and proteins play key roles during interaction, having a direct influence on the rebuilding of the cell wall architecture. The plant cell wall is involved in both susceptibility as well as resistance reactions. In this review we summarize important progress made in research on plant virus impact on cell wall remodeling. Analyses of essential defensive wall associated proteins in susceptible and resistant responses demonstrate that the components of cell wall metabolism can affect the spread of the virus as well as activate the apoplast- and symplast-based defense mechanisms, thus contributing to the complex network of the plant immune system. Although the cell wall reorganization during the plant-virus interaction remains a challenging task, the use of novel tools and methods to investigate its composition and structure will greatly contribute to our knowledge in the field.
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Affiliation(s)
- Edmund Kozieł
- Institute of Biology, Department of Botany, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Katarzyna Otulak-Kozieł
- Institute of Biology, Department of Botany, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Józef Julian Bujarski
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, United States
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Dort EN, Tanguay P, Hamelin RC. CRISPR/Cas9 Gene Editing: An Unexplored Frontier for Forest Pathology. FRONTIERS IN PLANT SCIENCE 2020; 11:1126. [PMID: 32793272 PMCID: PMC7387688 DOI: 10.3389/fpls.2020.01126] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/08/2020] [Indexed: 05/07/2023]
Abstract
CRISPR/Cas9 gene editing technology has taken the scientific community by storm since its development in 2012. First discovered in 1987, CRISPR/Cas systems act as an adaptive immune response in archaea and bacteria that defends against invading bacteriophages and plasmids. CRISPR/Cas9 gene editing technology modifies this immune response to function in eukaryotic cells as a highly specific, RNA-guided complex that can edit almost any genetic target. This technology has applications in all biological fields, including plant pathology. However, examples of its use in forest pathology are essentially nonexistent. The aim of this review is to give researchers a deeper understanding of the native CRISPR/Cas systems and how they were adapted into the CRISPR/Cas9 technology used today in plant pathology-this information is crucial for researchers aiming to use this technology in the pathosystems they study. We review the current applications of CRISPR/Cas9 in plant pathology and propose future directions for research in forest pathosystems where this technology is currently underutilized.
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Affiliation(s)
- Erika N. Dort
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
| | - Philippe Tanguay
- Laurentian Forestry Centre, Canadian Forest Service, Natural Resources Canada, Québec, QC, Canada
| | - Richard C. Hamelin
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Département des Sciences du bois et de la Forêt, Faculté de Foresterie et Géographie, Université Laval, Québec, QC, Canada
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Gerashchenkov GA, Rozhnova NA, Kuluev BR, Kiryanova OY, Gumerova GR, Knyazev AV, Vershinina ZR, Mikhailova EV, Chemeris DA, Matniyazov RT, Baimiev AK, Gubaidullin IM, Baimiev AK, Chemeris AV. Design of Guide RNA for CRISPR/Cas Plant Genome Editing. Mol Biol 2020. [DOI: 10.1134/s0026893320010069] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Kalinina NO, Khromov A, Love AJ, Taliansky ME. CRISPR Applications in Plant Virology: Virus Resistance and Beyond. PHYTOPATHOLOGY 2020; 110:18-28. [PMID: 31433273 DOI: 10.1094/phyto-07-19-0267-ia] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated genes (Cas) is a prokaryotic adaptive immune system which has been reprogrammed into a precise, simple, and efficient gene targeting technology. This emerging technology is revolutionizing various areas of life sciences, medicine, and biotechnology and has raised significant interest among plant biologists, both in basic science and in plant protection and breeding. In this review, we describe the basic principles of CRISPR/Cas systems, and how they can be deployed to model plants and crops for the control, monitoring, and study of the mechanistic aspects of plant virus infections. We discuss how Cas endonucleases can be used to engineer plant virus resistance by directly targeting viral DNA or RNA, as well as how they can inactivate host susceptibility genes. Additionally, other applications of CRISPR/Cas in plant virology such as virus diagnostics and imaging are reviewed. The review also provides a systemic comparison between CRISPR/Cas technology and RNA interference approaches, the latter of which has also been used for development of virus-resistant plants. Finally, we outline challenges to be solved before CRISPR/Cas can produce virus-resistant crop plants which can be marketed.
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Affiliation(s)
- Natalia O Kalinina
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Prospect Nauki 6, Pushchino, Moscow Region, 142290, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - Andrey Khromov
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Prospect Nauki 6, Pushchino, Moscow Region, 142290, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - Andrew J Love
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, U.K
| | - Michael E Taliansky
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Prospect Nauki 6, Pushchino, Moscow Region, 142290, Russia
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, U.K
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Zhang Y, Showalter AM. CRISPR/Cas9 Genome Editing Technology: A Valuable Tool for Understanding Plant Cell Wall Biosynthesis and Function. FRONTIERS IN PLANT SCIENCE 2020; 11:589517. [PMID: 33329650 PMCID: PMC7714752 DOI: 10.3389/fpls.2020.589517] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/23/2020] [Indexed: 05/05/2023]
Abstract
For the past 5 years, clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) technology has appeared in the molecular biology research spotlight. As a game-changing player in genome editing, CRISPR/Cas9 technology has revolutionized animal research, including medical research and human gene therapy as well as plant science research, particularly for crop improvement. One of the most common applications of CRISPR/Cas9 is to generate genetic knock-out mutants. Recently, several multiplex genome editing approaches utilizing CRISPR/Cas9 were developed and applied in various aspects of plant research. Here we summarize these approaches as they relate to plants, particularly with respect to understanding the biosynthesis and function of the plant cell wall. The plant cell wall is a polysaccharide-rich cell structure that is vital to plant cell formation, growth, and development. Humans are heavily dependent on the byproducts of the plant cell wall such as shelter, food, clothes, and fuel. Genes involved in the assembly of the plant cell wall are often highly redundant. To identify these redundant genes, higher-order knock-out mutants need to be generated, which is conventionally done by genetic crossing. Compared with genetic crossing, CRISPR/Cas9 multi-gene targeting can greatly shorten the process of higher-order mutant generation and screening, which is especially useful to characterize cell wall related genes in plant species that require longer growth time. Moreover, CRISPR/Cas9 makes it possible to knock out genes when null T-DNA mutants are not available or are genetically linked. Because of these advantages, CRISPR/Cas9 is becoming an ideal and indispensable tool to perform functional studies in plant cell wall research. In this review, we provide perspectives on how to design CRISPR/Cas9 to achieve efficient gene editing and multi-gene targeting in plants. We also discuss the recent development of the virus-based CRISPR/Cas9 system and the application of CRISPR/Cas9 to knock in genes. Lastly, we summarized current progress on using CRISPR/Cas9 for the characterization of plant cell wall-related genes.
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Affiliation(s)
- Yuan Zhang
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
- Department of Environmental & Plant Biology, Ohio University, Athens, OH, United States
| | - Allan M. Showalter
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
- Department of Environmental & Plant Biology, Ohio University, Athens, OH, United States
- *Correspondence: Allan M. Showalter,
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