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Bulle M, Venkatapuram AK, Abbagani S, Kirti PB. CRISPR/Cas9 based genome editing of Phytoene desaturase (PDS) gene in chilli pepper (Capsicum annuum L.). J Genet Eng Biotechnol 2024; 22:100380. [PMID: 38797550 PMCID: PMC11070243 DOI: 10.1016/j.jgeb.2024.100380] [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: 02/10/2024] [Revised: 04/08/2024] [Accepted: 04/21/2024] [Indexed: 05/29/2024]
Abstract
An effective CRISPR/Cas9 reagent delivery system has been developed in a commercially significant crop, the chilli pepper using a construct harboring two distinct gRNAs targeting exons 14 and 15 of the Phytoene desaturase (CaPDS) gene, whose loss-of-function mutation causes a photo-bleaching phenotype and impairs the biosynthesis of carotenoids. The construct carrying two sgRNAs was observed to create visible albino phenotypes in cotyledons regenerating on a medium containing 80 mg/L kanamycin, and plants regenerated therefrom after biolistic-mediated transfer of CRISPR/Cas9 reagents into chilli pepper cells. Analysis of CRISPR/Cas9 genome-editing events, including kanamycin screening of mutants and assessing homozygosity using the T7 endonuclease assay (T7E1), revealed 62.5 % of transformed plants exhibited successful editing at the target region and displayed both albino and mosaic phenotypes. Interestingly, the sequence analysis showed that insertions and substitutions were present in all the plant lines in the targeted CaPDS region. The detected mutations were mostly 12- to 24-bp deletions that disrupted the exon-intron junction, along with base substitutions and the insertion of 1-bp at the protospacer adjacent motif (PAM) region of the target site. The reduction in essential photosynthetic pigments (chlorophyll a, chlorophyll b and carotenoid) in knockout chilli pepper lines provided further evidence that the CaPDS gene had been functionally disrupted. In this present study, we report that the biolistic delivery of CRISPR/Cas9 reagents into chilli peppers is very effective and produces multiple mutation events in a short span of time.
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Affiliation(s)
- Mallesham Bulle
- Agri Biotech Foundation, PJTS Agricultural University Campus, Rajendranagar, Hyderabad 500030, Telangana, India.
| | - Ajay Kumar Venkatapuram
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sadanandam Abbagani
- Plant Biotechnology Research Unit, Department of Biotechnology, Kakatiya University, Warangal, Telangana 506 009, India
| | - P B Kirti
- Agri Biotech Foundation, PJTS Agricultural University Campus, Rajendranagar, Hyderabad 500030, Telangana, India
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Prado GS, Rocha DC, dos Santos LN, Contiliani DF, Nobile PM, Martinati-Schenk JC, Padilha L, Maluf MP, Lubini G, Pereira TC, Monteiro-Vitorello CB, Creste S, Boscariol-Camargo RL, Takita MA, Cristofani-Yaly M, de Souza AA. CRISPR technology towards genome editing of the perennial and semi-perennial crops citrus, coffee and sugarcane. FRONTIERS IN PLANT SCIENCE 2024; 14:1331258. [PMID: 38259920 PMCID: PMC10801916 DOI: 10.3389/fpls.2023.1331258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024]
Abstract
Gene editing technologies have opened up the possibility of manipulating the genome of any organism in a predicted way. CRISPR technology is the most used genome editing tool and, in agriculture, it has allowed the expansion of possibilities in plant biotechnology, such as gene knockout or knock-in, transcriptional regulation, epigenetic modification, base editing, RNA editing, prime editing, and nucleic acid probing or detection. This technology mostly depends on in vitro tissue culture and genetic transformation/transfection protocols, which sometimes become the major challenges for its application in different crops. Agrobacterium-mediated transformation, biolistics, plasmid or RNP (ribonucleoprotein) transfection of protoplasts are some of the commonly used CRISPR delivery methods, but they depend on the genotype and target gene for efficient editing. The choice of the CRISPR system (Cas9, Cas12), CRISPR mechanism (plasmid or RNP) and transfection technique (Agrobacterium spp., PEG solution, lipofection) directly impacts the transformation efficiency and/or editing rate. Besides, CRISPR/Cas technology has made countries rethink regulatory frameworks concerning genetically modified organisms and flexibilize regulatory obstacles for edited plants. Here we present an overview of the state-of-the-art of CRISPR technology applied to three important crops worldwide (citrus, coffee and sugarcane), considering the biological, methodological, and regulatory aspects of its application. In addition, we provide perspectives on recently developed CRISPR tools and promising applications for each of these crops, thus highlighting the usefulness of gene editing to develop novel cultivars.
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Affiliation(s)
- Guilherme Souza Prado
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
| | - Dhiôvanna Corrêia Rocha
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
- Institute of Biology, State University of Campinas (Unicamp), Campinas, Brazil
| | - Lucas Nascimento dos Santos
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
- Institute of Biology, State University of Campinas (Unicamp), Campinas, Brazil
| | - Danyel Fernandes Contiliani
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
- Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Paula Macedo Nobile
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
| | | | - Lilian Padilha
- Coffee Center of the Agronomic Institute of Campinas (IAC), Campinas, Brazil
- Embrapa Coffee, Brazilian Agricultural Research Corporation, Brasília, Federal District, Brazil
| | - Mirian Perez Maluf
- Coffee Center of the Agronomic Institute of Campinas (IAC), Campinas, Brazil
- Embrapa Coffee, Brazilian Agricultural Research Corporation, Brasília, Federal District, Brazil
| | - Greice Lubini
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Tiago Campos Pereira
- Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | | | - Silvana Creste
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
- Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
| | | | - Marco Aurélio Takita
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
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Shelake RM, Jadhav AM, Bhosale PB, Kim JY. Unlocking secrets of nature's chemists: Potential of CRISPR/Cas-based tools in plant metabolic engineering for customized nutraceutical and medicinal profiles. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108070. [PMID: 37816270 DOI: 10.1016/j.plaphy.2023.108070] [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: 07/18/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
Abstract
Plant species have evolved diverse metabolic pathways to effectively respond to internal and external signals throughout their life cycle, allowing adaptation to their sessile and phototropic nature. These pathways selectively activate specific metabolic processes, producing plant secondary metabolites (PSMs) governed by genetic and environmental factors. Humans have utilized PSM-enriched plant sources for millennia in medicine and nutraceuticals. Recent technological advances have significantly contributed to discovering metabolic pathways and related genes involved in the biosynthesis of specific PSM in different food crops and medicinal plants. Consequently, there is a growing demand for plant materials rich in nutrients and bioactive compounds, marketed as "superfoods". To meet the industrial demand for superfoods and therapeutic PSMs, modern methods such as system biology, omics, synthetic biology, and genome editing (GE) play a crucial role in identifying the molecular players, limiting steps, and regulatory circuitry involved in PSM production. Among these methods, clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR/Cas) is the most widely used system for plant GE due to its simple design, flexibility, precision, and multiplexing capabilities. Utilizing the CRISPR-based toolbox for metabolic engineering (ME) offers an ideal solution for developing plants with tailored preventive (nutraceuticals) and curative (therapeutic) metabolic profiles in an ecofriendly way. This review discusses recent advances in understanding the multifactorial regulation of metabolic pathways, the application of CRISPR-based tools for plant ME, and the potential research areas for enhancing plant metabolic profiles.
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Amol Maruti Jadhav
- Research Institute of Green Energy Convergence Technology (RIGET), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Pritam Bhagwan Bhosale
- Department of Veterinary Medicine, Research Institute of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea; Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea; Nulla Bio Inc, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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Awasthi P, Mishra AK, Kocábek T, Nath VS, Mishra S, Hazzouri KM, Sudalaimuthuasari N, Stajner N, Jakše J, Krofta K, Hájek T, Amiri KM. CRISPR/Cas9-mediated mutagenesis of the mediator complex subunits MED5a and MED5b genes impaired secondary metabolite accumulation in hop (Humulus lupulus). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107851. [PMID: 37354728 DOI: 10.1016/j.plaphy.2023.107851] [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: 02/24/2023] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 06/26/2023]
Abstract
Hop (Humulus lupulus L.) is an important commercial crop known for the biosynthesis of valuable specialized secondary metabolites in glandular trichomes (lupulin glands), which are used for the brewing industry. To achieve burgeoning market demands is the essentiality of comprehensive understanding of the mechanisms of biosynthesis of secondary metabolites in hop. Over the past year, several studies using structural biology and functional genomics approaches have shown that Mediator (MED) serves as an integrative hub for RNAP II-mediated transcriptional regulation of various physiological and cellular processes, including involvement of MED5a and MED5b in hyperaccumulation of phenylpropanoid in A. thaliana. In the present work, an unprecedented attempt was made to generate Hlmed5a/med5b double loci mutant lines in hop using a CRISPR/Cas9-based genome editing system. The Hlmed5a/med5b double loci mutant lines showed reduced expression of structural genes of the flavonoid, humulone, and terpenoid biosynthetic pathways, which was more pronounced in the lupulin gland compared to leaf tissue and was consistent with their reduced accumulation. Phenotypic and anatomical observations revealed that Hlmed5a/med5b double loci mutant line exhibited robust growth, earlier flowering, earlier cone maturity, reduced cone size, variations in floral structure patterns, and distorted lupulin glands without any remarkable changes in leaf morphology, intensity of leaf color, and chlorophyll content. Comparative transcriptome analysis of leaf and lupulin gland tissues indicates that the expression of enzymatic genes related to secondary metabolite biosynthesis, phytohormone biosynthesis, floral organs, flowering time, and trichome development, including other genes related to starch and sucrose metabolism and defense mechanisms, were differentially modulated in the Hlmed5a/med5b lines. The combined results from functional and transcriptomic analyses illuminates the pivotal function of HlMED5a and HlMED5b in homeostasis of secondary meatbolites accumulation in hop.
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Affiliation(s)
- Praveen Awasthi
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Zygmunta Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Ajay Kumar Mishra
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box. Al Ain 15551, United Arab Emirates.
| | - Tomáš Kocábek
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Vishnu Sukumari Nath
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box. Al Ain 15551, United Arab Emirates
| | - Sagarika Mishra
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box. Al Ain 15551, United Arab Emirates
| | - Khaled M Hazzouri
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box. Al Ain 15551, United Arab Emirates
| | - Naganeeswaran Sudalaimuthuasari
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box. Al Ain 15551, United Arab Emirates
| | - Natasa Stajner
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Karel Krofta
- Hop Research Institute, Co. Ltd., Kadaňská 2525, 438 46, Žatec, Czech Republic
| | - Tomáš Hájek
- University of South Bohemia, Faculty of Science, Branišovská 1716/31c, 370 05, České Budějovice, Czech Republic
| | - Khaled Ma Amiri
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box. Al Ain 15551, United Arab Emirates.
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Mipeshwaree Devi A, Khedashwori Devi K, Premi Devi P, Lakshmipriyari Devi M, Das S. Metabolic engineering of plant secondary metabolites: prospects and its technological challenges. FRONTIERS IN PLANT SCIENCE 2023; 14:1171154. [PMID: 37251773 PMCID: PMC10214965 DOI: 10.3389/fpls.2023.1171154] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/17/2023] [Indexed: 05/31/2023]
Abstract
Plants produce a wide range of secondary metabolites that play vital roles for their primary functions such as growth, defence, adaptations or reproduction. Some of the plant secondary metabolites are beneficial to mankind as nutraceuticals and pharmaceuticals. Metabolic pathways and their regulatory mechanism are crucial for targeting metabolite engineering. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-mediated system has been widely applied in genome editing with high accuracy, efficiency, and multiplex targeting ability. Besides its vast application in genetic improvement, the technique also facilitates a comprehensive profiling approach to functional genomics related to gene discovery involved in various plant secondary metabolic pathways. Despite these wide applications, several challenges limit CRISPR/Cas system applicability in genome editing in plants. This review highlights updated applications of CRISPR/Cas system-mediated metabolic engineering of plants and its challenges.
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Affiliation(s)
| | | | | | | | - Sudripta Das
- Plant Bioresources Division, Institute of Bioresources and Sustainable Development, Imphal, Manipur, India
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Cottrell MT. A Search for Diastatic Enzymes Endogenous to Humulus lupulus and Produced by Microbes Associated with Pellet Hops Driving “Hop Creep” of Dry Hopped Beer. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2022. [DOI: 10.1080/03610470.2022.2084327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Hop (Humulus lupulus L.) Essential Oils and Xanthohumol Derived from Extraction Process Using Solvents of Different Polarity. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050368] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This study evaluates the content of essential oils (EOs) and prenylated flavonoid Xanthohumol (XN) in extracts of Slovenian hops, cultivar Aurora, obtained by using fluids of different polarity. It is a continuation of our previous work, investigating the extraction of bitter acids from hops. Extraction was conducted semi-continuously, using sub- and supercritical fluids of different polarity, i.e., carbon dioxide (CO2) and propane as non-polar and dimethyl ether (DME) as the polar solvent. The experiments explored a temperature range between 20 °C and 80 °C and pressures ranging from 50 bar to 150 bar. The content of XN in extracts was analysed using high-performance liquid chromatography and experiments demonstrated the largest concentration of XN was obtained using DME. In order to analyse the EO components in extracts, connected with a distinct odour, the steam distillation of extracts was performed and GC analysis was employed. Hop oil derived from CO2 extracts at specific conditions, had the highest relative concentration of linalool, β-caryophyllene and α-humulene, and oil derived from propane extracts had the highest content of all other five selected components (myrcene, geraniol, farnesene, α-selinene and δ-cadinene). The relative content of the investigated EO components in DME extracts was similar to that in propane extracts.
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Gupta P, Hirschberg J. The Genetic Components of a Natural Color Palette: A Comprehensive List of Carotenoid Pathway Mutations in Plants. FRONTIERS IN PLANT SCIENCE 2022; 12:806184. [PMID: 35069664 PMCID: PMC8770946 DOI: 10.3389/fpls.2021.806184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/08/2021] [Indexed: 05/16/2023]
Abstract
Carotenoids comprise the most widely distributed natural pigments. In plants, they play indispensable roles in photosynthesis, furnish colors to flowers and fruit and serve as precursor molecules for the synthesis of apocarotenoids, including aroma and scent, phytohormones and other signaling molecules. Dietary carotenoids are vital to human health as a source of provitamin A and antioxidants. Hence, the enormous interest in carotenoids of crop plants. Over the past three decades, the carotenoid biosynthesis pathway has been mainly deciphered due to the characterization of natural and induced mutations that impair this process. Over the year, numerous mutations have been studied in dozens of plant species. Their phenotypes have significantly expanded our understanding of the biochemical and molecular processes underlying carotenoid accumulation in crops. Several of them were employed in the breeding of crops with higher nutritional value. This compendium of all known random and targeted mutants available in the carotenoid metabolic pathway in plants provides a valuable resource for future research on carotenoid biosynthesis in plant species.
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Affiliation(s)
| | - Joseph Hirschberg
- Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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Sub- and Supercritical Extraction of Slovenian Hops ( Humulus lupulus L.) Aurora Variety Using Different Solvents. PLANTS 2021; 10:plants10061137. [PMID: 34205132 PMCID: PMC8229442 DOI: 10.3390/plants10061137] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/27/2021] [Accepted: 05/31/2021] [Indexed: 02/07/2023]
Abstract
This work investigates the efficiency of supercritical fluid extraction of hops with a variety of solvents including carbon dioxide (CO2), propane, sulfur hexafluoride (SF6), and dimethyl ether (DME) at various densities (low-density and high-density). Operating parameters were 50 bar, 100 bar and 150 bar and 20 °C, 40 °C, 60 °C and 80 °C for all solvents, respectively. The influence of process parameters on the total yield of extraction and content of bitter acids in the extracts has been investigated. The mathematical model based on Fick's second law well described the experimental extraction results. Furthermore, HPLC analysis has been used to determine α- and β-acids in extracts. The yield of bitter compounds in hop extracts was largely influenced by the type of solvent, the temperature and pressure applied during extraction. The results show that CO2 and propane were roughly equivalent to DME in solvating power, while SF6 was a poor solvent at the same conditions. The highest yield as well as the highest concentration of bitter acids in extracts were obtained by using DME, where the optimal operating conditions were 40 °C and 100 bar for the extraction of α-acids (max. concentration 9.6%), 60 °C and 50 bar for the extraction of β-acids (4.5%) and 60 °C and 150 bar for the maximum extraction yield (25.6%).
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