1
|
Kumar J, Alok A, Steffenson BJ, Kianian S. A geminivirus crosses the monocot-dicot boundary and acts as a viral vector for gene silencing and genome editing. J Adv Res 2024; 61:35-45. [PMID: 37730118 DOI: 10.1016/j.jare.2023.09.013] [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: 07/24/2023] [Revised: 08/31/2023] [Accepted: 09/17/2023] [Indexed: 09/22/2023] Open
Abstract
INTRODUCTION Members of the family Geminiviridae have been reported to infect either a monocot plant or a dicot plant, but not both. This study reports a geminivirus, Wheat Dwarf India Virus (WDIV), first identified in wheat, that is capable of infecting both monocot and dicot plants and acting as a viral vector. OBJECTIVES This study was aimed at developing a broad host range viral vector system for reverse genetics and genome editing. METHODS Here we used a wheat isolate of WDIV and Ageratum yellow leaf curl betasatellite (AYLCB) for infectivity assays and vector development. We performed Agrobacterium-mediated inoculation of WDIV and AYLCB in wheat, oat, barley, corn, soybean, and tobacco. To examine the potential of WDIV to act as a viral vector, we modified the WDIV genome and cloned DNA fragments of the phytoene desaturase (PDS) genes from wheat and tobacco, separately. For gene editing experiments, tobacco lines expressing Cas9 were infiltrated with a WDIV-based vector carrying gRNA targeting the PDS gene. RESULTS About 80 to 90% of plants inoculated with infectious clones of WDIV alone or WDIV together with AYLCB showed mild symptoms, whereas some plants showed more prominent symptoms. WDIV and AYLCB were detected in the systemically infected leaves of all the plant species. Furthermore, the inoculation of the WDIV vector carrying PDS fragments induced silencing of the PDS gene in both wheat and tobacco plants. We also observed high-efficiency genome editing in the Cas9-expressing tobacco plants that were inoculated with WDIV vector-carrying gRNA. CONCLUSION Detection of WDIV in naturally infected wheat, barley, and sugarcane in the field and its ability to systemically infect wheat, oat, barley, corn, soybean, and tobacco under laboratory conditions, provides compelling evidence that WDIV is the first geminivirus identified with the capability of infecting both monocot and dicot plant species. The wide host range of WDIV can be exploited for developing a single vector system for high-throughput genome editing in many plant species.
Collapse
Affiliation(s)
- Jitendra Kumar
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, United States
| | - Anshu Alok
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, United States
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, United States
| | - Shahryar Kianian
- USDA-ARS Cereal Disease Laboratory, Saint Paul, MN 55108, United States.
| |
Collapse
|
2
|
Occhialini A, Lenaghan SC. Plastid engineering using episomal DNA. PLANT CELL REPORTS 2023:10.1007/s00299-023-03020-x. [PMID: 37127835 DOI: 10.1007/s00299-023-03020-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/11/2023] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE Novel episomal systems have the potential to accelerate plastid genetic engineering for application in plant synthetic biology. Plastids represent valuable subcellular compartments for genetic engineering of plants with intrinsic advantages to engineering the nucleus. The ability to perform site-specific transgene integration by homologous recombination (HR), coordination of transgene expression in operons, and high production of heterologous proteins, all make plastids an attractive target for synthetic biology. Typically, plastid engineering is performed by homologous recombination; however, episomal-replicating vectors have the potential to accelerate the design/build/test cycles for plastid engineering. By accelerating the timeline from design to validation, it will be possible to generate translational breakthroughs in fields ranging from agriculture to biopharmaceuticals. Episomal-based plastid engineering will allow precise single step metabolic engineering in plants enabling the installation of complex synthetic circuits with the ambitious goal of reaching similar efficiency and flexibility of to the state-of-the-art genetic engineering of prokaryotic systems. The prospect to design novel episomal systems for production of transplastomic marker-free plants will also improve biosafety for eventual release in agriculture.
Collapse
Affiliation(s)
- Alessandro Occhialini
- Department of Plant Sciences, University of Tennessee, 112 Plant Biotechnology Building 2505 E J Chapman Drive, Knoxville, TN, 37996, USA.
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, 2640 Morgan Circle Drive, Knoxville, TN, 37996, USA.
| | - Scott C Lenaghan
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, 2640 Morgan Circle Drive, Knoxville, TN, 37996, USA.
- Department of Food Science, University of Tennessee, 102 Food Safety and Processing Building 2600 River Dr., Knoxville, TN, 37996, USA.
| |
Collapse
|
3
|
Liu Q, Zhao C, Sun K, Deng Y, Li Z. Engineered biocontainable RNA virus vectors for non-transgenic genome editing across crop species and genotypes. MOLECULAR PLANT 2023; 16:616-631. [PMID: 36751129 DOI: 10.1016/j.molp.2023.02.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/13/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
CRISPR/Cas genome-editing tools provide unprecedented opportunities for basic plant biology research and crop breeding. However, the lack of robust delivery methods has limited the widespread adoption of these revolutionary technologies in plant science. Here, we report an efficient, non-transgenic CRISPR/Cas delivery platform based on the engineered tomato spotted wilt virus (TSWV), an RNA virus with a host range of over 1000 plant species. We eliminated viral elements essential for insect transmission to liberate genome space for accommodating large genetic cargoes without sacrificing the ability to infect plant hosts. The resulting non-insect-transmissible viral vectors enabled effective and stable in planta delivery of Cas12a and Cas9 nucleases as well as adenine and cytosine base editors. In systemically infected plant tissues, the deconstructed TSWV-derived vectors induced efficient somatic gene mutations and base conversions in multiple crop species with little genotype dependency. Plants with heritable, bi-allelic mutations could be readily regenerated by culturing the virus-infected tissues in vitro without antibiotic selection. Moreover, we showed that antiviral treatment with ribavirin during tissue culture cleared the viral vectors in 100% of regenerated plants and further augmented the recovery of heritable mutations. Because many plants are recalcitrant to stable transformation, the viral delivery system developed in this work provides a promising tool to overcome gene delivery bottlenecks for genome editing in various crop species and elite varieties.
Collapse
Affiliation(s)
- Qian Liu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Chenglu Zhao
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Kai Sun
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yinlu Deng
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhenghe Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China; Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou, China.
| |
Collapse
|
4
|
Mahmood MA, Naqvi RZ, Rahman SU, Amin I, Mansoor S. Plant Virus-Derived Vectors for Plant Genome Engineering. Viruses 2023; 15:v15020531. [PMID: 36851743 PMCID: PMC9958682 DOI: 10.3390/v15020531] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/25/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Advances in genome engineering (GE) tools based on sequence-specific programmable nucleases have revolutionized precise genome editing in plants. However, only the traditional approaches are used to deliver these GE reagents, which mostly rely on Agrobacterium-mediated transformation or particle bombardment. These techniques have been successfully used for the past decades for the genetic engineering of plants with some limitations relating to lengthy time-taking protocols and transgenes integration-related regulatory concerns. Nevertheless, in the era of climate change, we require certain faster protocols for developing climate-smart resilient crops through GE to deal with global food security. Therefore, some alternative approaches are needed to robustly deliver the GE reagents. In this case, the plant viral vectors could be an excellent option for the delivery of GE reagents because they are efficient, effective, and precise. Additionally, these are autonomously replicating and considered as natural specialists for transient delivery. In the present review, we have discussed the potential use of these plant viral vectors for the efficient delivery of GE reagents. We have further described the different plant viral vectors, such as DNA and RNA viruses, which have been used as efficient gene targeting systems in model plants, and in other important crops including potato, tomato, wheat, and rice. The achievements gained so far in the use of viral vectors as a carrier for GE reagent delivery are depicted along with the benefits and limitations of each viral vector. Moreover, recent advances have been explored in employing viral vectors for GE and adapting this technology for future research.
Collapse
Affiliation(s)
- Muhammad Arslan Mahmood
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad 38000, Pakistan
- Department of Biological Sciences, University of Sialkot, Sialkot 51310, Pakistan
| | - Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad 38000, Pakistan
| | - Saleem Ur Rahman
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad 38000, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad 38000, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad 38000, Pakistan
- International Center for Chemical and Biological Sciences, University of Karachi, Karachi 74000, Pakistan
- Correspondence:
| |
Collapse
|
5
|
Uranga M, Daròs JA. Tools and targets: The dual role of plant viruses in CRISPR-Cas genome editing. THE PLANT GENOME 2022:e20220. [PMID: 35698891 DOI: 10.1002/tpg2.20220] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/31/2022] [Indexed: 06/15/2023]
Abstract
The recent emergence of tools based on the clustered, regularly interspaced, short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins have revolutionized targeted genome editing, thus holding great promise to both basic plant science and precision crop breeding. Conventional approaches for the delivery of editing components rely on transformation technologies or transient delivery to protoplasts, both of which are time-consuming, laborious, and can raise legal concerns. Alternatively, plant RNA viruses can be used as transient delivery vectors of CRISPR-Cas reaction components, following the so-called virus-induced genome editing (VIGE). During the last years, researchers have been able to engineer viral vectors for the delivery of CRISPR guide RNAs and Cas nucleases. Considering that each viral vector is limited to its molecular biology properties and a specific host range, here we review recent advances for improving the VIGE toolbox with a special focus on strategies to achieve tissue-culture-free editing in plants. We also explore the utility of CRISPR-Cas technology to enhance biotic resistance with a special focus on plant virus diseases. This can be achieved by either targeting the viral genome or modifying essential host susceptibility genes that mediate in the infection process. Finally, we discuss the challenges and potential that VIGE holds in future breeding technologies.
Collapse
Affiliation(s)
- Mireia Uranga
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - University. Politècnica de València, Valencia, 46022, Spain
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - University. Politècnica de València, Valencia, 46022, Spain
| |
Collapse
|
6
|
Olivares F, Loyola R, Olmedo B, Miccono MDLÁ, Aguirre C, Vergara R, Riquelme D, Madrid G, Plantat P, Mora R, Espinoza D, Prieto H. CRISPR/Cas9 Targeted Editing of Genes Associated With Fungal Susceptibility in Vitis vinifera L. cv. Thompson Seedless Using Geminivirus-Derived Replicons. FRONTIERS IN PLANT SCIENCE 2021; 12:791030. [PMID: 35003180 PMCID: PMC8733719 DOI: 10.3389/fpls.2021.791030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/29/2021] [Indexed: 05/14/2023]
Abstract
The woody nature of grapevine (Vitis vinifera L.) has hindered the development of efficient gene editing strategies to improve this species. The lack of highly efficient gene transfer techniques, which, furthermore, are applied in multicellular explants such as somatic embryos, are additional technical handicaps to gene editing in the vine. The inclusion of geminivirus-based replicons in regular T-DNA vectors can enhance the expression of clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) elements, thus enabling the use of these multicellular explants as starting materials. In this study, we used Bean yellow dwarf virus (BeYDV)-derived replicon vectors to express the key components of CRISPR/Cas9 system in vivo and evaluate their editing capability in individuals derived from Agrobacterium-mediated gene transfer experiments of 'Thompson Seedless' somatic embryos. Preliminary assays using a BeYDV-derived vector for green fluorescent protein reporter gene expression demonstrated marker visualization in embryos for up to 33 days post-infiltration. A universal BeYDV-based vector (pGMV-U) was assembled to produce all CRISPR/Cas9 components with up to four independent guide RNA (gRNA) expression cassettes. With a focus on fungal tolerance, we used gRNA pairs to address considerably large deletions of putative grape susceptibility genes, including AUXIN INDUCED IN ROOT CULTURE 12 (VviAIR12), SUGARS WILL EVENTUALLY BE EXPORTED TRANSPORTER 4 (VviSWEET4), LESION INITIATION 2 (VviLIN2), and DIMERIZATION PARTNER-E2F-LIKE 1 (VviDEL1). The editing functionality of gRNA pairs in pGMV-U was evaluated by grapevine leaf agroinfiltration assays, thus enabling longer-term embryo transformations. These experiments allowed for the establishment of greenhouse individuals exhibiting a double-cut edited status for all targeted genes under different allele-editing conditions. After approximately 18 months, the edited grapevine plants were preliminary evaluated regarding its resistance to Erysiphe necator and Botrytis cinerea. Assays have shown that a transgene-free VviDEL1 double-cut edited line exhibits over 90% reduction in symptoms triggered by powdery mildew infection. These results point to the use of geminivirus-based replicons for gene editing in grapevine and other relevant fruit species.
Collapse
Affiliation(s)
- Felipe Olivares
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Rodrigo Loyola
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Blanca Olmedo
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - María de los Ángeles Miccono
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Carlos Aguirre
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Ricardo Vergara
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Danae Riquelme
- Phytopathology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Gabriela Madrid
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Philippe Plantat
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Roxana Mora
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Daniel Espinoza
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Humberto Prieto
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| |
Collapse
|
7
|
Bellido AM, Souza Canadá ED, Permingeat HR, Echenique V. Genetic Transformation of Apomictic Grasses: Progress and Constraints. FRONTIERS IN PLANT SCIENCE 2021; 12:768393. [PMID: 34804102 PMCID: PMC8602796 DOI: 10.3389/fpls.2021.768393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/05/2021] [Indexed: 05/17/2023]
Abstract
The available methods for plant transformation and expansion beyond its limits remain especially critical for crop improvement. For grass species, this is even more critical, mainly due to drawbacks in in vitro regeneration. Despite the existence of many protocols in grasses to achieve genetic transformation through Agrobacterium or biolistic gene delivery, their efficiencies are genotype-dependent and still very low due to the recalcitrance of these species to in vitro regeneration. Many plant transformation facilities for cereals and other important crops may be found around the world in universities and enterprises, but this is not the case for apomictic species, many of which are C4 grasses. Moreover, apomixis (asexual reproduction by seeds) represents an additional constraint for breeding. However, the transformation of an apomictic clone is an attractive strategy, as the transgene is immediately fixed in a highly adapted genetic background, capable of large-scale clonal propagation. With the exception of some species like Brachiaria brizantha which is planted in approximately 100 M ha in Brazil, apomixis is almost non-present in economically important crops. However, as it is sometimes present in their wild relatives, the main goal is to transfer this trait to crops to fix heterosis. Until now this has been a difficult task, mainly because many aspects of apomixis are unknown. Over the last few years, many candidate genes have been identified and attempts have been made to characterize them functionally in Arabidopsis and rice. However, functional analysis in true apomictic species lags far behind, mainly due to the complexity of its genomes, of the trait itself, and the lack of efficient genetic transformation protocols. In this study, we review the current status of the in vitro culture and genetic transformation methods focusing on apomictic grasses, and the prospects for the application of new tools assayed in other related species, with two aims: to pave the way for discovering the molecular pathways involved in apomixis and to develop new capacities for breeding purposes because many of these grasses are important forage or biofuel resources.
Collapse
Affiliation(s)
- Andrés M. Bellido
- Departamento de Agronomía, Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS – CCT – CONICET Bahía Blanca), Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | | | | | - Viviana Echenique
- Departamento de Agronomía, Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS – CCT – CONICET Bahía Blanca), Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| |
Collapse
|
8
|
Acha G, Vergara R, Muñoz M, Mora R, Aguirre C, Muñoz M, Kalazich J, Prieto H. A Traceable DNA-Replicon Derived Vector to Speed Up Gene Editing in Potato: Interrupting Genes Related to Undesirable Postharvest Tuber Traits as an Example. PLANTS 2021; 10:plants10091882. [PMID: 34579415 PMCID: PMC8468489 DOI: 10.3390/plants10091882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 11/30/2022]
Abstract
In potato (Solanum tuberosum L.), protoplast techniques are limited to a few genotypes; thus, the use of regular regeneration procedures of multicellular explants causes us to face complexities associated to CRISPR/Cas9 gene editing efficiency and final identification of individuals. Geminivirus-based replicons contained in T-DNAs could provide an improvement to these procedures considering their cargo capability. We built a Bean yellow dwarf virus-derived replicon vector, pGEF-U, that expresses all the editing reagents under a multi-guide RNA condition, and the Green Fluorescent Protein (GFP) marker gene. Agrobacterium-mediated gene transfer experiments were carried out on ‘Yagana-INIA’, a relevant local variety with no previous regeneration protocol. Assays showed that pGEF-U had GFP transient expression for up to 10 days post-infiltration when leaf explants were used. A dedicated potato genome analysis tool allowed for the design of guide RNA pairs to induce double cuts of genes associated to enzymatic browning (StPPO1 and 2) and to cold-induced sweetening (StvacINV1 and StBAM1). Monitoring GFP at 7 days post-infiltration, explants led to vector validation as well as to selection for regeneration (34.3% of starting explants). Plant sets were evaluated for the targeted deletion, showing individuals edited for StPPO1 and StBAM1 genes (1 and 4 lines, respectively), although with a transgenic condition. While no targeted deletion was seen in StvacINV1 and StPPO2 plant sets, stable GFP-expressing calli were chosen for analysis; we observed different repair alternatives, ranging from the expected loss of large gene fragments to those showing punctual insertions/deletions at both cut sites or incomplete repairs along the target region. Results validate pGEF-U for gene editing coupled to regular regeneration protocols, and both targeted deletion and single site editings encourage further characterization of the set of plants already generated.
Collapse
Affiliation(s)
- Giovana Acha
- Programa de Doctorado en Biotecnología, Universidad de Santiago, Santiago 9170020, Chile;
| | - Ricardo Vergara
- Laboratorio de Biotecnología, Instituto de Investigaciones Agropecuarias-La Platina, Santiago 8831314, Chile; (M.M.); (R.M.); (C.A.)
- Correspondence: (R.V.); (H.P.); Tel.: +56-2-2577-9129 (R.V. & H.P.)
| | - Marisol Muñoz
- Laboratorio de Biotecnología, Instituto de Investigaciones Agropecuarias-La Platina, Santiago 8831314, Chile; (M.M.); (R.M.); (C.A.)
| | - Roxana Mora
- Laboratorio de Biotecnología, Instituto de Investigaciones Agropecuarias-La Platina, Santiago 8831314, Chile; (M.M.); (R.M.); (C.A.)
| | - Carlos Aguirre
- Laboratorio de Biotecnología, Instituto de Investigaciones Agropecuarias-La Platina, Santiago 8831314, Chile; (M.M.); (R.M.); (C.A.)
| | - Manuel Muñoz
- Instituto de Investigaciones Agropecuarias-Remehue, Osorno 5290000, Chile;
| | - Julio Kalazich
- Carrera de Agronomía, Campus Osorno, Universidad de Los Lagos, Osorno 5290000, Chile;
| | - Humberto Prieto
- Laboratorio de Biotecnología, Instituto de Investigaciones Agropecuarias-La Platina, Santiago 8831314, Chile; (M.M.); (R.M.); (C.A.)
- Correspondence: (R.V.); (H.P.); Tel.: +56-2-2577-9129 (R.V. & H.P.)
| |
Collapse
|
9
|
Venkataraman S, Hefferon K. Application of Plant Viruses in Biotechnology, Medicine, and Human Health. Viruses 2021; 13:1697. [PMID: 34578279 PMCID: PMC8473230 DOI: 10.3390/v13091697] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 07/02/2021] [Accepted: 07/12/2021] [Indexed: 01/06/2023] Open
Abstract
Plant-based nanotechnology programs using virus-like particles (VLPs) and virus nanoparticles (VNPs) are emerging platforms that are increasingly used for a variety of applications in biotechnology and medicine. Tobacco mosaic virus (TMV) and potato virus X (PVX), by virtue of having high aspect ratios, make ideal platforms for drug delivery. TMV and PVX both possess rod-shaped structures and single-stranded RNA genomes encapsidated by their respective capsid proteins and have shown great promise as drug delivery systems. Cowpea mosaic virus (CPMV) has an icosahedral structure, and thus brings unique benefits as a nanoparticle. The uses of these three plant viruses as either nanostructures or expression vectors for high value pharmaceutical proteins such as vaccines and antibodies are discussed extensively in the following review. In addition, the potential uses of geminiviruses in medical biotechnology are explored. The uses of these expression vectors in plant biotechnology applications are also discussed. Finally, in this review, we project future prospects for plant viruses in the fields of medicine, human health, prophylaxis, and therapy of human diseases.
Collapse
Affiliation(s)
| | - Kathleen Hefferon
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada;
| |
Collapse
|
10
|
Ali Z, Mahfouz MM. CRISPR/Cas systems versus plant viruses: engineering plant immunity and beyond. PLANT PHYSIOLOGY 2021; 186:1770-1785. [PMID: 35237805 PMCID: PMC8331158 DOI: 10.1093/plphys/kiab220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 04/16/2021] [Indexed: 05/02/2023]
Abstract
Molecular engineering of plant immunity to confer resistance against plant viruses holds great promise for mitigating crop losses and improving plant productivity and yields, thereby enhancing food security. Several approaches have been employed to boost immunity in plants by interfering with the transmission or lifecycles of viruses. In this review, we discuss the successful application of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) (CRISPR/Cas) systems to engineer plant immunity, increase plant resistance to viruses, and develop viral diagnostic tools. Furthermore, we examine the use of plant viruses as delivery systems to engineer virus resistance in plants and provide insight into the limitations of current CRISPR/Cas approaches and the potential of newly discovered CRISPR/Cas systems to engineer better immunity and develop better diagnostics tools for plant viruses. Finally, we outline potential solutions to key challenges in the field to enable the practical use of these systems for crop protection and viral diagnostics.
Collapse
Affiliation(s)
- Zahir Ali
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Author for communication:
| |
Collapse
|
11
|
Jakubiec A, Sarokina A, Choinard S, Vlad F, Malcuit I, Sorokin AP. Replicating minichromosomes as a new tool for plastid genome engineering. NATURE PLANTS 2021; 7:932-941. [PMID: 34155372 DOI: 10.1038/s41477-021-00940-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 05/11/2021] [Indexed: 05/19/2023]
Abstract
Plant molecular farming, that is, using plants as hosts for production of therapeutic proteins and high-value compounds, has gained substantial interest in recent years. Chloroplasts in particular are an attractive subcellular compartment for expression of foreign genes. Here, we present a new method for transgene introduction and expression in chloroplasts that, unlike classically used approaches, does not require transgene insertion into the chloroplast genome. Instead, the transgene is amplified as a physically independent entity termed a 'minichromosome'. Amplification occurs in the presence of a helper protein that initiates the replication process via recognition of specific sequences flanking the transgene, resulting in accumulation of extremely high levels of transgene DNA. Importantly, we demonstrate that such amplified transgenes serve as a template for foreign protein expression, are maintained stably during plant development and are maternally transmitted to the progeny. These findings indicate that the minichromosome-based approach is an attractive tool for transgene expression in chloroplasts and for organelle genome engineering.
Collapse
Affiliation(s)
| | | | - Sandrine Choinard
- Algentech SAS, Evry-Courcouronnes, France
- Institut Jean-Pierre Bourgin (UMR1318), INRAE Centre Versailles-Grignon, Versailles, France
| | | | | | | |
Collapse
|
12
|
Mushtaq M, Ahmad Dar A, Skalicky M, Tyagi A, Bhagat N, Basu U, Bhat BA, Zaid A, Ali S, Dar TUH, Rai GK, Wani SH, Habib-Ur-Rahman M, Hejnak V, Vachova P, Brestic M, Çığ A, Çığ F, Erman M, EL Sabagh A. CRISPR-Based Genome Editing Tools: Insights into Technological Breakthroughs and Future Challenges. Genes (Basel) 2021; 12:797. [PMID: 34073848 PMCID: PMC8225059 DOI: 10.3390/genes12060797] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/11/2022] Open
Abstract
Genome-editing (GE) is having a tremendous influence around the globe in the life science community. Among its versatile uses, the desired modifications of genes, and more importantly the transgene (DNA)-free approach to develop genetically modified organism (GMO), are of special interest. The recent and rapid developments in genome-editing technology have given rise to hopes to achieve global food security in a sustainable manner. We here discuss recent developments in CRISPR-based genome-editing tools for crop improvement concerning adaptation, opportunities, and challenges. Some of the notable advances highlighted here include the development of transgene (DNA)-free genome plants, the availability of compatible nucleases, and the development of safe and effective CRISPR delivery vehicles for plant genome editing, multi-gene targeting and complex genome editing, base editing and prime editing to achieve more complex genetic engineering. Additionally, new avenues that facilitate fine-tuning plant gene regulation have also been addressed. In spite of the tremendous potential of CRISPR and other gene editing tools, major challenges remain. Some of the challenges are related to the practical advances required for the efficient delivery of CRISPR reagents and for precision genome editing, while others come from government policies and public acceptance. This review will therefore be helpful to gain insights into technological advances, its applications, and future challenges for crop improvement.
Collapse
Affiliation(s)
- Muntazir Mushtaq
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India; (M.M.); (A.A.D.)
| | - Aejaz Ahmad Dar
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India; (M.M.); (A.A.D.)
| | - Milan Skalicky
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
| | - Anshika Tyagi
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India;
| | - Nancy Bhagat
- School of Biotechnology, University of Jammu, Jammu 180006, India;
| | - Umer Basu
- Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India;
| | | | - Abbu Zaid
- Plant Physiology and Biochemistry Section, Department of Botany Aligarh Muslim University, Aigarh 202002, India;
| | - Sajad Ali
- Centre of Research for Development, University of Kashmir, Srinagar 190006, India;
| | | | - Gyanendra Kumar Rai
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India; (M.M.); (A.A.D.)
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Khudwani, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Jammu 192101, India
| | - Muhammad Habib-Ur-Rahman
- Department of Crop Science, Institute of Crop Science and Resource Conservation (INRES), University Bonn, 53115 Bonn, Germany;
| | - Vaclav Hejnak
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
| | - Pavla Vachova
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
| | - Marian Brestic
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
- Department of Plant Physiology, Slovak University of Agriculture, Nitra, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia
| | - Arzu Çığ
- Department of Horticulture, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey;
| | - Fatih Çığ
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey; (F.Ç.); (M.E.)
| | - Murat Erman
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey; (F.Ç.); (M.E.)
| | - Ayman EL Sabagh
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey; (F.Ç.); (M.E.)
- Department of Agronomy, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| |
Collapse
|
13
|
Yu Y, Wang X, Sun H, Liang Q, Wang W, Zhang C, Bian X, Cao Q, Li Q, Xie Y, Ma D, Li Z, Sun J. Improving CRISPR-Cas-mediated RNA targeting and gene editing using SPLCV replicon-based expression vectors in Nicotiana benthamiana. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1993-1995. [PMID: 32289196 PMCID: PMC7539982 DOI: 10.1111/pbi.13384] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 02/27/2020] [Accepted: 03/30/2020] [Indexed: 05/28/2023]
Affiliation(s)
- Yicheng Yu
- Jiangsu Key Laboratory of Phylogenomics and Comparative GenomicsSchool of Life SciencesJiangsu Normal UniversityXuzhouJiangsuChina
| | - Xiao Wang
- Jiangsu Key Laboratory of Phylogenomics and Comparative GenomicsSchool of Life SciencesJiangsu Normal UniversityXuzhouJiangsuChina
| | - Houjun Sun
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai DistrictXuzhouJiangsuChina
| | - Qiang Liang
- Jiangsu Key Laboratory of Phylogenomics and Comparative GenomicsSchool of Life SciencesJiangsu Normal UniversityXuzhouJiangsuChina
| | - Weichi Wang
- Jiangsu Key Laboratory of Phylogenomics and Comparative GenomicsSchool of Life SciencesJiangsu Normal UniversityXuzhouJiangsuChina
| | - Chengling Zhang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai DistrictXuzhouJiangsuChina
| | - Xiaofeng Bian
- Institute of Food CropsProvincial Key Laboratory of AgrobiologyJiangsu Academy of Agricultural SciencesNanjingJiangsuChina
| | - Qinghe Cao
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai DistrictXuzhouJiangsuChina
| | - Qiang Li
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai DistrictXuzhouJiangsuChina
| | - Yiping Xie
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai DistrictXuzhouJiangsuChina
| | - Daifu Ma
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai DistrictXuzhouJiangsuChina
| | - Zongyun Li
- Jiangsu Key Laboratory of Phylogenomics and Comparative GenomicsSchool of Life SciencesJiangsu Normal UniversityXuzhouJiangsuChina
| | - Jian Sun
- Jiangsu Key Laboratory of Phylogenomics and Comparative GenomicsSchool of Life SciencesJiangsu Normal UniversityXuzhouJiangsuChina
| |
Collapse
|
14
|
Medina-Puche L, Lozano-Duran R. Tailoring the cell: a glimpse of how plant viruses manipulate their hosts. CURRENT OPINION IN PLANT BIOLOGY 2019; 52:164-173. [PMID: 31731105 DOI: 10.1016/j.pbi.2019.09.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 09/22/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
Viruses are intracellular parasites that completely rely on the molecular machinery of the infected host to complete their cycle. Upon invasion of a susceptible cell, viruses dramatically reshape the intracellular environment to suit their needs, in a complex process that requires the fine manipulation of multiple aspects of the host cell biology, including those enabling replication of the viral genome, facilitating suppression or avoidance of anti-viral plant defence mechanisms, and supporting precise intra-cellular and inter-cellular trafficking of viral components. This tailoring of the cell to fit viral functions occurs through the coordinated action of fast-evolving, multifunctional viral proteins, which efficiently target host factors. In this review, we intend to offer a glimpse of how plant viruses manipulate their hosts from a cell biology perspective, focusing on recent advances covering three specific aspects of the viral infection: viral manipulation of organelle function; virus-induced formation of viral replication complexes through membrane remodelling; and viral evasion of autophagy.
Collapse
Affiliation(s)
- Laura Medina-Puche
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Rosa Lozano-Duran
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China.
| |
Collapse
|
15
|
Eckerstorfer MF, Dolezel M, Heissenberger A, Miklau M, Reichenbecher W, Steinbrecher RA, Waßmann F. An EU Perspective on Biosafety Considerations for Plants Developed by Genome Editing and Other New Genetic Modification Techniques (nGMs). Front Bioeng Biotechnol 2019; 7:31. [PMID: 30891445 PMCID: PMC6413072 DOI: 10.3389/fbioe.2019.00031] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 02/05/2019] [Indexed: 12/23/2022] Open
Abstract
The question whether new genetic modification techniques (nGM) in plant development might result in non-negligible negative effects for the environment and/or health is significant for the discussion concerning their regulation. However, current knowledge to address this issue is limited for most nGMs, particularly for recently developed nGMs, like genome editing, and their newly emerging variations, e.g., base editing. This leads to uncertainties regarding the risk/safety-status of plants which are developed with a broad range of different nGMs, especially genome editing, and other nGMs such as cisgenesis, transgrafting, haploid induction or reverse breeding. A literature survey was conducted to identify plants developed by nGMs which are relevant for future agricultural use. Such nGM plants were analyzed for hazards associated either (i) with their developed traits and their use or (ii) with unintended changes resulting from the nGMs or other methods applied during breeding. Several traits are likely to become particularly relevant in the future for nGM plants, namely herbicide resistance (HR), resistance to different plant pathogens as well as modified composition, morphology, fitness (e.g., increased resistance to cold/frost, drought, or salinity) or modified reproductive characteristics. Some traits such as resistance to certain herbicides are already known from existing GM crops and their previous assessments identified issues of concern and/or risks, such as the development of herbicide resistant weeds. Other traits in nGM plants are novel; meaning they are not present in agricultural plants currently cultivated with a history of safe use, and their underlying physiological mechanisms are not yet sufficiently elucidated. Characteristics of some genome editing applications, e.g., the small extent of genomic sequence change and their higher targeting efficiency, i.e., precision, cannot be considered an indication of safety per se, especially in relation to novel traits created by such modifications. All nGMs considered here can result in unintended changes of different types and frequencies. However, the rapid development of nGM plants can compromise the detection and elimination of unintended effects. Thus, a case-specific premarket risk assessment should be conducted for nGM plants, including an appropriate molecular characterization to identify unintended changes and/or confirm the absence of unwanted transgenic sequences.
Collapse
Affiliation(s)
| | - Marion Dolezel
- Department Landuse & Biosafety, Environment Agency Austria, Vienna, Austria
| | | | - Marianne Miklau
- Department Landuse & Biosafety, Environment Agency Austria, Vienna, Austria
| | - Wolfram Reichenbecher
- Department GMO Regulation, Biosafety, Federal Agency for Nature Conservation, Bonn, Germany
| | | | - Friedrich Waßmann
- Department GMO Regulation, Biosafety, Federal Agency for Nature Conservation, Bonn, Germany
| |
Collapse
|
16
|
Jeske H. Barcoding of Plant Viruses with Circular Single-Stranded DNA Based on Rolling Circle Amplification. Viruses 2018; 10:E469. [PMID: 30200312 PMCID: PMC6164888 DOI: 10.3390/v10090469] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 08/28/2018] [Accepted: 08/30/2018] [Indexed: 01/10/2023] Open
Abstract
The experience with a diagnostic technology based on rolling circle amplification (RCA), restriction fragment length polymorphism (RFLP) analyses, and direct or deep sequencing (Circomics) over the past 15 years is surveyed for the plant infecting geminiviruses, nanoviruses and associated satellite DNAs, which have had increasing impact on agricultural and horticultural losses due to global transportation and recombination-aided diversification. Current state methods for quarantine measures are described to identify individual DNA components with great accuracy and to recognize the crucial role of the molecular viral population structure as an important factor for sustainable plant protection.
Collapse
Affiliation(s)
- Holger Jeske
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart, Germany.
| |
Collapse
|
17
|
Petri C, Alburquerque N, Faize M, Scorza R, Dardick C. Current achievements and future directions in genetic engineering of European plum (Prunus domestica L.). Transgenic Res 2018; 27:225-240. [PMID: 29651659 PMCID: PMC5986827 DOI: 10.1007/s11248-018-0072-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 04/06/2018] [Indexed: 01/05/2023]
Abstract
In most woody fruit species, transformation and regeneration are difficult. However, European plum (Prunus domestica) has been shown to be amenable to genetic improvement technologies from classical hybridization, to genetic engineering, to rapid cycle crop breeding ('FasTrack' breeding). Since the first report on European plum transformation with marker genes in the early 90 s, numerous manuscripts have been published reporting the generation of new clones with agronomically interesting traits, such as pests, diseases and/or abiotic stress resistance, shorter juvenile period, dwarfing, continuous flowering, etc. This review focuses on the main advances in genetic transformation of European plum achieved to date, and the lines of work that are converting genetic engineering into a contemporary breeding tool for this species.
Collapse
Affiliation(s)
- Cesar Petri
- Departamento de Producción Vegetal, Instituto de Biotecnología Vegetal, UPCT, Campus Muralla del Mar, 30202, Cartagena, Murcia, Spain.
| | - Nuria Alburquerque
- Departamento de Mejora Vegetal, CEBAS-CSIC, Campus de Espinardo, 30100, Espinardo, Murcia, Spain
| | - Mohamed Faize
- Laboratory of Plant Biotechnology, Ecology and Ecosystem Valorization, Faculty of Sciences, University Chouaib Doukkali, 24000, El Jadida, Morocco
| | - Ralph Scorza
- Ag Biotech and Plant Breeding Consulting Services, Ralph Scorza LLC, Shepherdstown, WV, 25443, USA
| | - Chris Dardick
- USDA-ARS, Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, 25430, USA
| |
Collapse
|
18
|
Kushawaha AK, Rabindran R, Dasgupta I. Rolling circle amplification-based analysis of Sri Lankan cassava mosaic virus isolates from Tamil Nadu, India, suggests a low level of genetic variability. Virusdisease 2018; 29:61-67. [PMID: 29607360 DOI: 10.1007/s13337-018-0432-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 01/20/2018] [Indexed: 10/18/2022] Open
Abstract
Cassava mosaic disease is a widespread disease of cassava in south Asia and the African continent. In India, CMD is known to be caused by two single-stranded DNA viruses (geminiviruses), Indian cassava mosaic virus (ICMV) and Sri Lankan cassava mosdaic virus (SLCMV). Previously, the diversity of ICMV and SLCMV in India has been studied using PCR, a sequence-dependent method. To have a more in-depth study of the variability of the above viruses and to detect any novel geminiviruses associated with CMD, sequence-independent amplification using rolling circle amplification (RCA)-based methods were used. CMD affected cassava plants were sampled across eighty locations in nine districts of the southern Indian state of Tamil Nadu. Twelve complete sequence of coat protein genes of the resident geminiviruses, comprising 256 amino acid residues were generated from the above samples, which indicated changes at only six positions. RCA followed by RFLP of the 80 samples indicated that most samples (47) contained only SLCMV, followed by 8, which were infected jointly with ICMV and SLCMV. In 11 samples, the pattern did not match the expected patterns from either of the two viruses and hence, were variants. Sequence analysis of an average of 700 nucleotides from 31 RCA-generated fragments of the variants indicated identities of 97-99% with the sequence of a previously reported infectious clone of SLCMV. The evidence suggests low levels of genetic variability in the begomoviruses infecting cassava, mainly in the form of scattered single nucleotide changes.
Collapse
Affiliation(s)
- Akhilesh Kumar Kushawaha
- 1Department of Plant Molecular Biology, University of Delhi, South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Ramalingam Rabindran
- 2Center for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641003 India
| | - Indranil Dasgupta
- 1Department of Plant Molecular Biology, University of Delhi, South Campus, Benito Juarez Road, New Delhi, 110021 India
| |
Collapse
|
19
|
Chaudhary K, Chattopadhyay A, Pratap D. The evolution of CRISPR/Cas9 and their cousins: hope or hype? Biotechnol Lett 2018; 40:465-477. [PMID: 29344851 DOI: 10.1007/s10529-018-2506-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 01/08/2018] [Indexed: 12/14/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system allows biologists to edit genomic DNA of any cell in precise and specific way, entailing great potential for crop improvement, drug development and gene therapy. The system involves a nuclease (Cas9) and a designed guide RNA that are involved in wide range of applications such as genome modification, transcriptional modulation, genomic loci marking and RNA tracking. The limitation of the technique, in view of resistance of thymidine-rich genome to Cas9 cleavage, has now been overcome by the use of Cpf1 nuclease. In this review, we present an overview of CRISPR nucleases (Cas9 or Cpf1) with particular emphasis on human genome modification and compare their advantages and limitations. Furthermore, we summarize some of the pros and cons of CRISPR technology particularly in human therapeutics.
Collapse
Affiliation(s)
- Kulbhushan Chaudhary
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Anirudha Chattopadhyay
- Department of Plant Pathology, C.P. College of Agriculture, S.D. Agricultural University, S.K. Nagar, Gujrat, India
| | - Dharmendra Pratap
- Department of Genetics & Plant Breeding, Chaudhary Charan Singh University, Meerut, Uttar Pradesh, India.
| |
Collapse
|
20
|
Zaidi SSEA, Mansoor S. Viral Vectors for Plant Genome Engineering. FRONTIERS IN PLANT SCIENCE 2017; 8:539. [PMID: 28443125 PMCID: PMC5386974 DOI: 10.3389/fpls.2017.00539] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 03/27/2017] [Indexed: 05/19/2023]
Abstract
Recent advances in genome engineering (GE) has made it possible to precisely alter DNA sequences in plant cells, providing specifically engineered plants with traits of interest. Gene targeting efficiency depends on the delivery-method of both sequence-specific nucleases and repair templates, to plant cells. Typically, this is achieved using Agrobacterium mediated transformation or particle bombardment, both of which transform only a subset of cells in treated tissues. The alternate in planta approaches, stably integrating nuclease-encoding cassettes and repair templates into the plant genome, are time consuming, expensive and require extra regulations. More efficient GE reagents delivery methods are clearly needed if GE is to become routine, especially in economically important crops that are difficult to transform. Recently, autonomously replicating virus-based vectors have been demonstrated as efficient means of delivering GE reagents in plants. Both DNA viruses (Bean yellow dwarf virus, Wheat dwarf virus and Cabbage leaf curl virus) and RNA virus (Tobacco rattle virus) have demonstrated efficient gene targeting frequencies in model plants (Nicotiana benthamiana) and crops (potato, tomato, rice, and wheat). Here we discuss the recent advances using viral vectors for plant genome engineering, the current limitations and future directions.
Collapse
Affiliation(s)
- Syed Shan-e-Ali Zaidi
- Molecular Virology and Gene Silencing Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Shahid Mansoor
- Molecular Virology and Gene Silencing Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| |
Collapse
|
21
|
Lennon S, Dolan L. The New Phytologist Tansley Medal 2015. THE NEW PHYTOLOGIST 2016; 210:5. [PMID: 26919692 DOI: 10.1111/nph.13891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
|
22
|
Bhushan K, Pratap D, Sharma PK. Transcription activator‐like effector nucleases (TALENs): An efficient tool for plant genome editing. Eng Life Sci 2016. [DOI: 10.1002/elsc.201500126] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Kul Bhushan
- Advanced Centre for Plant Virology Indian Agricultural Research Institute New Delhi India
| | - Dharmendra Pratap
- Department of Genetics & Plant Breeding Ch. Charan Singh University Meerut Uttar Pradesh India
| | - Pradeep K. Sharma
- Department of Genetics & Plant Breeding Ch. Charan Singh University Meerut Uttar Pradesh India
| |
Collapse
|