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Golubova D, Tansley C, Su H, Patron NJ. Engineering Nicotiana benthamiana as a platform for natural product biosynthesis. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102611. [PMID: 39098308 DOI: 10.1016/j.pbi.2024.102611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/06/2024] [Accepted: 07/15/2024] [Indexed: 08/06/2024]
Abstract
Nicotiana benthamiana is a model plant, widely used for research. The susceptibility of young plants to Agrobacterium tumefaciens has been utilised for transient gene expression, enabling the production of recombinant proteins at laboratory and commercial scales. More recently, this technique has been used for the rapid prototyping of synthetic genetic circuits and for the elucidation and reconstruction of metabolic pathways. In the last few years, many complex metabolic pathways have been successfully reconstructed in this species. In addition, the availability of improved genomic resources and efficient gene editing tools have enabled the application of sophisticated metabolic engineering approaches to increase the purity and yield of target compounds. In this review, we discuss recent advances in the use of N. benthamiana for understanding and engineering plant metabolism, as well as efforts to improve the utility of this species as a production chassis for natural products.
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Affiliation(s)
- D Golubova
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - C Tansley
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK; Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - H Su
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - N J Patron
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK; Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.
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2
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Valli AA, Domingo-Calap ML, González de Prádena A, García JA, Cui H, Desbiez C, López-Moya JJ. Reconceptualizing transcriptional slippage in plant RNA viruses. mBio 2024:e0212024. [PMID: 39287447 DOI: 10.1128/mbio.02120-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Accepted: 08/19/2024] [Indexed: 09/19/2024] Open
Abstract
RNA viruses have evolved sophisticated strategies to exploit the limited encoded information within their typically compact genomes. One of them, named transcriptional slippage (TS), is characterized by the appearance of indels in nascent viral RNAs, leading to changes in the open reading frame (ORF). Although members of unrelated viral families express key proteins via TS, the available information about this phenomenon is still limited. In potyvirids (members of the Potyviridae family), TS has been defined by the insertion of an additional A at An motifs (n ≥ 6) in newly synthesized transcripts at a low frequency, modulated by nucleotides flanking the A-rich motif. Here, by using diverse experimental approaches and a collection of plant/virus combinations, we discover cases not following this definition. In summary, we observe (i) a high rate of single-nucleotide deletions at slippage motifs, (ii) overlapping ORFs acceded by slippage at an U8 stretch, and (iii) changes in slippage rates induced by factors not related to cognate viruses. Moreover, a survey of whole-genome sequences from potyvirids shows a widespread occurrence of species-specific An/Un (n ≥ 6) motifs. Even though many of them, but not all, lead to the production of truncated proteins rather than access to overlapping ORFs, these results suggest that slippage motifs appear more frequently than expected and play relevant roles during virus evolution. Considering the potential of this phenomenon to expand the viral proteome by acceding to overlapping ORFs and/or producing truncated proteins, a re-evaluation of TS significance during infections of RNA viruses is required.IMPORTANCETranscriptional slippage (TS) is used by RNA viruses as another strategy to maximize the coding information in their genomes. This phenomenon is based on a peculiar feature of viral replicases: they may produce indels in a small fraction of newly synthesized viral RNAs when transcribing certain motifs and then produce alternative proteins due to a change of the reading frame or truncated products by premature termination. Here, using plant-infecting RNA viruses as models, we discover cases expanding on previously established features of plant virus TS, prompting us to reconsider and redefine this expression strategy. An interesting conclusion from our study is that TS might be more relevant during RNA virus evolution and infection processes than previously assumed.
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Affiliation(s)
- Adrian A Valli
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - María Luisa Domingo-Calap
- Center for Research in Agricultural Genomics (CRAG-CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Spain
- Evolving Therapeutics SL., Parc Científic de la Universitat de València, Paterna, Spain
| | | | | | - Hongguang Cui
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education and College of Plant Protection, Hainan University, Haikou, Hainan, China
| | | | - Juan José López-Moya
- Center for Research in Agricultural Genomics (CRAG-CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Spain
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Wang JX, Han WH, Xie R, Zhang FB, Ge ZW, Ji SX, Liu SS, Wang XW. Metabolic and Molecular Insights Into Nicotiana benthamiana Trichome Exudates: An Ammunition Depot for Plant Resistance Against Insect Pests. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39262218 DOI: 10.1111/pce.15135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 07/02/2024] [Accepted: 08/20/2024] [Indexed: 09/13/2024]
Abstract
Nicotiana benthamiana, a widely acknowledged laboratory model plant for molecular studies, exhibits lethality to certain insect pests and can serve as a dead-end trap plant for pest control in the field. However, the underlying mechanism of N. benthamiana's resistance against insects remains unknown. Here, we elucidate that the lethal effect of N. benthamiana on the whitefly Bemisia tabaci arises from the toxic glandular trichome exudates. By comparing the metabolite profiles of trichome exudates, we found that 51 metabolites, including five O-acyl sugars (O-AS) with medium-chain acyl moieties, were highly accumulated in N. benthamiana. Silencing of two O-AS biosynthesis genes, branched-chain keto acid dehydrogenase (BCKD) and Isopropyl malate synthase-C (IPMS-C), significantly reduced the O-AS levels in N. benthamiana and its resistance against whiteflies. Additionally, we demonstrated that the higher expression levels of BCKD and IPMS-C in the trichomes of N. benthamiana contribute to O-AS synthesis and consequently enhance whitefly resistance. Furthermore, overexpression of NbBCKD and NbIPMS-C genes in the cultivated tobacco Nicotiana tabacum enhanced its resistance to whiteflies. Our study revealed the metabolic and molecular mechanisms underlying the lethal effect of N. benthamiana on whiteflies and presents a promising avenue for improving whitefly resistance.
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Affiliation(s)
- Jun-Xia Wang
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Wen-Hao Han
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Rui Xie
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Feng-Bin Zhang
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zhi-Wei Ge
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Shun-Xia Ji
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shu-Sheng Liu
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xiao-Wei Wang
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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Pizzio GA, Mayordomo C, Illescas-Miranda J, Coego A, Bono M, Sanchez-Olvera M, Martin-Vasquez C, Samantara K, Merilo E, Forment J, Estevez JC, Nebauer SG, Rodriguez PL. Basal ABA signaling balances transpiration and photosynthesis. PHYSIOLOGIA PLANTARUM 2024; 176:e14494. [PMID: 39210540 DOI: 10.1111/ppl.14494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024]
Abstract
The balance between the CO2 entry for photosynthesis and transpiration water loss is crucial for plant growth, and ABA signaling can affect this equilibrium. To test how ABA balances plant growth and environmental adaptation, we performed molecular genetics studies in the biotech crop Nicotiana benthamiana under well-watered or drought conditions. Studies on ABA signaling in crops are complicated by the multigenic nature of the PYR/PYL/RCAR ABA receptor family and its functional redundancy, which is particularly challenging in polyploid plants. We have generated a pentuple pyl mutant in the allotetraploid Nicotiana benthamiana through CRISPR/Cas9 gene editing. The pentuple mutant is impaired in 2 NbPYL1-like and 3 NbPYL8-like receptors, affecting the regulation of transpiration and several ABA-dependent transcriptional processes. RNA-seq and metabolite analysis revealed that the synthesis of galactinol, an essential precursor for the osmoprotective raffinose family of oligosaccharides, is ABA-dependent and impaired in the mutant under osmotic stress. In contrast, our results show that, under well-watered conditions, partial inactivation of ABA signaling leads to higher CO2 entry and photosynthesis in the mutant than in WT. Photosynthesis analyses revealed an increased CO2 diffusion capacity mediated by higher stomatal and mesophyll conductances, and higher substomatal CO2 concentration in the pentuple mutant. RNA-seq analyses revealed that genes associated with cell wall loosening (e.g., expansins) and porosity were strongly downregulated by ABA in WT. In summary, a partial relief of the ABA control on transpiration mediated by ABA receptors positively affects photosynthesis when water is not limited, at the expense of reduced water use efficiency.
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Affiliation(s)
- Gaston A Pizzio
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Cristian Mayordomo
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Jonatan Illescas-Miranda
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Alberto Coego
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Mar Bono
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Mayra Sanchez-Olvera
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Constanza Martin-Vasquez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Kajal Samantara
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Ebe Merilo
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Javier Forment
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Juan Carlos Estevez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Sergio G Nebauer
- Plant Production Department, Universitat Politècnica de València, Valencia, Spain
| | - Pedro L Rodriguez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
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Bai Y, Liu X, Baldwin IT. Using Synthetic Biology to Understand the Function of Plant Specialized Metabolites. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:629-653. [PMID: 38424065 DOI: 10.1146/annurev-arplant-060223-013842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Plant specialized metabolites (PSMs) are variably distributed across taxa, tissues, and ecological contexts; this variability has inspired many theories about PSM function, which, to date, remain poorly tested because predictions have outpaced the available data. Advances in mass spectrometry-based metabolomics have enabled unbiased PSM profiling, and molecular biology techniques have produced PSM-free plants; the combination of these methods has accelerated our understanding of the complex ecological roles that PSMs play in plants. Synthetic biology techniques and workflows are producing high-value, structurally complex PSMs in quantities and purities sufficient for both medicinal and functional studies. These workflows enable the reengineering of PSM transport, externalization, structural diversity, and production in novel taxa, facilitating rigorous tests of long-standing theoretical predictions about why plants produce so many different PSMs in particular tissues and ecological contexts. Plants use their chemical prowess to solve ecological challenges, and synthetic biology workflows are accelerating our understanding of these evolved functions.
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Affiliation(s)
- Yuechen Bai
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China; ,
| | - Xinyu Liu
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China; ,
| | - Ian T Baldwin
- Max Planck Institute for Chemical Ecology, Jena, Germany;
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Ludman M, Anita S, Fátyol K. Deficiency of multiple RNA silencing-associated genes may contribute to the increased susceptibility of Nicotiana benthamiana to viruses. PLANT CELL REPORTS 2024; 43:177. [PMID: 38898307 PMCID: PMC11186921 DOI: 10.1007/s00299-024-03262-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 06/06/2024] [Indexed: 06/21/2024]
Abstract
KEY MESSAGE Recently published high-quality reference genome assemblies indicate that, in addition to RDR1-deficiency, the loss of several key RNA silencing-associated genes may contribute to the hypersusceptibility of Nicotiana benthamiana to viruses.
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Affiliation(s)
- Márta Ludman
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi A0020U 4, Gödöllő, 2100, Hungary
| | - Schamberger Anita
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi A0020U 4, Gödöllő, 2100, Hungary
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, Budapest, 1117, Hungary
| | - Károly Fátyol
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi A0020U 4, Gödöllő, 2100, Hungary.
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Asadyar L, de Felippes FF, Bally J, Blackman CJ, An J, Sussmilch FC, Moghaddam L, Williams B, Blanksby SJ, Brodribb TJ, Waterhouse PM. Evidence for within-species transition between drought response strategies in Nicotiana benthamiana. THE NEW PHYTOLOGIST 2024. [PMID: 38863314 DOI: 10.1111/nph.19898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 05/23/2024] [Indexed: 06/13/2024]
Abstract
Nicotiana benthamiana is predominantly distributed in arid habitats across northern Australia. However, none of six geographically isolated accessions shows obvious xerophytic morphological features. To investigate how these tender-looking plants withstand drought, we examined their responses to water deprivation, assessed phenotypic, physiological, and cellular responses, and analysed cuticular wax composition and wax biosynthesis gene expression profiles. Results showed that the Central Australia (CA) accession, globally known as a research tool, has evolved a drought escape strategy with early vigour, short life cycle, and weak, water loss-limiting responses. By contrast, a northern Queensland (NQ) accession responded to drought by slowing growth, inhibiting flowering, increasing leaf cuticle thickness, and altering cuticular wax composition. Under water stress, NQ increased the heat stability and water impermeability of its cuticle by extending the carbon backbone of cuticular long-chain alkanes from c. 25 to 33. This correlated with rapid upregulation of at least five wax biosynthesis genes. In CA, the alkane chain lengths (c. 25) and gene expression profiles remained largely unaltered. This study highlights complex genetic and environmental control over cuticle composition and provides evidence for divergence into at least two fundamentally different drought response strategies within the N. benthamiana species in < 1 million years.
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Affiliation(s)
- Leila Asadyar
- School of Biology and Environmental Science, Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Qld, 4000, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland (UQ), Brisbane, Qld, 4072, Australia
| | - Felipe Fenselau de Felippes
- School of Biology and Environmental Science, Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Qld, 4000, Australia
| | - Julia Bally
- School of Biology and Environmental Science, Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Qld, 4000, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland (UQ), Brisbane, Qld, 4072, Australia
| | - Chris J Blackman
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland (UQ), Brisbane, Qld, 4072, Australia
- School of Natural Sciences, University of Tasmania (UTAS), Sandy Bay, Hobart, Tas., 7005, Australia
| | - Jiyuan An
- School of Biology and Environmental Science, Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Qld, 4000, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland (UQ), Brisbane, Qld, 4072, Australia
| | - Frances C Sussmilch
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland (UQ), Brisbane, Qld, 4072, Australia
- School of Natural Sciences, University of Tasmania (UTAS), Sandy Bay, Hobart, Tas., 7005, Australia
| | - Lalehvash Moghaddam
- School of Biology and Environmental Science, Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Qld, 4000, Australia
- School of Chemistry and Physics, Central Analytical Research Facility, Queensland University of Technology (QUT), Brisbane, Qld, 4000, Australia
| | - Brett Williams
- School of Biology and Environmental Science, Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Qld, 4000, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland (UQ), Brisbane, Qld, 4072, Australia
| | - Stephen J Blanksby
- School of Chemistry and Physics, Central Analytical Research Facility, Queensland University of Technology (QUT), Brisbane, Qld, 4000, Australia
| | - Timothy J Brodribb
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland (UQ), Brisbane, Qld, 4072, Australia
- School of Natural Sciences, University of Tasmania (UTAS), Sandy Bay, Hobart, Tas., 7005, Australia
| | - Peter M Waterhouse
- School of Biology and Environmental Science, Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Qld, 4000, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland (UQ), Brisbane, Qld, 4072, Australia
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Hayashi S, Souvan JM, Bally J, de Felippes FF, Waterhouse PM. Exploring the source of TYLCV resistance in Nicotiana benthamiana. FRONTIERS IN PLANT SCIENCE 2024; 15:1404160. [PMID: 38863537 PMCID: PMC11165019 DOI: 10.3389/fpls.2024.1404160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/08/2024] [Indexed: 06/13/2024]
Abstract
Tomato Yellow Leaf Curl Virus (TYLCV) is one of the most devastating pathogens of tomato, worldwide. It is vectored by the globally prevalent whitefly, Bemisia tabaci, and is asymptomatic in a wide range of plant species that act as a virus reservoir. The most successful crop protection for tomato in the field has been from resistance genes, of which five loci have been introgressed fromwild relatives. Of these, the Ty-1/Ty-3 locus, which encodes an RNA-dependent RNA polymerase 3 (RDR3), has been the most effective. Nevertheless, several TYLCV strains that break this resistance are beginning to emerge, increasing the need for new sources of resistance. Here we use segregation analysis and CRISPR-mediated gene dysfunctionalisation to dissect the differential response of two isolates of Nicotiana benthamiana to TYLCV infection. Our study indicates the presence of a novel non-RDR3, but yet to be identified, TYLCV resistance gene in a wild accession of N. benthamiana. This gene has the potential to be incorporated into tomatoes.
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Affiliation(s)
- Satomi Hayashi
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jacqueline M. Souvan
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, Australia
| | - Julia Bally
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, Queensland University of Technology, Brisbane, QLD, Australia
| | - Felipe F. de Felippes
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, Australia
| | - Peter M. Waterhouse
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, Queensland University of Technology, Brisbane, QLD, Australia
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Grützner R, König K, Horn C, Engler C, Laub A, Vogt T, Marillonnet S. A transient expression tool box for anthocyanin biosynthesis in Nicotiana benthamiana. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1238-1250. [PMID: 38124296 PMCID: PMC11022804 DOI: 10.1111/pbi.14261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/17/2023] [Accepted: 11/26/2023] [Indexed: 12/23/2023]
Abstract
Transient expression in Nicotiana benthamiana offers a robust platform for the rapid production of complex secondary metabolites. It has proven highly effective in helping identify genes associated with pathways responsible for synthesizing various valuable natural compounds. While this approach has seen considerable success, it has yet to be applied to uncovering genes involved in anthocyanin biosynthetic pathways. This is because only a single anthocyanin, delphinidin 3-O-rutinoside, can be produced in N. benthamiana by activation of anthocyanin biosynthesis using transcription factors. The production of other anthocyanins would necessitate the suppression of certain endogenous flavonoid biosynthesis genes while transiently expressing others. In this work, we present a series of tools for the reconstitution of anthocyanin biosynthetic pathways in N. benthamiana leaves. These tools include constructs for the expression or silencing of anthocyanin biosynthetic genes and a mutant N. benthamiana line generated using CRISPR. By infiltration of defined sets of constructs, the basic anthocyanins pelargonidin 3-O-glucoside, cyanidin 3-O-glucoside and delphinidin 3-O-glucoside could be obtained in high amounts in a few days. Additionally, co-infiltration of supplementary pathway genes enabled the synthesis of more complex anthocyanins. These tools should be useful to identify genes involved in the biosynthesis of complex anthocyanins. They also make it possible to produce novel anthocyanins not found in nature. As an example, we reconstituted the pathway for biosynthesis of Arabidopsis anthocyanin A5, a cyanidin derivative and achieved the biosynthesis of the pelargonidin and delphinidin variants of A5, pelargonidin A5 and delphinidin A5.
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Affiliation(s)
- Ramona Grützner
- Department of Cell and Metabolic BiologyLeibniz Institute of Plant BiochemistryHalleGermany
| | - Kristin König
- Department of Cell and Metabolic BiologyLeibniz Institute of Plant BiochemistryHalleGermany
| | - Claudia Horn
- Department of Cell and Metabolic BiologyLeibniz Institute of Plant BiochemistryHalleGermany
| | | | - Annegret Laub
- Department of Bioorganic ChemistryLeibniz Institute of Plant BiochemistryHalleGermany
| | - Thomas Vogt
- Department of Cell and Metabolic BiologyLeibniz Institute of Plant BiochemistryHalleGermany
| | - Sylvestre Marillonnet
- Department of Cell and Metabolic BiologyLeibniz Institute of Plant BiochemistryHalleGermany
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10
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Sankoh AF, Adjei J, Roberts DM, Burch-Smith TM. Comparing Methods for Detection and Quantification of Plasmodesmal Callose in Nicotiana benthamiana Leaves During Defense Responses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:427-431. [PMID: 38377039 DOI: 10.1094/mpmi-09-23-0152-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Callose, a β-(1,3)-d-glucan polymer, is essential for regulating intercellular trafficking via plasmodesmata (PD). Pathogens manipulate PD-localized proteins to enable intercellular trafficking by removing callose at PD or, conversely, by increasing callose accumulation at PD to limit intercellular trafficking during infection. Plant defense hormones like salicylic acid regulate PD-localized proteins to control PD and intercellular trafficking during immune defense responses such as systemic acquired resistance. Measuring callose deposition at PD in plants has therefore emerged as a popular parameter for assessing likely intercellular trafficking activity during plant immunity. Despite the popularity of this metric, there is no standard for how these measurements should be made. In this study, three commonly used methods for identifying and quantifying plasmodesmal callose by aniline blue staining were evaluated to determine the most effective in the Nicotiana benthamiana leaf model. The results reveal that the most reliable method used aniline blue staining and fluorescence microscopy to measure callose deposition in fixed tissue. Manual or semiautomated workflows for image analysis were also compared and found to produce similar results, although the semiautomated workflow produced a wider distribution of data points. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Amie F Sankoh
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996, U.S.A
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
| | - Joseph Adjei
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
| | - Daniel M Roberts
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996, U.S.A
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Ko SR, Lee S, Koo H, Seo H, Yu J, Kim YM, Kwon SY, Shin AY. High-quality chromosome-level genome assembly of Nicotiana benthamiana. Sci Data 2024; 11:386. [PMID: 38627408 PMCID: PMC11021556 DOI: 10.1038/s41597-024-03232-0] [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: 12/18/2023] [Accepted: 04/05/2024] [Indexed: 04/19/2024] Open
Abstract
Nicotiana benthamiana is a fundamental model organism in plant research. Recent advancements in genomic sequencing have revealed significant intraspecific genetic variations. This study addresses the pressing need for a precise genome sequence specific to its geographic origin by presenting a comprehensive genome assembly of the N. benthamiana LAB strain from the Republic of Korea (NbKLAB). We compare this assembly with the widely used NbLAB360 strain, shedding light on essential genomic differences between them. The outcome is a high-quality, chromosome-level genome assembly comprising 19 chromosomes, spanning 2,762 Mb, with an N50 of 142.6 Mb. Comparative analyses revealed notable variations, including 46,215 protein-coding genes, with an impressive 99.5% BUSCO completeness score. Furthermore, the NbKLAB assembly substantially improved the QV from 33% for NbLAB360 to 49%. This refined chromosomal genome assembly for N. benthamiana, in conjunction with comparative insights, provides a valuable resource for genomics research and molecular biology. This accomplishment forms a strong foundation for in-depth exploration into the intricacies of plant genetics and genomics, improved precision, and a comparative framework.
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Affiliation(s)
- Seo-Rin Ko
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Sanghee Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Biosystems and Bioengineering Program, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, 34113, Korea
| | - Hyunjin Koo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | | | | | - Yong-Min Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
- Digital Biotech Innovation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Biosystems and Bioengineering Program, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, 34113, Korea.
| | - Ah-Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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12
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Wang J, Zhang Q, Tung J, Zhang X, Liu D, Deng Y, Tian Z, Chen H, Wang T, Yin W, Li B, Lai Z, Dinesh-Kumar SP, Baker B, Li F. High-quality assembled and annotated genomes of Nicotiana tabacum and Nicotiana benthamiana reveal chromosome evolution and changes in defense arsenals. MOLECULAR PLANT 2024; 17:423-437. [PMID: 38273657 DOI: 10.1016/j.molp.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/08/2024] [Accepted: 01/21/2024] [Indexed: 01/27/2024]
Abstract
Nicotiana tabacum and Nicotiana benthamiana are widely used models in plant biology research. However, genomic studies of these species have lagged. Here we report the chromosome-level reference genome assemblies for N. benthamiana and N. tabacum with an estimated 99.5% and 99.8% completeness, respectively. Sensitive transcription start and termination site sequencing methods were developed and used for accurate gene annotation in N. tabacum. Comparative analyses revealed evidence for the parental origins and chromosome structural changes, leading to hybrid genome formation of each species. Interestingly, the antiviral silencing genes RDR1, RDR6, DCL2, DCL3, and AGO2 were lost from one or both subgenomes in N. benthamiana, while both homeologs were kept in N. tabacum. Furthermore, the N. benthamiana genome encodes fewer immune receptors and signaling components than that of N. tabacum. These findings uncover possible reasons underlying the hypersusceptible nature of N. benthamiana. We developed the user-friendly Nicomics (http://lifenglab.hzau.edu.cn/Nicomics/) web server to facilitate better use of Nicotiana genomic resources as well as gene structure and expression analyses.
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Affiliation(s)
- Jubin Wang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi Province, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330299, China
| | - Qingling Zhang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Jeffrey Tung
- Plant Gene Expression Center, Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94706, USA
| | - Xi Zhang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Dan Liu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yingtian Deng
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zhendong Tian
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Huilan Chen
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Taotao Wang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Weixiao Yin
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Bo Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Zhibing Lai
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Savithramma P Dinesh-Kumar
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Barbara Baker
- Plant Gene Expression Center, Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94706, USA.
| | - Feng Li
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
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13
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Chooi KM, Bell VA, Blouin AG, Sandanayaka M, Gough R, Chhagan A, MacDiarmid RM. The New Zealand perspective of an ecosystem biology response to grapevine leafroll disease. Adv Virus Res 2024; 118:213-272. [PMID: 38461030 DOI: 10.1016/bs.aivir.2024.02.001] [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] [Indexed: 03/11/2024]
Abstract
Grapevine leafroll-associated virus 3 (GLRaV-3) is a major pathogen of grapevines worldwide resulting in grapevine leafroll disease (GLD), reduced fruit yield, berry quality and vineyard profitability. Being graft transmissible, GLRaV-3 is also transmitted between grapevines by multiple hemipteran insects (mealybugs and soft scale insects). Over the past 20 years, New Zealand has developed and utilized integrated pest management (IPM) solutions that have slowly transitioned to an ecosystem-based biological response to GLD. These IPM solutions and combinations are based on a wealth of research within the temperate climates of New Zealand's nation-wide grape production. To provide context, the grapevine viruses present in the national vineyard estate and how these have been identified are described; the most pathogenic and destructive of these is GLRaV-3. We provide an overview of research on GLRaV-3 genotypes and biology within grapevines and describe the progressive development of GLRaV-3/GLD diagnostics based on molecular, serological, visual, and sensor-based technologies. Research on the ecology and control of the mealybugs Pseudococcus calceolariae and P. longispinus, the main insect vectors of GLRaV-3 in New Zealand, is described together with the implications of mealybug biological control agents and prospects to enhance their abundance and/or fitness in the vineyard. Virus transmission by mealybugs is described, with emphasis on understanding the interactions between GLRaV-3, vectors, and plants (grapevines, alternative hosts, or non-hosts of the virus). Disease management through grapevine removal and the economic influence of different removal strategies is detailed. Overall, the review summarizes research by an interdisciplinary team working in close association with the national industry body, New Zealand Winegrowers. Teamwork and communication across the whole industry has enabled implementation of research for the management of GLD.
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Affiliation(s)
- Kar Mun Chooi
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | - Vaughn A Bell
- The New Zealand Institute for Plant and Food Research Limited, Havelock North, New Zealand.
| | | | | | - Rebecca Gough
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | - Asha Chhagan
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | - Robin M MacDiarmid
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand; The University of Auckland, Auckland, New Zealand
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14
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Palukaitis P, Yoon JY. Defense signaling pathways in resistance to plant viruses: Crosstalk and finger pointing. Adv Virus Res 2024; 118:77-212. [PMID: 38461031 DOI: 10.1016/bs.aivir.2024.01.002] [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] [Indexed: 03/11/2024]
Abstract
Resistance to infection by plant viruses involves proteins encoded by plant resistance (R) genes, viz., nucleotide-binding leucine-rich repeats (NLRs), immune receptors. These sensor NLRs are activated either directly or indirectly by viral protein effectors, in effector-triggered immunity, leading to induction of defense signaling pathways, resulting in the synthesis of numerous downstream plant effector molecules that inhibit different stages of the infection cycle, as well as the induction of cell death responses mediated by helper NLRs. Early events in this process involve recognition of the activation of the R gene response by various chaperones and the transport of these complexes to the sites of subsequent events. These events include activation of several kinase cascade pathways, and the syntheses of two master transcriptional regulators, EDS1 and NPR1, as well as the phytohormones salicylic acid, jasmonic acid, and ethylene. The phytohormones, which transit from a primed, resting states to active states, regulate the remainder of the defense signaling pathways, both directly and by crosstalk with each other. This regulation results in the turnover of various suppressors of downstream events and the synthesis of various transcription factors that cooperate and/or compete to induce or suppress transcription of either other regulatory proteins, or plant effector molecules. This network of interactions results in the production of defense effectors acting alone or together with cell death in the infected region, with or without the further activation of non-specific, long-distance resistance. Here, we review the current state of knowledge regarding these processes and the components of the local responses, their interactions, regulation, and crosstalk.
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Affiliation(s)
- Peter Palukaitis
- Graduate School of Plant Protection and Quarantine, Jeonbuk National University, Jeonju, Jeollabuk-do, Republic of Korea.
| | - Ju-Yeon Yoon
- Graduate School of Plant Protection and Quarantine, Jeonbuk National University, Jeonju, Jeollabuk-do, Republic of Korea.
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15
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Vaucheret H, Voinnet O. The plant siRNA landscape. THE PLANT CELL 2024; 36:246-275. [PMID: 37772967 PMCID: PMC10827316 DOI: 10.1093/plcell/koad253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/12/2023] [Accepted: 09/28/2023] [Indexed: 09/30/2023]
Abstract
Whereas micro (mi)RNAs are considered the clean, noble side of the small RNA world, small interfering (si)RNAs are often seen as a noisy set of molecules whose barbarian acronyms reflect a large diversity of often elusive origins and functions. Twenty-five years after their discovery in plants, however, new classes of siRNAs are still being identified, sometimes in discrete tissues or at particular developmental stages, making the plant siRNA world substantially more complex and subtle than originally anticipated. Focusing primarily on the model Arabidopsis, we review here the plant siRNA landscape, including transposable elements (TE)-derived siRNAs, a vast array of non-TE-derived endogenous siRNAs, as well as exogenous siRNAs produced in response to invading nucleic acids such as viruses or transgenes. We primarily emphasize the extraordinary sophistication and diversity of their biogenesis and, secondarily, the variety of their known or presumed functions, including via non-cell autonomous activities, in the sporophyte, gametophyte, and shortly after fertilization.
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Affiliation(s)
- Hervé Vaucheret
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Olivier Voinnet
- Department of Biology, Swiss Federal Institute of Technology (ETH-Zurich), 8092 Zürich, Switzerland
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16
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Poulicard N, Pagán I, González-Jara P, Mora MÁ, Hily JM, Fraile A, Piñero D, García-Arenal F. Repeated loss of the ability of a wild pepper disease resistance gene to function at high temperatures suggests that thermoresistance is a costly trait. THE NEW PHYTOLOGIST 2024; 241:845-860. [PMID: 37920100 DOI: 10.1111/nph.19371] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/13/2023] [Indexed: 11/04/2023]
Abstract
Specificity in plant-pathogen gene-for-gene (GFG) interactions is determined by the recognition of pathogen proteins by the products of plant resistance (R) genes. The evolutionary dynamics of R genes in plant-virus systems is poorly understood. We analyse the evolution of the L resistance locus to tobamoviruses in the wild pepper Capsicum annuum var. glabriusculum (chiltepin), a crop relative undergoing incipient domestication. The frequency, and the genetic and phenotypic diversity, of the L locus was analysed in 41 chiltepin populations under different levels of human management over its distribution range in Mexico. The frequency of resistance was lower in Cultivated than in Wild populations. L-locus genetic diversity showed a strong spatial structure with no isolation-by-distance pattern, suggesting environment-specific selection, possibly associated with infection by the highly virulent tobamoviruses found in the surveyed regions. L alleles differed in recognition specificity and in the expression of resistance at different temperatures, broad-spectrum recognition of P0 + P1 pathotypes and expression above 32°C being ancestral traits that were repeatedly lost along L-locus evolution. Overall, loss of resistance co-occurs with incipient domestication and broad-spectrum resistance expressed at high temperatures has apparent fitness costs. These findings contribute to understand the role of fitness trade-offs in plant-virus coevolution.
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Affiliation(s)
- Nils Poulicard
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Israel Pagán
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Pablo González-Jara
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Miguel Ángel Mora
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Jean-Michel Hily
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Ciudad de México, Mexico
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
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17
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Wei M, Liu J, Wang S, Wang X, Liu H, Ma Q, Wang J, Shi W. Genetic Diversity and Phylogenetic Analysis of Zygophyllum loczyi in Northwest China's Deserts Based on the Resequencing of the Genome. Genes (Basel) 2023; 14:2152. [PMID: 38136974 PMCID: PMC10742952 DOI: 10.3390/genes14122152] [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: 10/01/2023] [Revised: 11/19/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
In order to study the genetics of local adaptation in all main deserts of northwest China, whole genomes of 169 individuals were resequenced, which covers 20 populations of Zygophyllum loczyi (Zygophyllales: Zygophylaceae). We describe more than 15 million single nucleotide polymorphisms and numerous InDels. The expected heterozygosity and PIC values associated with local adaptation varied significantly across biogeographic regions. Variation in environmental factors contributes largely to the population genetic structure of Z. loczyi. Bayesian analysis performed with STRUCTURE defined four genetic clusters, while the results of principle component analysis were similar. Our results shows that the Qaidam Desert group appears to be diverging into two branches characterized by significant geographic separation and gene flow with two neighboring deserts. Geological data assume that it is possible that the Taklamakan Desert was the original distribution site, and Z. loczyi could have migrated later on and expanded within other desert areas. The above findings provide insights into the processes involved in biogeography, phylogeny, and differentiation within the northwest deserts of China.
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Affiliation(s)
- Mengmeng Wei
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable, Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China; (M.W.); (J.L.); (X.W.); (J.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingdian Liu
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable, Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China; (M.W.); (J.L.); (X.W.); (J.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Suoming Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; (S.W.); (H.L.); (Q.M.)
| | - Xiyong Wang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable, Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China; (M.W.); (J.L.); (X.W.); (J.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Turpan Eremophytes Botanic Garden, The Chinese Academy of Sciences, Turpan 838008, China
| | - Haisuang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; (S.W.); (H.L.); (Q.M.)
| | - Qing Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; (S.W.); (H.L.); (Q.M.)
| | - Jiancheng Wang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable, Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China; (M.W.); (J.L.); (X.W.); (J.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Turpan Eremophytes Botanic Garden, The Chinese Academy of Sciences, Turpan 838008, China
| | - Wei Shi
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable, Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China; (M.W.); (J.L.); (X.W.); (J.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Turpan Eremophytes Botanic Garden, The Chinese Academy of Sciences, Turpan 838008, China
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18
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Sankoh AF, Adjei J, Roberts DM, Burch-Smith TM. Reliable detection and quantification of plasmodesmal callose in Nicotiana benthamiana leaves during defense responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.30.560305. [PMID: 37873219 PMCID: PMC10592870 DOI: 10.1101/2023.09.30.560305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Callose, a beta-(1,3)-D-glucan polymer, is essential for regulating intercellular trafficking via plasmodesmata (PD). Pathogens manipulate PD-localized proteins to enable intercellular trafficking by removing callose at PD, or conversely by increasing callose accumulation at PD to limit intercellular trafficking during infection. Plant defense hormones like salicylic acid regulate PD-localized proteins to control PD and intercellular trafficking during innate immune defense responses such as systemic acquired resistance. Measuring callose deposition at PD in plants has therefore emerged as a popular parameter for assessing the intercellular trafficking activity during plant immunity. Despite the popularity of this metric there is no standard for how these measurements should be made. In this study, three commonly used methods for identifying and quantifying PD callose by aniline blue staining were evaluated to determine the most effective in the Nicotiana benthamiana leaf model. The results reveal that the most reliable method used aniline blue staining and fluorescent microscopy to measure callose deposition in fixed tissue. Manual or semi-automated workflows for image analysis were also compared and found to produce similar results although the semi-automated workflow produced a wider distribution of data points.
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Affiliation(s)
- Amie F. Sankoh
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996 USA
- Donald Danforth Plant Science Center, Saint Louis, MO 63132 USA
| | - Joseph Adjei
- Donald Danforth Plant Science Center, Saint Louis, MO 63132 USA
| | - Daniel M. Roberts
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996 USA
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19
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Aydinoglu F, Kuloglu A. Nicotiana benthamiana as a model plant host for Fusarium verticillioides to investigate RNA interference, cross-kingdom RNA exchange, and competitive endogenous RNA (ceRNA) network. Mol Biol Rep 2023; 50:8061-8072. [PMID: 37540455 DOI: 10.1007/s11033-023-08698-6] [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: 04/25/2023] [Accepted: 07/18/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND Fusarium verticillioides is among the most devastating fungal pathogen of cereals. Therefore, it is crucial to employ effective and long-term strategies for managing F. verticillioides for sustainable agriculture. RNA interference (RNAi) being a natural defense mechanism of plants via regulation of gene expression, has emerged as a promising tool for eradicating pathogens. RNAi also operates between the host and pathogen through RNA exchange. RNAi interacts with competitive endogenous RNAs (ceRNAs) including long non-coding RNA (lncRNA), microRNA (miRNA), and mRNA. Due to the lack of an elaborate model to investigate all these mechanisms, this study aimed to establish a Nicotiana benthamiana (Nb)-F. verticillioides (Fv) phyto-pathosystem as an experimental model. METHODS AND RESULTS Nb seedlings were inoculated with Fv, and the pathogenicity was monitored morphologically, microscopically, biochemically, and transcriptionally. To observe the role of RNAi and RNA-exchange in pathogenicity, Nb-miR172 and Nb-miR399 targeting Nb-lncRNA-IPS (Induced by Phosphate Starvation1) and Nb-AP2 (Apetala2) and Nb-PHO2 (phosphate over-accumulator) ceRNA network and Fv-V-ATPase (Vesicle-fusing ATPase) targeted by Nb-miR172 were investigated. As a result, epidermal cell density, leaf area, petiole length, and chlorophyll content were reduced while the density of stomata and trichome and phenolic content and the activity of ascorbate peroxidase (APX) and glutathione reductase (GR) were increased in response to Fv infection in Nb. The expression of AP2 and PHO2 were downregulated against Fv but no significant changes were detected in IPS, miR172, and miR399 expression. CONCLUSION These findings suggested the Fv-Nb phyto-pathosystem as a useful experimental model to reveal genetic regulations.
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Affiliation(s)
- Fatma Aydinoglu
- Molecular Biology and Genetics Department, Gebze Technical University, Kocaeli, Turkey.
| | - Aslihan Kuloglu
- Molecular Biology and Genetics Department, Gebze Technical University, Kocaeli, Turkey
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20
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Vollheyde K, Dudley QM, Yang T, Oz MT, Mancinotti D, Fedi MO, Heavens D, Linsmith G, Chhetry M, Smedley MA, Harwood WA, Swarbreck D, Geu‐Flores F, Patron NJ. An improved Nicotiana benthamiana bioproduction chassis provides novel insights into nicotine biosynthesis. THE NEW PHYTOLOGIST 2023; 240:302-317. [PMID: 37488711 PMCID: PMC10952274 DOI: 10.1111/nph.19141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/28/2023] [Indexed: 07/26/2023]
Abstract
The model plant Nicotiana benthamiana is an increasingly attractive organism for the production of high-value, biologically active molecules. However, N. benthamiana accumulates high levels of pyridine alkaloids, in particular nicotine, which complicates the downstream purification processes. Here, we report a new assembly of the N. benthamiana genome as well as the generation of low-nicotine lines by CRISPR/Cas9-based inactivation of berberine bridge enzyme-like proteins (BBLs). Triple as well as quintuple mutants accumulated three to four times less nicotine than the respective control lines. The availability of lines without functional BBLs allowed us to probe their catalytic role in nicotine biosynthesis, which has remained obscure. Notably, chiral analysis revealed that the enantiomeric purity of nicotine was fully lost in the quintuple mutants. In addition, precursor feeding experiments showed that these mutants cannot facilitate the specific loss of C6 hydrogen that characterizes natural nicotine biosynthesis. Our work delivers an improved N. benthamiana chassis for bioproduction and uncovers the crucial role of BBLs in the stereoselectivity of nicotine biosynthesis.
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Affiliation(s)
- Katharina Vollheyde
- Department of Plant and Environmental SciencesUniversity of Copenhagen1871 FrederiksbergCopenhagenDenmark
| | | | - Ting Yang
- Department of Plant and Environmental SciencesUniversity of Copenhagen1871 FrederiksbergCopenhagenDenmark
| | - Mehmet T. Oz
- Earlham Institute, Norwich Research ParkNorwichNorfolkNR4 7UZUK
| | - Davide Mancinotti
- Department of Plant and Environmental SciencesUniversity of Copenhagen1871 FrederiksbergCopenhagenDenmark
| | | | - Darren Heavens
- Earlham Institute, Norwich Research ParkNorwichNorfolkNR4 7UZUK
| | - Gareth Linsmith
- Earlham Institute, Norwich Research ParkNorwichNorfolkNR4 7UZUK
| | - Monika Chhetry
- John Innes Centre, Norwich Research ParkNorwichNorfolkNR4 7UHUK
| | - Mark A. Smedley
- John Innes Centre, Norwich Research ParkNorwichNorfolkNR4 7UHUK
| | | | - David Swarbreck
- Earlham Institute, Norwich Research ParkNorwichNorfolkNR4 7UZUK
| | - Fernando Geu‐Flores
- Department of Plant and Environmental SciencesUniversity of Copenhagen1871 FrederiksbergCopenhagenDenmark
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21
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Ranawaka B, An J, Lorenc MT, Jung H, Sulli M, Aprea G, Roden S, Llaca V, Hayashi S, Asadyar L, LeBlanc Z, Ahmed Z, Naim F, de Campos SB, Cooper T, de Felippes FF, Dong P, Zhong S, Garcia-Carpintero V, Orzaez D, Dudley KJ, Bombarely A, Bally J, Winefield C, Giuliano G, Waterhouse PM. A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology. NATURE PLANTS 2023; 9:1558-1571. [PMID: 37563457 PMCID: PMC10505560 DOI: 10.1038/s41477-023-01489-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 07/11/2023] [Indexed: 08/12/2023]
Abstract
Nicotiana benthamiana is an invaluable model plant and biotechnology platform with a ~3 Gb allotetraploid genome. To further improve its usefulness and versatility, we have produced high-quality chromosome-level genome assemblies, coupled with transcriptome, epigenome, microRNA and transposable element datasets, for the ubiquitously used LAB strain and a related wild accession, QLD. In addition, single nucleotide polymorphism maps have been produced for a further two laboratory strains and four wild accessions. Despite the loss of five chromosomes from the ancestral tetraploid, expansion of intergenic regions, widespread segmental allopolyploidy, advanced diploidization and evidence of recent bursts of Copia pseudovirus (Copia) mobility not seen in other Nicotiana genomes, the two subgenomes of N. benthamiana show large regions of synteny across the Solanaceae. LAB and QLD have many genetic, metabolic and phenotypic differences, including disparate RNA interference responses, but are highly interfertile and amenable to genome editing and both transient and stable transformation. The LAB/QLD combination has the potential to be as useful as the Columbia-0/Landsberg errecta partnership, utilized from the early pioneering days of Arabidopsis genomics to today.
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Affiliation(s)
- Buddhini Ranawaka
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Jiyuan An
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia.
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia.
| | - Michał T Lorenc
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Hyungtaek Jung
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, Queensland, Australia
| | - Maria Sulli
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Giuseppe Aprea
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Sally Roden
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Victor Llaca
- Genomics Technologies, Corteva Agriscience, Johnston, IA, USA
| | - Satomi Hayashi
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Leila Asadyar
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Zacharie LeBlanc
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Zuba Ahmed
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Fatima Naim
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Samanta Bolzan de Campos
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Tal Cooper
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Felipe F de Felippes
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Pengfei Dong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Silin Zhong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Victor Garcia-Carpintero
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politècnica de Valencia, Valencia, Spain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politècnica de Valencia, Valencia, Spain
| | - Kevin J Dudley
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- QUT Central Analytical Research Facility, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Aureliano Bombarely
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politècnica de Valencia, Valencia, Spain
- Università degli Studi di Milano, Milan, Italy
| | - Julia Bally
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Christopher Winefield
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia.
- Department of Wine Food and Molecular Biosciences, Lincoln University, Lincoln, New Zealand.
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Peter M Waterhouse
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia.
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia.
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22
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Demurtas OC, Sulli M, Ferrante P, Mini P, Martí M, Aragonés V, Daròs JA, Giuliano G. Production of Saffron Apocarotenoids in Nicotiana benthamiana Plants Genome-Edited to Accumulate Zeaxanthin Precursor. Metabolites 2023; 13:729. [PMID: 37367887 DOI: 10.3390/metabo13060729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/30/2023] [Accepted: 06/03/2023] [Indexed: 06/28/2023] Open
Abstract
Crocins are glycosylated apocarotenoids with strong coloring power and anti-oxidant, anticancer, and neuro-protective properties. We previously dissected the saffron crocin biosynthesis pathway, and demonstrated that the CsCCD2 enzyme, catalyzing the carotenoid cleavage step, shows a strong preference for the xanthophyll zeaxanthin in vitro and in bacterio. In order to investigate substrate specificity in planta and to establish a plant-based bio-factory system for crocin production, we compared wild-type Nicotiana benthamiana plants, accumulating various xanthophylls together with α- and β-carotene, with genome-edited lines, in which all the xanthophylls normally accumulated in leaves were replaced by a single xanthophyll, zeaxanthin. These plants were used as chassis for the production in leaves of saffron apocarotenoids (crocins, picrocrocin) using two transient expression methods to overexpress CsCCD2: agroinfiltration and inoculation with a viral vector derived from tobacco etch virus (TEV). The results indicated the superior performance of the zeaxanthin-accumulating line and of the use of the viral vector to express CsCCD2. The results also suggested a relaxed substrate specificity of CsCCD2 in planta, cleaving additional carotenoid substrates.
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Affiliation(s)
- Olivia Costantina Demurtas
- Biotechnology and Agro-Industry Division, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, 00123 Rome, Italy
| | - Maria Sulli
- Biotechnology and Agro-Industry Division, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, 00123 Rome, Italy
| | - Paola Ferrante
- Biotechnology and Agro-Industry Division, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, 00123 Rome, Italy
| | - Paola Mini
- Biotechnology and Agro-Industry Division, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, 00123 Rome, Italy
| | - Maricarmen Martí
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022 Valencia, Spain
| | - Verónica Aragonés
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022 Valencia, Spain
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022 Valencia, Spain
| | - Giovanni Giuliano
- Biotechnology and Agro-Industry Division, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, 00123 Rome, Italy
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23
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Cunha AFA, Rodrigues PHD, Anghinoni AC, de Paiva VJ, Pinheiro DGDS, Campos ML. Mechanical wounding impacts the growth versus defense balance in tomato (Solanum lycopersicum). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 329:111601. [PMID: 36690279 DOI: 10.1016/j.plantsci.2023.111601] [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: 11/30/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 06/17/2023]
Abstract
Plants have evolved elaborate surveillance systems that allow them to perceive the attack by pests and pathogens and activate the appropriate defenses. Mechanical stimulation, such as mechanical wounding, represents one of the most reliable cues for the perception of potential herbivore aggressors. Here we demonstrate that mechanical wounding disturbs the growth versus defense balance in tomato, a physiological condition where growth reduction arises as a pleiotropic consequence of the activation of defense responses (or vice-versa). We observed that multiple lesions on tomato leaves impairs the formation of several growth-related traits, including shoot elongation, leaf expansion and time for flowering, while concomitantly activating the production of defense responses such as trichome formation and the upregulation of defense-related genes. We also provide genetic evidence that this wound-induced growth repression is possibly a consequence of tomato plants sensing the injuries via jasmonates (JAs), a class of plant hormones known to be master regulators of the plant growth versus defense balance. Besides providing a mechanistic explanation on how the growth and defense balance is shifted when plants are subjected to a specific type of mechanical stimulus, our results may offer a practical explanation for why tomato productivity is so negatively impacted by herbivore attack.
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Affiliation(s)
- Ana Flavia Aparecida Cunha
- Programa de Pós-Graduação em Biologia Vegetal, Universidade Federal de Mato Grosso, Cuiabá, MT 78060-900, Brazil; Integrative Plant Research Laboratory, Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil.
| | - Pedro Henrique Duarte Rodrigues
- Integrative Plant Research Laboratory, Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil.
| | - Ana Clara Anghinoni
- Integrative Plant Research Laboratory, Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil.
| | - Vinicius Juliani de Paiva
- Integrative Plant Research Laboratory, Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil.
| | - Daniel Gonçalves da Silva Pinheiro
- Integrative Plant Research Laboratory, Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil; Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Universidade Federal de Mato Grosso, Cuiabá, MT 78060-900, Brazil.
| | - Marcelo Lattarulo Campos
- Programa de Pós-Graduação em Biologia Vegetal, Universidade Federal de Mato Grosso, Cuiabá, MT 78060-900, Brazil; Integrative Plant Research Laboratory, Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil; Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Universidade Federal de Mato Grosso, Cuiabá, MT 78060-900, Brazil.
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24
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McCray TN, Azim MF, Burch-Smith TM. The dicot homolog of maize PPR103 carries a C-terminal DYW domain and is required for C-to-U editing of chloroplast RNA transcripts. RESEARCH SQUARE 2023:rs.3.rs-2574001. [PMID: 36865278 PMCID: PMC9980218 DOI: 10.21203/rs.3.rs-2574001/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
In plants, cytidine-to-uridine (C-to-U) editing is a crucial step in processing mitochondria and chloroplast-encoded transcripts. This editing requires nuclear-encoded proteins including members of the pentatricopeptide (PPR) family, especially PLS-type proteins carrying the DYW domain. IPI1/emb175/PPR103 is a nuclear gene encoding a PLS-type PPR protein essential for survival in Arabidopsis thaliana and maize. Arabidopsis IPI1 was identified as likely interacting with ISE2, a chloroplast-localized RNA helicase associated with C-to-U RNA editing in Arabidopsis and maize. Notably, while the Arabidopsis and Nicotiana IPI1 homologs possess complete DYW motifs at their C-termini, the maize homolog, ZmPPR103, lacks this triplet of residues which are essential for editing. We examined the function of ISE2 and IPI1 in chloroplast RNA processing in N. benthamiana. A combination of deep sequencing and Sanger sequencing revealed C-to-U editing at 41 sites in 18 transcripts, with 34 sites conserved in the closely related N. tabacum. Virus induced gene silencing of NbISE2 or NbIPI1 led to defective C-to-U revealed that they have overlapping roles at editing a site in the rpoB transcript but have distinct roles in editing other transcripts. This finding contrasts with maize ppr103 mutants that showed no defects in editing. The results indicate that NbISE2 and NbIPI1 are important for C-to-U editing in N. benthamiana chloroplasts, and they may function in a complex to edit specific sites while having antagonistic effects on editing others. That NbIPI1, carrying a DYW domain, is involved in organelle C-to-U RNA editing supports previous work showing that this domain catalyzes RNA editing.
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Affiliation(s)
- Tyra N. McCray
- School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Mohammad F. Azim
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996
- Donald Danforth Plant Science Center, St. Louis, MO 63132
| | - Tessa M. Burch-Smith
- School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996
- Donald Danforth Plant Science Center, St. Louis, MO 63132
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25
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Sestari I, Campos ML. Into a dilemma of plants: the antagonism between chemical defenses and growth. PLANT MOLECULAR BIOLOGY 2022; 109:469-482. [PMID: 34843032 DOI: 10.1007/s11103-021-01213-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/28/2021] [Indexed: 05/21/2023]
Abstract
Chemical defenses are imperative for plant survival, but their production is often associated with growth restrictions. Here we review the most recent theories to explain this complex dilemma of plants. Plants are a nutritional source for a myriad of pests and pathogens that depend on green tissues to complete their life cycle. Rather than remaining passive victims, plants utilize an arsenal of chemical defenses to fend off biotic attack. While the deployment of such barriers is imperative for survival, the production of these chemical defenses is typically associated with negative impacts on plant growth. Here we discuss the most recent theories which explain this highly dynamic growth versus defense dilemma. Firstly, we discuss the hypothesis that the antagonism between the accumulation of chemical defenses and growth is rooted in the evolutionary history of plants and may be a consequence of terrestrialization. Then, we revise the different paradigms available to explain the growth versus chemical defense antagonism, including recent findings that update these into more comprehensive and plausible theories. Finally, we highlight state-of-the-art strategies that are now allowing the activation of growth and the concomitant production of chemical barriers in plants. Growth versus chemical defense antagonism imposes large ecological and economic costs, including increased crop susceptibility to pests and pathogens. In a world where these plant enemies are the main problem to increase food production, we believe that this review will summarize valuable information for future studies aiming to breed highly defensive plants without the typical accompanying penalties to growth.
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Affiliation(s)
- Ivan Sestari
- Coordenadoria Especial de Ciências Biológicas e Agronômicas, Universidade Federal de Santa Catarina, Curitibanos, SC, Brazil
| | - Marcelo Lattarulo Campos
- Integrative Plant Research Laboratory, Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil.
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26
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Pierroz G. Genomics reveal a complicated past and suggest a possible future for Nicotiana benthamiana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:5-6. [PMID: 35789508 DOI: 10.1111/tpj.15869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
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27
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Cauz‐Santos LA, Dodsworth S, Samuel R, Christenhusz MJM, Patel D, Shittu T, Jakob A, Paun O, Chase MW. Genomic insights into recent species divergence in Nicotiana benthamiana and natural variation in Rdr1 gene controlling viral susceptibility. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:7-18. [PMID: 35535507 PMCID: PMC9543217 DOI: 10.1111/tpj.15801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 05/31/2023]
Abstract
One of the most commonly encountered and frequently cited laboratory organisms worldwide is classified taxonomically as Nicotiana benthamiana (Solanaceae), an accession of which, typically referred to as LAB, is renowned for its unique susceptibility to a wide range of plant viruses and hence capacity to be transformed using a variety of methods. This susceptibility is the result of an insertion and consequent loss of function in the RNA-dependent RNA polymerase 1 (Rdr1) gene. However, the origin and age of LAB and the evolution of N. benthamiana across its wide distribution in Australia remain relatively underexplored. Here, we have used multispecies coalescent methods on genome-wide single nucleotide polymorphisms (SNPs) to assess species limits, phylogenetic relationships and divergence times within N. benthamiana. Our results show that the previous taxonomic concept of this species in fact comprises five geographically, morphologically and genetically distinct species, one of which includes LAB. We provide clear evidence that LAB is closely related to accessions collected further north in the Northern Territory; this species split much earlier, c. 1.1 million years ago, from their common ancestor than the other four in this clade and is morphologically the most distinctive. We also found that the Rdr1 gene insertion is variable among accessions from the northern portions of the Northern Territory. Furthermore, this long-isolated species typically grows in sheltered sites in subtropical/tropical monsoon areas of northern Australia, contradicting the previously advanced hypothesis that this species is an extremophile that has traded viral resistance for precocious development.
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Affiliation(s)
- Luiz A. Cauz‐Santos
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
| | - Steven Dodsworth
- School of Biological SciencesUniversity of PortsmouthKing Henry Building, King Henry 1 StreetPortsmouthPO1 2DYUK
- School of Life SciencesUniversity of Bedfordshire, University SquareLutonBedfordshireLU1 3JUUK
| | - Rosabelle Samuel
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
| | | | - Denise Patel
- School of Life SciencesUniversity of Bedfordshire, University SquareLutonBedfordshireLU1 3JUUK
| | - Taiwo Shittu
- School of Life SciencesUniversity of Bedfordshire, University SquareLutonBedfordshireLU1 3JUUK
| | - Aljaž Jakob
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
| | - Ovidiu Paun
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
| | - Mark W. Chase
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
- Royal Botanic GardensKewRichmondTW9 3DSUK
- Department of Environment and AgricultureCurtin UniversityPerthWestern AustraliaAustralia
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28
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Shahzad GIR, Passera A, Maldera G, Casati P, Marcello I, Bianco PA. Biocontrol Potential of Endophytic Plant-Growth-Promoting Bacteria against Phytopathogenic Viruses: Molecular Interaction with the Host Plant and Comparison with Chitosan. Int J Mol Sci 2022; 23:6990. [PMID: 35805989 PMCID: PMC9266900 DOI: 10.3390/ijms23136990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/16/2022] Open
Abstract
Endophytic plant-growth-promoting bacteria (ePGPB) are interesting tools for pest management strategies. However, the molecular interactions underlying specific biocontrol effects, particularly against phytopathogenic viruses, remain unexplored. Herein, we investigated the antiviral effects and triggers of induced systemic resistance mediated by four ePGPB (Paraburkholderia fungorum strain R8, Paenibacillus pasadenensis strain R16, Pantoea agglomerans strain 255-7, and Pseudomonas syringae strain 260-02) against four viruses (Cymbidium Ring Spot Virus-CymRSV; Cucumber Mosaic Virus-CMV; Potato Virus X-PVX; and Potato Virus Y-PVY) on Nicotiana benthamiana plants under controlled conditions and compared them with a chitosan-based resistance inducer product. Our studies indicated that ePGPB- and chitosan-treated plants presented well-defined biocontrol efficacy against CymRSV and CMV, unlike PVX and PVY. They exhibited significant reductions in symptom severity while promoting plant height compared to nontreated, virus-infected controls. However, these phenotypic traits showed no association with relative virus quantification. Moreover, the tested defense-related genes (Enhanced Disease Susceptibility-1 (EDS1), Non-expressor of Pathogenesis-related genes-1 (NPR1), and Pathogenesis-related protein-2B (PR2B)) implied the involvement of a salicylic-acid-related defense pathway triggered by EDS1 gene upregulation.
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Affiliation(s)
| | | | | | | | - Iriti Marcello
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroecology, University of Milan, 20133 Milan, Italy; (G.-i.-R.S.); (A.P.); (G.M.); (P.C.); (P.A.B.)
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29
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Sharifzadeh M, Mottaghi-Dastjerdi N, Soltany Rezae Raad M. A Review of Virus-Like Particle-Based SARS-CoV-2 Vaccines in Clinical Trial Phases. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH 2022; 21:e127042. [PMID: 35873011 PMCID: PMC9293385 DOI: 10.5812/ijpr-127042] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/16/2022] [Accepted: 01/29/2022] [Indexed: 11/28/2022]
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic has affected more than 269 million worldwide, with more than five million deaths as of early December 2021. The main concerns in this pandemic include the asymptomatic nature of COVID-19, leading to the infection of many healthy people, the infectious nature of the pathogen, and its high spreading rate. The disease features have highlighted the importance of controlling this pandemic via vaccines. There has been a worldwide race to produce better, more protective, and efficacious vaccines. Simultaneously, different new variants of the virus are emerging. Therefore, there is a concern about the efficacy of the vaccines against new variants. The platform used for COVID-19 vaccine development needs to be flexible enough to enable the manufacturer to react suitably to new virus variants. We performed a comprehensive search in the online databases of PubMed, Scopus, Google Scholar, clinicaltrials.gov, WHO, ICTRP, and Cochrane until December 10th, 2021. There are 331 candidate vaccines in clinical development, with 194 in the preclinical stage and 137 in different clinical phases. Eleven platforms have been used for the development of COVID-19 vaccines, including inactivated/live attenuated virus, protein subunit, virus-like particle (VLP), non-replicating/replicating viral vectors (VVnr or VVr), VVr or VVnr plus antigen-presenting cell, bacterial antigen-spore expression vector, DNA, and RNA. The VLP-based vaccine platform is a safe, highly immunogenic, and flexible platform for developing vaccines. This review focuses on VLP-based vaccine platforms and explicitly discusses the six VLP-based COVID-19 vaccines in clinical trial phases.
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Affiliation(s)
- Mohammad Sharifzadeh
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Negar Mottaghi-Dastjerdi
- Department of Pharmacognosy and Pharmaceutical Biotechnology, School of Pharmacy, Iran University of Medical Sciences, Tehran, Iran
- Corresponding Author: Department of Pharmacognosy and Pharmaceutical Biotechnology, School of Pharmacy, Iran University of Medical Sciences, Tehran, Iran. Tel/Fax: +98-2144606181,
| | - Mohammad Soltany Rezae Raad
- Department of Pharmaceutical Biotechnology and Pharmaceutical Biotechnology Research Center, School of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
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Wylie S, Li H. Historical and Scientific Evidence for the Origin and Cultural Importance to Australia's First-Nations Peoples of the Laboratory Accession of Nicotiana benthamiana, a Model for Plant Virology. Viruses 2022; 14:771. [PMID: 35458501 PMCID: PMC9027518 DOI: 10.3390/v14040771] [Citation(s) in RCA: 4] [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: 03/21/2022] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 02/01/2023] Open
Abstract
Nicotiana benthamiana is an indigenous plant species distributed across northern Australia. The laboratory accession (LAB) of N. benthamiana has become widely adopted as a model host for plant viruses, and it is distinct from other accessions morphologically, physiologically, and by having an attenuation-of-function mutation in the RNA-dependent RNA polymerase 1 (NbRdr1) gene, referred to as NbRdr1m. Recent historical evidence suggested LAB was derived from a 1936 collection by John Cleland at The Granites of the Northern Territory, although no scientific evidence was provided. We provide scientific evidence and further historical evidence supporting the origin of LAB as The Granites. Analysis of a herbarium specimen of N. benthamiana collected by Cleland in 1936 revealed that The Granites population contains plants heterozygous for the NbRdr1 locus, having both the functional NbRdr1 and the mutant NbRdr1m alleles. N. benthamiana was an important cultural asset actively utilised as the narcotic Pituri (chewing tobacco) by the Warlpiri Aboriginal people at the site, who prevented women of child-bearing age from consuming it. We propose that Aboriginal people selected some of the unique traits of LAB that have subsequently facilitated its adoption as a model plant, such as lack of seed dormancy, fast maturity, low nornicotine content, and gracility.
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Affiliation(s)
- Steve Wylie
- Plant Biotechnology Research Group (Virology), Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch 6150, Australia;
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Rai A, Sivalingam PN, Senthil-Kumar M. A spotlight on non-host resistance to plant viruses. PeerJ 2022; 10:e12996. [PMID: 35382007 PMCID: PMC8977066 DOI: 10.7717/peerj.12996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 02/02/2022] [Indexed: 01/11/2023] Open
Abstract
Plant viruses encounter a range of host defenses including non-host resistance (NHR), leading to the arrest of virus replication and movement in plants. Viruses have limited host ranges, and adaptation to a new host is an atypical phenomenon. The entire genotypes of plant species which are imperceptive to every single isolate of a genetically variable virus species are described as non-hosts. NHR is the non-specific resistance manifested by an innately immune non-host due to pre-existing and inducible defense responses, which cannot be evaded by yet-to-be adapted plant viruses. NHR-to-plant viruses are widespread, but the phenotypic variation is often not detectable within plant species. Therefore, molecular and genetic mechanisms of NHR need to be systematically studied to enable exploitation in crop protection. This article comprehensively describes the possible mechanisms of NHR against plant viruses. Also, the previous definition of NHR to plant viruses is insufficient, and the main aim of this article is to sensitize plant pathologists to the existence of NHR to plant viruses and to highlight the need for immediate and elaborate research in this area.
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Affiliation(s)
- Avanish Rai
- National Institute of Plant Genome Research, New Delhi, India
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32
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Xu W, Guo Y, Li H, Sivasithamparam K, Jones MGK, Chen X, Wylie SJ. Differential Symptom Development and Viral RNA Loads in 10 Nicotiana benthamiana Accessions Infected with the Tobamovirus Yellow Tailflower Mild Mottle Virus. PLANT DISEASE 2022; 106:984-989. [PMID: 34735277 DOI: 10.1094/pdis-08-21-1697-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Yellow tailflower mild mottle virus (YTMMV, genus Tobamovirus) was identified from wild plants of solanaceous species in Australia. Nicotiana benthamiana is a species indigenous to the arid north of Australia. N. benthamiana accession RA-4 (the lab type), which has a mutant, functionally defective, RNA-dependent RNA polymerase 1 (Rdr1) gene (Nb-Rdr1m), has played a significant role in plant virology, but little study has been done regarding responses to virus infection by other accessions of N. benthamiana. All wild-collected N. benthamiana accessions used in this study harbored wild-type Rdr1 genes (Nb-Rdr1). We compared symptoms of YTMMV infection and viral RNA load on RA-4 and nine wild-collected accessions of N. benthamiana from mainland Western Australia, an island, and the Northern Territory. After inoculation with YTMMV, RA-4 plants responded with systemic hypersensitivity and all individuals were dead 35 days postinoculation (dpi). Plants of wild-collected accessions exhibited a range of symptoms, from mild to severe, and some, but not all, died in the same period. Quantitative reverse transcription PCR revealed that the Rdr1 mutation was not a predictor of viral RNA load or symptom severity. For example, wild-collected A019412 plants carried more than twice the viral RNA load of RA-4 plants, but symptom expression was moderate. For plants of most accessions, viral RNA load did not increase after 10 dpi. The exception was plants of accession Barrow-1, in which viral RNA load was low until 15 dpi, after which it increased more than 29-fold. This study revealed differential responses by N. benthamiana accessions to infection by an isolate of YTMMV. The Rdr1 gene, whether mutant or wild-type, did not appear to influence viral RNA load or disease expression. Genetic diversity of the 10 N. benthamiana accessions in some cases reflected geographical location, but in other accessions this was not so.
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Affiliation(s)
- Weinan Xu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Plant Biotechnology Research Group (Virology), Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch 6150, Australia
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yuxia Guo
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Hua Li
- Plant Biotechnology Research Group (Virology), Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch 6150, Australia
| | - Krishnapillai Sivasithamparam
- Plant Biotechnology Research Group (Virology), Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch 6150, Australia
| | - Michael G K Jones
- Plant Biotechnology Research Group (Virology), Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch 6150, Australia
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Stephen J Wylie
- Plant Biotechnology Research Group (Virology), Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch 6150, Australia
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Pizzio GA, Mayordomo C, Lozano-Juste J, Garcia-Carpintero V, Vazquez-Vilar M, Nebauer SG, Kaminski KP, Ivanov NV, Estevez JC, Rivera-Moreno M, Albert A, Orzaez D, Rodriguez PL. PYL1- and PYL8-like ABA Receptors of Nicotiana benthamiana Play a Key Role in ABA Response in Seed and Vegetative Tissue. Cells 2022; 11:795. [PMID: 35269417 PMCID: PMC8909036 DOI: 10.3390/cells11050795] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/16/2022] [Accepted: 02/20/2022] [Indexed: 02/04/2023] Open
Abstract
To face the challenges of climate change and sustainable food production, it is essential to develop crop genome editing techniques to pinpoint key genes involved in abiotic stress signaling. The identification of those prevailing abscisic acid (ABA) receptors that mediate plant-environment interactions is quite challenging in polyploid plants because of the high number of genes in the PYR/PYL/RCAR ABA receptor family. Nicotiana benthamiana is a biotechnological crop amenable to genome editing, and given the importance of ABA signaling in coping with drought stress, we initiated the analysis of its 23-member family of ABA receptors through multiplex CRISPR/Cas9-mediated editing. We generated several high-order mutants impaired in NbPYL1-like and NbPYL8-like receptors, which showed certain insensitivity to ABA for inhibition of seedling establishment, growth, and development of shoot and lateral roots as well as reduced sensitivity to the PYL1-agonist cyanabactin (CB). However, in these high-order mutants, regulation of transpiration was not affected and was responsive to ABA treatment. This reveals a robust and redundant control of transpiration in this allotetraploid plant that probably reflects its origin from the extreme habitat of central Australia.
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Affiliation(s)
- Gaston A. Pizzio
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, ES-46022 Valencia, Spain; (G.A.P.); (C.M.); (J.L.-J.); (V.G.-C.); (M.V.-V.); (D.O.)
| | - Cristian Mayordomo
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, ES-46022 Valencia, Spain; (G.A.P.); (C.M.); (J.L.-J.); (V.G.-C.); (M.V.-V.); (D.O.)
| | - Jorge Lozano-Juste
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, ES-46022 Valencia, Spain; (G.A.P.); (C.M.); (J.L.-J.); (V.G.-C.); (M.V.-V.); (D.O.)
| | - Victor Garcia-Carpintero
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, ES-46022 Valencia, Spain; (G.A.P.); (C.M.); (J.L.-J.); (V.G.-C.); (M.V.-V.); (D.O.)
| | - Marta Vazquez-Vilar
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, ES-46022 Valencia, Spain; (G.A.P.); (C.M.); (J.L.-J.); (V.G.-C.); (M.V.-V.); (D.O.)
| | - Sergio G. Nebauer
- Plant Production Department, Universitat Politècnica de València, ES-46022 Valencia, Spain;
| | - Kacper P. Kaminski
- PMI R&D, Philip Morris Products S.A., Quai Jean Renaud 5, CH-2000 Neuchâtel, Switzerland; (K.P.K.); (N.V.I.)
| | - Nikolai V. Ivanov
- PMI R&D, Philip Morris Products S.A., Quai Jean Renaud 5, CH-2000 Neuchâtel, Switzerland; (K.P.K.); (N.V.I.)
| | - Juan C. Estevez
- Centro Singular de Investigación en Química e Bioloxía Molecular (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Maria Rivera-Moreno
- Instituto de Química-Física Rocasolano, Departamento de Cristalografía y Biología Estructural, CSIC, ES-28006 Madrid, Spain; (M.R.-M.); (A.A.)
| | - Armando Albert
- Instituto de Química-Física Rocasolano, Departamento de Cristalografía y Biología Estructural, CSIC, ES-28006 Madrid, Spain; (M.R.-M.); (A.A.)
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, ES-46022 Valencia, Spain; (G.A.P.); (C.M.); (J.L.-J.); (V.G.-C.); (M.V.-V.); (D.O.)
| | - Pedro L. Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, ES-46022 Valencia, Spain; (G.A.P.); (C.M.); (J.L.-J.); (V.G.-C.); (M.V.-V.); (D.O.)
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Tsai WA, Shafiei-Peters JR, Mitter N, Dietzgen RG. Effects of Elevated Temperature on the Susceptibility of Capsicum Plants to Capsicum Chlorosis Virus Infection. Pathogens 2022; 11:pathogens11020200. [PMID: 35215143 PMCID: PMC8879237 DOI: 10.3390/pathogens11020200] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 02/01/2023] Open
Abstract
Capsicum, an important vegetable crop in Queensland, Australia, is vulnerable to both elevated temperatures and capsicum chlorosis virus (CaCV). Thus, it is imperative to understand the genetic responses of capsicum plants (Capsicum annuum) to CaCV under elevated temperature conditions. Here, we challenged susceptible plants (cv. Yolo Wonder) with CaCV and investigated the effects of elevated temperature on symptom expression, the accumulation of virus-derived short interfering RNA (vsiRNA) and viral RNA, and the expression of plant defense-associated genes. CaCV-inoculated plants initially showed more severe symptoms and higher viral concentrations at a higher temperature (HT, 35 °C) than at ambient temperature (AT, 25 °C). However, symptom recovery and reduced viral RNA accumulation were seen in the CaCV-infected plants grown at HT at later stages of infection. We also observed that HT enhanced the accumulation of vsiRNAs and that, concurrently, RNA interference (RNAi)-related genes, including Dicer-like2 (DCL2), DCL4, RNA-dependent RNA polymerase 1 (RdRp1), RdRp6, and Argonaute2 (AGO2), were upregulated early during infection. Moreover, continuous high levels of vsiRNAs were observed during later stages of CaCV infection at HT. Overall, our investigation suggests that HT facilitates CaCV replication during early infection stages. However, this appears to lead to an early onset of antiviral RNA silencing, resulting in a subsequent recovery from CaCV in systemic leaves.
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Boccia M, Grzech D, Lopes AA, O’Connor SE, Caputi L. Directed Biosynthesis of New to Nature Alkaloids in a Heterologous Nicotiana benthamiana Expression Host. FRONTIERS IN PLANT SCIENCE 2022; 13:919443. [PMID: 35812900 PMCID: PMC9257203 DOI: 10.3389/fpls.2022.919443] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/24/2022] [Indexed: 05/17/2023]
Abstract
Plants produce a wide variety of pharmacologically active molecules classified as natural products. Derivatization of these natural products can modulate or improve the bioactivity of the parent compound. Unfortunately, chemical derivatization of natural products is often difficult or impractical. Here we use the newly discovered biosynthetic genes for two monoterpene indole alkaloids, alstonine and stemmadenine acetate, to generate analogs of these compounds. We reconstitute these biosynthetic genes in the heterologous host Nicotiana benthamiana along with an unnatural starting substrate to produce the corresponding new-to-nature alkaloid product.
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Affiliation(s)
- Marianna Boccia
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Dagny Grzech
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Adriana A. Lopes
- Biotechnology Unit, Universidade de Ribeirão Preto (UNAERP), Ribeirão Preto, Brazil
| | - Sarah E. O’Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
- *Correspondence: Sarah E. O’Connor,
| | - Lorenzo Caputi
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
- Lorenzo Caputi,
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Jansing J, Bortesi L. Knockout of Glycosyltransferases in Nicotiana benthamiana by Genome Editing to Improve Glycosylation of Plant-Produced Proteins. Methods Mol Biol 2022; 2480:241-284. [PMID: 35616867 DOI: 10.1007/978-1-0716-2241-4_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Plants are excellent production hosts for the in vivo synthesis of complex glycosylated proteins such as antibodies. The plant N-glycosylation machinery is largely similar to that found in humans and other mammalian organisms, which is an advantage in comparison to microbial production systems in particular. However, there are some differences in the identity and chemical linkage of the sugars that plants and mammals use to build their N-glycans. These differences can affect important properties of glycosylated proteins produced recombinantly in plants. Here we describe the complete procedure of multiplex targeted gene knockout with CRISPR/Cas9 in Nicotiana benthamiana in order to eliminate the undesirable sugars α-1,3-fucose and β-1,2-xylose from the plant N-glycans. The workflow includes target gene identification, guide RNA design and testing, plant transformation, and the analysis of the regenerated transgenic plants by Sanger sequencing, immunoblot, and mass-spectrometric analysis of recombinant and endogenous proteins.
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Affiliation(s)
- Julia Jansing
- Aachen-Maastricht Institute for Biobased Materials (AMIBM), Maastricht University, Geleen, The Netherlands.
| | - Luisa Bortesi
- Aachen-Maastricht Institute for Biobased Materials (AMIBM), Maastricht University, Geleen, The Netherlands
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37
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Spiegel H, Schillberg S, Nölke G. Production of Recombinant Proteins by Agrobacterium-Mediated Transient Expression. Methods Mol Biol 2022; 2480:89-102. [PMID: 35616859 DOI: 10.1007/978-1-0716-2241-4_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The agroinfiltration of plant tissue is a robust method that allows the rapid and transient expression of recombinant proteins. Using wild-type plants as biomass, agroinfiltration exploits the ability of plants to synthesize even complex multimeric proteins that require oxidative folding and/or post-translational modifications, while avoiding the expensive and time-consuming creation of stably transformed plant lines. Here we describe a generic method for the transient expression of recombinant proteins in Nicotiana benthamiana at the small to medium laboratory scale, including appropriate binary vectors, the design and cloning of expression constructs, the transformation, selection, and cultivation of recombinant Agrobacterium tumefaciens, the infiltration of plants using a syringe or vacuum device, and finally the extraction of recombinant proteins from plant tissues.
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Affiliation(s)
- Holger Spiegel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany.
| | - Stefan Schillberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
- Department of Phytopathology, Justus Liebig University Giessen, Giessen, Germany
| | - Greta Nölke
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
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González-Grandío E, Demirer GS, Jackson CT, Yang D, Ebert S, Molawi K, Keller H, Landry MP. Carbon nanotube biocompatibility in plants is determined by their surface chemistry. J Nanobiotechnology 2021; 19:431. [PMID: 34930290 PMCID: PMC8686619 DOI: 10.1186/s12951-021-01178-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 12/02/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Agriculture faces significant global challenges including climate change and an increasing food demand due to a growing population. Addressing these challenges will require the adoption of transformative innovations into biotechnology practice, such as nanotechnology. Recently, nanomaterials have emerged as unmatched tools for their use as biosensors, or as biomolecule delivery vehicles. Despite their increasingly prolific use, plant-nanomaterial interactions remain poorly characterized, drawing into question the breadth of their utility and their broader environmental compatibility. RESULTS Herein, we characterize the response of Arabidopsis thaliana to single walled carbon nanotube (SWNT) exposure with two different surface chemistries commonly used for biosensing and nucleic acid delivery: oligonucleotide adsorbed-pristine SWNTs, and polyethyleneimine-SWNTs loaded with plasmid DNA (PEI-SWNTs), both introduced by leaf infiltration. We observed that pristine SWNTs elicit a mild stress response almost undistinguishable from the infiltration process, indicating that these nanomaterials are well-tolerated by the plant. However, PEI-SWNTs induce a much larger transcriptional reprogramming that involves stress, immunity, and senescence responses. PEI-SWNT-induced transcriptional profile is very similar to that of mutant plants displaying a constitutive immune response or treated with stress-priming agrochemicals. We selected molecular markers from our transcriptomic analysis and identified PEI as the main cause of this adverse reaction. We show that PEI-SWNT response is concentration-dependent and, when persistent over time, leads to cell death. We probed a panel of PEI variant-functionalized SWNTs across two plant species and identified biocompatible SWNT surface functionalizations. CONCLUSIONS While SWNTs themselves are well tolerated by plants, SWNTs surface-functionalized with positively charged polymers become toxic and produce cell death. We use molecular markers to identify more biocompatible SWNT formulations. Our results highlight the importance of nanoparticle surface chemistry on their biocompatibility and will facilitate the use of functionalized nanomaterials for agricultural improvement.
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Affiliation(s)
- Eduardo González-Grandío
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Gözde S Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.,Department of Plant Biology and Genome Center, University of California, Davis, CA, USA
| | - Christopher T Jackson
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Darwin Yang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Sophia Ebert
- BASF, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Kian Molawi
- BASF, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Harald Keller
- BASF, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA. .,Innovative Genomics Institute (IGI), Berkeley, CA, USA. .,California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, CA, USA. .,Chan-Zuckerberg Biohub, San Francisco, CA, USA.
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Mateos-Fernández R, Moreno-Giménez E, Gianoglio S, Quijano-Rubio A, Gavaldá-García J, Estellés L, Rubert A, Rambla JL, Vazquez-Vilar M, Huet E, Fernández-del-Carmen A, Espinosa-Ruiz A, Juteršek M, Vacas S, Navarro I, Navarro-Llopis V, Primo J, Orzáez D. Production of Volatile Moth Sex Pheromones in Transgenic Nicotiana benthamiana Plants. BIODESIGN RESEARCH 2021; 2021:9891082. [PMID: 37849952 PMCID: PMC10521740 DOI: 10.34133/2021/9891082] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/31/2021] [Indexed: 10/19/2023] Open
Abstract
Plant-based bioproduction of insect sex pheromones has been proposed as an innovative strategy to increase the sustainability of pest control in agriculture. Here, we describe the engineering of transgenic plants producing (Z)-11-hexadecenol (Z11-16OH) and (Z)-11-hexadecenyl acetate (Z11-16OAc), two main volatile components in many Lepidoptera sex pheromone blends. We assembled multigene DNA constructs encoding the pheromone biosynthetic pathway and stably transformed them into Nicotiana benthamiana plants. The constructs contained the Amyelois transitella AtrΔ11 desaturase gene, the Helicoverpa armigera fatty acyl reductase HarFAR gene, and the Euonymus alatus diacylglycerol acetyltransferase EaDAct gene in different configurations. All the pheromone-producing plants showed dwarf phenotypes, the severity of which correlated with pheromone levels. All but one of the recovered lines produced high levels of Z11-16OH, but very low levels of Z11-16OAc, probably as a result of recurrent truncations at the level of the EaDAct gene. Only one plant line (SxPv1.2) was recovered that harboured an intact pheromone pathway and which produced moderate levels of Z11-16OAc (11.8 μg g-1 FW) and high levels of Z11-16OH (111.4 μg g-1). Z11-16OAc production was accompanied in SxPv1.2 by a partial recovery of the dwarf phenotype. SxPv1.2 was used to estimate the rates of volatile pheromone release, which resulted in 8.48 ng g-1 FW per day for Z11-16OH and 9.44 ng g-1 FW per day for Z11-16OAc. Our results suggest that pheromone release acts as a limiting factor in pheromone biodispenser strategies and establish a roadmap for biotechnological improvements.
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Affiliation(s)
- Rubén Mateos-Fernández
- Institute for Plant Molecular and Cell Biology (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Elena Moreno-Giménez
- Institute for Plant Molecular and Cell Biology (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Silvia Gianoglio
- Institute for Plant Molecular and Cell Biology (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Alfredo Quijano-Rubio
- Institute for Plant Molecular and Cell Biology (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Jose Gavaldá-García
- Institute for Plant Molecular and Cell Biology (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Lucía Estellés
- Institute for Plant Molecular and Cell Biology (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Alba Rubert
- Institute for Plant Molecular and Cell Biology (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - José Luis Rambla
- Institute for Plant Molecular and Cell Biology (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), Valencia, Spain
- Jaume I University, Castellon de la Plana, Spain
| | - Marta Vazquez-Vilar
- Institute for Plant Molecular and Cell Biology (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Estefanía Huet
- Institute for Plant Molecular and Cell Biology (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Asunción Fernández-del-Carmen
- Institute for Plant Molecular and Cell Biology (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Ana Espinosa-Ruiz
- Institute for Plant Molecular and Cell Biology (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Mojca Juteršek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Sandra Vacas
- Centro de Ecología Química Agrícola, Instituto Agroforestal del Mediterráneo, Universitat Politècnica de València, Valencia, Spain
| | | | - Vicente Navarro-Llopis
- Centro de Ecología Química Agrícola, Instituto Agroforestal del Mediterráneo, Universitat Politècnica de València, Valencia, Spain
| | - Jaime Primo
- Centro de Ecología Química Agrícola, Instituto Agroforestal del Mediterráneo, Universitat Politècnica de València, Valencia, Spain
| | - Diego Orzáez
- Institute for Plant Molecular and Cell Biology (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), Valencia, Spain
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40
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Nosaki S, Hoshikawa K, Ezura H, Miura K. Transient protein expression systems in plants and their applications. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:297-304. [PMID: 34782815 PMCID: PMC8562577 DOI: 10.5511/plantbiotechnology.21.0610a] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/10/2021] [Indexed: 06/01/2023]
Abstract
The production of recombinant proteins is important in academic research to identify protein functions. Moreover, recombinant enzymes are used in the food and chemical industries, and high-quality proteins are required for diagnostic, therapeutic, and pharmaceutical applications. Though many recombinant proteins are produced by microbial or mammalian cell-based expression systems, plants have been promoted as alternative, cost-effective, scalable, safe, and sustainable expression systems. The development and improvement of transient expression systems have significantly reduced the period of protein production and increased the yield of recombinant proteins in plants. In this review, we consider the importance of plant-based expression systems for recombinant protein production and as genetic engineering tools.
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Affiliation(s)
- Shohei Nosaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Ken Hoshikawa
- Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki 305-8686, Japan
| | - Hiroshi Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Kenji Miura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
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Molina-Hidalgo FJ, Vazquez-Vilar M, D'Andrea L, Demurtas OC, Fraser P, Giuliano G, Bock R, Orzáez D, Goossens A. Engineering Metabolism in Nicotiana Species: A Promising Future. Trends Biotechnol 2021; 39:901-913. [PMID: 33341279 DOI: 10.1016/j.tibtech.2020.11.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 12/31/2022]
Abstract
Molecular farming intends to use crop plants as biofactories for high value-added compounds following application of a wide range of biotechnological tools. In particular, the conversion of nonfood crops into efficient biofactories is expected to be a strong asset in the development of a sustainable bioeconomy. The 'nonfood' status combined with the high metabolic versatility and the capacity of high-yield cultivation highlight the plant genus Nicotiana as one of the most appropriate 'chassis' for molecular farming. Nicotiana species are a rich source of valuable industrial, active pharmaceutical ingredients and nutritional compounds, synthesized from highly complex biosynthetic networks. Here, we review and discuss approaches currently used to design enriched Nicotiana species for molecular farming using new plant breeding techniques (NPBTs).
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Affiliation(s)
- Francisco Javier Molina-Hidalgo
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Marta Vazquez-Vilar
- Instituto de Biología Molecular y Celular de Plantas (IBMCP-UPV-CSIC), Valencia, Spain
| | - Lucio D'Andrea
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Olivia C Demurtas
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Paul Fraser
- School of Biological Sciences, Royal Holloway, University of London, London, UK
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Diego Orzáez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP-UPV-CSIC), Valencia, Spain
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium.
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Albert NW, Butelli E, Moss SM, Piazza P, Waite CN, Schwinn KE, Davies KM, Martin C. Discrete bHLH transcription factors play functionally overlapping roles in pigmentation patterning in flowers of Antirrhinum majus. THE NEW PHYTOLOGIST 2021; 231:849-863. [PMID: 33616943 PMCID: PMC8248400 DOI: 10.1111/nph.17142] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 11/30/2020] [Indexed: 05/08/2023]
Abstract
Floral pigmentation patterning is important for pollinator attraction as well as aesthetic appeal. Patterning of anthocyanin accumulation is frequently associated with variation in activity of the Myb, bHLH and WDR transcription factor complex (MBW) that regulates anthocyanin biosynthesis. Investigation of two classic mutants in Antirrhinum majus, mutabilis and incolorata I, showed they affect a gene encoding a bHLH protein belonging to subclade bHLH-2. The previously characterised gene, Delila, which encodes a bHLH-1 protein, has a bicoloured mutant phenotype, with residual lobe-specific pigmentation conferred by Incolorata I. Both Incolorata I and Delila induce expression of the anthocyanin biosynthetic gene DFR. Rosea 1 (Myb) and WDR1 proteins compete for interaction with Delila, but interact positively to promote Incolorata I activity. Delila positively regulates Incolorata I and WDR1 expression. Hierarchical regulation can explain the bicoloured patterning of delila mutants, through effects on both regulatory gene expression and the activity of promoters of biosynthetic genes like DFR that mediate MBW regulation. bHLH-1 and bHLH-2 proteins contribute to establishing patterns of pigment distribution in A. majus flowers in two ways: through functional redundancy in regulating anthocyanin biosynthetic gene expression, and through differences between the proteins in their ability to regulate genes encoding transcription factors.
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Affiliation(s)
- Nick W. Albert
- Plant & Food Research Food Industry Science CentreFitzherbert Science CentreBatchelar RoadPalmerston North4474New Zealand
| | | | - Sarah M.A. Moss
- Plant & Food Research Food Industry Science CentreFitzherbert Science CentreBatchelar RoadPalmerston North4474New Zealand
| | - Paolo Piazza
- Oxford Genomics CentreUniversity of OxfordRoosevelt DriveOxford,OX3 7BNUK
| | - Chethi N. Waite
- Plant & Food Research Food Industry Science CentreFitzherbert Science CentreBatchelar RoadPalmerston North4474New Zealand
| | - Kathy E. Schwinn
- Plant & Food Research Food Industry Science CentreFitzherbert Science CentreBatchelar RoadPalmerston North4474New Zealand
| | - Kevin M. Davies
- Plant & Food Research Food Industry Science CentreFitzherbert Science CentreBatchelar RoadPalmerston North4474New Zealand
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43
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Drapal M, Enfissi EMA, Fraser PD. Metabolic effects of agro-infiltration on N. benthamiana accessions. Transgenic Res 2021; 30:303-315. [PMID: 33909228 PMCID: PMC8080481 DOI: 10.1007/s11248-021-00256-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/10/2021] [Indexed: 02/07/2023]
Abstract
Over the recent years, Nicotiana benthamiana has gained great importance as a chassis for the production of high value, low volume pharmaceuticals and/or active pharmaceutical ingredients (APIs). The process involving infiltration of the N. benthamiana leaves with Agrobacterium spp, harbouring vectors with the gene of interest, facilitates transient expression. To date, little information is available on the effect of the agro-infiltration process on the metabolome of N. benthamiana, which is necessary to improve the process for large-scale, renewable manufacturing of high value compounds and medical products. Hence, the objective of the present study was to assess metabolic adaptation of N. benthamiana as a response to the presence of Agrobacterium. The present study elucidated changes of the steady-state metabolism in the agroinfiltrated leaf area, the area around the infection and the rest of the plant. Furthermore, the study discusses the phenotypic advantages of the N. benthamiana lab strain, optimised for agro-infiltration, compared to three other wild accessions. Results showed that the lab strain has a different metabolic composition and showed less alterations of the phenylpropanoid pathway and cell wall remodelling in the agroinfiltrated leaf areas, for example chlorogenic acid, cadaverine and C18:0-2-glycerol ester. In conclusion, both of these alterations present potential candidates to improve the phenotype of the N. benthamiana lab strain for a more efficient transient expression process.
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Affiliation(s)
- Margit Drapal
- Biochemistry, Royal Holloway University of London, Egham, UK
| | | | - Paul D Fraser
- Biochemistry, Royal Holloway University of London, Egham, UK.
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Schiavinato M, Bodrug‐Schepers A, Dohm JC, Himmelbauer H. Subgenome evolution in allotetraploid plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:672-688. [PMID: 33547826 PMCID: PMC8251528 DOI: 10.1111/tpj.15190] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/25/2021] [Accepted: 01/29/2021] [Indexed: 05/02/2023]
Abstract
Polyploidization is a well-known speciation and adaptation mechanism. Traces of former polyploidization events were discovered within many genomes, and especially in plants. Allopolyploidization by interspecific hybridization between two species is common. Among hybrid plants, many are domesticated species of agricultural interest and many of their genomes and of their presumptive parents have been sequenced. Hybrid genomes remain challenging to analyse because of the presence of multiple subgenomes. The genomes of hybrids often undergo rearrangement and degradation over time. Based on 10 hybrid plant genomes from six different genera, with hybridization dating from 10,000 to 5 million years ago, we assessed subgenome degradation, subgenomic intermixing and biased subgenome fractionation. The restructuring of hybrid genomes does not proceed proportionally with the age of the hybrid. The oldest hybrids in our data set display completely different fates: whereas the subgenomes of the tobacco plant Nicotiana benthamiana are in an advanced stage of degradation, the subgenomes of quinoa (Chenopodium quinoa) are exceptionally well conserved by structure and sequence. We observed statistically significant biased subgenome fractionation in seven out of 10 hybrids, which had different ages and subgenomic intermixing levels. Hence, we conclude that no correlation exists between biased fractionation and subgenome intermixing. Lastly, domestication may encourage or hinder subgenome intermixing, depending on the evolutionary context. In summary, comparative analysis of hybrid genomes and their presumptive parents allowed us to determine commonalities and differences between their evolutionary fates. In order to facilitate the future analysis of further hybrid genomes, we automated the analysis steps within manticore, which is publicly available at https://github.com/MatteoSchiavinato/manticore.git.
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Affiliation(s)
- Matteo Schiavinato
- Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)Institute of Computational BiologyMuthgasse 18Vienna1190Austria
| | - Alexandrina Bodrug‐Schepers
- Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)Institute of Computational BiologyMuthgasse 18Vienna1190Austria
| | - Juliane C. Dohm
- Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)Institute of Computational BiologyMuthgasse 18Vienna1190Austria
| | - Heinz Himmelbauer
- Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)Institute of Computational BiologyMuthgasse 18Vienna1190Austria
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45
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LeBlanc Z, Waterhouse P, Bally J. Plant-Based Vaccines: The Way Ahead? Viruses 2020; 13:E5. [PMID: 33375155 PMCID: PMC7822169 DOI: 10.3390/v13010005] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/16/2020] [Accepted: 12/19/2020] [Indexed: 12/20/2022] Open
Abstract
Severe virus outbreaks are occurring more often and spreading faster and further than ever. Preparedness plans based on lessons learned from past epidemics can guide behavioral and pharmacological interventions to contain and treat emergent diseases. Although conventional biologics production systems can meet the pharmaceutical needs of a community at homeostasis, the COVID-19 pandemic has created an abrupt rise in demand for vaccines and therapeutics that highlight the gaps in this supply chain's ability to quickly develop and produce biologics in emergency situations given a short lead time. Considering the projected requirements for COVID-19 vaccines and the necessity for expedited large scale manufacture the capabilities of current biologics production systems should be surveyed to determine their applicability to pandemic preparedness. Plant-based biologics production systems have progressed to a state of commercial viability in the past 30 years with the capacity for production of complex, glycosylated, "mammalian compatible" molecules in a system with comparatively low production costs, high scalability, and production flexibility. Continued research drives the expansion of plant virus-based tools for harnessing the full production capacity from the plant biomass in transient systems. Here, we present an overview of vaccine production systems with a focus on plant-based production systems and their potential role as "first responders" in emergency pandemic situations.
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Affiliation(s)
- Zacharie LeBlanc
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD 4000, Australia;
| | - Peter Waterhouse
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD 4000, Australia;
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Queensland University of Technology (QUT), Brisbane, QLD 4000, Australia
| | - Julia Bally
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD 4000, Australia;
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46
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Ranawaka B, Tanurdzic M, Waterhouse P, Naim F. An optimised chromatin immunoprecipitation (ChIP) method for starchy leaves of Nicotiana benthamiana to study histone modifications of an allotetraploid plant. Mol Biol Rep 2020; 47:9499-9509. [PMID: 33237398 PMCID: PMC7723940 DOI: 10.1007/s11033-020-06013-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/16/2020] [Indexed: 10/26/2022]
Abstract
All flowering plants have evolved through multiple rounds of polyploidy throughout the evolutionary process. Intergenomic interactions between subgenomes in polyploid plants are predicted to induce chromatin modifications such as histone modifications to regulate expression of gene homoeologs. Nicotiana benthamiana is an ancient allotetraploid plant with ecotypes collected from climatically diverse regions of Australia. Studying the chromatin landscape of this unique collection will likely shed light on the importance of chromatin modifications in gene regulation in polyploids as well its implications in adaptation of plants in environmentally diverse conditions. Generally, chromatin immunoprecipitation and high throughput DNA sequencing (ChIP-seq) is used to study chromatin modifications. However, due to the starchy nature of mature N. benthamiana leaves, previously published protocols were unsuitable. The higher amounts of starch in leaves that co-precipitated with nuclei hindered downstream processing of DNA. Here we present an optimised ChIP protocol for N. benthamiana leaves to facilitate comparison of chromatin modifications in two closely related ecotypes. Several steps of ChIP were optimised including tissue harvesting, nuclei isolation, nuclei storage, DNA shearing and DNA recovery. Commonly available antibodies targeting histone 3 lysine 4 trimethylation (H3K4me3) and histone 3 lysine 9 dimethylation (H3K9me2) histone modifications were used and success of ChIP was confirmed by PCR and next generation sequencing. Collectively, our optimised method is the first comprehensive ChIP method for mature starchy leaves of N. benthamiana to enable studies of chromatin landscape at the genome-wide scale.
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Affiliation(s)
- Buddhini Ranawaka
- Centre for Agriculture and Bioeconomy, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
| | - Milos Tanurdzic
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Peter Waterhouse
- Centre for Agriculture and Bioeconomy, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Fatima Naim
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
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47
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Qu H, Jackson MA, Yap K, Harvey PJ, Gilding EK, Craik DJ. Production of a structurally validated cyclotide in rice suspension cells is enabled by a supporting biosynthetic enzyme. PLANTA 2020; 252:97. [PMID: 33155076 DOI: 10.1007/s00425-020-03505-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/26/2020] [Indexed: 05/22/2023]
Abstract
We demonstrate the production of a structurally correct cyclotide in rice suspension cells with co-expression of a ligase-type AEP, which unlocks monocotyledons as production platforms to produce cyclotides. Cyclotides are a class of backbone-cyclic plant peptides that harbor a cystine knot composed of three disulfide bonds. These structural features make cyclotides particularly stable, and thus they have attracted significant attention for their use in biotechnological applications such as drug design. Currently, chemical synthesis is the predominant strategy to produce cyclotides for research purposes. However, synthetic production becomes costly both economically and environmentally at large scale. Plants offer an attractive alternative to chemical synthesis because of their lower cost and environmental footprint. In this study, rice suspension cells were engineered to produce the prototypical cyclotide, kalata B1 (kB1), a cyclotide with insecticidal properties from the African plant Oldenlandia affinis. Engineered rice cells produced structurally validated kB1 at yields of 64.21 µg/g (DW), which was dependent on the co-expression of a peptide ligase-competent asparaginyl endopeptidase OaAEP1b from O. affinis. Without co-expression, kB1 was predominantly produced as linear peptide. Through HPLC-MS co-elution, reduction, alkylation, enzymatic digestion, and proton NMR analysis, kB1 produced in rice was shown to be structurally identical to native kB1. This study reports the first example of an engineered plant suspension cell culture with the required molecular machinery for efficient production and cyclisation of a heterologous cyclotide.
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Affiliation(s)
- Haiou Qu
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Mark A Jackson
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kuok Yap
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Peta J Harvey
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Edward K Gilding
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia.
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48
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Incarbone M, Scheer H, Hily JM, Kuhn L, Erhardt M, Dunoyer P, Altenbach D, Ritzenthaler C. Characterization of a DCL2-Insensitive Tomato Bushy Stunt Virus Isolate Infecting Arabidopsis thaliana. Viruses 2020; 12:E1121. [PMID: 33023227 PMCID: PMC7650723 DOI: 10.3390/v12101121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 12/17/2022] Open
Abstract
Tomato bushy stunt virus (TBSV), the type member of the genus Tombusvirus in the family Tombusviridae is one of the best studied plant viruses. The TBSV natural and experimental host range covers a wide spectrum of plants including agricultural crops, ornamentals, vegetables and Nicotiana benthamiana. However, Arabidopsis thaliana, the well-established model organism in plant biology, genetics and plant-microbe interactions is absent from the list of known TBSV host plant species. Most of our recent knowledge of the virus life cycle has emanated from studies in Saccharomyces cerevisiae, a surrogate host for TBSV that lacks crucial plant antiviral mechanisms such as RNA interference (RNAi). Here, we identified and characterized a TBSV isolate able to infect Arabidopsis with high efficiency. We demonstrated by confocal and 3D electron microscopy that in Arabidopsis TBSV-BS3Ng replicates in association with clustered peroxisomes in which numerous spherules are induced. A dsRNA-centered immunoprecipitation analysis allowed the identification of TBSV-associated host components including DRB2 and DRB4, which perfectly localized to replication sites, and NFD2 that accumulated in larger viral factories in which peroxisomes cluster. By challenging knock-out mutants for key RNAi factors, we showed that TBSV-BS3Ng undergoes a non-canonical RNAi defensive reaction. In fact, unlike other RNA viruses described, no 22nt TBSV-derived small RNA are detected in the absence of DCL4, indicating that this virus is DCL2-insensitive. The new Arabidopsis-TBSV-BS3Ng pathosystem should provide a valuable new model for dissecting plant-virus interactions in complement to Saccharomyces cerevisiae.
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Affiliation(s)
- Marco Incarbone
- Institut de Biologie de Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France; (H.S.); (M.E.); (P.D.)
| | - Hélene Scheer
- Institut de Biologie de Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France; (H.S.); (M.E.); (P.D.)
| | - Jean-Michel Hily
- IFV, Le Grau-Du-Roi, Université de Strasbourg, INRAE, SVQV UNR-A 1131, 68000 Colmar, France;
| | - Lauriane Kuhn
- Plateforme protéomique Strasbourg Esplanade FR1589 du CNRS, Université de Strasbourg, 67000 Strasbourg, France;
| | - Mathieu Erhardt
- Institut de Biologie de Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France; (H.S.); (M.E.); (P.D.)
| | - Patrice Dunoyer
- Institut de Biologie de Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France; (H.S.); (M.E.); (P.D.)
| | - Denise Altenbach
- Bioreba AG, Christoph Merian Ring 7, CH-4153 Reinach, Switzerland;
| | - Christophe Ritzenthaler
- Institut de Biologie de Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France; (H.S.); (M.E.); (P.D.)
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49
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Kourelis J, Malik S, Mattinson O, Krauter S, Kahlon PS, Paulus JK, van der Hoorn RAL. Evolution of a guarded decoy protease and its receptor in solanaceous plants. Nat Commun 2020; 11:4393. [PMID: 32879321 PMCID: PMC7468133 DOI: 10.1038/s41467-020-18069-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/03/2020] [Indexed: 12/26/2022] Open
Abstract
Rcr3 is a secreted protease of tomato that is targeted by fungal effector Avr2, a secreted protease inhibitor of the fungal pathogen Cladosporium fulvum. The Avr2-Rcr3 complex is recognized by receptor-like protein Cf-2, triggering hypersensitive cell death (HR) and disease resistance. Avr2 also targets Rcr3 paralog Pip1, which is not required for Avr2 recognition but contributes to basal resistance. Thus, Rcr3 acts as a guarded decoy in this interaction, trapping the fungus into a recognition event. Here we show that Rcr3 evolved > 50 million years ago (Mya), whereas Cf-2 evolved <6Mya by co-opting the pre-existing Rcr3 in the Solanum genus. Ancient Rcr3 homologs present in tomato, potato, eggplants, pepper, petunia and tobacco can be inhibited by Avr2 with the exception of tobacco Rcr3. Four variant residues in Rcr3 promote Avr2 inhibition, but the Rcr3 that co-evolved with Cf-2 lacks three of these residues, indicating that the Rcr3 co-receptor is suboptimal for Avr2 binding. Pepper Rcr3 triggers HR with Cf-2 and Avr2 when engineered for enhanced inhibition by Avr2. Nicotiana benthamiana (Nb) is a natural null mutant carrying Rcr3 and Pip1 alleles with deleterious frame-shift mutations. Resurrected NbRcr3 and NbPip1 alleles were active proteases and further NbRcr3 engineering facilitated Avr2 inhibition, uncoupled from HR signalling. The evolution of a receptor co-opting a conserved pathogen target contrasts with other indirect pathogen recognition mechanisms.
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Affiliation(s)
- Jiorgos Kourelis
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB, Oxford, UK
| | - Shivani Malik
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB, Oxford, UK
| | - Oliver Mattinson
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB, Oxford, UK
| | - Sonja Krauter
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB, Oxford, UK
| | - Parvinderdeep S Kahlon
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB, Oxford, UK
| | - Judith K Paulus
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB, Oxford, UK
| | - Renier A L van der Hoorn
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB, Oxford, UK.
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Histidine-Rich Defensins from the Solanaceae and Brasicaceae Are Antifungal and Metal Binding Proteins. J Fungi (Basel) 2020; 6:jof6030145. [PMID: 32847065 PMCID: PMC7557933 DOI: 10.3390/jof6030145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/08/2020] [Accepted: 08/19/2020] [Indexed: 01/01/2023] Open
Abstract
Plant defensins are best known for their antifungal activity and contribution to the plant immune system. The defining feature of plant defensins is their three-dimensional structure known as the cysteine stabilized alpha-beta motif. This protein fold is remarkably tolerant to sequence variation with only the eight cysteines that contribute to the stabilizing disulfide bonds absolutely conserved across the family. Mature defensins are typically 46–50 amino acids in length and are enriched in lysine and/or arginine residues. Examination of a database of approximately 1200 defensin sequences revealed a subset of defensin sequences that were extended in length and were enriched in histidine residues leading to their classification as histidine-rich defensins (HRDs). Using these initial HRD sequences as a query, a search of the available sequence databases identified over 750 HRDs in solanaceous plants and 20 in brassicas. Histidine residues are known to contribute to metal binding functions in proteins leading to the hypothesis that HRDs would have metal binding properties. A selection of the HRD sequences were recombinantly expressed and purified and their antifungal and metal binding activity was characterized. Of the four HRDs that were successfully expressed all displayed some level of metal binding and two of four had antifungal activity. Structural characterization of the other HRDs identified a novel pattern of disulfide linkages in one of the HRDs that is predicted to also occur in HRDs with similar cysteine spacing. Metal binding by HRDs represents a specialization of the plant defensin fold outside of antifungal activity.
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