1
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Hunt H, Leape S, Sidhu JS, Ajmera I, Lynch JP, Ratcliffe RG, Sweetlove LJ. A role for fermentation in aerobic conditions as revealed by computational analysis of maize root metabolism during growth by cell elongation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1553-1570. [PMID: 37831626 DOI: 10.1111/tpj.16478] [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: 05/31/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 10/15/2023]
Abstract
The root is a well-studied example of cell specialisation, yet little is known about the metabolism that supports the transport functions and growth of different root cell types. To address this, we used computational modelling to study metabolism in the elongation zone of a maize lateral root. A functional-structural model captured the cell-anatomical features of the root and modelled how they changed as the root elongated. From these data, we derived constraints for a flux balance analysis model that predicted metabolic fluxes of the 11 concentric rings of cells in the root. We discovered a distinct metabolic flux pattern in the cortical cell rings, endodermis and pericycle (but absent in the epidermis) that involved a high rate of glycolysis and production of the fermentation end-products lactate and ethanol. This aerobic fermentation was confirmed experimentally by metabolite analysis. The use of fermentation in the model was not obligatory but was the most efficient way to meet the specific demands for energy, reducing power and carbon skeletons of expanding cells. Cytosolic acidification was avoided in the fermentative mode due to the substantial consumption of protons by lipid synthesis. These results expand our understanding of fermentative metabolism beyond that of hypoxic niches and suggest that fermentation could play an important role in the metabolism of aerobic tissues.
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Affiliation(s)
- Hilary Hunt
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Stefan Leape
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Jagdeep Singh Sidhu
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Ishan Ajmera
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Jonathan P Lynch
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - R George Ratcliffe
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Lee J Sweetlove
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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2
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Vrobel O, Tarkowski P. Can plant hormonomics be built on simple analysis? A review. PLANT METHODS 2023; 19:107. [PMID: 37833752 PMCID: PMC10576392 DOI: 10.1186/s13007-023-01090-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/08/2023] [Indexed: 10/15/2023]
Abstract
The field of plant hormonomics focuses on the qualitative and quantitative analysis of the hormone complement in plant samples, akin to other omics sciences. Plant hormones, alongside primary and secondary metabolites, govern vital processes throughout a plant's lifecycle. While active hormones have received significant attention, studying all related compounds provides valuable insights into internal processes. Conventional single-class plant hormone analysis employs thorough sample purification, short analysis and triple quadrupole tandem mass spectrometry. Conversely, comprehensive hormonomics analysis necessitates minimal purification, robust and efficient separation and better-performing mass spectrometry instruments. This review summarizes the current status of plant hormone analysis methods, focusing on sample preparation, advances in chromatographic separation and mass spectrometric detection, including a discussion on internal standard selection and the potential of derivatization. Moreover, current approaches for assessing the spatiotemporal distribution are evaluated. The review touches on the legitimacy of the term plant hormonomics by exploring the current status of methods and outlining possible future trends.
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Affiliation(s)
- Ondřej Vrobel
- Department of Biochemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
- Czech Advanced Technology and Research Institute, Palacky University, Olomouc, Czech Republic
- Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, Olomouc, Czech Republic
| | - Petr Tarkowski
- Czech Advanced Technology and Research Institute, Palacky University, Olomouc, Czech Republic.
- Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, Olomouc, Czech Republic.
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3
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Wang R, Li X, Zhu S, Zhang D, Han S, Li Z, Lu J, Chu H, Xiao J, Li S. Integrated flow cytometric and proteomics analyses reveal the regulatory network underlying sugarcane protoplast responses to fusion. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107918. [PMID: 37619268 DOI: 10.1016/j.plaphy.2023.107918] [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: 05/28/2023] [Revised: 07/19/2023] [Accepted: 07/26/2023] [Indexed: 08/26/2023]
Abstract
BACKGROUND Somatic cell fusion is a process that transfers cytoplasmic and nuclear genes to create new germplasm resources. But our limited understanding of the physiological and molecular mechanisms that shape protoplast responses to fusion. METHOD We employed flow cytometry, cytology, proteomics, and gene expression analysis to examine the sugarcane (Saccharum spp.) protoplast fusion. RESULTS Flow cytometry analysis revealed the fusion rate of protoplasts was 1.95%, the FSC value and SSC of heterozygous cells was 1.17-1.47 times higher than that of protoplasts. The protoplasts viability decreased and the MDA increased after fusion. During fusion, the cell membranes were perforated to different degrees, nuclear activity was weakened, while microtubules depolymerized and formed several short rod like structures in the protoplasts. The most abundant proteins during fusion were mainly involved in RNA processing and modification, cell cycle control, cell division, chromosome partition, nuclear structure, extracellular structures, and nucleotide transport and metabolism. Moreover, the expression of key regeneration genes, such as WUS, GAUT, CESA, PSK, Aux/IAA, Cdc2, Cyclin D3, Cyclin A, and Cyclin B, was significantly altered following fusion. PURPOSE AND SIGNIFICANCE Overall, our findings provide a theoretical basis that increases our knowledge of the mechanisms underlying protoplast fusion.
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Affiliation(s)
- Rui Wang
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, 530004, China; Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, 530004, China.
| | - Xinzhu Li
- School of Biomedical Engineering, South-Central Minzu University, No. 182, Minzu Avenue, Wuhan, 430074, China.
| | - Shuifang Zhu
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, 530004, China; Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, 530004, China.
| | - Demei Zhang
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, 530004, China; Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, 530004, China.
| | - Shijian Han
- Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, 530004, China.
| | - Zhigang Li
- Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, 530004, China.
| | - Jiahui Lu
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, 530004, China; Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, 530004, China.
| | - Haiwei Chu
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, 530004, China; Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, 530004, China.
| | - Jiming Xiao
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, 530004, China; Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, 530004, China.
| | - Suli Li
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, 530004, China; Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, 530004, China.
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4
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Cook TM, Isenegger D, Dutta S, Sahab S, Kay P, Aboobucker SI, Biswas E, Heerschap S, Nikolau BJ, Dong L, Lübberstedt T. Overcoming roadblocks for in vitro nurseries in plants: induction of meiosis. FRONTIERS IN PLANT SCIENCE 2023; 14:1204813. [PMID: 37332695 PMCID: PMC10272530 DOI: 10.3389/fpls.2023.1204813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/17/2023] [Indexed: 06/20/2023]
Abstract
Efforts to increase genetic gains in breeding programs of flowering plants depend on making genetic crosses. Time to flowering, which can take months to decades depending on the species, can be a limiting factor in such breeding programs. It has been proposed that the rate of genetic gain can be increased by reducing the time between generations by circumventing flowering through the in vitro induction of meiosis. In this review, we assess technologies and approaches that may offer a path towards meiosis induction, the largest current bottleneck for in vitro plant breeding. Studies in non-plant, eukaryotic organisms indicate that the in vitro switch from mitotic cell division to meiosis is inefficient and occurs at very low rates. Yet, this has been achieved with mammalian cells by the manipulation of a limited number of genes. Therefore, to experimentally identify factors that switch mitosis to meiosis in plants, it is necessary to develop a high-throughput system to evaluate a large number of candidate genes and treatments, each using large numbers of cells, few of which may gain the ability to induce meiosis.
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Affiliation(s)
- Tanner M. Cook
- Iowa State University, Department of Agronomy, Ames, IA, United States
| | - Daniel Isenegger
- Agriculture Victoria, Agribio, La Trobe University, Melbourne, VIC, Australia
| | - Somak Dutta
- Iowa State University, Department of Statistics, Ames, IA, United States
| | - Sareena Sahab
- Agriculture Victoria, Agribio, La Trobe University, Melbourne, VIC, Australia
| | - Pippa Kay
- Agriculture Victoria, Agribio, La Trobe University, Melbourne, VIC, Australia
| | | | - Eva Biswas
- Iowa State University, Department of Statistics, Ames, IA, United States
| | - Seth Heerschap
- Iowa State University, Department of Electrical and Computer Engineering, Ames, IA, United States
| | - Basil J. Nikolau
- Iowa State University, Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Ames, IA, United States
| | - Liang Dong
- Iowa State University, Department of Electrical and Computer Engineering, Ames, IA, United States
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Son S, Kwon M, Im JH. A New Approach for Wounding Research: MYC2 Gene Expression and Protein Stability in Wounded Arabidopsis Protoplasts. PLANTS 2021; 10:plants10081518. [PMID: 34451563 PMCID: PMC8399638 DOI: 10.3390/plants10081518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/14/2021] [Accepted: 07/23/2021] [Indexed: 11/22/2022]
Abstract
Wounding is a constant threat to plant survival throughout their lifespan; therefore, understanding the biological responses to wounds at the cellular level is important. The protoplast system is versatile for molecular biology, however, no wounding studies on this system have been reported. We established a new approach for wounding research using mechanically damaged Arabidopsis mesophyll protoplasts. Wounded protoplasts showed typical wounding responses, such as increased MPK6 kinase activity and upregulated JAZ1 expression. We also assessed expression profiles and protein stability of the basic helix-loop-helix transcription factor MYC2 in wounded protoplasts. Promoter activity, gene expression, and protein stability of MYC2 were compromised, but recovered in the early stage of wounding. In the late stage, the promoter activity and expression of MYC2 were increased, but the protein stability was not changed. According to the results of the present study, this new cell-based approach will be of use in various molecular studies on plant wounding.
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Affiliation(s)
- Seungmin Son
- Department of Life Sciences, Korea University, 145 Anamro, Sungbuk-gu, Seoul 136701, Korea;
- National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea
| | - Miye Kwon
- Jeju Biodiversity Research Institute (JBRI), Jeju Technopark (JTP), Jeju 63608, Korea
- Correspondence: (M.K.); (J.H.I.); Tel.: +82-64-720-2817 (M.K.); +1-517-353-0458 (J.H.I.)
| | - Jong Hee Im
- Department of Life Sciences, Korea University, 145 Anamro, Sungbuk-gu, Seoul 136701, Korea;
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA
- Correspondence: (M.K.); (J.H.I.); Tel.: +82-64-720-2817 (M.K.); +1-517-353-0458 (J.H.I.)
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6
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Antoniadi I, Skalický V, Sun G, Ma W, Galbraith DW, Novák O, Ljung K. Fluorescence activated cell sorting-A selective tool for plant cell isolation and analysis. Cytometry A 2021; 101:725-736. [PMID: 34028996 DOI: 10.1002/cyto.a.24461] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/27/2021] [Accepted: 05/03/2021] [Indexed: 12/13/2022]
Abstract
Instrumentation for flow cytometry and sorting is designed around the assumption that samples are single-cell suspensions. However, with few exceptions, higher plants comprise complex multicellular tissues and organs, in which the individual cells are held together by shared cell walls. Single-cell suspensions can be obtained through digestion of the cells walls and release of the so-called protoplasts (plants without their cell wall). Here we describe best practices for protoplast preparation, and for analysis through flow cytometry and cell sorting. Finally, the numerous downstream applications involving sorted protoplasts are discussed.
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Affiliation(s)
- Ioanna Antoniadi
- Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Vladimír Skalický
- Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences and Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Guiling Sun
- School of Life Sciences, Henan University, Institute of Plant Stress Biology, Kaifeng, China
| | - Wen Ma
- School of Life Sciences, Henan University, Institute of Plant Stress Biology, Kaifeng, China
| | - David W Galbraith
- Department of Biomedical Engineering, University of Arizona, School of Plant Sciences, BIO5 Institute, Arizona Cancer Center, Tucson, Arizona, USA.,School of Life Sciences, Henan University, Institute of Plant Stress Biology, Kaifeng, China
| | - Ondřej Novák
- Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.,Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences and Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Karin Ljung
- Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
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7
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Ren R, Gao J, Yin D, Li K, Lu C, Ahmad S, Wei Y, Jin J, Zhu G, Yang F. Highly Efficient Leaf Base Protoplast Isolation and Transient Expression Systems for Orchids and Other Important Monocot Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:626015. [PMID: 33659015 PMCID: PMC7917215 DOI: 10.3389/fpls.2021.626015] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/25/2021] [Indexed: 05/21/2023]
Abstract
Versatile protoplast platforms greatly facilitate the development of modern botany. However, efficient protoplast-based systems are still challenging for numerous horticultural plants and crops. Orchids are globally cultivated ornamental and medicinal monocot plants, but few efficient protoplast isolation and transient expression systems have been developed. In this study, we established a highly efficient orchid protoplast isolation protocol by selecting suitable source materials and optimizing the enzymatic conditions, which required optimal D-mannitol concentrations (0.4-0.6 M) combined with optimal 1.2% cellulose and 0.6% macerozyme, 5 μM of 2-mercaptoethanol and 6 h digestion. Tissue- and organ-specific protoplasts were successfully isolated from young leaves [∼3.22 × 106/g fresh weight (FW)], flower pedicels (∼5.26 × 106/g FW), and young root tips (∼7.66 × 105/g FW) of Cymbidium orchids. This protocol recommends the leaf base tissues (the tender part of young leaves attached to the stem) as better source materials. High yielding viable protoplasts were isolated from the leaf base of Cymbidium (∼2.50 × 107/g FW), Phalaenopsis (1.83 × 107/g FW), Paphiopedilum (1.10 × 107/g FW), Dendrobium (8.21 × 106/g FW), Arundina (3.78 × 106/g FW) orchids, and other economically important monocot crops including maize (Zea mays) (3.25 × 107/g FW) and rice (Oryza sativa) (4.31 × 107/g FW), which showed marked advantages over previous mesophyll protoplast isolation protocols. Leaf base protoplasts of Cymbidium orchids were used for polyethylene glycol (PEG)-mediated transfection, and a transfection efficiency of more than 80% was achieved. This leaf base protoplast system was applied successfully to analyze the CsDELLA-mediated gibberellin signaling in Cymbidium orchids. We investigated the subcellular localization of the CsDELLA-green fluorescent protein fusion and analyzed the role of CsDELLA in the regulation of gibberellin to flowering-related genes via efficient transient overexpression and gene silencing of CsDELLA in Cymbidium protoplasts. This protoplast isolation and transient expression system is the most efficient based on the documented results to date. It can be widely used for cellular and molecular studies in orchids and other economically important monocot crops, especially for those lacking an efficient genetic transformation system in vivo.
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Affiliation(s)
- Rui Ren
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jie Gao
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Dongmei Yin
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Kai Li
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Chuqiao Lu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Sagheer Ahmad
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yonglu Wei
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jianpeng Jin
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Genfa Zhu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Fengxi Yang
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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8
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Abstract
Flow cytometry and sorting represents a valuable and mature experimental platform for the analysis of cellular populations. Applications involving higher plants started to emerge around 40 years ago and are now widely employed both to provide unique information regarding basic and applied questions in the biosciences and to advance agricultural productivity in practical ways. Further development of this platform is being actively pursued, and this promises additional progress in our understanding of the interactions of cells within complex tissues and organs. Higher plants offer unique challenges in terms of flow cytometric analysis, first since their organs and tissues are, almost without exception, three-dimensional assemblies of different cell types held together by tough cell walls, and, second, because individual plant cells are generally larger than those of mammals.This chapter, which updates work last reviewed in 2014 [Galbraith DW (2014) Flow cytometry and sorting in Arabidopsis. In: Sanchez Serrano JJ, Salinas J (eds) Arabidopsis Protocols, 3rd ed. Methods in molecular biology, vol 1062. Humana Press, Totowa, pp 509-537], describes the application of techniques of flow cytometry and sorting to the model plant species Arabidopsis thaliana, in particular emphasizing (a) fluorescence labeling in vivo of specific cell types and of subcellular components, (b) analysis using both conventional cytometers and spectral analyzers, (c) fluorescence-activated sorting of protoplasts and nuclei, and (d) transcriptome analyses using sorted protoplasts and nuclei, focusing on population analyses at the level of single protoplasts and nuclei. Since this is an update, details of new experimental methods are emphasized.
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Affiliation(s)
- David W Galbraith
- University of Arizona, School of Plant Sciences and Bio5 Institute, Tucson, AZ, USA. .,Henan University, Institute of Plant Stress Biology, School of Life Sciences, Kaifeng, China.
| | - Guiling Sun
- Henan University, Institute of Plant Stress Biology, School of Life Sciences, Kaifeng, China
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9
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Ren R, Gao J, Lu C, Wei Y, Jin J, Wong SM, Zhu G, Yang F. Highly Efficient Protoplast Isolation and Transient Expression System for Functional Characterization of Flowering Related Genes in Cymbidium Orchids. Int J Mol Sci 2020; 21:ijms21072264. [PMID: 32218171 PMCID: PMC7177621 DOI: 10.3390/ijms21072264] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 11/16/2022] Open
Abstract
Protoplast systems have been proven powerful tools in modern plant biology. However, successful preparation of abundant viable protoplasts remains a challenge for Cymbidium orchids. Herein, we established an efficient protoplast isolation protocol from orchid petals through optimization of enzymatic conditions. It requires optimal D-mannitol concentration (0.5 M), enzyme concentration (1.2 % (w/v) cellulose and 0.6 % (w/v) macerozyme) and digestion time (6 h). With this protocol, the highest yield (3.50 × 107/g fresh weight of orchid tissue) and viability (94.21%) of protoplasts were obtained from flower petals of Cymbidium. In addition, we achieved high transfection efficiency (80%) through the optimization of factors affecting polyethylene glycol (PEG)-mediated protoplast transfection including incubation time, final PEG4000 concentration and plasmid DNA amount. This highly efficient protoplast-based transient expression system (PTES) was further used for protein subcellular localization, bimolecular fluorescence complementation (BiFC) assay and gene regulation studies of flowering related genes in Cymbidium orchids. Taken together, our protoplast isolation and transfection protocol is highly efficient, stable and time-saving. It can be used for gene function and molecular analyses in orchids and other economically important monocot crops.
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Affiliation(s)
- Rui Ren
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (R.R.); (J.G.); (C.L.); (Y.W.); (J.J.)
| | - Jie Gao
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (R.R.); (J.G.); (C.L.); (Y.W.); (J.J.)
| | - Chuqiao Lu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (R.R.); (J.G.); (C.L.); (Y.W.); (J.J.)
| | - Yonglu Wei
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (R.R.); (J.G.); (C.L.); (Y.W.); (J.J.)
| | - Jianpeng Jin
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (R.R.); (J.G.); (C.L.); (Y.W.); (J.J.)
| | - Sek-Man Wong
- Department of Biological Sciences, National University of Singapore (NUS), 14 Science Drive 4, Singapore 117543, Singapore;
- National University of Singapore Suzhou Research Institute (NUSRI), Suzhou Industrial Park, Suzhou 215000, China
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Genfa Zhu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (R.R.); (J.G.); (C.L.); (Y.W.); (J.J.)
- Correspondence: (G.Z.); (F.Y.)
| | - Fengxi Yang
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (R.R.); (J.G.); (C.L.); (Y.W.); (J.J.)
- Correspondence: (G.Z.); (F.Y.)
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Shameer K, Naika MB, Shafi KM, Sowdhamini R. Decoding systems biology of plant stress for sustainable agriculture development and optimized food production. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 145:19-39. [DOI: 10.1016/j.pbiomolbio.2018.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 10/23/2018] [Accepted: 12/06/2018] [Indexed: 12/13/2022]
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11
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Huang R, Shu S, Liu M, Wang C, Jiang B, Jiang J, Yang C, Zhang S. Nuclear Prohibitin3 Maintains Genome Integrity and Cell Proliferation in the Root Meristem through Minichromosome Maintenance 2. PLANT PHYSIOLOGY 2019; 179:1669-1691. [PMID: 30674698 PMCID: PMC6446790 DOI: 10.1104/pp.18.01463] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 01/08/2019] [Indexed: 05/30/2023]
Abstract
The nucleo-mitochondrial dual-localized proteins can act as gene expression regulators; however, few instances of these proteins have been described in plants. Arabidopsis (Arabidopsis thaliana) PROHIBITIN 3 (PHB3) is involved in stress responses and developmental processes, but it is unknown how these roles are achieved at the molecular level in the nucleus. In this study, we show that nucleo-mitochondrial PHB3 plays an essential role in regulating genome stability and cell proliferation. PHB3 is up-regulated by DNA damage agents, and the stress-induced PHB3 proteins accumulate in the nucleus. Loss of function of PHB3 results in DNA damage and defective maintenance of the root stem cell niche. Subsequently, the expression patterns and levels of the root stem cell regulators are altered and down-regulated, respectively. In addition, the phb3 mutant shows aberrant cell division and altered expression of cell cycle-related genes, such as CycB1 and Cyclin dependent kinase 1 Moreover, the minichromosome maintenance (MCM) genes, e.g. MCM2, MCM3, MCM4, MCM5, MCM6, and MCM7, are up-regulated in the phb3 mutant. Reducing the MCM2 expression level substantially recovers the DNA damage in the phb3 mutant and partially rescues the altered cell proliferation and root deficiency of phb3 seedlings. PHB3 acts as a transcriptional coregulator that represses MCM2 expression by competitively binding to the promoter E2F-cis-acting elements with E2Fa so as to modulate primary root growth. Collectively, these findings indicate that nuclear-localized PHB3 acts as a transcriptional coregulator that suppresses MCM2 expression to sustain genome integrity and cell proliferation for stem cell niche maintenance in Arabidopsis.
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Affiliation(s)
- Ruihua Huang
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Si Shu
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Mengling Liu
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Chao Wang
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Bei Jiang
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Jieming Jiang
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Chengwei Yang
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Shengchun Zhang
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631, China
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12
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Libault M. Transcriptional Reprogramming of Legume Genomes: Perspective and Challenges Associated With Single-Cell and Single Cell-Type Approaches During Nodule Development. FRONTIERS IN PLANT SCIENCE 2018; 9:1600. [PMID: 30467509 PMCID: PMC6237103 DOI: 10.3389/fpls.2018.01600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 10/17/2018] [Indexed: 05/11/2023]
Abstract
Transcriptomic approaches revealed thousands of genes differentially or specifically expressed during nodulation, a biological process resulting from the symbiosis between leguminous plant roots and rhizobia, atmospheric nitrogen-fixing symbiotic bacteria. Ultimately, nodulation will lead to the development of a new root organ, the nodule. Through functional genomic studies, plant transcriptomes have been used by scientists to reveal plant genes potentially controlling nodulation. However, it is important to acknowledge that the physiology, transcriptomic programs, and biochemical properties of the plant cells involved in nodulation are continuously regulated. They also differ between the different cell-types composing the nodules. To generate a more accurate picture of the transcriptome, epigenome, proteome, and metabolome of the cells infected by rhizobia and cells composing the nodule, there is a need to implement plant single-cell and single cell-types strategies and methods. Accessing such information would allow a better understanding of the infection of plant cells by rhizobia and will help understanding the complex interactions existing between rhizobia and the plant cells. In this mini-review, we are reporting the current knowledge on legume nodulation gained by plant scientists at the level of single cell-types, and provide perspectives on single cell/single cell-type approaches when applied to legume nodulation.
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Affiliation(s)
- Marc Libault
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Centre for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
- Center for Root and Rhizobiome Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
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13
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Binek A, Rojo D, Godzien J, Rupérez FJ, Nuñez V, Jorge I, Ricote M, Vázquez J, Barbas C. Flow Cytometry Has a Significant Impact on the Cellular Metabolome. J Proteome Res 2018; 18:169-181. [PMID: 30362351 DOI: 10.1021/acs.jproteome.8b00472] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The characterization of specialized cell subpopulations in a heterogeneous tissue is essential for understanding organ function in health and disease. A popular method of cell isolation is fluorescence-activated cell sorting (FACS) based on probes that bind surface or intracellular markers. In this study, we analyze the impact of FACS on the cell metabolome of mouse peritoneal macrophages. Compared with directly pelleted macrophages, FACS-treated cells had an altered content of metabolites related to the plasma membrane, activating a mechanosensory signaling cascade causing inflammation-like stress. The procedure also triggered alterations related to energy consumption and cell damage. The observed changes mostly derive from the physical impact on cells during their passage through the instrument. These findings provide evidence of FACS-induced biochemical changes, which should be taken into account in the design of robust metabolic assays of cells separated by flow cytometry.
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Affiliation(s)
- Aleksandra Binek
- Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III , Madrid 28029 , Spain 1
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia , Universidad CEU San Pablo , Campus Montepríncipe , Madrid 28668 , Spain
| | - Joanna Godzien
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia , Universidad CEU San Pablo , Campus Montepríncipe , Madrid 28668 , Spain
| | - Francisco Javier Rupérez
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia , Universidad CEU San Pablo , Campus Montepríncipe , Madrid 28668 , Spain
| | - Vanessa Nuñez
- Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III , Madrid 28029 , Spain 1
| | - Inmaculada Jorge
- Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III , Madrid 28029 , Spain 1.,CIBER de Enfermedades Cardiovasculares (CIBER CV), Madrid 28029 , Spain
| | - Mercedes Ricote
- Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III , Madrid 28029 , Spain 1
| | - Jesús Vázquez
- Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III , Madrid 28029 , Spain 1.,CIBER de Enfermedades Cardiovasculares (CIBER CV), Madrid 28029 , Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia , Universidad CEU San Pablo , Campus Montepríncipe , Madrid 28668 , Spain
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14
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Rivas-Ubach A, Liu Y, Bianchi TS, Tolić N, Jansson C, Paša-Tolić L. Moving beyond the van Krevelen Diagram: A New Stoichiometric Approach for Compound Classification in Organisms. Anal Chem 2018; 90:6152-6160. [PMID: 29671593 DOI: 10.1021/acs.analchem.8b00529] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
van Krevelen diagrams (O/C vs H/C ratios of elemental formulas) have been widely used in studies to obtain an estimation of the main compound categories present in environmental samples. However, the limits defining a specific compound category based solely on O/C and H/C ratios of elemental formulas have never been accurately listed or proposed to classify metabolites in biological samples. Furthermore, while O/C vs H/C ratios of elemental formulas can provide an overview of the compound categories, such classification is inefficient because of the large overlap among different compound categories along both axes. We propose a more accurate compound classification for biological samples analyzed by high-resolution mass spectrometry based on an assessment of the C/H/O/N/P stoichiometric ratios of over 130 000 elemental formulas of compounds classified in 6 main categories: lipids, peptides, amino sugars, carbohydrates, nucleotides, and phytochemical compounds (oxy-aromatic compounds). Our multidimensional stoichiometric compound classification (MSCC) constraints showed a highly accurate categorization of elemental formulas to the main compound categories in biological samples with over 98% of accuracy representing a substantial improvement over any classification based on the classic van Krevelen diagram. This method represents a signficant step forward in environmental research, especially ecological stoichiometry and eco-metabolomics studies, by providing a novel and robust tool to improve our understanding of the ecosystem structure and function through the chemical characterization of biological samples.
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Affiliation(s)
- Albert Rivas-Ubach
- Environmental Molecular Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Yina Liu
- Environmental Molecular Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States.,Geochemical and Environmental Research Group , Texas A&M University , College Station , Texas 77845 , United States
| | - Thomas S Bianchi
- Department of Geological Sciences , University of Florida , Gainesville , Florida 32611-2120 , United States
| | - Nikola Tolić
- Environmental Molecular Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Christer Jansson
- Environmental Molecular Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
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15
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Cell-Type Specific Metabolic Flux Analysis: A Challenge for Metabolic Phenotyping and a Potential Solution in Plants. Metabolites 2017; 7:metabo7040059. [PMID: 29137184 PMCID: PMC5746739 DOI: 10.3390/metabo7040059] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/09/2017] [Accepted: 11/10/2017] [Indexed: 12/22/2022] Open
Abstract
Stable isotope labelling experiments are used routinely in metabolic flux analysis (MFA) to determine the metabolic phenotype of cells and tissues. A complication arises in multicellular systems because single cell measurements of transcriptomes, proteomes and metabolomes in multicellular organisms suggest that the metabolic phenotype will differ between cell types. In silico analysis of simulated metabolite isotopomer datasets shows that cellular heterogeneity confounds conventional MFA because labelling data averaged over multiple cell types does not necessarily yield averaged flux values. A potential solution to this problem—the use of cell-type specific reporter proteins as a source of cell-type specific labelling data—is proposed and the practicality of implementing this strategy in the roots of Arabidopsis thaliana seedlings is explored. A protocol for the immunopurification of ectopically expressed green fluorescent protein (GFP) from Arabidopsis thaliana seedlings using a GFP-binding nanobody is developed, and through GC-MS analysis of protein hydrolysates it is established that constitutively expressed GFP reports accurately on the labelling of total protein in root tissues. It is also demonstrated that the constitutive expression of GFP does not perturb metabolism. The principal obstacle to the implementation of the method in tissues with cell-type specific GFP expression is the sensitivity of the GC-MS system.
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16
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Libault M, Pingault L, Zogli P, Schiefelbein J. Plant Systems Biology at the Single-Cell Level. TRENDS IN PLANT SCIENCE 2017; 22:949-960. [PMID: 28970001 DOI: 10.1016/j.tplants.2017.08.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/14/2017] [Accepted: 08/21/2017] [Indexed: 05/19/2023]
Abstract
Our understanding of plant biology is increasingly being built upon studies using 'omics and system biology approaches performed at the level of the entire plant, organ, or tissue. Although these approaches open new avenues to better understand plant biology, they suffer from the cellular complexity of the analyzed sample. Recent methodological advances now allow plant scientists to overcome this limitation and enable biological analyses of single-cells or single-cell-types. Coupled with the development of bioinformatics and functional genomics resources, these studies provide opportunities for high-resolution systems analyses of plant phenomena. In this review, we describe the recent advances, current challenges, and future directions in exploring the biology of single-cells and single-cell-types to enhance our understanding of plant biology as a system.
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Affiliation(s)
- Marc Libault
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
| | - Lise Pingault
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Prince Zogli
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - John Schiefelbein
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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17
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Linn J, Ren M, Berkowitz O, Ding W, van der Merwe MJ, Whelan J, Jost R. Root Cell-Specific Regulators of Phosphate-Dependent Growth. PLANT PHYSIOLOGY 2017; 174:1969-1989. [PMID: 28465462 PMCID: PMC5490885 DOI: 10.1104/pp.16.01698] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 05/01/2017] [Indexed: 05/07/2023]
Abstract
Cellular specialization in abiotic stress responses is an important regulatory feature driving plant acclimation. Our in silico approach of iterative coexpression, interaction, and enrichment analyses predicted root cell-specific regulators of phosphate starvation response networks in Arabidopsis (Arabidopsis thaliana). This included three uncharacterized genes termed Phosphate starvation-induced gene interacting Root Cell Enriched (PRCE1, PRCE2, and PRCE3). Root cell-specific enrichment of 12 candidates was confirmed in promoter-GFP lines. T-DNA insertion lines of 11 genes showed changes in phosphate status and growth responses to phosphate availability compared with the wild type. Some mutants (cbl1, cipk2, prce3, and wdd1) displayed strong biomass gain irrespective of phosphate supply, while others (cipk14, mfs1, prce1, prce2, and s6k2) were able to sustain growth under low phosphate supply better than the wild type. Notably, root or shoot phosphate accumulation did not strictly correlate with organ growth. Mutant response patterns markedly differed from those of master regulators of phosphate homeostasis, PHOSPHATE STARVATION RESPONSE1 (PHR1) and PHOSPHATE2 (PHO2), demonstrating that negative growth responses in the latter can be overcome when cell-specific regulators are targeted. RNA sequencing analysis highlighted the transcriptomic plasticity in these mutants and revealed PHR1-dependent and -independent regulatory circuits with gene coexpression profiles that were highly correlated to the quantified physiological traits. The results demonstrate how in silico prediction of cell-specific, stress-responsive genes uncovers key regulators and how their manipulation can have positive impacts on plant growth under abiotic stress.
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Affiliation(s)
- Joshua Linn
- Department of Animal, Plant, and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, VIC 3083, Australia
| | - Meiyan Ren
- Department of Animal, Plant, and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, VIC 3083, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant, and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, VIC 3083, Australia
| | - Wona Ding
- College of Science and Technology, Ningbo University, Ningbo, 315211 Zhejiang Province, People's Republic of China
| | - Margaretha J van der Merwe
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, Western Australia, WA 6009, Australia
| | - James Whelan
- Department of Animal, Plant, and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, VIC 3083, Australia
| | - Ricarda Jost
- Department of Animal, Plant, and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, VIC 3083, Australia
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18
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Novák O, Antoniadi I, Ljung K. High-Resolution Cell-Type Specific Analysis of Cytokinins in Sorted Root Cell Populations of Arabidopsis thaliana. Methods Mol Biol 2017; 1497:231-248. [PMID: 27864770 DOI: 10.1007/978-1-4939-6469-7_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We describe a method combining fluorescence-activated cell sorting (FACS) with one-step miniaturized isolation and accurate quantification of cytokinins (CKs) using ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) to measure these phytohormones in specific cell types of Arabidopsis thaliana roots. The methodology provides information of unprecedented resolution about spatial distributions of CKs, and thus should facilitate attempts to elucidate regulatory networks involved in root developmental processes.
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Affiliation(s)
- Ondřej Novák
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany AS CR & Faculty of Science, Palacký University, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic.
| | - Ioanna Antoniadi
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden
| | - Karin Ljung
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden
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19
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Laser microdissection of tomato fruit cell and tissue types for transcriptome profiling. Nat Protoc 2016; 11:2376-2388. [PMID: 27809311 DOI: 10.1038/nprot.2016.146] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This protocol enables transcriptome profiling of specific cell or tissue types that are isolated from tomato using laser microdissection (LM). To prepare tissue for LM, fruit samples are first fixed in optimal cutting temperature (OCT) medium and frozen in molds. The tissue is then sectioned using a cryostat before being dissected using an LM instrument. The RNAs contained in the harvested cells are purified and subjected to two rounds of amplification to yield sufficient quantities of RNA to generate cDNA libraries. Unlike several other techniques that are used to isolate specific cell types, LM has the advantage of being readily applied to any plant species without having to generate transgenic plants. Using the protocols described here, LM-mediated cell-type transcriptomic analysis of two samples requires ∼8 d from tissue harvest to RNA sequencing (RNA-seq), whereas each additional sample, up to a total of 12 samples, requires ∼1 additional day for the LM step. RNA obtained using this method has been successfully used for deep-coverage transcriptome profiling, which is a particularly effective strategy for identifying genes that are differentially expressed between cell or tissue types.
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20
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Braguy J, Zurbriggen MD. Synthetic strategies for plant signalling studies: molecular toolbox and orthogonal platforms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:118-38. [PMID: 27227549 DOI: 10.1111/tpj.13218] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/11/2016] [Accepted: 05/13/2016] [Indexed: 05/15/2023]
Abstract
Plants deploy a wide array of signalling networks integrating environmental cues with growth, defence and developmental responses. The high level of complexity, redundancy and connection between several pathways hampers a comprehensive understanding of involved functional and regulatory mechanisms. The implementation of synthetic biology approaches is revolutionizing experimental biology in prokaryotes, yeasts and animal systems and can likewise contribute to a new era in plant biology. This review gives an overview on synthetic biology approaches for the development and implementation of synthetic molecular tools and techniques to interrogate, understand and control signalling events in plants, ranging from strategies for the targeted manipulation of plant genomes up to the spatiotemporally resolved control of gene expression using optogenetic approaches. We also describe strategies based on the partial reconstruction of signalling pathways in orthogonal platforms, like yeast, animal and in vitro systems. This allows a targeted analysis of individual signalling hubs devoid of interconnectivity with endogenous interacting components. Implementation of the interdisciplinary synthetic biology tools and strategies is not exempt of challenges and hardships but simultaneously most rewarding in terms of the advances in basic and applied research. As witnessed in other areas, these original theoretical-experimental avenues will lead to a breakthrough in the ability to study and comprehend plant signalling networks.
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Affiliation(s)
- Justine Braguy
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Universitätstrasse 1, Building 26.12.U1.25, Düsseldorf, 40225, Germany
- King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Universitätstrasse 1, Building 26.12.U1.25, Düsseldorf, 40225, Germany
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21
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Bergau N, Navarette Santos A, Henning A, Balcke GU, Tissier A. Autofluorescence as a Signal to Sort Developing Glandular Trichomes by Flow Cytometry. FRONTIERS IN PLANT SCIENCE 2016; 7:949. [PMID: 27446176 PMCID: PMC4923063 DOI: 10.3389/fpls.2016.00949] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/14/2016] [Indexed: 05/04/2023]
Abstract
The industrial relevance of a number of metabolites produced in plant glandular trichomes (GTs) has spurred research on these specialized organs for a number of years. Most of the research, however, has focused on the elucidation of secondary metabolite pathways and comparatively little has been undertaken on the development and differentiation of GTs. One way to gain insight into these developmental processes is to generate stage-specific transcriptome and metabolome data. The difficulty for this resides in the isolation of early stages of development of the GTs. Here we describe a method for the separation and isolation of intact young and mature type VI trichomes from the wild tomato species Solanum habrochaites. The final and key step of the method uses cell sorting based on distinct autofluorescence signals of the young and mature trichomes. We demonstrate that sorting by flow cytometry allows recovering pure fractions of young and mature trichomes. Furthermore, we show that the sorted trichomes can be used for transcript and metabolite analyses. Because many plant tissues or cells have distinct autofluorescence components, the principles of this method can be generally applicable for the isolation of specific cell types without prior labeling.
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Affiliation(s)
- Nick Bergau
- Department of Cell and Metabolic Biology, Leibniz-Institute of Plant BiochemistryHalle, Germany
| | | | - Anja Henning
- Department of Cell and Metabolic Biology, Leibniz-Institute of Plant BiochemistryHalle, Germany
| | - Gerd U. Balcke
- Department of Cell and Metabolic Biology, Leibniz-Institute of Plant BiochemistryHalle, Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz-Institute of Plant BiochemistryHalle, Germany
- *Correspondence: Alain Tissier,
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