1
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Balasubramanian VK, Veličković D, Rubio Wilhelmi MDM, Anderton CR, Stewart CN, DiFazio S, Blumwald E, Ahkami AH. Spatiotemporal metabolic responses to water deficit stress in distinct leaf cell-types of poplar. FRONTIERS IN PLANT SCIENCE 2024; 15:1346853. [PMID: 38495374 PMCID: PMC10940329 DOI: 10.3389/fpls.2024.1346853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/12/2024] [Indexed: 03/19/2024]
Abstract
The impact of water-deficit (WD) stress on plant metabolism has been predominantly studied at the whole tissue level. However, plant tissues are made of several distinct cell types with unique and differentiated functions, which limits whole tissue 'omics'-based studies to determine only an averaged molecular signature arising from multiple cell types. Advancements in spatial omics technologies provide an opportunity to understand the molecular mechanisms underlying plant responses to WD stress at distinct cell-type levels. Here, we studied the spatiotemporal metabolic responses of two poplar (Populus tremula× P. alba) leaf cell types -palisade and vascular cells- to WD stress using matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI). We identified unique WD stress-mediated metabolic shifts in each leaf cell type when exposed to early and prolonged WD stresses and recovery from stress. During water-limited conditions, flavonoids and phenolic metabolites were exclusively accumulated in leaf palisade cells. However, vascular cells mainly accumulated sugars and fatty acids during stress and recovery conditions, respectively, highlighting the functional divergence of leaf cell types in response to WD stress. By comparing our MALDI-MSI metabolic data with whole leaf tissue gas chromatography-mass spectrometry (GC-MS)-based metabolic profile, we identified only a few metabolites including monosaccharides, hexose phosphates, and palmitic acid that showed a similar accumulation trend at both cell-type and whole leaf tissue levels. Overall, this work highlights the potential of the MSI approach to complement the whole tissue-based metabolomics techniques and provides a novel spatiotemporal understanding of plant metabolic responses to WD stress. This will help engineer specific metabolic pathways at a cellular level in strategic perennial trees like poplars to help withstand future aberrations in environmental conditions and to increase bioenergy sustainability.
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Affiliation(s)
- Vimal Kumar Balasubramanian
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Dušan Veličković
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | | | - Christopher R. Anderton
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - C. Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, United States
| | - Stephen DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California Davis, Davis, CA, United States
| | - Amir H. Ahkami
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
- Adjoint Faculty, School of Biological Science (SBS), Washington State University (WSU), Pullman, WA, United States
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2
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Mihailova G, Tchorbadjieva M, Rakleova G, Georgieva K. Differential Accumulation of sHSPs Isoforms during Desiccation of the Resurrection Plant Haberlea rhodopensis Friv. under Optimal and High Temperature. LIFE (BASEL, SWITZERLAND) 2023; 13:life13010238. [PMID: 36676187 PMCID: PMC9863180 DOI: 10.3390/life13010238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/06/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023]
Abstract
Haberlea rhodopensis belongs to the small group of angiosperms that can survive desiccation to air-dry state and quickly restore their metabolism upon rehydration. In the present study, we investigated the accumulation of sHSPs and the extent of non-photochemical quenching during the downregulation of photosynthesis in H. rhodopensis leaves under desiccation at optimum (23 °C) and high temperature (38 °C). Desiccation of plants at 38 °C caused a stronger reduction in photosynthetic activity and corresponding enhancement in thermal energy dissipation. The accumulation of sHSPs was investigated by Western blot. While no expression of sHPSs was detected in the unstressed control sample, exposure of well-hydrated plants to high temperature induced an accumulation of sHSPs. Only a faint signal was observed at 50% RWC when dehydration was applied at 23 °C. Several cross-reacting polypeptide bands in the range of 16.5-19 kDa were observed in plants desiccated at high temperature. Two-dimensional electrophoresis and immunoblotting revealed the presence of several sHSPs with close molecular masses and pIs in the range of 5-8.0 that differed for each stage of treatment. At the latest stages of desiccation, fourteen different sHSPs could be distinguished, indicating that sHSPs might play a crucial role in H. rhodopensis under dehydration at high temperatures.
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Affiliation(s)
- Gergana Mihailova
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
- Correspondence: ; Tel.: +359-2-979-2688
| | - Magdalena Tchorbadjieva
- Department of Biochemistry, Faculty of Biology, Sofia University, 8 Dragan Tsankov Blvd., 1164 Sofia, Bulgaria
| | - Goritsa Rakleova
- Department of Biochemistry, Faculty of Biology, Sofia University, 8 Dragan Tsankov Blvd., 1164 Sofia, Bulgaria
| | - Katya Georgieva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
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3
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Kawa D, Brady SM. Root cell types as an interface for biotic interactions. TRENDS IN PLANT SCIENCE 2022; 27:1173-1186. [PMID: 35792025 DOI: 10.1016/j.tplants.2022.06.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/04/2022] [Accepted: 06/09/2022] [Indexed: 05/27/2023]
Abstract
Root responses to environmental stresses show a high level of cell type and developmental stage specificity. Interactions with beneficial and pathogenic organisms - including microbes and parasites - elicit a set of transcriptional responses unique to each root cell type, often dependent on their differentiation state. Localized changes to the cell wall and to the integrity of root cell types can serve as a physical barrier for a range of pests. Conversely, certain microorganisms weaken existing barriers within root cell types. Interactions with microorganisms vary between roots of different developmental origins and cellular architectures. Here we provide an overview of the molecular, architectural, and structural properties of root cell types crucial to both maintaining beneficial interactions and protecting from pathogens.
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Affiliation(s)
- Dorota Kawa
- Department of Plant Biology and Genome Center, University of California, Davis, CA 95616, USA.
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, CA 95616, USA.
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4
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Berkowitz O, Xu Y, Liew LC, Wang Y, Zhu Y, Hurgobin B, Lewsey MG, Whelan J. RNA-seq analysis of laser microdissected Arabidopsis thaliana leaf epidermis, mesophyll and vasculature defines tissue-specific transcriptional responses to multiple stress treatments. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:938-955. [PMID: 33974297 DOI: 10.1111/tpj.15314] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/28/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
Acclimation of plants to adverse conditions requires the coordination of gene expression and signalling pathways between tissues and cell types. As the energy and carbon capturing organs, leaves are significantly affected by abiotic and biotic stresses. However, tissue- or cell type-specific analyses of stress responses have focussed on the Arabidopsis root. Here, we comparatively explore the transcriptomes of three leaf tissues (epidermis, mesophyll, vasculature) after induction of diverse stress pathways by chemical stimuli (antimycin A, 3-amino-1,2,4-triazole, methyl viologen, salicylic acid) and ultraviolet light in Arabidopsis using laser capture microdissection followed by RNA sequencing. Stimulation of stress pathways caused an overall reduction in the number of genes expressed in a tissue-specific manner, though a small subset gained or changed their tissue specificity. We find no evidence of a common stress response, with only a few genes consistently responsive to two or more treatments in the analysed tissues. However, differentially expressed genes overlap between tissues for individual treatments. A focussed analysis provided evidence for an interaction of auxin and ethylene that mediates retrograde signalling during mitochondrial dysfunction specifically in the epidermis, and a gene regulatory network defined the hierarchy of interactions. Taken together, we have generated an extensive reference dataset that will be valuable for future experiments analysing transcriptional responses on a tissue or single-cell level. Our results will enable the tailoring of the tissue-specific engineering of stress-tolerant plants.
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Affiliation(s)
- Oliver Berkowitz
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Yue Xu
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Lim Chee Liew
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Yan Wang
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Yanqiao Zhu
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Bhavna Hurgobin
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Mathew G Lewsey
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - James Whelan
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
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5
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Misra BB, Assmann SM, Chen S. Plant single-cell and single-cell-type metabolomics. TRENDS IN PLANT SCIENCE 2014; 19:637-46. [PMID: 24946988 DOI: 10.1016/j.tplants.2014.05.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 05/22/2014] [Accepted: 05/23/2014] [Indexed: 05/19/2023]
Abstract
In conjunction with genomics, transcriptomics, and proteomics, plant metabolomics is providing large data sets that are paving the way towards a comprehensive and holistic understanding of plant growth, development, defense, and productivity. However, dilution effects from organ- and tissue-based sampling of metabolomes have limited our understanding of the intricate regulation of metabolic pathways and networks at the cellular level. Recent advances in metabolomics methodologies, along with the post-genomic expansion of bioinformatics knowledge and functional genomics tools, have allowed the gathering of enriched information on individual cells and single cell types. Here we review progress, current status, opportunities, and challenges presented by single cell-based metabolomics research in plants.
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Affiliation(s)
- Biswapriya B Misra
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA
| | - Sarah M Assmann
- Department of Biology, Penn State University, 208 Mueller Laboratory, University Park, PA 16802, USA
| | - Sixue Chen
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA; Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA.
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Pintó-Marijuan M, Munné-Bosch S. Photo-oxidative stress markers as a measure of abiotic stress-induced leaf senescence: advantages and limitations. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3845-57. [PMID: 24683180 DOI: 10.1093/jxb/eru086] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Inside chloroplasts, several abiotic stresses (including drought, high light, salinity, or extreme temperatures) induce a reduction in CO2 assimilation rates with a consequent increase in reactive oxygen species (ROS) production, ultimately leading to leaf senescence and yield loss. Photo-oxidation processes should therefore be mitigated to prevent leaf senescence, and plants have evolved several mechanisms to either prevent the formation of ROS or eliminate them. Technology evolution during the past decade has brought faster and more precise methodologies to quantify ROS production effects and damage, and the capacities of plants to withstand oxidative stress. Nevertheless, it is very difficult to disentangle photo-oxidative processes that bring leaf defence and acclimation, from those leading to leaf senescence (and consequently death). It is important to avoid the mistake of discussing results on leaf extracts as being equivalent to chloroplast extracts without taking into account that other organelles, such as peroxisomes, mitochondria, or the apoplast also significantly contribute to the overall ROS production within the cell. Another important aspect is that studies on abiotic stress-induced leaf senescence in crops do not always include a time-course evolution of studied processes, which limits our knowledge about what photo-oxidative stress processes are required to irreversibly induce the senescence programme. This review will summarize the current technologies used to evaluate the extent of photo-oxidative stress in plants, and discuss their advantages and limitations in characterizing abiotic stress-induced leaf senescence in crops.
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Affiliation(s)
- Marta Pintó-Marijuan
- Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain
| | - Sergi Munné-Bosch
- Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain
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7
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Barkla BJ, Castellanos-Cervantes T, de León JLD, Matros A, Mock HP, Perez-Alfocea F, Salekdeh GH, Witzel K, Zörb C. Elucidation of salt stress defense and tolerance mechanisms of crop plants using proteomics--current achievements and perspectives. Proteomics 2014; 13:1885-900. [PMID: 23723162 DOI: 10.1002/pmic.201200399] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 04/12/2013] [Accepted: 04/24/2013] [Indexed: 12/18/2022]
Abstract
Salinity is a major threat limiting the productivity of crop plants. A clear demand for improving the salinity tolerance of the major crop plants is imposed by the rapidly growing world population. This review summarizes the achievements of proteomic studies to elucidate the response mechanisms of selected model and crop plants to cope with salinity stress. We also aim at identifying research areas, which deserve increased attention in future proteome studies, as a prerequisite to identify novel targets for breeding strategies. Such areas include the impact of plant-microbial communities on the salinity tolerance of crops under field conditions, the importance of hormone signaling in abiotic stress tolerance, and the significance of control mechanisms underlying the observed changes in the proteome patterns. We briefly highlight the impact of novel tools for future proteome studies and argue for the use of integrated approaches. The evaluation of genetic resources by means of novel automated phenotyping facilities will have a large impact on the application of proteomics especially in combination with metabolomics or transcriptomics.
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8
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Brosché M, Blomster T, Salojärvi J, Cui F, Sipari N, Leppälä J, Lamminmäki A, Tomai G, Narayanasamy S, Reddy RA, Keinänen M, Overmyer K, Kangasjärvi J. Transcriptomics and functional genomics of ROS-induced cell death regulation by RADICAL-INDUCED CELL DEATH1. PLoS Genet 2014; 10:e1004112. [PMID: 24550736 PMCID: PMC3923667 DOI: 10.1371/journal.pgen.1004112] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 12/02/2013] [Indexed: 11/18/2022] Open
Abstract
Plant responses to changes in environmental conditions are mediated by a network of signaling events leading to downstream responses, including changes in gene expression and activation of cell death programs. Arabidopsis thaliana RADICAL-INDUCED CELL DEATH1 (RCD1) has been proposed to regulate plant stress responses by protein-protein interactions with transcription factors. Furthermore, the rcd1 mutant has defective control of cell death in response to apoplastic reactive oxygen species (ROS). Combining transcriptomic and functional genomics approaches we first used microarray analysis in a time series to study changes in gene expression after apoplastic ROS treatment in rcd1. To identify a core set of cell death regulated genes, RCD1-regulated genes were clustered together with other array experiments from plants undergoing cell death or treated with various pathogens, plant hormones or other chemicals. Subsequently, selected rcd1 double mutants were constructed to further define the genetic requirements for the execution of apoplastic ROS induced cell death. Through the genetic analysis we identified WRKY70 and SGT1b as cell death regulators functioning downstream of RCD1 and show that quantitative rather than qualitative differences in gene expression related to cell death appeared to better explain the outcome. Allocation of plant energy to defenses diverts resources from growth. Recently, a plant response termed stress-induced morphogenic response (SIMR) was proposed to regulate the balance between defense and growth. Using a rcd1 double mutant collection we show that SIMR is mostly independent of the classical plant defense signaling pathways and that the redox balance is involved in development of SIMR. Reactive oxygen species (ROS) are utilized in plants as signaling molecules to regulate development, stress responses and cell death. One extreme form of defense uses programmed cell death (PCD) in a scorched earth strategy to deliberately kill off cells invaded by a pathogen. Compared to animals, the regulation of plant PCD remains largely uncharacterized, particularly with regard to how ROS regulate changes in gene expression leading to PCD. Using comparative transcriptome analysis of mutants deficient in PCD regulation and publicly available cell death microarray data, we show that quantitative rather than qualitative differences in cell death gene expression appear to better explain the cell death response. In a genetic analysis with double mutants we also found the transcription factor WRKY70 and a component of ubiquitin mediated protein degradation, SGT1b, to be involved in regulation of ROS induced PCD.
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Affiliation(s)
- Mikael Brosché
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
- Institute of Technology, University of Tartu, Tartu, Estonia
- * E-mail:
| | - Tiina Blomster
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Jarkko Salojärvi
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Fuqiang Cui
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Nina Sipari
- Department of Biology, University of Eastern Finland, Joensuu, Finland
| | - Johanna Leppälä
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Airi Lamminmäki
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Gloria Tomai
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Shaman Narayanasamy
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Ramesha A. Reddy
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Markku Keinänen
- Department of Biology, University of Eastern Finland, Joensuu, Finland
| | - Kirk Overmyer
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Jaakko Kangasjärvi
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
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9
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Voo SS, Lange BM. Sample preparation for single cell transcriptomics: essential oil glands in Citrus fruit peel as an example. Methods Mol Biol 2014; 1153:203-212. [PMID: 24777799 DOI: 10.1007/978-1-4939-0606-2_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Many plant natural products are synthesized in specialized cells and tissues. To learn more about metabolism in these cells, they have to be studied in isolation. Here, we describe a protocol for the isolation of epithelial cells that surround secretory cavities in Citrus fruit peel. Cells isolated using laser microdissection are suitable for RNA isolation and downstream transcriptome analyses.
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Affiliation(s)
- Siau Sie Voo
- Institute of Biological Chemistry, M.J. Murdock Metabolomics Laboratory, Washington State University, Clark Hall, Room 341, Pullman, WA, 99164-6340, USA
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10
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Poschenrieder C, Cabot C, Martos S, Gallego B, Barceló J. Do toxic ions induce hormesis in plants? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 212:15-25. [PMID: 24094050 DOI: 10.1016/j.plantsci.2013.07.012] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 07/14/2013] [Accepted: 07/30/2013] [Indexed: 06/02/2023]
Abstract
The concept of hormesis in plants is critically reviewed, taking growth stimulation by low concentrations of toxic trace elements as a reference. The importance of both non-adaptive and adaptive mechanisms underlying ion-induced hormetic growth responses is highlighted. The activation of defense mechanisms by metal ions and pathogenic elicitors and the cross talk between the signals induced by metal ions and biotic stressors are considered. The production of reactive oxygen species and, consequently, the induction of stress-induced antioxidants, are key mechanisms in metal ion-induced hormesis in plants. It is concluded that in the current scientific literature, hormesis is used as an "umbrella" term that includes a wide range of different mechanisms. It is recommended that the term hormesis be used in plant toxicology as a descriptive term for the stimulated phase in growth response curves that is induced by low concentrations of toxic metal ions without evidence of the underlying mechanisms. If the mechanisms underlying the stimulated growth phase have been identified, specific terms, such as amelioration, defense gene activation, priming or acclimation, should be used.
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Affiliation(s)
- Charlotte Poschenrieder
- Lab. Fisiología Vegetal, Facultad Biociencias, Universidad Autónoma de Barcelona, E-08193 Bellaterra, Spain.
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11
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Verbruggen N, Hanikenne M, Clemens S. A more complete picture of metal hyperaccumulation through next-generation sequencing technologies. FRONTIERS IN PLANT SCIENCE 2013; 4:388. [PMID: 24098304 PMCID: PMC3787545 DOI: 10.3389/fpls.2013.00388] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Accepted: 09/11/2013] [Indexed: 05/04/2023]
Abstract
The mechanistic understanding of metal hyperaccumulation has benefitted immensely from the use of molecular genetics tools developed for Arabidopsis thaliana. The revolution in DNA sequencing will enable even greater strides in the near future, this time not restricted to the family Brassicaceae. Reference genomes are within reach for many ecologically interesting species including heterozygous outbreeders. They will allow deep RNA-seq transcriptome studies and the re-sequencing of contrasting individuals to unravel the genetic basis of phenotypic variation. Cell-type specific transcriptome analyses, which will be essential for the dissection of metal translocation pathways in hyperaccumulators, can be achieved through the combination of RNA-seq and translatome approaches. Affordable high-resolution genotyping of many individuals enables the elucidation of quantitative trait loci in intra- and interspecific crosses as well as through genome-wide association mapping across large panels of accessions. Furthermore, genome-wide scans have the power to detect loci under recent selection. Together these approaches will lead to a detailed understanding of the evolutionary path towards the emergence of hyperaccumulation traits.
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Affiliation(s)
- Nathalie Verbruggen
- Plant Physiology and Molecular Genetics, Bioengineering School, Faculty of Sciences, Université Libre de BruxellesBrussels, Belgium
| | - Marc Hanikenne
- Functional Genomics and Plant Molecular Imaging, Center for Protein Engineering, Department of Life Sciences, University of LiègeLiège, Belgium
- PhytoSYSTEMS, University of LiègeLiège, Belgium
| | - Stephan Clemens
- Department of Plant Physiology, University of BayreuthBayreuth, Germany
- Bayreuth Center for Molecular Biosciences, University of BayreuthBayreuth, Germany
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12
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Wuest SE, Schmid MW, Grossniklaus U. Cell-specific expression profiling of rare cell types as exemplified by its impact on our understanding of female gametophyte development. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:41-9. [PMID: 23276786 DOI: 10.1016/j.pbi.2012.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 12/03/2012] [Indexed: 05/20/2023]
Abstract
Expression profiling of single cells can yield insights into cell specification, cellular differentiation processes, and cell type-specific responses to environmental stimuli. Recent work has established excellent tools to perform genome-wide expression studies of individual cell types, even if the cells of interest occur at low frequency within an organ. We review the advances and impact of gene expression studies of rare cell types, as exemplified by recently gained insights into the development and function of the angiosperm female gametophyte. The detailed transcriptional characterization of different stages during female gametophyte development has significantly helped to improve our understanding of cellular specification or cell-cell communication processes. Next-generation sequencing approaches--used increasingly for expression profiling--will now allow for comparative approaches that focus on agriculturally, ecologically or evolutionarily relevant aspects of plant reproduction.
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Affiliation(s)
- Samuel E Wuest
- Institute of Evolutionary Biology and Environmental Studies & Zürich-Basel Plant Science Center, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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13
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Wang D, Mills ES, Deal RB. Technologies for systems-level analysis of specific cell types in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 197:21-29. [PMID: 23116668 PMCID: PMC4037754 DOI: 10.1016/j.plantsci.2012.08.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 08/21/2012] [Accepted: 08/22/2012] [Indexed: 05/08/2023]
Abstract
The study of biological processes at cell type resolution requires the isolation of the specific cell types from an organism, but this presents a great technical challenge. In recent years a number of methods have been developed that allow deep analyses of the epigenome, transcriptome, and ribosome-associated mRNA populations in individual cell types. The application of these methods has lead to a clearer understanding of important issues in plant biology, including cell fate specification and cell type-specific responses to the environment. In this review, we discuss current mechanical- and affinity-based technologies available for isolation and analysis of individual cell types in a plant. The integration of these methods is proposed as a means of achieving a holistic view of cellular processes at all levels, from chromatin dynamics to metabolomics. Finally, we explore the limitations of current methods and the needs for future technological development.
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Affiliation(s)
- Dongxue Wang
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - E. Shannon Mills
- Graduate program in Genetics and Molecular Biology of the Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA 30322, USA
| | - Roger B. Deal
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- To whom correspondence should be addressed:
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Rogers ED, Jackson T, Moussaieff A, Aharoni A, Benfey PN. Cell type-specific transcriptional profiling: implications for metabolite profiling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:5-17. [PMID: 22449039 PMCID: PMC3315153 DOI: 10.1111/j.1365-313x.2012.04888.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Plant development and survival is centered on complex regulatory networks composed of genes, proteins, hormone pathways, metabolites and signaling pathways. The recent advancements in whole genome biology have furthered our understanding of the interactions between these networks. As a result, numerous cell type-specific transcriptome profiles have been generated that have elucidated complex gene regulatory networks occurring at the cellular level, many of which were masked during whole-organ analysis. Modern technologies have also allowed researchers to generate multiple whole-organ metabolite profiles; however, only a limited number have been generated at the level of individual cells. Recent advancements in the isolation of individual cell populations have made cell type-specific metabolite profiles possible, enabling the enhanced detection and quantification of metabolites that were formerly unavailable when considering the whole organ. The comparison of metabolite and transcriptome profiles from the same cells has been a valuable resource to generate predictions regarding specific metabolite activity and function. In this review, we focus on recent studies that demonstrate the value of cell type-specific transcriptional profiles and their comparison with profiles generated from whole organs. Advancements in the isolation of single-cell populations will be highlighted, and the potential application towards generating detailed metabolic profiles will be discussed.
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Affiliation(s)
- Eric D. Rogers
- Department of Biologyand Duke Center for Systems Biology, Duke University, Durham, NC, USA 27708
| | - Terry Jackson
- Department of Biologyand Duke Center for Systems Biology, Duke University, Durham, NC, USA 27708
| | - Arieh Moussaieff
- Department of Plant Sciences, Weizmann Institute, Rehovot, 76100, Israel
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute, Rehovot, 76100, Israel
| | - Philip N. Benfey
- Department of Biologyand Duke Center for Systems Biology, Duke University, Durham, NC, USA 27708
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Loiacono FV, De Tullio MC. Why we should stop inferring simple correlations between antioxidants and plant stress resistance: towards the antioxidomic era. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2012; 16:160-7. [PMID: 22433077 DOI: 10.1089/omi.2011.0099] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A large number of studies have investigated the relationship between different forms of abiotic stress and antioxidants. However, misconceptions and technical flaws often affect studies on this important topic. Reactive oxygen species (ROS) generated under stress conditions should not be considered just as potential threats, because they are essential components of the signaling mechanism inducing plant defenses. Similarly, the complexity of the antioxidant system should be considered, to avoid misleading oversimplifications. Recent literature is discussed, highlighting the importance of accurate experimental setups for obtaining reliable results in this delicate field of research. A tentative "troubleshooting guide" is provided to help researchers interested in improving the quality of their work on the role of antioxidants in plant stress resistance. Significant advancements in the field could be reached with the development of antioxidomics, defined here as a new branch of research at the crossroads of other disciplines including metabolomics and proteomics, studying the complex relationship among antioxidants and their functions.
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Affiliation(s)
- F Vanessa Loiacono
- Department of Applied Plant Sciences and Plant Biotechnology, University of Natural Resources and Applied Life Sciences, Institute of Horticulture, Fruit-Growing and Viticulture, Vienna, Austria
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Abstract
Soil salinity devastates agriculture. It reduces crop yields and makes arable land unsuitable for later use. Many species have evolved highly efficient strategies to sense, transduce, and build up tolerance to high salinity and even sensitive species have endogenous mechanism for coping with this stress. These underlying physiological and metabolic mechanisms can be unraveled using metabolomics. Here we describe detailed protocols of how to extract polar metabolites for analysis using GC-MS and LC-MS. We also touch briefly on considerations that should be taken into account when designing the experiment and how the resulting data may be analyzed and visualized in a biological context.
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Affiliation(s)
- Ute Roessner
- ACPFG Centre for Plant Functional Genomics and Metabolomics Australia, University of Melbourne, Melbourne, VIC, Australia.
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Taylor-Teeples M, Ron M, Brady SM. Novel biological insights revealed from cell type-specific expression profiling. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:601-7. [PMID: 21704550 DOI: 10.1016/j.pbi.2011.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 05/27/2011] [Accepted: 05/30/2011] [Indexed: 05/20/2023]
Abstract
Transcriptional regulation plays a major role in defining cell identity. Analysis of cell type-resolution expression profiling datasets is moving beyond cataloging gene expression patterns to reveal novel biological insights. Recently developed expression maps of the shoot apical meristem and gametophytes can be used as tools to help define novel cell types and pathways. Already these maps have revealed cell type-specific epigenetic regulatory mechanisms that play important roles in development. Further examples are provided that demonstrate how cell type-specific expression profiling can also be used to uncover genes and pathways in development and response to stress that would be nearly impossible to identify using traditional genetics.
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Affiliation(s)
- Mallorie Taylor-Teeples
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
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