1
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Muthego D, Moloi SJ, Brown AP, Goche T, Chivasa S, Ngara R. Exogenous abscisic acid treatment regulates protein secretion in sorghum cell suspension cultures. PLANT SIGNALING & BEHAVIOR 2023; 18:2291618. [PMID: 38100609 PMCID: PMC10730228 DOI: 10.1080/15592324.2023.2291618] [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: 08/17/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023]
Abstract
Drought stress adversely affects plant growth, often leading to total crop failure. Upon sensing soil water deficits, plants switch on biosynthesis of abscisic acid (ABA), a stress hormone for drought adaptation. Here, we used exogenous ABA application to dark-grown sorghum cell suspension cultures as an experimental system to understand how a drought-tolerant crop responds to ABA. We evaluated intracellular and secreted proteins using isobaric tags for relative and absolute quantification. While the abundance of only ~ 7% (46 proteins) intracellular proteins changed in response to ABA, ~32% (82 proteins) of secreted proteins identified in this study were ABA responsive. This shows that the extracellular matrix is disproportionately targeted and suggests it plays a vital role in sorghum adaptation to drought. Extracellular proteins responsive to ABA were predominantly defense/detoxification and cell wall-modifying enzymes. We confirmed that sorghum plants exposed to drought stress activate genes encoding the same proteins identified in the in vitro cell culture system with ABA. Our results suggest that ABA activates defense and cell wall remodeling systems during stress response. This could underpin the success of sorghum adaptation to drought stress.
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Affiliation(s)
- Dakalo Muthego
- Department of Plant Sciences, University of the Free State, Phuthaditjhaba, South Africa
| | - Sellwane J. Moloi
- Department of Plant Sciences, University of the Free State, Phuthaditjhaba, South Africa
| | | | - Tatenda Goche
- Department of Biosciences, Durham University, Durham, UK
- Department of Crop Science, Bindura University of Science Education, Bindura, Zimbabwe
| | | | - Rudo Ngara
- Department of Plant Sciences, University of the Free State, Phuthaditjhaba, South Africa
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2
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Lastochkina O, Yuldashev R, Avalbaev A, Allagulova C, Veselova S. The Contribution of Hormonal Changes to the Protective Effect of Endophytic Bacterium Bacillus subtilis on Two Wheat Genotypes with Contrasting Drought Sensitivities under Osmotic Stress. Microorganisms 2023; 11:2955. [PMID: 38138099 PMCID: PMC10745732 DOI: 10.3390/microorganisms11122955] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/29/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
A comparative analysis was conducted to evaluate the effects of seed priming with endophytic bacterium Bacillus subtilis 10-4 (BS) on the hormonal system and cell wall tolerance (lipid peroxidation (LPO), electrolyte leakage (EL), and root lignin deposition) of two Triticum aestivum L. (wheat) varieties with contrasting drought sensitivities (Ekada 70-drought-tolerant (DT); Salavat Yulaev-drought-sensitive (DS)) under normal conditions and 12% polyethylene glycol-6000 (PEG)-induced osmotic stress. The results showed that under normal conditions, the growth stimulation in wheat plants by BS was attributed to changes in the hormonal balance, particularly an increase in endogenous indole-3-acetic acid (IAA) accumulation. However, under stress, a significant hormonal imbalance was observed in wheat seedlings, characterized by a pronounced accumulation of abscisic acid (ABA) and a decrease in the levels of IAA and cytokinins (CK). These effects were reflected in the inhibition of plant growth. BS exhibited a protective effect on stressed plants, as evidenced by a significantly lower amplitude of stress-induced changes in the hormonal system: maintaining the content of IAA at a level close to the control, reducing stress-induced ABA accumulation, and preventing CK depletion. These effects were further reflected in the normalization of growth parameters in dehydrated seedlings, as well as a decrease in leaf chlorophyll degradation, LPO, and EL, along with an increase in lignin deposition in the basal part of the roots in both genotypes. Overall, the findings demonstrate that BS, producing phytohormones, specifically IAA and ABA, had a more pronounced protective effect on DT plants, as evidenced by a smaller amplitude of stress-induced hormonal changes, higher leaf chlorophyll content, root lignin deposition, and lower cell membrane damage (LPO) and permeability (EL) compared to DS plants.
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Affiliation(s)
- Oksana Lastochkina
- Institute of Biochemistry and Genetics—Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 71 Pr. Oktyabrya, 450054 Ufa, Russia (A.A.); (S.V.)
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3
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Huang Y, Yang R, Luo H, Yuan Y, Diao Z, Li J, Gong S, Yu G, Yao H, Zhang H, Cai Y. Arabidopsis Protein Phosphatase PIA1 Impairs Plant Drought Tolerance by Serving as a Common Negative Regulator in ABA Signaling Pathway. PLANTS (BASEL, SWITZERLAND) 2023; 12:2716. [PMID: 37514328 PMCID: PMC10384177 DOI: 10.3390/plants12142716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/16/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023]
Abstract
Reversible phosphorylation of proteins is a ubiquitous regulatory mechanism in vivo that can respond to external changes, and plays an extremely important role in cell signal transduction. Protein phosphatase 2C is the largest protein phosphatase family in higher plants. Recently, it has been found that some clade A members can negatively regulate ABA signaling pathways. However, the functions of several subgroups of Arabidopsis PP2C other than clade A have not been reported, and whether other members of the PP2C family also participate in the regulation of ABA signaling pathways remains to be studied. In this study, based on the previous screening and identification work of PP2C involved in the ABA pathway, the clade F member PIA1 encoding a gene of the PP2C family, which was down-regulated after ABA treatment during the screening, was selected as the target. Overexpression of PIA1 significantly down-regulated the expression of ABA marker gene RD29A in Arabidopsis protoplasts, and ABA-responsive elements have been found in the cis-regulatory elements of PIA1 by promoter analysis. When compared to Col-0, transgenic plants overexpressing PIA1 were less sensitive to ABA, whereas pia1 showed the opposite trait in seed germination, root growth, and stomatal opening experiments. Under drought stress, SOD, POD, CAT, and APX activities of PIA1 overexpression lines were lower than Col-0 and pia1, while the content of H2O2 was higher, leading to its lowest survival rate in test plants, which were consistent with the significant inhibition of the expression of ABA-dependent stress-responsive genes RD29B, ABI5, ABF3, and ABF4 in the PIA1 transgenic background after ABA treatment. Using yeast two-hybrid and luciferase complementation assays, PIA1 was found to interact with multiple ABA key signaling elements, including 2 RCARs and 6 SnRK2s. Our results indicate that PIA1 may reduce plant drought tolerance by functioning as a common negative regulator involved in ABA signaling pathway.
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Affiliation(s)
- Yan Huang
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625000, China
| | - Rongqian Yang
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625000, China
| | - Huiling Luo
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625000, China
| | - Yuan Yuan
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625000, China
| | - Zhihong Diao
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625000, China
| | - Junhao Li
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625000, China
| | - Shihe Gong
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625000, China
| | - Guozhi Yu
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625000, China
| | - Huipeng Yao
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625000, China
| | - Huaiyu Zhang
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625000, China
| | - Yi Cai
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625000, China
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4
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Peng KC, Siao W, Hsieh HL. FAR-RED INSENSITIVE 219 and phytochrome B corepress shade avoidance via modulating nuclear speckle formation. PLANT PHYSIOLOGY 2023; 192:1449-1465. [PMID: 36869668 PMCID: PMC10231371 DOI: 10.1093/plphys/kiad103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 06/01/2023]
Abstract
Plants can sense the shade from neighboring plants by detecting a reduction of the red:far-red light (R:FR) ratio. Phytochrome B (phyB) is the primary photoreceptor that perceives shade light and regulates jasmonic acid (JA) signaling. However, the molecular mechanisms underlying phyB and JA signaling integration in shade responses remain largely unknown. Here, we show the interaction of phyB and FAR-RED INSENSITIVE 219 (FIN219)/JASMONATE RESISTANT1 (JAR1) in a functional demand manner in Arabidopsis (Arabidopsis thaliana) seedling development. Genetic evidence and interaction studies indicated that phyB and FIN219 synergistically and negatively regulate shade-induced hypocotyl elongation. Moreover, phyB interacted with various isoforms of FIN219 under high and low R:FR light. Methyl jasmonate (MeJA) treatment, FIN219 mutation, and PHYBOE digalactosyldiacylglycerol synthase1-1 (dgd1-1) plants, which show increased levels of JA, altered the patterns of phyB-associated nuclear speckles under the same conditions. Surprisingly, PHYBOE dgd1-1 showed a shorter hypocotyl phenotype than its parental mutants under shade conditions. Microarray assays using PHYBOE and PHYBOE fin219-2 indicated that PHYB overexpression substantially affects defense response-related genes under shade light and coregulates expression of auxin-responsive genes with FIN219. Thus, our findings reveal that phyB substantially crosstalks with JA signaling through FIN219 to modulate seedling development under shade light.
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Affiliation(s)
- Kai-Chun Peng
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Wei Siao
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 106, Taiwan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Hsu-Liang Hsieh
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 106, Taiwan
- Department of Life Science, College of Life Science, National Taiwan University, Taipei 106, Taiwan
- Master Program in Global Agriculture Technology and Genomic Science, National Taiwan University, Taipei 106, Taiwan
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5
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Shi W, Wang X, Liu H, Cai Z, Lu C, Chen Y. A novel ABA-insensitive mutant in Arabidopsis reveals molecular network of ABA-induced anthocyanin accumulation and abiotic stress tolerance. JOURNAL OF PLANT PHYSIOLOGY 2022; 278:153810. [PMID: 36162212 DOI: 10.1016/j.jplph.2022.153810] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/03/2022] [Accepted: 09/03/2022] [Indexed: 06/16/2023]
Abstract
Abscisic acid (ABA) plays primary regulatory roles in abiotic stress tolerance and seed germination. Here, we report a unique novel Arabidopsis abscisic acid-insensitive mutant, abr (abscisic acid resistance), which was able to germinate in medium containing high ABA concentrations and tolerant to abiotic stress tolerance. We observed that abr mutant accumulated more anthocyanins by ABA treatment than did the wild type (WT). Dimethylthiourea (DMTU, an H2O2 scavenger) was effective in inhibiting ABA-induced anthocyanins accumulation. RNA-seq showed that the expression of anthocyanins synthesis, antioxidant enzyme and stress-related genes were specifically increased in ABA-treated abr seedlings, suggesting that the abr mutation affects stress response as well as ABA responses. Interestingly, seedlings accumulating anthocyanins exhibited more tolerance to mannitol and NaCl compared to wild type. We propose that ABA-induced H2O2 generation triggers the foliar anthocyanins accumulation, which, in turn, enhances the abiotic stress tolerance in abr mutant.
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Affiliation(s)
- Weijia Shi
- College of Biological Sciences and Biotechnology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China
| | - Xiaojing Wang
- College of Biological Sciences and Biotechnology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China
| | - Huan Liu
- College of Biological Sciences and Biotechnology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China
| | - Zian Cai
- College of Biological Sciences and Biotechnology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China
| | - Cunfu Lu
- College of Biological Sciences and Biotechnology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China.
| | - Yuzhen Chen
- College of Biological Sciences and Biotechnology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China.
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6
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Balasubramanian VK, Purvine SO, Liang Y, Kelly RT, Pasa-Tolic L, Chrisler WB, Blumwald E, Stewart CN, Zhu Y, Ahkami AH. Cell-Type-Specific Proteomics Analysis of a Small Number of Plant Cells by Integrating Laser Capture Microdissection with a Nanodroplet Sample Processing Platform. Curr Protoc 2021; 1:e153. [PMID: 34043287 DOI: 10.1002/cpz1.153] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Plant organs and tissues contain multiple cell types, which are well organized in 3-dimensional structure to efficiently perform physiological functions such as homeostasis and response to environmental perturbation and pathogen infection. It is critically important to perform molecular measurements at the cell-type-specific level to discover mechanisms and unique features of cell populations that govern differentiation and respond to external perturbations. Although mass spectrometry-based proteomics has been demonstrated as an enabling discovery tool for studying plant physiology, conventional approaches require millions of cells to generate robust biological conclusions. Such requirements mask the cell-to-cell heterogeneities and limit the comprehensive profiling of plant proteins at spatially resolved and cell-type-specific resolutions. This article describes a recently developed proteomics workflow for studying a small number of plant cells by integrating laser capture microdissection, microfluidic nanodroplet-based sample preparation, and ultrasensitive liquid chromatography-mass spectrometry. Using poplar as a model tree species, we provide detailed protocols, including plant leaf and root tissue harvest, sample preparation, cryosectioning, laser microdissection, protein digestion, mass spectrometry measurement, and data analysis. We show that the workflow enables the precise identification and quantification of thousands of proteins from hundreds of isolated plant root and leaf cells. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Plant tissue fixation and embedding Support Protocol 1: Preparation of 2.5% CMC solution Support Protocol 2: Slow freezing of CMC blocks to avoid crack development in the block Basic Protocol 2: Preparation of cryosections Alternate Protocol: Using a vacuum manifold to dehydrate the cryosection slides (primarily for root tissues) Basic Protocol 3: Laser capture microdissection of specific types of plant cells Basic Protocol 4: Nanodroplet-based sample preparation for ultrasensitive proteomic analysis Support Protocol 3: Fabrication of nanowell chips Basic Protocol 5: Liquid chromatography and mass spectrometry.
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Affiliation(s)
- Vimal K Balasubramanian
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - Yiran Liang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - William B Chrisler
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, California
| | - C Neal Stewart
- Department of Plant Sciences, Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, Tennessee
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - Amir H Ahkami
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
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7
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Advances in Wheat Physiology in Response to Drought and the Role of Plant Growth Promoting Rhizobacteria to Trigger Drought Tolerance. Microorganisms 2021; 9:microorganisms9040687. [PMID: 33810405 PMCID: PMC8066330 DOI: 10.3390/microorganisms9040687] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/20/2021] [Accepted: 03/22/2021] [Indexed: 11/17/2022] Open
Abstract
In the coming century, climate change and the increasing human population are likely leading agriculture to face multiple challenges. Agricultural production has to increase while preserving natural resources and protecting the environment. Drought is one of the major abiotic problems, which limits the growth and productivity of crops and impacts 1–3% of all land.To cope with unfavorable water-deficit conditions, plants use through sophisticated and complex mechanisms that help to perceive the stress signal and enable optimal crop yield are required. Among crop production, wheat is estimated to feed about one-fifth of humanity, but faces more and more drought stress periods, partially due to climate change. Plant growth promoting rhizobacteria are a promising and interesting way to develop productive and sustainable agriculture despite environmental stress. The current review focuses on drought stress effects on wheat and how plant growth-promoting rhizobacteria trigger drought stress tolerance of wheat by highlighting several mechanisms. These bacteria can lead to better growth and higher yield through the production of phytohormones, osmolytes, antioxidants, volatile compounds, exopolysaccharides and 1-aminocyclopropane-1-carboxylate deaminase. Based on the available literature, we provide a comprehensive review of mechanisms involved in drought resilience and how bacteria may alleviate this constraint
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8
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Baggs EL, Monroe JG, Thanki AS, O'Grady R, Schudoma C, Haerty W, Krasileva KV. Convergent Loss of an EDS1/PAD4 Signaling Pathway in Several Plant Lineages Reveals Coevolved Components of Plant Immunity and Drought Response. THE PLANT CELL 2020; 32:2158-2177. [PMID: 32409319 PMCID: PMC7346574 DOI: 10.1105/tpc.19.00903] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 04/28/2020] [Accepted: 05/12/2020] [Indexed: 05/19/2023]
Abstract
Plant innate immunity relies on nucleotide binding leucine-rich repeat receptors (NLRs) that recognize pathogen-derived molecules and activate downstream signaling pathways. We analyzed the variation in NLR gene copy number and identified plants with a low number of NLR genes relative to sister species. We specifically focused on four plants from two distinct lineages, one monocot lineage (Alismatales) and one eudicot lineage (Lentibulariaceae). In these lineages, the loss of NLR genes coincides with loss of the well-known downstream immune signaling complex ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1)/PHYTOALEXIN DEFICIENT 4 (PAD4). We expanded our analysis across whole proteomes and found that other characterized immune genes were absent only in Lentibulariaceae and Alismatales. Additionally, we identified genes of unknown function that were convergently lost together with EDS1/PAD4 in five plant species. Gene expression analyses in Arabidopsis (Arabidopsis thaliana) and Oryza sativa revealed that several homologs of the candidates are differentially expressed during pathogen infection, drought, and abscisic acid treatment. Our analysis provides evolutionary evidence for the rewiring of plant immunity in some plant lineages, as well as the coevolution of the EDS1/PAD4 pathway and drought responses.
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Affiliation(s)
- Erin L Baggs
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
- University of California Berkeley, Berkeley, California 94720
| | - J Grey Monroe
- University of California Davis, Davis, California 95616
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Anil S Thanki
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
| | - Ruby O'Grady
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Christian Schudoma
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
| | - Ksenia V Krasileva
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
- University of California Berkeley, Berkeley, California 94720
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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9
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He J, Zhang RX, Kim DS, Sun P, Liu H, Liu Z, Hetherington AM, Liang YK. ROS of Distinct Sources and Salicylic Acid Separate Elevated CO 2-Mediated Stomatal Movements in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:542. [PMID: 32457781 PMCID: PMC7225777 DOI: 10.3389/fpls.2020.00542] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 04/09/2020] [Indexed: 05/12/2023]
Abstract
Elevated CO2 (eCO2) often reduces leaf stomatal aperture and density thus impacts plant physiology and productivity. We have previously demonstrated that the Arabidopsis BIG protein distinguishes between the processes of eCO2-induced stomatal closure and eCO2-inhibited stomatal opening. However, the mechanistic basis of this action is not fully understood. Here we show that eCO2-elicited reactive oxygen species (ROS) production in big mutants was compromised in stomatal closure induction but not in stomatal opening inhibition. Pharmacological and genetic studies show that ROS generated by both NADPH oxidases and cell wall peroxidases contribute to eCO2-induced stomatal closure, whereas inhibition of light-induced stomatal opening by eCO2 may rely on the ROS derived from NADPH oxidases but not from cell wall peroxidases. As with JA and ABA, SA is required for eCO2-induced ROS generation and stomatal closure. In contrast, none of these three signals has a significant role in eCO2-inhibited stomatal opening, unveiling the distinct roles of plant hormonal signaling pathways in the induction of stomatal closure and the inhibition of stomatal opening by eCO2. In conclusion, this study adds SA to a list of plant hormones that together with ROS from distinct sources distinguish two branches of eCO2-mediated stomatal movements.
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Affiliation(s)
- Jingjing He
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, China
| | - Ruo-Xi Zhang
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, China
| | - Dae Sung Kim
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, China
| | - Peng Sun
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, China
| | - Honggang Liu
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhongming Liu
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, China
| | - Alistair M. Hetherington
- School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, United Kingdom
| | - Yun-Kuan Liang
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, China
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10
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Wei M, Zhuang Y, Li H, Li P, Huo H, Shu D, Huang W, Wang S. The cloning and characterization of hypersensitive to salt stress mutant, affected in quinolinate synthase, highlights the involvement of NAD in stress-induced accumulation of ABA and proline. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:85-98. [PMID: 31733117 DOI: 10.1111/tpj.14613] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 10/28/2019] [Accepted: 11/01/2019] [Indexed: 05/22/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD), a ubiquitous coenzyme, is required for many physiological reactions and processes. However, it remains largely unknown how NAD affects plant response to salt stress. We isolated a salt-sensitive mutant named hypersensitive to salt stress (hss) from an ethyl methanesulfonate-induced mutation population. A point mutation was identified by MutMap in the encoding region of Quinolinate Synthase (QS) gene required for the de novo synthesis of NAD. This point mutation caused a substitution of amino acid in the highly-conserved NadA domain of QS, resulting in an impairment of NAD biosynthesis in the mutant. Molecular and chemical complementation have restored the response of the hss mutant to salt stress, indicating that the decreased NAD contents in the mutant were responsible for its hypersensitivity to salt stress. Furthermore, the endogenous levels of abscisic acid (ABA) and proline were also reduced in stress-treated hss mutant. The application of ABA or proline could alleviate stress-induced oxidative damage of the mutant and partially rescue its hypersensitivity to salt stress, but not affect NAD concentration. Taken together, our results demonstrated that the NadA domain of QS is important for NAD biosynthesis, and NAD participates in plant response to salt stress by affecting stress-induced accumulation of ABA and proline.
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Affiliation(s)
- Ming Wei
- CAS Center for Excellence in Molecular Plant Sciences, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong Zhuang
- CAS Center for Excellence in Molecular Plant Sciences, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Li
- CAS Center for Excellence in Molecular Plant Sciences, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Penghui Li
- CAS Center for Excellence in Molecular Plant Sciences, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Heqiang Huo
- Mid-Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Apopka, FL, 32703, USA
| | - Dan Shu
- CAS Center for Excellence in Molecular Plant Sciences, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Weizao Huang
- CAS Center for Excellence in Molecular Plant Sciences, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Songhu Wang
- CAS Center for Excellence in Molecular Plant Sciences, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, 05282, Myanmar
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11
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Wang L, Zou Y, Kaw HY, Wang G, Sun H, Cai L, Li C, Meng LY, Li D. Recent developments and emerging trends of mass spectrometric methods in plant hormone analysis: a review. PLANT METHODS 2020; 16:54. [PMID: 32322293 PMCID: PMC7161177 DOI: 10.1186/s13007-020-00595-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 04/04/2020] [Indexed: 05/18/2023]
Abstract
Plant hormones are naturally occurring small molecule compounds which are present at trace amounts in plant. They play a pivotal role in the regulation of plant growth. The biological activity of plant hormones depends on their concentrations in the plant, thus, accurate determination of plant hormone is paramount. However, the complex plant matrix, wide polarity range and low concentration of plant hormones are the main hindrances to effective analyses of plant hormone even when state-of-the-art analytical techniques are employed. These factors substantially influence the accuracy of analytical results. So far, significant progress has been realized in the analysis of plant hormones, particularly in sample pretreatment techniques and mass spectrometric methods. This review describes the classic extraction and modern microextraction techniques used to analyze plant hormone. Advancements in solid phase microextraction (SPME) methods have been driven by the ever-increasing requirement for dynamic and in vivo identification of the spatial distribution of plant hormones in real-life plant samples, which would contribute greatly to the burgeoning field of plant hormone investigation. In this review, we describe advances in various aspects of mass spectrometry methods. Many fragmentation patterns are analyzed to provide the theoretical basis for the establishment of a mass spectral database for the analysis of plant hormones. We hope to provide a technical guide for further discovery of new plant hormones. More than 140 research studies on plant hormone published in the past decade are reviewed, with a particular emphasis on the recent advances in mass spectrometry and sample pretreatment techniques in the analysis of plant hormone. The potential progress for further research in plant hormones analysis is also highlighted.
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Affiliation(s)
- Liyuan Wang
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
| | - Yilin Zou
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
| | - Han Yeong Kaw
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
| | - Gang Wang
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
| | - Huaze Sun
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
| | - Long Cai
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
| | - Chengyu Li
- State Key Laboratory of Application of Rare Earth Resources, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 China
| | - Long-Yue Meng
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
- Department of Environmental Science, Yanbian University, Yanji, 133002 China
| | - Donghao Li
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
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12
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Plasma membrane proteome analyses of Arabidopsis thaliana suspension-cultured cells during cold or ABA treatment: Relationship with freezing tolerance and growth phase. J Proteomics 2020; 211:103528. [DOI: 10.1016/j.jprot.2019.103528] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/28/2019] [Accepted: 09/15/2019] [Indexed: 11/22/2022]
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13
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Dubiel M, Beeckman T, Smagghe G, Van Damme EJM. Arabidopsis Lectin EULS3 Is Involved in ABA Signaling in Roots. FRONTIERS IN PLANT SCIENCE 2020; 11:437. [PMID: 32362905 PMCID: PMC7181964 DOI: 10.3389/fpls.2020.00437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/25/2020] [Indexed: 05/18/2023]
Abstract
The Arabidopsis thaliana lectin ArathEULS3 is upregulated in particular stress conditions and upon abscisic acid (ABA) treatment. ABA is a plant hormone important for plant growth and stress responses. During stress ABA is perceived by PYR/PYL/RCAR receptors, inhibiting protein phosphatases PP2Cs thereby enabling SNRK2s kinases to start downstream phosphorylation cascades and signaling. PYL9, one of the ABA receptors was identified as an interacting partner for ArathEULS3. Promoter::GUS activity studies revealed the expression of ArathEULS3 in the central root cylinder and the cells flanking young lateral root primordia, and showed enhanced expression in root tips after ABA treatment. Transcript levels for ArathEULS3 increased after exposure to ABA and osmotic treatments. ArathEULS3 CRISPR KO mutants served as a tool to expand the knowledge on the role of ArathEULS3 in plant development. KO lines revealed a longer root system compared to WT plants, and showed reduced sensitivity to ABA, salt, and osmotic conditions. Additionally it was noted that the KO mutants had more emerged lateral roots when grown in high osmotic conditions. Together these data suggest that ArathEULS3 may be an important player in ABA responses in roots.
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Affiliation(s)
- Malgorzata Dubiel
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Ghent, Belgium
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Els J. M. Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Ghent, Belgium
- Center for Advanced Light Microscopy, Ghent University, Ghent, Belgium
- *Correspondence: Els J. M. Van Damme,
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14
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Eggplant Germination is Promoted by Hydrogen Peroxide and Temperature in an Independent but Overlapping Manner. Molecules 2019; 24:molecules24234270. [PMID: 31771170 PMCID: PMC6930571 DOI: 10.3390/molecules24234270] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/12/2019] [Accepted: 11/21/2019] [Indexed: 12/27/2022] Open
Abstract
Hydrogen peroxide promotes seed germination, but the molecular mechanisms underlying this process are unclear. This study presents the results of eggplant (Solanum melongena) germination analyses conducted at two different temperatures and follows the effect of hydrogen peroxide treatment on seed germination and the seed proteome. Hydrogen peroxide was found to promote eggplant germination in a way not dissimilar to that of increased temperature stimuli. LC–MS profiling detected 729 protein families, 77 of which responded to a temperature increase or hydrogen peroxide treatment. These differentially abundant proteins were found to be involved in a number of processes, including protein and amino acid metabolism, carbohydrate metabolism, and the glyoxylate cycle. There was a very low overlap between hydrogen peroxide and temperature-responsive proteins, highlighting the differences behind the seemingly similar outcomes. Furthermore, the observed changes from the seed proteome indicate that hydrogen peroxide treatment diminished the seed endogenous hydrogen peroxide pool and that a part of manifested positive hydrogen peroxide effect might be related to altered sensitivity to abscisic acid.
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15
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Zhang H, Liu P, Guo T, Zhao H, Bensaddek D, Aebersold R, Xiong L. Arabidopsis proteome and the mass spectral assay library. Sci Data 2019; 6:278. [PMID: 31757973 DOI: 10.6084/m9.figshare.c.4647293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/27/2019] [Indexed: 05/26/2023] Open
Abstract
Arabidopsis is an important model organism and the first plant with its genome completely sequenced. Knowledge from studying this species has either direct or indirect applications for agriculture and human health. Quantitative proteomics by data-independent acquisition mass spectrometry (SWATH/DIA-MS) was recently developed and is considered as a high-throughput, massively parallel targeted approach for accurate proteome quantification. In this approach, a high-quality and comprehensive spectral library is a prerequisite. Here, we generated an expression atlas of 10 organs of Arabidopsis and created a library consisting of 15,514 protein groups, 187,265 unique peptide sequences, and 278,278 precursors. The identified protein groups correspond to ~56.5% of the predicted proteome. Further proteogenomics analysis identified 28 novel proteins. We applied DIA-MS using this library to quantify the effect of abscisic acid on Arabidopsis. We were able to recover 8,793 protein groups of which 1,787 were differentially expressed. MS data are available via ProteomeXchange with identifier PXD012708 and PXD012710 for data-dependent acquisition and PXD014032 for DIA analyses.
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Affiliation(s)
- Huoming Zhang
- King Abdallah University of Science and Technology, Core Labs, Thuwal, Kingdom of Saudi Arabia.
| | - Pei Liu
- Division of Biological and Environmental Science and Engineering, King Abdallah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Tiannan Guo
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Huayan Zhao
- Division of Biological and Environmental Science and Engineering, King Abdallah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Dalila Bensaddek
- King Abdallah University of Science and Technology, Core Labs, Thuwal, Kingdom of Saudi Arabia
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Faculry of Science, University of Zurich, Zurich, Switzerland
| | - Liming Xiong
- Division of Biological and Environmental Science and Engineering, King Abdallah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Department of Biology, Hong Kong Baptist University, Kowlong Tong, Hong Kong, SAR, China
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16
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Zhang H, Liu P, Guo T, Zhao H, Bensaddek D, Aebersold R, Xiong L. Arabidopsis proteome and the mass spectral assay library. Sci Data 2019. [PMID: 31757973 DOI: 10.1038/s41597-019-0294-0)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Arabidopsis is an important model organism and the first plant with its genome completely sequenced. Knowledge from studying this species has either direct or indirect applications for agriculture and human health. Quantitative proteomics by data-independent acquisition mass spectrometry (SWATH/DIA-MS) was recently developed and is considered as a high-throughput, massively parallel targeted approach for accurate proteome quantification. In this approach, a high-quality and comprehensive spectral library is a prerequisite. Here, we generated an expression atlas of 10 organs of Arabidopsis and created a library consisting of 15,514 protein groups, 187,265 unique peptide sequences, and 278,278 precursors. The identified protein groups correspond to ~56.5% of the predicted proteome. Further proteogenomics analysis identified 28 novel proteins. We applied DIA-MS using this library to quantify the effect of abscisic acid on Arabidopsis. We were able to recover 8,793 protein groups of which 1,787 were differentially expressed. MS data are available via ProteomeXchange with identifier PXD012708 and PXD012710 for data-dependent acquisition and PXD014032 for DIA analyses.
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Affiliation(s)
- Huoming Zhang
- King Abdallah University of Science and Technology, Core Labs, Thuwal, Kingdom of Saudi Arabia.
| | - Pei Liu
- Division of Biological and Environmental Science and Engineering, King Abdallah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Tiannan Guo
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Huayan Zhao
- Division of Biological and Environmental Science and Engineering, King Abdallah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Dalila Bensaddek
- King Abdallah University of Science and Technology, Core Labs, Thuwal, Kingdom of Saudi Arabia
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Faculry of Science, University of Zurich, Zurich, Switzerland
| | - Liming Xiong
- Division of Biological and Environmental Science and Engineering, King Abdallah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Department of Biology, Hong Kong Baptist University, Kowlong Tong, Hong Kong, SAR, China
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17
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Zhang H, Liu P, Guo T, Zhao H, Bensaddek D, Aebersold R, Xiong L. Arabidopsis proteome and the mass spectral assay library. Sci Data 2019; 6:278. [PMID: 31757973 PMCID: PMC6874543 DOI: 10.1038/s41597-019-0294-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/27/2019] [Indexed: 12/19/2022] Open
Abstract
Arabidopsis is an important model organism and the first plant with its genome completely sequenced. Knowledge from studying this species has either direct or indirect applications for agriculture and human health. Quantitative proteomics by data-independent acquisition mass spectrometry (SWATH/DIA-MS) was recently developed and is considered as a high-throughput, massively parallel targeted approach for accurate proteome quantification. In this approach, a high-quality and comprehensive spectral library is a prerequisite. Here, we generated an expression atlas of 10 organs of Arabidopsis and created a library consisting of 15,514 protein groups, 187,265 unique peptide sequences, and 278,278 precursors. The identified protein groups correspond to ~56.5% of the predicted proteome. Further proteogenomics analysis identified 28 novel proteins. We applied DIA-MS using this library to quantify the effect of abscisic acid on Arabidopsis. We were able to recover 8,793 protein groups of which 1,787 were differentially expressed. MS data are available via ProteomeXchange with identifier PXD012708 and PXD012710 for data-dependent acquisition and PXD014032 for DIA analyses. Measurement(s) | Proteome | Technology Type(s) | mass spectrometry assay • computational modeling technique | Sample Characteristic - Organism | Arabidopsis thaliana |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.9959036
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Affiliation(s)
- Huoming Zhang
- King Abdallah University of Science and Technology, Core Labs, Thuwal, Kingdom of Saudi Arabia.
| | - Pei Liu
- Division of Biological and Environmental Science and Engineering, King Abdallah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Tiannan Guo
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Huayan Zhao
- Division of Biological and Environmental Science and Engineering, King Abdallah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Dalila Bensaddek
- King Abdallah University of Science and Technology, Core Labs, Thuwal, Kingdom of Saudi Arabia
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Faculry of Science, University of Zurich, Zurich, Switzerland
| | - Liming Xiong
- Division of Biological and Environmental Science and Engineering, King Abdallah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.,Department of Biology, Hong Kong Baptist University, Kowlong Tong, Hong Kong, SAR, China
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18
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Pontiggia D, Spinelli F, Fabbri C, Licursi V, Negri R, De Lorenzo G, Mattei B. Changes in the microsomal proteome of tomato fruit during ripening. Sci Rep 2019; 9:14350. [PMID: 31586085 PMCID: PMC6778153 DOI: 10.1038/s41598-019-50575-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 08/23/2019] [Indexed: 11/09/2022] Open
Abstract
The variations in the membrane proteome of tomato fruit pericarp during ripening have been investigated by mass spectrometry-based label-free proteomics. Mature green (MG30) and red ripe (R45) stages were chosen because they are pivotal in the ripening process: MG30 corresponds to the end of cellular expansion, when fruit growth has stopped and fruit starts ripening, whereas R45 corresponds to the mature fruit. Protein patterns were markedly different: among the 1315 proteins identified with at least two unique peptides, 145 significantly varied in abundance in the process of fruit ripening. The subcellular and biochemical fractionation resulted in GO term enrichment for organelle proteins in our dataset, and allowed the detection of low-abundance proteins that were not detected in previous proteomic studies on tomato fruits. Functional annotation showed that the largest proportion of identified proteins were involved in cell wall metabolism, vesicle-mediated transport, hormone biosynthesis, secondary metabolism, lipid metabolism, protein synthesis and degradation, carbohydrate metabolic processes, signalling and response to stress.
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Affiliation(s)
- Daniela Pontiggia
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Francesco Spinelli
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Claudia Fabbri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Valerio Licursi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy.,Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Rodolfo Negri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy.,Foundation Cenci Bolognetti-Institut Pasteur, Rome, Italy
| | - Giulia De Lorenzo
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy. .,Foundation Cenci Bolognetti-Institut Pasteur, Rome, Italy.
| | - Benedetta Mattei
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
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19
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Broekgaarden C, Pelgrom KTB, Bucher J, van Dam NM, Grosser K, Pieterse CMJ, van Kaauwen M, Steenhuis G, Voorrips RE, de Vos M, Vosman B, Worrich A, van Wees SCM. Combining QTL mapping with transcriptome and metabolome profiling reveals a possible role for ABA signaling in resistance against the cabbage whitefly in cabbage. PLoS One 2018; 13:e0206103. [PMID: 30399182 PMCID: PMC6219772 DOI: 10.1371/journal.pone.0206103] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/05/2018] [Indexed: 11/18/2022] Open
Abstract
Whiteflies are among the world's most significant agricultural pests and chemical insecticides are extensively used to reduce crop damage to acceptable levels. However, nearly all insecticides pose a threat to the environment and alternative control methods, such as breeding of crop varieties that are inherently insect-resistant, are needed. Previously, a strong source of plant-age dependent resistance to the cabbage whitefly (Aleyrodes proletella) has been identified in the modern white cabbage (Brassica oleracea var. capitata) variety Rivera. However, nothing is known about the molecular mechanisms or the genes involved in this resistance. In the present study, a multidisciplinary approach combining transcriptome and metabolome profiling with genetic mapping was used to identify the molecular players of whitefly resistance in cabbage. Transcriptome profiles of young (susceptible) and older (resistant) Rivera plants were analyzed using RNA sequencing. While many genes involved in general processes were differentially expressed between both ages, several defense-related processes were overrepresented in the transcriptome profile of older plants. Hormone measurements revealed that jasmonic acid (JA) levels decreased upon whitefly infestation at both plant ages. Interestingly, abscisic acid (ABA) levels showed contrasting effects in response to whitefly infestation: ABA levels were reduced in young plants but induced in older plants upon whitefly feeding. Auxin levels were significantly lower in older plants compared with young plants, independent of whitefly presence, while glucosinolate levels were higher. Additionally, whitefly performance was monitored in an F2 population derived from a cross between Rivera and the susceptible white cabbage variety Christmas Drumhead. Significant QTL intervals were mapped on chromosome 2 and 9 for oviposition rate and whitefly adult survival, respectively. Several genes that were higher expressed in older plants and located in the identified QTL intervals were orthologous to Arabidopsis genes that have been related to ABA signaling, suggesting a role for ABA in the regulation of resistance towards whiteflies. Our results show that combining different omics approaches is a useful strategy to identify candidate genes underlying insect resistance.
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Affiliation(s)
- Colette Broekgaarden
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, the Netherlands
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
- Keygene N.V., Wageningen, the Netherlands
| | - Koen T. B. Pelgrom
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Johan Bucher
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Nicole M. van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Friedrich Schiller University Jena, Institute of Biodiversity, Jena, Germany
| | - Katharine Grosser
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Friedrich Schiller University Jena, Institute of Biodiversity, Jena, Germany
| | - Corné M. J. Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, the Netherlands
| | - Martijn van Kaauwen
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Greet Steenhuis
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Roeland E. Voorrips
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
| | | | - Ben Vosman
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Anja Worrich
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Friedrich Schiller University Jena, Institute of Biodiversity, Jena, Germany
| | - Saskia C. M. van Wees
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, the Netherlands
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20
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Černý M, Habánová H, Berka M, Luklová M, Brzobohatý B. Hydrogen Peroxide: Its Role in Plant Biology and Crosstalk with Signalling Networks. Int J Mol Sci 2018; 19:E2812. [PMID: 30231521 PMCID: PMC6163176 DOI: 10.3390/ijms19092812] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/13/2018] [Accepted: 09/15/2018] [Indexed: 12/30/2022] Open
Abstract
Hydrogen peroxide (H₂O₂) is steadily gaining more attention in the field of molecular biology research. It is a major REDOX (reduction⁻oxidation reaction) metabolite and at high concentrations induces oxidative damage to biomolecules, which can culminate in cell death. However, at concentrations in the low nanomolar range, H₂O₂ acts as a signalling molecule and in many aspects, resembles phytohormones. Though its signalling network in plants is much less well characterized than are those of its counterparts in yeast or mammals, accumulating evidence indicates that the role of H₂O₂-mediated signalling in plant cells is possibly even more indispensable. In this review, we summarize hydrogen peroxide metabolism in plants, the sources and sinks of this compound and its transport via peroxiporins. We outline H₂O₂ perception, its direct and indirect effects and known targets in the transcriptional machinery. We focus on the role of H₂O₂ in plant growth and development and discuss the crosstalk between it and phytohormones. In addition to a literature review, we performed a meta-analysis of available transcriptomics data which provided further evidence for crosstalk between H₂O₂ and light, nutrient signalling, temperature stress, drought stress and hormonal pathways.
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Affiliation(s)
- Martin Černý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
- Phytophthora Research Centre, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic.
| | - Hana Habánová
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
- CEITEC-Central European Institute of Technology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
- Brno Ph.D. Talent, South Moravian Centre for International Mobility, 602 00 Brno, Czech Republic.
| | - Miroslav Berka
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
| | - Markéta Luklová
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
- CEITEC-Central European Institute of Technology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
| | - Břetislav Brzobohatý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
- CEITEC-Central European Institute of Technology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
- Institute of Biophysics AS CR, 613 00 Brno, Czech Republic.
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21
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Alberto D, Couée I, Pateyron S, Sulmon C, Gouesbet G. Low doses of triazine xenobiotics mobilize ABA and cytokinin regulations in a stress- and low-energy-dependent manner. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 274:8-22. [PMID: 30080643 DOI: 10.1016/j.plantsci.2018.04.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/25/2018] [Accepted: 04/28/2018] [Indexed: 06/08/2023]
Abstract
The extent of residual contaminations of pesticides through drift, run-off and leaching is a potential threat to non-target plant communities. Arabidopsis thaliana responds to low doses of the herbicide atrazine, and of its degradation products, desethylatrazine and hydroxyatrazine, not only in the long term, but also under conditions of short-term exposure. In order to investigate underlying molecular mechanisms of low-dose responses and to decipher commonalities and specificities between different chemical treatments, parallel transcriptomic studies of the early effects of the atrazine-desethylatrazine-hydroxyatrazine chemical series were undertaken using whole-genome microarrays. All of the triazines under study produced coordinated and specific changes in gene expression. Hydroxyatrazine-responsive genes were mainly linked to root development, whereas atrazine and desethylatrazine mostly affected molecular signaling networks implicated in stress and hormone responses. Analysis of signaling-related genes, promoter sites and shared-function interaction networks highlighted the involvement of energy-, stress-, abscisic acid- and cytokinin-regulated processes, and emphasized the importance of cold-, heat- and drought-related signaling in the perception of low doses of triazines. These links between low-dose xenobiotic impacts and stress-hormone crosstalk pathways give novel insights into plant-pesticide interactions and plant-pollution interactions that are essential for toxicity evaluation in the context of environmental risk assessment.
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Affiliation(s)
- Diana Alberto
- Université de Rennes 1 / Centre National de la Recherche Scientifique, UMR 6553 ECOBIO, Rennes, F-35000, France
| | - Ivan Couée
- Université de Rennes 1 / Centre National de la Recherche Scientifique, UMR 6553 ECOBIO, Rennes, F-35000, France
| | - Stéphanie Pateyron
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Orsay, France; Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Orsay, France
| | - Cécile Sulmon
- Université de Rennes 1 / Centre National de la Recherche Scientifique, UMR 6553 ECOBIO, Rennes, F-35000, France
| | - Gwenola Gouesbet
- Université de Rennes 1 / Centre National de la Recherche Scientifique, UMR 6553 ECOBIO, Rennes, F-35000, France.
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22
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Van Ruyskensvelde V, Van Breusegem F, Van Der Kelen K. Post-transcriptional regulation of the oxidative stress response in plants. Free Radic Biol Med 2018; 122:181-192. [PMID: 29496616 DOI: 10.1016/j.freeradbiomed.2018.02.032] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/22/2018] [Accepted: 02/23/2018] [Indexed: 12/30/2022]
Abstract
Due to their sessile lifestyle, plants can be exposed to several kinds of stresses that will increase the production of reactive oxygen species (ROS), such as hydrogen peroxide, singlet oxygen, and hydroxyl radicals, in the plant cells and activate several signaling pathways that cause alterations in the cellular metabolism. Nevertheless, when ROS production outreaches a certain level, oxidative damage to nucleic acids, lipids, metabolites, and proteins will occur, finally leading to cell death. Until now, the most comprehensive and detailed readout of oxidative stress responses is undoubtedly obtained at the transcriptome level. However, transcript levels often do not correlate with the corresponding protein levels. Indeed, together with transcriptional regulations, post-transcriptional, translational, and/or post-translational regulations will shape the active proteome. Here, we review the current knowledge on the post-transcriptional gene regulation during the oxidative stress responses in planta.
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Affiliation(s)
- Valerie Van Ruyskensvelde
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium.
| | - Katrien Van Der Kelen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
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23
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Ha JH, Kim JH, Kim SG, Sim HJ, Lee G, Halitschke R, Baldwin IT, Kim JI, Park CM. Shoot phytochrome B modulates reactive oxygen species homeostasis in roots via abscisic acid signaling in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:790-798. [PMID: 29570885 DOI: 10.1111/tpj.13902] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 02/26/2018] [Accepted: 03/02/2018] [Indexed: 05/14/2023]
Abstract
Underground roots normally reside in darkness. However, they are often exposed to ambient light that penetrates through cracks in the soil layers which can occur due to wind, heavy rain or temperature extremes. In response to light exposure, roots produce reactive oxygen species (ROS) which promote root growth. It is known that ROS-induced growth promotion facilitates rapid escape of the roots from non-natural light. Meanwhile, long-term exposure of the roots to light elicits a ROS burst, which causes oxidative damage to cellular components, necessitating that cellular levels of ROS should be tightly regulated in the roots. Here we demonstrate that the red/far-red light photoreceptor phytochrome B (phyB) stimulates the biosynthesis of abscisic acid (ABA) in the shoots, and notably the shoot-derived ABA signals induce a peroxidase-mediated ROS detoxification reaction in the roots. Accordingly, while ROS accumulate in the roots of the phyb mutant that exhibits reduced primary root growth in the light, such an accumulation of ROS did not occur in the dark-grown phyb roots that exhibited normal growth. These observations indicate that mobile shoot-to-root ABA signaling links shoot phyB-mediated light perception with root ROS homeostasis to help roots adapt to unfavorable light exposure. We propose that ABA-mediated shoot-to-root phyB signaling contributes to the synchronization of shoot and root growth for optimal propagation and performance in plants.
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Affiliation(s)
- Jun-Ho Ha
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Ju-Heon Kim
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Sang-Gyu Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea
| | - Hee-Jung Sim
- Gyeongnam Department of Environmental Toxicology and Chemistry, Korea Institute of Toxicology, Gyeongnam, 52834, Korea
| | - Gisuk Lee
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Rayko Halitschke
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Jeong-Il Kim
- Department of Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju, 61186, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
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24
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Endo T, Shimada T, Nakata Y, Fujii H, Matsumoto H, Nakajima N, Ikoma Y, Omura M. Abscisic acid affects expression of citrus FT homologs upon floral induction by low temperature in Satsuma mandarin (Citrus unshiu Marc.). TREE PHYSIOLOGY 2018; 38:755-771. [PMID: 29182786 DOI: 10.1093/treephys/tpx145] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/20/2017] [Indexed: 06/07/2023]
Abstract
After a long juvenile period, citrus trees undergo seasonal flowering cycles. Under natural conditions, citrus flowering is regulated mainly by low ambient temperatures around 15-20 °C and water deficit stress. Recent studies have revealed that fluctuations in the expression of citrus homologs of FLOWERING LOCUS T (FT, encoding a flowering integrator) are correlated with their presumed role as flower-promoting signals. Previous ectopic expression analyses have demonstrated the flower-promoting function of citrus FT homologs. In this study, we examined whether abscisic acid (ABA) affects the expression of FT homologs and the flowering induced by low ambient temperatures. Application of exogenous ABA to potted Satsuma mandarin (Citrus unshiu Marc.) trees resulted in transient accumulation of citrus FT homolog transcripts. The promoter of one citrus FT homolog, CiFT3, was active in transgenic A. thaliana (Arabidopsis thaliana) and responded to exogenous and endogenous ABA. CiFT3 is preferentially expressed in shoots, and its expression was affected by flower-inductive treatments. Endogenous ABA accumulated in mandarin shoots during the floral induction period at 15 °C and under field conditions. The accumulation of ABA was correlated with the accumulation of FT homolog transcripts and flowering intensity. It was consistent with changes in the expression of genes related to ABA metabolism. The abundance of carotenoid precursors that serve as substrates for ABA biosynthesis decreased in leaves during the accumulation of ABA. Our data indicate that ABA and carotenoid precursors in leaves influence the flowering of mandarin trees induced by low temperature.
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Affiliation(s)
- Tomoko Endo
- Institute of Fruit Tree and Tea Science (NIFTS), National Agriculture and Food Research Organization (NARO), Shizuoka 424-0292, Japan
| | - Takehiko Shimada
- Institute of Fruit Tree and Tea Science (NIFTS), National Agriculture and Food Research Organization (NARO), Shizuoka 424-0292, Japan
| | - Yumi Nakata
- Institute of Fruit Tree and Tea Science (NIFTS), National Agriculture and Food Research Organization (NARO), Shizuoka 424-0292, Japan
| | - Hiroshi Fujii
- Institute of Fruit Tree and Tea Science (NIFTS), National Agriculture and Food Research Organization (NARO), Shizuoka 424-0292, Japan
| | - Hikaru Matsumoto
- Institute of Fruit Tree and Tea Science (NIFTS), National Agriculture and Food Research Organization (NARO), Shizuoka 424-0292, Japan
| | - Naoko Nakajima
- Institute of Fruit Tree and Tea Science (NIFTS), National Agriculture and Food Research Organization (NARO), Shizuoka 424-0292, Japan
| | - Yoshinori Ikoma
- Institute of Fruit Tree and Tea Science (NIFTS), National Agriculture and Food Research Organization (NARO), Shizuoka 424-0292, Japan
| | - Mitsuo Omura
- Faculty of Agriculture, Shizuoka University, Shizuoka 422-8529, Japan
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25
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Nwugo CC, Sengoda VG, Tian L, Lin H. Characterization of physiological and molecular processes associated with potato response to Zebra chip disease. HORTICULTURE RESEARCH 2017; 4:17069. [PMID: 29238599 PMCID: PMC5717366 DOI: 10.1038/hortres.2017.69] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 10/22/2017] [Accepted: 10/30/2017] [Indexed: 05/29/2023]
Abstract
Transcriptional analyses identified molecular mechanisms associated with the response of leaf and root potato tissues to 'Candidatus. Liberibacter solanacearum' (Lso) infection, presumptive causal agent of zebra chip disease (ZC). Putative Lso infection affected several host processes including defense response-, regulation-, starch metabolism- and energy production-related processes. Interestingly, while proteinase inhibitors were strongly upregulated in leaf tissues, a concomitant downregulation was observed in root tissues. Quantitative polymerase chain reaction (qPCR) analysis suggests that alternative splicing might play a role. Furthermore, the transcriptional expression of redox homeostasis-related genes, including superoxide dismutase, showed the most inconsistent response to Lso in leaf and root tissues, highlighting potential targets of Lso susceptibility. Additionally, a net increase in gene expression in ZC-affected tissues despite the concomitant downregulation of photosynthesis-related processes, suggests a putative Lso-mediated low resource-use-efficiency. Subsequent nutritional analyses revealed a hypothesized Lso-mediated increase in nutrient accumulation, particularly a 210 and 108% increases in the potassium concentration of ZC-affected leaf and root tissues, respectively, suggesting an important role for potassium in ZC pathophysiology. This study highlights insights of above and below ground tissues in molecular and physiological aspects associated with potato response to ZC.
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Affiliation(s)
- Chika C Nwugo
- San Joaquin Valley Agricultural Sciences Center, USDA-ARS, Parlier, CA 93658, USA
| | - Venkatesan G Sengoda
- California Seed and Plant Labs, Sacramento, CA 95668, USA
- USDA-ARS, Yakima Agricultural Research Laboratory, Wapato, WA 98951, USA
| | - Li Tian
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Hong Lin
- San Joaquin Valley Agricultural Sciences Center, USDA-ARS, Parlier, CA 93658, USA
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26
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Waese J, Fan J, Pasha A, Yu H, Fucile G, Shi R, Cumming M, Kelley LA, Sternberg MJ, Krishnakumar V, Ferlanti E, Miller J, Town C, Stuerzlinger W, Provart NJ. ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology. THE PLANT CELL 2017; 29:1806-1821. [PMID: 28808136 PMCID: PMC5590499 DOI: 10.1105/tpc.17.00073] [Citation(s) in RCA: 219] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 07/17/2017] [Accepted: 08/09/2017] [Indexed: 05/17/2023]
Abstract
A big challenge in current systems biology research arises when different types of data must be accessed from separate sources and visualized using separate tools. The high cognitive load required to navigate such a workflow is detrimental to hypothesis generation. Accordingly, there is a need for a robust research platform that incorporates all data and provides integrated search, analysis, and visualization features through a single portal. Here, we present ePlant (http://bar.utoronto.ca/eplant), a visual analytic tool for exploring multiple levels of Arabidopsis thaliana data through a zoomable user interface. ePlant connects to several publicly available web services to download genome, proteome, interactome, transcriptome, and 3D molecular structure data for one or more genes or gene products of interest. Data are displayed with a set of visualization tools that are presented using a conceptual hierarchy from big to small, and many of the tools combine information from more than one data type. We describe the development of ePlant in this article and present several examples illustrating its integrative features for hypothesis generation. We also describe the process of deploying ePlant as an "app" on Araport. Building on readily available web services, the code for ePlant is freely available for any other biological species research.
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Affiliation(s)
- Jamie Waese
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Jim Fan
- Department of Computer Science, University of Waterloo, Ontario N2L 3G1, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Hans Yu
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Geoffrey Fucile
- SIB Swiss Institute of Bioinformatics, sciCORE Computing Center, University of Basel, CH-4056 Basel, Switzerland
| | - Ruian Shi
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Matthew Cumming
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | | | | | | | - Erik Ferlanti
- Araport.org/J. Craig Venter Institute, Rockville, Maryland 20850
| | - Jason Miller
- Araport.org/J. Craig Venter Institute, Rockville, Maryland 20850
| | - Chris Town
- Araport.org/J. Craig Venter Institute, Rockville, Maryland 20850
| | - Wolfgang Stuerzlinger
- School of Interactive Arts and Technology, Simon Fraser University, British Columbia V3T 0A3, Canada
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
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27
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Bi B, Tang J, Han S, Guo J, Miao Y. Sinapic acid or its derivatives interfere with abscisic acid homeostasis during Arabidopsis thaliana seed germination. BMC PLANT BIOLOGY 2017; 17:99. [PMID: 28587634 PMCID: PMC5461752 DOI: 10.1186/s12870-017-1048-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 05/25/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND Sinapic acid and its esters have broad functions in different stages of seed germination and plant development and are thought to play a role in protecting against ultraviolet irradiation. To better understand the interactions between sinapic acid esters and seed germination processes in response to various stresses, we analyzed the role of the plant hormone abscisic acid (ABA) in the regulation of sinapic acid esters involved in seed germination and early seedling growth. RESULTS We found that exogenous sinapic acid promotes seed germination in a dose-dependent manner in Arabidopsis thaliana. High-performance liquid chromatography mass spectrometry analysis showed that exogenous sinapic acid increased the sinapoylcholine content of imbibed seeds. Furthermore, sinapic acid affected ABA catabolism, resulting in reduced ABA levels and increased levels of the ABA-glucose ester. Using mutants deficient in the synthesis of sinapate esters, we showed that the germination of mutant sinapoylglucose accumulator 2 (sng2) and bright trichomes 1 (brt1) seeds was more sensitive to ABA than the wild-type. Moreover, Arabidopsis mutants deficient in either abscisic acid deficient 2 (ABA2) or abscisic acid insensitive 3 (ABI3) displayed increased expression of the sinapoylglucose:choline sinapoyltransferase (SCT) and sinapoylcholine esterase (SCE) genes with sinapic acid treatment. This treatment also affected the accumulation of sinapoylcholine and free choline during seed germination. CONCLUSIONS We demonstrated that sinapoylcholine, which constitutes the major phenolic component in seeds among various minor sinapate esters, affected ABA homeostasis during seed germination and early seedling growth in Arabidopsis. Our findings provide insights into the role of sinapic acid and its esters in regulating ABA-mediated inhibition of Arabidopsis seed germination in response to drought stress.
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Affiliation(s)
- Baodi Bi
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Jingliang Tang
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Shuang Han
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Jinggong Guo
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Yuchen Miao
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng, 475001, China.
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28
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Soto-Suárez M, Serrato AJ, Rojas-González JA, Bautista R, Sahrawy M. Transcriptomic and proteomic approach to identify differentially expressed genes and proteins in Arabidopsis thaliana mutants lacking chloroplastic 1 and cytosolic FBPases reveals several levels of metabolic regulation. BMC PLANT BIOLOGY 2016; 16:258. [PMID: 27905870 PMCID: PMC5134223 DOI: 10.1186/s12870-016-0945-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/22/2016] [Indexed: 05/11/2023]
Abstract
BACKGROUND During the photosynthesis, two isoforms of the fructose-1,6-bisphosphatase (FBPase), the chloroplastidial (cFBP1) and the cytosolic (cyFBP), catalyse the first irreversible step during the conversion of triose phosphates (TP) to starch or sucrose, respectively. Deficiency in cyFBP and cFBP1 isoforms provokes an imbalance of the starch/sucrose ratio, causing a dramatic effect on plant development when the plastidial enzyme is lacking. RESULTS We study the correlation between the transcriptome and proteome profile in rosettes and roots when cFBP1 or cyFBP genes are disrupted in Arabidopsis thaliana knock-out mutants. By using a 70-mer oligonucleotide microarray representing the genome of Arabidopsis we were able to identify 1067 and 1243 genes whose expressions are altered in the rosettes and roots of the cfbp1 mutant respectively; whilst in rosettes and roots of cyfbp mutant 1068 and 1079 genes are being up- or down-regulated respectively. Quantitative real-time PCR validated 100% of a set of 14 selected genes differentially expressed according to our microarray analysis. Two-dimensional (2-D) gel electrophoresis-based proteomic analysis revealed quantitative differences in 36 and 26 proteins regulated in rosettes and roots of cfbp1, respectively, whereas the 18 and 48 others were regulated in rosettes and roots of cyfbp mutant, respectively. The genes differentially expressed and the proteins more or less abundant revealed changes in protein metabolism, RNA regulation, cell signalling and organization, carbon metabolism, redox regulation, and transport together with biotic and abiotic stress. Notably, a significant set (25%) of the proteins identified were also found to be regulated at a transcriptional level. CONCLUSION This transcriptomic and proteomic analysis is the first comprehensive and comparative study of the gene/protein re-adjustment that occurs in photosynthetic and non-photosynthetic organs of Arabidopsis mutants lacking FBPase isoforms.
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Affiliation(s)
- Mauricio Soto-Suárez
- Departamento de Bioquímica, Biología Molecular y Celular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, 18008 Granada, Spain
- Present address: Corporación Colombiana de Investigación Agropecuaria, CORPOICA, Km 14 vía Mosquera, Mosquera, Cundinamarca Colombia
| | - Antonio J. Serrato
- Departamento de Bioquímica, Biología Molecular y Celular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, 18008 Granada, Spain
| | - José A. Rojas-González
- Departamento de Bioquímica, Biología Molecular y Celular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, 18008 Granada, Spain
| | - Rocío Bautista
- Plataforma Andaluza de Bioinformática/SCBI, Edificio de Bioinnovación, Parque Tecnológico de Andalucía, Universidad de Málaga, C/ Severo Ochoa 34, 29590 Campanillas, Spain
| | - Mariam Sahrawy
- Departamento de Bioquímica, Biología Molecular y Celular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, 18008 Granada, Spain
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29
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Thalmann M, Pazmino D, Seung D, Horrer D, Nigro A, Meier T, Kölling K, Pfeifhofer HW, Zeeman SC, Santelia D. Regulation of Leaf Starch Degradation by Abscisic Acid Is Important for Osmotic Stress Tolerance in Plants. THE PLANT CELL 2016; 28:1860-78. [PMID: 27436713 PMCID: PMC5006701 DOI: 10.1105/tpc.16.00143] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 07/05/2016] [Accepted: 07/19/2016] [Indexed: 05/18/2023]
Abstract
Starch serves functions that range over a timescale of minutes to years, according to the cell type from which it is derived. In guard cells, starch is rapidly mobilized by the synergistic action of β-AMYLASE1 (BAM1) and α-AMYLASE3 (AMY3) to promote stomatal opening. In the leaves, starch typically accumulates gradually during the day and is degraded at night by BAM3 to support heterotrophic metabolism. During osmotic stress, starch is degraded in the light by stress-activated BAM1 to release sugar and sugar-derived osmolytes. Here, we report that AMY3 is also involved in stress-induced starch degradation. Recently isolated Arabidopsis thaliana amy3 bam1 double mutants are hypersensitive to osmotic stress, showing impaired root growth. amy3 bam1 plants close their stomata under osmotic stress at similar rates as the wild type but fail to mobilize starch in the leaves. (14)C labeling showed that amy3 bam1 plants have reduced carbon export to the root, affecting osmolyte accumulation and root growth during stress. Using genetic approaches, we further demonstrate that abscisic acid controls the activity of BAM1 and AMY3 in leaves under osmotic stress through the AREB/ABF-SnRK2 kinase-signaling pathway. We propose that differential regulation and isoform subfunctionalization define starch-adaptive plasticity, ensuring an optimal carbon supply for continued growth under an ever-changing environment.
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Affiliation(s)
- Matthias Thalmann
- Department of Plant and Microbial Biology, University of Zürich, 8008 Zürich, Switzerland
| | - Diana Pazmino
- Department of Plant and Microbial Biology, University of Zürich, 8008 Zürich, Switzerland
| | - David Seung
- Institute for Agricultural Sciences, ETH Zürich, 8092 Zürich, Switzerland
| | - Daniel Horrer
- Department of Plant and Microbial Biology, University of Zürich, 8008 Zürich, Switzerland
| | - Arianna Nigro
- Department of Plant and Microbial Biology, University of Zürich, 8008 Zürich, Switzerland
| | - Tiago Meier
- Department of Plant and Microbial Biology, University of Zürich, 8008 Zürich, Switzerland
| | - Katharina Kölling
- Institute for Agricultural Sciences, ETH Zürich, 8092 Zürich, Switzerland
| | - Hartwig W Pfeifhofer
- Institut für Pflanzenwissenschaften, Karl-Franzens-Universität Graz, 8010 Graz, Austria
| | - Samuel C Zeeman
- Institute for Agricultural Sciences, ETH Zürich, 8092 Zürich, Switzerland
| | - Diana Santelia
- Department of Plant and Microbial Biology, University of Zürich, 8008 Zürich, Switzerland
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30
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Sah SK, Reddy KR, Li J. Abscisic Acid and Abiotic Stress Tolerance in Crop Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:571. [PMID: 27200044 DOI: 10.3389/fpls.2016.00571/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 04/13/2016] [Indexed: 05/27/2023]
Abstract
Abiotic stress is a primary threat to fulfill the demand of agricultural production to feed the world in coming decades. Plants reduce growth and development process during stress conditions, which ultimately affect the yield. In stress conditions, plants develop various stress mechanism to face the magnitude of stress challenges, although that is not enough to protect them. Therefore, many strategies have been used to produce abiotic stress tolerance crop plants, among them, abscisic acid (ABA) phytohormone engineering could be one of the methods of choice. ABA is an isoprenoid phytohormone, which regulates various physiological processes ranging from stomatal opening to protein storage and provides adaptation to many stresses like drought, salt, and cold stresses. ABA is also called an important messenger that acts as the signaling mediator for regulating the adaptive response of plants to different environmental stress conditions. In this review, we will discuss the role of ABA in response to abiotic stress at the molecular level and ABA signaling. The review also deals with the effect of ABA in respect to gene expression.
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Affiliation(s)
- Saroj K Sah
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Mississippi State, Mississippi, MS, USA
| | - Kambham R Reddy
- Department of Plant and Soil Sciences, Mississippi State University Mississippi State, Mississippi, MS, USA
| | - Jiaxu Li
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Mississippi State, Mississippi, MS, USA
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31
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Sah SK, Reddy KR, Li J. Abscisic Acid and Abiotic Stress Tolerance in Crop Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:571. [PMID: 27200044 PMCID: PMC4855980 DOI: 10.3389/fpls.2016.00571] [Citation(s) in RCA: 563] [Impact Index Per Article: 70.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 04/13/2016] [Indexed: 05/17/2023]
Abstract
Abiotic stress is a primary threat to fulfill the demand of agricultural production to feed the world in coming decades. Plants reduce growth and development process during stress conditions, which ultimately affect the yield. In stress conditions, plants develop various stress mechanism to face the magnitude of stress challenges, although that is not enough to protect them. Therefore, many strategies have been used to produce abiotic stress tolerance crop plants, among them, abscisic acid (ABA) phytohormone engineering could be one of the methods of choice. ABA is an isoprenoid phytohormone, which regulates various physiological processes ranging from stomatal opening to protein storage and provides adaptation to many stresses like drought, salt, and cold stresses. ABA is also called an important messenger that acts as the signaling mediator for regulating the adaptive response of plants to different environmental stress conditions. In this review, we will discuss the role of ABA in response to abiotic stress at the molecular level and ABA signaling. The review also deals with the effect of ABA in respect to gene expression.
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Affiliation(s)
- Saroj K. Sah
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, Mississippi, MS, USA
| | - Kambham R. Reddy
- Department of Plant and Soil Sciences, Mississippi State UniversityMississippi State, Mississippi, MS, USA
| | - Jiaxu Li
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, Mississippi, MS, USA
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32
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Abstract
Gibberellins (GAs) are plant hormones that promote a wide range of developmental processes. While GA signalling is well understood, little is known about how GA is transported or how GA distribution is regulated. Here we utilize fluorescently labelled GAs (GA-Fl) to screen for Arabidopsis mutants deficient in GA transport. We show that the NPF3 transporter efficiently transports GA across cell membranes in vitro and GA-Fl in vivo. NPF3 is expressed in root endodermis and repressed by GA. NPF3 is targeted to the plasma membrane and subject to rapid BFA-dependent recycling. We show that abscisic acid (ABA), an antagonist of GA, is also transported by NPF3 in vitro. ABA promotes NPF3 expression and GA-Fl uptake in plants. On the basis of these results, we propose that GA distribution and activity in Arabidopsis is partly regulated by NPF3 acting as an influx carrier and that GA-ABA interaction may occur at the level of transport.
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33
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Yoo MJ, Ma T, Zhu N, Liu L, Harmon AC, Wang Q, Chen S. Genome-wide identification and homeolog-specific expression analysis of the SnRK2 genes in Brassica napus guard cells. PLANT MOLECULAR BIOLOGY 2016; 91:211-27. [PMID: 26898295 DOI: 10.1007/s11103-016-0456-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/15/2016] [Indexed: 05/22/2023]
Abstract
Sucrose non-fermenting-1-related protein kinase 2 (SnRK2) proteins constitute a small plant-specific serine/threonine kinase family involved in abscisic acid (ABA) signaling and plant responses to biotic and abiotic stresses. Although SnRK2s have been well-studied in Arabidopsis thaliana, little is known about SnRK2s in Brassica napus. Here we identified 30 putative sequences encoding 10 SnRK2 proteins in the B. napus genome and the expression profiles of a subset of 14 SnRK2 genes in guard cells of B. napus. In agreement with its polyploid origin, B. napus maintains both homeologs from its diploid parents. The results of quantitative real-time PCR (qRT-PCR) and reanalysis of RNA-Seq data showed that certain BnSnRK2 genes were commonly expressed in leaf tissues in different varieties of B. napus. In particular, qRT-PCR results showed that 12 of the 14 BnSnRK2s responded to drought stress in leaves and in ABA-treated guard cells. Among them, BnSnRK2.4 and BnSnRK2.6 were of interest because of their robust responsiveness to ABA treatment and drought stress. Notably, BnSnRK2 genes exhibited up-regulation of different homeologs, particularly in response to abiotic stress. The homeolog expression bias in BnSnRK2 genes suggests that parental origin of genes might be responsible for efficient regulation of stress responses in polyploids. This work has laid a foundation for future functional characterization of the different BnSnKR2 homeologs in B. napus and its parents, especially their functions in guard cell signaling and stress responses.
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Affiliation(s)
- Mi-Jeong Yoo
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Tianyi Ma
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Ning Zhu
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Lihong Liu
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, 310058, China
| | - Alice C Harmon
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Qiaomei Wang
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, 310058, China
| | - Sixue Chen
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA.
- Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL, 32611, USA.
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32610, USA.
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Wang J, Yao L, Li B, Meng Y, Ma X, Lai Y, Si E, Ren P, Yang K, Shang X, Wang H. Comparative Proteomic Analysis of Cultured Suspension Cells of the Halophyte Halogeton glomeratus by iTRAQ Provides Insights into Response Mechanisms to Salt Stress. FRONTIERS IN PLANT SCIENCE 2016; 7:110. [PMID: 26904073 PMCID: PMC4746295 DOI: 10.3389/fpls.2016.00110] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 01/21/2016] [Indexed: 05/23/2023]
Abstract
Soil salinity severely threatens land use capability and crop yields worldwide. An analysis of the molecular mechanisms of salt tolerance in halophytes will contribute to the development of salt-tolerant crops. In this study, a combination of physiological characteristics and iTRAQ-based proteomic approaches was conducted to investigate the molecular mechanisms underlying the salt response of suspension cell cultures of halophytic Halogeton glomeratus. These cells showed halophytic growth responses comparable to those of the whole plant. In total, 97 up-regulated proteins and 192 down-regulated proteins were identified as common to both 200 and 400 mM NaCl concentration treatments. Such salinity responsive proteins were mainly involved in energy, carbohydrate metabolism, stress defense, protein metabolism, signal transduction, cell growth, and cytoskeleton metabolism. Effective regulatory protein expression related to energy, stress defense, and carbohydrate metabolism play important roles in the salt-tolerance of H. glomeratus suspension cell cultures. However, known proteins regulating Na(+) efflux from the cytoplasm and its compartmentalization into the vacuole did not change significantly under salinity stress suggesting our existing knowledge concerning Na(+) extrusion and compartmentalization in halophytes needs to be evaluated further. Such data are discussed in the context of our current understandings of the mechanisms involved in the salinity response of the halophyte, H. glomeratus.
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Affiliation(s)
- Juncheng Wang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm EnhancementLanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural UniversityLanzhou, China
| | - Lirong Yao
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm EnhancementLanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural UniversityLanzhou, China
| | - Baochun Li
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm EnhancementLanzhou, China
- Department of Botany, College of Life Science and Technology, Gansu Agricultural UniversityLanzhou, China
| | - Yaxiong Meng
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm EnhancementLanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural UniversityLanzhou, China
| | - Xiaole Ma
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm EnhancementLanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural UniversityLanzhou, China
| | - Yong Lai
- Department of Agriculture and Forestry, College of Agriculture and Animal Husbandry, Qinghai UniversityXining, China
| | - Erjing Si
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm EnhancementLanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural UniversityLanzhou, China
| | - Panrong Ren
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm EnhancementLanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural UniversityLanzhou, China
| | - Ke Yang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm EnhancementLanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural UniversityLanzhou, China
| | - Xunwu Shang
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural UniversityLanzhou, China
| | - Huajun Wang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm EnhancementLanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural UniversityLanzhou, China
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Circulating Fibroblast Growth Factor 21 Is A Sensitive Biomarker for Severe Ischemia/reperfusion Injury in Patients with Liver Transplantation. Sci Rep 2016; 6:19776. [PMID: 26806156 PMCID: PMC4726235 DOI: 10.1038/srep19776] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 11/05/2015] [Indexed: 02/07/2023] Open
Abstract
Hepatic ischemia/reperfusion (I/R) injury is a major cause of morbidity and mortality after liver surgery. Therefore, it is important to identity reliable biomarkers to assist early diagnosis of hepatic I/R injury. This study aimed to investigate the potential of serum levels of fibroblast growth factor 21 (FGF21) as a biomarker for hepatic I/R injury in patients with liver transplantation. Two independent cohorts of liver transplantation patients were recruited for determination of serum levels of FGF21, ALT, and AST. The results demonstrated that serum FGF21 at 2 hours post-reperfusion in cohort-1 exhibited an approximately 20-fold elevation relative to those in healthy subjects. In blood samples dynamically collected in cohort-2, a dramatic increase in serum FGF21 levels (~25-fold) was observed at two hours after surgery, whereas the peak levels of serum ALT and AST were detected only after 24 hours. Temporal correlation analysis demonstrated a significant association of peak serum levels of FGF21 at 2 hours with the magnitude of the increase in both serum ALT and AST levels at 24 hours post transplantation. In conclusion, serum FGF21 may represent a sensitive and specific prognostic biomarker for early detection of I/R injury in patients with liver transplantation.
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Černý M, Novák J, Habánová H, Cerna H, Brzobohatý B. Role of the proteome in phytohormonal signaling. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:1003-15. [PMID: 26721743 DOI: 10.1016/j.bbapap.2015.12.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 11/30/2015] [Accepted: 12/16/2015] [Indexed: 02/07/2023]
Abstract
Phytohormones are orchestrators of plant growth and development. A lot of time and effort has been invested in attempting to comprehend their complex signaling pathways but despite success in elucidating some key components, molecular mechanisms in the transduction pathways are far from being resolved. The last decade has seen a boom in the analysis of phytohormone-responsive proteins. Abscisic acid, auxin, brassinosteroids, cytokinin, ethylene, gibberellins, nitric oxide, oxylipins, strigolactones, salicylic acid--all have been analyzed to various degrees. For this review, we collected data from proteome-wide analyses resulting in a list of over 2000 annotated proteins from Arabidopsis proteomics and nearly 500 manually filtered protein families merged from all the data available from different species. We present the currently accepted model of phytohormone signaling, highlight the contributions made by proteomic-based research and describe the key nodes in phytohormone signaling networks, as revealed by proteome analysis. These include ubiquitination and proteasome mediated degradation, calcium ion signaling, redox homeostasis, and phosphoproteome dynamics. Finally, we discuss potential pitfalls and future perspectives in the field. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Affiliation(s)
- Martin Černý
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
| | - Jan Novák
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
| | - Hana Habánová
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
| | - Hana Cerna
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
| | - Břetislav Brzobohatý
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
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Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits. Mol Genet Genomics 2015; 291:323-36. [PMID: 26334613 DOI: 10.1007/s00438-015-1111-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 08/24/2015] [Indexed: 10/23/2022]
Abstract
Studies in diploid parental species of polyploid plants are important to understand their contributions to the formation of plant and species evolution. Coffea eugenioides is a diploid species that is considered to be an ancestor of allopolyploid Coffea arabica together with Coffea canephora. Despite its importance in the evolutionary history of the main economic species of coffee, no study has focused on C. eugenioides molecular genetics. RNA-seq creates the possibility to generate reference transcriptomes and identify coding genes and potential candidates related to important agronomic traits. Therefore, the main objectives were to obtain a global overview of transcriptionally active genes in this species using next-generation sequencing and to analyze specific genes that were highly expressed in leaves and fruits with potential exploratory characteristics for breeding and understanding the evolutionary biology of coffee. A de novo assembly generated 36,935 contigs that were annotated using eight databases. We observed a total of ~5000 differentially expressed genes between leaves and fruits. Several genes exclusively expressed in fruits did not exhibit similarities with sequences in any database. We selected ten differentially expressed unigenes in leaves and fruits to evaluate transcriptional profiles using qPCR. Our study provides the first gene catalog for C. eugenioides and enhances the knowledge concerning the mechanisms involved in the C. arabica homeologous. Furthermore, this work will open new avenues for studies into specific genes and pathways in this species, especially related to fruit, and our data have potential value in assisted breeding applications.
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Geilen K, Böhmer M. Dynamic subnuclear relocalisation of WRKY40 in response to Abscisic acid in Arabidopsis thaliana. Sci Rep 2015; 5:13369. [PMID: 26293691 PMCID: PMC4642543 DOI: 10.1038/srep13369] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 07/23/2015] [Indexed: 11/20/2022] Open
Abstract
WRKY18, WRKY40 and WRKY60 are members of the WRKY transcription factor family and function as transcriptional regulators in ABA signal transduction in Arabidopsis thaliana. Here we show that WRKY18 and WRKY40, but not WRKY60, co-localise with PIF3, PIF4 and PHYB to Phytochrome B-containing nuclear bodies (PNBs). Localisation to the PNBs is phosphorylation-dependent and is inhibited by the general Ser/Thr-kinase inhibitor Staurosporine. Upon ABA treatment, WRKY40 relocalises from PNBs to the nucleoplasm in an OST1-dependent manner. This stimulus-induced relocalisation was not observed in response to other abiotic or biotic stimuli, including NaCl, MeJA or flg22 treatment. Bimolecular fluorescence complementation experiments indicate that while PIF3, PIF4 and PHYB physically interact in these bodies, PHYB, PIF3 and PIF4 do not interact with the two WRKY transcription factors, which may suggest a more general role for these bodies in regulation of transcriptional activity.
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Affiliation(s)
- Katja Geilen
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität, Münster, Germany
| | - Maik Böhmer
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität, Münster, Germany
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Fukao Y. Discordance between protein and transcript levels detected by selected reaction monitoring. PLANT SIGNALING & BEHAVIOR 2015; 10:e1017697. [PMID: 26039477 PMCID: PMC4623550 DOI: 10.1080/15592324.2015.1017697] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 02/04/2015] [Accepted: 02/05/2015] [Indexed: 05/25/2023]
Abstract
Expression levels between transcript and protein are not always correlated. In the present study, the abundance of protein PDR9/ABCG37 in 3 Arabidopsis pdr9/abcg37 mutant alleles was evaluated using selected reaction monitoring analysis. The results showed that protein and mRNA expression levels were similar in 2 mutant alleles. The mRNA expression levels in another mutant, determined by both semi-quantitative and quantitative RT-PCR, were similar to the wild-type, although the abundance of protein was about half the abundance of the wild-type. These results suggested that using only mRNA expression levels to infer protein abundance, compare mutants or responses to various stimuli may lead to incorrect interpretation and conclusions.
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Affiliation(s)
- Yoichiro Fukao
- Plant Global Education Project; Graduate School of Biological Sciences; Nara Institute of Science and Technology; Takayama, Ikoma, Japan
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40
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Shabala S, Pottosin I. Regulation of potassium transport in plants under hostile conditions: implications for abiotic and biotic stress tolerance. PHYSIOLOGIA PLANTARUM 2014; 151:257-79. [PMID: 24506225 DOI: 10.1111/ppl.12165] [Citation(s) in RCA: 274] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/15/2013] [Accepted: 01/13/2014] [Indexed: 05/18/2023]
Abstract
Intracellular potassium homeostasis is a prerequisite for the optimal operation of plant metabolic machinery and plant's overall performance. It is controlled by K(+) uptake, efflux and intracellular and long-distance relocation, mediated by a large number of K(+) -selective and non-selective channels and transporters located at both plasma and vacuolar membranes. All abiotic and biotic stresses result in a significant disturbance to intracellular potassium homeostasis. In this work, we discuss molecular mechanisms and messengers mediating potassium transport and homeostasis focusing on four major environmental stresses: salinity, drought, flooding and biotic factors. We argue that cytosolic K(+) content may be considered as one of the 'master switches' enabling plant transition from the normal metabolism to 'hibernated state' during first hours after the stress exposure and then to a recovery phase. We show that all these stresses trigger substantial disturbance to K(+) homeostasis and provoke a feedback control on K(+) channels and transporters expression and post-translational regulation of their activity, optimizing K(+) absorption and usage, and, at the extreme end, assisting the programmed cell death. We discuss specific modes of regulation of the activity of K(+) channels and transporters by membrane voltage, intracellular Ca(2+) , reactive oxygen species, polyamines, phytohormones and gasotransmitters, and link this regulation with plant-adaptive responses to hostile environments.
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Affiliation(s)
- Sergey Shabala
- School of Agricultural Science, University of Tasmania, Hobart, Tas, 7001, Australia
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Abscisic acid sensor RCAR7/PYL13, specific regulator of protein phosphatase coreceptors. Proc Natl Acad Sci U S A 2014; 111:5741-6. [PMID: 24706923 DOI: 10.1073/pnas.1322085111] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The plant hormone abscisic acid (ABA) acts both as a developmental signal and as an integrator of environmental cues such as drought and cold. ABA perception recruits an ABA-binding regulatory component [regulatory component of ABA receptor (RCAR)/PYR1/PYL] and an associated protein phosphatase 2C (PP2C). Phytohormone binding inactivates the phosphatase activity of the coreceptor, permitting phosphorelay of the ABA signal via downstream protein kinases. RCARs and PP2C coreceptors are represented by small protein families comprising 14 and 9 members in Arabidopsis, respectively. The specificity of the RCAR-PP2C interaction and the constraints contributing to specific combinations are poorly understood. In this contribution, we analyzed RCAR7/PYL13, which is characterized by three variant amino acid residues in the conserved ABA-binding pocket. RCAR7 regulated the phosphatase activity of the PP2Cs ABI1, ABI2, and PP2CA in vitro at nanomolar ABA levels; however, it was unable to regulate the structurally related hypersensitive to ABA 1 (HAB1). Site-directed mutagenesis of HAB1 established ABA-dependent regulation by RCAR7. Conversion of the noncanonical amino acid residues of RCAR7 into the consensus ABA-binding pocket did not perceptibly change receptor function. Ectopic expression of RCAR7 in Arabidopsis resulted in ABA hypersensitivity affecting gene regulation, seed germination, and stomatal closure. The RCAR7 loss-of-function mutant revealed no changes in ABA responses, similar to the RCAR9 knockout line, whereas the combined deficiency of RCAR7 and RCAR9 resulted in ABA-insensitive seed germination. The study shows a role of RCAR7 in early plant development, proves its ABA receptor function, and identifies structural constraints of RCAR7-PP2C interaction.
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Wu L, Hu X, Tang H, Han Z, Chen Y. Valid application of western blotting. Mol Biol Rep 2014; 41:3517-20. [PMID: 24510387 DOI: 10.1007/s11033-014-3215-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 01/28/2014] [Indexed: 11/27/2022]
Abstract
Western blotting is a powerful and commonly used tool to identify and quantify a specific protein in a complex mixture. However, the systematic errors in the application of western blotting analysis are frequently to be found, which may compromise the interpretation of results. To make a valid application of western blotting, it is essential to begin with three independent biological replicates. Subsequently, a more reliable normalization method is in urgent need for western blotting analysis and using reference proteins is the currently preferred method of normalization. Additionally, identification of valid reference proteins is crucial for western blotting analysis and it should be examined carefully in relation to the cell or tissue types when using housekeeping proteins as internal standards.
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Affiliation(s)
- Liuji Wu
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain Crops, Zhengzhou, 450002, China
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Wu L, Wang S, Chen X, Wang X, Wu L, Zu X, Chen Y. Proteomic and phytohormone analysis of the response of maize (Zea mays L.) seedlings to sugarcane mosaic virus. PLoS One 2013; 8:e70295. [PMID: 23894637 PMCID: PMC3720893 DOI: 10.1371/journal.pone.0070295] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Accepted: 06/22/2013] [Indexed: 12/27/2022] Open
Abstract
Background Sugarcane mosaic virus (SCMV) is an important virus pathogen in crop production, causing serious losses in grain and forage yields in susceptible cultivars. Control strategies have been developed, but only marginal successes have been achieved. For the efficient control of this virus, a better understanding of its interactions and associated resistance mechanisms at the molecular level is required. Methodology/Principal Findings The responses of resistant and susceptible genotypes of maize to SCMV and the molecular basis of the resistance were studied using a proteomic approach based on two-dimensional polyacrylamide gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS/MS) analysis. Ninety-six protein spots showed statistically significant differences in intensity after SCMV inoculation. The classification of differentially expressed proteins showed that SCMV-responsive proteins were mainly involved in energy and metabolism, stress and defense responses, and photosynthesis. Most of the proteins identified were located in chloroplasts, chloroplast membranes, and the cytoplasm. Analysis of changes in phytohormone levels after virus inoculation suggested that salicylic acid, abscisic acid, jasmonic acid, and azelaic acid may played important roles in the maize response to SCMV infection. Conclusions/Significance Among these identified proteins, 19 have not been identified previously as virus-responsive proteins, and seven were new and did not have assigned functions. These proteins may be candidate proteins for future investigation, and they may present new biological functions and play important roles in plant-virus interactions. The behavioural patterns of the identified proteins suggest the existence of defense mechanisms operating during the early stages of infection that differed in two genotypes. In addition, there are overlapping and specific phytohormone responses to SCMV infection between resistant and susceptible maize genotypes. This study may provide important insights into the molecular events during plant responses to virus infection.
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Affiliation(s)
- Liuji Wu
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain Crops, Zhengzhou, China
- Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Zhengzhou, China
| | - Shunxi Wang
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain Crops, Zhengzhou, China
| | - Xiao Chen
- Henan Province Seed Control Station, Zhengzhou, China
| | - Xintao Wang
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain Crops, Zhengzhou, China
| | - Liancheng Wu
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain Crops, Zhengzhou, China
- Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Zhengzhou, China
| | - Xiaofeng Zu
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain Crops, Zhengzhou, China
| | - Yanhui Chen
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain Crops, Zhengzhou, China
- Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Zhengzhou, China
- * E-mail:
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Naika M, Shameer K, Sowdhamini R. Comparative analyses of stress-responsive genes in Arabidopsis thaliana: insight from genomic data mining, functional enrichment, pathway analysis and phenomics. MOLECULAR BIOSYSTEMS 2013; 9:1888-908. [PMID: 23645342 DOI: 10.1039/c3mb70072k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Biotic and abiotic stresses adversely affect agriculture by reducing crop growth and productivity worldwide. To investigate the abiotic stress-responsive genes in Arabidopsis thaliana, we compiled a dataset of stress signals and differentially upregulated genes (>= 2.5 fold change) from Stress-responsive transcription Factors DataBase (STIFDB) with additional set of stress signals and genes curated from PubMed and Gene Expression Omnibus. A dataset of 3091 genes differentially upregulated due to 14 different stress signals (abscisic acid, aluminum, cold, cold-drought-salt, dehydration, drought, heat, iron, light, NaCl, osmotic stress, oxidative stress, UV-B and wounding) were curated and used for the analysis. Details about stress-responsive enriched genes and their association with stress signals can be obtained from STIFDB2 database . The gene-stress-signal data were analyzed using an enrichment-based meta-analysis framework consisting of two different ontologies (Gene Ontology and Plant Ontology), biological pathway and functional domain annotations. We found several shared and distinct biological processes, cellular components and molecular functions associated with stress-responsive genes. Pathway analysis revealed that stress-responsive genes perturbed the pathways under the "Metabolic pathways" category. We also found several shared and stress-signal specific protein domains, suggesting functional mechanisms regulating stress-response. Phenomic characteristics of abiotic stress-responsive genes were ascertained for several stresses and found to be shared by multiple stresses in both anatomy and temporal categories of Plant Ontology. We found several constitutive stress-responsive genes that are differentially upregulated due to perturbation of different stress signals, for example a gene (AT1G68440) involved in phenylpropanoid metabolism and polyamine catabolism as responsive to seven different stress signals. We also performed structure-function prediction of five genes associated responsive to multiple abiotic stress signals. We envisage that results from our analysis that provide insight into functional repertoire, metabolic pathways and phenomic characteristics common and specifically associated with stress signals would help to understand abiotic stress regulome in Arabidopsis thaliana and may also help to develop an improved plant variety using molecular breeding and genetic engineering techniques that are rapidly stress-responsive and tolerant.
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Affiliation(s)
- Mahantesha Naika
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, 560065, India.
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Caparrós-Martín JA, McCarthy-Suárez I, Culiáñez-Macià FA. HAD hydrolase function unveiled by substrate screening: enzymatic characterization of Arabidopsis thaliana subclass I phosphosugar phosphatase AtSgpp. PLANTA 2013; 237:943-54. [PMID: 23179445 PMCID: PMC3607736 DOI: 10.1007/s00425-012-1809-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 11/02/2012] [Indexed: 05/18/2023]
Abstract
This work presents the isolation and the biochemical characterization of the Arabidopsis thaliana gene AtSgpp. This gene shows homology with the Arabidopsis low molecular weight phosphatases AtGpp1 and AtGpp2 and the yeast counterpart GPP1 and GPP2, which have a high specificity for DL-glycerol-3-phosphate. In addition, it exhibits homology with DOG1 and DOG2 that dephosphorylate 2-deoxy-D-glucose-6-phosphate. Using a comparative genomic approach, we identified the AtSgpp gene as a conceptual translated haloacid dehalogenase-like hydrolase HAD protein. AtSgpp (locus tag At2g38740), encodes a protein with a predicted Mw of 26.7 kDa and a pI of 4.6. Its sequence motifs and expected structure revealed that AtSgpp belongs to the HAD hydrolases subfamily I, with the C1-type cap domain. In the presence of Mg(2+) ions, the enzyme has a phosphatase activity over a wide range of phosphosugars substrates (pH optima at 7.0 and K m in the range of 3.6-7.7 mM). AtSgpp promiscuity is preferentially detectable on D-ribose-5-phosphate, 2-deoxy-D-ribose-5-phosphate, 2-deoxy-D-glucose-6-phosphate, D-mannose-6-phosphate, D-fructose-1-phosphate, D-glucose-6-phosphate, DL-glycerol-3-phosphate, and D-fructose-6-phosphate, as substrates. AtSgpp is ubiquitously expressed throughout development in most plant organs, mainly in sepal and guard cell. Interestingly, expression is affected by abiotic and biotic stresses, being the greatest under Pi starvation and cyclopentenone oxylipins induction. Based on both, substrate lax specificity and gene expression, the physiological function of AtSgpp in housekeeping detoxification, modulation of sugar-phosphate balance and Pi homeostasis, is provisionally assigned.
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Affiliation(s)
- José A. Caparrós-Martín
- Instituto de Biología Molecular y Celular de Plantas ‘‘Eduardo Primo Yúfera’’ (UPV-CSIC), Universidad Politécnica de Valencia, Ciudad Politécnica de la Innovación (CPI), C/Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Iva McCarthy-Suárez
- Instituto de Biología Molecular y Celular de Plantas ‘‘Eduardo Primo Yúfera’’ (UPV-CSIC), Universidad Politécnica de Valencia, Ciudad Politécnica de la Innovación (CPI), C/Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Francisco A. Culiáñez-Macià
- Instituto de Biología Molecular y Celular de Plantas ‘‘Eduardo Primo Yúfera’’ (UPV-CSIC), Universidad Politécnica de Valencia, Ciudad Politécnica de la Innovación (CPI), C/Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
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Alvarez S, Roy Choudhury S, Hicks LM, Pandey S. Quantitative Proteomics-Based Analysis Supports a Significant Role of GTG Proteins in Regulation of ABA Response in Arabidopsis Roots. J Proteome Res 2013; 12:1487-501. [DOI: 10.1021/pr301159u] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Sophie Alvarez
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis,
Missouri 63132, United States
| | - Swarup Roy Choudhury
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis,
Missouri 63132, United States
| | - Leslie M. Hicks
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis,
Missouri 63132, United States
| | - Sona Pandey
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis,
Missouri 63132, United States
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47
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Osakabe Y, Arinaga N, Umezawa T, Katsura S, Nagamachi K, Tanaka H, Ohiraki H, Yamada K, Seo SU, Abo M, Yoshimura E, Shinozaki K, Yamaguchi-Shinozaki K. Osmotic stress responses and plant growth controlled by potassium transporters in Arabidopsis. THE PLANT CELL 2013; 25:609-624. [PMID: 23396830 DOI: 10.2307/41812291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Osmotic adjustment plays a fundamental role in water stress responses and growth in plants; however, the molecular mechanisms governing this process are not fully understood. Here, we demonstrated that the KUP potassium transporter family plays important roles in this process, under the control of abscisic acid (ABA) and auxin. We generated Arabidopsis thaliana multiple mutants for K(+) uptake transporter 6 (KUP6), KUP8, KUP2/SHORT HYPOCOTYL3, and an ABA-responsive potassium efflux channel, guard cell outward rectifying K(+) channel (GORK). The triple mutants, kup268 and kup68 gork, exhibited enhanced cell expansion, suggesting that these KUPs negatively regulate turgor-dependent growth. Potassium uptake experiments using (86)radioactive rubidium ion ((86)Rb(+)) in the mutants indicated that these KUPs might be involved in potassium efflux in Arabidopsis roots. The mutants showed increased auxin responses and decreased sensitivity to an auxin inhibitor (1-N-naphthylphthalamic acid) and ABA in lateral root growth. During water deficit stress, kup68 gork impaired ABA-mediated stomatal closing, and kup268 and kup68 gork decreased survival of drought stress. The protein kinase SNF1-related protein kinases 2E (SRK2E), a key component of ABA signaling, interacted with and phosphorylated KUP6, suggesting that KUP functions are regulated directly via an ABA signaling complex. We propose that the KUP6 subfamily transporters act as key factors in osmotic adjustment by balancing potassium homeostasis in cell growth and drought stress responses.
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Affiliation(s)
- Yuriko Osakabe
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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48
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Osakabe Y, Arinaga N, Umezawa T, Katsura S, Nagamachi K, Tanaka H, Ohiraki H, Yamada K, Seo SU, Abo M, Yoshimura E, Shinozaki K, Yamaguchi-Shinozaki K. Osmotic stress responses and plant growth controlled by potassium transporters in Arabidopsis. THE PLANT CELL 2013; 25:609-24. [PMID: 23396830 PMCID: PMC3608781 DOI: 10.1105/tpc.112.105700] [Citation(s) in RCA: 207] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Osmotic adjustment plays a fundamental role in water stress responses and growth in plants; however, the molecular mechanisms governing this process are not fully understood. Here, we demonstrated that the KUP potassium transporter family plays important roles in this process, under the control of abscisic acid (ABA) and auxin. We generated Arabidopsis thaliana multiple mutants for K(+) uptake transporter 6 (KUP6), KUP8, KUP2/SHORT HYPOCOTYL3, and an ABA-responsive potassium efflux channel, guard cell outward rectifying K(+) channel (GORK). The triple mutants, kup268 and kup68 gork, exhibited enhanced cell expansion, suggesting that these KUPs negatively regulate turgor-dependent growth. Potassium uptake experiments using (86)radioactive rubidium ion ((86)Rb(+)) in the mutants indicated that these KUPs might be involved in potassium efflux in Arabidopsis roots. The mutants showed increased auxin responses and decreased sensitivity to an auxin inhibitor (1-N-naphthylphthalamic acid) and ABA in lateral root growth. During water deficit stress, kup68 gork impaired ABA-mediated stomatal closing, and kup268 and kup68 gork decreased survival of drought stress. The protein kinase SNF1-related protein kinases 2E (SRK2E), a key component of ABA signaling, interacted with and phosphorylated KUP6, suggesting that KUP functions are regulated directly via an ABA signaling complex. We propose that the KUP6 subfamily transporters act as key factors in osmotic adjustment by balancing potassium homeostasis in cell growth and drought stress responses.
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Affiliation(s)
- Yuriko Osakabe
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- Gene Discovery Research Group, RIKEN Plant Science Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Naoko Arinaga
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Taishi Umezawa
- Gene Discovery Research Group, RIKEN Plant Science Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Shogo Katsura
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Keita Nagamachi
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hidenori Tanaka
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Haruka Ohiraki
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kohji Yamada
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - So-Uk Seo
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Mitsuru Abo
- Laboratory of Analytical Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Etsuro Yoshimura
- Laboratory of Analytical Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Plant Science Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Kazuko Yamaguchi-Shinozaki
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki 305-8686, Japan
- Address correspondence to
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49
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Dai S, Chen S. Single-cell-type proteomics: toward a holistic understanding of plant function. Mol Cell Proteomics 2012; 11:1622-30. [PMID: 22982375 DOI: 10.1074/mcp.r112.021550] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Multicellular organisms such as plants contain different types of cells with specialized functions. Analyzing the protein characteristics of each type of cell will not only reveal specific cell functions, but also enhance understanding of how an organism works. Most plant proteomics studies have focused on using tissues and organs containing a mixture of different cells. Recent single-cell-type proteomics efforts on pollen grains, guard cells, mesophyll cells, root hairs, and trichomes have shown utility. We expect that high resolution proteomic analyses will reveal novel functions in single cells. This review provides an overview of recent developments in plant single-cell-type proteomics. We discuss application of the approach for understanding important cell functions, and we consider the technical challenges of extending the approach to all plant cell types. Finally, we consider the integration of single-cell-type proteomics with transcriptomics and metabolomics with the goal of providing a holistic understanding of plant function.
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Affiliation(s)
- Shaojun Dai
- Department of Biology, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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50
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Obata T, Fernie AR. The use of metabolomics to dissect plant responses to abiotic stresses. Cell Mol Life Sci 2012; 69:3225-43. [PMID: 22885821 PMCID: PMC3437017 DOI: 10.1007/s00018-012-1091-5] [Citation(s) in RCA: 456] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Revised: 07/09/2012] [Accepted: 07/09/2012] [Indexed: 12/15/2022]
Abstract
Plant metabolism is perturbed by various abiotic stresses. As such the metabolic network of plants must be reconfigured under stress conditions in order to allow both the maintenance of metabolic homeostasis and the production of compounds that ameliorate the stress. The recent development and adoption of metabolomics and systems biology approaches enable us not only to gain a comprehensive overview, but also a detailed analysis of crucial components of the plant metabolic response to abiotic stresses. In this review we introduce the analytical methods used for plant metabolomics and describe their use in studies related to the metabolic response to water, temperature, light, nutrient limitation, ion and oxidative stresses. Both similarity and specificity of the metabolic responses against diverse abiotic stress are evaluated using data available in the literature. Classically discussed stress compounds such as proline, γ-amino butyrate and polyamines are reviewed, and the widespread importance of branched chain amino acid metabolism under stress condition is discussed. Finally, where possible, mechanistic insights into metabolic regulatory processes are discussed.
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Affiliation(s)
- Toshihiro Obata
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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