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Gonzalez S, Swift J, Yaaran A, Xu J, Miller C, Illouz-Eliaz N, Nery JR, Busch W, Zait Y, Ecker JR. Arabidopsis transcriptome responses to low water potential using high-throughput plate assays. eLife 2024; 12:RP84747. [PMID: 38904663 PMCID: PMC11192529 DOI: 10.7554/elife.84747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024] Open
Abstract
Soil-free assays that induce water stress are routinely used to investigate drought responses in the plant Arabidopsis thaliana. Due to their ease of use, the research community often relies on polyethylene glycol (PEG), mannitol, and salt (NaCl) treatments to reduce the water potential of agar media, and thus induce drought conditions in the laboratory. However, while these types of stress can create phenotypes that resemble those of water deficit experienced by soil-grown plants, it remains unclear how these treatments compare at the transcriptional level. Here, we demonstrate that these different methods of lowering water potential elicit both shared and distinct transcriptional responses in Arabidopsis shoot and root tissue. When we compared these transcriptional responses to those found in Arabidopsis roots subject to vermiculite drying, we discovered many genes induced by vermiculite drying were repressed by low water potential treatments on agar plates (and vice versa). Additionally, we also tested another method for lowering water potential of agar media. By increasing the nutrient content and tensile strength of agar, we show the 'hard agar' (HA) treatment can be leveraged as a high-throughput assay to investigate natural variation in Arabidopsis growth responses to low water potential.
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Affiliation(s)
- Stephen Gonzalez
- Plant Biology Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
| | - Joseph Swift
- Plant Biology Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
| | - Adi Yaaran
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food, and Environment, The Hebrew University of JerusalemRehovotIsrael
| | - Jiaying Xu
- Plant Biology Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
| | - Charlotte Miller
- Plant Biology Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
| | - Natanella Illouz-Eliaz
- Plant Biology Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
| | - Wolfgang Busch
- Plant Biology Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
| | - Yotam Zait
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food, and Environment, The Hebrew University of JerusalemRehovotIsrael
| | - Joseph R Ecker
- Plant Biology Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
- Genomic Analysis Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
- Howard Hughes Medical Institute, The Salk Institute for Biological StudiesLa JollaUnited States
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2
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Chakraborty N, Raghuram N. Life, death and resurrection of plant GPCRs. PLANT MOLECULAR BIOLOGY 2023; 111:221-232. [PMID: 36495361 DOI: 10.1007/s11103-022-01323-3] [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: 07/06/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
The activation of G-protein coupled receptors (GPCRs) by extracellular ligands constitutes the first step of heterotrimeric G-protein signalling in animals. In plants, canonical GPCRs have been known for over 25 years, often in association with agronomically important functions. But their role in plant G-protein signalling and even their annotation as GPCR was contested in the last decade, only to be revisited in the light of more recent evidences. In this first ever review on plant GPCRs, we catalogue all the plant GPCRs described to date and discuss the evidences for and against their role in plants in general and G-protein signalling in particular. We argue against writing off GPCRs and point to the missing links to be investigated to establish firm conclusions either way.
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Affiliation(s)
- Navjyoti Chakraborty
- Centre for Sustainable Nitrogen and Nutrient Management, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, 110078, India
| | - Nandula Raghuram
- Centre for Sustainable Nitrogen and Nutrient Management, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, 110078, India.
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Yu Y, Portolés S, Ren Y, Sun G, Wang XF, Zhang H, Guo S. The key clock component ZEITLUPE (ZTL) negatively regulates ABA signaling by degradation of CHLH in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:995907. [PMID: 36176682 PMCID: PMC9513469 DOI: 10.3389/fpls.2022.995907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
Ubiquitination-mediated protein degradation plays important roles in ABA signal transduction and delivering responses to chloroplast stress signals in plants, but additional E3 ligases of protein ubiquitination remain to be identified to understand the complex signaling network. Here we reported that ZEITLUPE (ZTL), an F-box protein, negatively regulates abscisic acid (ABA) signaling during ABA-inhibited early seedling growth and ABA-induced stomatal closure in Arabidopsis thaliana. Using molecular biology and biochemistry approaches, we demonstrated that ZTL interacts with and ubiquitinates its substrate, CHLH/ABAR (Mg-chelatase H subunit/putative ABA receptor), to modulate CHLH stability via the 26S proteasome pathway. CHLH acts genetically downstream of ZTL in ABA and drought stress signaling. Interestingly, ABA conversely induces ZTL phosphorylation, and high levels of ABA also induce CHLH proteasomal degradation, implying that phosphorylated ZTL protein may enhance the affinity to CHLH, leading to the increased degradation of CHLH after ABA treatment. Taken together, our results revealed a possible mechanism of reciprocal regulation between ABA signaling and the circadian clock, which is thought to be essential for plant fitness and survival.
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Affiliation(s)
- Yongtao Yu
- National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Sergi Portolés
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yi Ren
- National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Guangyu Sun
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Xiao-Fang Wang
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Huihui Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Shaogui Guo
- National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
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4
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Zeng WQ, Sun HT, Wang L, Lu XJ, Zhang XL. Cloning and expression analyses of a Pyrabactin Resistance 1 (PYR1) gene from Magnolia sieboldii K. Koch. Bioengineered 2021; 12:3358-3366. [PMID: 34224313 PMCID: PMC8806413 DOI: 10.1080/21655979.2021.1947168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Magnolia sieboldii K. Koch is endemic to China and has high medicinal and ornamental values. However, its seed exhibits morphophysiological dormancy, and the molecular mechanisms of which are not clearly understood. To reveal the regulation mechanism of the ABA signal in seed dormancy, the M. sieboldii ABA receptor Pyrabactin Resistance 1 (PYR1) gene was cloned and analyzed. Analysis of the MsPYR1 sequence analysis showed that the full-length cDNA contained a complete open reading frame of 987 bp and encoded a predicted protein of 204 amino acid residues. The protein had a relative molecular weight of 22.661 kDa and theoretical isoelectric point of 5.01. The transcript levels of MsPYR1 were immediately upregulated at 16 DAI and then decreased at 40 DAI. The highest transcript level of MsPYR1 was found in the dry seeds, indicating that the MsPYR1 gene may play an important role in the regulation of dormancy. The MsPYR1 gene cDNA was successfully expressed in E. coli Rosetta (DE3), and the protein bands were consistent with the prediction. The Anti-MsPYR1antibody could detect the expression of MsPYR1 in M. sieboldii. The results provided a foundation for further study of the function of the MsPYR1 gene.ABBREVIATIONSABA: Abscisic acid; MPD: morphophysiological; PYR1: Pyrabactin Resistance1; PYL: Pyr1-Like; RCAR: Regulatory Components of Aba Receptors; PP2C: protein phosphatases 2C; SnRK2: sucrose non-fermenting1-related protein kinase2; DAI: day after imbibition; NCBI: National Center for Biotechnology Information; BCA: Bicinchoninic acid; CDD: Conserved Domains.
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Affiliation(s)
- Wan-Qi Zeng
- Department of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Hong-Tao Sun
- Department of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Lei Wang
- Department of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Xiu-Jun Lu
- Department of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Xiao-Lin Zhang
- Department of Forestry, Shenyang Agricultural University, Shenyang, China.,State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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5
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van der Woude L, Piotrowski M, Klaasse G, Paulus JK, Krahn D, Ninck S, Kaschani F, Kaiser M, Novák O, Ljung K, Bulder S, van Verk M, Snoek BL, Fiers M, Martin NI, van der Hoorn RAL, Robert S, Smeekens S, van Zanten M. The chemical compound 'Heatin' stimulates hypocotyl elongation and interferes with the Arabidopsis NIT1-subfamily of nitrilases. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1523-1540. [PMID: 33768644 PMCID: PMC8360157 DOI: 10.1111/tpj.15250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/22/2021] [Indexed: 05/17/2023]
Abstract
Temperature passively affects biological processes involved in plant growth. Therefore, it is challenging to study the dedicated temperature signalling pathways that orchestrate thermomorphogenesis, a suite of elongation growth-based adaptations that enhance leaf-cooling capacity. We screened a chemical library for compounds that restored hypocotyl elongation in the pif4-2-deficient mutant background at warm temperature conditions in Arabidopsis thaliana to identify modulators of thermomorphogenesis. The small aromatic compound 'Heatin', containing 1-iminomethyl-2-naphthol as a pharmacophore, was selected as an enhancer of elongation growth. We show that ARABIDOPSIS ALDEHYDE OXIDASES redundantly contribute to Heatin-mediated hypocotyl elongation. Following a chemical proteomics approach, the members of the NITRILASE1-subfamily of auxin biosynthesis enzymes were identified among the molecular targets of Heatin. Our data reveal that nitrilases are involved in promotion of hypocotyl elongation in response to high temperature and Heatin-mediated hypocotyl elongation requires the NITRILASE1-subfamily members, NIT1 and NIT2. Heatin inhibits NIT1-subfamily enzymatic activity in vitro and the application of Heatin accordingly results in the accumulation of NIT1-subfamily substrate indole-3-acetonitrile in vivo. However, levels of the NIT1-subfamily product, bioactive auxin (indole-3-acetic acid), were also significantly increased. It is likely that the stimulation of hypocotyl elongation by Heatin might be independent of its observed interaction with NITRILASE1-subfamily members. However, nitrilases may contribute to the Heatin response by stimulating indole-3-acetic acid biosynthesis in an indirect way. Heatin and its functional analogues present novel chemical entities for studying auxin biology.
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Affiliation(s)
- Lennard van der Woude
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Markus Piotrowski
- Department of Molecular Genetics and Physiology of PlantsFaculty of Biology and BiotechnologyUniversitätsstraße 150Bochum44801Germany
| | - Gruson Klaasse
- Department of Chemical Biology & Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUniversity UtrechtUniversiteitsweg 99Utrecht3584 CGthe Netherlands
| | - Judith K. Paulus
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Daniel Krahn
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Sabrina Ninck
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Farnusch Kaschani
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Markus Kaiser
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Ondřej Novák
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
- Laboratory of Growth RegulatorsThe Czech Academy of Sciences & Faculty of ScienceInstitute of Experimental BotanyPalacký UniversityŠlechtitelů 27Olomouc78371Czech Republic
| | - Karin Ljung
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
| | - Suzanne Bulder
- Bejo Zaden B.V.Trambaan 1Warmenhuizen1749 CZthe Netherlands
| | - Marcel van Verk
- Plant‐Microbe InteractionsInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
- KeygeneAgro Business Park 90Wageningen6708 PWthe Netherlands
- Theoretical Biology and BioinformaticsInstitute of Biodynamics and BiocomplexityUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Basten L. Snoek
- Theoretical Biology and BioinformaticsInstitute of Biodynamics and BiocomplexityUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Martijn Fiers
- BioscienceWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
| | - Nathaniel I. Martin
- Department of Chemical Biology & Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUniversity UtrechtUniversiteitsweg 99Utrecht3584 CGthe Netherlands
- Biological Chemistry GroupSylvius LaboratoriesInstitute of Biology LeidenLeiden UniversitySylviusweg 72Leiden2333 BEthe Netherlands
| | - Renier A. L. van der Hoorn
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Stéphanie Robert
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
| | - Sjef Smeekens
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Martijn van Zanten
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
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6
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Ruiz-Partida R, Rosario SM, Lozano-Juste J. An Update on Crop ABA Receptors. PLANTS 2021; 10:plants10061087. [PMID: 34071543 PMCID: PMC8229007 DOI: 10.3390/plants10061087] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/06/2021] [Accepted: 05/13/2021] [Indexed: 11/19/2022]
Abstract
The hormone abscisic acid (ABA) orchestrates the plant stress response and regulates sophisticated metabolic and physiological mechanisms essential for survival in a changing environment. Plant ABA receptors were described more than 10 years ago, and a considerable amount of information is available for the model plant Arabidopsis thaliana. Unfortunately, this knowledge is still very limited in crops that hold the key to feeding a growing population. In this review, we summarize genomic, genetic and structural data obtained in crop ABA receptors. We also provide an update on ABA perception in major food crops, highlighting specific and common features of crop ABA receptors.
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Affiliation(s)
- Rafael Ruiz-Partida
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV), Calle Ingeniero Fausto Elio s/n, Edificio 8E, 46022 Valencia, Spain; (R.R.-P.); (S.M.R.)
| | - Sttefany M. Rosario
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV), Calle Ingeniero Fausto Elio s/n, Edificio 8E, 46022 Valencia, Spain; (R.R.-P.); (S.M.R.)
- Laboratorio de Biología Molecular, Facultad de Ciencias Agronómicas y Veterinarias, Universidad Autónoma de Santo Domingo (UASD), Camino de Engombe, Santo Domingo 10904, Dominican Republic
| | - Jorge Lozano-Juste
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV), Calle Ingeniero Fausto Elio s/n, Edificio 8E, 46022 Valencia, Spain; (R.R.-P.); (S.M.R.)
- Correspondence:
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7
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Jin YN, Cui ZH, Ma K, Yao JL, Ruan YY, Guo ZF. Characterization of ZmCOLD1, novel GPCR-Type G Protein genes involved in cold stress from Zea mays L. and the evolution analysis with those from other species. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:619-632. [PMID: 33854288 PMCID: PMC7981359 DOI: 10.1007/s12298-021-00966-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/27/2021] [Accepted: 03/03/2021] [Indexed: 06/12/2023]
Abstract
Maize is one of the most vital staple crops worldwide. G proteins modulate plentiful signaling pathways, and G protein-coupled receptor-type G proteins (GPCRs) are highly conserved membrane proteins in plants. However, researches on maize G proteins and GPCRs are scarce. In this study, we identified three novel GPCR-Type G Protein (GTG) genes from chromosome 10 (Chr 10) in maize, designated as ZmCOLD1-10A, ZmCOLD1-10B and ZmCOLD1-10C. Their amino acid sequences had high similarity to TaCOLD1 from wheat and OsCOLD1 from rice. They contained the basic characteristics of GTG/COLD1 proteins, including GPCR-like topology, the conserved hydrophilic loop (HL) domain, DUF3735 (domain of unknown function 3735) domain, GTPase-activating domain, and ATP/GTP-binding domain. Subcellular localization analyses of ZmCOLD1 proteins suggested that ZmCOLD1 proteins localized on plasma membrane (PM) and endoplasmic reticulum (ER). Furthermore, amino acid sequence alignment verified the conservation of the key 187th amino acid T in maize and other wild maize-relative species. Evolutionary relationship among plants GTG/COLD1 proteins family displayed strong group-specificity. Expression analysis indicated that ZmCOLD1-10A was cold-induced and inhibited by light. Together, these results suggested that ZmCOLD1 genes had potential value to improve cold tolerance and to contribute crops growth and molecular breeding.
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Affiliation(s)
- Ya-Nan Jin
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866 China
- College of Life Science, Inner Mongolia University for the Nationalities, Tongliao, 028000 China
| | - Zhen-hai Cui
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866 China
| | - Ke Ma
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866 China
| | - Jia-Lu Yao
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866 China
| | - Yan-Ye Ruan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866 China
| | - Zhi-Fu Guo
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866 China
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8
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Visscher AM, Castillo-Lorenzo E, Toorop PE, Junio da Silva L, Yeo M, Pritchard HW. Pseudophoenix ekmanii (Arecaceae) seeds at suboptimal temperature show reduced imbibition rates and enhanced expression of genes related to germination inhibition. PLANT BIOLOGY (STUTTGART, GERMANY) 2020; 22:1041-1051. [PMID: 32609914 DOI: 10.1111/plb.13156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
Pseudophoenix ekmanii is a critically endangered palm species that can be found in the southeast of the Dominican Republic. The temperatures to which P. ekmanii seeds are exposed upon dispersal range from 32 to 23 °C (max and min) and can reach a low of approximately 20 °C in January. Our aim was to analyse the effect of suboptimal (20 °C) and optimal (30 °C) germination temperature on seed imbibition, moisture content, embryo growth and gene expression patterns in this tropical palm species. Seed imbibition was tracked using whole seeds, while moisture content was assessed for individual seed sections. Embryo and whole seed size were measured before and after full imbibition. For transcriptome sequencing, mRNA was extracted from embryo tissues only and the resulting reads were mapped against the Elaeis guineensis reference genome. Differentially expressed genes were identified after statistical analysis and subsequently probed for enrichment of Gene Ontology categories 'Biological process' and 'Cellular component'. Our results show that prolonged exposure to 20 °C slows whole seed and embryo imbibition and causes germination to be both delayed and inhibited. Embryonic transcriptome patterns associated with the negative regulation of germination by suboptimal temperature include up-regulation of ABA biosynthesis genes, ABA-responsive genes, as well as other genes previously related to physiological dormancy and inhibition of germination. Thus, our manuscript provides the first insights into the gene expression patterns involved in the response to suboptimal temperature during seed imbibition in a tropical palm species.
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Affiliation(s)
- A M Visscher
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, West Sussex, United Kingdom
| | - E Castillo-Lorenzo
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, West Sussex, United Kingdom
- Department of Natural Capital and Plant Health, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, West Sussex, United Kingdom
| | - P E Toorop
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, West Sussex, United Kingdom
| | - L Junio da Silva
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, West Sussex, United Kingdom
| | - M Yeo
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, West Sussex, United Kingdom
| | - H W Pritchard
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, West Sussex, United Kingdom
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9
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Liu Z, Li N, Zhang Y, Li Y. Transcriptional repression of GIF1 by the KIX-PPD-MYC repressor complex controls seed size in Arabidopsis. Nat Commun 2020; 11:1846. [PMID: 32296056 PMCID: PMC7160150 DOI: 10.1038/s41467-020-15603-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 03/12/2020] [Indexed: 11/17/2022] Open
Abstract
Seed size is a key agronomic trait that greatly determines plant yield. Elucidating the molecular mechanism underlying seed size regulation is also an important question in developmental biology. Here, we show that the KIX-PPD-MYC-GIF1 pathway plays a crucial role in seed size control in Arabidopsis thaliana. Disruption of KIX8/9 and PPD1/2 causes large seeds due to increased cell proliferation and cell elongation in the integuments. KIX8/9 and PPD1/2 interact with transcription factors MYC3/4 to form the KIX-PPD-MYC complex in Arabidopsis. The KIX-PPD-MYC complex associates with the typical G-box sequence in the promoter of GRF-INTERACTING FACTOR 1 (GIF1), which promotes seed growth, and represses its expression. Genetic analyses support that KIX8/9, PPD1/2, MYC3/4, and GIF1 function in a common pathway to control seed size. Thus, our results reveal a genetic and molecular mechanism by which the transcription factors MYC3/4 recruit KIX8/9 and PPD1/2 to the promoter of GIF1 and repress its expression, thereby determining seed size in Arabidopsis. Seed size is an important determinant of plant yield. Here, Liu et al. show that a KIX-PPD repressor complex and MYC transcription factors interact with the G-box motif in the promoter of GRF-INTERACTING FACTOR 1 to regulate seed size by influencing cell proliferation and elongation in the integument.
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Affiliation(s)
- Zupei Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100039, Beijing, China
| | - Na Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yueying Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100039, Beijing, China
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, China. .,University of Chinese Academy of Sciences, 100039, Beijing, China.
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10
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Liu XS, Liang CC, Hou SG, Wang X, Chen DH, Shen JL, Zhang W, Wang M. The LRR-RLK Protein HSL3 Regulates Stomatal Closure and the Drought Stress Response by Modulating Hydrogen Peroxide Homeostasis. FRONTIERS IN PLANT SCIENCE 2020; 11:548034. [PMID: 33329622 PMCID: PMC7728693 DOI: 10.3389/fpls.2020.548034] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 10/26/2020] [Indexed: 05/14/2023]
Abstract
Guard cells shrink in response to drought stress and abscisic acid (ABA) signaling, thereby reducing stomatal aperture. Hydrogen peroxide (H2O2) is an important signaling molecule acting to induce stomatal closure. As yet, the molecular basis of control over the level of H2O2 in the guard cells remains largely unknown. Here, the leucine-rich repeat (LRR)-receptor-like kinase (RLK) protein HSL3 has been shown to have the ability to negatively regulate stomatal closure by modulating the level of H2O2 in the guard cells. HSL3 was markedly up-regulated by treating plants with either ABA or H2O2, as well as by dehydration. In the loss-of-function hsl3 mutant, both stomatal closure and the activation of anion currents proved to be hypersensitive to ABA treatment, and the mutant was more tolerant than the wild type to moisture deficit; the overexpression of HSL3 had the opposite effect. In the hsl3 mutant, the transcription of NADPH oxidase gene RbohF involved in H2O2 production showed marked up-regulation, as well as the level of catalase activity was weakly inducible by ABA, allowing H2O2 to accumulate in the guard cells. HSL3 was concluded to participate in the regulation of the response to moisture deficit through ABA-induced stomatal closure triggered by the accumulation of H2O2 in the guard cells.
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Affiliation(s)
- Xuan-shan Liu
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Chao-chao Liang
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Shu-guo Hou
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, China
| | - Xin Wang
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Dong-hua Chen
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Jian-lin Shen
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Wei Zhang
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
- *Correspondence: Mei Wang,
| | - Mei Wang
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
- Wei Zhang,
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11
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Joglekar S, Suliman M, Bartsch M, Halder V, Maintz J, Bautor J, Zeier J, Parker JE, Kombrink E. Chemical Activation of EDS1/PAD4 Signaling Leading to Pathogen Resistance in Arabidopsis. PLANT & CELL PHYSIOLOGY 2018; 59:1592-1607. [PMID: 29931201 DOI: 10.1093/pcp/pcy106] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Indexed: 05/20/2023]
Abstract
In a chemical screen we identified thaxtomin A (TXA), a phytotoxin from plant pathogenic Streptomyces scabies, as a selective and potent activator of FLAVIN-DEPENDENT MONOOXYGENASE1 (FMO1) expression in Arabidopsis (Arabidopsis thaliana). TXA induction of FMO1 was unrelated to the production of reactive oxygen species (ROS), plant cell death or its known inhibition of cellulose synthesis. TXA-stimulated FMO1 expression was strictly dependent on ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1) and PHYTOALEXIN DEFICIENT4 (PAD4) but independent of salicylic acid (SA) synthesis via ISOCHORISMATE SYNTHASE1 (ICS1). TXA induced the expression of several EDS1/PAD4-regulated genes, including EDS1, PAD4, SENESCENCE ASSOCIATED GENE101 (SAG101), ICS1, AGD2-LIKE DEFENSE RESPONSE PROTEIN1 (ALD1) and PATHOGENESIS-RELATED PROTEIN1 (PR1), and accumulation of SA. Notably, enhanced ALD1 expression did not result in accumulation of the product pipecolic acid (PIP), which promotes FMO1 expression during biologically induced systemic acquired resistance. TXA treatment preferentially stimulated expression of PAD4 compared with EDS1, which was mirrored by PAD4 protein accumulation, suggesting that TXA leads to increased PAD4 availability to form EDS1-PAD4 signaling complexes. Also, TXA treatment of Arabidopsis plants led to enhanced disease resistance to bacterial and oomycete infection, which was dependent on EDS1 and PAD4, as well as on FMO1 and ICS1. Collectively, the data identify TXA as a potentially useful chemical tool to conditionally activate and interrogate EDS1- and PAD4-controlled pathways in plant immunity.
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Affiliation(s)
- Shachi Joglekar
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Mohamed Suliman
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Michael Bartsch
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Vivek Halder
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Jens Maintz
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Jaqueline Bautor
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Jürgen Zeier
- Department of Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Jane E Parker
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Erich Kombrink
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Köln, Germany
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12
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Ma Z, Bykova NV, Igamberdiev AU. Cell signaling mechanisms and metabolic regulation of germination and dormancy in barley seeds. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.cj.2017.08.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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13
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Li K, Xu C, Huang J, Liu W, Zhang L, Wan W, Tao H, Li L, Lin S, Harrison A, He H. Prediction and identification of the effectors of heterotrimeric G proteins in rice (Oryza sativa L.). Brief Bioinform 2017; 18:270-278. [PMID: 26970777 DOI: 10.1093/bib/bbw021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Indexed: 11/14/2022] Open
Abstract
Heterotrimeric G protein signaling cascades are one of the primary metazoan sensing mechanisms linking a cell to environment. However, the number of experimentally identified effectors of G protein in plant is limited. We have therefore studied which tools are best suited for predicting G protein effectors in rice. Here, we compared the predicting performance of four classifiers with eight different encoding schemes on the effectors of G proteins by using 10-fold cross-validation. Four methods were evaluated: random forest, naive Bayes, K-nearest neighbors and support vector machine. We applied these methods to experimentally identified effectors of G proteins and randomly selected non-effector proteins, and tested their sensitivity and specificity. The result showed that random forest classifier with composition of K-spaced amino acid pairs and composition of motif or domain (CKSAAP_PROSITE_200) combination method yielded the best performance, with accuracy and the Mathew's correlation coefficient reaching 74.62% and 0.49, respectively. We have developed G-Effector, an online predictor, which outperforms BLAST, PSI-BLAST and HMMER on predicting the effectors of G proteins. This provided valuable guidance for the researchers to select classifiers combined with different feature selection encoding schemes. We used G-Effector to screen the effectors of G protein in rice, and confirmed the candidate effectors by gene co-expression data. Interestingly, one of the top 15 candidates, which did not appear in the training data set, was validated in a previous research work. Therefore, the candidate effectors list in this article provides both a clue for researchers as to their function and a framework of validation for future experimental work. It is accessible at http://bioinformatics.fafu.edu.cn/geffector.
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Affiliation(s)
- Kuan Li
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China
| | - Chaoqun Xu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jian Huang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, China; State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, China; Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou, China
| | - Lina Zhang
- Department of Biology, University of California at San Diego, La Jolla, California, USA
| | - Weifeng Wan
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huan Tao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ling Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute of Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Shoukai Lin
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Andrew Harrison
- Department of Mathematical Sciences, University of Essex, Wivenhoe Park, Colchester, UK
| | - Huaqin He
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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14
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Lievens L, Pollier J, Goossens A, Beyaert R, Staal J. Abscisic Acid as Pathogen Effector and Immune Regulator. FRONTIERS IN PLANT SCIENCE 2017; 8:587. [PMID: 28469630 PMCID: PMC5395610 DOI: 10.3389/fpls.2017.00587] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 03/31/2017] [Indexed: 05/18/2023]
Abstract
Abscisic acid (ABA) is a sesquiterpene signaling molecule produced in all kingdoms of life. To date, the best known functions of ABA are derived from its role as a major phytohormone in plant abiotic stress resistance. Different organisms have developed different biosynthesis and signal transduction pathways related to ABA. Despite this, there are also intriguing common themes where ABA often suppresses host immune responses and is utilized by pathogens as an effector molecule. ABA also seems to play an important role in compatible mutualistic interactions such as mycorrhiza and rhizosphere bacteria with plants, and possibly also the animal gut microbiome. The frequent use of ABA in inter-species communication could be a possible reason for the wide distribution and re-invention of ABA as a signaling molecule in different organisms. In humans and animal models, it has been shown that ABA treatment or nutrient-derived ABA is beneficial in inflammatory diseases like colitis and type 2 diabetes, which confer potential to ABA as an interesting nutraceutical or pharmacognostic drug. The anti-inflammatory activity, cellular metabolic reprogramming, and other beneficial physiological and psychological effects of ABA treatment in humans and animal models has sparked an interest in this molecule and its signaling pathway as a novel pharmacological target. In contrast to plants, however, very little is known about the ABA biosynthesis and signaling in other organisms. Genes, tools and knowledge about ABA from plant sciences and studies of phytopathogenic fungi might benefit biomedical studies on the physiological role of endogenously generated ABA in humans.
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Affiliation(s)
- Laurens Lievens
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, VIBGhent, Belgium
- Department of Biomedical Molecular Biology, Ghent UniversityGhent, Belgium
| | - Jacob Pollier
- VIB-UGent Center for Plant Systems Biology, VIBGhent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
| | - Alain Goossens
- VIB-UGent Center for Plant Systems Biology, VIBGhent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
| | - Rudi Beyaert
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, VIBGhent, Belgium
- Department of Biomedical Molecular Biology, Ghent UniversityGhent, Belgium
| | - Jens Staal
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, VIBGhent, Belgium
- Department of Biomedical Molecular Biology, Ghent UniversityGhent, Belgium
- *Correspondence: Jens Staal
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15
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Verslues PE. ABA and cytokinins: challenge and opportunity for plant stress research. PLANT MOLECULAR BIOLOGY 2016; 91:629-640. [PMID: 26910054 DOI: 10.1007/s11103-016-0458-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 02/19/2016] [Indexed: 06/05/2023]
Abstract
Accumulation of the stress hormone abscisic acid (ABA) induces many cellular mechanisms associated with drought resistance. Recent years have seen a rapid advance in our knowledge of how increased ABA levels are perceived by ABA receptors, particularly the PYL/RCAR receptors, but there has been relatively less new information about how ABA accumulation is controlled and matched to stress severity. ABA synthesis and catabolism, conjugation and deconjugation to glucose, and ABA transport all are involved in controlling ABA levels. This highly buffered system of ABA metabolism represents both a challenge and opportunity in developing a mechanistic understanding of how plants detect and respond to drought. Recent data have also shown that direct manipulation of cytokinin levels in transgenic plants has dramatic effect on drought phenotypes and prompted new interest in the role of cytokinins and cytokinin signaling in drought. Both ABA and cytokinins will continue to be major foci of drought research but likely with different trajectories both in terms of basic research and in translational research aimed at increasing plant performance during drought.
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Affiliation(s)
- Paul E Verslues
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128 Sec. 2 Academia Rd, Nankang Dist., Taipei, 11529, Taiwan.
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16
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Trusov Y, Botella JR. Plant G-Proteins Come of Age: Breaking the Bond with Animal Models. Front Chem 2016; 4:24. [PMID: 27252940 PMCID: PMC4877378 DOI: 10.3389/fchem.2016.00024] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/04/2016] [Indexed: 11/29/2022] Open
Abstract
G-proteins are universal signal transducers mediating many cellular responses. Plant G-protein signaling has been modeled on the well-established animal paradigm but accumulated experimental evidence indicates that G-protein-dependent signaling in plants has taken a very different evolutionary path. Here we review the differences between plant and animal G-proteins reported over past two decades. Most importantly, while in animal systems the G-protein signaling cycle is activated by seven transmembrane-spanning G-protein coupled receptors, the existence of these type of receptors in plants is highly controversial. Instead plant G-proteins have been proven to be functionally associated with atypical receptors such as the Arabidopsis RGS1 and a number of receptor-like kinases. We propose that, instead of the GTP/GDP cycle used in animals, plant G-proteins are activated/de-activated by phosphorylation/de-phosphorylation. We discuss the need of a fresh new look at these signaling molecules and provide a hypothetical model that departs from the accepted animal paradigm.
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Affiliation(s)
- Yuri Trusov
- School of Agriculture and Food Sciences, University of Queensland Brisbane, QLD, Australia
| | - José R Botella
- School of Agriculture and Food Sciences, University of Queensland Brisbane, QLD, Australia
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17
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Shang Y, Dai C, Lee MM, Kwak JM, Nam KH. BRI1-Associated Receptor Kinase 1 Regulates Guard Cell ABA Signaling Mediated by Open Stomata 1 in Arabidopsis. MOLECULAR PLANT 2016; 9:447-460. [PMID: 26724418 DOI: 10.1016/j.molp.2015.12.014] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 11/30/2015] [Accepted: 12/14/2015] [Indexed: 05/08/2023]
Abstract
Stomatal movements are critical in regulating gas exchange for photosynthesis and water balance between plant tissues and the atmosphere. The plant hormone abscisic acid (ABA) plays key roles in regulating stomatal closure under various abiotic stresses. In this study, we revealed a novel role of BAK1 in guard cell ABA signaling. We found that the brassinosteroid (BR) signaling mutant bak1 lost more water than wild-type plants and showed ABA insensitivity in stomatal closure. ABA-induced OST1 expression and reactive oxygen species (ROS) production were also impaired in bak1. Unlike direct treatment with H2O2, overexpression of OST1 did not completely rescue the insensitivity of bak1 to ABA. We demonstrated that BAK1 forms a complex with OST1 near the plasma membrane and that the BAK1/OST1 complex is increased in response to ABA in planta. Brassinolide, the most active BR, exerted a negative effect on ABA-induced formation of the BAK1/OST1 complex and OST1 expression. Moreover, we found that BAK1 and ABI1 oppositely regulate OST1 phosphorylation in vitro, and that ABI1 interacts with BAK1 and inhibits the interaction of BAK1 and OST1. Taken together, our results suggest that BAK1 regulates ABA-induced stomatal closure in guard cells.
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Affiliation(s)
- Yun Shang
- Department of Biological Sciences, Sookmyung Women's University, Seoul 140-742, Republic of Korea
| | - Changbo Dai
- Department of Systems Biology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Myeong Min Lee
- Department of Systems Biology, Yonsei University, Seoul 120-749, Republic of Korea
| | - June M Kwak
- Department of New Biology, Center for Plant Aging Research, Institute for Basic Science, Daegu Gyeongbuk Institute of Science and Technology, Daegu 711-873, Republic of Korea
| | - Kyoung Hee Nam
- Department of Biological Sciences, Sookmyung Women's University, Seoul 140-742, Republic of Korea.
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18
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Transcriptome analysis of Arabidopsis GCR1 mutant reveals its roles in stress, hormones, secondary metabolism and phosphate starvation. PLoS One 2015; 10:e0117819. [PMID: 25668726 PMCID: PMC4357605 DOI: 10.1371/journal.pone.0117819] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/30/2014] [Indexed: 12/19/2022] Open
Abstract
The controversy over the existence or the need for G-protein coupled receptors (GPCRs) in plant G-protein signalling has overshadowed a more fundamental quest for the role of AtGCR1, the most studied and often considered the best candidate for GPCR in plants. Our whole transcriptome microarray analysis of the GCR1-knock-out mutant (gcr1-5) in Arabidopsis thaliana revealed 350 differentially expressed genes spanning all chromosomes. Many of them were hitherto unknown in the context of GCR1 or G-protein signalling, such as in phosphate starvation, storage compound and fatty acid biosynthesis, cell fate, etc. We also found some GCR1-responsive genes/processes that are reported to be regulated by heterotrimeric G-proteins, such as biotic and abiotic stress, hormone response and secondary metabolism. Thus, GCR1 could have G-protein-mediated as well as independent roles and regardless of whether it works as a GPCR, further analysis of the organism-wide role of GCR1 has a significance of its own.
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19
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Ruggieri V, Francese G, Sacco A, D’Alessandro A, Rigano MM, Parisi M, Milone M, Cardi T, Mennella G, Barone A. An association mapping approach to identify favourable alleles for tomato fruit quality breeding. BMC PLANT BIOLOGY 2014; 14:337. [PMID: 25465385 PMCID: PMC4266912 DOI: 10.1186/s12870-014-0337-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 11/17/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Genome Wide Association Studies (GWAS) have been recently used to dissect complex quantitative traits and identify candidate genes affecting phenotype variation of polygenic traits. In order to map loci controlling variation in tomato marketable and nutritional fruit traits, we used a collection of 96 cultivated genotypes, including Italian, Latin American, and other worldwide-spread landraces and varieties. Phenotyping was carried out by measuring ten quality traits and metabolites in red ripe fruits. In parallel, genotyping was carried out by using the Illumina Infinium SolCAP array, which allows data to be collected from 7,720 single nucleotide polymorphism (SNP) markers. RESULTS The Mixed Linear Model used to detect associations between markers and traits allowed population structure and relatedness to be evidenced within our collection, which have been taken into consideration for association analysis. GWAS identified 20 SNPs that were significantly associated with seven out of ten traits considered. In particular, our analysis revealed two markers associated with phenolic compounds, three with ascorbic acid, β-carotene and trans-lycopene, six with titratable acidity, and only one with pH and fresh weight. Co-localization of a group of associated loci with candidate genes/QTLs previously reported in other studies validated the approach. Moreover, 19 putative genes in linkage disequilibrium with markers were found. These genes might be involved in the biosynthetic pathways of the traits analyzed or might be implied in their transcriptional regulation. Finally, favourable allelic combinations between associated loci were identified that could be pyramided to obtain new improved genotypes. CONCLUSIONS Our results led to the identification of promising candidate loci controlling fruit quality that, in the future, might be transferred into tomato genotypes by Marker Assisted Selection or genetic engineering, and highlighted that intraspecific variability might be still exploited for enhancing tomato fruit quality.
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Affiliation(s)
- Valentino Ruggieri
- />Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Gianluca Francese
- />Consiglio per la Ricerca e la Sperimentazione in Agricoltura - Centro di Ricerca per l’Orticoltura (CRA-ORT), Via Cavalleggeri 25, 84098 Pontecagnano, SA Italy
| | - Adriana Sacco
- />Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Antonietta D’Alessandro
- />Consiglio per la Ricerca e la Sperimentazione in Agricoltura - Centro di Ricerca per l’Orticoltura (CRA-ORT), Via Cavalleggeri 25, 84098 Pontecagnano, SA Italy
| | - Maria Manuela Rigano
- />Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Mario Parisi
- />Consiglio per la Ricerca e la Sperimentazione in Agricoltura - Centro di Ricerca per l’Orticoltura (CRA-ORT), Via Cavalleggeri 25, 84098 Pontecagnano, SA Italy
| | - Marco Milone
- />Consiglio per la Ricerca e la Sperimentazione in Agricoltura - Centro di Ricerca per l’Orticoltura (CRA-ORT), Via Cavalleggeri 25, 84098 Pontecagnano, SA Italy
| | - Teodoro Cardi
- />Consiglio per la Ricerca e la Sperimentazione in Agricoltura - Centro di Ricerca per l’Orticoltura (CRA-ORT), Via Cavalleggeri 25, 84098 Pontecagnano, SA Italy
| | - Giuseppe Mennella
- />Consiglio per la Ricerca e la Sperimentazione in Agricoltura - Centro di Ricerca per l’Orticoltura (CRA-ORT), Via Cavalleggeri 25, 84098 Pontecagnano, SA Italy
| | - Amalia Barone
- />Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
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Mei C, Jiang SC, Lu YF, Wu FQ, Yu YT, Liang S, Feng XJ, Portoles Comeras S, Lu K, Wu Z, Wang XF, Zhang DP. Arabidopsis pentatricopeptide repeat protein SOAR1 plays a critical role in abscisic acid signalling. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5317-30. [PMID: 25005137 PMCID: PMC4157714 DOI: 10.1093/jxb/eru293] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A dominant suppressor of the ABAR overexpressor, soar1-1D, from CHLH/ABAR [coding for Mg-chelatase H subunit/putative abscisic acid (ABA) receptor (ABAR)] overexpression lines was screened to explore the mechanism of the ABAR-mediated ABA signalling. The SOAR1 gene encodes a pentatricopeptide repeat (PPR) protein which localizes to both the cytosol and nucleus. Down-regulation of SOAR1 strongly enhances, but up-regulation of SOAR1 almost completely impairs, ABA responses, revealing that SOAR1 is a critical, negative, regulator of ABA signalling. Further genetic evidence supports that SOAR1 functions downstream of ABAR and probably upstream of an ABA-responsive transcription factor ABI5. Changes in the SOAR1 expression alter expression of a subset of ABA-responsive genes including ABI5. These findings provide important information to elucidate further the functional mechanism of PPR proteins and the complicated ABA signalling network.
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Affiliation(s)
- Chao Mei
- MOE Systems Biology and Bioinformatics Laboratory, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shang-Chuan Jiang
- MOE Systems Biology and Bioinformatics Laboratory, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yan-Fen Lu
- MOE Systems Biology and Bioinformatics Laboratory, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fu-Qing Wu
- MOE Systems Biology and Bioinformatics Laboratory, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yong-Tao Yu
- MOE Systems Biology and Bioinformatics Laboratory, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shan Liang
- MOE Systems Biology and Bioinformatics Laboratory, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiu-Jing Feng
- MOE Systems Biology and Bioinformatics Laboratory, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Sergi Portoles Comeras
- MOE Systems Biology and Bioinformatics Laboratory, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Kai Lu
- MOE Systems Biology and Bioinformatics Laboratory, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhen Wu
- MOE Systems Biology and Bioinformatics Laboratory, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiao-Fang Wang
- MOE Systems Biology and Bioinformatics Laboratory, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Da-Peng Zhang
- MOE Systems Biology and Bioinformatics Laboratory, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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21
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Tsugama D, Liu S, Takano T. A bZIP protein, VIP1, interacts with Arabidopsis heterotrimeric G protein β subunit, AGB1. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 71:240-6. [PMID: 23974356 DOI: 10.1016/j.plaphy.2013.07.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 07/31/2013] [Indexed: 05/05/2023]
Abstract
Heterotrimeric G proteins (Gα, Gβ, Gγ) are signaling molecules conserved among eukaryotic species. The G proteins transmit signals via protein-protein interactions. By a yeast two-hybrid screen, we identified a bZIP protein, VIP1, as an Arabidopsis thaliana Gβ (AGB1)-interacting partner. The interaction between AGB1 and VIP1 was confirmed by an in vitro GST pull-down assay and a bimolecular fluorescence complementation (BiFC) assay. VIP1 was previously reported to be a regulator of osmosensory signaling. Interestingly, the BiFC pattern between AGB1 and VIP1 was speckled when cells were incubated in a hypotonic solution, but not when cells were incubated in a mannitol-containing hypertonic solution, suggesting that the subcellular localization of the AGB1-VIP1 complex is regulated by extracellular osmolarity and/or turgor pressure.
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Affiliation(s)
- Daisuke Tsugama
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo-shi, Tokyo, 188-0002, Japan
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22
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Zhang XF, Jiang T, Wu Z, Du SY, Yu YT, Jiang SC, Lu K, Feng XJ, Wang XF, Zhang DP. Cochaperonin CPN20 negatively regulates abscisic acid signaling in Arabidopsis. PLANT MOLECULAR BIOLOGY 2013; 83:205-18. [PMID: 23783410 PMCID: PMC3777161 DOI: 10.1007/s11103-013-0082-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 05/26/2013] [Indexed: 05/08/2023]
Abstract
Previous study showed that the magnesium-protoporphyrin IX chelatase H subunit (CHLH/ABAR) positively regulates abscisic acid (ABA) signaling. Here, we investigated the functions of a CHLH/ABAR interaction protein, the chloroplast co-chaperonin 20 (CPN20) in ABA signaling in Arabidopsis thaliana. We showed that down-expression of the CPN20 gene increases, but overexpression of the CPN20 gene reduces, ABA sensitivity in the major ABA responses including ABA-induced seed germination inhibition, postgermination growth arrest, promotion of stomatal closure and inhibition of stomatal opening. Genetic evidence supports that CPN20 functions downstream or at the same node of CHLH/ABAR, but upstream of the WRKY40 transcription factor. The other CPN20 interaction partners CPN10 and CPN60 are not involved in ABA signaling. Our findings show that CPN20 functions negatively in the ABAR-WRKY40 coupled ABA signaling independently of its co-chaperonin role, and provide a new insight into the role of co-chaperones in the regulation of plant responses to environmental cues.
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Affiliation(s)
- Xiao-Feng Zhang
- MOE Systems Biology and Bioinformatics Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Tao Jiang
- MOE Systems Biology and Bioinformatics Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Zhen Wu
- MOE Systems Biology and Bioinformatics Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Shu-Yuan Du
- MOE Systems Biology and Bioinformatics Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Yong-Tao Yu
- MOE Systems Biology and Bioinformatics Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Shang-Chuan Jiang
- MOE Systems Biology and Bioinformatics Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Kai Lu
- MOE Systems Biology and Bioinformatics Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Xiu-Jing Feng
- MOE Systems Biology and Bioinformatics Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Xiao-Fang Wang
- MOE Systems Biology and Bioinformatics Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Da-Peng Zhang
- MOE Systems Biology and Bioinformatics Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084 China
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Tsugama D, Liu S, Takano T. Arabidopsis heterotrimeric G protein β subunit, AGB1, regulates brassinosteroid signalling independently of BZR1. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:3213-23. [PMID: 23814276 PMCID: PMC3733146 DOI: 10.1093/jxb/ert159] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The Arabidopsis thaliana heterotrimeric G protein β subunit, AGB1, is involved in both abscisic acid (ABA) signalling and brassinosteroid (BR) signalling, but it is unclear how AGB1 regulates these signalling pathways. A key transcription factor downstream of BR, BZR1, and its gain-of-function mutant, bzr1-1, were overexpressed in an AGB1-null mutant, agb1-1, to examine their effects on the BR hyposensitivity and the ABA hypersensitivity of agb1-1, and to examine whether AGB1 regulates the functions of BZR1. Because the amino acid sequence of AGB1 contains 17 putative modification motifs of glycogen synthase kinase 3/SHAGGY-like protein kinases (GSKs), which are known components of BR signalling, the interaction between AGB1 and one of the Arabidopsis GSKs, BIN2, was examined. Expression of bzr1-1 alleviated the effects of a BR biosynthesis inhibitor, brassinazole, in both the wild type and agb1-1, and overexpression of BZR1 alleviated the effects of ABA in both the wild type and agb1-1. AGB1 did not affect the phosphorylation state of BZR1 in vivo. AGB1 interacted with BIN2 in vitro, but did not affect the phosphorylation state of BIN2. The results suggest that AGB1 interacts with BIN2, but regulates the BR signalling in a BZR1-independent manner.
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Affiliation(s)
- Daisuke Tsugama
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo-shi, Tokyo 188-0002, Japan
| | - Shenkui Liu
- Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin 150040, PR China
| | - Tetsuo Takano
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo-shi, Tokyo 188-0002, Japan
- *To whom correspondence should be addressed. E-mail:
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24
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Urano D, Chen JG, Botella JR, Jones AM. Heterotrimeric G protein signalling in the plant kingdom. Open Biol 2013. [PMID: 23536550 DOI: 10.1098/rsob.12.0186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
Abstract
In animals, heterotrimeric G proteins, comprising α-, β-and γ-subunits, perceive extracellular stimuli through cell surface receptors, and transmit signals to ion channels, enzymes and other effector proteins to affect numerous cellular behaviours. In plants, G proteins have structural similarities to the corresponding molecules in animals but transmit signals by atypical mechanisms and effector proteins to control growth, cell proliferation, defence, stomate movements, channel regulation, sugar sensing and some hormonal responses. In this review, we summarize the current knowledge on the molecular regulation of plant G proteins, their effectors and the physiological functions studied mainly in two model organisms: Arabidopsis thaliana and rice (Oryza sativa). We also look at recent progress on structural analyses, systems biology and evolutionary studies.
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Affiliation(s)
- Daisuke Urano
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
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25
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Urano D, Chen JG, Botella JR, Jones AM. Heterotrimeric G protein signalling in the plant kingdom. Open Biol 2013; 3:120186. [PMID: 23536550 PMCID: PMC3718340 DOI: 10.1098/rsob.120186] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 03/05/2013] [Indexed: 12/18/2022] Open
Abstract
In animals, heterotrimeric G proteins, comprising α-, β-and γ-subunits, perceive extracellular stimuli through cell surface receptors, and transmit signals to ion channels, enzymes and other effector proteins to affect numerous cellular behaviours. In plants, G proteins have structural similarities to the corresponding molecules in animals but transmit signals by atypical mechanisms and effector proteins to control growth, cell proliferation, defence, stomate movements, channel regulation, sugar sensing and some hormonal responses. In this review, we summarize the current knowledge on the molecular regulation of plant G proteins, their effectors and the physiological functions studied mainly in two model organisms: Arabidopsis thaliana and rice (Oryza sativa). We also look at recent progress on structural analyses, systems biology and evolutionary studies.
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Affiliation(s)
- Daisuke Urano
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - José Ramón Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Alan M. Jones
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA
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26
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Du SY, Zhang XF, Lu Z, Xin Q, Wu Z, Jiang T, Lu Y, Wang XF, Zhang DP. Roles of the different components of magnesium chelatase in abscisic acid signal transduction. PLANT MOLECULAR BIOLOGY 2012; 80:519-37. [PMID: 23011401 PMCID: PMC3472068 DOI: 10.1007/s11103-012-9965-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 08/26/2012] [Indexed: 05/12/2023]
Abstract
The H subunit of Mg-chelatase (CHLH) was shown to regulate abscisic acid (ABA) signaling and the I subunit (CHLI) was also reported to modulate ABA signaling in guard cells. However, it remains essentially unknown whether and how the Mg-chelatase-catalyzed Mg-protoporphyrin IX-production differs from ABA signaling. Using a newly-developed surface plasmon resonance system, we showed that ABA binds to CHLH, but not to the other Mg-chelatase components/subunits CHLI, CHLD (D subunit) and GUN4. A new rtl1 mutant allele of the CHLH gene in Arabidopsis thaliana showed ABA-insensitive phenotypes in both stomatal movement and seed germination. Upregulation of CHLI1 resulted in ABA hypersensitivity in seed germination, while downregulation of CHLI conferred ABA insensitivity in stomatal response in Arabidopsis. We showed that CHLH and CHLI, but not CHLD, regulate stomatal sensitivity to ABA in tobacco (Nicotiana benthamiana). The overexpression lines of the CHLD gene showed wild-type ABA sensitivity in Arabidopsis. Both the GUN4-RNA interference and overexpression lines of Arabidopsis showed wild-type phenotypes in the major ABA responses. These findings provide clear evidence that the Mg-chelatase-catalyzed Mg-ProtoIX production is distinct from ABA signaling, giving information to understand the mechanism by which the two cellular processes differs at the molecular level.
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Affiliation(s)
- Shu-Yuan Du
- MOE Systems Biology and Bioinformatics Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Xiao-Feng Zhang
- MOE Systems Biology and Bioinformatics Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Zekuan Lu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Qi Xin
- College of Biological Sciences, China Agricultural University, Beijing, 100094 China
| | - Zhen Wu
- MOE Systems Biology and Bioinformatics Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Tao Jiang
- College of Biological Sciences, China Agricultural University, Beijing, 100094 China
| | - Yan Lu
- College of Biological Sciences, China Agricultural University, Beijing, 100094 China
| | - Xiao-Fang Wang
- MOE Systems Biology and Bioinformatics Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Da-Peng Zhang
- MOE Systems Biology and Bioinformatics Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084 China
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27
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Abstract
Background Computational sequence analysis, that is, prediction of local sequence properties, homologs, spatial structure and function from the sequence of a protein, offers an efficient way to obtain needed information about proteins under study. Since reliable prediction is usually based on the consensus of many computer programs, meta-severs have been developed to fit such needs. Most meta-servers focus on one aspect of sequence analysis, while others incorporate more information, such as PredictProtein for local sequence feature predictions, SMART for domain architecture and sequence motif annotation, and GeneSilico for secondary and spatial structure prediction. However, as predictions of local sequence properties, three-dimensional structure and function are usually intertwined, it is beneficial to address them together. Results We developed a MEta-Server for protein Sequence Analysis (MESSA) to facilitate comprehensive protein sequence analysis and gather structural and functional predictions for a protein of interest. For an input sequence, the server exploits a number of select tools to predict local sequence properties, such as secondary structure, structurally disordered regions, coiled coils, signal peptides and transmembrane helices; detect homologous proteins and assign the query to a protein family; identify three-dimensional structure templates and generate structure models; and provide predictive statements about the protein's function, including functional annotations, Gene Ontology terms, enzyme classification and possible functionally associated proteins. We tested MESSA on the proteome of Candidatus Liberibacter asiaticus. Manual curation shows that three-dimensional structure models generated by MESSA covered around 75% of all the residues in this proteome and the function of 80% of all proteins could be predicted. Availability MESSA is free for non-commercial use at http://prodata.swmed.edu/MESSA/
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28
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Jaffé FW, Freschet GEC, Valdes BM, Runions J, Terry MJ, Williams LE. G protein-coupled receptor-type G proteins are required for light-dependent seedling growth and fertility in Arabidopsis. THE PLANT CELL 2012; 24:3649-68. [PMID: 23001037 PMCID: PMC3480293 DOI: 10.1105/tpc.112.098681] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 07/13/2012] [Accepted: 08/28/2012] [Indexed: 05/20/2023]
Abstract
G protein-coupled receptor-type G proteins (GTGs) are highly conserved membrane proteins in plants, animals, and fungi that have eight to nine predicted transmembrane domains. They have been classified as G protein-coupled receptor-type G proteins that function as abscisic acid (ABA) receptors in Arabidopsis thaliana. We cloned Arabidopsis GTG1 and GTG2 and isolated new T-DNA insertion alleles of GTG1 and GTG2 in both Wassilewskija and Columbia backgrounds. These gtg1 gtg2 double mutants show defects in fertility, hypocotyl and root growth, and responses to light and sugars. Histological studies of shoot tissue reveal cellular distortions that are particularly evident in the epidermal layer. Stable expression of GTG1(pro):GTG1-GFP (for green fluorescent protein) in Arabidopsis and transient expression in tobacco (Nicotiana tabacum) indicate that GTG1 is localized primarily to Golgi bodies and to the endoplasmic reticulum. Microarray analysis comparing gene expression profiles in the wild type and double mutant revealed differences in expression of genes important for cell wall function, hormone response, and amino acid metabolism. The double mutants isolated here respond normally to ABA in seed germination assays, root growth inhibition, and gene expression analysis. These results are inconsistent with their proposed role as ABA receptors but demonstrate that GTGs are fundamentally important for plant growth and development.
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Affiliation(s)
- Felix W. Jaffé
- Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Gian-Enrico C. Freschet
- Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Billy M. Valdes
- Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - John Runions
- Oxford Brookes University, Department of Biological and Medical Sciences, Oxford OX3 0BP, United Kingdom
| | - Matthew J. Terry
- Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Lorraine E. Williams
- Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
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29
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Lim CW, Baek W, Lim S, Lee SC. ABA signal transduction from ABA receptors to ion channels. Genes Genomics 2012. [DOI: 10.1007/s13258-012-0081-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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30
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Ben-Ari G. The ABA signal transduction mechanism in commercial crops: learning from Arabidopsis. PLANT CELL REPORTS 2012; 31:1357-69. [PMID: 22660953 DOI: 10.1007/s00299-012-1292-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 05/22/2012] [Accepted: 05/22/2012] [Indexed: 05/08/2023]
Abstract
The phytohormone abscisic acid (ABA) affects a wide range of stages of plant development as well as the plant's response to biotic and abiotic stresses. Manipulation of ABA signaling in commercial crops holds promising potential for improving crop yields. Several decades of research have been invested in attempts to identify the first components of the ABA signaling cascade. It was only in 2009, that two independent groups identified the PYR/PYL/RCAR protein family as the plant ABA receptor. This finding was followed by a surge of studies on ABA signal transduction, many of them using Arabidopsis as their model. The ABA signaling cascade was found to consist of a double-negative regulatory mechanism assembled from three protein families. These include the ABA receptors, the PP2C family of inhibitors, and the kinase family, SnRK2. It was found that ABA-bound PYR/RCARs inhibit PP2C activity, and that PP2Cs inactivate SnRK2s. Researchers today are examining how the elucidation of the ABA signaling cascade in Arabidopsis can be applied to improvements in commercial agriculture. In this article, we have attempted to review recent studies which address this issue. In it, we discuss various approaches useful in identifying the genetic and protein components involved. Finally, we suggest possible commercial applications of genetic manipulation of ABA signaling to improve crop yields.
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Affiliation(s)
- Giora Ben-Ari
- Institute of Plant Sciences, The Volcani Center, ARO, Bet Dagan, Israel.
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31
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Two G-protein-coupled-receptor candidates, Cand2 and Cand7, are involved in Arabidopsis root growth mediated by the bacterial quorum-sensing signals N-acyl-homoserine lactones. Biochem Biophys Res Commun 2011; 417:991-5. [PMID: 22206669 DOI: 10.1016/j.bbrc.2011.12.066] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 12/14/2011] [Indexed: 11/21/2022]
Abstract
Many Gram-negative bacteria use N-acyl-homoserine lactones (AHLs) as quorum sensing (QS) signaling molecules to coordinate their group behavior. Recently, it was shown that plants can perceive and respond to these bacterial AHLs. However, little is known about the molecular mechanism underlying the response of plants to bacterial QS signals. In this study, we show that the promotion of root elongation in wild type Arabidopsis thaliana induced by the AHLs N-3-oxo-hexanoyl-homoserine lactone (3OC6-HSL) or N-3-oxo-octanoyl-homoserine lactone (3OC8-HSL) was completely abolished in plants with loss-of-function mutations in two candidate G-protein Coupled Receptors (GPCRs), Cand2 and Cand7. Furthermore, real-time PCR analysis revealed that the expression levels of Cand2 and Cand7 were elevated in plants treated with 3OC6-HSL or 3OC8-HSL. These results suggest that Cand2 and Cand7 are involved in the regulation of root growth by bacterial AHLs and that GPCRs play a role in mediating interactions between plants and microbes.
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32
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Sturla L, Fresia C, Guida L, Grozio A, Vigliarolo T, Mannino E, Millo E, Bagnasco L, Bruzzone S, De Flora A, Zocchi E. Binding of abscisic acid to human LANCL2. Biochem Biophys Res Commun 2011; 415:390-5. [DOI: 10.1016/j.bbrc.2011.10.079] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 10/14/2011] [Indexed: 10/16/2022]
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Araújo WL, Fernie AR, Nunes-Nesi A. Control of stomatal aperture: a renaissance of the old guard. PLANT SIGNALING & BEHAVIOR 2011; 6:1305-11. [PMID: 21847028 PMCID: PMC3258058 DOI: 10.4161/psb.6.9.16425] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Stomata, functionally specialized small pores on the surfaces of leaves, regulate the flow of gases in and out of plants. The pore is opened by an increase in osmotic pressure in the guard cells, resulting in the uptake of water. The subsequent increase in cell volume inflates the guard cell and culminates with the opening of the pore. Although guard cells can be regarded as one of the most thoroughly investigated cell types, our knowledge of the signaling pathways which regulate guard cell function remains fragmented. Recent research in guard cells has led to several new hypotheses, however, it is still a matter of debate as to whether guard cells function autonomously or are subject to regulation by their neighboring mesophyll cells.This review synthesizes what is known about the mechanisms and genes critical for modulating stomatal movement. Recent progress on the regulation of guard cell function is reviewed here including the involvement of environmental signals such as light, the concentration of atmospheric CO2 and endogenous plant hormones. In addition we re-evaluate the important role of organic acids such as malate and fumarate play in guard cell metabolism in this process.
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Affiliation(s)
- Wagner L Araújo
- Max-Planck Institute for Molecular Plant Physiology; Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck Institute for Molecular Plant Physiology; Potsdam-Golm, Germany
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal; Universidade Federal de Viçosa; Max-Planck Partner Group; MG, Viçosa, Brazil
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Takezawa D, Komatsu K, Sakata Y. ABA in bryophytes: how a universal growth regulator in life became a plant hormone? JOURNAL OF PLANT RESEARCH 2011; 124:437-53. [PMID: 21416316 DOI: 10.1007/s10265-011-0410-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 02/11/2011] [Indexed: 05/03/2023]
Abstract
Abscisic acid (ABA) is not a plant-specific compound but one found in organisms across kingdoms from bacteria to animals, suggesting that it is a ubiquitous and versatile substance that can modulate physiological functions of various organisms. Recent studies have shown that plants developed an elegant system for ABA sensing and early signal transduction mechanisms to modulate responses to environmental stresses for survival in terrestrial conditions. ABA-induced increase in stress tolerance has been reported not only in vascular plants but also in non-vascular bryophytes. Since bryophytes are the key group of organisms in the context of plant evolution, clarification of their ABA-dependent processes is important for understanding evolutionary adaptation of land plants. Molecular approaches using Physcomitrella patens have revealed that ABA plays a role in dehydration stress tolerance in mosses, which comprise a major group of bryophytes. Furthermore, we recently reported that signaling machinery for ABA responses is also conserved in liverworts, representing the most basal members of extant land plant lineage. Conservation of the mechanism for ABA sensing and responses in angiosperms and basal land plants suggests that acquisition of this mechanism for stress tolerance in vegetative tissues was one of the critical evolutionary events for adaptation to the land. This review describes the role of ABA in basal land plants as well as non-land plant organisms and further elaborates on recent progress in molecular studies of model bryophytes by comparative and functional genomic approaches.
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Affiliation(s)
- Daisuke Takezawa
- Graduate School of Science and Engineering, Institute for Environmental Science and Technology, Saitama University, Saitama 338-8570, Japan.
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35
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Guo J, Yang X, Weston DJ, Chen JG. Abscisic acid receptors: past, present and future. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2011; 53:469-79. [PMID: 21554537 DOI: 10.1111/j.1744-7909.2011.01044.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Jin-Gui Chen (Corresponding author) Abscisic acid (ABA) is the key plant stress hormone. Consistent with the earlier studies in support of the presence of both membrane- and cytoplasm-localized ABA receptors, recent studies have identified multiple ABA receptors located in various subcellular locations. These include a chloroplast envelope-localized receptor (the H subunit of Chloroplast Mg(2+) -chelatase/ABA Receptor), two plasma membrane-localized receptors (G-protein Coupled Receptor 2 and GPCR-type G proteins), and one cytosol/nucleus-localized Pyrabactin Resistant (PYR)/PYR-Like (PYL)/Regulatory Component of ABA Receptor 1 (RCAR). Although the downstream molecular events for most of the identified ABA receptors are currently unknown, one of them, PYR/PYL/RCAR was found to directly bind and regulate the activity of a long-known central regulator of ABA signaling, the A-group protein phosphatase 2C (PP2C). Together with the Sucrose Non-fermentation Kinase Subfamily 2 (SnRK2s) protein kinases, a central signaling complex (ABA-PYR-PP2Cs-SnRK2s) that is responsible for ABA signal perception and transduction is supported by abundant genetic, physiological, biochemical and structural evidence. The identification of multiple ABA receptors has advanced our understanding of ABA signal perception and transduction while adding an extra layer of complexity.
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Affiliation(s)
- Jianjun Guo
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114-2790, USA
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36
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Klingler JP, Batelli G, Zhu JK. ABA receptors: the START of a new paradigm in phytohormone signalling. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:3199-210. [PMID: 20522527 PMCID: PMC3107536 DOI: 10.1093/jxb/erq151] [Citation(s) in RCA: 164] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The phytohormone abscisic acid (ABA) plays a central role in plant development and in plant adaptation to both biotic and abiotic stressors. In recent years, knowledge of ABA metabolism and signal transduction has advanced rapidly to provide detailed glimpses of the hormone's activities at the molecular level. Despite this progress, many gaps in understanding have remained, particularly at the early stages of ABA perception by the plant cell. The search for an ABA receptor protein has produced multiple candidates, including GCR2, GTG1, and GTG2, and CHLH. In addition to these candidates, in 2009 several research groups converged on a novel family of Arabidopsis proteins that bind ABA, and thereby interact directly with a class of protein phosphatases that are well known as critical players in ABA signal transduction. The PYR/PYL/RCAR receptor family is homologous to the Bet v 1-fold and START domain proteins. It consists of 14 members, nearly all of which appear capable of participating in an ABA receptor-signal complex that responds to the hormone by activating the transcription of ABA-responsive genes. Evidence is provided here that PYR/PYL/RCAR receptors can also drive the phosphorylation of the slow anion channel SLAC1 to provide a fast and timely response to the ABA signal. Crystallographic studies have vividly shown the mechanics of ABA binding to PYR/PYL/RCAR receptors, presenting a model that bears some resemblance to the binding of gibberellins to GID1 receptors. Since this ABA receptor family is highly conserved in crop species, its discovery is likely to usher a new wave of progress in the elucidation and manipulation of plant stress responses in agricultural settings.
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Affiliation(s)
- John P. Klingler
- Plant Stress Genomics Research Center, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
- Department of Botany and Plant Sciences, 2150 Batchelor Hall, University of California at Riverside, Riverside, California 92521, USA
| | - Giorgia Batelli
- Plant Stress Genomics Research Center, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
- Department of Botany and Plant Sciences, 2150 Batchelor Hall, University of California at Riverside, Riverside, California 92521, USA
| | - Jian-Kang Zhu
- Plant Stress Genomics Research Center, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
- Department of Botany and Plant Sciences, 2150 Batchelor Hall, University of California at Riverside, Riverside, California 92521, USA
- To whom correspondence should be addressed: E-mail:
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37
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Shang Y, Yan L, Liu ZQ, Cao Z, Mei C, Xin Q, Wu FQ, Wang XF, Du SY, Jiang T, Zhang XF, Zhao R, Sun HL, Liu R, Yu YT, Zhang DP. The Mg-chelatase H subunit of Arabidopsis antagonizes a group of WRKY transcription repressors to relieve ABA-responsive genes of inhibition. THE PLANT CELL 2010; 22:1909-35. [PMID: 20543028 PMCID: PMC2910980 DOI: 10.1105/tpc.110.073874] [Citation(s) in RCA: 375] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 04/10/2010] [Accepted: 05/25/2010] [Indexed: 05/17/2023]
Abstract
The phytohormone abscisic acid (ABA) plays a vital role in plant development and response to environmental challenges, but the complex networks of ABA signaling pathways are poorly understood. We previously reported that a chloroplast protein, the magnesium-protoporphyrin IX chelatase H subunit (CHLH/ABAR), functions as a receptor for ABA in Arabidopsis thaliana. Here, we report that ABAR spans the chloroplast envelope and that the cytosolic C terminus of ABAR interacts with a group of WRKY transcription factors (WRKY40, WRKY18, and WRKY60) that function as negative regulators of ABA signaling in seed germination and postgermination growth. WRKY40, a central negative regulator, inhibits expression of ABA-responsive genes, such as ABI5. In response to a high level of ABA signal that recruits WRKY40 from the nucleus to the cytosol and promotes ABAR-WRKY40 interaction, ABAR relieves the ABI5 gene of inhibition by repressing WRKY40 expression. These findings describe a unique ABA signaling pathway from the early signaling events to downstream gene expression.
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Affiliation(s)
- Yi Shang
- Protein Science Laboratory of the Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lu Yan
- Protein Science Laboratory of the Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
- College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | - Zhi-Qiang Liu
- Protein Science Laboratory of the Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
- College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | - Zheng Cao
- Protein Science Laboratory of the Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
- College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | - Chao Mei
- Protein Science Laboratory of the Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qi Xin
- Protein Science Laboratory of the Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
- College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | - Fu-Qing Wu
- Protein Science Laboratory of the Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
- College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | - Xiao-Fang Wang
- Protein Science Laboratory of the Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
- College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | - Shu-Yuan Du
- Protein Science Laboratory of the Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Tao Jiang
- Protein Science Laboratory of the Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
- College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | - Xiao-Feng Zhang
- Protein Science Laboratory of the Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Rui Zhao
- Protein Science Laboratory of the Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
- College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | - Hai-Li Sun
- Protein Science Laboratory of the Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
- College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | - Rui Liu
- Protein Science Laboratory of the Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
- College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | - Yong-Tao Yu
- Protein Science Laboratory of the Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Da-Peng Zhang
- Protein Science Laboratory of the Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Address correspondence to
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Muschietti J, McCormick S. Abscisic acid (ABA) receptors: light at the end of the tunnel. F1000 BIOLOGY REPORTS 2010; 2. [PMID: 20948817 PMCID: PMC2948352 DOI: 10.3410/b2-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The plant hormone abscisic acid (ABA) plays a role in several aspects of plant growth and development. Understanding how this hormonal stimulus is sensed and transduced turned out to be one of the major tasks in the field of plant signaling. A series of recent papers proposed several different proteins that could receive the ABA signal and initiate the signaling cascade. The winner appears to be PYR/PYL/RCAR (PYrabactin Resistance/PYrabactin Resistance-Like/Regulatory Component of Abscisic acid Receptor) proteins, as crystal structures were recently published. The crystal structures support the idea that upon ABA binding to a PYR/PYL/RCAR protein, the activity of a phosphatase 2C, with known repressive activity on ABA signaling, is inhibited.
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Affiliation(s)
- Jorge Muschietti
- Instituto de Ingeniería Genética y Biología Molecular (INGEBI-CONICET)Vuelta de Obligado 2490, Piso 2, C1428ADN, Buenos AiresArgentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos AiresBuenos AiresArgentina
| | - Sheila McCormick
- Plant Gene Expression Center, US Department of Agriculture/Agricultural Research ServiceAlbany, CA 94710USA
- Department of Plant and Microbial Biology, University of California at Berkeley800 Buchanan Street, Albany, CA 94710USA
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39
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Cutler SR, Rodriguez PL, Finkelstein RR, Abrams SR. Abscisic acid: emergence of a core signaling network. ANNUAL REVIEW OF PLANT BIOLOGY 2010; 61:651-79. [PMID: 20192755 DOI: 10.1146/annurev-arplant-042809-112122] [Citation(s) in RCA: 1736] [Impact Index Per Article: 124.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Abscisic acid (ABA) regulates numerous developmental processes and adaptive stress responses in plants. Many ABA signaling components have been identified, but their interconnections and a consensus on the structure of the ABA signaling network have eluded researchers. Recently, several advances have led to the identification of ABA receptors and their three-dimensional structures, and an understanding of how key regulatory phosphatase and kinase activities are controlled by ABA. A new model for ABA action has been proposed and validated, in which the soluble PYR/PYL/RCAR receptors function at the apex of a negative regulatory pathway to directly regulate PP2C phosphatases, which in turn directly regulate SnRK2 kinases. This model unifies many previously defined signaling components and highlights the importance of future work focused on defining the direct targets of SnRK2s and PP2Cs, dissecting the mechanisms of hormone interactions (i.e., cross talk) and defining connections between this new negative regulatory pathway and other factors implicated in ABA signaling.
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Affiliation(s)
- Sean R Cutler
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA.
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Kim TH, Böhmer M, Hu H, Nishimura N, Schroeder JI. Guard cell signal transduction network: advances in understanding abscisic acid, CO2, and Ca2+ signaling. ANNUAL REVIEW OF PLANT BIOLOGY 2010; 61:561-91. [PMID: 20192751 PMCID: PMC3056615 DOI: 10.1146/annurev-arplant-042809-112226] [Citation(s) in RCA: 811] [Impact Index Per Article: 57.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Stomatal pores are formed by pairs of specialized epidermal guard cells and serve as major gateways for both CO(2) influx into plants from the atmosphere and transpirational water loss of plants. Because they regulate stomatal pore apertures via integration of both endogenous hormonal stimuli and environmental signals, guard cells have been highly developed as a model system to dissect the dynamics and mechanisms of plant-cell signaling. The stress hormone ABA and elevated levels of CO(2) activate complex signaling pathways in guard cells that are mediated by kinases/phosphatases, secondary messengers, and ion channel regulation. Recent research in guard cells has led to a new hypothesis for how plants achieve specificity in intracellular calcium signaling: CO(2) and ABA enhance (prime) the calcium sensitivity of downstream calcium-signaling mechanisms. Recent progress in identification of early stomatal signaling components are reviewed here, including ABA receptors and CO(2)-binding response proteins, as well as systems approaches that advance our understanding of guard cell-signaling mechanisms.
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Affiliation(s)
| | | | - Honghong Hu
- University of California, San Diego, Division of Biological Sciences, Section of Cell and Developmental Biology, La Jolla, California 92093-0116
| | - Noriyuki Nishimura
- University of California, San Diego, Division of Biological Sciences, Section of Cell and Developmental Biology, La Jolla, California 92093-0116
| | - Julian I. Schroeder
- University of California, San Diego, Division of Biological Sciences, Section of Cell and Developmental Biology, La Jolla, California 92093-0116
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41
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Li S, Xu C, Yang Y, Xia G. Functional analysis of TaDi19A, a salt-responsive gene in wheat. PLANT, CELL & ENVIRONMENT 2010; 33:117-29. [PMID: 19895399 DOI: 10.1111/j.1365-3040.2009.02063.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A salinity stress upregulated expressed sequence tag (EST) was selected from a suppression subtractive hybridization cDNA library, constructed from the salinity-tolerant wheat cultivar Shanrong No. 3. Sequence analysis showed that the corresponding gene (named TaDi19A) belonged to the Di19 family. TaDi19A was constitutively expressed in both the root and leaf of wheat seedlings grown under non-stressed conditions, but was substantially up-regulated by the imposition of stress (salinity, osmotic stress and cold), or the supply of stress-related hormones [abscisic acid (ABA) and ethylene]. The heterologous over-expression of TaDi19A in Arabidopsis thaliana increased the plants' sensitivity to salinity stress, ABA and mannitol during the germination stage. Root elongation in these transgenic lines showed a reduced tolerance to salinity stress and a reduced sensitivity to ethophon. The expression of the ABA signal pathway genes ABI1, RAB18, ERD15 and ABF3, and SOS2 (SOS pathway) was altered in the transgenic lines. TaDi19A plays a role in the plant's response to abiotic stress, and some possible mechanisms of its action are proposed.
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Affiliation(s)
- Shuo Li
- School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong, China
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42
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Attwood TK, Kell DB, McDermott P, Marsh J, Pettifer SR, Thorne D. Calling International Rescue: knowledge lost in literature and data landslide! Biochem J 2009; 424:317-33. [PMID: 19929850 PMCID: PMC2805925 DOI: 10.1042/bj20091474] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Accepted: 09/29/2009] [Indexed: 11/17/2022]
Abstract
We live in interesting times. Portents of impending catastrophe pervade the literature, calling us to action in the face of unmanageable volumes of scientific data. But it isn't so much data generation per se, but the systematic burial of the knowledge embodied in those data that poses the problem: there is so much information available that we simply no longer know what we know, and finding what we want is hard - too hard. The knowledge we seek is often fragmentary and disconnected, spread thinly across thousands of databases and millions of articles in thousands of journals. The intellectual energy required to search this array of data-archives, and the time and money this wastes, has led several researchers to challenge the methods by which we traditionally commit newly acquired facts and knowledge to the scientific record. We present some of these initiatives here - a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia and the Semantic Biochemical Journal experiment. With their promises to provide new ways of interacting with the literature, and new and more powerful tools to access and extract the knowledge sequestered within it, we ask what advances they make and what obstacles to progress still exist? We explore these questions, and, as you read on, we invite you to engage in an experiment with us, a real-time test of a new technology to rescue data from the dormant pages of published documents. We ask you, please, to read the instructions carefully. The time has come: you may turn over your papers...
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Key Words
- dynamic document content
- interactive pdf
- linking documents with research data
- manuscript mark-up
- mark-up standards
- semantic publishing
- bj, biochemical journal
- cohse, conceptual open hypermedia services environment
- doi, digital object identifier
- go, gene ontology
- gpcr, g protein-coupled receptor
- html, hypertext mark-up language
- iupac, international union of pure and applied chemistry
- ntd, neglected tropical diseases
- obo, open biomedical ontologies
- pdb, protein data bank
- pdf, portable document format
- plos, public library of science
- pmc, pubmed central
- ptm, post-translational modification
- rsc, royal society of chemistry
- sda, structured digital abstract
- stm, scientific, technical and medical
- ud, utopia documents
- xml, extensible mark-up language
- xmp, extensible metadata platform
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Affiliation(s)
- Teresa K Attwood
- School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, UK.
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Santiago J, Rodrigues A, Saez A, Rubio S, Antoni R, Dupeux F, Park SY, Márquez JA, Cutler SR, Rodriguez PL. Modulation of drought resistance by the abscisic acid receptor PYL5 through inhibition of clade A PP2Cs. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 60:575-88. [PMID: 19624469 DOI: 10.1111/j.1365-313x.2009.03981.x] [Citation(s) in RCA: 354] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Abscisic acid (ABA) is a key phytohormone involved in adaption to environmental stress and regulation of plant development. Clade A protein phosphatases type 2C (PP2Cs), such as HAB1, are key negative regulators of ABA signaling in Arabidopsis. To obtain further insight into regulation of HAB1 function by ABA, we have screened for HAB1-interacting partners using a yeast two-hybrid approach. Three proteins were identified, PYL5, PYL6 and PYL8, which belong to a 14-member subfamily of the Bet v1-like superfamily. HAB1-PYL5 interaction was confirmed using BiFC and co-immunoprecipitation assays. PYL5 over-expression led to a globally enhanced response to ABA, in contrast to the opposite phenotype reported for HAB1-over-expressing plants. F(2) plants that over-expressed both HAB1 and PYL5 showed an enhanced response to ABA, indicating that PYL5 antagonizes HAB1 function. PYL5 and other members of its protein family inhibited HAB1, ABI1 and ABI2 phosphatase activity in an ABA-dependent manner. Isothermal titration calorimetry revealed saturable binding of (+)ABA to PYL5, with K(d) values of 1.1 mum or 38 nm in the absence or presence of the PP2C catalytic core of HAB1, respectively. Our work indicates that PYL5 is a cytosolic and nuclear ABA receptor that activates ABA signaling through direct inhibition of clade A PP2Cs. Moreover, we show that enhanced resistance to drought can be obtained through PYL5-mediated inhibition of clade A PP2Cs.
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Affiliation(s)
- Julia Santiago
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - UPV, ES-46022 Valencia, Spain
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Rodríguez-Gacio MDC, Matilla-Vázquez MA, Matilla AJ. Seed dormancy and ABA signaling: the breakthrough goes on. PLANT SIGNALING & BEHAVIOR 2009; 4:1035 - 49. [PMID: 19875942 PMCID: PMC2819511 DOI: 10.4161/psb.4.11.9902] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Accepted: 06/05/2009] [Indexed: 05/18/2023]
Abstract
The seed is an important organ of higher plants regarding plant survival and species dispersion. The transition between seed dormancy and germination represents a critical stage in the plant life cycle and it is an important ecological and commercial trait. A dynamic balance of synthesis and catabolism of two antagonistic hormones, abscisic acid (ABA) and giberellins (GAs), controls the equilibrium between seed dormancy and germination. Embryonic ABA plays a central role in induction and maintenance of seed dormancy, and also inhibits the transition from embryonic to germination growth. Therefore, the ABA metabolism must be highly regulated at both temporal and spatial levels during phase of dessication tolerance. On the other hand, the ABA levels do not depend exclusively on the seeds because sometimes it becomes a strong sink and imports it from the roots and rhizosphere through the xylem and/or phloem. All theses events are discussed in depth here. Likewise, the role of some recently characterized genes belonging to seeds of woody species and related to ABA signaling, are also included. Finally, although four possible ABA receptors have been reported, not much is known about how they mediate ABA signalling transduction. However, new publications seem to shown that almost all these receptors lack several properties to consider them as such.
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Abstract
Heterotrimeric G proteins (Galpha, Gbeta/Ggamma subunits) constitute one of the most important components of cell signaling cascade. G Protein Coupled Receptors (GPCRs) perceive many extracellular signals and transduce them to heterotrimeric G proteins, which further transduce these signals intracellular to appropriate downstream effectors and thereby play an important role in various signaling pathways. GPCRs exist as a superfamily of integral membrane protein receptors that contain seven transmembrane alpha-helical regions, which bind to a wide range of ligands. Upon activation by a ligand, the GPCR undergoes a conformational change and then activate the G proteins by promoting the exchange of GDP/GTP associated with the Galpha subunit. This leads to the dissociation of Gbeta/Ggamma dimer from Galpha. Both these moieties then become free to act upon their downstream effectors and thereby initiate unique intracellular signaling responses. After the signal propagation, the GTP of Galpha-GTP is hydrolyzed to GDP and Galpha becomes inactive (Galpha-GDP), which leads to its re-association with the Gbeta/Ggamma dimer to form the inactive heterotrimeric complex. The GPCR can also transduce the signal through G protein independent pathway. GPCRs also regulate cell cycle progression. Till to date thousands of GPCRs are known from animal kingdom with little homology among them, but only single GPCR has been identified in plant system. The Arabidopsis GPCR was reported to be cell cycle regulated and also involved in ABA and in stress signaling. Here I have described a general mechanism of signal transduction through GPCR/G proteins, structure of GPCRs, family of GPCRs and plant GPCR and its role.
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Affiliation(s)
- Narendra Tuteja
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India.
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46
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Sturla L, Fresia C, Guida L, Bruzzone S, Scarfì S, Usai C, Fruscione F, Magnone M, Millo E, Basile G, Grozio A, Jacchetti E, Allegretti M, De Flora A, Zocchi E. LANCL2 is necessary for abscisic acid binding and signaling in human granulocytes and in rat insulinoma cells. J Biol Chem 2009; 284:28045-28057. [PMID: 19667068 DOI: 10.1074/jbc.m109.035329] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Abscisic acid (ABA) is a plant hormone regulating fundamental physiological functions in plants, such as response to abiotic stress. Recently, ABA was shown to be produced and released by human granulocytes, by insulin-producing rat insulinoma cells, and by human and murine pancreatic beta cells. ABA autocrinally stimulates the functional activities specific for each cell type through a receptor-operated signal transduction pathway, sequentially involving a pertussis toxin-sensitive receptor/G-protein complex, cAMP, CD38-produced cADP-ribose and intracellular calcium. Here we show that the lanthionine synthetase C-like protein LANCL2 is required for ABA binding on the membrane of human granulocytes and that LANCL2 is necessary for transduction of the ABA signal into the cell-specific functional responses in granulocytes and in rat insulinoma cells. Co-expression of LANCL2 and CD38 in the human HeLa cell line reproduces the ABA-signaling pathway. Results obtained with granulocytes and CD38(+)/LANCL2(+) HeLa transfected with a chimeric G-protein (G alpha(q/i)) suggest that the pertussis toxin-sensitive G-protein coupled to LANCL2 is a G(i). Identification of LANCL2 as a critical component of the ABA-sensing protein complex will enable the screening of synthetic ABA antagonists as prospective new anti-inflammatory and anti-diabetic agents.
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Affiliation(s)
- Laura Sturla
- Department of Experimental Medicine, Section of Biochemistry, and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV 1, Genova 16132
| | - Chiara Fresia
- Department of Experimental Medicine, Section of Biochemistry, and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV 1, Genova 16132
| | - Lucrezia Guida
- Department of Experimental Medicine, Section of Biochemistry, and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV 1, Genova 16132
| | - Santina Bruzzone
- Department of Experimental Medicine, Section of Biochemistry, and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV 1, Genova 16132
| | - Sonia Scarfì
- Department of Experimental Medicine, Section of Biochemistry, and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV 1, Genova 16132; Advanced Biotechnology Center, Largo R. Benzi 10, Genova 16132
| | - Cesare Usai
- Institute of Biophysics, National Research Council, Via De Marini 6, Genova 16149
| | | | - Mirko Magnone
- Department of Experimental Medicine, Section of Biochemistry, and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV 1, Genova 16132
| | - Enrico Millo
- Department of Experimental Medicine, Section of Biochemistry, and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV 1, Genova 16132
| | - Giovanna Basile
- Department of Experimental Medicine, Section of Biochemistry, and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV 1, Genova 16132
| | - Alessia Grozio
- Department of Experimental Medicine, Section of Biochemistry, and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV 1, Genova 16132
| | - Emanuela Jacchetti
- Institute of Biophysics, National Research Council, Via De Marini 6, Genova 16149
| | | | - Antonio De Flora
- Department of Experimental Medicine, Section of Biochemistry, and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV 1, Genova 16132.
| | - Elena Zocchi
- Department of Experimental Medicine, Section of Biochemistry, and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV 1, Genova 16132; Advanced Biotechnology Center, Largo R. Benzi 10, Genova 16132.
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Wu FQ, Xin Q, Cao Z, Liu ZQ, Du SY, Mei C, Zhao CX, Wang XF, Shang Y, Jiang T, Zhang XF, Yan L, Zhao R, Cui ZN, Liu R, Sun HL, Yang XL, Su Z, Zhang DP. The magnesium-chelatase H subunit binds abscisic acid and functions in abscisic acid signaling: new evidence in Arabidopsis. PLANT PHYSIOLOGY 2009; 150:1940-54. [PMID: 19535472 PMCID: PMC2719140 DOI: 10.1104/pp.109.140731] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Accepted: 06/14/2009] [Indexed: 05/20/2023]
Abstract
Using a newly developed abscisic acid (ABA)-affinity chromatography technique, we showed that the magnesium-chelatase H subunit ABAR/CHLH (for putative abscisic acid receptor/chelatase H subunit) specifically binds ABA through the C-terminal half but not the N-terminal half. A set of potential agonists/antagonists to ABA, including 2-trans,4-trans-ABA, gibberellin, cytokinin-like regulator 6-benzylaminopurine, auxin indole-3-acetic acid, auxin-like substance naphthalene acetic acid, and jasmonic acid methyl ester, did not bind ABAR/CHLH. A C-terminal C370 truncated ABAR with 369 amino acid residues (631-999) was shown to bind ABA, which may be a core of the ABA-binding domain in the C-terminal half. Consistently, expression of the ABAR/CHLH C-terminal half truncated proteins fused with green fluorescent protein (GFP) in wild-type plants conferred ABA hypersensitivity in all major ABA responses, including seed germination, postgermination growth, and stomatal movement, and the expression of the same truncated proteins fused with GFP in an ABA-insensitive cch mutant of the ABAR/CHLH gene restored the ABA sensitivity of the mutant in all of the ABA responses. However, the effect of expression of the ABAR N-terminal half fused with GFP in the wild-type plants was limited to seedling growth, and the restoring effect of the ABA sensitivity of the cch mutant was limited to seed germination. In addition, we identified two new mutant alleles of ABAR/CHLH from the mutant pool in the Arabidopsis Biological Resource Center via Arabidopsis (Arabidopsis thaliana) Targeting-Induced Local Lesions in Genomes. The abar-2 mutant has a point mutation resulting in the N-terminal Leu-348-->Phe, and the abar-3 mutant has a point mutation resulting in the N-terminal Ser-183-->Phe. The two mutants show altered ABA-related phenotypes in seed germination and postgermination growth but not in stomatal movement. These findings support the idea that ABAR/CHLH is an ABA receptor and reveal that the C-terminal half of ABAR/CHLH plays a central role in ABA signaling, which is consistent with its ABA-binding ability, but the N-terminal half is also functionally required, likely through a regulatory action on the C-terminal half.
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Affiliation(s)
- Fu-Qing Wu
- State Key Laboratory of Plant Physiology and Biochemistry , China Agricultural University, Beijing 100094, China
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48
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Abstract
Plant growth and development is regulated by a structurally unrelated collection of small molecules called plant hormones. During the last 15 years the number of known plant hormones has grown from five to at least ten. Furthermore, many of the proteins involved in plant hormone signalling pathways have been identified, including receptors for many of the major hormones. Strikingly, the ubiquitin-proteasome pathway plays a central part in most hormone-signalling pathways. In addition, recent studies confirm that hormone signalling is integrated at several levels during plant growth and development.
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49
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Ton J, Flors V, Mauch-Mani B. The multifaceted role of ABA in disease resistance. TRENDS IN PLANT SCIENCE 2009; 14:310-7. [PMID: 19443266 DOI: 10.1016/j.tplants.2009.03.006] [Citation(s) in RCA: 475] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 03/20/2009] [Accepted: 03/23/2009] [Indexed: 05/18/2023]
Abstract
Long known only for its role in abiotic stress tolerance, recent evidence shows that abscisic acid (ABA) also has a prominent role in biotic stress. Although it acts as a negative regulator of disease resistance, ABA can also promote plant defense and is involved in a complicated network of synergistic and antagonistic interactions. Its role in disease resistance depends on the type of pathogen, its specific way of entering the host and, hence, the timing of the defense response and the type of affected plant tissue. Here, we discuss the controversial evidence pointing to either a repression or a promotion of resistance by ABA. Furthermore, we propose a model in which both possibilities are integrated.
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Affiliation(s)
- Jurriaan Ton
- Rothamsted Research, West Common, Harpenden, Herts, AL5 2JQ, UK
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50
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Abstract
The plant hormones are a structurally unrelated collection of small molecules derived from various essential metabolic pathways. These compounds are important regulators of plant growth and mediate responses to both biotic and abiotic stresses. During the last ten years there have been many exciting advances in our understanding of plant hormone biology, including new discoveries in the areas of hormone biosynthesis, transport, perception and response. Receptors for many of the major hormones have now been identified, providing new opportunities to study the chemical specificity of hormone signaling. These studies also reveal a surprisingly important role for the ubiquitin-proteasome pathway in hormone signaling. In addition, recent work confirms that hormone signaling interacts at multiple levels during plant growth and development. In the future, a major challenge will be to understand how the information conveyed by these simple compounds is integrated during plant growth.
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