201
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Affiliation(s)
- Agustina Buet
- Instituto de Fisiología Vegetal (INFIVE); Universidad Nacional de La Plata (UNLP) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Buenos Aires Argentina
| | - Marcela Simontacchi
- Instituto de Fisiología Vegetal (INFIVE); Universidad Nacional de La Plata (UNLP) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Buenos Aires Argentina
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202
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Gayomba SR, Zhai Z, Jung HI, Vatamaniuk OK. Local and systemic signaling of iron status and its interactions with homeostasis of other essential elements. FRONTIERS IN PLANT SCIENCE 2015; 6:716. [PMID: 26442030 PMCID: PMC4568396 DOI: 10.3389/fpls.2015.00716] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 08/27/2015] [Indexed: 05/03/2023]
Abstract
Iron (Fe) is essential for plant growth and development. However, alkaline soils, which occupy approximately 30% of the world's arable lands, are considered Fe-limiting for plant growth because insoluble Fe (III) chelates prevail under these conditions. In contrast, high bioavailability of Fe in acidic soils can be toxic to plants due to the ability of Fe ions to promote oxidative stress. Therefore, plants have evolved sophisticated mechanisms to sense and respond to the fluctuation of Fe availability in the immediate environment and to the needs of developing shoot tissues to preclude deficiency while avoiding toxicity. In this review, we focus on recent advances in our understanding of local and systemic signaling of Fe status with emphasis on the contribution of Fe, its interaction with other metals and metal ligands in triggering molecular responses that regulate Fe uptake and partitioning in the plant body.
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Affiliation(s)
| | | | | | - Olena K. Vatamaniuk
- *Correspondence: Olena K. Vatamaniuk, Soil and Crop Sciences Section, School of Integrative Plant Sciences, Cornell University, 360 Tower Road, 608 Bradfield Hall, Ithaca, NY 14853, USA,
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203
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Zargar SM, Fujiwara M, Inaba S, Kobayashi M, Kurata R, Ogata Y, Fukao Y. Correlation analysis of proteins responsive to Zn, Mn, or Fe deficiency in Arabidopsis roots based on iTRAQ analysis. PLANT CELL REPORTS 2015; 34:157-66. [PMID: 25366567 DOI: 10.1007/s00299-014-1696-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 09/21/2014] [Accepted: 10/07/2014] [Indexed: 05/25/2023]
Abstract
For discovering the functional correlation between the identified and quantified proteins by iTRAQ analysis, here we propose a correlation analysis method with cosine correlation coefficients as a powerful tool. iTRAQ analysis is a quantitative proteomics approach that enables identification and quantification of a large number of proteins. In order to obtain proteins responsive to Zn, Mn, or Fe mineral deficiency, we conducted iTRAQ analysis using a microsomal fraction of protein extractions from Arabidopsis root tissues. We identified and quantified 730 common proteins in three biological replicates with less than 1 % false discovery rate. To determine the role of these proteins in tolerating mineral deficiencies and their relation to each other, we calculated cosine correlation coefficients and represented the outcomes on a correlation map for visual understanding of functional relations among the identified proteins. Functionally similar proteins were gathered into the same clusters. Interestingly, a cluster of proteins (FRO2, IRT1, AHA2, PDR9/ABCG37, and GLP5) highly responsive to Fe deficiency was identified, which included both known and unknown novel proteins involved in tolerating Fe deficiency. We propose that the correlation analysis with the cosine correlation coefficients is a powerful method for finding important proteins of interest to several biological processes through comprehensive data sets.
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Affiliation(s)
- Sajad Majeed Zargar
- Plant Global Education Project Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama, 8916-5, Ikoma, 630-0192, Japan
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204
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Strehmel N, Böttcher C, Schmidt S, Scheel D. Profiling of secondary metabolites in root exudates of Arabidopsis thaliana. PHYTOCHEMISTRY 2014; 108:35-46. [PMID: 25457500 DOI: 10.1016/j.phytochem.2014.10.003] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 10/01/2014] [Accepted: 10/08/2014] [Indexed: 05/20/2023]
Abstract
To explore the chemical composition of root exudates of the model plant Arabidopsis thaliana a workflow for nontargeted metabolite profiling of the semipolar fraction of root exudates was developed. It comprises hydroponic plant cultivation and sampling of root exudates under sterile conditions, sample preparation by solid-phase extraction and analysis by reversed-phase UPLC/ESI-QTOFMS. Following the established workflow, root exudates of six-week-old plants were profiled and a set of reproducibly occurring molecular features was compiled. To structurally elucidate the corresponding metabolites, accurate mass tandem mass spectrometry and on-line hydrogen/deuterium exchange were applied. Currently, a total of 103 compounds were detected and annotated by elemental composition of which more than 90 were structurally characterized or classified. Among them, 42 compounds were rigorously identified using an authenticated standard. The compounds identified so far include nucleosides, deoxynucleosides, aromatic amino acids, anabolites and catabolites of glucosinolates, dipeptides, indolics, salicylic and jasmonic acid catabolites, coumarins, mono-, di- and trilignols, hydroxycinnamic acid derivatives and oxylipins and exemplify the high chemical diversity of plant root exudates.
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205
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Kobayashi T, Nakanishi Itai R, Nishizawa NK. Iron deficiency responses in rice roots. RICE (NEW YORK, N.Y.) 2014; 7:27. [PMID: 26224556 PMCID: PMC4884003 DOI: 10.1186/s12284-014-0027-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Iron (Fe) is an essential element for most living organisms. To acquire sparingly soluble Fe from the rhizosphere, rice roots rely on two Fe acquisition pathways. The first of these pathways involves Fe(III) chelators specific to graminaceous plants, the mugineic acid family phytosiderophores, and the second involves absorption of Fe(2+). Key components in this response include enzymes involved in the biosynthesis of deoxymugineic acid (OsNAS1, OsNAS2, OsNAAT1, and OsDMAS1), the deoxymugineic acid efflux transporter (TOM1), the Fe(III)-deoxymugineic acid transporter (OsYSL15), and Fe(2+) transporters (OsIRT1, OsIRT2, and OsNRAMP1). In whole roots, these proteins are expressed in a coordinated manner with strong transcriptional induction in response to Fe deficiency. Radial transport of Fe to xylem and phloem is also mediated by the mugineic acid family phytosiderophores, as well as other chelators and their transporters, including Fe(II)-nicotianamine transporter (OsYSL2), phenolics efflux transporters (PEZ1 and PEZ2), and citrate efflux transporter (OsFRDL1). Among these, OsYSL2 is strongly induced under conditions of Fe deficiency. Both transcriptional induction and potential feedback repression mediate the expressional regulation of the genes involved in Fe uptake and translocation in response to Fe deficiency. The transcription factors IDEF1, IDEF2, and OsIRO2 are responsible for transcriptional induction, whereas the ubiquitin ligases OsHRZ1 and OsHRZ2, as well as the transcription factors OsIRO3 and OsbHLH133, are thought to mediate negative regulation. Furthermore, IDEF1 and OsHRZs bind Fe and other metals, and are therefore candidate Fe sensors. The interacting functions of these regulators are thought to fine tune the expression of proteins involved in Fe uptake and translocation.
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Affiliation(s)
- Takanori Kobayashi
- />Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012 Japan
- />Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa, 921-8836 Japan
| | - Reiko Nakanishi Itai
- />Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Naoko K. Nishizawa
- />Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa, 921-8836 Japan
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206
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Vacuolar-Iron-Transporter1-Like proteins mediate iron homeostasis in Arabidopsis. PLoS One 2014; 9:e110468. [PMID: 25360591 PMCID: PMC4215979 DOI: 10.1371/journal.pone.0110468] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 09/13/2014] [Indexed: 12/12/2022] Open
Abstract
Iron deficiency is a nutritional problem in plants and reduces crop productivity, quality and yield. With the goal of improving the iron (Fe) storage properties of plants, we have investigated the function of three Arabidopsis proteins with homology to Vacuolar Iron Transporter1 (AtVIT1). Heterologous expression of Vacuolar Iron Transporter-Like1 (AtVTL1; At1g21140), AtVTL2 (At1g76800) or AtVTL5 (At3g25190) in the yeast vacuolar Fe transport mutant, Δccc1, restored growth in the presence of 4 mM Fe. Isolated vacuoles from yeast expressing either of the VTL genes in the Δccc1 background had a three- to four-fold increase in Fe concentration compared to vacuoles isolated from the untransformed mutant. Transiently expressed GFP-tagged AtVTL1 was localized exclusively and AtVTL2 was localized primarily to the vacuolar membrane of onion epidermis cells. Seedling root growth of the Arabidopsis nramp3/nramp4 and vit1-1 mutants was decreased compared to the wild type when seedlings were grown under Fe deficiency. When expressed under the 35S promoter in the nramp3/nramp4 or vit1-1 backgrounds, AtVTL1, AtVTL2 or AtVTL5 restored root growth in both mutants. The seed Fe concentration in the nramp3/nramp4 mutant overexpressing AtVTL1, AtVTL2 or AtVTL5 was between 50 and 60% higher than in non-transformed double mutants or wild-type plants. We conclude that the VTL proteins catalyze Fe transport into vacuoles and thus contribute to the regulation of Fe homeostasis in planta.
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207
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Siwinska J, Kadzinski L, Banasiuk R, Gwizdek-Wisniewska A, Olry A, Banecki B, Lojkowska E, Ihnatowicz A. Identification of QTLs affecting scopolin and scopoletin biosynthesis in Arabidopsis thaliana. BMC PLANT BIOLOGY 2014; 14:280. [PMID: 25326030 PMCID: PMC4252993 DOI: 10.1186/s12870-014-0280-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 10/09/2014] [Indexed: 05/08/2023]
Abstract
BACKGROUND Scopoletin and its glucoside scopolin are important secondary metabolites synthesized in plants as a defense mechanism against various environmental stresses. They belong to coumarins, a class of phytochemicals with significant biological activities that is widely used in medical application and cosmetics industry. Although numerous studies showed that a variety of coumarins occurs naturally in several plant species, the details of coumarins biosynthesis and its regulation is not well understood. It was shown previously that coumarins (predominantly scopolin and scopoletin) occur in Arabidopsis thaliana (Arabidopsis) roots, but until now nothing is known about natural variation of their accumulation in this model plant. Therefore, the genetic architecture of coumarins biosynthesis in Arabidopsis has not been studied before. RESULTS Here, the variation in scopolin and scopoletin content was assessed by comparing seven Arabidopsis accessions. Subsequently, a quantitative trait locus (QTL) mapping was performed with an Advanced Intercross Recombinant Inbred Lines (AI-RILs) mapping population EstC (Est-1 × Col). In order to reveal the genetic basis of both scopolin and scopoletin biosynthesis, two sets of methanol extracts were made from Arabidopsis roots and one set was additionally subjected to enzymatic hydrolysis prior to quantification done by high-performance liquid chromatography (HPLC). We identified one QTL for scopolin and five QTLs for scopoletin accumulation. The identified QTLs explained 13.86% and 37.60% of the observed phenotypic variation in scopolin and scopoletin content, respectively. In silico analysis of genes located in the associated QTL intervals identified a number of possible candidate genes involved in coumarins biosynthesis. CONCLUSIONS Together, our results demonstrate for the first time that Arabidopsis is an excellent model for studying the genetic and molecular basis of natural variation in coumarins biosynthesis in plants. It additionally provides a basis for fine mapping and cloning of the genes involved in scopolin and scopoletin biosynthesis. Importantly, we have identified new loci for this biosynthetic process.
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Affiliation(s)
- Joanna Siwinska
- />Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, ul. Kladki 24, Gdansk, 80-822 Poland
| | - Leszek Kadzinski
- />Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, ul. Kladki 24, Gdansk, 80-822 Poland
| | - Rafal Banasiuk
- />Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, ul. Kladki 24, Gdansk, 80-822 Poland
| | - Anna Gwizdek-Wisniewska
- />Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, ul. Kladki 24, Gdansk, 80-822 Poland
| | - Alexandre Olry
- />Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, Vandœuvre-lès-Nancy, 54505 France
- />INRA, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, Vandœuvre-lès-Nancy, 54505 France
| | - Bogdan Banecki
- />Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, ul. Kladki 24, Gdansk, 80-822 Poland
| | - Ewa Lojkowska
- />Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, ul. Kladki 24, Gdansk, 80-822 Poland
| | - Anna Ihnatowicz
- />Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, ul. Kladki 24, Gdansk, 80-822 Poland
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208
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Zamioudis C, Hanson J, Pieterse CMJ. β-Glucosidase BGLU42 is a MYB72-dependent key regulator of rhizobacteria-induced systemic resistance and modulates iron deficiency responses in Arabidopsis roots. THE NEW PHYTOLOGIST 2014; 204:368-79. [PMID: 25138267 DOI: 10.1111/nph.12980] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 07/04/2014] [Indexed: 05/03/2023]
Abstract
Selected soil-borne rhizobacteria can trigger an induced systemic resistance (ISR) that is effective against a broad spectrum of pathogens. In Arabidopsis thaliana, the root-specific transcription factor MYB72 is required for the onset of ISR, but is also associated with plant survival under conditions of iron deficiency. Here, we investigated the role of MYB72 in both processes. To identify MYB72 target genes, we analyzed the root transcriptomes of wild-type Col-0, mutant myb72 and complemented 35S:FLAG-MYB72/myb72 plants in response to ISR-inducing Pseudomonas fluorescens WCS417. Five WCS417-inducible genes were misregulated in myb72 and complemented in 35S:FLAG-MYB72/myb72. Amongst these, we uncovered β-glucosidase BGLU42 as a novel component of the ISR signaling pathway. Overexpression of BGLU42 resulted in constitutive disease resistance, whereas the bglu42 mutant was defective in ISR. Furthermore, we found 195 genes to be constitutively upregulated in MYB72-overexpressing roots in the absence of WCS417. Many of these encode enzymes involved in the production of iron-mobilizing phenolic metabolites under conditions of iron deficiency. We provide evidence that BGLU42 is required for their release into the rhizosphere. Together, this work highlights a thus far unidentified link between the ability of beneficial rhizobacteria to stimulate systemic immunity and mechanisms induced by iron deficiency in host plants.
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Affiliation(s)
- Christos Zamioudis
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, PO Box 800.56, 3508 TB, Utrecht, the Netherlands
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209
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Moran Lauter AN, Peiffer GA, Yin T, Whitham SA, Cook D, Shoemaker RC, Graham MA. Identification of candidate genes involved in early iron deficiency chlorosis signaling in soybean (Glycine max) roots and leaves. BMC Genomics 2014; 15:702. [PMID: 25149281 PMCID: PMC4161901 DOI: 10.1186/1471-2164-15-702] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 08/12/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Iron is an essential micronutrient for all living things, required in plants for photosynthesis, respiration and metabolism. A lack of bioavailable iron in soil leads to iron deficiency chlorosis (IDC), causing a reduction in photosynthesis and interveinal yellowing of leaves. Soybeans (Glycine max (L.) Merr.) grown in high pH soils often suffer from IDC, resulting in substantial yield losses. Iron efficient soybean cultivars maintain photosynthesis and have higher yields under IDC-promoting conditions than inefficient cultivars. RESULTS To capture signaling between roots and leaves and identify genes acting early in the iron efficient cultivar Clark, we conducted a RNA-Seq study at one and six hours after replacing iron sufficient hydroponic media (100 μM iron(III) nitrate nonahydrate) with iron deficient media (50 μM iron(III) nitrate nonahydrate). At one hour of iron stress, few genes were differentially expressed in leaves but many were already changing expression in roots. By six hours, more genes were differentially expressed in the leaves, and a massive shift was observed in the direction of gene expression in both roots and leaves. Further, there was little overlap in differentially expressed genes identified in each tissue and time point. CONCLUSIONS Genes involved in hormone signaling, regulation of DNA replication and iron uptake utilization are key aspects of the early iron-efficiency response. We observed dynamic gene expression differences between roots and leaves, suggesting the involvement of many transcription factors in eliciting rapid changes in gene expression. In roots, genes involved iron uptake and development of Casparian strips were induced one hour after iron stress. In leaves, genes involved in DNA replication and sugar signaling responded to iron deficiency. The differentially expressed genes (DEGs) and signaling components identified here represent new targets for soybean improvement.
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Affiliation(s)
- Adrienne N Moran Lauter
- />USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, 1565 Agronomy Hall, Ames, IA 50011 USA
| | - Gregory A Peiffer
- />USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, 1565 Agronomy Hall, Ames, IA 50011 USA
| | - Tengfei Yin
- />Department of Statistics, Iowa State University, Ames, Iowa 50011 USA
| | - Steven A Whitham
- />Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011 USA
| | - Dianne Cook
- />Department of Statistics, Iowa State University, Ames, Iowa 50011 USA
| | - Randy C Shoemaker
- />USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, 1565 Agronomy Hall, Ames, IA 50011 USA
- />Department of Agronomy, Iowa State University, Ames, Iowa 50011 USA
| | - Michelle A Graham
- />USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, 1565 Agronomy Hall, Ames, IA 50011 USA
- />Department of Agronomy, Iowa State University, Ames, Iowa 50011 USA
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210
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Schmidt H, Günther C, Weber M, Spörlein C, Loscher S, Böttcher C, Schobert R, Clemens S. Metabolome analysis of Arabidopsis thaliana roots identifies a key metabolic pathway for iron acquisition. PLoS One 2014; 9:e102444. [PMID: 25058345 PMCID: PMC4109925 DOI: 10.1371/journal.pone.0102444] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 06/19/2014] [Indexed: 01/07/2023] Open
Abstract
Fe deficiency compromises both human health and plant productivity. Thus, it is important to understand plant Fe acquisition strategies for the development of crop plants which are more Fe-efficient under Fe-limited conditions, such as alkaline soils, and have higher Fe density in their edible tissues. Root secretion of phenolic compounds has long been hypothesized to be a component of the reduction strategy of Fe acquisition in non-graminaceous plants. We therefore subjected roots of Arabidopsis thaliana plants grown under Fe-replete and Fe-deplete conditions to comprehensive metabolome analysis by gas chromatography-mass spectrometry and ultra-pressure liquid chromatography electrospray ionization quadrupole time-of-flight mass spectrometry. Scopoletin and other coumarins were found among the metabolites showing the strongest response to two different Fe-limited conditions, the cultivation in Fe-free medium and in medium with an alkaline pH. A coumarin biosynthesis mutant defective in ortho-hydroxylation of cinnamic acids was unable to grow on alkaline soil in the absence of Fe fertilization. Co-cultivation with wild-type plants partially rescued the Fe deficiency phenotype indicating a contribution of extracellular coumarins to Fe solubilization. Indeed, coumarins were detected in root exudates of wild-type plants. Direct infusion mass spectrometry as well as UV/vis spectroscopy indicated that coumarins are acting both as reductants of Fe(III) and as ligands of Fe(II).
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Affiliation(s)
- Holger Schmidt
- Department of Plant Physiology, University of Bayreuth, Bayreuth, Germany
| | - Carmen Günther
- Department of Plant Physiology, University of Bayreuth, Bayreuth, Germany
| | - Michael Weber
- Department of Plant Physiology, University of Bayreuth, Bayreuth, Germany
| | - Cornelia Spörlein
- Department of Organic Chemistry, University of Bayreuth, Bayreuth, Germany
| | - Sebastian Loscher
- Department of Organic Chemistry, University of Bayreuth, Bayreuth, Germany
| | - Christoph Böttcher
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - Rainer Schobert
- Department of Organic Chemistry, University of Bayreuth, Bayreuth, Germany
- Bayreuth Center for Molecular Biosciences, University of Bayreuth, Bayreuth, Germany
| | - Stephan Clemens
- Department of Plant Physiology, University of Bayreuth, Bayreuth, Germany
- Bayreuth Center for Molecular Biosciences, University of Bayreuth, Bayreuth, Germany
- * E-mail:
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211
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Kobayashi T, Nishizawa NK. Iron sensors and signals in response to iron deficiency. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 224:36-43. [PMID: 24908504 DOI: 10.1016/j.plantsci.2014.04.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 04/03/2014] [Accepted: 04/03/2014] [Indexed: 05/03/2023]
Abstract
The transcription of genes involved in iron acquisition in plants is induced under iron deficiency, but our understanding of iron sensors and signals remains limited. Iron Deficiency-responsive Element-binding Factor 1 (IDEF1) and Hemerythrin motif-containing Really Interesting New Gene- and Zinc-finger proteins (HRZs)/BRUTUS (BTS) have recently emerged as candidate iron sensors because of their functions as potent regulators of iron deficiency responses and their iron-binding properties. IDEF1 is a central transcriptional regulator of graminaceous genes involved in iron uptake and utilization, predominantly during the early stages of iron deficiency. HRZs/BTS are E3 ubiquitin ligases and negative regulators of iron deficiency responses in both graminaceous and non-graminaceous plants. Rice OsHRZ1 and OsHRZ2 are also potent regulators of iron accumulation. Characterizing these putative iron sensors also provides clues to understanding the nature of iron signals, which may involve ionized iron itself, other metals, oxygen, redox status, heme and iron-sulfur clusters, in addition to metabolites affected by iron deficiency. Systemic iron responses may also be regulated by phloem-mobile iron and its chelators such as nicotianamine. Iron sensors and signals will be identified by demonstration of signal transmission by IDEF1, HRZs/BTS, or unknown factors.
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Affiliation(s)
- Takanori Kobayashi
- Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan; Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan.
| | - Naoko K Nishizawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan.
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212
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Lima MRM, Diaz SO, Lamego I, Grusak MA, Vasconcelos MW, Gil AM. Nuclear magnetic resonance metabolomics of iron deficiency in soybean leaves. J Proteome Res 2014; 13:3075-87. [PMID: 24738838 DOI: 10.1021/pr500279f] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Iron (Fe) deficiency is an important agricultural concern that leads to lower yields and crop quality. A better understanding of the condition at the metabolome level could contribute to the design of strategies to ameliorate Fe-deficiency problems. Fe-sufficient and Fe-deficient soybean leaf extracts and whole leaves were analyzed by liquid (1)H nuclear magnetic resonance (NMR) and high-resolution magic-angle spinning NMR spectroscopy, respectively. Overall, 30 compounds were measurable and identifiable (comprising amino and organic acids, fatty acids, carbohydrates, alcohols, polyphenols, and others), along with 22 additional spin systems (still unassigned). Thus, metabolite differences between treatment conditions could be evaluated for different compound families simultaneously. Statistically relevant metabolite changes upon Fe deficiency included higher levels of alanine, asparagine/aspartate, threonine, valine, GABA, acetate, choline, ethanolamine, hypoxanthine, trigonelline, and polyphenols and lower levels of citrate, malate, ethanol, methanol, chlorogenate, and 3-methyl-2-oxovalerate. The data indicate that the main metabolic impacts of Fe deficiency in soybean include enhanced tricarboxylic acid cycle activity, enhanced activation of oxidative stress protection mechanisms and enhanced amino acid accumulation. Metabolites showing accumulation differences in Fe-starved but visually asymptomatic leaves could serve as biomarkers for early detection of Fe-deficiency stress.
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Affiliation(s)
- Marta R M Lima
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto , Rua Dr. António Bernardino Almeida, 4200-072 Porto, Portugal
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213
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Vasconcelos MW, Clemente TE, Grusak MA. Evaluation of constitutive iron reductase (AtFRO2) expression on mineral accumulation and distribution in soybean (Glycine max. L). FRONTIERS IN PLANT SCIENCE 2014; 5:112. [PMID: 24765096 PMCID: PMC3982063 DOI: 10.3389/fpls.2014.00112] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 03/10/2014] [Indexed: 05/20/2023]
Abstract
Iron is an important micronutrient in human and plant nutrition. Adequate iron nutrition during crop production is central for assuring appropriate iron concentrations in the harvestable organs, for human food or animal feed. The whole-plant movement of iron involves several processes, including the reduction of ferric to ferrous iron at several locations throughout the plant, prior to transmembrane trafficking of ferrous iron. In this study, soybean plants that constitutively expressed the AtFRO2 iron reductase gene were analyzed for leaf iron reductase activity, as well as the effect of this transgene's expression on root, leaf, pod wall, and seed mineral concentrations. High Fe supply, in combination with the constitutive expression of AtFRO2, resulted in significantly higher concentrations of different minerals in roots (K, P, Zn, Ca, Ni, Mg, and Mo), pod walls (Fe, K, P, Cu, and Ni), leaves (Fe, P, Cu, Ca, Ni, and Mg) and seeds (Fe, Zn, Cu, and Ni). Leaf and pod wall iron concentrations increased as much as 500% in transgenic plants, while seed iron concentrations only increased by 10%, suggesting that factors other than leaf and pod wall reductase activity were limiting the translocation of iron to seeds. Protoplasts isolated from transgenic leaves had three-fold higher reductase activity than controls. Expression levels of the iron storage protein, ferritin, were higher in the transgenic leaves than in wild-type, suggesting that the excess iron may be stored as ferritin in the leaves and therefore unavailable for phloem loading and delivery to the seeds. Also, citrate and malate levels in the roots and leaves of transgenic plants were significantly higher than in wild-type, suggesting that organic acid production could be related to the increased accumulation of minerals in roots, leaves, and pod walls, but not in the seeds. All together, these results suggest a more ubiquitous role for the iron reductase in whole-plant mineral accumulation and distribution.
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Affiliation(s)
- Marta W. Vasconcelos
- Centro de Biotecnologia e Química Fina, Escola Superior de Biotecnologia, Centro Regional do Porto da Universidade Católica PortuguesaPorto, Portugal
- Department of Pediatrics, USDA-ARS Children’s Nutrition Research Center, Baylor College of MedicineHouston, TX, USA
| | - Thomas E. Clemente
- Center for Biotechnology – Plant Science Initiative, University of Nebraska-LincolnLincoln, NE, USA
| | - Michael A. Grusak
- Department of Pediatrics, USDA-ARS Children’s Nutrition Research Center, Baylor College of MedicineHouston, TX, USA
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Grillet L, Mari S, Schmidt W. Iron in seeds - loading pathways and subcellular localization. FRONTIERS IN PLANT SCIENCE 2014; 4:535. [PMID: 24427161 PMCID: PMC3877777 DOI: 10.3389/fpls.2013.00535] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 12/11/2013] [Indexed: 05/04/2023]
Abstract
Iron (Fe) is one of the most abundant elements on earth, but its limited bioavailability poses a major constraint for agriculture and constitutes a serious problem in human health. Due to an improved understanding of the mechanisms that control Fe homeostasis in plants, major advances toward engineering biofortified crops have been made during the past decade. Examples of successful biofortification strategies are, however, still scarce and the process of Fe loading into seeds is far from being well understood in most crop species. In particular in grains where the embryo represents the main storage compartment such as legumes, increasing the seed Fe content remains a challenging task. This review aims at placing the recently identified actors in Fe transport into the unsolved puzzle of grain filling, taking the differences of Fe distribution between various species into consideration. We summarize the current knowledge on Fe transport between symplasmic and apoplasmic compartments, and provide models for Fe trafficking and localization in different seed types that may help to develop high seed Fe germplasms.
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Affiliation(s)
- Louis Grillet
- Institute of Plant and Microbial BiologyAcademia Sinica, Taipei, Taiwan
| | - Stéphane Mari
- Plant Biology, Institut National pour la Recherche AgronomiqueMontpellier, France
| | - Wolfgang Schmidt
- Institute of Plant and Microbial BiologyAcademia Sinica, Taipei, Taiwan
- *Correspondence: Wolfgang Schmidt, Institute of Plant and Microbial Biology, Academia Sinica, Academia Road 128, Taipei 11529, Taiwan e-mail:
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215
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Ricachenevsky FK, Sperotto RA. There and back again, or always there? The evolution of rice combined strategy for Fe uptake. FRONTIERS IN PLANT SCIENCE 2014; 5:189. [PMID: 24860581 PMCID: PMC4030153 DOI: 10.3389/fpls.2014.00189] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 04/22/2014] [Indexed: 05/04/2023]
Affiliation(s)
- Felipe K. Ricachenevsky
- Laboratório de Fisiologia Vegetal, Departamento de Botânica, Centro de Biotecnologia, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil
- *Correspondence:
| | - Raul A. Sperotto
- Programa de Pós-Graduação em Biotecnologia, Centro de Ciências Biológicas e da Saúde, Centro Universitário UNIVATESLajeado, Brazil
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216
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Shimizu BI. 2-Oxoglutarate-dependent dioxygenases in the biosynthesis of simple coumarins. FRONTIERS IN PLANT SCIENCE 2014; 5:549. [PMID: 25404933 PMCID: PMC4217350 DOI: 10.3389/fpls.2014.00549] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 09/25/2014] [Indexed: 05/18/2023]
Abstract
Coumarins are natural plant products that have been the subject of extensive phytochemical and pharmacological research studies in the past few decades. The core structure of coumarins is derived from the respective cinnamates via ortho-hydroxylation of the aromatic ring, trans/cis isomerization, and lactonization. Various substitution patterns of coumarins have been reported, whereas the biosynthesis of coumarins remains elusive. Ortho-hydroxylation is a key step in simple coumarin biosynthesis as a branch point from the lignin biosynthetic pathway. 2-Oxoglutarate-dependent dioxygenases (2OGDs) from plants convert cinnamate derivatives into simple coumarins through the process of ortho-hydroxylation. This review describes the 2OGDs involved in coumarin biosynthesis and their substrate specificities.
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Affiliation(s)
- Bun-Ichi Shimizu
- *Correspondence: Bun-Ichi Shimizu, Department of Life Sciences, Graduate School of Life Sciences, Toyo University, Itakura, Gunma 3740193, Japan e-mail:
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217
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ABCG Transporters and Their Role in the Biotic Stress Response. SIGNALING AND COMMUNICATION IN PLANTS 2014. [DOI: 10.1007/978-3-319-06511-3_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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218
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Nakano RT, Yamada K, Bednarek P, Nishimura M, Hara-Nishimura I. ER bodies in plants of the Brassicales order: biogenesis and association with innate immunity. FRONTIERS IN PLANT SCIENCE 2014; 5:73. [PMID: 24653729 PMCID: PMC3947992 DOI: 10.3389/fpls.2014.00073] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 02/12/2014] [Indexed: 05/20/2023]
Abstract
The endoplasmic reticulum (ER) forms highly organized network structures composed of tubules and cisternae. Many plant species develop additional ER-derived structures, most of which are specific for certain groups of species. In particular, a rod-shaped structure designated as the ER body is produced by plants of the Brassicales order, which includes Arabidopsis thaliana. Genetic analyses and characterization of A. thaliana mutants possessing a disorganized ER morphology or lacking ER bodies have provided insights into the highly organized mechanisms responsible for the formation of these unique ER structures. The accumulation of proteins specific for the ER body within the ER plays an important role in the formation of ER bodies. However, a mutant that exhibits morphological defects of both the ER and ER bodies has not been identified. This suggests that plants in the Brassicales order have evolved novel mechanisms for the development of this unique organelle, which are distinct from those used to maintain generic ER structures. In A. thaliana, ER bodies are ubiquitous in seedlings and roots, but rare in rosette leaves. Wounding of rosette leaves induces de novo formation of ER bodies, suggesting that these structures are associated with resistance against pathogens and/or herbivores. ER bodies accumulate a large amount of β-glucosidases, which can produce substances that potentially protect against invading pests. Biochemical studies have determined that the enzymatic activities of these β-glucosidases are enhanced during cell collapse. These results suggest that ER bodies are involved in plant immunity, although there is no direct evidence of this. In this review, we provide recent perspectives of ER and ER body formation in A. thaliana, and discuss clues for the functions of ER bodies. We highlight defense strategies against biotic stress that are unique for the Brassicales order, and discuss how ER structures could contribute to these strategies.
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Affiliation(s)
- Ryohei T. Nakano
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Kenji Yamada
- Department of Cell Biology, National Institute for Basic BiologyOkazaki, Japan
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies (Sokendai)Okazaki, Japan
| | - Paweł Bednarek
- Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznañ, Poland
| | - Mikio Nishimura
- Department of Cell Biology, National Institute for Basic BiologyOkazaki, Japan
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies (Sokendai)Okazaki, Japan
| | - Ikuko Hara-Nishimura
- Department of Botany, Graduate School of Science, Kyoto UniversityKyoto, Japan
- *Correspondence: Ikuko Hara-Nishimura, Laboratory of Plant Molecular and Cell Biology, Department of Botany, Graduate School of Science, Kyoto University, Kita-Shirakawa Oiwake-cho, Sakyo-ku, 606-8502 Kyoto, Japan e-mail:
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219
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Pan IC, Schmidt W. Functional implications of K63-linked ubiquitination in the iron deficiency response of Arabidopsis roots. FRONTIERS IN PLANT SCIENCE 2014; 4:542. [PMID: 24427162 PMCID: PMC3877749 DOI: 10.3389/fpls.2013.00542] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 12/12/2013] [Indexed: 05/02/2023]
Abstract
Iron is an essential micronutrient that plays important roles as a redox cofactor in a variety of processes, many of which are related to DNA metabolism. The E2 ubiquitin conjugase UBC13, the only E2 protein that is capable of catalyzing the formation of non-canonical K63-linked ubiquitin chains, has been associated with the DNA damage tolerance pathway in eukaryotes, critical for maintenance of genome stability and integrity. We previously showed that UBC13 and an interacting E3 ubiquitin ligase, RGLG, affect the differentiation of root epidermal cells in Arabidopsis. When grown on iron-free media, Arabidopsis plants develops root hairs that are branched at their base, a response that has been interpreted as an adaption to reduced iron availability. Mutations in UBC13A abolished the branched root hair phenotype. Unexpectedly, mutations in RGLG genes caused constitutive root hair branching. Based on recent results that link endocytotic turnover of plasma membrane-bound PIN transporters to K63-linked ubiquitination, we reinterpreted our results in a context that classifies the root hair phenotype of iron-deficient plants as a consequence of altered auxin distribution. We show here that UBC13A/B and RGLG1/2 are involved in DNA damage repair and hypothesize that UBC13 protein becomes limited under iron-deficient conditions to prioritize DNA metabolism. The data suggest that genes involved in combating detrimental effects on genome stability may represent essential components in the plant's stress response.
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Affiliation(s)
- I-Chun Pan
- Institute of Plant and Microbial Biology, Academia SinicaTaipei, Taiwan
| | - Wolfgang Schmidt
- Institute of Plant and Microbial Biology, Academia SinicaTaipei, Taiwan
- Biotechnology Center, National Chung-Hsing UniversityTaichung, Taiwan
- Genome and Systems Biology Degree Program, College of Life Science, National Taiwan UniversityTaipei, Taiwan
- *Correspondence: Wolfgang Schmidt, Institute of Plant and Microbial Biology, Academia Sinica, Academia Road 128, Taipei 11529, Taiwan e-mail:
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