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Jain D, Schmidt W. Protein Phosphorylation Orchestrates Acclimations of Arabidopsis Plants to Environmental pH. Mol Cell Proteomics 2024; 23:100685. [PMID: 38000714 PMCID: PMC10837763 DOI: 10.1016/j.mcpro.2023.100685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 10/18/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
Environment pH (pHe) is a key parameter dictating a surfeit of conditions critical to plant survival and fitness. To elucidate the mechanisms that recalibrate cytoplasmic and apoplastic pH homeostasis, we conducted a comprehensive proteomic/phosphoproteomic inventory of plants subjected to transient exposure to acidic or alkaline pH, an approach that covered the majority of protein-coding genes of the reference plant Arabidopsis thaliana. Our survey revealed a large set-of so far undocumented pHe-dependent phospho-sites, indicative of extensive post-translational regulation of proteins involved in the acclimation to pHe. Changes in pHe altered both electrogenic H+ pumping via P-type ATPases and H+/anion co-transport processes, putatively leading to altered net trans-plasma membrane translocation of H+ ions. In pH 7.5 plants, the transport (but not the assimilation) of nitrogen via NRT2-type nitrate and AMT1-type ammonium transporters was induced, conceivably to increase the cytosolic H+ concentration. Exposure to both acidic and alkaline pH resulted in a marked repression of primary root elongation. No such cessation was observed in nrt2.1 mutants. Alkaline pH decreased the number of root hairs in the wild type but not in nrt2.1 plants, supporting a role of NRT2.1 in developmental signaling. Sequestration of iron into the vacuole via alterations in protein abundance of the vacuolar iron transporter VTL5 was inversely regulated in response to high and low pHe, presumptively in anticipation of associated changes in iron availability. A pH-dependent phospho-switch was also observed for the ABC transporter PDR7, suggesting changes in activity and, possibly, substrate specificity. Unexpectedly, the effect of pHe was not restricted to roots and provoked pronounced changes in the shoot proteome. In both roots and shoots, the plant-specific TPLATE complex components AtEH1 and AtEH2-essential for clathrin-mediated endocytosis-were differentially phosphorylated at multiple sites in response to pHe, indicating that the endocytic cargo protein trafficking is orchestrated by pHe.
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Affiliation(s)
- Dharmesh Jain
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei, Taiwan; Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan; Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Wolfgang Schmidt
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei, Taiwan; Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan; Biotechnology Center, National Chung-Hsing University, Taichun, Taiwan; Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei, Taiwan.
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2
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Kılıç M, Käpylä V, Gollan PJ, Aro EM, Rintamäki E. PSI Photoinhibition and Changing CO 2 Levels Initiate Retrograde Signals to Modify Nuclear Gene Expression. Antioxidants (Basel) 2023; 12:1902. [PMID: 38001755 PMCID: PMC10669900 DOI: 10.3390/antiox12111902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/10/2023] [Accepted: 10/16/2023] [Indexed: 11/26/2023] Open
Abstract
Photosystem I (PSI) is a critical component of the photosynthetic machinery in plants. Under conditions of environmental stress, PSI becomes photoinhibited, leading to a redox imbalance in the chloroplast. PSI photoinhibition is caused by an increase in electron pressure within PSI, which damages the iron-sulfur clusters. In this study, we investigated the susceptibility of PSI to photoinhibition in plants at different concentrations of CO2, followed by global gene expression analyses of the differentially treated plants. PSI photoinhibition was induced using a specific illumination protocol that inhibited PSI with minimal effects on PSII. Unexpectedly, the varying CO2 levels combined with the PSI-PI treatment neither increased nor decreased the likelihood of PSI photodamage. All PSI photoinhibition treatments, independent of CO2 levels, upregulated genes generally involved in plant responses to excess iron and downregulated genes involved in iron deficiency. PSI photoinhibition also induced genes encoding photosynthetic proteins that act as electron acceptors from PSI. We propose that PSI photoinhibition causes a release of iron from damaged iron-sulfur clusters, which initiates a retrograde signal from the chloroplast to the nucleus to modify gene expression. In addition, the deprivation of CO2 from the air initiated a signal that induced flavonoid biosynthesis genes, probably via jasmonate production.
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Affiliation(s)
| | | | | | | | - Eevi Rintamäki
- Molecular Plant Biology, Department of Life Technologies, University of Turku, 20014 Turku, Finland; (M.K.); (V.K.); (P.J.G.); (E.-M.A.)
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Liu Z, Qiu J, Shen Z, Wang C, Jiang N, Shi H, Kou Y. The E3 ubiquitin ligase OsRGLG5 targeted by the Magnaporthe oryzae effector AvrPi9 confers basal resistance against rice blast. PLANT COMMUNICATIONS 2023; 4:100626. [PMID: 37177781 PMCID: PMC10504590 DOI: 10.1016/j.xplc.2023.100626] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 03/29/2023] [Accepted: 05/09/2023] [Indexed: 05/15/2023]
Abstract
Rice blast, caused by Magnaporthe oryzae, is one of the most devastating diseases of rice. During infection, M. oryzae secretes effectors to facilitate blast development. Among these effectors, the avirulence factor AvrPi9 is recognized by Pi9, a broad-spectrum blast resistance protein that triggers Pi9-mediated resistance in rice. However, little is known about the interaction between AvrPi9 and Pi9 and how AvrPi9 exerts virulence to promote infection. In this study, we found that ectopic expression of AvrPi9 in the Pi9-lacking cultivar TP309 suppressed basal resistance against M. oryzae. Furthermore, we identified an AvrPi9-interacting protein in rice, which we named OsRGLG5, encoding a functional RING-type E3 ubiquitin ligase. During infection, AvrPi9 was ubiquitinated and degraded by OsRGLG5. Meanwhile, AvrPi9 affected the stability of OsRGLG5. Infection assays revealed that OsRGLG5 is a positive regulator of basal resistance against M. oryzae, but it is not essential for Pi9-mediated blast resistance in rice. In conclusion, our results revealed that OsRGLG5 is targeted by the M. oryzae effector AvrPi9 and positively regulates basal resistance against rice blast.
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Affiliation(s)
- Zhiquan Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Jiehua Qiu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Zhenan Shen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Congcong Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Nan Jiang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Huanbin Shi
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Yanjun Kou
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
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Hsieh EJ, Liao SW, Chang CY, Tseng CH, Wang SL, Grillet L. L-DOPA induces iron accumulation in roots of Ipomoea aquatica and Arabidopsis thaliana in a pH-dependent manner. BOTANICAL STUDIES 2023; 64:24. [PMID: 37620733 PMCID: PMC10449704 DOI: 10.1186/s40529-023-00396-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023]
Abstract
BACKGROUND Iron deficiency is the leading cause of anemia worldwide, particularly in countries with predominant plant-based diets. Plants constitute the main source of dietary iron. Increasing their iron concentration could reduce the occurrence of anemia. The water spinach Ipomoea aquatica is consumed as a vegetable throughout Asia and tolerates high iron concentrations making it an attractive candidate for iron biofortification. L-DOPA is an allelopathic molecule secreted by some legumes. L-DOPA can trigger the expression of Fe deficiency-inducible genes, and could potentially be used as a biostimulant to increase Fe concentration. RESULTS L-DOPA significantly affected root growth of water spinach, and triggered a massive accumulation of Fe in roots. Both effects were exacerbated when L-DOPA was dissolved in KOH, which is surprising given that L-DOPA is less stable at high pH. To check whether a higher pH could indeed increase the bioactivity of L-DOPA, we used Arabidopsis thaliana, which grows at lower pH than water spinach, and subjected the plants to L-DOPA treatments at pH 5.5 and pH 6.0, which are both within the optimal range for Arabidopsis nutrition. At pH 6.0, the root growth of Arabidopsis was more strongly inhibited than at pH 5.5. We found that at higher pH, L-DOPA oxidizes to form a melanin precipitate. CONCLUSIONS We concluded that the oxidation of L-DOPA that we observed upon solubilization in KOH, or in nutrient solutions at slightly higher pH produces melanin-related molecules that are more potent than L-DOPA itself to trigger the primary root growth inhibition, Fe uptake and root Fe accumulation in water spinach and Arabidopsis.
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Affiliation(s)
- En-Jung Hsieh
- College of Agriculture and Bioresources, Department of Agricultural Chemistry, National Taiwan University, Building No. 2, Rm. 209A No. 1, Sec. 4, Roosevelt Rd, Taipei, 10617, Taiwan
| | - Siao-Wei Liao
- College of Agriculture and Bioresources, Department of Agricultural Chemistry, National Taiwan University, Building No. 2, Rm. 209A No. 1, Sec. 4, Roosevelt Rd, Taipei, 10617, Taiwan
| | - Ching-Yuan Chang
- College of Agriculture and Bioresources, Department of Agricultural Chemistry, National Taiwan University, Building No. 2, Rm. 209A No. 1, Sec. 4, Roosevelt Rd, Taipei, 10617, Taiwan
| | - Chu-Han Tseng
- College of Agriculture and Bioresources, Department of Agricultural Chemistry, National Taiwan University, Building No. 2, Rm. 209A No. 1, Sec. 4, Roosevelt Rd, Taipei, 10617, Taiwan
| | - Shan-Li Wang
- College of Agriculture and Bioresources, Department of Agricultural Chemistry, National Taiwan University, Building No. 2, Rm. 209A No. 1, Sec. 4, Roosevelt Rd, Taipei, 10617, Taiwan
| | - Louis Grillet
- College of Agriculture and Bioresources, Department of Agricultural Chemistry, National Taiwan University, Building No. 2, Rm. 209A No. 1, Sec. 4, Roosevelt Rd, Taipei, 10617, Taiwan.
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Singh A, Gracheva M, Kovács Kis V, Keresztes Á, Sági-Kazár M, Müller B, Pankaczi F, Ahmad W, Kovács K, May Z, Tolnai G, Homonnay Z, Fodor F, Klencsár Z, Solti Á. Apoplast utilisation of nanohaematite initiates parallel suppression of RIBA1 and FRO1&3 in Cucumis sativus. NANOIMPACT 2023; 29:100444. [PMID: 36470408 DOI: 10.1016/j.impact.2022.100444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/13/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
Nanoscale Fe containing particles can penetrate the root apoplast. Nevertheless, cell wall size exclusion questions that for Fe mobilisation, a close contact between the membrane integrating FERRIC REDUCTASE OXIDASE (FRO) enzymes and Fe containing particles is required. Haematite nanoparticle suspension, size of 10-20 nm, characterized by 57Fe Mössbauer spectroscopy, TEM, ICP and SAED was subjected to Fe utilisation by the flavin secreting model plant cucumber (Cucumis sativus). Alterations in the structure and distribution of the particles were revealed by 57Fe Mössbauer spectroscopy, HRTEM and EDS element mapping. Biological utilisation of Fe resulted in a suppression of Fe deficiency responses (expression of CsFRO 1, 2 & 3 and RIBOFLAVIN A1; CsRIBA1 genes and root ferric chelate reductase activity). Haematite nanoparticles were stacked in the middle lamella of the apoplast. Fe mobilisation is evidenced by the reduction in the particle size. Fe release from nanoparticles does not require a contact with the plasma membrane. Parallel suppression in the CsFRO 1&3 and CsRIBA1 transcript amounts support that flavin biosynthesis is an inclusive Fe deficiency response involved in the reduction-based Fe utilisation of Cucumis sativus roots. CsFRO2 is suggested to play a role in the intracellular Fe homeostasis.
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Affiliation(s)
- Amarjeet Singh
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest H-1117, Hungary; PhD School of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest H-1117, Hungary
| | - Maria Gracheva
- Laboratory of Nuclear Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest H-1117, Hungary; Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest H-1117, Hungary; Centre for Energy Research, Eötvös Loránd Research Network, Konkoly-Thege Miklós út. 29-33, Budapest H-1121, Hungary
| | - Viktória Kovács Kis
- Centre for Energy Research, Eötvös Loránd Research Network, Konkoly-Thege Miklós út. 29-33, Budapest H-1121, Hungary; Institute of Environmental Sciences, University of Pannonia, Egyetem út. 10, Veszprém H-8200, Hungary
| | - Áron Keresztes
- Department of Plant Anatomy, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest H-1117, Hungary
| | - Máté Sági-Kazár
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest H-1117, Hungary; PhD School of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest H-1117, Hungary
| | - Brigitta Müller
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest H-1117, Hungary
| | - Fruzsina Pankaczi
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest H-1117, Hungary; PhD School of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest H-1117, Hungary
| | - Waqas Ahmad
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest H-1117, Hungary; PhD School of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest H-1117, Hungary
| | - Krisztina Kovács
- Laboratory of Nuclear Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest H-1117, Hungary
| | - Zoltán May
- Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok körútja 2, Budapest H-1117, Hungary
| | | | - Zoltán Homonnay
- Laboratory of Nuclear Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest H-1117, Hungary
| | - Ferenc Fodor
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest H-1117, Hungary
| | - Zoltán Klencsár
- Centre for Energy Research, Eötvös Loránd Research Network, Konkoly-Thege Miklós út. 29-33, Budapest H-1121, Hungary
| | - Ádám Solti
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest H-1117, Hungary.
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Retzer K, Moulinier-Anzola J, Lugsteiner R, Konstantinova N, Schwihla M, Korbei B, Luschnig C. Endosomally Localized RGLG-Type E3 RING-Finger Ligases Modulate Sorting of Ubiquitylation-Mimic PIN2. Int J Mol Sci 2022; 23:6767. [PMID: 35743207 PMCID: PMC9224344 DOI: 10.3390/ijms23126767] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/07/2022] [Accepted: 06/14/2022] [Indexed: 11/26/2022] Open
Abstract
Intracellular sorting and the abundance of sessile plant plasma membrane proteins are imperative for sensing and responding to environmental inputs. A key determinant for inducing adjustments in protein localization and hence functionality is their reversible covalent modification by the small protein modifier ubiquitin, which is for example responsible for guiding proteins from the plasma membrane to endosomal compartments. This mode of membrane protein sorting control requires the catalytic activity of E3 ubiquitin ligases, amongst which members of the RING DOMAIN LIGASE (RGLG) family have been implicated in the formation of lysine 63-linked polyubiquitin chains, serving as a prime signal for endocytic vacuolar cargo sorting. Nevertheless, except from some indirect implications for such RGLG activity, no further evidence for their role in plasma membrane protein sorting has been provided so far. Here, by employing RGLG1 reporter proteins combined with assessment of plasma membrane protein localization in a rglg1 rglg2 loss-of-function mutant, we demonstrate a role for RGLGs in cargo trafficking between plasma membrane and endosomal compartments. Specifically, our findings unveil a requirement for RGLG1 association with endosomal sorting compartments for fundamental aspects of plant morphogenesis, underlining a vital importance for ubiquitylation-controlled intracellular sorting processes.
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Affiliation(s)
| | | | | | | | | | - Barbara Korbei
- Department of Applied Genetics and Cell Biology, Institute of Molecular Plant Biology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; (K.R.); (J.M.-A.); (R.L.); (N.K.); (M.S.)
| | - Christian Luschnig
- Department of Applied Genetics and Cell Biology, Institute of Molecular Plant Biology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; (K.R.); (J.M.-A.); (R.L.); (N.K.); (M.S.)
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Mackinnon E, Stone SL. The Ubiquitin Proteasome System and Nutrient Stress Response. FRONTIERS IN PLANT SCIENCE 2022; 13:867419. [PMID: 35665152 PMCID: PMC9161090 DOI: 10.3389/fpls.2022.867419] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Plants utilize different molecular mechanisms, including the Ubiquitin Proteasome System (UPS) that facilitates changes to the proteome, to mitigate the impact of abiotic stresses on growth and development. The UPS encompasses the ubiquitination of selected substrates followed by the proteasomal degradation of the modified proteins. Ubiquitin ligases, or E3s, are central to the UPS as they govern specificity and facilitate the attachment of one or more ubiquitin molecules to the substrate protein. From recent studies, the UPS has emerged as an important regulator of the uptake and translocation of essential macronutrients and micronutrients. In this review, we discuss select E3s that are involved in regulating nutrient uptake and responses to stress conditions, including limited or excess levels of nitrogen, phosphorus, iron, and copper.
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Perea-García A, Puig S, Peñarrubia L. The role of post-transcriptional modulators of metalloproteins in response to metal deficiencies. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1735-1750. [PMID: 34849747 DOI: 10.1093/jxb/erab521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Copper and iron proteins have a wide range of functions in living organisms. Metal assembly into metalloproteins is a complex process, where mismetalation is detrimental and energy consuming to cells. Under metal deficiency, metal distribution is expected to reach a metalation ranking, prioritizing essential versus dispensable metalloproteins, while avoiding interference with other metals and protecting metal-sensitive processes. In this review, we propose that post-transcriptional modulators of metalloprotein mRNA (ModMeR) are good candidates in metal prioritization under metal-limited conditions. ModMeR target high quota or redundant metalloproteins and, by adjusting their synthesis, ModMeR act as internal metal distribution valves. Inappropriate metalation of ModMeR targets could compete with metal delivery to essential metalloproteins and interfere with metal-sensitive processes, such as chloroplastic photosynthesis and mitochondrial respiration. Regulation of ModMeR targets could increase or decrease the metal flow through interconnected pathways in cellular metal distribution, helping to achieve adequate differential metal requirements. Here, we describe and compare ModMeR that function in response to copper and iron deficiencies. Specifically, we describe copper-miRNAs from Arabidopsis thaliana and diverse iron ModMeR from yeast, mammals, and bacteria under copper and iron deficiencies, as well as the influence of oxidative stress. Putative functions derived from their role as ModMeR are also discussed.
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Affiliation(s)
- Ana Perea-García
- Departament de Bioquímica i Biologia Molecular and Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, Burjassot, Valencia, Spain
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Sergi Puig
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Lola Peñarrubia
- Departament de Bioquímica i Biologia Molecular and Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, Burjassot, Valencia, Spain
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Hsieh EJ, Lin WD, Schmidt W. Genomically Hardwired Regulation of Gene Activity Orchestrates Cellular Iron Homeostasis in Arabidopsis. RNA Biol 2021; 19:143-161. [PMID: 35067184 PMCID: PMC8786333 DOI: 10.1080/15476286.2021.2024024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/09/2021] [Accepted: 12/26/2021] [Indexed: 10/26/2022] Open
Abstract
Iron (Fe) is an essential micronutrient which plays pivotal roles as electron donor and catalyst across organisms. In plants, variable, often insufficient Fe supply necessitates mechanisms that constantly attune Fe uptake rates and recalibrate cellular Fe homoeostasis. Here, we show that short-term (0.5, 6, and 12 h) exposure of Arabidopsis thaliana plants to Fe deficiency triggered massive changes in gene activity governed by transcription and alternative splicing (AS), regulatory layers that were to a large extent mutually exclusive. Such preclusion was not observed for genes that are directly involved in the acquisition of Fe, which appears to be concordantly regulated by both expression and AS. Generally, genes with lower splice site strengths and higher intron numbers were more likely to be regulated by AS, no dependence on gene architecture was observed for transcriptionally controlled genes. Conspicuously, specific processes were associated with particular genomic features and biased towards either regulatory mode, suggesting that genomic hardwiring is functionally biased. Early changes in splicing patterns were, in many cases, congruent with later changes in transcript or protein abundance, thus contributing to the pronounced transcriptome-proteome discordance observed in plants.
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Affiliation(s)
- En-Jung Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Wen-Dar Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Wolfgang Schmidt
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan
- Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei, Taiwan
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Gautam CK, Tsai HH, Schmidt W. IRONMAN tunes responses to iron deficiency in concert with environmental pH. PLANT PHYSIOLOGY 2021; 187:1728-1745. [PMID: 34618058 PMCID: PMC8566206 DOI: 10.1093/plphys/kiab329] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 05/13/2021] [Indexed: 05/16/2023]
Abstract
Iron (Fe) is an essential mineral element that governs the composition of natural plant communities and limits crop yield in agricultural ecosystems due to its extremely low availability in most soils, particularly at alkaline pH. To extract sufficient Fe from the soil under such conditions, some plants, including Arabidopsis (Arabidopsis thaliana), secrete Fe-mobilizing phenylpropanoids, which mobilize sparingly soluble Fe hydroxides by reduction and chelation. We show here that ectopic expression of the peptides IRONMAN (IMA1) and IMA2 improves growth on calcareous soil by inducing biosynthesis and secretion of the catecholic coumarin 7,8-dihydroxy-6-methoxycoumarin (fraxetin) via increased expression of MYB72 and SCOPOLETIN 8-HYDROXYLASE, a response that is strictly dependent on elevated environmental pH (pHe). By contrast, transcription of the cytochrome P450 family protein CYP82C4, catalyzing the subsequent hydroxylation of fraxetin to sideretin, which forms less stable complexes with iron, was strongly repressed under such conditions. We concluded that IMA peptides regulate processes supporting Fe uptake at both acidic and elevated pH by controlling gene expression upstream of or in concert with a putative pHe signal, adapting the plant to prevailing edaphic conditions. This regulatory pattern confers tolerance to calcareous soils by extending the pH range in which Fe can be efficiently absorbed from the soil. Our results further suggest that pHe calibrates the activities of components of the Fe deficiency response, accentuating processes that are most efficient under the prevailing conditions. Altering the expression of IMA peptides provides a route for generating plants adapted to calcareous soils.
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Affiliation(s)
- Chandan Kumar Gautam
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung 40227, Taiwan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Huei-Hsuan Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Wolfgang Schmidt
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei 11529, Taiwan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung 40227, Taiwan
- Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
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11
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Huang T, Suen D. Iron insufficiency in floral buds impairs pollen development by disrupting tapetum function. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:244-267. [PMID: 34310779 PMCID: PMC9292431 DOI: 10.1111/tpj.15438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 06/25/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Reduction of crop yield due to iron (Fe) deficiency has always been a concern in agriculture. How Fe insufficiency in floral buds affects pollen development remains unexplored. Here, plants transferred to Fe-deficient medium at the reproductive stage had reduced floral Fe content and viable pollen and showed a defective pollen outer wall, all restored by supplying floral buds with Fe. A comparison of differentially expressed genes (DEGs) in Fe-deficient leaves, roots, and anthers suggested that changes in several cellular processes were unique to anthers, including increased lipid degradation. Co-expression analysis revealed that ABORTED MICROSPORES (AMS), DEFECTIVE IN TAPETAL DEVELOPMENT AND FUNCTION1, and BASIC HELIX-LOOP-HELIX 089/091/010 encode key upstream transcription factors of Fe deficiency-responsive DEGs involved in tapetum function and development, including tapetal ROS homeostasis, programmed cell death, and pollen outer wall formation-related lipid metabolism. Analysis of RESPIRATORY-BURST OXIDASE HOMOLOG E (RBOHE) gain- and loss-of-function under Fe deficiency indicated that RBOHE- and Fe-dependent regulation cooperatively control anther reactive oxygen species levels and pollen development. Since DEGs in Fe-deficient anthers were not significantly enriched in genes related to mitochondrial function, the changes in mitochondrial status under Fe deficiency, including respiration activity, density, and morphology, were probably because the Fe amount was insufficient to maintain proper mitochondrial protein function in anthers. To sum up, Fe deficiency in anthers may affect Fe-dependent protein function and impact upstream transcription factors and their downstream genes, resulting in extensively impaired tapetum function and pollen development.
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Affiliation(s)
- Tzu‐Hsiang Huang
- Agricultural Biotechnology Research CenterAcademia SinicaTaipei11529Taiwan
- Molecular and Biological Agricultural Sciences ProgramTaiwan International Graduate ProgramAcademia Sinica and National Chung‐Hsing UniversityTaipei11529Taiwan
- Graduate Institute of BiotechnologyNational Chung‐Hsing UniversityTaichung40227Taiwan
| | - Der‐Fen Suen
- Agricultural Biotechnology Research CenterAcademia SinicaTaipei11529Taiwan
- Molecular and Biological Agricultural Sciences ProgramTaiwan International Graduate ProgramAcademia Sinica and National Chung‐Hsing UniversityTaipei11529Taiwan
- Biotechnology CenterNational Chung‐Hsing UniversityTaichung40227Taiwan
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12
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Kroh GE, Pilon M. Iron deficiency and the loss of chloroplast iron-sulfur cluster assembly trigger distinct transcriptome changes in Arabidopsis rosettes. Metallomics 2020; 12:1748-1764. [PMID: 33047775 DOI: 10.1039/d0mt00175a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Regulation of mRNA abundance revealed a genetic program for plant leaf acclimation to iron (Fe) limitation. The transcript for SUFB, a key component of the plastid iron-sulfur (Fe-S) assembly pathway is down-regulated early after Fe deficiency, and prior to down-regulation of mRNAs encoding abundant chloroplast Fe containing proteins, which should economize the use of Fe. What controls this system is unclear. We utilized RNA-seq. aimed to identify differentially expressed transcripts that are co-regulated with SUFB after Fe deficiency in leaves. To distinguish if lack of Fe or lack of Fe-S cofactors and associated loss of enzymatic and photosynthetic activity trigger transcriptome reprogramming, WT plants on low Fe were compared with an inducible sufb-RNAi knockdown. Fe deficiency targeted a limited set of genes and predominantly affected transcripts for chloroplast localized proteins. A set of glutaredoxin transcripts was concertedly down-regulated early after Fe deficiency, however when these same genes were down-regulated by RNAi the effect on known chloroplast Fe deficiency marker proteins was minimal. In promoters of differentially expressed genes, binding motifs for AP2/ERF transcription factors were most abundant and three AP2/ERF transcription factors were also differentially expressed early after low Fe treatment. Surprisingly, Fe deficiency in a WT on low Fe and a sufb-RNAi knockdown presented very little overlap in differentially expressed genes. sufb-RNAi produced expression patterns expected for Fe excess and up-regulation of a transcript for another Fe-S assembly component not affected by low Fe. These findings indicate that Fe scarcity, not Fe utilization, triggers reprogramming of the transcriptome in leaves.
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Affiliation(s)
- Gretchen Elizabeth Kroh
- Biology Department, Colorado State University, 2515 W. Pitkin Street, Fort Collins, CO 80523-1878, USA.
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13
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Park EY, Tsuyuki KM, Parsons EM, Jeong J. PRC2-mediated H3K27me3 modulates shoot iron homeostasis in Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2020; 15:1784549. [PMID: 32594838 PMCID: PMC8550290 DOI: 10.1080/15592324.2020.1784549] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Plants use intricate mechanisms to adapt to changing iron conditions because iron is essential and also one of the most limiting nutrients for plant growth. Furthermore, iron is potentially toxic in excess and must be tightly regulated. Previously, we showed that chromatin remodeling via histone 3 lysine 27 trimethylation (H3K27me3) modulates the expression of FIT-dependent genes under iron deficiency in roots. This study builds on our previous findings, showing that H3K27me3 also modulates iron regulation in shoots. In the clf mutant, which lacks the predominant H3K27 tri-methyltransferase, we detected increased iron translocation to shoots under iron deficiency as compared to wild type. Transcriptomic analysis of shoots also revealed differential expression of genes consistent with higher iron levels in clf shoots than wild type shoots under iron-deficient conditions. In addition, we verify that YSL1 and IMA1, two genes involved in signaling iron status from shoots to roots, are direct targets of H3K27me3 and reveal iron-dependent deposition of H3K27me3 on these loci. This study contributes to a better understanding of the molecular mechanisms behind iron regulation in plants, as the effect of PRC2-mediated H3K27me3 on iron homeostasis genes expressed in the shoots has not been previously reported to our knowledge.
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Affiliation(s)
- Emily Y. Park
- Department of Biology, Amherst College, Amherst, MA, USA
| | | | | | - Jeeyon Jeong
- Department of Biology, Amherst College, Amherst, MA, USA
- CONTACT Jeeyon Jeong Department of Biology Amherst College, Amherst, MA, USA
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14
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Cheng N, Yu H, Rao X, Park S, Connolly EL, Hirschi KD, Nakata PA. Alteration of iron responsive gene expression in Arabidopsis glutaredoxin S17 loss of function plants with or without iron stress. PLANT SIGNALING & BEHAVIOR 2020; 15:1758455. [PMID: 32351167 PMCID: PMC8570760 DOI: 10.1080/15592324.2020.1758455] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 05/25/2023]
Abstract
Iron (Fe) is a mineral nutrient and a metal cofactor essential for plants. Iron limitation can have detrimental effects on plant growth and development, while excess iron inside plant cells leads to oxidative damage. As a result, plants have evolved complex regulatory networks to respond to fluctuations in cellular iron concentrations. The mechanisms that regulate these responses however, are not fully understood. Heterologous expression of an Arabidopsis thaliana monothiol glutaredoxin S17 (GRXS17) suppresses the over-accumulation of iron in the Saccharomyces cerevisiae Grx3/Grx4 mutant and disruption of GRXS17 causes plant sensitivity to exogenous oxidants and iron deficiency stress. GRXS17 may act as an important regulator in the plant's ability to respond to iron deficiency stress and maintain redox homeostasis. Here, we extend this investigation by analyzing iron-responsive gene expression of the Fer-like iron deficiency-induced transcription factor (FIT) network (FIT, IRT1, FRO1, and FRO2) and the bHLH transcription factor POPEYE (PYE) network (PYE, ZIF1, FRO3, NAS4, and BTS) in GRXS17 KO plants and wildtype controls grown under iron sufficiency and deficiency conditions. Our findings suggest that GRXS17 is required for tolerance to iron deficiency, and plays a negative regulatory role under conditions of iron sufficiency.
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Affiliation(s)
- Ninghui Cheng
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Han Yu
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Xiaolan Rao
- BioDiscovery Institute and Department of Biological Sciences, College of Sciences, University of North Texas, Denton, TX, USA
| | - Sunghun Park
- Department of Horticulture and Natural Resources, Kansas State University, Manhattan, KS, USA
| | - Erin L. Connolly
- Department of Plant Science, Penn State University, State College, PA, USA
| | - Kendal D. Hirschi
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Paul A. Nakata
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
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15
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Kroh GE, Pilon M. Regulation of Iron Homeostasis and Use in Chloroplasts. Int J Mol Sci 2020; 21:E3395. [PMID: 32403383 PMCID: PMC7247011 DOI: 10.3390/ijms21093395] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/08/2020] [Accepted: 05/09/2020] [Indexed: 01/20/2023] Open
Abstract
Iron (Fe) is essential for life because of its role in protein cofactors. Photosynthesis, in particular photosynthetic electron transport, has a very high demand for Fe cofactors. Fe is commonly limiting in the environment, and therefore photosynthetic organisms must acclimate to Fe availability and avoid stress associated with Fe deficiency. In plants, adjustment of metabolism, of Fe utilization, and gene expression, is especially important in the chloroplasts during Fe limitation. In this review, we discuss Fe use, Fe transport, and mechanisms of acclimation to Fe limitation in photosynthetic lineages with a focus on the photosynthetic electron transport chain. We compare Fe homeostasis in Cyanobacteria, the evolutionary ancestors of chloroplasts, with Fe homeostasis in green algae and in land plants in order to provide a deeper understanding of how chloroplasts and photosynthesis may cope with Fe limitation.
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Affiliation(s)
| | - Marinus Pilon
- Department of Biology, Colorado State University Department of Biology, Fort Collins, CO 80523, USA;
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16
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Role of the Ubiquitin Proteasome System in Plant Response to Abiotic Stress. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 343:65-110. [PMID: 30712675 DOI: 10.1016/bs.ircmb.2018.05.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ubiquitination is a prevalent post-translation modification system that is involved in almost all aspects of eukaryotic biology. It involves the attachment of ubiquitin, a small, highly conserved protein to selected substrates. The most notable function of ubiquitin is the targeting of modified proteins to the multi-proteolytic 26S proteasome complex for degradation. The ubiquitin proteasome system (UPS) regulates the abundance of numerous enzymes, structural and regulatory proteins ensuring proper cellular function. Plants utilize the UPS to facilitate cellular changes required to respond to and tolerate adverse growth conditions. In this review, the regulatory role of the UPS in responses to abiotic stress is discussed, particularly the function of ubiquitin-dependent degradation in the suppression, activation and attenuation or termination of stress signaling.
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17
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iTRAQ-based analysis of the Arabidopsis proteome reveals insights into the potential mechanisms of anthocyanin accumulation regulation in response to phosphate deficiency. J Proteomics 2018; 184:39-53. [PMID: 29920325 DOI: 10.1016/j.jprot.2018.06.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/01/2018] [Accepted: 06/07/2018] [Indexed: 01/18/2023]
Abstract
Phosphate (Pi) deficiency significantly limits plant growth in natural and agricultural systems. Accumulation of anthocyanins in shoots is a common response of Arabidopsis thaliana to Pi deficiency. To elucidate the mechanisms underlying Pi deficiency-induced anthocyanin accumulation, we employed a proteomic approach based on isobaric tags for relative and absolute quantification (iTRAQ) to investigate protein expression profiles of Arabidopsis thaliana seedlings subjected to Pi deficiency for 7 days. In total, 5,106 proteins were identified, of which 156 displayed significant changes in abundance upon Pi deficiency. Bioinformatics analysis indicated that flavonoid biosynthesis was the most significantly elevated metabolic process under Pi deficiency. We further examined the potential role of the flavonoid biosynthetic pathway using a dihydroflavonol 4-reductase (DFR) mutant (tt3) and quantitative RT-PCR (qRT-PCR) analysis, and found that the tt3 mutant was deprived of transcriptional up-regulation of three genes related to anthocyanin biosynthesis, modification and transport under Pi deficiency. These results showed that Pi deficiency probably enhances the anthocyanin accumulation by promoting the flavonoid biosynthesis. The exact functions of these proteins remain to be examined. Nevertheless, our study increases the understanding of the mechanisms implicated in the anthocyanin accumulation induced by Pi deficiency and adaptive responses of plants to Pi starvation.
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18
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Tsai HH, Rodríguez-Celma J, Lan P, Wu YC, Vélez-Bermúdez IC, Schmidt W. Scopoletin 8-Hydroxylase-Mediated Fraxetin Production Is Crucial for Iron Mobilization. PLANT PHYSIOLOGY 2018; 177:194-207. [PMID: 29559590 PMCID: PMC5933141 DOI: 10.1104/pp.18.00178] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 03/12/2018] [Indexed: 05/05/2023]
Abstract
Iron (Fe) is an essential mineral nutrient and an important factor for the composition of natural plant communities. Low Fe availability in aerated soils with neutral or alkaline pH has led to the evolution of elaborate mechanisms that extract Fe from the soil solution. In Arabidopsis (Arabidopsis thaliana), Fe is acquired by an orchestrated strategy that comprises mobilization, chelation, and reduction of Fe3+ prior to its uptake. Here, we show that At3g12900, previously annotated as scopoletin 8-hydroxylase (S8H), participates in Fe acquisition by mediating the biosynthesis of fraxetin (7,8-dihydroxy-6-methoxycoumarin), a coumarin derived from the scopoletin pathway. S8H is highly induced in roots of Fe-deficient plants both at the transcript and protein levels. Mutants defective in the expression of S8H showed increased sensitivity to growth on pH 7.0 media supplemented with an immobile source of Fe and reduced secretion of fraxetin. Transgenic lines overexpressing S8H exhibited an opposite phenotype. Homozygous s8h mutants grown on media with immobilized Fe accumulated significantly more scopolin, the storage form of scopoletin, supporting the designated function of S8H in scopoletin hydroxylation. Fraxetin exhibited Fe-reducing properties in vitro with higher rates being observed at neutral relative to acidic pH. Supplementing the media containing immobile Fe with fraxetin partially rescued the s8h mutants. In natural Arabidopsis accessions differing in their performance on media containing immobilized Fe, the amount of secreted fraxetin was highly correlated with growth and Fe and chlorophyll content, indicating that fraxetin secretion is a decisive factor for calcicole-calcifuge behavior (i.e. the ability/inability to thrive on alkaline soils) of plants.
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Affiliation(s)
- Huei-Hsuan Tsai
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung 40227, Taiwan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | | | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, P.R. China
| | - Yu-Ching Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | | | - Wolfgang Schmidt
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei 11529, Taiwan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung 40227, Taiwan
- Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
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19
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Suen DF, Schmidt W. OTU5 tunes environmental responses by sustaining chromatin structure. PLANT SIGNALING & BEHAVIOR 2018; 13:e1435963. [PMID: 29393726 PMCID: PMC5933914 DOI: 10.1080/15592324.2018.1435963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 01/24/2018] [Indexed: 06/07/2023]
Abstract
Phenotypic plasticity is dependent on the correct interpretation of environmental cues. We recently showed that the deubiquitinase OTU5 is required for orchestrating internal and external signals, tuning the morphogenesis of epidermal cells to the prevailing conditions. Homozygous otu5 mutants developed long and dense root hairs, resembling phosphate-deficient plants. The phenotype of otu5 plants was similar to that of arp6 plants, which carries a mutation that compromises the deposition of H2A.Z. Homozygous otu5 arp6 double mutants exhibited a synergistic phenotype, suggesting that the two mutations are functionally related. In a multi-omics approach comprising genome-wide DNA methylation, detection of various post-translational histone modifications as well as transcriptomic and proteomic surveys, we found that OTU5 is critical for maintaining the abundance of stimulus-responsive proteins, probably by modulating chromatin structure. It is concluded that changes in protein abundance and phenotypic readout in response to environmental signals are regulated by a complex interplay between various levels of gene expression.
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Affiliation(s)
- Der-Fen Suen
- Agricultural Biotechnology Research Center, Taipei, Taiwan
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20
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Tsai HH, Schmidt W. Mobilization of Iron by Plant-Borne Coumarins. TRENDS IN PLANT SCIENCE 2017; 22:538-548. [PMID: 28385337 DOI: 10.1016/j.tplants.2017.03.008] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 03/06/2017] [Accepted: 03/13/2017] [Indexed: 05/19/2023]
Abstract
Iron is one of the most abundant elements in soils, but its low phytoavailability at high pH restricts plant communities on alkaline soils to taxa that have evolved efficient strategies to increase iron solubility. Recent evidence provides support for a previously underestimated role of root-secreted coumarins in mobilizing iron through reduction and chelation as part of an orchestrated strategy evolved to improve the acquisition of iron from recalcitrant pools. Understanding the mechanisms that tune the production of iron-mobilizing coumarins and their intricate interplay with other biosynthesis pathways could yield clues for deciphering the molecular basis of 'iron efficiency' - the ability of plants to thrive on soils with limited iron availability - and may open avenues for generating iron-fortified crops.
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Affiliation(s)
- Huei Hsuan Tsai
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei 11529, Taiwan; Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung 40227, Taiwan; Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Wolfgang Schmidt
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei 11529, Taiwan; Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan; Biotechnology Center, National Chung-Hsing University, Taichung 40227, Taiwan; Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei 10617, Taiwan.
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21
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Li W, Lan P. The Understanding of the Plant Iron Deficiency Responses in Strategy I Plants and the Role of Ethylene in This Process by Omic Approaches. FRONTIERS IN PLANT SCIENCE 2017; 8:40. [PMID: 28174585 PMCID: PMC5259694 DOI: 10.3389/fpls.2017.00040] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/09/2017] [Indexed: 05/19/2023]
Abstract
Iron (Fe) is an essential plant micronutrient but is toxic in excess. Fe deficiency chlorosis is a major constraint for plant growth and causes severe losses of crop yields and quality. Under Fe deficiency conditions, plants have developed sophisticated mechanisms to keep cellular Fe homeostasis via various physiological, morphological, metabolic, and gene expression changes to facilitate the availability of Fe. Ethylene has been found to be involved in the Fe deficiency responses of plants through pharmacological studies or by the use of ethylene mutants. However, how ethylene is involved in the regulations of Fe starvation responses remains not fully understood. Over the past decade, omics approaches, mainly focusing on the RNA and protein levels, have been used extensively to investigate global gene expression changes under Fe-limiting conditions, and thousands of genes have been found to be regulated by Fe status. Similarly, proteome profiles have uncovered several hallmark processes that help plants adapt to Fe shortage. To find out how ethylene participates in the Fe deficiency response and explore putatively novel regulators for further investigation, this review emphasizes the integration of those genes and proteins, derived from omics approaches, regulated both by Fe deficiency, and ethylene into a systemic network by gene co-expression analysis.
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Affiliation(s)
- Wenfeng Li
- Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, College of Biology and the Environment, Nanjing Forestry UniversityNanjing, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of SciencesNanjing, China
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of SciencesNanjing, China
- *Correspondence: Ping Lan
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22
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Rodríguez-Celma J, Tsai YH, Wen TN, Wu YC, Curie C, Schmidt W. Systems-wide analysis of manganese deficiency-induced changes in gene activity of Arabidopsis roots. Sci Rep 2016; 6:35846. [PMID: 27804982 PMCID: PMC5090222 DOI: 10.1038/srep35846] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 10/06/2016] [Indexed: 11/09/2022] Open
Abstract
Manganese (Mn) is pivotal for plant growth and development, but little information is available regarding the strategies that evolved to improve Mn acquisition and cellular homeostasis of Mn. Using an integrated RNA-based transcriptomic and high-throughput shotgun proteomics approach, we generated a comprehensive inventory of transcripts and proteins that showed altered abundance in response to Mn deficiency in roots of the model plant Arabidopsis. A suite of 22,385 transcripts was consistently detected in three RNA-seq runs; LC-MS/MS-based iTRAQ proteomics allowed the unambiguous determination of 11,606 proteins. While high concordance between mRNA and protein expression (R = 0.87) was observed for transcript/protein pairs in which both gene products accumulated differentially upon Mn deficiency, only approximately 10% of the total alterations in the abundance of proteins could be attributed to transcription, indicating a large impact of protein-level regulation. Differentially expressed genes spanned a wide range of biological functions, including the maturation, translation, and transport of mRNAs, as well as primary and secondary metabolic processes. Metabolic analysis by UPLC-qTOF-MS revealed that the steady-state levels of several major glucosinolates were significantly altered upon Mn deficiency in both roots and leaves, possibly as a compensation for increased pathogen susceptibility under conditions of Mn deficiency.
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Affiliation(s)
- Jorge Rodríguez-Celma
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Taipei, Taiwan
| | - Yi-Hsiu Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Taipei, Taiwan
| | - Tuan-Nan Wen
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Taipei, Taiwan
| | - Yu-Ching Wu
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Taipei, Taiwan
| | - Catherine Curie
- Biochimie et Physiologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Institut National pour la Recherche Agronomique, Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, INRA/SupAgro, Université Montpellier 2, Montpellier, France
| | - Wolfgang Schmidt
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei, Taiwan
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23
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Nagels Durand A, Iñigo S, Ritter A, Iniesto E, De Clercq R, Staes A, Van Leene J, Rubio V, Gevaert K, De Jaeger G, Pauwels L, Goossens A. The Arabidopsis Iron-Sulfur Protein GRXS17 is a Target of the Ubiquitin E3 Ligases RGLG3 and RGLG4. PLANT & CELL PHYSIOLOGY 2016; 57:1801-1813. [PMID: 27497447 DOI: 10.1093/pcp/pcw122] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/05/2016] [Indexed: 06/06/2023]
Abstract
The stability of signaling proteins in eukaryotes is often controlled by post-translational modifiers. For polyubiquitination, specificity is assured by E3 ubiquitin ligases. Although plant genomes encode hundreds of E3 ligases, only few targets are known, even in the model Arabidopsis thaliana. Here, we identified the monothiol glutaredoxin GRXS17 as a substrate of the Arabidopsis E3 ubiquitin ligases RING DOMAIN LIGASE 3 (RGLG3) and RGLG4 using a substrate trapping approach involving tandem affinity purification of RING-dead versions. Simultaneously, we used a ubiquitin-conjugating enzym (UBC) panel screen to pinpoint UBC30 as a cognate E2 UBC capable of interacting with RGLG3 and RGLG4 and mediating auto-ubiquitination of RGLG3 and ubiquitination of GRXS17 in vitro. Accordingly, GRXS17 is ubiquitinated and degraded in an RGLG3- and RGLG4-dependent manner in planta. The truncated hemoglobin GLB3 also interacted with RGLG3 and RGLG4 but appeared to obstruct RGLG3 ubiquitination activity rather than being its substrate. Our results suggest that the RGLG family is intimately linked to the essential element iron.
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Affiliation(s)
- Astrid Nagels Durand
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium These authors contributed equally to this work
| | - Sabrina Iñigo
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium These authors contributed equally to this work
| | - Andrés Ritter
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - Elisa Iniesto
- Plant Molecular Genetics Department, National Centre for Biotechnology (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Campus Universidad Autónoma, Madrid, Spain
| | - Rebecca De Clercq
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - An Staes
- Medical Biotechnology Center, VIB, B-9000 Ghent, Belgium Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - Vicente Rubio
- Plant Molecular Genetics Department, National Centre for Biotechnology (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Campus Universidad Autónoma, Madrid, Spain
| | - Kris Gevaert
- Medical Biotechnology Center, VIB, B-9000 Ghent, Belgium Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - Laurens Pauwels
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium These authors contributed equally to this work
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium These authors contributed equally to this work.
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Muhammad D, Schmittling S, Williams C, Long TA. More than meets the eye: Emergent properties of transcription factors networks in Arabidopsis. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:64-74. [PMID: 27485161 DOI: 10.1016/j.bbagrm.2016.07.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/10/2016] [Accepted: 07/27/2016] [Indexed: 11/30/2022]
Abstract
Uncovering and mathematically modeling Transcription Factor Networks (TFNs) are the first steps in engineering plants with traits that are better equipped to respond to changing environments. Although several plant TFNs are well known, the framework for systematically modeling complex characteristics such as switch-like behavior, oscillations, and homeostasis that emerge from them remain elusive. This review highlights literature that provides, in part, experimental and computational techniques for characterizing TFNs. This review also outlines methodologies that have been used to mathematically model the dynamic characteristics of TFNs. We present several examples of TFNs in plants that are involved in developmental and stress response. In several cases, advanced algorithms capture or quantify emergent properties that serve as the basis for robustness and adaptability in plant responses. Increasing the use of mathematical approaches will shed new light on these regulatory properties that control plant growth and development, leading to mathematical models that predict plant behavior. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
| | - Selene Schmittling
- Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, USA
| | - Cranos Williams
- Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, USA
| | - Terri A Long
- Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA.
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25
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Salazar-Henao JE, Vélez-Bermúdez IC, Schmidt W. The regulation and plasticity of root hair patterning and morphogenesis. Development 2016; 143:1848-58. [DOI: 10.1242/dev.132845] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Root hairs are highly specialized cells found in the epidermis of plant roots that play a key role in providing the plant with water and mineral nutrients. Root hairs have been used as a model system for understanding both cell fate determination and the morphogenetic plasticity of cell differentiation. Indeed, many studies have shown that the fate of root epidermal cells, which differentiate into either root hair or non-hair cells, is determined by a complex interplay of intrinsic and extrinsic cues that results in a predictable but highly plastic pattern of epidermal cells that can vary in shape, size and function. Here, we review these studies and discuss recent evidence suggesting that environmental information can be integrated at multiple points in the root hair morphogenetic pathway and affects multifaceted processes at the chromatin, transcriptional and post-transcriptional levels.
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Affiliation(s)
| | | | - Wolfgang Schmidt
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
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26
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Meisrimler CN, Wienkoop S, Lyon D, Geilfus CM, Lüthje S. Long-term iron deficiency: Tracing changes in the proteome of different pea (Pisum sativum L.) cultivars. J Proteomics 2016; 140:13-23. [PMID: 27012544 DOI: 10.1016/j.jprot.2016.03.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 03/01/2016] [Accepted: 03/10/2016] [Indexed: 12/11/2022]
Abstract
UNLABELLED Iron deficiency (-Fe) is one of the major problems in crop production. Dicots, like pea (Pisum sativum L.), are Strategy I plants, which induce a group of specific enzymes such as Fe(III)-chelate reductase (FRO), Fe responsive transporter (IRT) and H(+)-ATPase (HA) at the root plasma membrane under -Fe. Different species and cultivars have been shown to react diversely to -Fe. Furthermore, different kinds of experimental set-ups for -Fe have to be distinguished: i) short-term vs. long-term, ii) constant vs. acute alteration and iii) buffered vs. unbuffered systems. The presented work compares the effects of constant long-term -Fe in an unbuffered system on roots of four different pea cultivars in a timely manner (12, 19 and 25days). To differentiate the effects of -Fe and plant development, control plants (+Fe) were analyzed in comparison to -Fe plants. Besides physiological measurements, an integrative study was conducted using a comprehensive proteome analysis. Proteins, related to stress adaptation (e.g. HSP), reactive oxygen species related proteins and proteins of the mitochondrial electron transport were identified to be changed in their abundance. Regulations and possible functions of identified proteins are discussed. SIGNIFICANCE Pea (Pisum sativum L.) belongs to the legume family (Fabaceae) and is an important crop plant due to high Fe, starch and protein contents. According to FAOSTAT data (September 2015), world production of the garden pea quadrupled from 1970 to 2012. Since the initial studies by Gregor Mendel, the garden pea became the most-characterized legume and has been used in numerous investigations in plant biochemistry and physiology, but is not well represented in the "omics"-related fields. A major limitation in pea production is the Fe availability from soils. Adaption mechanisms to Fe deficiency vary between species, and even cultivars have been shown to react diversely. A label-free proteomic approach, in combination with physiological measurements, was chosen to observe four different pea cultivars for 5 to 25days. Physiological and proteome data showed that cultivar Blauwschokker and Vroege were more susceptible to -Fe than cultivar Kelvedon (highly efficient) and GftR (semi-efficient). Proteomic data hint that the adaptation process to long-term -Fe takes place between days 19 and 25. Results show that adaptation processes of efficient cultivars are able to postpone secondary negative effects of long-term -Fe, possibly by stabilizing the protein metabolic processing and the mitochondrial electron transport components. This maintains the cellular energy proliferation, keeps ROS production low and postpones the mitochondrial cell death signal.
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Affiliation(s)
- Claudia-Nicole Meisrimler
- University of Hamburg, Biocenter Klein Flottbek and Botanical Garden, Oxidative Stress and Plant Proteomics Group, Ohnhorststraße 18, D-22609 Hamburg, Germany; CEA, IBEB, Laboratoire de biologie du développement des plantes, Saint-Paul-lez-Durance F-13108, France; CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance F-13108, France; Aix Marseille Université, BVME UMR7265, Marseille F-13284, France.
| | - Stefanie Wienkoop
- University of Vienna, Dept. of Ecogenomics and Systems Biology, Althanstrasse 14, A-1090 Vienna, Austria.
| | - David Lyon
- University of Vienna, Dept. of Ecogenomics and Systems Biology, Althanstrasse 14, A-1090 Vienna, Austria.
| | - Christoph-Martin Geilfus
- University of Kiel, Institute for Plant Nutrition and Soil Science, Hermann-Rodewald-Str. 2, 24118 Kiel, Germany.
| | - Sabine Lüthje
- University of Hamburg, Biocenter Klein Flottbek and Botanical Garden, Oxidative Stress and Plant Proteomics Group, Ohnhorststraße 18, D-22609 Hamburg, Germany.
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Shama LNS, Mark FC, Strobel A, Lokmer A, John U, Mathias Wegner K. Transgenerational effects persist down the maternal line in marine sticklebacks: gene expression matches physiology in a warming ocean. Evol Appl 2016; 9:1096-1111. [PMID: 27695518 PMCID: PMC5039323 DOI: 10.1111/eva.12370] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Accepted: 01/28/2016] [Indexed: 12/25/2022] Open
Abstract
Transgenerational effects can buffer populations against environmental change, yet little is known about underlying mechanisms, their persistence or the influence of environmental cue timing. We investigated mitochondrial respiratory capacity (MRC) and gene expression of marine sticklebacks that experienced acute or developmental acclimation to simulated ocean warming (21°C) across three generations. Previous work showed that acute acclimation of grandmothers to 21°C led to lower (optimized) offspring MRCs. Here, developmental acclimation of mothers to 21°C led to higher, but more efficient offspring MRCs. Offspring with a 21°C × 17°C grandmother-mother environment mismatch showed metabolic compensation: their MRCs were as low as offspring with a 17°C thermal history across generations. Transcriptional analyses showed primarily maternal but also grandmaternal environment effects: genes involved in metabolism and mitochondrial protein biosynthesis were differentially expressed when mothers developed at 21°C, whereas 21°C grandmothers influenced genes involved in hemostasis and apoptosis. Genes involved in mitochondrial respiration all showed higher expression when mothers developed at 21° and lower expression in the 21°C × 17°C group, matching the phenotypic pattern for MRCs. Our study links transcriptomics to physiology under climate change, and demonstrates that mechanisms underlying transgenerational effects persist across multiple generations with specific outcomes depending on acclimation type and environmental mismatch between generations.
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Affiliation(s)
- Lisa N S Shama
- Coastal Ecology Section Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung Wadden Sea Station Sylt Germany
| | - Felix C Mark
- Integrative Ecophysiology Section Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung Bremerhaven Germany
| | - Anneli Strobel
- Integrative Ecophysiology Section Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung Bremerhaven Germany; Man Society Environment (MGU) Department of Environmental Sciences University of Basel Switzerland
| | - Ana Lokmer
- Coastal Ecology Section Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung Wadden Sea Station Sylt Germany
| | - Uwe John
- Ecological Chemistry Section Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung Bremerhaven Germany
| | - K Mathias Wegner
- Coastal Ecology Section Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung Wadden Sea Station Sylt Germany
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28
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Sanchez-Lucas R, Mehta A, Valledor L, Cabello-Hurtado F, Romero-Rodrıguez MC, Simova-Stoilova L, Demir S, Rodriguez-de-Francisco LE, Maldonado-Alconada AM, Jorrin-Prieto AL, Jorrín-Novo JV. A year (2014-2015) of plants in Proteomics journal. Progress in wet and dry methodologies, moving from protein catalogs, and the view of classic plant biochemists. Proteomics 2016; 16:866-76. [PMID: 26621614 DOI: 10.1002/pmic.201500351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/26/2015] [Accepted: 11/04/2015] [Indexed: 12/23/2022]
Abstract
The present review is an update of the previous one published in Proteomics 2015 Reviews special issue [Jorrin-Novo, J. V. et al., Proteomics 2015, 15, 1089-1112] covering the July 2014-2015 period. It has been written on the bases of the publications that appeared in Proteomics journal during that period and the most relevant ones that have been published in other high-impact journals. Methodological advances and the contribution of the field to the knowledge of plant biology processes and its translation to agroforestry and environmental sectors will be discussed. This review has been organized in four blocks, with a starting general introduction (literature survey) followed by sections focusing on the methodology (in vitro, in vivo, wet, and dry), proteomics integration with other approaches (systems biology and proteogenomics), biological information, and knowledge (cell communication, receptors, and signaling), ending with a brief mention of some other biological and translational topics to which proteomics has made some contribution.
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Affiliation(s)
- Rosa Sanchez-Lucas
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia (CENARGEN), Brasília, DF, Brazil
| | - Luis Valledor
- Department of Biology of Organisms and Systems (BOS), University of Oviedo, Oviedo, Spain
| | | | - M Cristina Romero-Rodrıguez
- Centro Multidisciplinario de Investigaciones Tecnológicas, and Departamento de Fitoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Lyudmila Simova-Stoilova
- Plant Molecular Biology Department, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Sekvan Demir
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Luis E Rodriguez-de-Francisco
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain.,INTEC-Sto. Domingo, Santo Domingo, República Dominicana
| | - Ana M Maldonado-Alconada
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Ana L Jorrin-Prieto
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Jesus V Jorrín-Novo
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
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Zhang S, Zhang Y, Cao Y, Lei Y, Jiang H. Quantitative Proteomic Analysis Reveals Populus cathayana Females Are More Sensitive and Respond More Sophisticatedly to Iron Deficiency than Males. J Proteome Res 2016; 15:840-50. [PMID: 26842668 DOI: 10.1021/acs.jproteome.5b00750] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Previous studies have shown that there are significant sexual differences in the morphological and physiological responses of Populus cathayana Rehder to nitrogen and phosphorus deficiencies, but little is known about the sex-specific differences in responses to iron deficiency. In this study, the effects of iron deficiency on the morphology, physiology, and proteome of P. cathayana males and females were investigated. The results showed that iron deficiency (25 days) significantly decreased height growth, photosynthetic rate, chlorophyll content, and tissue iron concentration in both sexes. A comparison between the sexes indicated that iron-deficient males had less height inhibition and photosynthesis system II or chloroplast ultrastructural damage than iron-deficient females. iTRAQ-based quantitative proteomic analysis revealed that 144 and 68 proteins were decreased in abundance (e.g., proteins involved in photosynthesis, carbohydrate and energy metabolism, and gene expression regulation) and 78 and 39 proteins were increased in abundance (e.g., proteins involved in amino acid metabolism and stress response) according to the criterion of ratio ≥1.5 in females and males, respectively. A comparison between the sexes indicated that iron-deficient females exhibited a greater change in the proteins involved in photosynthesis, carbon and energy metabolism, the redox system, and stress responsive proteins. This study reveals females are more sensitive and have a more sophisticated response to iron deficiency compared with males and provides new insights into differential sexual responses to nutrient deficiency.
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Affiliation(s)
- Sheng Zhang
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences , Chengdu 610041, China
| | - Yunxiang Zhang
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences , Chengdu 610041, China.,University of Chinese Academy of Sciences , Beijing 100039, China
| | | | - Yanbao Lei
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences , Chengdu 610041, China
| | - Hao Jiang
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences , Chengdu 610041, China
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30
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Salazar-Henao JE, Schmidt W. An Inventory of Nutrient-Responsive Genes in Arabidopsis Root Hairs. FRONTIERS IN PLANT SCIENCE 2016; 7:237. [PMID: 26973680 PMCID: PMC4771725 DOI: 10.3389/fpls.2016.00237] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 02/12/2016] [Indexed: 05/07/2023]
Abstract
Root hairs, single cell extensions of root epidermal cells that are critically involved in the acquisition of mineral nutrients, have proven to be an excellent model system for studying plant cell growth. More recently, omics-based systems biology approaches have extended the model function of root hairs toward functional genomic studies. While such studies are extremely useful to decipher the complex mechanisms underlying root hair morphogenesis, their importance for the performance and fitness of the plant puts root hairs in the spotlight of research aimed at elucidating aspects with more practical implications. Here, we mined transcriptomic and proteomic surveys to catalog genes that are preferentially expressed in root hairs and responsive to nutritional signals. We refer to this group of genes as the root hair trophomorphome. Our analysis shows that the activity of genes within the trophomorphome is regulated at both the transcriptional and post-transcriptional level with the mode of regulation being related to the function of the gene product. A core set of proteins functioning in cell wall modification and protein transport was defined as the backbone of the trophomorphome. In addition, our study shows that homeostasis of reactive oxygen species and redox regulation plays a key role in root hair trophomorphogenesis.
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Affiliation(s)
| | - 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
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