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Zhu Z, Krall L, Li Z, Xi L, Luo H, Li S, He M, Yang X, Zan H, Gilbert M, Gombos S, Wang T, Neuhäuser B, Jacquot A, Lejay L, Zhang J, Liu J, Schulze WX, Wu XN. Transceptor NRT1.1 and receptor-kinase QSK1 complex controls PM H +-ATPase activity under low nitrate. Curr Biol 2024; 34:1479-1491.e6. [PMID: 38490203 DOI: 10.1016/j.cub.2024.02.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 01/09/2024] [Accepted: 02/27/2024] [Indexed: 03/17/2024]
Abstract
NRT1.1, a nitrate transceptor, plays an important role in nitrate binding, sensing, and nitrate-dependent lateral root (LR) morphology. However, little is known about NRT1.1-mediated nitrate signaling transduction through plasma membrane (PM)-localized proteins. Through in-depth phosphoproteome profiling using membranes of Arabidopsis roots, we identified receptor kinase QSK1 and plasma membrane H+-ATPase AHA2 as potential downstream components of NRT1.1 signaling in a mild low-nitrate (LN)-dependent manner. QSK1, as a functional kinase and molecular link, physically interacts with NRT1.1 and AHA2 at LN and specifically phosphorylates AHA2 at S899. Importantly, we found that LN, not high nitrate (HN), induces formation of the NRT1.1-QSK1-AHA2 complex in order to repress the proton efflux into the apoplast by increased phosphorylation of AHA2 at S899. Loss of either NRT1.1 or QSK1 thus results in a higher T947/S899 phosphorylation ratio on AHA2, leading to enhanced pump activity and longer LRs under LN. Our results uncover a regulatory mechanism in which NRT1.1, under LN conditions, promotes coreceptor QSK1 phosphorylation and enhances the NRT1.1-QSK1 complex formation to transduce LN sensing to the PM H+-ATPase AHA2, controlling the phosphorylation ratio of activating and inhibitory phosphorylation sites on AHA2. This then results in altered proton pump activity, apoplast acidification, and regulation of NRT1.1-mediated LR growth.
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Affiliation(s)
- Zhe Zhu
- Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science and School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Leonard Krall
- Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science and School of Life Sciences, Yunnan University, Kunming 650500, China.
| | - Zhi Li
- Department of Plant Systems Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Hongxiu Luo
- Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science and School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Shalan Li
- Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science and School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Mingjie He
- Department of Plant Systems Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Xiaolin Yang
- Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science and School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Haitao Zan
- Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science and School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Max Gilbert
- Department of Plant Systems Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Sven Gombos
- Department of Plant Systems Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Ting Wang
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China
| | - Benjamin Neuhäuser
- Nutritional Crop Physiology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Aurore Jacquot
- IPSiM, University Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Laurence Lejay
- IPSiM, University Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Jingbo Zhang
- National Academy of Agriculture Green Development, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Junzhong Liu
- Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science and School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, 70599 Stuttgart, Germany.
| | - Xu Na Wu
- Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science and School of Life Sciences, Yunnan University, Kunming 650500, China.
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Olt P, Ding W, Schulze WX, Ludewig U. The LaCLE35 peptide modifies rootlet density and length in cluster roots of white lupin. Plant Cell Environ 2024; 47:1416-1431. [PMID: 38226783 DOI: 10.1111/pce.14799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/24/2023] [Accepted: 12/16/2023] [Indexed: 01/17/2024]
Abstract
White lupin (lupinus albus L.) forms special bottlebrush-like root structures called cluster roots (CR) when phosphorus is low, to remobilise sparingly soluble phosphates in the soil. The molecular mechanisms that control the CR formation remain unknown. Root development in other plants is regulated by CLE (CLAVATA3/ EMBRYO SURROUNDING REGION (ESR)-RELATED) peptides, which provide more precise control mechanisms than common phytohormones. This makes these peptides interesting candidates to be involved in CR formation, where fine tuning to environmental factors is required. In this study we present an analysis of CLE peptides in white lupin. The peptides LaCLE35 (RGVHy PSGANPLHN) and LaCLE55 (RRVHy PSCHy PDPLHN) reduced root growth and altered CR in hydroponically cultured white lupins. We demonstrate that rootlet density and rootlet length were locally, but not systemically, impaired by exogenously applied CLE35. The peptide was identified in the xylem sap. The inhibitory effect of CLE35 on root growth was attributed to arrested cell elongation in root tips. Taken together, CLE peptides affect both rootlet density and rootlet length, which are two critical factors for CR formation, and may be involved in fine tuning this peculiar root structure that is present in a few crops and many Proteaceae species, under low phosphorus availability.
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Affiliation(s)
- Philipp Olt
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart, Germany
| | - Wenli Ding
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart, Germany
| | - Waltraud X Schulze
- Institute of Biology, Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Uwe Ludewig
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart, Germany
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3
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Li Z, Na Wu X, Jacquot A, Chaput V, Adamo M, Neuhäuser B, Straub T, Lejay L, Schulze WX. Phosphoregulation in the N-terminus of NRT2.1 affects nitrate uptake by controlling the interaction of NRT2.1 with NAR2.1 and kinase HPCAL1 in Arabidopsis. J Exp Bot 2024; 75:2127-2142. [PMID: 38066636 DOI: 10.1093/jxb/erad490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/06/2023] [Indexed: 03/28/2024]
Abstract
NRT2.1, the major high affinity nitrate transporter in roots, can be phosphorylated at five different sites within the N- and the C-terminus. Here, we characterized the functional relationship of two N-terminal phosphorylation sites, S21 and S28, in Arabidopsis. Based on a site-specific correlation network, we identified a receptor kinase (HPCAL1, AT5G49770), phosphorylating NRT2.1 at S21 and resulting in active nitrate uptake. HPCAL1 itself was regulated by phosphorylation at S839 and S870 within its kinase domain. In the active state, when S839 was dephosphorylated and S870 was phosphorylated, HPCAL1 was found to interact with the N-terminus of NRT2.1, mainly when S28 was dephosphorylated. Phosphorylation of NRT2.1 at S21 resulted in a reduced interaction of NRT2.1 with its activator NAR2.1, but nitrate transport activity remained. By contrast, phosphorylated NRT2.1 at S28 enhanced the interaction with NAR2.1, but reduced the interaction with HPCAL1. Here we identified HPCAL1 as the kinase affecting this phospho-switch through phosphorylation of NRT2.1 at S21.
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Affiliation(s)
- Zhi Li
- Department of Plant Systems Biology, University of Hohenheim, D-70593, Stuttgart, Germany
| | - Xu Na Wu
- Department of Plant Systems Biology, University of Hohenheim, D-70593, Stuttgart, Germany
| | - Aurore Jacquot
- BPMP, University Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Valentin Chaput
- BPMP, University Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Mattia Adamo
- BPMP, University Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Benjamin Neuhäuser
- Department of Crop Physiology, University of Hohenheim, D-70593, Stuttgart, Germany
| | - Tatsiana Straub
- Department of Plant Systems Biology, University of Hohenheim, D-70593, Stuttgart, Germany
| | - Laurence Lejay
- BPMP, University Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, D-70593, Stuttgart, Germany
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Liese A, Eichstädt B, Lederer S, Schulz P, Oehlschläger J, Matschi S, Feijó JA, Schulze WX, Konrad KR, Romeis T. Imaging of plant calcium-sensor kinase conformation monitors real time calcium-dependent decoding in planta. Plant Cell 2024; 36:276-297. [PMID: 37433056 DOI: 10.1093/plcell/koad196] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 06/14/2023] [Accepted: 07/10/2023] [Indexed: 07/13/2023]
Abstract
Changes in cytosolic calcium (Ca2+) concentration are among the earliest reactions to a multitude of stress cues. While a plethora of Ca2+-permeable channels may generate distinct Ca2+ signatures and contribute to response specificities, the mechanisms by which Ca2+ signatures are decoded are poorly understood. Here, we developed a genetically encoded Förster resonance energy transfer (FRET)-based reporter that visualizes the conformational changes in Ca2+-dependent protein kinases (CDPKs/CPKs). We focused on two CDPKs with distinct Ca2+-sensitivities, highly Ca2+-sensitive Arabidopsis (Arabidopsis thaliana) AtCPK21 and rather Ca2+-insensitive AtCPK23, to report conformational changes accompanying kinase activation. In tobacco (Nicotiana tabacum) pollen tubes, which naturally display coordinated spatial and temporal Ca2+ fluctuations, CPK21-FRET, but not CPK23-FRET, reported oscillatory emission ratio changes mirroring cytosolic Ca2+ changes, pointing to the isoform-specific Ca2+-sensitivity and reversibility of the conformational change. In Arabidopsis guard cells, CPK21-FRET-monitored conformational dynamics suggest that CPK21 serves as a decoder of signal-specific Ca2+ signatures in response to abscisic acid and the flagellin peptide flg22. Based on these data, CDPK-FRET is a powerful approach for tackling real-time live-cell Ca2+ decoding in a multitude of plant developmental and stress responses.
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Affiliation(s)
- Anja Liese
- Department for Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany
- Dahlem Centre of Plant Sciences, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Bernadette Eichstädt
- Dahlem Centre of Plant Sciences, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Sarah Lederer
- Department for Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany
| | - Philipp Schulz
- Dahlem Centre of Plant Sciences, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Jan Oehlschläger
- Department for Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany
| | - Susanne Matschi
- Department for Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany
| | - José A Feijó
- Department of Cell Biology & Molecular Genetics, University of Maryland, 2136 Bioscience Research Bldg, College Park, MD 20742-5815, USA
| | - Waltraud X Schulze
- Plant Systems Biology, Universität Hohenheim, D-70593 Stuttgart, Germany
| | - Kai R Konrad
- Julius-Von-Sachs Institute for Biosciences, Julius Maximilians Universität Würzburg, D-97082 Würzburg, Germany
| | - Tina Romeis
- Department for Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany
- Dahlem Centre of Plant Sciences, Freie Universität Berlin, D-14195 Berlin, Germany
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Ahmad B, Lerma-Reyes R, Mukherjee T, Nguyen HV, Weber AL, Schulze WX, Comer JR, Schrick K. Nuclear localization of HD-Zip IV transcription factor GLABRA2 is driven by Importin α. bioRxiv 2023:2023.11.03.565550. [PMID: 37961624 PMCID: PMC10635128 DOI: 10.1101/2023.11.03.565550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
GLABRA2 (GL2), a class IV homeodomain leucine-zipper (HD-Zip IV) transcription factor (TF) from Arabidopsis , is a developmental regulator of specialized cell types in the epidermis. GL2 contains a putative monopartite nuclear localization sequence (NLS) partially overlapping with its homeodomain (HD). We demonstrate that NLS deletion or alanine substitution of its basic residues (KRKRKK) affects nuclear localization and results in a loss-of-function phenotype. Fusion of the predicted NLS (GTNKRKRKKYHRH) to the fluorescent protein EYFP is sufficient for its nuclear localization in roots and trichomes. The functional NLS is evolutionarily conserved in a distinct subset of HD-Zip IV members including PROTODERMAL FACTOR2 (PDF2). Despite partial overlap of the NLS with the HD, genetic dissection of the NLS from PDF2 indicates that nuclear localization and DNA binding are separable functions. Affinity purification of GL2 from plant tissues followed by mass spectrometry-based proteomics identified Importin α (IMPα) isoforms as potential GL2 interactors. NLS structural prediction and molecular docking studies with IMPα-3 revealed major interacting residues. Split-ubiquitin cytosolic yeast two-hybrid assays suggest interaction between GL2 and four IMPα isoforms from Arabidopsis. Direct interactions were verified in vitro by co-immunoprecipitation with recombinant proteins. IMPα triple mutants ( impα- 1,2,3 ) exhibit defects in EYFP:GL2 nuclear localization in trichomes but not in roots, consistent with tissue-specific and redundant functions of IMPα isoforms in Arabidopsis . Taken together, our findings provide mechanistic evidence for IMPα-dependent nuclear localization of GL2 and other HD-Zip IV TFs in plants. One sentence summary GLABRA2, a representative HD-Zip IV transcription factor from Arabidopsis , contains an evolutionarily conserved monopartite nuclear localization sequence that is recognized by Importin α for translocation to the nucleus, a process that is necessary for cell-type differentiation of the epidermis.
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Kränzlein M, Schmöckel SM, Geilfus CM, Schulze WX, Altenbuchinger M, Hrenn H, Roessner U, Zörb C. Lipid remodeling of contrasting maize ( Zea mays L.) hybrids under repeated drought. Front Plant Sci 2023; 14:1050079. [PMID: 37235021 PMCID: PMC10206266 DOI: 10.3389/fpls.2023.1050079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 04/17/2023] [Indexed: 05/28/2023]
Abstract
The role of recovery after drought has been proposed to play a more prominent role during the whole drought-adaption process than previously thought. Two maize hybrids with comparable growth but contrasting physiological responses were investigated using physiological, metabolic, and lipidomic tools to understand the plants' strategies of lipid remodeling in response to repeated drought stimuli. Profound differences in adaptation between hybrids were discovered during the recovery phase, which likely gave rise to different degrees of lipid adaptability to the subsequent drought event. These differences in adaptability are visible in galactolipid metabolism and fatty acid saturation patterns during recovery and may lead to a membrane dysregulation in the sensitive maize hybrid. Moreover, the more drought-tolerant hybrid displays more changes of metabolite and lipid abundance with a higher number of differences within individual lipids, despite a lower physiological response, while the responses in the sensitive hybrid are higher in magnitude but lower in significance on the level of individual lipids and metabolites. This study suggests that lipid remodeling during recovery plays a key role in the drought response of plants.
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Affiliation(s)
- Markus Kränzlein
- Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | | | | | - Waltraud X. Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Michael Altenbuchinger
- Department of Medical Bioinformatics, University Medical Center Göttingen, Göttingen, Germany
| | - Holger Hrenn
- Core Facility Hohenheim, University of Hohenheim, Stuttgart, Germany
| | - Ute Roessner
- Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Christian Zörb
- Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
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7
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Gombos S, Miras M, Howe V, Xi L, Pottier M, Kazemein Jasemi NS, Schladt M, Ejike JO, Neumann U, Hänsch S, Kuttig F, Zhang Z, Dickmanns M, Xu P, Stefan T, Baumeister W, Frommer WB, Simon R, Schulze WX. A high-confidence Physcomitrium patens plasmodesmata proteome by iterative scoring and validation reveals diversification of cell wall proteins during evolution. New Phytol 2023; 238:637-653. [PMID: 36636779 DOI: 10.1111/nph.18730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
Plasmodesmata (PD) facilitate movement of molecules between plant cells. Regulation of this movement is still not understood. Plasmodesmata are hard to study, being deeply embedded within cell walls and incorporating several membrane types. Thus, structure and protein composition of PD remain enigmatic. Previous studies of PD protein composition identified protein lists with few validations, making functional conclusions difficult. We developed a PD scoring approach in iteration with large-scale systematic localization, defining a high-confidence PD proteome of Physcomitrium patens (HC300). HC300, together with bona fide PD proteins from literature, were placed in Pddb. About 65% of proteins in HC300 were not previously PD-localized. Callose-degrading glycolyl hydrolase family 17 (GHL17) is an abundant protein family with representatives across evolutionary scale. Among GHL17s, we exclusively found members of one phylogenetic clade with PD localization and orthologs occur only in species with developed PD. Phylogenetic comparison was expanded to xyloglucan endotransglucosylases/hydrolases and Exordium-like proteins, which also diversified into PD-localized and non-PD-localized members on distinct phylogenetic clades. Our high-confidence PD proteome HC300 provides insights into diversification of large protein families. Iterative and systematic large-scale localization across plant species strengthens the reliability of HC300 as basis for exploring structure, function, and evolution of this important organelle.
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Affiliation(s)
- Sven Gombos
- Department of Plant Systems Biology, University of Hohenheim, 70593, Stuttgart, Germany
| | - Manuel Miras
- Department of Molecular Physiology, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Vicky Howe
- Department of Developmental Genetics, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, 70593, Stuttgart, Germany
| | - Mathieu Pottier
- Department of Molecular Physiology, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Neda S Kazemein Jasemi
- Department of Developmental Genetics, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Moritz Schladt
- Department of Molecular Physiology, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - J Obinna Ejike
- Department of Molecular Physiology, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Ulla Neumann
- Central Microscopy, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Sebastian Hänsch
- Center for Advanced Imaging, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Franziska Kuttig
- Department of Developmental Genetics, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Zhaoxia Zhang
- Department of Plant Systems Biology, University of Hohenheim, 70593, Stuttgart, Germany
| | - Marcel Dickmanns
- Department of Molecular Physiology, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Peng Xu
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Thorsten Stefan
- Department of Plant Systems Biology, University of Hohenheim, 70593, Stuttgart, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Wolf B Frommer
- Department of Molecular Physiology, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
- Institute for Transformative Biomolecules, Nagoya University, Nagoya, 464-0813, Japan
| | - Rüdiger Simon
- Department of Developmental Genetics, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, 70593, Stuttgart, Germany
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Wang J, Xi L, Wu XN, König S, Rohr L, Neumann T, Weber J, Harter K, Schulze WX. PEP7 acts as a peptide ligand for the receptor kinase SIRK1 to regulate aquaporin-mediated water influx and lateral root growth. Mol Plant 2022; 15:1615-1631. [PMID: 36131543 DOI: 10.1016/j.molp.2022.09.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/11/2022] [Accepted: 09/19/2022] [Indexed: 06/15/2023]
Abstract
Plant receptors constitute a large protein family that regulates various aspects of development and responses to external cues. Functional characterization of this protein family and the identification of their ligands remain major challenges in plant biology. Previously, we identified plasma membrane-intrinsic sucrose-induced receptor kinase 1 (SIRK1) and Qian Shou kinase 1 (QSK1) as receptor/co-receptor pair involved in the regulation of aquaporins in response to osmotic conditions induced by sucrose. In this study, we identified a member of the elicitor peptide (PEP) family, namely PEP7, as the specific ligand of th receptor kinase SIRK1. PEP7 binds to the extracellular domain of SIRK1 with a binding constant of 1.44 ± 0.79 μM and is secreted to the apoplasm specifically in response to sucrose treatment. Stabilization of a signaling complex involving SIRK1, QSK1, and aquaporins as substrates is mediated by alterations in the external sucrose concentration or by PEP7 application. Moreover, the presence of PEP7 induces the phosphorylation of aquaporins in vivo and enhances water influx into protoplasts. Disturbed water influx, in turn, led to delayed lateral root development in the pep7 mutant. The loss-of-function mutant of SIRK1 is not responsive to external PEP7 treatment regarding kinase activity, aquaporin phosphorylation, water influx activity, and lateral root development. Taken together, our data indicate that the PEP7/SIRK1/QSK1 complex represents a crucial perception and response module that mediates sucrose-controlled water flux in plants and lateral root development.
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Affiliation(s)
- Jiahui Wang
- Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Xu Na Wu
- Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany; School of Life Science, Center for Life Sciences, Yunnan University, 650091 Kunming, People's Republic of China
| | - Stefanie König
- Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Leander Rohr
- Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Theresia Neumann
- Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Jan Weber
- Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Klaus Harter
- Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany.
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Hui J, An X, Li Z, Neuhäuser B, Ludewig U, Wu X, Schulze WX, Chen F, Feng G, Lambers H, Zhang F, Yuan L. The mycorrhiza-specific ammonium transporter ZmAMT3;1 mediates mycorrhiza-dependent nitrogen uptake in maize roots. Plant Cell 2022; 34:4066-4087. [PMID: 35880836 PMCID: PMC9516061 DOI: 10.1093/plcell/koac225] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/18/2022] [Indexed: 06/15/2023]
Abstract
Most plant species can form symbioses with arbuscular mycorrhizal fungi (AMFs), which may enhance the host plant's acquisition of soil nutrients. In contrast to phosphorus nutrition, the molecular mechanism of mycorrhizal nitrogen (N) uptake remains largely unknown, and its physiological relevance is unclear. Here, we identified a gene encoding an AMF-inducible ammonium transporter, ZmAMT3;1, in maize (Zea mays) roots. ZmAMT3;1 was specifically expressed in arbuscule-containing cortical cells and the encoded protein was localized at the peri-arbuscular membrane. Functional analysis in yeast and Xenopus oocytes indicated that ZmAMT3;1 mediated high-affinity ammonium transport, with the substrate NH4+ being accessed, but likely translocating uncharged NH3. Phosphorylation of ZmAMT3;1 at the C-terminus suppressed transport activity. Using ZmAMT3;1-RNAi transgenic maize lines grown in compartmented pot experiments, we demonstrated that substantial quantities of N were transferred from AMF to plants, and 68%-74% of this capacity was conferred by ZmAMT3;1. Under field conditions, the ZmAMT3;1-dependent mycorrhizal N pathway contributed >30% of postsilking N uptake. Furthermore, AMFs downregulated ZmAMT1;1a and ZmAMT1;3 protein abundance and transport activities expressed in the root epidermis, suggesting a trade-off between mycorrhizal and direct root N-uptake pathways. Taken together, our results provide a comprehensive understanding of mycorrhiza-dependent N uptake in maize and present a promising approach to improve N-acquisition efficiency via plant-microbe interactions.
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Affiliation(s)
- Jing Hui
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, MOE, China Agricultural University, Beijing, 100193, China
| | - Xia An
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, MOE, China Agricultural University, Beijing, 100193, China
| | - Zhibo Li
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, MOE, China Agricultural University, Beijing, 100193, China
| | - Benjamin Neuhäuser
- Department of Nutritional Crop Physiology, Institute of Crop Science, University of Hohenheim, Stuttgart, 70593, Germany
| | - Uwe Ludewig
- Department of Nutritional Crop Physiology, Institute of Crop Science, University of Hohenheim, Stuttgart, 70593, Germany
| | - Xuna Wu
- Department of Plant Systems Biology, Institute for Physiology and Biotechnology of Plants, University of Hohenheim, Stuttgart, 70593, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, Institute for Physiology and Biotechnology of Plants, University of Hohenheim, Stuttgart, 70593, Germany
| | - Fanjun Chen
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, MOE, China Agricultural University, Beijing, 100193, China
| | - Gu Feng
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, MOE, China Agricultural University, Beijing, 100193, China
| | - Hans Lambers
- School of Biological Science and Institute of Agriculture, University of Western Australia, Perth, WA6009, Australia
| | - Fusuo Zhang
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, MOE, China Agricultural University, Beijing, 100193, China
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10
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Han Y, Hong W, Xiong C, Lambers H, Sun Y, Xu Z, Schulze WX, Cheng L. Combining analyses of metabolite profiles and phosphorus fractions to explore high phosphorus utilization efficiency in maize. J Exp Bot 2022; 73:4184-4203. [PMID: 35303743 DOI: 10.1093/jxb/erac117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Phosphorus (P) limitation is a significant factor restricting crop production in agricultural systems, and enhancing the internal P utilization efficiency (PUE) of crops plays an important role in ensuring sustainable P use in agriculture. To better understand how P is remobilized to affect crop growth, we first screened P-efficient (B73 and GEMS50) and P-inefficient (Liao5114) maize genotypes at the same shoot P content, and then analyzed P pools and performed non-targeted metabolomic analyses to explore changes in cellular P fractions and metabolites in maize genotypes with contrasting PUE. We show that lipid P and nucleic acid P concentrations were significantly lower in lower leaves of P-efficient genotypes, and these P pools were remobilized to a major extent in P-efficient genotypes. Broad metabolic alterations were evident in leaves of P-efficient maize genotypes, particularly affecting products of phospholipid turnover and phosphorylated compounds, and the shikimate biosynthesis pathway. Taken together, our results suggest that P-efficient genotypes have a high capacity to remobilize lipid P and nucleic acid P and promote the shikimate pathway towards efficient P utilization in maize.
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Affiliation(s)
- Yang Han
- Department of Plant Nutrient, College of Resources and Environmental Sciences, Academy of National Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, PR China
| | - Wanting Hong
- Department of Plant Nutrient, College of Resources and Environmental Sciences, Academy of National Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, PR China
| | - Chuanyong Xiong
- Department of Plant Nutrient, College of Resources and Environmental Sciences, Academy of National Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, PR China
| | - Hans Lambers
- Department of Plant Nutrient, College of Resources and Environmental Sciences, Academy of National Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, PR China
- School of Biological Sciences and UWA Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Yan Sun
- Department of Plant Nutrient, College of Resources and Environmental Sciences, Academy of National Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, PR China
| | - Zikai Xu
- Department of Plant Nutrient, College of Resources and Environmental Sciences, Academy of National Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, PR China
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, D-70593 Stuttgart, Germany
| | - Lingyun Cheng
- Department of Plant Nutrient, College of Resources and Environmental Sciences, Academy of National Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, PR China
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11
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He M, Wang J, Herold S, Xi L, Schulze WX. A Rapid and Universal Workflow for Label-Free-Quantitation-Based Proteomic and Phosphoproteomic Studies in Cereals. Curr Protoc 2022; 2:e425. [PMID: 35674286 DOI: 10.1002/cpz1.425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Proteomics and phosphoproteomics are robust tools to analyze dynamics of post-transcriptional processes during growth and development. A variety of experimental methods and workflows have been published, but most of them were developed for model plants and have not been adapted to high-throughput platforms. Here, we describe an experimental workflow for proteome and phosphoproteome studies tailored to cereal crop tissues. The workflow consists of two parallel parts that are suitable for analyzing protein/phosphoprotein from total proteins and the microsomal membrane fraction. We present phosphoproteomic data regarding quantification coverage and analytical reproducibility for example preparations from maize root and shoot, wheat leaf, and a microsomal protein preparation from maize leaf. To enable users to adjust for tissue specific requirements, we provide two different methods of protein clean-up: traditional ethanol precipitation (PC) and a recently developed technology termed single-pot, solid-phase-enhanced sample preparation (SP3). Both the PC and SP3 methods are effective in the removal of unwanted substances in total protein crude extracts. In addition, two different methods of phosphopeptide enrichment are presented: a TiO2 -based method and Fe(III)-NTA cartridges on a robotized platform. Although the overall number of phosphopeptides is stable across protein clean-up and phosphopeptide enrichment methods, there are differences in the preferred phosphopeptides in each enrichment method. The preferred protocol depends on laboratory capabilities and research objective. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Total protein crude extraction Basic Protocol 2: Total protein clean-up with ethanol precipitation Alternate Protocol 1: Total protein clean-up with SP3 method Basic Protocol 3: Microsomal fraction protein extraction Basic Protocol 4: Protein concentration determination by Bradford assay Basic Protocol 5: In-solution digestion with trypsin Basic Protocol 6: Phosphopeptide enrichment with TiO2 Alternate Protocol 2: Phosphopeptide enrichment with Fe(III)-NTA cartridges Basic Protocol 7: Peptide desalting with C18 material Basic Protocol 8: LC-MS/MS analysis of (phospho)peptides and spectrum matching.
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Affiliation(s)
- Mingjie He
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Jiahui Wang
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Sandra Herold
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
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12
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Stefan T, Wu XN, Zhang Y, Fernie A, Schulze WX. Regulatory Modules of Metabolites and Protein Phosphorylation in Arabidopsis Genotypes With Altered Sucrose Allocation. Front Plant Sci 2022; 13:891405. [PMID: 35665154 PMCID: PMC9161306 DOI: 10.3389/fpls.2022.891405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
Multi-omics data sets are increasingly being used for the interpretation of cellular processes in response to environmental cues. Especially, the posttranslational modification of proteins by phosphorylation is an important regulatory process affecting protein activity and/or localization, which, in turn, can have effects on metabolic processes and metabolite levels. Despite this importance, relationships between protein phosphorylation status and metabolite abundance remain largely underexplored. Here, we used a phosphoproteomics-metabolomics data set collected at the end of day and night in shoots and roots of Arabidopsis to propose regulatory relationships between protein phosphorylation and accumulation or allocation of metabolites. For this purpose, we introduced a novel, robust co-expression measure suited to the structure of our data sets, and we used this measure to construct metabolite-phosphopeptide networks. These networks were compared between wild type and plants with perturbations in key processes of sugar metabolism, namely, sucrose export (sweet11/12 mutant) and starch synthesis (pgm mutant). The phosphopeptide-metabolite network turned out to be highly sensitive to perturbations in sugar metabolism. Specifically, KING1, the regulatory subunit of SnRK1, was identified as a primary candidate connecting protein phosphorylation status with metabolism. We additionally identified strong changes in the fatty acid network of the sweet11/12 mutant, potentially resulting from a combination of fatty acid signaling and metabolic overflow reactions in response to high internal sucrose concentrations. Our results further suggest novel protein-metabolite relationships as candidates for future targeted research.
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Affiliation(s)
- Thorsten Stefan
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Xu Na Wu
- College for Life Science, Yunnan University, Kunming, China
| | - Youjun Zhang
- Department of Central Metabolism, Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
- Center of Plant System Biology and Biotechnology, Plovdiv, Bulgaria
| | - Alisdair Fernie
- Department of Central Metabolism, Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
- Center of Plant System Biology and Biotechnology, Plovdiv, Bulgaria
| | - Waltraud X. Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
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13
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He M, Li X, Mang M, Li Z, Ludewig U, Schulze WX. A systems-biology approach identifies co-expression modules in response to low phosphate supply in maize lines of different breeding history. Plant J 2022; 109:1249-1270. [PMID: 34897849 DOI: 10.1111/tpj.15630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Plants cope with low phosphorus availability by adjusting growth and metabolism through transcriptomic and proteomic adaptations. We hypothesize that selected genotypes with distinct phosphorous (P) use efficiency covering the breeding history of European Flint heterotic pool provide a tool to reveal general and genotype-specific molecular responses to P limitation. We reconstructed protein and gene co-expression networks by weighted correlation network analysis and related these to phosphate deficiency-induced traits. In roots, low phosphate supply resulted in a decreasing abundance of proteins in the oxidative pentose phosphate pathway and a negative correlation with root and shoot phosphate content. We observed an increase in abundance and positive correlation with root and shoot phosphate content for proteins in sucrose biosynthesis, lipid metabolism, respiration and RNA processing. Purple acid phosphatases, superoxide dismutase and phenylalanine ammonia lyase were identified as being upregulated under low phosphate in all genotypes. Overall, correlations between protein and mRNA abundance changes were limited, with ribosomal proteins and the ubiquitin protein degradation pathway exclusively responding with protein abundance changes. Carbohydrate, phospho- and sulfo-lipid metabolism showed abundance changes at the protein and mRNA levels. These partially non-overlapping proteomic and transcriptomic adjustments to low phosphate suggest sugar and lipid metabolism as metabolic processes associated with improved P use efficiency specifically in Founder Flint lines. We identified a mitogen-activated protein kinase-kinase as a potential genotype-specific regulator of sucrose metabolism at low phosphate in Founder Flint line EP1. We conclude that, during breedingt of Elite Flint lines, regulation of primary metabolism has changed to result in a distinct low phosphate response in Founder lines.
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Affiliation(s)
- Mingjie He
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Xuelian Li
- Department of Nutritional Crop Physiology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Melissa Mang
- Department of Nutritional Crop Physiology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Zhi Li
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Uwe Ludewig
- Department of Nutritional Crop Physiology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, 70593, Germany
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14
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Pertl-Obermeyer H, Gimeno A, Kuchler V, Servili E, Huang S, Fang H, Lang V, Sydow K, Pöckl M, Schulze WX, Obermeyer G. pH modulates interaction of 14-3-3 proteins with pollen plasma membrane H+ ATPases independently from phosphorylation. J Exp Bot 2022; 73:168-181. [PMID: 34467995 DOI: 10.1093/jxb/erab387] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Pollen grains transport the sperm cells through the style tissue via a fast-growing pollen tube to the ovaries where fertilization takes place. Pollen tube growth requires a precisely regulated network of cellular as well as molecular events including the activity of the plasma membrane H+ ATPase, which is known to be regulated by reversible protein phosphorylation and subsequent binding of 14-3-3 isoforms. Immunodetection of the phosphorylated penultimate threonine residue of the pollen plasma membrane H+ ATPase (LilHA1) of Lilium longiflorum pollen revealed a sudden increase in phosphorylation with the start of pollen tube growth. In addition to phosphorylation, pH modulated the binding of 14-3-3 isoforms to the regulatory domain of the H+ ATPase, whereas metabolic components had only small effects on 14-3-3 binding, as tested with in vitro assays using recombinant 14-3-3 isoforms and phosphomimicking substitutions of the threonine residue. Consequently, local H+ influxes and effluxes as well as pH gradients in the pollen tube tip are generated by localized regulation of the H+ ATPase activity rather than by heterogeneous localized distribution in the plasma membrane.
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Affiliation(s)
- Heidi Pertl-Obermeyer
- Membrane Biophysics, Department of Biosciences, University of Salzburg, Billrothstr. 11, 5020 Salzburg, Austria
- MorphoPhysics, Department of Chemistry and Physics of Materials, University of Salzburg, Jakob-Haringer-Str. 2a, 5020 Salzburg, Austria
| | - Ana Gimeno
- Membrane Biophysics, Department of Biosciences, University of Salzburg, Billrothstr. 11, 5020 Salzburg, Austria
| | - Verena Kuchler
- Membrane Biophysics, Department of Biosciences, University of Salzburg, Billrothstr. 11, 5020 Salzburg, Austria
| | - Evrim Servili
- Membrane Biophysics, Department of Biosciences, University of Salzburg, Billrothstr. 11, 5020 Salzburg, Austria
- Inst. Recherche Experimentale & Clinique, University of Louvain, Ave. Hippocrate, Woluwe-Saint Lambert, Belgium
| | - Shuai Huang
- Membrane Biophysics, Department of Biosciences, University of Salzburg, Billrothstr. 11, 5020 Salzburg, Austria
- Southern University of Science and Technology, Shenzen, PR China
| | - Han Fang
- Membrane Biophysics, Department of Biosciences, University of Salzburg, Billrothstr. 11, 5020 Salzburg, Austria
- Spinal Chord Injury & Tissue Regeneration Centre, Paracelsus Medical University, Strubergasse, Salzburg, Austria
| | - Veronika Lang
- Membrane Biophysics, Department of Biosciences, University of Salzburg, Billrothstr. 11, 5020 Salzburg, Austria
- STRATEC GmbH, Sonystraße 20, Anif, Austria
| | - Katharina Sydow
- Membrane Biophysics, Department of Biosciences, University of Salzburg, Billrothstr. 11, 5020 Salzburg, Austria
| | - Magdalena Pöckl
- Membrane Biophysics, Department of Biosciences, University of Salzburg, Billrothstr. 11, 5020 Salzburg, Austria
| | - Waltraud X Schulze
- Plant Systems Biology, University of Hohenheim, Garbenstraße 30, 70599 Stuttgart, Germany
| | - Gerhard Obermeyer
- Membrane Biophysics, Department of Biosciences, University of Salzburg, Billrothstr. 11, 5020 Salzburg, Austria
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15
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Chu LC, Offenborn JN, Steinhorst L, Wu XN, Xi L, Li Z, Jacquot A, Lejay L, Kudla J, Schulze WX. Plasma membrane calcineurin B-like calcium-ion sensor proteins function in regulating primary root growth and nitrate uptake by affecting global phosphorylation patterns and microdomain protein distribution. New Phytol 2021; 229:2223-2237. [PMID: 33098106 DOI: 10.1111/nph.17017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/27/2020] [Indexed: 05/25/2023]
Abstract
The collective function of calcineurin B-like (CBL) calcium ion (Ca2+ ) sensors and CBL-interacting protein kinases (CIPKs) in decoding plasma-membrane-initiated Ca2+ signals to convey developmental and adaptive responses to fluctuating nitrate availability remained to be determined. Here, we generated a cbl-quintuple mutant in Arabidopsis thaliana devoid of these Ca2+ sensors at the plasma membrane and performed comparative phenotyping, nitrate flux determination, phosphoproteome analyses, and studies of membrane domain protein distribution in response to low and high nitrate availability. We observed that CBL proteins exert multifaceted regulation of primary and lateral root growth and nitrate fluxes. Accordingly, we found that loss of plasma membrane Ca2+ sensor function simultaneously affected protein phosphorylation of numerous membrane proteins, including several nitrate transporters, proton pumps, and aquaporins, as well as their distribution within plasma membrane microdomains, and identified a specific phosphorylation and domain distribution pattern during distinct phases of low and high nitrate responses. Collectively, these analyses reveal a central and coordinative function of CBL-CIPK-mediated signaling in conveying plant adaptation to fluctuating nitrate availability and identify a crucial role of Ca2+ signaling in regulating the composition and dynamics of plasma membrane microdomains.
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Affiliation(s)
- Liang-Cui Chu
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Jan Niklas Offenborn
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, Münster, 48149, Germany
| | - Leonie Steinhorst
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, Münster, 48149, Germany
| | - Xu Na Wu
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Zhi Li
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Aurore Jacquot
- BPMP, Université de Montpellier, CNRS, INRAE, Institut Agro, Montpellier, 34060, France
| | - Laurence Lejay
- BPMP, Université de Montpellier, CNRS, INRAE, Institut Agro, Montpellier, 34060, France
| | - Jörg Kudla
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, Münster, 48149, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, 70593, Germany
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16
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Schulze WX, Altenbuchinger M, He M, Kränzlein M, Zörb C. Proteome profiling of repeated drought stress reveals genotype-specific responses and memory effects in maize. Plant Physiol Biochem 2021; 159:67-79. [PMID: 33341081 DOI: 10.1016/j.plaphy.2020.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Drought has become a major stress for agricultural productivity in temperate regions, such as central Europe. Thus, information on how crop plants respond to drought is important to develop tolerant hybrids and to ensure yield stability. Posttranscriptional regulation through changed protein abundances is an important mechanism of short-term response to stress events that has not yet been widely exploited in breeding strategies. Here, we investigated the response to repeated drought exposure of a tolerant and a sensitive maize hybrid in order to understand general protein abundance changes induced by singular drought or repeated drought events. In general, drought affected protein abundance of multiple pathways in the plant. We identified starch metabolism, aquaporin abundance, PSII proteins and histones as strongly associated with typical drought-induced phenotypes such as increased membrane leakage, osmolality or effects on stomatal conductance and assimilation rate. In addition, we found a strong effect of drought on nutrient assimilation, especially the sulfur metabolism. In general, pre-experience of mild drought before exposure to a more severe drought resulted in visible adaptations resulting in dampened phenotypes as well as lower magnitude of protein abundance changes.
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Affiliation(s)
- Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, 70593, Stuttgart, Germany.
| | - Michael Altenbuchinger
- Research Group Computational Biology, University of Hohenheim, 70593, Stuttgart, Germany
| | - Mingjie He
- Department of Plant Systems Biology, University of Hohenheim, 70593, Stuttgart, Germany
| | - Markus Kränzlein
- Institute of Crop Sciences, University of Hohenheim, 70593, Stuttgart, Germany
| | - Christian Zörb
- Institute of Crop Sciences, University of Hohenheim, 70593, Stuttgart, Germany
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17
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Xi L, Schulze WX, Wu XN. Phosphoproteomic Analysis of Plant Membranes. Methods Mol Biol 2021; 2200:441-451. [PMID: 33175392 DOI: 10.1007/978-1-0716-0880-7_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Mass spectrometry (MS) is a powerful tool to investigate plant phosphorylation dynamics on a system-wide scale (phosphoproteomics). Plant membrane phosphoproteomics enables elucidating regulatory patterns in membranes, such as kinase-target relationships in different signaling pathways. Here, we present "ShortPhos," an efficient and simple phosphoproteomics protocol for research on plant membrane proteins, which allows fast and efficient identification and quantification of phosphopeptides from small amounts of starting plant material and/or membrane proteins. This method improves upon the efficiency of plant membrane phosphoproteomics profiling and can be applied to the study of membrane-based signaling networks.
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Affiliation(s)
- Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Xu Na Wu
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany.
- School of Life Sciences, Center for Life Sciences, Yunnan University, Kunming, China.
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18
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Abstract
Protein phosphorylation is an important cellular regulatory mechanism affecting the activity, localization, conformation, and interaction of proteins. Protein phosphorylation is catalyzed by kinases, and thus kinases are the enzymes regulating cellular signaling cascades. In the model plant Arabidopsis, 940 genes encode for kinases. The substrate proteins of kinases are phosphorylated at defined sites, which consist of common patterns around the phosphorylation site, known as phosphorylation motifs. The discovery of kinase specificity with a preference of phosphorylation of certain motifs and application of such motifs in deducing signaling cascades helped to reveal underlying regulation mechanisms, and facilitated the prediction of kinase-target pairs. In this mini-review, we took advantage of retrieved data as examples to present the functions of kinase families along with their commonly found phosphorylation motifs from their substrates.
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Affiliation(s)
- Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany.
| | - Zhaoxia Zhang
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Sandra Herold
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Sarah Kassem
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Xu Na Wu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
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19
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Long L, Pedas PR, Kristensen RK, Schulze WX, Husted S, Zhang G, Schjoerring JK, Yuan L. High light intensity aggravates latent manganese deficiency in maize. J Exp Bot 2020; 71:6116-6127. [PMID: 32737981 DOI: 10.1093/jxb/eraa366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/30/2020] [Indexed: 06/11/2023]
Abstract
Manganese (Mn) plays an important role in the oxygen-evolving complex, where energy from light absorption is used for water splitting. Although changes in light intensity and Mn status can interfere with the functionality of the photosynthetic apparatus, the interaction between these two factors and the underlying mechanisms remain largely unknown. Here, maize seedlings were grown hydroponically and exposed to two different light intensities under Mn-sufficient or -deficient conditions. No visual Mn deficiency symptoms appeared even though the foliar Mn concentration in the Mn-deficient treatments was reduced to 2 µg g-1. However, the maximum quantum yield efficiency of PSII and the net photosynthetic rate declined significantly, indicating latent Mn deficiency. The reduction in photosynthetic performance by Mn depletion was further aggravated when plants were exposed to high light intensity. Integrated transcriptomic and proteomic analyses showed that a considerable number of genes encoding proteins in the photosynthetic apparatus were only suppressed by a combination of Mn deficiency and high light, thus indicating interactions between changes in Mn nutritional status and light intensity. We conclude that high light intensity aggravates latent Mn deficiency in maize by interfering with the abundance of PSII proteins.
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Affiliation(s)
- Lizhi Long
- Key Lab of Plant-Soil Interaction, MOE, College Resources and Environmental Sciences, China Agricultural University, Beijing, China
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej, Frederiksberg C, Denmark
- Department of Agronomy, Zhejiang University, Hangzhou, China
| | - Pai R Pedas
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej, Frederiksberg C, Denmark
| | - Rebekka K Kristensen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej, Frederiksberg C, Denmark
| | - Waltraud X Schulze
- Institute for Physiology and Biotechnology of Plants, University of Hohenheim, Garbenstraße, Stuttgart, Germany
| | - Søren Husted
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej, Frederiksberg C, Denmark
| | - Guoping Zhang
- Department of Agronomy, Zhejiang University, Hangzhou, China
| | - Jan K Schjoerring
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej, Frederiksberg C, Denmark
| | - Lixing Yuan
- Key Lab of Plant-Soil Interaction, MOE, College Resources and Environmental Sciences, China Agricultural University, Beijing, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
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20
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Durian G, Sedaghatmehr M, Matallana-Ramirez LP, Schilling SM, Schaepe S, Guerra T, Herde M, Witte CP, Mueller-Roeber B, Schulze WX, Balazadeh S, Romeis T. Calcium-Dependent Protein Kinase CPK1 Controls Cell Death by In Vivo Phosphorylation of Senescence Master Regulator ORE1. Plant Cell 2020; 32:1610-1625. [PMID: 32111670 PMCID: PMC7203915 DOI: 10.1105/tpc.19.00810] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/27/2020] [Accepted: 02/28/2020] [Indexed: 05/20/2023]
Abstract
Calcium-regulated protein kinases are key components of intracellular signaling in plants that mediate rapid stress-induced responses to changes in the environment. To identify in vivo phosphorylation substrates of CALCIUM-DEPENDENT PROTEIN KINASE1 (CPK1), we analyzed the conditional expression of constitutively active CPK1 in conjunction with in vivo phosphoproteomics. We identified Arabidopsis (Arabidopsis thaliana) ORESARA1 (ORE1), the developmental master regulator of senescence, as a direct CPK1 phosphorylation substrate. CPK1 phosphorylates ORE1 at a hotspot within an intrinsically disordered region. This augments transcriptional activation by ORE1 of its downstream target gene BIFUNCTIONAL NUCLEASE1 (BFN1). Plants that overexpress ORE1, but not an ORE1 variant lacking the CPK1 phosphorylation hotspot, promote early senescence. Furthermore, ORE1 is required for enhanced cell death induced by CPK1 signaling. Our data validate the use of conditional expression of an active enzyme combined with phosphoproteomics to decipher specific kinase target proteins of low abundance, of transient phosphorylation, or in yet-undescribed biological contexts. Here, we have identified that senescence is not just under molecular surveillance manifested by stringent gene regulatory control over ORE1 In addition, the decision to die is superimposed by an additional layer of control toward ORE1 via its posttranslational modification linked to the calcium-regulatory network through CPK1.
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Affiliation(s)
- Guido Durian
- Department of Plant Biochemistry, Dahlem Centre of Plant Sciences, Institute for Biology, Freie Universität Berlin, 14195 Berlin, Germany
- University of Turku, Molecular Plant Biology, Department of Biochemistry, FI-20014 Turku, Finland
| | - Mastoureh Sedaghatmehr
- University of Potsdam, Institute of Biochemistry and Biology, 14476 Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, Cooperative Research Group, 14476 Potsdam, Germany
| | - Lilian P Matallana-Ramirez
- University of Potsdam, Institute of Biochemistry and Biology, 14476 Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, Cooperative Research Group, 14476 Potsdam, Germany
| | - Silke M Schilling
- Department of Plant Biochemistry, Dahlem Centre of Plant Sciences, Institute for Biology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Sieke Schaepe
- Department of Plant Biochemistry, Dahlem Centre of Plant Sciences, Institute for Biology, Freie Universität Berlin, 14195 Berlin, Germany
| | | | - Marco Herde
- Department of Plant Biochemistry, Dahlem Centre of Plant Sciences, Institute for Biology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Claus-Peter Witte
- Department of Plant Biochemistry, Dahlem Centre of Plant Sciences, Institute for Biology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Bernd Mueller-Roeber
- University of Potsdam, Institute of Biochemistry and Biology, 14476 Potsdam, Germany
| | - Waltraud X Schulze
- Max Planck Institute of Molecular Plant Physiology, Department of Metabolic Networks, 14476 Potsdam, Germany
| | - Salma Balazadeh
- University of Potsdam, Institute of Biochemistry and Biology, 14476 Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, Cooperative Research Group, 14476 Potsdam, Germany
| | - Tina Romeis
- Department of Plant Biochemistry, Dahlem Centre of Plant Sciences, Institute for Biology, Freie Universität Berlin, 14195 Berlin, Germany
- Leibniz Institute of Plant Biochemistry, Department Biochemistry of Plant Interactions, 06120 Halle (Saale), Germany
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21
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Dier M, Hüther L, Schulze WX, Erbs M, Köhler P, Weigel HJ, Manderscheid R, Zörb C. Elevated Atmospheric CO 2 Concentration Has Limited Effect on Wheat Grain Quality Regardless of Nitrogen Supply. J Agric Food Chem 2020; 68:3711-3721. [PMID: 32105067 DOI: 10.1021/acs.jafc.9b07817] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Elevated atmospheric CO2 concentrations (e[CO2]) can decrease the grain quality of wheat. However, little information exists concerning interactions between e[CO2] and nitrogen fertilization on important grain quality traits. To investigate this, a 2-year free air CO2 enrichment (FACE) experiment was conducted with two CO2 (393 and 600 ppm) and three (deficiency, adequate, and excess) nitrogen levels. Concentrations of flour proteins (albumins/globulins, gliadins, and glutenins) and key minerals (iron, zinc, and sulfur) and baking quality (loaf volume) were markedly increased by increasing nitrogen levels and varied between years. e[CO2] resulted in slightly decreased albumin/globulin and total gluten concentration under all nitrogen conditions, whereas loaf volume and mineral concentrations remained unaffected. Two-dimensional gel electrophoresis revealed strong effects of nitrogen supply and year on the grain proteome. Under adequate nitrogen, the grain proteome was affected by e[CO2] with 19 downregulated and 17 upregulated protein spots. The downregulated proteins comprised globulins but no gluten proteins. e[CO2] resulted in decreased crude protein concentration at maximum loaf volume. The present study contrasts with other FACE studies showing markedly stronger negative impacts of e[CO2] on chemical grain quality, and the reasons for that might be differences between genotypes, soil conditions, or the extent of growth stimulation by e[CO2].
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Affiliation(s)
- Markus Dier
- Institute of Crop Science, Quality of Plant Products, University of Hohenheim, Emil-Wolff-Str. 25, D-70599 Stuttgart, Germany
- Thünen Institute of Biodiversity, Bundesallee 65, D-38116 Braunschweig, Germany
| | - Liane Hüther
- Institute of Animal Nutrition, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Bundesallee 37, D-38116 Braunschweig, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Garbenstr. 30, D-70593 Stuttgart, Germany
| | - Martin Erbs
- German Agricultural Research Alliance-Deutsche Agrarforschungsallianz (DAFA), Bundesallee 50, D-38116 Braunschweig, Germany
- Thünen Institute of Biodiversity, Bundesallee 65, D-38116 Braunschweig, Germany
| | - Peter Köhler
- Biotask AG, Schelztorstr. 54-56, D-73728 Esslingen, Germany
| | - Hans-Joachim Weigel
- Thünen Institute of Biodiversity, Bundesallee 65, D-38116 Braunschweig, Germany
| | - Remy Manderscheid
- Thünen Institute of Biodiversity, Bundesallee 65, D-38116 Braunschweig, Germany
| | - Christian Zörb
- Institute of Crop Science, Quality of Plant Products, University of Hohenheim, Emil-Wolff-Str. 25, D-70599 Stuttgart, Germany
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22
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Li X, Sanagi M, Lu Y, Nomura Y, Stolze SC, Yasuda S, Saijo Y, Schulze WX, Feil R, Stitt M, Lunn JE, Nakagami H, Sato T, Yamaguchi J. Protein Phosphorylation Dynamics Under Carbon/Nitrogen-Nutrient Stress and Identification of a Cell Death-Related Receptor-Like Kinase in Arabidopsis. Front Plant Sci 2020; 11:377. [PMID: 32308664 PMCID: PMC7145971 DOI: 10.3389/fpls.2020.00377] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/16/2020] [Indexed: 05/03/2023]
Abstract
Nutrient availability, in particular the availability of sugar [carbon (C)] and nitrogen (N), is important for the regulation of plant metabolism and development. In addition to independent utilization of C and N nutrients, plants sense and respond to the balance of C and N nutrients (C/N-nutrient) available to them. High C/low N-nutrient stress has been shown to arrest early post-germinative growth while promoting progression to senescence in Arabidopsis. Although several signaling components of the C/N-nutrient response have been identified, the inclusive molecular basis of plant C/N-nutrient response remains unclear. This proteome analysis evaluated phosphorylation dynamics in response to high C/low N-nutrient stress. Phosphoproteomics under conditions of C/N-nutrient stress showed a global change in the phosphorylation status of proteins, including plasma membrane H+-ATPase, carbon and nitrogen metabolic enzymes and signaling proteins such as protein kinases and transcription factors. Further analyses suggested that SNF1-related protein kinase 1 (SnRK1) is involved in primary C/N-nutrient signal mediation via the transcriptional regulation of C/N-regulatory kinases. We also identified a leucine-rich repeat receptor-like kinase with extracellular malectin-like domain, named as LMK1, which was shown to possess cell death induction activity in plant leaves. These results provide important insight into the C/N-nutrient signaling pathways connecting nutrition stress to various cellular and physiological processes in plants.
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Affiliation(s)
- Xingwen Li
- Faculty of Science and Graduate School of Life Sciences, Hokkaido University, Sapporo, Japan
| | - Miho Sanagi
- Faculty of Science and Graduate School of Life Sciences, Hokkaido University, Sapporo, Japan
| | - Yu Lu
- Faculty of Science and Graduate School of Life Sciences, Hokkaido University, Sapporo, Japan
| | - Yuko Nomura
- Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | | | - Shigetaka Yasuda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Yusuke Saijo
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Waltraud X. Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, Golm, Germany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Golm, Germany
| | - John E. Lunn
- Max Planck Institute of Molecular Plant Physiology, Golm, Germany
| | - Hirofumi Nakagami
- Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- *Correspondence: Hirofumi Nakagami,
| | - Takeo Sato
- Faculty of Science and Graduate School of Life Sciences, Hokkaido University, Sapporo, Japan
- Takeo Sato,
| | - Junji Yamaguchi
- Faculty of Science and Graduate School of Life Sciences, Hokkaido University, Sapporo, Japan
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23
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Wu X, Liu T, Zhang Y, Duan F, Neuhäuser B, Ludewig U, Schulze WX, Yuan L. Ammonium and nitrate regulate NH4+ uptake activity of Arabidopsis ammonium transporter AtAMT1;3 via phosphorylation at multiple C-terminal sites. J Exp Bot 2019; 70:4919-4930. [PMID: 31087098 PMCID: PMC6760267 DOI: 10.1093/jxb/erz230] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 05/04/2019] [Indexed: 05/03/2023]
Abstract
In plants, nutrient transporters require tight regulation to ensure optimal uptake in complex environments. The activities of many nutrient transporters are post-translationally regulated by reversible phosphorylation, allowing rapid adaptation to variable environmental conditions. Here, we show that the Arabidopsis root epidermis-expressed ammonium transporter AtAMT1;3 was dynamically (de-)phosphorylated at multiple sites in the cytosolic C-terminal region (CTR) responding to ammonium and nitrate signals. Under ammonium resupply rapid phosphorylation of a Thr residue (T464) in the conserved part of the CTR (CTRC) effectively inhibited AtAMT1;3-dependent NH4+ uptake. Moreover, phosphorylation of Thr (T494), one of three phosphorylation sites in the non-conserved part of the CTR (CRTNC), moderately decreased the NH4+ transport activity of AtAMT1;3, as deduced from functional analysis of phospho-mimic mutants in yeast, oocytes, and transgenic Arabidopsis. Double phospho-mutants indicated a role of T494 in fine-tuning the NH4+ transport activity when T464 was non-phosphorylated. Transient dephosphorylation of T494 with nitrate resupply closely paralleled a transient increase in ammonium uptake. These results suggest that T464 phosphorylation at the CTRC acts as a prime switch to prevent excess ammonium influx, while T494 phosphorylation at the CTRNC fine tunes ammonium uptake in response to nitrate. This provides a sophisticated regulatory mechanism for plant ammonium transporters to achieve optimal ammonium uptake in response to various nitrogen forms.
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Affiliation(s)
- Xiangyu Wu
- Key Lab of Plant-Soil Interaction, MOE, College Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Ting Liu
- Key Lab of Plant-Soil Interaction, MOE, College Resources and Environmental Sciences, China Agricultural University, Beijing, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Yongjian Zhang
- Key Lab of Plant-Soil Interaction, MOE, College Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Fengying Duan
- Key Lab of Plant-Soil Interaction, MOE, College Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Benjamin Neuhäuser
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart, Germany
| | - Uwe Ludewig
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart, Germany
| | - Waltraud X Schulze
- Institute for Physiology and Biotechnology of Plants, Plant Systems Biology, University of Hohenheim, Garbenstraße, Stuttgart, Germany
| | - Lixing Yuan
- Key Lab of Plant-Soil Interaction, MOE, College Resources and Environmental Sciences, China Agricultural University, Beijing, China
- Correspondence:
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24
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Grison MS, Kirk P, Brault ML, Wu XN, Schulze WX, Benitez-Alfonso Y, Immel F, Bayer EM. Plasma Membrane-Associated Receptor-like Kinases Relocalize to Plasmodesmata in Response to Osmotic Stress. Plant Physiol 2019; 181:142-160. [PMID: 31300470 PMCID: PMC6716232 DOI: 10.1104/pp.19.00473] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/02/2019] [Indexed: 05/17/2023]
Abstract
Plasmodesmata act as key elements in intercellular communication, coordinating processes related to plant growth, development, and responses to environmental stresses. While many of the developmental, biotic, and abiotic signals are primarily perceived at the plasma membrane (PM) by receptor proteins, plasmodesmata also cluster receptor-like activities; whether these two pathways interact is currently unknown. Here, we show that specific PM-located Leu-rich-repeat receptor-like-kinases, Qiān Shŏu kinase (QSK1) and inflorescence meristem kinase2, which under optimal growth conditions are absent from plasmodesmata, rapidly relocate and cluster to the pores in response to osmotic stress. This process is remarkably fast, is not a general feature of PM-associated proteins, and is independent of sterol and sphingolipid membrane composition. Focusing on QSK1, previously reported to be involved in stress responses, we show that relocalization in response to mannitol depends on QSK1 phosphorylation. Loss-of-function mutation in QSK1 results in delayed lateral root (LR) development, and the mutant is affected in the root response to mannitol stress. Callose-mediated plasmodesmata regulation is known to regulate LR development. We found that callose levels are reduced in the qsk1 mutant background with a root phenotype resembling ectopic expression of PdBG1, an enzyme that degrades callose at the pores. Both the LR and callose phenotypes can be complemented by expression of wild-type and phosphomimic QSK1 variants, but not by phosphodead QSK1 mutant, which fails to relocalize at plasmodesmata. Together, the data indicate that reorganization of receptor-like-kinases to plasmodesmata is important for the regulation of callose and LR development as part of the plant response to osmotic stress.
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Affiliation(s)
- Magali S Grison
- Laboratoire de Biogenèse Membranaire, UMR5200 Centre National de la Recherche Scientifique, Université de Bordeaux, 71 Avenue Edouard Bourlaux, 33883 Villenave d'Ornon cedex, France
| | - Philip Kirk
- Centre for Plant Science, School of Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Marie L Brault
- Laboratoire de Biogenèse Membranaire, UMR5200 Centre National de la Recherche Scientifique, Université de Bordeaux, 71 Avenue Edouard Bourlaux, 33883 Villenave d'Ornon cedex, France
| | - Xu Na Wu
- Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Yoselin Benitez-Alfonso
- Centre for Plant Science, School of Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Françoise Immel
- Laboratoire de Biogenèse Membranaire, UMR5200 Centre National de la Recherche Scientifique, Université de Bordeaux, 71 Avenue Edouard Bourlaux, 33883 Villenave d'Ornon cedex, France
| | - Emmanuelle M Bayer
- Laboratoire de Biogenèse Membranaire, UMR5200 Centre National de la Recherche Scientifique, Université de Bordeaux, 71 Avenue Edouard Bourlaux, 33883 Villenave d'Ornon cedex, France
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25
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Wu XN, Chu L, Xi L, Pertl-Obermeyer H, Li Z, Sklodowski K, Sanchez-Rodriguez C, Obermeyer G, Schulze WX. Sucrose-induced Receptor Kinase 1 is Modulated by an Interacting Kinase with Short Extracellular Domain. Mol Cell Proteomics 2019; 18:1556-1571. [PMID: 31147492 PMCID: PMC6683012 DOI: 10.1074/mcp.ra119.001336] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/08/2019] [Indexed: 12/22/2022] Open
Abstract
Sucrose as a product of photosynthesis is the major carbohydrate translocated from photosynthetic leaves to growing nonphotosynthetic organs such as roots and seeds. These growing tissues, besides carbohydrate supply, require uptake of water through aquaporins to enhance cell expansion during growth. Previous work revealed Sucrose Induced Receptor Kinase, SIRK1, to control aquaporin activity via phosphorylation in response to external sucrose stimulation. Here, we present the regulatory role of AT3G02880 (QSK1), a receptor kinase with a short external domain, in modulation of SIRK1 activity. Our results suggest that SIRK1 autophosphorylates at Ser-744 after sucrose treatment. Autophosphorylated SIRK1 then interacts with and transphosphorylates QSK1 and QSK2. Upon interaction with QSK1, SIRK1 phosphorylates aquaporins at their regulatory C-terminal phosphorylation sites. Consequently, in root protoplast swelling assays, the qsk1qsk2 mutant showed reduced water influx rates under iso-osmotic sucrose stimulation, confirming an involvement in the same signaling pathway as the receptor kinase SIRK1. Large-scale phosphoproteomics comparing single mutant sirk1, qsk1, and double mutant sirk1 qsk1 revealed that aquaporins were regulated by phosphorylation depending on an activated receptor kinase complex of SIRK1, as well as QSK1. QSK1 thereby acts as a coreceptor stabilizing and enhancing SIRK1 activity and recruiting substrate proteins, such as aquaporins.
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Affiliation(s)
- Xu Na Wu
- ‡Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Liangcui Chu
- ‡Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Lin Xi
- ‡Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Heidi Pertl-Obermeyer
- §Molecular Plant Biophysics and Biochemistry, Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Zhi Li
- ‡Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Kamil Sklodowski
- ¶Department of Biology, ETH Zürich, Universitätsstrasse 2, 8092 Zürich, Switzerland
| | | | - Gerhard Obermeyer
- §Molecular Plant Biophysics and Biochemistry, Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Waltraud X Schulze
- ‡Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany.
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26
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Haj Ahmad F, Wu XN, Stintzi A, Schaller A, Schulze WX. The Systemin Signaling Cascade As Derived from Time Course Analyses of the Systemin-responsive Phosphoproteome. Mol Cell Proteomics 2019; 18:1526-1542. [PMID: 31138643 PMCID: PMC6683004 DOI: 10.1074/mcp.ra119.001367] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/20/2019] [Indexed: 11/06/2022] Open
Abstract
Systemin is a small peptide with important functions in plant wound response signaling. Although the transcriptional responses of systemin action are well described, the signaling cascades involved in systemin perception and signal transduction at the protein level are poorly understood. Here we used a tomato cell suspension culture system to profile phosphoproteomic responses induced by systemin and its inactive Thr17Ala analog, allowing us to reconstruct a systemin-specific kinase/phosphatase signaling network. Our time-course analysis revealed early phosphorylation events at the plasma membrane, such as dephosphorylation of H+-ATPase, rapid phosphorylation of NADPH-oxidase and Ca2+-ATPase. Later responses involved transient phosphorylation of small GTPases, vesicle trafficking proteins and transcription factors. Based on a correlation analysis of systemin-induced phosphorylation profiles, we predicted substrate candidates for 44 early systemin-responsive kinases, which includes receptor kinases and downstream kinases such as MAP kinases, as well as nine phosphatases. We propose a regulatory module in which H+-ATPase LHA1 is rapidly de-phosphorylated at its C-terminal regulatory residue T955 by phosphatase PLL5, resulting in the alkalization of the growth medium within 2 mins of systemin treatment. We found the MAP kinase MPK2 to have increased phosphorylation level at its activating TEY-motif at 15 min post-treatment. The predicted interaction of MPK2 with LHA1 was confirmed by in vitro kinase assays, suggesting that the H+-ATPase LHA1 is re-activated by MPK2 later in the systemin response. Our data set provides a resource of proteomic events involved in systemin signaling that will be valuable for further in-depth functional studies in elucidation of systemin signaling cascades.
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Affiliation(s)
- Fatima Haj Ahmad
- ‡University of Hohenheim, Institute of Molecular Plant Physiology, 70593 Stuttgart, Germany
| | - Xu Na Wu
- ‡University of Hohenheim, Institute of Molecular Plant Physiology, 70593 Stuttgart, Germany
| | - Annick Stintzi
- ‡University of Hohenheim, Institute of Molecular Plant Physiology, 70593 Stuttgart, Germany
| | - Andreas Schaller
- ‡University of Hohenheim, Institute of Molecular Plant Physiology, 70593 Stuttgart, Germany
| | - Waltraud X Schulze
- ‡University of Hohenheim, Institute of Molecular Plant Physiology, 70593 Stuttgart, Germany.
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27
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Millar AH, Heazlewood JL, Giglione C, Holdsworth MJ, Bachmair A, Schulze WX. The Scope, Functions, and Dynamics of Posttranslational Protein Modifications. Annu Rev Plant Biol 2019; 70:119-151. [PMID: 30786234 DOI: 10.1146/annurev-arplant-050718-100211] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Assessing posttranslational modification (PTM) patterns within protein molecules and reading their functional implications present grand challenges for plant biology. We combine four perspectives on PTMs and their roles by considering five classes of PTMs as examples of the broader context of PTMs. These include modifications of the N terminus, glycosylation, phosphorylation, oxidation, and N-terminal and protein modifiers linked to protein degradation. We consider the spatial distribution of PTMs, the subcellular distribution of modifying enzymes, and their targets throughout the cell, and we outline the complexity of compartmentation in understanding of PTM function. We also consider PTMs temporally in the context of the lifetime of a protein molecule and the need for different PTMs for assembly, localization, function, and degradation. Finally, we consider the combined action of PTMs on the same proteins, their interactions, and the challenge ahead of integrating PTMs into an understanding of protein function in plants.
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Affiliation(s)
- A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia;
| | - Joshua L Heazlewood
- School of BioSciences, University of Melbourne, Melbourne, Victoria 3010, Australia;
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell, CNRS UMR9198, F-91198 Gif-sur-Yvette Cedex, France;
| | - Michael J Holdsworth
- School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom;
| | - Andreas Bachmair
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria;
| | - Waltraud X Schulze
- Systembiologie der Pflanze, Universität Hohenheim, 70599 Stuttgart, Germany;
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28
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Xi L, Wu XN, Gilbert M, Schulze WX. Classification and Interactions of LRR Receptors and Co-receptors Within the Arabidopsis Plasma Membrane - An Overview. Front Plant Sci 2019; 10:472. [PMID: 31057579 PMCID: PMC6477698 DOI: 10.3389/fpls.2019.00472] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 03/28/2019] [Indexed: 05/18/2023]
Abstract
Receptor kinases (RK) constitute the largest protein kinase family in plants. In particular, members of the leucine-rich repeat-receptor kinases (LRR-RKs) are involved in the perception of various signals at the plasma membrane. Experimental evidence over the past years revealed a conserved activation mechanism through ligand-inducible heterodimer formation: a ligand is recognized by a receptor kinase with a large extracellular domain (ECD). This ligand binding receptor directly interacts with a so-called co-receptor with a small ECD for ligand fixation and kinase activation. A large proportion of LRR-RKs is functionally still uncharacterized and the dynamic complexity of the plasma membrane makes it difficult to precisely define receptor kinase heterodimer pairs and their functions. In this review, we give an overview of the current knowledge of LRR receptor and co-receptor functions. We use ECD lengths to classify the LRR receptor kinase family and describe different interaction properties of ligand-binding receptors and their respective co-receptor from a network perspective.
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29
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Abstract
Biological processes consist of several consecutive and interacting steps as, for example, in signal transduction cascades or metabolic reaction chains. These processes are regulated by protein-protein interactions and the formation of larger protein complexes, which also occur within biological membranes. To gain a large-scale overview of complex-forming proteins and the composition of such complexes within the cellular membranes of Arabidopsis roots, we use the combination of size-exclusion chromatography and mass spectrometry. First, we identified complex-forming proteins by a retention shift analysis relative to expected retention times of monomeric proteins during size-exclusion chromatography. In a second step we predicted complex composition through pairwise correlation of elution profiles. As result we present an interactome of 963 proteins within cellular membranes of Arabidopsis roots. Identification of complex-forming proteins was highly robust between two independently grown root proteomes. The protein complex composition derived from pairwise correlations of coeluting proteins reproducibly identified stable protein complexes (ribosomes, proteasome, mitochondrial respiratory chain supercomplexes) but showed higher variance between replicates regarding transient interactions (e.g., interactions with kinases) within membrane protein complexes.
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Affiliation(s)
- Max Gilbert
- Department of Plant Systems Biology , Universität Hohenheim , 70593 Stuttgart , Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology , Universität Hohenheim , 70593 Stuttgart , Germany
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Zhang X, Högy P, Wu X, Schmid I, Wang X, Schulze WX, Jiang D, Fangmeier A. Physiological and Proteomic Evidence for the Interactive Effects of Post-Anthesis Heat Stress and Elevated CO 2 on Wheat. Proteomics 2018; 18:e1800262. [PMID: 30307109 DOI: 10.1002/pmic.201800262] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/11/2018] [Indexed: 01/08/2023]
Abstract
Elevated CO2 promotes leaf photosynthesis and improves crop grain yield. However, as a major anthropogenic greenhouse gas, CO2 contributes to more frequent and severe heat stress, which threatens crop productivity. The combined effects of elevated CO2 and heat stress are complex, and the underlying mechanisms are poorly understood. In the present study, the effects of elevated CO2 and high-temperature on foliar physiological traits and the proteome of spring wheat grown under two CO2 concentrations (380 and 550 µmol mol-1 ) and two temperature conditions (ambient and post-anthesis heat stress) are examined. Elevated CO2 increases leaf photosynthetic traits, biomass, and grain yield, while heat stress depresses photosynthesis and yield. Temperature-induced impacts on chlorophyll content and grain yield are not significantly different under the two CO2 concentrations. Analysis of the leaf proteome reveals that proteins involved in photosynthesis as well as antioxidant and protein synthesis pathways are significantly downregulated due to the combination of elevated CO2 and heat stress. Correspondingly, plants treated with elevated CO2 and heat stress exhibit decreased green leaf area, photosynthetic rate, antioxidant enzyme activities, and 1000-kernel weight. The present study demonstrates that future post-anthesis heat episodes will diminish the positive effects of elevated CO2 and negatively impact wheat production.
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Affiliation(s)
- Xiaxiang Zhang
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, P.R. China.,National Technology Innovation Center for Regional Wheat Production, National Engineering and Technology Center for Information Agriculture, Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, P.R. China
| | - Petra Högy
- Institute of Landscape and Plant Ecology, University of Hohenheim, August-von-Hartmann-Str. 3, 70599, Stuttgart, Germany
| | - Xuna Wu
- Department of Plant Systems Biology, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Iris Schmid
- Institute of Landscape and Plant Ecology, University of Hohenheim, August-von-Hartmann-Str. 3, 70599, Stuttgart, Germany
| | - Xiulin Wang
- National Technology Innovation Center for Regional Wheat Production, National Engineering and Technology Center for Information Agriculture, Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, P.R. China
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Dong Jiang
- National Technology Innovation Center for Regional Wheat Production, National Engineering and Technology Center for Information Agriculture, Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, P.R. China
| | - Andreas Fangmeier
- Institute of Landscape and Plant Ecology, University of Hohenheim, August-von-Hartmann-Str. 3, 70599, Stuttgart, Germany
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Pertl-Obermeyer H, Lackner P, Schulze WX, Hoepflinger MC, Hoeftberger M, Foissner I, Obermeyer G. Dissecting the subcellular membrane proteome reveals enrichment of H+ (co-)transporters and vesicle trafficking proteins in acidic zones of Chara internodal cells. PLoS One 2018; 13:e0201480. [PMID: 30157181 PMCID: PMC6114288 DOI: 10.1371/journal.pone.0201480] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/16/2018] [Indexed: 02/06/2023] Open
Abstract
The Characeae are multicellular green algae with very close relationship to land plants. Their internodal cells have been the subject of numerous (electro-)physiological studies. When exposed to light, internodal cells display alternating bands of low and high pH along their surface in order to facilitate carbon uptake required for photosynthesis. Here we investigated for the first time the subcellular membrane protein composition of acidic and alkaline regions in internodal cells of Chara australis R. Br. using MS-proteomics. The identified peptides were annotated to Chara unigenes using a custom-made Chara database generated from a transcriptome analysis and to orthologous Arabidopsis genes using TAIR (The Arabidopsis Information Resource) database. Apart from providing the first public-available, functionally-annotated sequence database for Chara australis, the proteome study, which is supported by immunodetection, identified several membrane proteins associated with acidic regions that contain a high density of specific plasma membrane (PM) invaginations, the charasomes, which locally increase the membrane area to overcome diffusion limitation in membrane transport. An increased abundance of PM H+ ATPases at charasomes is consistent with their role in the acidification of the environment, but the characean PM H+ ATPase sequence suggests a different regulation compared to higher plant PM H+ ATPases. A higher abundance of H+ co-transporters in the charasome-rich, acidic regions possibly reflects enhanced uptake of ions and nutrients. The increase in mitochondrial proteins confirms earlier findings about the accumulation of cortical mitochondria in the acidic zones. The significant enrichment of clathrin heavy chains and clathrin adaptor proteins as well as other proteins involved in trafficking indicate a higher activity of membrane transport in the charasome-rich than in charasome-poor areas. New and unexpected data, for instance the upregulation and abundance of vacuolar transporters correlating with the charasome-rich, acidic cell regions account for new perspectives in the formation of charasomes.
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Affiliation(s)
- Heidi Pertl-Obermeyer
- Molecular Plant Biophysics and Biochemistry, Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Peter Lackner
- Bioinformatics of Allergens, Department of Biosciences, University of Salzburg, Salzburg, Austria
| | | | - Marion C. Hoepflinger
- Plant Cell Dynamics, Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Margit Hoeftberger
- Plant Cell Dynamics, Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Ilse Foissner
- Plant Cell Dynamics, Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Gerhard Obermeyer
- Molecular Plant Biophysics and Biochemistry, Department of Biosciences, University of Salzburg, Salzburg, Austria
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Wu XN, Xi L, Pertl-Obermeyer H, Li Z, Chu LC, Schulze WX. Highly Efficient Single-Step Enrichment of Low Abundance Phosphopeptides from Plant Membrane Preparations. Front Plant Sci 2017; 8:1673. [PMID: 29042862 PMCID: PMC5632542 DOI: 10.3389/fpls.2017.01673] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 09/12/2017] [Indexed: 05/30/2023]
Abstract
Mass spectrometry (MS)-based large scale phosphoproteomics has facilitated the investigation of plant phosphorylation dynamics on a system-wide scale. However, generating large scale data sets for membrane phosphoproteins usually requires fractionation of samples and extended hands-on laboratory time. To overcome these limitations, we developed "ShortPhos," an efficient and simple phosphoproteomics protocol optimized for research on plant membrane proteins. The optimized workflow allows fast and efficient identification and quantification of phosphopeptides, even from small amounts of starting plant materials. "ShortPhos" can produce label-free datasets with a high quantitative reproducibility. In addition, the "ShortPhos" protocol recovered more phosphorylation sites from membrane proteins, especially plasma membrane and vacuolar proteins, when compared to our previous workflow and other membrane-based data in the PhosPhAt 4.0 database. We applied "ShortPhos" to study kinase-substrate relationships within a nitrate-induction experiment on Arabidopsis roots. The "ShortPhos" identified significantly more known kinase-substrate relationships compared to previous phosphoproteomics workflows, producing new insights into nitrate-induced signaling pathways.
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Ishihara H, Moraes TA, Pyl ET, Schulze WX, Obata T, Scheffel A, Fernie AR, Sulpice R, Stitt M. Growth rate correlates negatively with protein turnover in Arabidopsis accessions. Plant J 2017; 91:416-429. [PMID: 28419597 DOI: 10.1111/tpj.13576] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 03/17/2017] [Accepted: 04/10/2017] [Indexed: 05/22/2023]
Abstract
Previous studies with Arabidopsis accessions revealed that biomass correlates negatively to dusk starch content and total protein, and positively to the maximum activities of enzymes in photosynthesis. We hypothesized that large accessions have lower ribosome abundance and lower rates of protein synthesis, and that this is compensated by lower rates of protein degradation. This would increase growth efficiency and allow more investment in photosynthetic machinery. We analysed ribosome abundance and polysome loading in 19 accessions, modelled the rates of protein synthesis and compared them with the observed rate of growth. Large accessions contained less ribosomes than small accessions, due mainly to cytosolic ribosome abundance falling at night in large accessions. The modelled rates of protein synthesis resembled those required for growth in large accessions, but were up to 30% in excess in small accessions. We then employed 13 CO2 pulse-chase labelling to measure the rates of protein synthesis and degradation in 13 accessions. Small accessions had a slightly higher rate of protein synthesis and much higher rates of protein degradation than large accessions. Protein turnover was negligible in large accessions but equivalent to up to 30% of synthesised protein day-1 in small accessions. We discuss to what extent the decrease in growth in small accessions can be quantitatively explained by known costs of protein turnover and what factors may lead to the altered diurnal dynamics and increase of ribosome abundance in small accessions, and propose that there is a trade-off between protein turnover and maximisation of growth rate.
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Affiliation(s)
- Hirofumi Ishihara
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Thiago Alexandre Moraes
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Eva-Theresa Pyl
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Waltraud X Schulze
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
- Department of Plant Systems Biology, University of Hohenheim, Garbenstraße 30, Stuttgart, 70599, Germany
| | - Toshihiro Obata
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - André Scheffel
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Ronan Sulpice
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
- Plant Systems Biology Laboratory, Plant and AgriBiosciences Research Centre, Botany and Plant Science, National University of Ireland Galway, Galway, H91 TK33, Ireland
| | - Mark Stitt
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
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Fasbender L, Maurer D, Kreuzwieser J, Kreuzer I, Schulze WX, Kruse J, Becker D, Alfarraj S, Hedrich R, Werner C, Rennenberg H. The carnivorous Venus flytrap uses prey-derived amino acid carbon to fuel respiration. New Phytol 2017; 214:597-606. [PMID: 28042877 DOI: 10.1111/nph.14404] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 11/23/2016] [Indexed: 06/06/2023]
Abstract
The present study was performed to elucidate the fate of carbon (C) and nitrogen (N) derived from protein of prey caught by carnivorous Dionaea muscipula. For this, traps were fed 13 C/15 N-glutamine (Gln). The release of 13 CO2 was continuously monitored by isotope ratio infrared spectrometry. After 46 h, the allocation of C and N label into different organs was determined and tissues were subjected to metabolome, proteome and transcriptome analyses. Nitrogen of Gln fed was already separated from its C skeleton in the decomposing fluid secreted by the traps. Most of the Gln-C and Gln-N recovered inside plants were localized in fed traps. Among nonfed organs, traps were a stronger sink for Gln-C compared to Gln-N, and roots were a stronger sink for Gln-N compared to Gln-C. A significant amount of the Gln-C was respired as indicated by 13 C-CO2 emission, enhanced levels of metabolites of respiratory Gln degradation and increased abundance of proteins of respiratory processes. Transcription analyses revealed constitutive expression of enzymes involved in Gln metabolism in traps. It appears that prey not only provides building blocks of cellular constituents of carnivorous Dionaea muscipula, but also is used for energy generation by respiratory amino acid degradation.
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Affiliation(s)
- Lukas Fasbender
- Institute of Forest Sciences, Chair of Ecosystem Physiology, University of Freiburg, Georges-Köhler-Allee 53/54, Freiburg, 79110, Germany
| | - Daniel Maurer
- Institute of Forest Sciences, Chair of Tree Physiology, University of Freiburg, Georges-Köhler-Allee 53/54, Freiburg, 79110, Germany
| | - Jürgen Kreuzwieser
- Institute of Forest Sciences, Chair of Tree Physiology, University of Freiburg, Georges-Köhler-Allee 53/54, Freiburg, 79110, Germany
| | - Ines Kreuzer
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, 97070, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Jörg Kruse
- Institute of Forest Sciences, Chair of Tree Physiology, University of Freiburg, Georges-Köhler-Allee 53/54, Freiburg, 79110, Germany
| | - Dirk Becker
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, 97070, Germany
| | - Saleh Alfarraj
- College of Science, King Saud University, PO Box 2455, Riyadh, 11451, Saudi Arabia
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, 97070, Germany
- College of Science, King Saud University, PO Box 2455, Riyadh, 11451, Saudi Arabia
| | - Christiane Werner
- Institute of Forest Sciences, Chair of Ecosystem Physiology, University of Freiburg, Georges-Köhler-Allee 53/54, Freiburg, 79110, Germany
| | - Heinz Rennenberg
- Institute of Forest Sciences, Chair of Tree Physiology, University of Freiburg, Georges-Köhler-Allee 53/54, Freiburg, 79110, Germany
- College of Science, King Saud University, PO Box 2455, Riyadh, 11451, Saudi Arabia
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Zakhartsev M, Medvedeva I, Orlov Y, Akberdin I, Krebs O, Schulze WX. Metabolic model of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation. BMC Plant Biol 2016; 16:262. [PMID: 28031032 PMCID: PMC5192601 DOI: 10.1186/s12870-016-0868-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 08/05/2016] [Indexed: 05/12/2023]
Abstract
BACKGROUND Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of these metabolic and underlying regulatory processes allow a detailed understanding of carbon distribution within the plant and the formation of associated phenotypic traits. Sucrose translocation from 'source' tissues (e.g. mesophyll) to 'sink' tissues (e.g. root) is tightly bound to the proton gradient across the membranes. The plant sucrose transporters are grouped into efflux exporters (SWEET family) and proton-symport importers (SUC, STP families). To better understand regulation of sucrose export from source tissues and sucrose import into sink tissues, there is a need for a metabolic model that takes in account the tissue organisation of Arabidopsis thaliana with corresponding metabolic specificities of respective tissues in terms of sucrose and proton production/utilization. An ability of the model to operate under different light modes ('light' and 'dark') and correspondingly in different energy producing modes is particularly important in understanding regulatory modules. RESULTS Here, we describe a multi-compartmental model consisting of a mesophyll cell with plastid and mitochondrion, a phloem cell, as well as a root cell with mitochondrion. In this model, the phloem was considered as a non-growing transport compartment, the mesophyll compartment was considered as both autotrophic (growing on CO2 under light) and heterotrophic (growing on starch in darkness), and the root was always considered as heterotrophic tissue dependent on sucrose supply from the mesophyll compartment. In total, the model includes 413 balanced compounds interconnected by 400 transformers. The structured metabolic model accounts for central carbon metabolism, photosynthesis, photorespiration, carbohydrate metabolism, energy and redox metabolisms, proton metabolism, biomass growth, nutrients uptake, proton gradient generation and sucrose translocation between tissues. Biochemical processes in the model were associated with gene-products (742 ORFs). Flux Balance Analysis (FBA) of the model resulted in balanced carbon, nitrogen, proton, energy and redox states under both light and dark conditions. The main H+-fluxes were reconstructed and their directions matched with proton-dependent sucrose translocation from 'source' to 'sink' under any light condition. CONCLUSIONS The model quantified the translocation of sucrose between plant tissues in association with an integral balance of protons, which in turn is defined by operational modes of the energy metabolism.
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Affiliation(s)
- Maksim Zakhartsev
- Department of Plant Systems Biology, University of Hohenheim, Fruwirthstraße 12, 70599 Stuttgart, Germany
| | - Irina Medvedeva
- Novosibirsk State University, Pirogova 2, 630090 Novosibirsk, Russia
| | - Yury Orlov
- The Federal Research Center Institute of Cytology and Genetics, Russian Academy of Sciences, Lavrentyeva 10, 630090 Novosibirsk, Russia
| | - Ilya Akberdin
- The Federal Research Center Institute of Cytology and Genetics, Russian Academy of Sciences, Lavrentyeva 10, 630090 Novosibirsk, Russia
- Biology Department, San Diego State University, San Diego, CA 92182-4614 USA
| | - Olga Krebs
- Heidelberg Institute of Theoretical Sciences, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Waltraud X. Schulze
- Department of Plant Systems Biology, University of Hohenheim, Fruwirthstraße 12, 70599 Stuttgart, Germany
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Menz J, Li Z, Schulze WX, Ludewig U. Early nitrogen-deprivation responses in Arabidopsis roots reveal distinct differences on transcriptome and (phospho-) proteome levels between nitrate and ammonium nutrition. Plant J 2016; 88:717-734. [PMID: 27419465 DOI: 10.1111/tpj.13272] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 06/30/2016] [Accepted: 07/08/2016] [Indexed: 05/07/2023]
Abstract
Plant roots acquire nitrogen predominantly as ammonium and nitrate, which besides serving as nutrients, also have signaling roles. Re-addition of nitrate to starved plants rapidly re-programs the metabolism and gene expression, but the earliest responses to nitrogen deprivation are unknown. Here, the early transcriptional and (phospho)proteomic responses of roots to nitrate or ammonium deprivation were analyzed. The rapid transcriptional repression of known nitrate-induced genes proceeded the tissue NO3- concentration drop, with the transcription factor genes LBD37/38 and HRS1/HHO1 among those with earliest significant change. Similar rapid transcriptional repression occurred in loss-of-function mutants of the nitrate response factor NLP7 and some transcripts were stabilized by nitrate. In contrast, an early transcriptional response to ammonium deprivation was almost completely absent. However, ammonium deprivation induced a rapid and transient perturbation of the proteome and a differential phosphorylation pattern in proteins involved in adjusting the pH and cation homeostasis, plasma membrane H+ , NH4+ , K+ and water fluxes. Fewer differential phosphorylation patterns in transporters, kinases and other proteins occurred with nitrate deprivation. The deprivation responses were not just opposite to the re-supply responses, but identified NO3- deprivation-induced mRNA decay and signaling candidates potentially reporting the external nitrate status to the cell.
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Affiliation(s)
- Jochen Menz
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstr. 20, 70593, Stuttgart, Germany
| | - Zhi Li
- Institute for Physiology and Biotechnology of Plants, Plant Systems Biology, University of Hohenheim, Garbenstraße 30, 70593, Stuttgart, Germany
| | - Waltraud X Schulze
- Institute for Physiology and Biotechnology of Plants, Plant Systems Biology, University of Hohenheim, Garbenstraße 30, 70593, Stuttgart, Germany
| | - Uwe Ludewig
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstr. 20, 70593, Stuttgart, Germany
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Thieme CJ, Rojas-Triana M, Stecyk E, Schudoma C, Zhang W, Yang L, Miñambres M, Walther D, Schulze WX, Paz-Ares J, Scheible WR, Kragler F. Corrigendum: Endogenous Arabidopsis messenger RNAs transported to distant tissues. Nat Plants 2016; 2:16195. [PMID: 27869791 DOI: 10.1038/nplants.2016.195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
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Zakhartsev M, Pertl-Obermeyer H, Schulze WX. From Phosphoproteome to Modeling of Plant Signaling Pathways. Methods Mol Biol 2016; 1394:245-259. [PMID: 26700054 DOI: 10.1007/978-1-4939-3341-9_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Quantitative proteomic experiments in recent years became almost routine in many aspects of biology. Particularly the quantification of peptides and corresponding phosphorylated counterparts from a single experiment is highly important for understanding of dynamics of signaling pathways. We developed an analytical method to quantify phosphopeptides (pP) in relation to the quantity of the corresponding non-phosphorylated parent peptides (P). We used mixed-mode solid-phase extraction to purify total peptides from tryptic digest and separated them from most of the phosphorous-containing compounds (e.g., phospholipids, nucleotides) which enhances pP enrichment on TiO2 beads. Phosphoproteomic data derived with this designed method allows quantifying pP/P stoichiometry, and qualifying experimental data for mathematical modeling.
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Affiliation(s)
- Maksim Zakhartsev
- Plant Systems Biology, Plant Physiology, University of Hohenheim, Fruwirthstrasse 12, 70599, Stuttgart, Germany.
| | - Heidi Pertl-Obermeyer
- Plant Systems Biology, Plant Physiology, University of Hohenheim, Fruwirthstrasse 12, 70599, Stuttgart, Germany
| | - Waltraud X Schulze
- Plant Systems Biology, Plant Physiology, University of Hohenheim, Fruwirthstrasse 12, 70599, Stuttgart, Germany
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Pertl-Obermeyer H, Wu XN, Schrodt J, Müdsam C, Obermeyer G, Schulze WX. Identification of Cargo for Adaptor Protein (AP) Complexes 3 and 4 by Sucrose Gradient Profiling. Mol Cell Proteomics 2016; 15:2877-89. [PMID: 27371946 DOI: 10.1074/mcp.m116.060129] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Indexed: 11/06/2022] Open
Abstract
Intracellular vesicle trafficking is a fundamental process in eukaryotic cells. It enables cellular polarity and exchange of proteins between subcellular compartments such as the plasma membrane or the vacuole. Adaptor protein complexes participate in the vesicle formation by specific selection of the transported cargo. We investigated the role of the adaptor protein complex 3 (AP-3) and adaptor protein complex 4 (AP-4) in this selection process by screening for AP-3 and AP-4 dependent cargo proteins. Specific cargo proteins are expected to be mis-targeted in knock-out mutants of adaptor protein complex components. Thus, we screened for altered distribution profiles across a density gradient of membrane proteins in wild type versus ap-3β and ap-4β knock-out mutants. In ap-3β mutants, especially proteins with transport functions, such as aquaporins and plasma membrane ATPase, as well as vesicle trafficking proteins showed differential protein distribution profiles across the density gradient. In the ap-4β mutant aquaporins but also proteins from lipid metabolism were differentially distributed. These proteins also showed differential phosphorylation patterns in ap-3β and ap-4β compared with wild type. Other proteins, such as receptor kinases were depleted from the AP-3 mutant membrane system, possibly because of degradation after mis-targeting. In AP-4 mutants, membrane fractions were depleted for cytochrome P450 proteins, cell wall proteins and receptor kinases. Analysis of water transport capacity in wild type and mutant mesophyll cells confirmed aquaporins as cargo proteins of AP-3 and AP-4. The combination of organelle density gradients with proteome analysis turned out as a suitable experimental strategy for large-scale analyses of protein trafficking.
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Affiliation(s)
- Heidi Pertl-Obermeyer
- From the ‡Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Xu Na Wu
- From the ‡Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Jens Schrodt
- From the ‡Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Christina Müdsam
- ¶Molecular Plant Physiology, University of Erlangen, Staudtstraβe 5, 91058 Erlangen, Germany
| | - Gerhard Obermeyer
- §Molecular Plant Biophysics and Biochemistry, Department of Molecular Biology, University of Salzburg, Billrothstraβe 11, 5020 Salzburg, Austria
| | - Waltraud X Schulze
- From the ‡Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany;
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Bemm F, Becker D, Larisch C, Kreuzer I, Escalante-Perez M, Schulze WX, Ankenbrand M, Van de Weyer AL, Krol E, Al-Rasheid KA, Mithöfer A, Weber AP, Schultz J, Hedrich R. Venus flytrap carnivorous lifestyle builds on herbivore defense strategies. Genome Res 2016; 26:812-25. [PMID: 27197216 PMCID: PMC4889972 DOI: 10.1101/gr.202200.115] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 04/07/2016] [Indexed: 11/24/2022]
Abstract
Although the concept of botanical carnivory has been known since Darwin's time, the molecular mechanisms that allow animal feeding remain unknown, primarily due to a complete lack of genomic information. Here, we show that the transcriptomic landscape of the Dionaea trap is dramatically shifted toward signal transduction and nutrient transport upon insect feeding, with touch hormone signaling and protein secretion prevailing. At the same time, a massive induction of general defense responses is accompanied by the repression of cell death-related genes/processes. We hypothesize that the carnivory syndrome of Dionaea evolved by exaptation of ancient defense pathways, replacing cell death with nutrient acquisition.
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Affiliation(s)
- Felix Bemm
- Center for Computational and Theoretical Biology, Campus Hubland Nord; Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, D-97218 Würzburg, Germany
| | - Dirk Becker
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University of Würzburg, 97082 Würzburg, Germany
| | - Christina Larisch
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University of Würzburg, 97082 Würzburg, Germany
| | - Ines Kreuzer
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University of Würzburg, 97082 Würzburg, Germany
| | - Maria Escalante-Perez
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University of Würzburg, 97082 Würzburg, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Markus Ankenbrand
- Center for Computational and Theoretical Biology, Campus Hubland Nord; Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, D-97218 Würzburg, Germany; Department of Animal Ecology and Tropical Biology, Biocenter, Am Hubland, 97074 Würzburg, Germany
| | - Anna-Lena Van de Weyer
- Center for Computational and Theoretical Biology, Campus Hubland Nord; Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, D-97218 Würzburg, Germany
| | - Elzbieta Krol
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University of Würzburg, 97082 Würzburg, Germany
| | - Khaled A Al-Rasheid
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University of Würzburg, 97082 Würzburg, Germany; Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Axel Mithöfer
- Bioorganic Chemistry Department, Max-Planck-Institute for Chemical Ecology, 07745 Jena, Germany
| | - Andreas P Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Jörg Schultz
- Center for Computational and Theoretical Biology, Campus Hubland Nord; Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, D-97218 Würzburg, Germany
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University of Würzburg, 97082 Würzburg, Germany
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41
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Figueroa CM, Feil R, Ishihara H, Watanabe M, Kölling K, Krause U, Höhne M, Encke B, Plaxton WC, Zeeman SC, Li Z, Schulze WX, Hoefgen R, Stitt M, Lunn JE. Trehalose 6-phosphate coordinates organic and amino acid metabolism with carbon availability. Plant J 2016; 85:410-23. [PMID: 26714615 DOI: 10.1111/tpj.13114] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/14/2015] [Accepted: 12/21/2015] [Indexed: 05/18/2023]
Abstract
Trehalose 6-phosphate (Tre6P) is an essential signal metabolite in plants, linking growth and development to carbon metabolism. The sucrose-Tre6P nexus model postulates that Tre6P acts as both a signal and negative feedback regulator of sucrose levels. To test this model, short-term metabolic responses to induced increases in Tre6P levels were investigated in Arabidopsis thaliana plants expressing the Escherichia coli Tre6P synthase gene (otsA) under the control of an ethanol-inducible promoter. Increased Tre6P levels led to a transient decrease in sucrose content, post-translational activation of nitrate reductase and phosphoenolpyruvate carboxylase, and increased levels of organic and amino acids. Radio-isotope ((14)CO2) and stable isotope ((13)CO2) labelling experiments showed no change in the rates of photoassimilate export in plants with elevated Tre6P, but increased labelling of organic acids. We conclude that high Tre6P levels decrease sucrose levels by stimulating nitrate assimilation and anaplerotic synthesis of organic acids, thereby diverting photoassimilates away from sucrose to generate carbon skeletons and fixed nitrogen for amino acid synthesis. These results are consistent with the sucrose-Tre6P nexus model, and implicate Tre6P in coordinating carbon and nitrogen metabolism in plants.
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Affiliation(s)
- Carlos M Figueroa
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Hirofumi Ishihara
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Mutsumi Watanabe
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Katharina Kölling
- Department of Biology, Institute of Agricultural Sciences, ETH Zurich, Zurich, 8092, Switzerland
| | - Ursula Krause
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Melanie Höhne
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Beatrice Encke
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - William C Plaxton
- Department of Biology and Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Samuel C Zeeman
- Department of Biology, Institute of Agricultural Sciences, ETH Zurich, Zurich, 8092, Switzerland
| | - Zhi Li
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - John E Lunn
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
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42
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Abstract
Phosphorylation of substrate proteins by protein kinases can lead to activation or inactivation of signaling pathways or metabolic processes. Precise understanding of activity and specificity of protein kinases are important questions in characterization of kinase functions. Here, we describe a procedure to study kinase activity and specificity using kinase-GFP complexes purified from plant material and synthetic peptides as substrates. Magnetic GFP beads allow purifying receptor-like kinase-GFP complexes from microsomal fractions. Kinase-GFP complexes are then incubated with ATP and the synthetic peptides for kinase reaction. Phosphorylation of substrate peptides is then identified and quantified by mass spectrometry.
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Affiliation(s)
- Xu Na Wu
- Department of Plant Systems Biology, Universität Hohenheim, Fruwirthstraße 12, Stuttgart, 70593, Germany
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43
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Dautel R, Wu XN, Heunemann M, Schulze WX, Harter K. The Sensor Histidine Kinases AHK2 and AHK3 Proceed into Multiple Serine/Threonine/Tyrosine Phosphorylation Pathways in Arabidopsis thaliana. Mol Plant 2016; 9:182-186. [PMID: 26485051 DOI: 10.1016/j.molp.2015.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/03/2015] [Accepted: 10/09/2015] [Indexed: 05/07/2023]
Affiliation(s)
- Rebecca Dautel
- Department of Plant Physiology, Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Xu Na Wu
- Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Michael Heunemann
- Department of Plant Physiology, Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Klaus Harter
- Department of Plant Physiology, Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany.
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44
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Pertl-Obermeyer H, Trentmann O, Duscha K, Neuhaus HE, Schulze WX. Quantitation of Vacuolar Sugar Transporter Abundance Changes Using QconCAT Synthtetic Peptides. Front Plant Sci 2016; 7:411. [PMID: 27148277 PMCID: PMC4828444 DOI: 10.3389/fpls.2016.00411] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/17/2016] [Indexed: 05/19/2023]
Abstract
Measurements of protein abundance changes are important for biological conclusions on protein-related processes such as activity or complex formation. Proteomic analyses in general are almost routine tasks in many laboratories, but a precise and quantitative description of (absolute) protein abundance changes require careful experimental design and precise data quality. Today, a vast choice of metabolic labeling and label-free quantitation protocols are available, but the trade-off between quantitative precision and proteome coverage of quantified proteins including missing value problems remain. Here, we provide an example of a targeted proteomic approach using artificial standard proteins consisting of concatenated peptides of interest (QconCAT) to specifically quantify abiotic stress-induced abundance changes in low abundant vacuolar transporters. An advantage of this approach is the reliable quantitation of alimited set of low-abundant target proteins throughout different conditions. We show that vacuolar ATPase AVP1 and sugar transporters of the ERDL (early responsive to dehydration-like) family and TMT2 (tonoplast monosaccharide transporter 2) showed increased abundance upon salt stress.
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Affiliation(s)
| | - Oliver Trentmann
- Plant Physiology, University of KaiserslauternKaiserslautern, Germany
| | - Kerstin Duscha
- Plant Physiology, University of KaiserslauternKaiserslautern, Germany
| | | | - Waltraud X. Schulze
- Department of Plant Systems Biology, University of HohenheimStuttgart, Germany
- *Correspondence: Waltraud X. Schulze,
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45
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Szymanski WG, Zauber H, Erban A, Gorka M, Wu XN, Schulze WX. Cytoskeletal Components Define Protein Location to Membrane Microdomains. Mol Cell Proteomics 2015; 14:2493-509. [PMID: 26091700 PMCID: PMC4563731 DOI: 10.1074/mcp.m114.046904] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 03/02/2015] [Indexed: 11/06/2022] Open
Abstract
The plasma membrane is an important compartment that undergoes dynamic changes in composition upon external or internal stimuli. The dynamic subcompartmentation of proteins in ordered low-density (DRM) and disordered high-density (DSM) membrane phases is hypothesized to require interactions with cytoskeletal components. Here, we systematically analyzed the effects of actin or tubulin disruption on the distribution of proteins between membrane density phases. We used a proteomic screen to identify candidate proteins with altered submembrane location, followed by biochemical or cell biological characterization in Arabidopsis thaliana. We found that several proteins, such as plasma membrane ATPases, receptor kinases, or remorins resulted in a differential distribution between membrane density phases upon cytoskeletal disruption. Moreover, in most cases, contrasting effects were observed: Disruption of actin filaments largely led to a redistribution of proteins from DRM to DSM membrane fractions while disruption of tubulins resulted in general depletion of proteins from the membranes. We conclude that actin filaments are necessary for dynamic movement of proteins between different membrane phases and that microtubules are not necessarily important for formation of microdomains as such, but rather they may control the protein amount present in the membrane phases.
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Affiliation(s)
- Witold G Szymanski
- From the ‡Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Henrik Zauber
- §Max-Delbrück Center of Molecular Medicine, Robert-Rössle-Straβe 10, 13092 Berlin, Germany
| | - Alexander Erban
- From the ‡Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Michal Gorka
- From the ‡Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Xu Na Wu
- From the ‡Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Waltraud X Schulze
- ¶University of Hohenheim, Department of Plant Systems Biology, 70593 Stuttgart, Germany
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46
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Li Z, Phillip D, Neuhäuser B, Schulze WX, Ludewig U. Protein Dynamics in Young Maize Root Hairs in Response to Macro- and Micronutrient Deprivation. J Proteome Res 2015; 14:3362-71. [DOI: 10.1021/acs.jproteome.5b00399] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Zhi Li
- Department
of Plant Systems Biology, University of Hohenheim, Garbenstraße
30, 70599 Stuttgart, Germany
| | - Daniel Phillip
- Institute
of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Benjamin Neuhäuser
- Institute
of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Waltraud X. Schulze
- Department
of Plant Systems Biology, University of Hohenheim, Garbenstraße
30, 70599 Stuttgart, Germany
| | - Uwe Ludewig
- Institute
of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstraße 20, 70599 Stuttgart, Germany
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47
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Thieme CJ, Rojas-Triana M, Stecyk E, Schudoma C, Zhang W, Yang L, Miñambres M, Walther D, Schulze WX, Paz-Ares J, Scheible WR, Kragler F. Endogenous Arabidopsis messenger RNAs transported to distant tissues. Nat Plants 2015; 1:15025. [PMID: 27247031 DOI: 10.1038/nplants.2015.25] [Citation(s) in RCA: 238] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 02/10/2015] [Indexed: 05/06/2023]
Abstract
The concept that proteins and small RNAs can move to and function in distant body parts is well established. However, non-cell-autonomy of small RNA molecules raises the question: To what extent are protein-coding messenger RNAs (mRNAs) exchanged between tissues in plants? Here we report the comprehensive identification of 2,006 genes producing mobile RNAs in Arabidopsis thaliana. The analysis of variant ecotype transcripts that were present in heterografted plants allowed the identification of mRNAs moving between various organs under normal or nutrient-limiting conditions. Most of these mobile transcripts seem to follow the phloem-dependent allocation pathway transporting sugars from photosynthetic tissues to roots via the vasculature. Notably, a high number of transcripts also move in the opposite, root-to-shoot direction and are transported to specific tissues including flowers. Proteomic data on grafted plants indicate the presence of proteins from mobile RNAs, allowing the possibility that they may be translated at their destination site. The mobility of a high number of mRNAs suggests that a postulated tissue-specific gene expression profile might not be predictive for the actual plant body part in which a transcript exerts its function.
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Affiliation(s)
- Christoph J Thieme
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam 14476, Germany
| | - Monica Rojas-Triana
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401, USA
| | - Ewelina Stecyk
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam 14476, Germany
| | - Christian Schudoma
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam 14476, Germany
| | - Wenna Zhang
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam 14476, Germany
| | - Lei Yang
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam 14476, Germany
| | - Miguel Miñambres
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Cientificas, Campus de Cantoblanco, Madrid 28049, Spain
| | - Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam 14476, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart 70593, Germany
| | - Javier Paz-Ares
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Cientificas, Campus de Cantoblanco, Madrid 28049, Spain
| | - Wolf-Rüdiger Scheible
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam 14476, Germany
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401, USA
| | - Friedrich Kragler
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam 14476, Germany
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48
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Abstract
Protein phosphorylation events on serine, threonine, and tyrosine residues are the most pervasive protein covalent bond modifications in plant signaling. Both low and high throughput studies reveal the importance of phosphorylation in plant molecular biology. Although becoming more and more common, the proteome-wide screening on phosphorylation by experiments remains time consuming and costly. Therefore, in silico prediction methods are proposed as a complementary analysis tool to enhance the phosphorylation site identification, develop biological hypothesis, or help experimental design. These methods build statistical models based on the experimental data, and they do not have some of the technical-specific bias, which may have advantage in proteome-wide analysis. More importantly computational methods are very fast and cheap to run, which makes large-scale phosphorylation identifications very practical for any types of biological study. Thus, the phosphorylation prediction tools become more and more popular. In this chapter, we will focus on plant specific phosphorylation site prediction tools, with essential illustration of technical details and application guidelines. We will use Musite, PhosPhAt and PlantPhos as the representative tools. We will present the results on the prediction of the Arabidopsis protein phosphorylation events to give users a general idea of the performance range of the three tools, together with their strengths and limitations. We believe these prediction tools will contribute more and more to the plant phosphorylation research community.
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Affiliation(s)
- Qiuming Yao
- Department of Computer Science and Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
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49
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Abstract
The family of transmembrane receptor kinase is the largest protein kinase family in Arabidopsis. However many of these kinases have yet uncharacterized functions and little is known about direct substrates of these kinases. Here, we present a large-scale phosphoproteomics method involving label-free quantitation-based comparative phosphopeptide profiling of knockout mutants in receptor-like kinases. This approach, among other physiological and cell biological experiments, is one step in understanding the functional roles of plant kinases in the context of their signaling networks.
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Affiliation(s)
- Xu Na Wu
- Department of Plant Systems Biology, Universität Hohenheim, Fruwirthstraße 12, Stuttgart, 70593, Germany
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50
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Abstract
Plant kinases are one of the largest protein families in Arabidopsis. There are almost 600 membrane-located receptor kinases and almost 400 soluble kinases with distinct functions in signal transduction. In this minireview we discuss phylogeny and functional context of prominent members from major protein kinase subfamilies in plants.
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Affiliation(s)
- Monika Zulawski
- Max Planck Institute of molecular Plant Physiology, 14470, Potsdam, Germany
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