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Chandran AEJ, Finkler A, Hait TA, Kiere Y, David S, Pasmanik-Chor M, Shkolnik D. Calcium regulation of the Arabidopsis Na+/K+ transporter HKT1;1 improves seed germination under salt stress. PLANT PHYSIOLOGY 2024; 194:1834-1852. [PMID: 38057162 PMCID: PMC10904324 DOI: 10.1093/plphys/kiad651] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/02/2023] [Accepted: 11/09/2023] [Indexed: 12/08/2023]
Abstract
Calcium is known to improve seed-germination rates under salt stress. We investigated the involvement of calcium ions (Ca2+) in regulating HIGH-AFFINITY K+ TRANSPORTER 1 (HKT1; 1), which encodes a Na+/K+ transporter, and its post-translational regulator TYPE 2C PROTEIN PHOSPHATASE 49 (PP2C49), in germinating Arabidopsis (Arabidopsis thaliana) seedlings. Germination rates of hkt1 mutant seeds under salt stress remained unchanged by CaCl2 treatment in wild-type Arabidopsis, whereas pp2c49 mutant seeds displayed improved salt-stress tolerance in the absence of CaCl2 supplementation. Analysis of HKT1;1 and PP2C49 promoter activity revealed that CaCl2 treatment results in radicle-focused expression of HKT1;1 and reduction of the native radicle-exclusive expression of PP2C49. Ion-content analysis indicated that CaCl2 treatment improves K+ retention in germinating wild-type seedlings under salt stress, but not in hkt1 seedlings. Transgenic seedlings designed to exclusively express HKT1;1 in the radicle during germination displayed higher germination rates under salt stress than the wild type in the absence of CaCl2 treatment. Transcriptome analysis of germinating seedlings treated with CaCl2, NaCl, or both revealed 118 upregulated and 94 downregulated genes as responsive to the combined treatment. Bioinformatics analysis of the upstream sequences of CaCl2-NaCl-treatment-responsive upregulated genes revealed the abscisic acid response element CACGTGTC, a potential CaM-binding transcription activator-binding motif, as most prominent. Our findings suggest a key role for Ca2+ in mediating salt-stress responses during germination by regulating genes that function to maintain Na+ and K+ homeostasis, which is vital for seed germination under salt stress.
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Affiliation(s)
- Ancy E J Chandran
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Aliza Finkler
- School of Plant Sciences and Food Security, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tom Aharon Hait
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yvonne Kiere
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Sivan David
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Metsada Pasmanik-Chor
- School of Plant Sciences and Food Security, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Doron Shkolnik
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 7610001, Israel
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2
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PhosPhAt 4.0: An Updated Arabidopsis Database for Searching Phosphorylation Sites and Kinase-Target Interactions. Methods Mol Biol 2021; 2358:189-202. [PMID: 34270056 DOI: 10.1007/978-1-0716-1625-3_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The PhosPhAt 4.0 database contains information on Arabidopsis phosphorylation sites identified by mass spectrometry in large-scale experiments from different research groups. So far PhosPhAt 4.0 has been one of the most significant large-scale data resources for plant phosphorylation studies. Functionalities of the web application, besides display of phosphorylation sites, include phosphorylation site prediction and kinase-target relationships retrieval. Here, we present an overview and user instructions for the PhosPhAt 4.0 database, with strong emphasis on recent renewals regarding protein annotation by SUBA4.0 and Mapman4, and additional phosphorylation site information imported from other databases, such as UniProt. Here, we provide a user guide for the retrieval of phosphorylation motifs from the kinase-target database and how to visualize these results. The improvements incorporated into the PhosPhAt 4.0 database have produced much more functionality and user flexibility for phosphoproteomic analysis.
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3
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Salladini E, Jørgensen MLM, Theisen FF, Skriver K. Intrinsic Disorder in Plant Transcription Factor Systems: Functional Implications. Int J Mol Sci 2020; 21:E9755. [PMID: 33371315 PMCID: PMC7767404 DOI: 10.3390/ijms21249755] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 01/07/2023] Open
Abstract
Eukaryotic cells are complex biological systems that depend on highly connected molecular interaction networks with intrinsically disordered proteins as essential components. Through specific examples, we relate the conformational ensemble nature of intrinsic disorder (ID) in transcription factors to functions in plants. Transcription factors contain large regulatory ID-regions with numerous orphan sequence motifs, representing potential important interaction sites. ID-regions may affect DNA-binding through electrostatic interactions or allosterically as for the bZIP transcription factors, in which the DNA-binding domains also populate ensembles of dynamic transient structures. The flexibility of ID is well-suited for interaction networks requiring efficient molecular adjustments. For example, Radical Induced Cell Death1 depends on ID in transcription factors for its numerous, structurally heterogeneous interactions, and the JAZ:MYC:MED15 regulatory unit depends on protein dynamics, including binding-associated unfolding, for regulation of jasmonate-signaling. Flexibility makes ID-regions excellent targets of posttranslational modifications. For example, the extent of phosphorylation of the NAC transcription factor SOG1 regulates target gene expression and the DNA-damage response, and phosphorylation of the AP2/ERF transcription factor DREB2A acts as a switch enabling heat-regulated degradation. ID-related phase separation is emerging as being important to transcriptional regulation with condensates functioning in storage and inactivation of transcription factors. The applicative potential of ID-regions is apparent, as removal of an ID-region of the AP2/ERF transcription factor WRI1 affects its stability and consequently oil biosynthesis. The highlighted examples show that ID plays essential functional roles in plant biology and has a promising potential in engineering.
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Affiliation(s)
| | | | | | - Karen Skriver
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark; (E.S.); (M.L.M.J.); (F.F.T.)
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4
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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. THE PLANT CELL 2020; 32:1610-1625. [PMID: 32111670 PMCID: PMC7203915 DOI: 10.1105/tpc.19.00810] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [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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5
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Korkuć P, Walther D. Towards understanding the crosstalk between protein post-translational modifications: Homo- and heterotypic PTM pair distances on protein surfaces are not random. Proteins 2016; 85:78-92. [DOI: 10.1002/prot.25200] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/29/2016] [Accepted: 10/20/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Paula Korkuć
- Max Planck Institute for Molecular Plant Physiology; Am Mühlenberg 1 Potsdam-Golm 14476 Germany
| | - Dirk Walther
- Max Planck Institute for Molecular Plant Physiology; Am Mühlenberg 1 Potsdam-Golm 14476 Germany
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6
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Torres MP, Dewhurst H, Sundararaman N. Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease. Mol Cell Proteomics 2016; 15:3513-3528. [PMID: 27697855 PMCID: PMC5098047 DOI: 10.1074/mcp.m116.062331] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Indexed: 01/09/2023] Open
Abstract
Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable body of potential regulatory elements that impact hundreds of different biological processes important in eukaryotic biology and human health.
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Affiliation(s)
- Matthew P Torres
- From the School of Biological Sciences; Georgia Institute of Technology; Atlanta, Georgia 30332
| | - Henry Dewhurst
- From the School of Biological Sciences; Georgia Institute of Technology; Atlanta, Georgia 30332
| | - Niveda Sundararaman
- From the School of Biological Sciences; Georgia Institute of Technology; Atlanta, Georgia 30332
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7
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Korkuć P, Walther D. Spatial proximity statistics suggest a regulatory role of protein phosphorylation on compound binding. Proteins 2016; 84:565-79. [PMID: 26817627 DOI: 10.1002/prot.25001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/12/2016] [Accepted: 01/18/2016] [Indexed: 01/07/2023]
Abstract
Phosphorylation is an important post-translational modification that regulates protein function by the attachment of negatively charged phosphate groups to phosphorylatable amino acid residues. As a mode of action, an influence of phosphorylation on the binding of compounds to proteins has been discussed and described for a number of proteins in the literature. However, a systematic statistical survey probing for enriched phosphorylation sites close to compound binding sites in support of this notion and with properly chosen random reference distributions has not been presented yet. Using high-resolution protein structures from the Protein Data Bank including their co-crystallized non-covalently bound compounds and experimentally determined phosphorylation sites, we analyzed the pairwise distance distributions of phosphorylation and compound binding sites on protein surfaces. We found that phosphorylation sites are indeed located at significantly closer distances to compounds than expected by chance holding true specifically also for the subset of compound binding sites serving as catalytic sites of metabolic reactions. This tendency was particularly evident when treating phosphorylation sites as collective sets supporting the relevance of phosphorylation hotspots. Interestingly, phosphorylation sites were found to be closer to negatively charged than to positively charged compounds suggesting a stronger modulation of the binding of negatively charged compounds in dependence on phosphorylation status than on positively charged compounds. The enrichment of phosphorylation sites near compound binding sites confirms a regulatory role of phosphorylation in compound binding and provides a solid statistical basis for the literature-reported selected events.
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Affiliation(s)
- Paula Korkuć
- Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Dirk Walther
- Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
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8
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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. MOLECULAR 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] [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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9
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Friso G, van Wijk KJ. Posttranslational Protein Modifications in Plant Metabolism. PLANT PHYSIOLOGY 2015; 169:1469-87. [PMID: 26338952 PMCID: PMC4634103 DOI: 10.1104/pp.15.01378] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 09/02/2015] [Indexed: 05/18/2023]
Abstract
Posttranslational modifications (PTMs) of proteins greatly expand proteome diversity, increase functionality, and allow for rapid responses, all at relatively low costs for the cell. PTMs play key roles in plants through their impact on signaling, gene expression, protein stability and interactions, and enzyme kinetics. Following a brief discussion of the experimental and bioinformatics challenges of PTM identification, localization, and quantification (occupancy), a concise overview is provided of the major PTMs and their (potential) functional consequences in plants, with emphasis on plant metabolism. Classic examples that illustrate the regulation of plant metabolic enzymes and pathways by PTMs and their cross talk are summarized. Recent large-scale proteomics studies mapped many PTMs to a wide range of metabolic functions. Unraveling of the PTM code, i.e. a predictive understanding of the (combinatorial) consequences of PTMs, is needed to convert this growing wealth of data into an understanding of plant metabolic regulation.
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Affiliation(s)
- Giulia Friso
- School for Integrative Plant Sciences, Section Plant Biology, Cornell University, Ithaca, New York 14853
| | - Klaas J van Wijk
- School for Integrative Plant Sciences, Section Plant Biology, Cornell University, Ithaca, New York 14853
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10
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Chaki M, Kovacs I, Spannagl M, Lindermayr C. Computational prediction of candidate proteins for S-nitrosylation in Arabidopsis thaliana. PLoS One 2014; 9:e110232. [PMID: 25333472 PMCID: PMC4204854 DOI: 10.1371/journal.pone.0110232] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 09/17/2014] [Indexed: 02/04/2023] Open
Abstract
Nitric oxide (NO) is an important signaling molecule that regulates many physiological processes in plants. One of the most important regulatory mechanisms of NO is S-nitrosylation-the covalent attachment of NO to cysteine residues. Although the involvement of cysteine S-nitrosylation in the regulation of protein functions is well established, its substrate specificity remains unknown. Identification of candidates for S-nitrosylation and their target cysteine residues is fundamental for studying the molecular mechanisms and regulatory roles of S-nitrosylation in plants. Several experimental methods that are based on the biotin switch have been developed to identify target proteins for S-nitrosylation. However, these methods have their limits. Thus, computational methods are attracting considerable attention for the identification of modification sites in proteins. Using GPS-SNO version 1.0, a recently developed S-nitrosylation site-prediction program, a set of 16,610 candidate proteins for S-nitrosylation containing 31,900 S-nitrosylation sites was isolated from the entire Arabidopsis proteome using the medium threshold. In the compartments "chloroplast," "CUL4-RING ubiquitin ligase complex," and "membrane" more than 70% of the proteins were identified as candidates for S-nitrosylation. The high number of identified candidates in the proteome reflects the importance of redox signaling in these compartments. An analysis of the functional distribution of the predicted candidates showed that proteins involved in signaling processes exhibited the highest prediction rate. In a set of 46 proteins, where 53 putative S-nitrosylation sites were already experimentally determined, the GPS-SNO program predicted 60 S-nitrosylation sites, but only 11 overlap with the results of the experimental approach. In general, a computer-assisted method for the prediction of targets for S-nitrosylation is a very good tool; however, further development, such as including the three dimensional structure of proteins in such analyses, would improve the identification of S-nitrosylation sites.
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Affiliation(s)
- Mounira Chaki
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Izabella Kovacs
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Manuel Spannagl
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Christian Lindermayr
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
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11
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Bigeard J, Rayapuram N, Bonhomme L, Hirt H, Pflieger D. Proteomic and phosphoproteomic analyses of chromatin-associated proteins from Arabidopsis thaliana. Proteomics 2014; 14:2141-55. [PMID: 24889360 DOI: 10.1002/pmic.201400072] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/28/2014] [Accepted: 05/26/2014] [Indexed: 11/09/2022]
Abstract
The nucleus is the organelle where basically all DNA-related processes take place in eukaryotes, such as replication, transcription, and splicing as well as epigenetic regulation. The identification and description of the nuclear proteins is one of the requisites toward a comprehensive understanding of the biological functions accomplished in the nucleus. Many of the regulatory mechanisms of protein functions rely on their PTMs among which phosphorylation is probably one of the most important properties affecting enzymatic activity, interaction with other molecules, localization, or stability. So far, the nuclear and subnuclear proteome and phosphoproteome of the model plant Arabidopsis thaliana have been the subject of very few studies. In this work, we developed a purification protocol of Arabidopsis chromatin-associated proteins and performed proteomic and phosphoproteomic analyses identifying a total of 879 proteins of which 198 were phosphoproteins that were mainly involved in chromatin remodeling, transcriptional regulation, and RNA processing. From 230 precisely localized phosphorylation sites (phosphosites), 52 correspond to hitherto unidentified sites. This protocol and data thereby obtained should be a valuable resource for many domains of plant research.
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Affiliation(s)
- Jean Bigeard
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA/CNRS/Université d'Evry Val d'Essonne/Saclay Plant Sciences, Evry, France
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12
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Bigeard J, Rayapuram N, Pflieger D, Hirt H. Phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins. Proteomics 2014; 14:2127-40. [PMID: 24889195 DOI: 10.1002/pmic.201400073] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/28/2014] [Accepted: 05/26/2014] [Indexed: 12/25/2022]
Abstract
In eukaryotes, most of the DNA is located in the nucleus where it is organized with histone proteins in a higher order structure as chromatin. Chromatin and chromatin-associated proteins contribute to DNA-related processes such as replication and transcription as well as epigenetic regulation. Protein functions are often regulated by PTMs among which phosphorylation is one of the most abundant PTM. Phosphorylation of proteins affects important properties, such as enzyme activity, protein stability, or subcellular localization. We here describe the main specificities of protein phosphorylation in plants and review the current knowledge on phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins. We also outline some future challenges to further elucidate protein phosphorylation and chromatin regulation.
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Affiliation(s)
- Jean Bigeard
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA/CNRS/Université d'Evry Val d'Essonne/Saclay Plant Sciences, Evry, France
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13
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Wu X, Sklodowski K, Encke B, Schulze WX. A kinase-phosphatase signaling module with BSK8 and BSL2 involved in regulation of sucrose-phosphate synthase. J Proteome Res 2014; 13:3397-409. [PMID: 24924143 DOI: 10.1021/pr5003164] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
External supply of sucrose to carbon-starved Arabidopsis seedlings induced changes in phosphorylation of Brassinosteroid Signaling Kinase 8 (BSK8) at two different sites. Serine S(20) lies within a phosphorylation hotspot at the N-terminal region of the protein, while S(213) is located within the kinase domain of BSK8. Upon sucrose supply phosphorylation of BSK8(S20) and BSK8(S213) showed opposite behavior with increasing phosphorylation of S(213) and decreased phosphorylation of S(20) at 5 min after sucrose supply. Here we aim to systematically analyze the effects of BSK8 mutations on downstream cellular regulatory events and characterize molecular functions of BSK8 and its phosphorylation. Comparative phosphoproteomic profiling of a bsk8 knockout mutant and wild type revealed potential targets in sucrose metabolism. Activity of sucrose-phosphate synthase (SPS) was decreased by phosphorylation at S(152), and SPS phosphorylation inversely correlated with sucrose-induced BSK8 activity. Furthermore, BSK8 was found to interact with BSL2, a Kelch-type phosphatase. On the basis of a combination of kinase activity measurements, SPS activity assays, and phosphorylation site mutations in BSK8 at S(20) and S(213), we conclude that regulation of SPS by BSK8 occurs through activation of a phosphatase that in turn may dephosphorylate SPS and thus activates the enzyme.
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Affiliation(s)
- XuNa Wu
- Max Planck Institute for Molecular Plant Physiology , Am Mühlenberg 1, 14476 Golm, Germany
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14
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van Wijk KJ, Friso G, Walther D, Schulze WX. Meta-Analysis of Arabidopsis thaliana Phospho-Proteomics Data Reveals Compartmentalization of Phosphorylation Motifs. THE PLANT CELL 2014; 26:2367-2389. [PMID: 24894044 PMCID: PMC4114939 DOI: 10.1105/tpc.114.125815] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 03/27/2014] [Accepted: 05/09/2014] [Indexed: 05/18/2023]
Abstract
Protein (de)phosphorylation plays an important role in plants. To provide a robust foundation for subcellular phosphorylation signaling network analysis and kinase-substrate relationships, we performed a meta-analysis of 27 published and unpublished in-house mass spectrometry-based phospho-proteome data sets for Arabidopsis thaliana covering a range of processes, (non)photosynthetic tissue types, and cell cultures. This resulted in an assembly of 60,366 phospho-peptides matching to 8141 nonredundant proteins. Filtering the data for quality and consistency generated a set of medium and a set of high confidence phospho-proteins and their assigned phospho-sites. The relation between single and multiphosphorylated peptides is discussed. The distribution of p-proteins across cellular functions and subcellular compartments was determined and showed overrepresentation of protein kinases. Extensive differences in frequency of pY were found between individual studies due to proteomics and mass spectrometry workflows. Interestingly, pY was underrepresented in peroxisomes but overrepresented in mitochondria. Using motif-finding algorithms motif-x and MMFPh at high stringency, we identified compartmentalization of phosphorylation motifs likely reflecting localized kinase activity. The filtering of the data assembly improved signal/noise ratio for such motifs. Identified motifs were linked to kinases through (bioinformatic) enrichment analysis. This study also provides insight into the challenges/pitfalls of using large-scale phospho-proteomic data sets to nonexperts.
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Affiliation(s)
- Klaas J van Wijk
- Department of Plant Biology, Cornell University, Ithaca, New York 14850
| | - Giulia Friso
- Department of Plant Biology, Cornell University, Ithaca, New York 14850
| | - Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, 14476 Golm, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
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Duan G, Walther D, Schulze WX. Reconstruction and analysis of nutrient-induced phosphorylation networks in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2013; 4:540. [PMID: 24400017 PMCID: PMC3872036 DOI: 10.3389/fpls.2013.00540] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/12/2013] [Indexed: 05/23/2023]
Abstract
Elucidating the dynamics of molecular processes in living organisms in response to external perturbations is a central goal in modern systems biology. We investigated the dynamics of protein phosphorylation events in Arabidopsis thaliana exposed to changing nutrient conditions. Phosphopeptide expression levels were detected at five consecutive time points over a time interval of 30 min after nutrient resupply following prior starvation. The three tested inorganic, ionic nutrients NH(+) 4, NO(-) 3, PO(3-) 4 elicited similar phosphosignaling responses that were distinguishable from those invoked by the sugars mannitol, sucrose. When embedded in the protein-protein interaction network of Arabidopsis thaliana, phosphoproteins were found to exhibit a higher degree compared to average proteins. Based on the time-series data, we reconstructed a network of regulatory interactions mediated by phosphorylation. The performance of different network inference methods was evaluated by the observed likelihood of physical interactions within and across different subcellular compartments and based on gene ontology semantic similarity. The dynamic phosphorylation network was then reconstructed using a Pearson correlation method with added directionality based on partial variance differences. The topology of the inferred integrated network corresponds to an information dissemination architecture, in which the phosphorylation signal is passed on to an increasing number of phosphoproteins stratified into an initiation, processing, and effector layer. Specific phosphorylation peptide motifs associated with the distinct layers were identified indicating the action of layer-specific kinases. Despite the limited temporal resolution, combined with information on subcellular location, the available time-series data proved useful for reconstructing the dynamics of the molecular signaling cascade in response to nutrient stress conditions in the plant Arabidopsis thaliana.
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Affiliation(s)
- Guangyou Duan
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Dirk Walther
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Waltraud X. Schulze
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
- Department of Plant Systems Biology, Universität HohenheimStuttgart, Germany
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Beltrao P, Bork P, Krogan NJ, van Noort V. Evolution and functional cross-talk of protein post-translational modifications. Mol Syst Biol 2013; 9:714. [PMID: 24366814 PMCID: PMC4019982 DOI: 10.1002/msb.201304521] [Citation(s) in RCA: 257] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 11/18/2013] [Accepted: 11/22/2013] [Indexed: 12/19/2022] Open
Abstract
Protein post-translational modifications (PTMs) allow the cell to regulate protein activity and play a crucial role in the response to changes in external conditions or internal states. Advances in mass spectrometry now enable proteome wide characterization of PTMs and have revealed a broad functional role for a range of different types of modifications. Here we review advances in the study of the evolution and function of PTMs that were spurred by these technological improvements. We provide an overview of studies focusing on the origin and evolution of regulatory enzymes as well as the evolutionary dynamics of modification sites. Finally, we discuss different mechanisms of altering protein activity via post-translational regulation and progress made in the large-scale functional characterization of PTM function.
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Affiliation(s)
- Pedro Beltrao
- European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI)CambridgeUK
| | - Peer Bork
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Max‐Delbruck‐Centre for Molecular MedicineBerlin‐BuchGermany
| | - Nevan J. Krogan
- Department of Cellular and Molecular PharmacologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
- California Institute for Quantitative BiosciencesSan FranciscoCaliforniaUSA
- J. David Gladstone InstitutesSan FranciscoCaliforniaUSA
| | - Vera van Noort
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
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17
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Wu XN, Sanchez Rodriguez C, Pertl-Obermeyer H, Obermeyer G, Schulze WX. Sucrose-induced receptor kinase SIRK1 regulates a plasma membrane aquaporin in Arabidopsis. Mol Cell Proteomics 2013; 12:2856-73. [PMID: 23820729 PMCID: PMC3790296 DOI: 10.1074/mcp.m113.029579] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Revised: 06/30/2013] [Indexed: 11/06/2022] Open
Abstract
The transmembrane receptor kinase family is the largest protein kinase family in Arabidopsis, and it contains the highest fraction of proteins with yet uncharacterized functions. Here, we present functions of SIRK1, a receptor kinase that was previously identified with rapid transient phosphorylation after sucrose resupply to sucrose-starved seedlings. SIRK1 was found to be an active kinase with increasing activity in the presence of an external sucrose supply. In sirk1 T-DNA insertional mutants, the sucrose-induced phosphorylation patterns of several membrane proteins were strongly reduced; in particular, pore-gating phosphorylation sites in aquaporins were affected. SIRK1-GFP fusions were found to directly interact with aquaporins in affinity pull-down experiments on microsomal membrane vesicles. Furthermore, protoplast swelling assays of sirk1 mutants and SIRK1-GFP expressing lines confirmed a direct functional interaction of receptor kinase SIRK1 and aquaporins as substrates for phosphorylation. A lack of SIRK1 expression resulted in the failure of mutant protoplasts to control water channel activity upon changes in external sucrose concentrations. We propose that SIRK1 is involved in the regulation of sucrose-specific osmotic responses through direct interaction with and activation of an aquaporin via phosphorylation and that the duration of this response is controlled by phosphorylation-dependent receptor internalization.
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Affiliation(s)
- Xu Na Wu
- Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm, Germany
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18
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Sugita M, Ichinose M, Ide M, Sugita C. Architecture of the PPR gene family in the moss Physcomitrella patens. RNA Biol 2013; 10:1439-45. [PMID: 23645116 PMCID: PMC3858427 DOI: 10.4161/rna.24772] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Pentatricopeptide repeat (PPR) proteins are widespread in eukaryotes and in particular, include several hundred members in land plants. The majority of PPR proteins are localized in mitochondria and plastids, where they play a crucial role in various aspects of RNA metabolism at the post-transcriptional level in gene expression. However, many of their functions remain to be characterized. In contrast to vascular plants, the moss Physcomitrella patens has only 105 PPR genes. This number may represent a minimum set of PPR proteins required for post-transcriptional regulation in plant organelles. Here, we review the overall structure of the P. patens PPR gene family and the current status of the functional characterization of moss PPR proteins.
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Affiliation(s)
- Mamoru Sugita
- Center for Gene Research; Nagoya University; Chikusa-ku; Nagoya, Japan
| | - Mizuho Ichinose
- Center for Gene Research; Nagoya University; Chikusa-ku; Nagoya, Japan
| | - Mizuki Ide
- Center for Gene Research; Nagoya University; Chikusa-ku; Nagoya, Japan
| | - Chieko Sugita
- Center for Gene Research; Nagoya University; Chikusa-ku; Nagoya, Japan
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19
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Zulawski M, Braginets R, Schulze WX. PhosPhAt goes kinases--searchable protein kinase target information in the plant phosphorylation site database PhosPhAt. Nucleic Acids Res 2012; 41:D1176-84. [PMID: 23172287 PMCID: PMC3531128 DOI: 10.1093/nar/gks1081] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Reversible phosphorylation is a key mechanism for regulating protein function. Thus it is of high interest to know which kinase can phosphorylate which proteins. Comprehensive information about phosphorylation sites in Arabidopsis proteins is hosted within the PhosPhAt database (http://phosphat.mpimp-golm.mpg.de). However, our knowledge of the kinases that phosphorylate those sites is dispersed throughout the literature and very difficult to access, particularly for investigators seeking to interpret large scale and high-throughput experiments. Therefore, we aimed to compile information on kinase–substrate interactions and kinase-specific regulatory information and make this available via a new functionality embedded in PhosPhAt. Our approach involved systematic surveying of the literature for regulatory information on the members of the major kinase families in Arabidopsis thaliana, such as CDPKs, MPK(KK)s, AGC kinases and SnRKs, as well as individual kinases from other families. To date, we have researched more than 4450 kinase-related publications, which collectively contain information on about 289 kinases. Users can now query the PhosPhAt database not only for experimental and predicted phosphorylation sites of individual proteins, but also for known substrates for a given kinase or kinase family. Further developments include addition of new phosphorylation sites and visualization of clustered phosphorylation events, known as phosphorylation hotspots.
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Affiliation(s)
- Monika Zulawski
- Max Planck Institut für molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Golm, Germany
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