1
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Bailey M, Ivanauskaite A, Grimmer J, Akintewe O, Payne AC, Osborne R, Labandera AM, Etherington RD, Rantala M, Baginsky S, Mulo P, Gibbs DJ. Retraction Note: The Arabidopsis NOT4A E3 ligase promotes PGR3 expression and regulates chloroplast translation. Nat Commun 2022; 13:2913. [PMID: 35595752 PMCID: PMC9122975 DOI: 10.1038/s41467-022-30354-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Mark Bailey
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK.,Plant Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | | | - Julia Grimmer
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Saale, Germany
| | | | - Adrienne C Payne
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Rory Osborne
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | | | | | - Marjaana Rantala
- Molecular Plant Biology, University of Turku, 20520, Turku, Finland
| | - Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Saale, Germany.,Biochemistry of Plants, Faculty for Biology and Biotechnology, Ruhr-University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Paula Mulo
- Molecular Plant Biology, University of Turku, 20520, Turku, Finland
| | - Daniel J Gibbs
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK.
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2
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Rödiger A, Agne B, Dobritzsch D, Helm S, Müller F, Pötzsch N, Baginsky S. Chromoplast differentiation in bell pepper (Capsicum annuum) fruits. Plant J 2021; 105:1431-1442. [PMID: 33258209 DOI: 10.1111/tpj.15104] [Citation(s) in RCA: 12] [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: 09/15/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 05/21/2023]
Abstract
We report here a detailed analysis of the proteome adjustments that accompany chromoplast differentiation from chloroplasts during bell pepper (Capsicum annuum) fruit ripening. While the two photosystems are disassembled and their constituents degraded, the cytochrome b6 f complex, the ATPase complex, and Calvin cycle enzymes are maintained at high levels up to fully mature chromoplasts. This is also true for ferredoxin (Fd) and Fd-dependent NADP reductase, suggesting that ferredoxin retains a central role in the chromoplasts' redox metabolism. There is a significant increase in the amount of enzymes of the typical metabolism of heterotrophic plastids, such as the oxidative pentose phosphate pathway (OPPP) and amino acid and fatty acid biosynthesis. Enzymes of chlorophyll catabolism and carotenoid biosynthesis increase in abundance, supporting the pigment reorganization that goes together with chromoplast differentiation. The majority of plastid encoded proteins decline but constituents of the plastid ribosome and AccD increase in abundance. Furthermore, the amount of plastid terminal oxidase (PTOX) remains unchanged despite a significant increase in phytoene desaturase (PDS) levels, suggesting that the electrons from phytoene desaturation are consumed by another oxidase. This may be a particularity of non-climacteric fruits such as bell pepper that lack a respiratory burst at the onset of fruit ripening.
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Affiliation(s)
- Anja Rödiger
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
- Biochemistry of Plants, Biology and Biotechnology, Ruhr-University Bochum, Bochum, Germany
| | - Birgit Agne
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
- Biochemistry of Plants, Biology and Biotechnology, Ruhr-University Bochum, Bochum, Germany
| | - Dirk Dobritzsch
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Stefan Helm
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Fränze Müller
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
- Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Nina Pötzsch
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Sacha Baginsky
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
- Biochemistry of Plants, Biology and Biotechnology, Ruhr-University Bochum, Bochum, Germany
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3
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Rödiger A, Galonska J, Bergner E, Agne B, Helm S, Alseekh S, Fernie AR, Thieme D, Hoehenwarter W, Hause G, Pfannschmidt T, Baginsky S. Working day and night: plastid casein kinase 2 catalyses phosphorylation of proteins with diverse functions in light- and dark-adapted plastids. Plant J 2020; 104:546-558. [PMID: 32745315 DOI: 10.1111/tpj.14944] [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] [Received: 08/08/2019] [Revised: 07/15/2020] [Accepted: 07/21/2020] [Indexed: 06/11/2023]
Abstract
Casein kinase 2 is a ubiquitous protein kinase that has puzzled researchers for several decades because of its pleiotropic activity. Here, we set out to identify the in vivo targets of plastid casein kinase 2 (pCK2) in Arabidopsis thaliana. Survey phosphoproteome analyses were combined with targeted analyses with wild-type and pck2 knockdown mutants to identify potential pCK2 targets by their decreased phosphorylation state in the mutant. To validate potential substrates, we complemented the pck2 knockdown line with tandem affinity tag (TAP)-tagged pCK2 and found it to restore growth parameters, as well as many, but not all, putative pCK2-dependent phosphorylation events. We further performed a targeted analysis at the end-of-night to increase the specificity of target protein identification. This analysis confirmed light-independent phosphorylation of several pCK2 target proteins. Based on the aforementioned data, we define a set of in vivo pCK2-targets that span different chloroplast functions, such as metabolism, transcription, translation and photosynthesis. The pleiotropy of pCK2 functions is also manifested by altered state transition kinetics during short-term acclimation and significant alterations in the mutant metabolism, supporting its function in photosynthetic regulation. Thus, our data expand our understanding on chloroplast phosphorylation networks and provide insights into kinase networks in the regulation of chloroplast functions.
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Affiliation(s)
- Anja Rödiger
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Charles Tanford Proteinzentrum, Kurt-Mothes-Str. 3a, Halle (Saale), 06120, Germany
| | - Johann Galonska
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Charles Tanford Proteinzentrum, Kurt-Mothes-Str. 3a, Halle (Saale), 06120, Germany
| | - Elena Bergner
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Charles Tanford Proteinzentrum, Kurt-Mothes-Str. 3a, Halle (Saale), 06120, Germany
| | - Birgit Agne
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Charles Tanford Proteinzentrum, Kurt-Mothes-Str. 3a, Halle (Saale), 06120, Germany
| | - Stefan Helm
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Charles Tanford Proteinzentrum, Kurt-Mothes-Str. 3a, Halle (Saale), 06120, Germany
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, Potsdam, 14476, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, Potsdam, 14476, Germany
| | - Domenika Thieme
- Leibniz-Institut für Pflanzenbiochemie, Weinbergweg 3, Halle (Saale), 06120, Germany
| | - Wolfgang Hoehenwarter
- Leibniz-Institut für Pflanzenbiochemie, Weinbergweg 3, Halle (Saale), 06120, Germany
| | - Gerd Hause
- Biocentre, Martin-Luther-University Halle-Wittenberg, Weinbergweg 22, Halle (Saale), 06120, Germany
| | | | - Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Charles Tanford Proteinzentrum, Kurt-Mothes-Str. 3a, Halle (Saale), 06120, Germany
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4
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Hristou A, Grimmer J, Baginsky S. The Secret Life of Chloroplast Precursor Proteins in the Cytosol. Mol Plant 2020; 13:1111-1113. [PMID: 32679264 DOI: 10.1016/j.molp.2020.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 05/11/2023]
Affiliation(s)
- Athina Hristou
- Biochemistry of Plants, Faculty of Biochemistry and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Julia Grimmer
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Charles Tanford Proteinzentrum, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany
| | - Sacha Baginsky
- Biochemistry of Plants, Faculty of Biochemistry and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801 Bochum, Germany; Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Charles Tanford Proteinzentrum, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany.
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5
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Grimmer J, Helm S, Dobritzsch D, Hause G, Shema G, Zahedi RP, Baginsky S. Mild proteasomal stress improves photosynthetic performance in Arabidopsis chloroplasts. Nat Commun 2020; 11:1662. [PMID: 32245955 PMCID: PMC7125294 DOI: 10.1038/s41467-020-15539-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 08/04/2019] [Accepted: 03/13/2020] [Indexed: 11/09/2022] Open
Abstract
The proteasome is an essential protein-degradation machinery in eukaryotic cells that controls protein turnover and thereby the biogenesis and function of cell organelles. Chloroplasts import thousands of nuclear-encoded precursor proteins from the cytosol, suggesting that the bulk of plastid proteins is transiently exposed to the cytosolic proteasome complex. Therefore, there is a cytosolic equilibrium between chloroplast precursor protein import and proteasomal degradation. We show here that a shift in this equilibrium, induced by mild genetic proteasome impairment, results in elevated precursor protein abundance in the cytosol and significantly increased accumulation of functional photosynthetic complexes in protein import-deficient chloroplasts. Importantly, a proteasome lid mutant shows improved photosynthetic performance, even in the absence of an import defect, signifying that functional precursors are continuously degraded. Hence, turnover of plastid precursors in the cytosol represents a mechanism to constrain thylakoid membrane assembly and photosynthetic electron transport.
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Affiliation(s)
- Julia Grimmer
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Saale, Germany
| | - Stefan Helm
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Saale, Germany
| | - Dirk Dobritzsch
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Saale, Germany
| | - Gerd Hause
- Biocenter of the University, Martin-Luther-University Halle-Wittenberg, Weinbergweg 22, 06120, Halle, Saale, Germany
| | - Gerta Shema
- Leibniz-Institut für Analytische Wissenschaften -ISAS- e.V., Bunsen-Kirchhoff-Straße 11, 44139, Dortmund, Germany
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften -ISAS- e.V., Bunsen-Kirchhoff-Straße 11, 44139, Dortmund, Germany
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Côte Ste-Catherine Road, Montreal, QC, H3T 1E2, Canada
| | - Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Saale, Germany.
- Biochemistry of Plants, Faculty for Biology and Biotechnology, Ruhr-University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany.
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6
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Schäfer P, Helm S, Köhler D, Agne B, Baginsky S. Consequences of impaired 1-MDa TIC complex assembly for the abundance and composition of chloroplast high-molecular mass protein complexes. PLoS One 2019; 14:e0213364. [PMID: 30865669 PMCID: PMC6415892 DOI: 10.1371/journal.pone.0213364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 10/24/2018] [Accepted: 02/20/2019] [Indexed: 12/28/2022] Open
Abstract
We report a systematic analysis of chloroplast high-molecular mass protein complexes using a combination of native gel electrophoresis and absolute protein quantification by MSE. With this experimental setup, we characterized the effect of the tic56-3 mutation in the 1-MDa inner envelope translocase (TIC) on the assembly of the chloroplast proteome. We show that the tic56-3 mutation results in a reduction of the 1-MDa TIC complex to approximately 10% of wildtype levels. Hierarchical clustering confirmed the association of malate dehydrogenase (MDH) with an envelope-associated FtsH/FtsHi complex and suggested the association of a glycine-rich protein with the 1-MDa TIC complex. Depletion of this complex leads to a reduction of chloroplast ATPase to approx. 75% of wildtype levels, while the abundance of the FtsH/FtsHi complex is increased to approx. 140% of wildtype. The accumulation of the major photosynthetic complexes is not affected by the mutation, suggesting that tic56-3 plants can sustain a functional photosynthetic machinery despite a significant reduction of the 1-MDa TIC complex. Together our analysis expands recent efforts to catalogue the native molecular masses of chloroplast proteins and provides information on the consequences of impaired accumulation of the 1-MDa TIC translocase for chloroplast proteome assembly.
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Affiliation(s)
- Peter Schäfer
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Halle (Saale), Germany
| | - Stefan Helm
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Halle (Saale), Germany
| | - Daniel Köhler
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Halle (Saale), Germany
| | - Birgit Agne
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Halle (Saale), Germany
| | - Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Halle (Saale), Germany
- * E-mail:
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7
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Frank J, Happeck R, Meier B, Hoang MTT, Stribny J, Hause G, Ding H, Morsomme P, Baginsky S, Peiter E. Chloroplast-localized BICAT proteins shape stromal calcium signals and are required for efficient photosynthesis. New Phytol 2019; 221:866-880. [PMID: 30169890 DOI: 10.1111/nph.15407] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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] [Received: 02/21/2018] [Accepted: 07/17/2018] [Indexed: 05/18/2023]
Abstract
The photosynthetic machinery of plants must be regulated to maximize the efficiency of light reactions and CO2 fixation. Changes in free Ca2+ in the stroma of chloroplasts have been observed at the transition between light and darkness, and also in response to stress stimuli. Such Ca2+ dynamics have been proposed to regulate photosynthetic capacity. However, the molecular mechanisms of Ca2+ fluxes in the chloroplasts have been unknown. By employing a Ca2+ reporter-based approach, we identified two chloroplast-localized Ca2+ transporters in Arabidopsis thaliana, BICAT1 and BICAT2, that determine the amplitude of the darkness-induced Ca2+ signal in the chloroplast stroma. BICAT2 mediated Ca2+ uptake across the chloroplast envelope, and its knockout mutation strongly dampened the dark-induced [Ca2+ ]stroma signal. Conversely, this Ca2+ transient was increased in knockout mutants of BICAT1, which transports Ca2+ into the thylakoid lumen. Knockout mutation of BICAT2 caused severe defects in chloroplast morphology, pigmentation and photosynthetic light reactions, rendering bicat2 mutants barely viable under autotrophic growth conditions, while bicat1 mutants were less affected. These results show that BICAT transporters play a role in chloroplast Ca2+ homeostasis. They are also involved in the regulation of photosynthesis and plant productivity. Further work will be required to reveal whether the effect on photosynthesis is a direct result of their role as Ca2+ transporters.
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Affiliation(s)
- Julia Frank
- Institute for Biochemistry and Biotechnology, Faculty of Natural Sciences I, Martin Luther University Halle-Wittenberg, D-06120, Halle (Saale), Germany
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, D-06120, Halle (Saale), Germany
| | - Ricardo Happeck
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, D-06120, Halle (Saale), Germany
| | - Bastian Meier
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, D-06120, Halle (Saale), Germany
| | - Minh Thi Thanh Hoang
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, D-06120, Halle (Saale), Germany
| | - Jiri Stribny
- Louvain Institute of Biomolecular Science and Technology (LIBST), Université Catholique de Louvain, B-1348, Louvain-la-Neuve, Belgium
| | - Gerd Hause
- Biocenter, Martin Luther University Halle-Wittenberg, D-06120, Halle (Saale), Germany
| | - Haidong Ding
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, D-06120, Halle (Saale), Germany
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
| | - Pierre Morsomme
- Louvain Institute of Biomolecular Science and Technology (LIBST), Université Catholique de Louvain, B-1348, Louvain-la-Neuve, Belgium
| | - Sacha Baginsky
- Institute for Biochemistry and Biotechnology, Faculty of Natural Sciences I, Martin Luther University Halle-Wittenberg, D-06120, Halle (Saale), Germany
| | - Edgar Peiter
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, D-06120, Halle (Saale), Germany
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8
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Rödiger A, Baginsky S. Tailored Use of Targeted Proteomics in Plant-Specific Applications. Front Plant Sci 2018; 9:1204. [PMID: 30174680 PMCID: PMC6107752 DOI: 10.3389/fpls.2018.01204] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 07/26/2018] [Indexed: 05/03/2023]
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Abstract
Label-free peptide quantification is a promising approach for the large-scale characterization of proteome dynamics at low cost. Here, we describe a method for absolute label-free quantification using an untargeted approach for peptide fragmentation referred to as MSE. We show that spiked external standards provide sufficient accuracy for the quantification of proteins in complex samples resulting in similar protein quantification results as spectral counting. As an advantage, label-free quantification also works for small numbers of samples whereas spectral counting requires large datasets to result in a similar robustness. The sensitivity of protein identification increases significantly when ion mobility separation is included in addition to the standard LC-MS setup in the analysis workflow. Ion mobility decreases sample complexity and serves as an additional separation criterion to align a parent ion with its product ions after MSE fragmentation. As a drawback, quantification of high abundance proteins becomes inaccurate because of detector saturation. We describe here a suitable workflow to achieve good sensitivity for protein quantification and give initial guidance on data interpretation. To achieve good identification and quantification accuracy, the protein amount loaded onto the column should not exceed 400-600 ng. In a dynamic range window of 3-4 orders of magnitude, robust quantification can be obtained with complex samples comprising up to 2000-3000 proteins.
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Affiliation(s)
- Stefan Helm
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Weinbergweg 22, 06120, Halle (Saale), Germany
| | - Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Weinbergweg 22, 06120, Halle (Saale), Germany.
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10
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Hempel F, Stenzel I, Heilmann M, Krishnamoorthy P, Menzel W, Golbik R, Helm S, Dobritzsch D, Baginsky S, Lee J, Hoehenwarter W, Heilmann I. MAPKs Influence Pollen Tube Growth by Controlling the Formation of Phosphatidylinositol 4,5-Bisphosphate in an Apical Plasma Membrane Domain. Plant Cell 2017; 29:3030-3050. [PMID: 29167320 PMCID: PMC5757277 DOI: 10.1105/tpc.17.00543] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/12/2017] [Accepted: 11/18/2017] [Indexed: 05/19/2023]
Abstract
An apical plasma membrane domain enriched in the regulatory phospholipid phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] is critical for polar tip growth of pollen tubes. How the biosynthesis of PtdIns(4,5)P2 by phosphatidylinositol 4-phosphate 5-kinases (PI4P 5-kinases) is controlled by upstream signaling is currently unknown. The pollen-expressed PI4P 5-kinase PIP5K6 is required for clathrin-mediated endocytosis and polar tip growth in pollen tubes. Here, we identify PIP5K6 as a target of the pollen-expressed mitogen-activated protein kinase MPK6 and characterize the regulatory effects. Based on an untargeted mass spectrometry approach, phosphorylation of purified recombinant PIP5K6 by pollen tube extracts could be attributed to MPK6. Recombinant MPK6 phosphorylated residues T590 and T597 in the variable insert of the catalytic domain of PIP5K6, and this modification inhibited PIP5K6 activity in vitro. PIP5K6 interacted with MPK6 in yeast two-hybrid tests, immuno-pull-down assays, and by bimolecular fluorescence complementation at the apical plasma membrane of pollen tubes. In vivo, MPK6 expression resulted in reduced plasma membrane association of a fluorescent PtdIns(4,5)P2 reporter and decreased endocytosis without impairing membrane association of PIP5K6. Effects of PIP5K6 expression on pollen tube growth and cell morphology were attenuated by coexpression of MPK6 in a phosphosite-dependent manner. Our data indicate that MPK6 controls PtdIns(4,5)P2 production and membrane trafficking in pollen tubes, possibly contributing to directional growth.
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Affiliation(s)
- Franziska Hempel
- Department of Cellular Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Irene Stenzel
- Department of Cellular Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Mareike Heilmann
- Department of Cellular Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Praveen Krishnamoorthy
- Department of Cellular Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Wilhelm Menzel
- Department of Cellular Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Ralph Golbik
- Department of Microbial Biotechnology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Stefan Helm
- Department of Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Dirk Dobritzsch
- Department of Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Sacha Baginsky
- Department of Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Justin Lee
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany
| | - Wolfgang Hoehenwarter
- Proteome Analytics, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany
| | - Ingo Heilmann
- Department of Cellular Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
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11
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Schönberg A, Rödiger A, Mehwald W, Galonska J, Christ G, Helm S, Thieme D, Majovsky P, Hoehenwarter W, Baginsky S. Identification of STN7/STN8 kinase targets reveals connections between electron transport, metabolism and gene expression. Plant J 2017; 90:1176-1186. [PMID: 28295753 DOI: 10.1111/tpj.13536] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [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: 12/20/2016] [Revised: 03/03/2017] [Accepted: 03/06/2017] [Indexed: 05/18/2023]
Abstract
The thylakoid-associated kinases STN7 and STN8 are involved in short- and long-term acclimation of photosynthetic electron transport to changing light conditions. Here we report the identification of STN7/STN8 in vivo targets that connect photosynthetic electron transport with metabolism and gene expression. Comparative phosphoproteomics with the stn7 and stn8 single and double mutants identified two proteases, one RNA-binding protein, a ribosomal protein, the large subunit of Rubisco and a ferredoxin-NADP reductase as targets for the thylakoid-associated kinases. Phosphorylation of three of the above proteins can be partially complemented by STN8 in the stn7 single mutant, albeit at lower efficiency, while phosphorylation of the remaining three proteins strictly depends on STN7. The properties of the STN7-dependent phosphorylation site are similar to those of phosphorylated light-harvesting complex proteins entailing glycine or another small hydrophobic amino acid in the -1 position. Our analysis uncovers the STN7/STN8 kinases as mediators between photosynthetic electron transport, its immediate downstream sinks and long-term adaptation processes affecting metabolite accumulation and gene expression.
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Affiliation(s)
- Anna Schönberg
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Weinbergweg 22, 06120, Halle (Saale), Germany
| | - Anja Rödiger
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Weinbergweg 22, 06120, Halle (Saale), Germany
| | - Wiebke Mehwald
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Weinbergweg 22, 06120, Halle (Saale), Germany
| | - Johann Galonska
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Weinbergweg 22, 06120, Halle (Saale), Germany
| | - Gideon Christ
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Weinbergweg 22, 06120, Halle (Saale), Germany
| | - Stefan Helm
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Weinbergweg 22, 06120, Halle (Saale), Germany
| | - Domenika Thieme
- Proteomeanalytik, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Petra Majovsky
- Proteomeanalytik, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | | | - Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Weinbergweg 22, 06120, Halle (Saale), Germany
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12
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Zufferey M, Montandon C, Douet V, Demarsy E, Agne B, Baginsky S, Kessler F. The novel chloroplast outer membrane kinase KOC1 is a required component of the plastid protein import machinery. J Biol Chem 2017; 292:6952-6964. [PMID: 28283569 DOI: 10.1074/jbc.m117.776468] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 01/12/2017] [Revised: 02/28/2017] [Indexed: 11/06/2022] Open
Abstract
The biogenesis and maintenance of cell organelles such as mitochondria and chloroplasts require the import of many proteins from the cytosol, a process that is controlled by phosphorylation. In the case of chloroplasts, the import of hundreds of different proteins depends on translocons at the outer and inner chloroplast membrane (TOC and TIC, respectively) complexes. The essential protein TOC159 functions thereby as an import receptor. It has an N-terminal acidic (A-) domain that extends into the cytosol, controls receptor specificity, and is highly phosphorylated in vivo However, kinases that phosphorylate the TOC159 A-domain to enable protein import have remained elusive. Here, using co-purification with TOC159 from Arabidopsis, we discovered a novel component of the chloroplast import machinery, the regulatory kinase at the outer chloroplast membrane 1 (KOC1). We found that KOC1 is an integral membrane protein facing the cytosol and stably associates with TOC. Moreover, KOC1 phosphorylated the A-domain of TOC159 in vitro, and in mutant koc1 chloroplasts, preprotein import efficiency was diminished. koc1 Arabidopsis seedlings had reduced survival rates after transfer from the dark to the light in which protein import into plastids is required to rapidly complete chloroplast biogenesis. In summary, our data indicate that KOC1 is a functional component of the TOC machinery that phosphorylates import receptors, supports preprotein import, and contributes to efficient chloroplast biogenesis.
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Affiliation(s)
- Mónica Zufferey
- From the Laboratory of Plant Physiology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Cyrille Montandon
- the College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853
| | - Véronique Douet
- From the Laboratory of Plant Physiology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Emilie Demarsy
- the Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland, and
| | - Birgit Agne
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, 06099 Halle (Saale), Germany
| | - Sacha Baginsky
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, 06099 Halle (Saale), Germany
| | - Felix Kessler
- From the Laboratory of Plant Physiology, University of Neuchâtel, 2000 Neuchâtel, Switzerland,
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13
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Agne B, Köhler D, Baginsky S. Protein import-independent functions of Tic56, a component of the 1-MDa translocase at the inner chloroplast envelope membrane. Plant Signal Behav 2017; 12:e1284726. [PMID: 28125316 PMCID: PMC5399903 DOI: 10.1080/15592324.2017.1284726] [Citation(s) in RCA: 12] [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] [Indexed: 05/17/2023]
Abstract
Tic56 is an essential subunit of a 1-MDa protein complex at the inner chloroplast envelope membrane that comprises Tic100, Tic214 and the protein conducting channel protein Tic20-I. The complex was characterized as the "general protein import translocase" because mutants in either of its subunits have a severe growth phenotype and fail to assemble a photosynthetic machinery. In a recent publication we show that the albino phenotype of tic56-1 mutants results at least in part from a defect in ribosome assembly and a deficiency in plastid translation. We furthermore could not detect any impairment of protein import activity with plastids from tic56-3 mutants, despite a lack of full-length Tic56 and a decreased abundance of other 1-MDa complex subunits. These findings suggest that the 1-MDa complex consists of subunits that have functions other than protein import.
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Affiliation(s)
- Birgit Agne
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Weinbergweg, Halle (Saale), Germany
| | - Daniel Köhler
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Weinbergweg, Halle (Saale), Germany
| | - Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Weinbergweg, Halle (Saale), Germany
- CONTACT Sacha Baginsky Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany
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14
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Köhler D, Helm S, Agne B, Baginsky S. Importance of Translocon Subunit Tic56 for rRNA Processing and Chloroplast Ribosome Assembly. Plant Physiol 2016; 172:2429-2444. [PMID: 27733515 PMCID: PMC5129725 DOI: 10.1104/pp.16.01393] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 10/11/2016] [Indexed: 05/20/2023]
Abstract
Toc159-containing complexes at the outer chloroplast envelope membrane form stable supercomplexes with a 1-MD translocon at the inner chloroplast envelope membrane of which Tic56 is one essential subunit. While the single mutants tic56-1 and ppi2 (toc159) have an albino phenotype and are able to grow heterotrophically, we find the double mutant to be embryo lethal. Comprehensive quantitative proteome profiling with both single mutants in combination with GeneChip analyses identified a posttranscriptional defect in the accumulation of plastid ribosomal proteins and diminished expression of plastid encoded proteins. In the tic56-1 mutant, the assembly of functional ribosomes is furthermore hampered by a processing defect of the plastid 23S rRNA. Spectinomycin-treatment of wild-type plants phenocopies the molecular phenotype of plastid proteome accumulation in tic56-1 and to a smaller degree also ppi2 plastids, suggesting that a defect in plastid translation is largely responsible for the phenotype of both import mutants. Import experiments with the tic56-3 mutant revealed no significant defect in the import of small ribosomal protein 16 in the absence of full-length Tic56, suggesting that the defect in ribosome assembly in tic56-1 may be independent of a function of Tic56 in protein import. Our data establish a previously unknown link between plastid protein import, the processing of plastid rRNAs, and the assembly of plastid ribosomes and provide further knowledge on the function of the translocon components and the molecular basis for their albino phenotype.
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Affiliation(s)
- Daniel Köhler
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, 06120 Halle (Saale), Germany
| | - Stefan Helm
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, 06120 Halle (Saale), Germany
| | - Birgit Agne
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, 06120 Halle (Saale), Germany
| | - Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, 06120 Halle (Saale), Germany
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15
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Richter AS, Gartmann H, Fechler M, Rödiger A, Baginsky S, Grimm B. Identification of four plastid-localized protein kinases. FEBS Lett 2016; 590:1749-56. [PMID: 27214872 DOI: 10.1002/1873-3468.12223] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 12/16/2023]
Abstract
In chloroplasts, protein phosphorylation regulates important processes, including metabolism, photosynthesis, gene expression, and signaling. Because the hitherto known plastid protein kinases represent only a fraction of existing kinases, we aimed at the identification of novel plastid-localized protein kinases that potentially phosphorylate enzymes of the tetrapyrrole biosynthesis (TBS) pathway. We screened publicly available databases for proteins annotated as putative protein kinase family proteins with predicted chloroplast localization. Additionally, we analyzed chloroplast fractions which were separated by sucrose density gradient centrifugation by mass spectrometry. We identified four new candidates for protein kinases, which were confirmed to be plastid localized by expression of GFP-fusion proteins in tobacco leaves. A phosphorylation assay with the purified kinases confirmed the protein kinase activity for two of them.
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Affiliation(s)
- Andreas S Richter
- Humboldt Universität zu Berlin, Institute of Biology/Plant Physiology, Berlin, Germany
| | - Hans Gartmann
- Humboldt Universität zu Berlin, Institute of Biology/Plant Physiology, Berlin, Germany
| | - Mona Fechler
- Humboldt Universität zu Berlin, Institute of Biology/Plant Physiology, Berlin, Germany
| | - Anja Rödiger
- Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Sacha Baginsky
- Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Bernhard Grimm
- Humboldt Universität zu Berlin, Institute of Biology/Plant Physiology, Berlin, Germany
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16
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Abstract
The development of new software tools, improved mass spectrometry equipment, a suite of optimized scan types, and better-quality phosphopeptide affinity capture have paved the way for an explosion of mass spectrometry data on phosphopeptides. Because phosphoproteomics achieves good sensitivity, most studies use complete cell extracts for phosphopeptide enrichment and identification without prior enrichment of proteins or subcellular compartments. As a consequence, the phosphoproteome of cell organelles often comes as a by-product from large-scale studies and is commonly assembled from these in meta-analyses. This review aims at providing some guidance on the limitations of meta-analyses that combine data from analyses with different scopes, reports on the current status of knowledge on chloroplast phosphorylation targets, provides initial insights into phosphorylation site conservation in different plant species, and highlights emerging information on the integration of gene expression with metabolism and photosynthesis by means of protein phosphorylation.
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Affiliation(s)
- Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany
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17
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Lu Q, Helm S, Rödiger A, Baginsky S. On the Extent of Tyrosine Phosphorylation in Chloroplasts. Plant Physiol 2015; 169:996-1000. [PMID: 26243617 PMCID: PMC4587464 DOI: 10.1104/pp.15.00921] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 07/29/2015] [Indexed: 05/20/2023]
Abstract
Reanalysis of published mass spectrometry data on Tyr-phosphorylated chloroplast proteins indicates that the majority of peptide spectrum matches reporting Tyr phosphorylation are ambiguous.
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Affiliation(s)
- Qintao Lu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (Q.L.); andInstitute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany (S.H., A.R., S.B.)
| | - Stefan Helm
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (Q.L.); andInstitute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany (S.H., A.R., S.B.)
| | - Anja Rödiger
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (Q.L.); andInstitute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany (S.H., A.R., S.B.)
| | - Sacha Baginsky
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (Q.L.); andInstitute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany (S.H., A.R., S.B.)
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18
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Schönberg A, Baginsky S. The Peptide Microarray ChloroPhos1.0: A Screening Tool for the Identification of Arabidopsis thaliana Chloroplast Protein Kinase Substrates. Methods Mol Biol 2015; 1306:147-57. [PMID: 25930700 DOI: 10.1007/978-1-4939-2648-0_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
We designed the peptide microarray ChloroPhos1.0 to screen for substrates of chloroplast protein kinases. The peptides represented on the microarray were selected from phosphoproteomics data, and the identified chloroplast phosphopeptides were spotted as 15-mers on a glass slide with the phosphorylation site centered. Altogether, 905 distinct peptides from chloroplast proteins are present on the array. Here we describe how the array can be used to identify the target protein spectrum of chloroplast kinases. We present the method and discuss limitations and challenges associated with the determination of phosphorylation activity on peptide substrates in vitro.
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Affiliation(s)
- Anna Schönberg
- Department of Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Weinbergweg 22, Halle (Saale), 06120, Germany
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19
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Köhler D, Montandon C, Hause G, Majovsky P, Kessler F, Baginsky S, Agne B. Characterization of chloroplast protein import without Tic56, a component of the 1-megadalton translocon at the inner envelope membrane of chloroplasts. Plant Physiol 2015; 167:972-90. [PMID: 25588737 PMCID: PMC4348784 DOI: 10.1104/pp.114.255562] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 01/14/2015] [Indexed: 05/17/2023]
Abstract
We report on the characterization of Tic56, a unique component of the recently identified 1-MD translocon at the inner envelope membrane of chloroplasts (TIC) in Arabidopsis (Arabidopsis thaliana) comprising Tic20, Tic100, and Tic214. We isolated Tic56 by copurification with Tandem Affinity Purification-tagged Toc159 in the absence of precursor protein, indicating spontaneous and translocation-independent formation of the translocon at the outer envelope membrane of chloroplasts (TOC) and TIC supercomplexes. Tic56 mutant plants have an albino phenotype and are unable to grow without an external carbon source. Using specific enrichment of protein amino termini, we analyzed the tic56-1 and plastid protein import2 (toc159) mutants to assess the in vivo import capacity of plastids in mutants of an outer and inner envelope component of the anticipated TOC-TIC supercomplex. Inboth mutants, we observed processing of several import substrates belonging to various pathways. Our results suggest that despite the severe developmental defects, protein import into Tic56-deficient plastids is functional to a considerable degree, indicating the existence of alternative translocases at the inner envelope membrane.
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20
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Betterle N, Ballottari M, Baginsky S, Bassi R. High light-dependent phosphorylation of photosystem II inner antenna CP29 in monocots is STN7 independent and enhances nonphotochemical quenching. Plant Physiol 2015; 167:457-71. [PMID: 25501945 PMCID: PMC4326754 DOI: 10.1104/pp.114.252379] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Phosphorylation of the photosystem II antenna protein CP29 has been reported to be induced by excess light and further enhanced by low temperature, increasing resistance to these stressing factors. Moreover, high light-induced CP29 phosphorylation was specifically found in monocots, both C3 and C4, which include the large majority of food crops. Recently, knockout collections have become available in rice (Oryza sativa), a model organism for monocots. In this work, we have used reverse genetics coupled to biochemical and physiological analysis to elucidate the molecular basis of high light-induced phosphorylation of CP29 and the mechanisms by which it exerts a photoprotective effect. We found that kinases and phosphatases involved in CP29 phosphorylation are distinct from those reported to act in State 1-State 2 transitions. In addition, we elucidated the photoprotective role of CP29 phosphorylation in reducing singlet oxygen production and enhancing excess energy dissipation. We thus established, in monocots, a mechanistic connection between phosphorylation of CP29 and nonphotochemical quenching, two processes so far considered independent from one another.
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Affiliation(s)
- Nico Betterle
- Dipartimento di Biotecnologie, Università di Verona, 37134 Verona, Italy (N.B., M.B., R.B.); andInstitute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany (S.B.)
| | - Matteo Ballottari
- Dipartimento di Biotecnologie, Università di Verona, 37134 Verona, Italy (N.B., M.B., R.B.); andInstitute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany (S.B.)
| | - Sacha Baginsky
- Dipartimento di Biotecnologie, Università di Verona, 37134 Verona, Italy (N.B., M.B., R.B.); andInstitute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany (S.B.)
| | - Roberto Bassi
- Dipartimento di Biotecnologie, Università di Verona, 37134 Verona, Italy (N.B., M.B., R.B.); andInstitute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany (S.B.)
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21
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Köhler D, Dobritzsch D, Hoehenwarter W, Helm S, Steiner JM, Baginsky S. Identification of protein N-termini in Cyanophora paradoxa cyanelles: transit peptide composition and sequence determinants for precursor maturation. Front Plant Sci 2015; 6:559. [PMID: 26257763 PMCID: PMC4510345 DOI: 10.3389/fpls.2015.00559] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 07/07/2015] [Indexed: 05/06/2023]
Abstract
Glaucophyta, rhodophyta, and chloroplastida represent the three main evolutionary lineages that diverged from a common ancestor after primary endosymbiosis. Comparative analyses between members of these three lineages are a rich source of information on ancestral plastid features. We analyzed the composition and the cleavage site of cyanelle transit peptides from the glaucophyte Cyanophora paradoxa by terminal amine labeling of substrates (TAILS), and compared their characteristics to those of representatives of the chloroplastida. Our data show that transit peptide architecture is similar between members of these two lineages. This entails a comparable modular structure, an overrepresentation of serine or alanine and similarities in the amino acid composition around the processing peptidase cleavage site. The most distinctive difference is the overrepresentation of phenylalanine in the N-terminal 1-10 amino acids of cyanelle transit peptides. A quantitative proteome analysis with periplasm-free cyanelles identified 42 out of 262 proteins without the N-terminal phenylalanine, suggesting that the requirement for phenylalanine in the N-terminal region is not absolute. Proteins in this set are on average of low abundance, suggesting that either alternative import pathways are operating specifically for low abundance proteins or that the gene model annotation is incorrect for proteins with fewer EST sequences. We discuss these two possibilities and provide examples for both interpretations.
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Affiliation(s)
- Daniel Köhler
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, BiozentrumHalle (Saale), Germany
| | - Dirk Dobritzsch
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, BiozentrumHalle (Saale), Germany
| | | | - Stefan Helm
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, BiozentrumHalle (Saale), Germany
| | - Jürgen M. Steiner
- Plant Physiology, Institute of Biology, Martin-Luther-University Halle-WittenbergHalle (Saale), Germany
| | - Sacha Baginsky
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, BiozentrumHalle (Saale), Germany
- *Correspondence: Sacha Baginsky, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany
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Lu Q, Ding S, Reiland S, Rödiger A, Roschitzki B, Xue P, Gruissem W, Lu C, Baginsky S. Identification and characterization of chloroplast casein kinase II from Oryza sativa (rice). J Exp Bot 2015; 66:175-87. [PMID: 25316064 DOI: 10.1093/jxb/eru405] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [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: 05/08/2023]
Abstract
Plastid casein kinase II is an important regulator of transcription, posttranscriptional processes, and, most likely, different metabolic functions in dicotyledonous species. Here we report the identification and characterization of pCKII from the monocotyledonous species Oryza sativa. OspCKII activity was enriched from isolated rice chloroplasts using heparin-Sepharose chromatography, in which it co-elutes with the transcriptionally active chromosome (TAC) and several ribosomal proteins. Inclusion mass scanning of the kinase-active fraction identified the gene model for OspCKII. Transient expression of GFP fused to the 184 N-terminal amino acids of the OspCKII sequence in rice confirmed the chloroplastic localization of the kinase. OspCKII activity shows the characteristic features of casein kinase II, such as the utilization of GTP as phosphate donor, inhibition by low concentrations of heparin and poly-lysine, and utilization of the canonical pCKII motif E-S-E-G-E in the model substrate RNP29. Phosphoproteome analysis of a protein extract from rice leaves combined with a meta-analysis with published phosphoproteomics data revealed differences in the target protein spectrum between rice and Arabidopsis. Consistently, several pCKII phosphorylation sites in dicotyledonous plants are not conserved in monocots and algae, suggesting that details of pCKII regulation in plastids have changed during evolution.
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Affiliation(s)
- Qingtao Lu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shunhua Ding
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Sonja Reiland
- Department of Biology, Plant Biotechnology, ETH Zurich, 8092 Zurich, Switzerland
| | - Anja Rödiger
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Bernd Roschitzki
- Functional Genomics Center Zurich, University of Zurich \ ETH Zurich, 8057 Zurich, Switzerland
| | - Peng Xue
- Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wilhelm Gruissem
- Department of Biology, Plant Biotechnology, ETH Zurich, 8092 Zurich, Switzerland Functional Genomics Center Zurich, University of Zurich \ ETH Zurich, 8057 Zurich, Switzerland
| | - Congming Lu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Sacha Baginsky
- Department of Biology, Plant Biotechnology, ETH Zurich, 8092 Zurich, Switzerland
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23
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Schönberg A, Bergner E, Helm S, Agne B, Dünschede B, Schünemann D, Schutkowski M, Baginsky S. The peptide microarray "ChloroPhos1.0" identifies new phosphorylation targets of plastid casein kinase II (pCKII) in Arabidopsis thaliana. PLoS One 2014; 9:e108344. [PMID: 25295873 PMCID: PMC4189921 DOI: 10.1371/journal.pone.0108344] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 08/19/2014] [Indexed: 11/18/2022] Open
Abstract
We report the development of a peptide microarray based on previously determined phosphorylation sites in chloroplast proteins. Altogether, 905 peptides were spotted as 15mers in nine replicates onto glass slides. We used the microarray for in vitro phosphorylation experiments and specifically assessed the peptide substrate spectrum of chloroplast casein kinase II (pCKII). To this end, native pCKII from Arabidopsis thaliana and Sinapis alba chloroplasts was enriched by Heparin-Sepharose chromatography and its activity on the microarray was compared to the activity of a recombinant Arabidopsis pCKII. All three kinase preparations phosphorylated a similar set of peptides that were clearly distinct from those phosphorylated by bovine heart protein kinase A (PKA) in control experiments. The majority of the pCKII phosphorylation targets are involved in plastid gene expression, supporting the earlier denomination of pCKII as plastid transcription kinase (PTK). In addition we identified Alb3 as pCKII substrate that is essential for the integration of light-harvesting complex subunits (LHC) into the thylakoid membrane. Plastid CKII phosphorylation activity was characterized in greater detail in vitro with recombinant wildtype Alb3 and phosphorylation site mutants as substrates, establishing S424 as the pCKII phosphorylation site. Our data show that the peptide microarray ChloroPhos1.0 is a suitable tool for the identification of new kinase downstream targets in vitro that can be validated subsequently by in vivo experiments.
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Affiliation(s)
- Anna Schönberg
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Elena Bergner
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Stefan Helm
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Birgit Agne
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Beatrix Dünschede
- Molecular Biology of Plant Organelles, Ruhr-University Bochum, Bochum, Germany
| | - Danja Schünemann
- Molecular Biology of Plant Organelles, Ruhr-University Bochum, Bochum, Germany
| | - Mike Schutkowski
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
- Steinbeis-Forschungszentrum, Peptide Microarrays, Halle (Saale), Germany
| | - Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
- * E-mail:
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25
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Joaquín-Ramos A, Huerta-Ocampo JÁ, Barrera-Pacheco A, De León-Rodríguez A, Baginsky S, Barba de la Rosa AP. Comparative proteomic analysis of amaranth mesophyll and bundle sheath chloroplasts and their adaptation to salt stress. J Plant Physiol 2014; 171:1423-1435. [PMID: 25046763 DOI: 10.1016/j.jplph.2014.06.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [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: 03/10/2014] [Revised: 06/17/2014] [Accepted: 06/19/2014] [Indexed: 06/03/2023]
Abstract
The effect of salt stress was analyzed in chloroplasts of Amaranthus cruentus var. Amaranteca, a plant NAD-malic enzyme (NAD-ME) type. Morphology of chloroplasts from bundle sheath (BSC) and mesophyll (MC) was observed by transmission electron microscopy (TEM). BSC and MC from control plants showed similar morphology, however under stress, changes in BSC were observed. The presence of ribulose bisphosphate carboxylase/oxygenase (RuBisCO) was confirmed by immunohistochemical staining in both types of chloroplasts. Proteomic profiles of thylakoid protein complexes from BSC and MC, and their changes induced by salt stress were analyzed by blue-native polyacrylamide gel electrophoresis followed by SDS-PAGE (2-D BN/SDS-PAGE). Differentially accumulated protein spots were analyzed by LC-MS/MS. Although A. cruentus photosynthetic tissue showed the Kranz anatomy, the thylakoid proteins showed some differences at photosystem structure level. Our results suggest that A. cruentus var. Amaranteca could be better classified as a C3-C4 photosynthetic plant.
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Affiliation(s)
- Ahuitzolt Joaquín-Ramos
- IPICyT, Instituto Potosino de Investigación Científica y Tecnológica A.C., Camino a la Presa San José No. 2055, Lomas 4a Sección, San Luis Potosí, S.L.P. 78216, Mexico
| | - José Á Huerta-Ocampo
- IPICyT, Instituto Potosino de Investigación Científica y Tecnológica A.C., Camino a la Presa San José No. 2055, Lomas 4a Sección, San Luis Potosí, S.L.P. 78216, Mexico
| | - Alberto Barrera-Pacheco
- IPICyT, Instituto Potosino de Investigación Científica y Tecnológica A.C., Camino a la Presa San José No. 2055, Lomas 4a Sección, San Luis Potosí, S.L.P. 78216, Mexico
| | - Antonio De León-Rodríguez
- IPICyT, Instituto Potosino de Investigación Científica y Tecnológica A.C., Camino a la Presa San José No. 2055, Lomas 4a Sección, San Luis Potosí, S.L.P. 78216, Mexico
| | - Sacha Baginsky
- Martin-Luther-Universität Halle-Wittenberg, Institut für Biochemie, Abteilung Pflanzenbiochemie, Weinbergweg 22 (Biozentrum), 06120 Halle (Saale), Germany
| | - Ana P Barba de la Rosa
- IPICyT, Instituto Potosino de Investigación Científica y Tecnológica A.C., Camino a la Presa San José No. 2055, Lomas 4a Sección, San Luis Potosí, S.L.P. 78216, Mexico.
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Grimmer J, Rödiger A, Hoehenwarter W, Helm S, Baginsky S. The RNA-binding protein RNP29 is an unusual Toc159 transport substrate. Front Plant Sci 2014; 5:258. [PMID: 24982663 PMCID: PMC4059279 DOI: 10.3389/fpls.2014.00258] [Citation(s) in RCA: 5] [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: 04/16/2014] [Accepted: 05/20/2014] [Indexed: 05/08/2023]
Abstract
The precursors of RNP29 and Ferredoxin (Fd2) were previously identified in the cytosol of ppi2 plant cells with their N-terminal amino acid acetylated. Here, we explore whether precursor accumulation in ppi2 is characteristic for Toc159 client proteins, by characterizing the import properties of the RNP29 precursor in comparison to Fd2 and other Toc159-dependent or independent substrates. We find specific accumulation of the RNP29 precursor in ppi2 but not in wild type or ppi1 protoplasts. With the exception of Lhcb4, precursor accumulation is also detected with all other tested constructs in ppi2. However, RNP29 is clearly different from the other proteins because only precursor but almost no mature protein is detectable in protoplast extracts. Co-transformation of RNP29 with Toc159 complements its plastid import, supporting the hypothesis that RNP29 is a Toc159-dependent substrate. Exchange of the second amino acid in the RNP29 transit peptide to Glu or Asn prevents methionine excision but not N-terminal acetylation, suggesting that different N-acetyltransferases may act on chloroplast precursor proteins in vivo. All different RNP29 constructs are efficiently imported into wild type but not into ppi2 plastids, arguing for a minor impact of the N-terminal amino acid on the import process.
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Affiliation(s)
- Julia Grimmer
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-WittenbergHalle (Saale), Germany
| | - Anja Rödiger
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-WittenbergHalle (Saale), Germany
| | | | - Stefan Helm
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-WittenbergHalle (Saale), Germany
| | - Sacha Baginsky
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-WittenbergHalle (Saale), Germany
- *Correspondence: Sacha Baginsky, Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany e-mail:
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Helm S, Dobritzsch D, Rödiger A, Agne B, Baginsky S. Protein identification and quantification by data-independent acquisition and multi-parallel collision-induced dissociation mass spectrometry (MS(E)) in the chloroplast stroma proteome. J Proteomics 2013; 98:79-89. [PMID: 24361574 DOI: 10.1016/j.jprot.2013.12.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [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: 09/06/2013] [Revised: 10/30/2013] [Accepted: 12/02/2013] [Indexed: 11/18/2022]
Abstract
UNLABELLED We report here a systematic evaluation of a multiplex mass spectrometry method coupled with ion mobility separation (HD-MS(E)) for the identification and quantification of proteins in the chloroplast stroma. We show that this method allows the robust quantification of reference proteins in mixtures, and it detects concentration differences with high sensitivity when three replicas are performed. Applied to the analysis of the chloroplast stroma proteome, HD-MS(E) identified and quantified many chloroplast proteins that were not previously identified in large-scale proteome analyses, suggesting HD-MS(E) as a suitable complementary tool for discovery proteomics. We find that HD-MS(E) tends to underestimate protein abundances at concentrations above 25fmol, which is likely due to ion transmission loss and detector saturation. This limitation can be circumvented by omitting the ion mobility separation step in the HD-MS(E) workflow. The robustness of protein quantification is influenced by the selection of peptides and their intensity distribution, therefore critical scrutiny of quantification results is required. Based on the HD-MS(E) quantification of chloroplast stroma proteins we performed a meta-analysis and compared published quantitative data with our results, using a parts per million normalization scheme. Important pathways in the chloroplast stroma show quantitative stability against different experimental conditions and quantification strategies. BIOLOGICAL SIGNIFICANCE Our analysis establishes MS(E)-based Hi3 quantification as a tool for the absolute quantification of proteins in the chloroplast stroma. The meta-analysis performed with a parts per million normalization scheme shows that quantitative proteomics data acquired in different labs and with different quantification strategies yield comparable results for some metabolic pathways, while others show a higher variability. Our data therefore indicate that such meta-analyses allow distinguishing robust from fine-controlled metabolic pathways.
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Affiliation(s)
- Stefan Helm
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany
| | - Dirk Dobritzsch
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany
| | - Anja Rödiger
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany
| | - Birgit Agne
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany
| | - Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany.
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Motohashi R, Rödiger A, Agne B, Baerenfaller K, Baginsky S. Common and specific protein accumulation patterns in different albino/pale-green mutants reveals regulon organization at the proteome level. Plant Physiol 2012; 160:2189-201. [PMID: 23027667 PMCID: PMC3510140 DOI: 10.1104/pp.112.204032] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Research interest in proteomics is increasingly shifting toward the reverse genetic characterization of gene function at the proteome level. In plants, several distinct gene defects perturb photosynthetic capacity, resulting in the loss of chlorophyll and an albino or pale-green phenotype. Because photosynthesis is interconnected with the entire plant metabolism and its regulation, all albino plants share common characteristics that are determined by the switch from autotrophic to heterotrophic growth. Reverse genetic characterizations of such plants often cannot distinguish between specific consequences of a gene defect from generic effects in response to perturbations in photosynthetic capacity. Here, we set out to define common and specific features of protein accumulation in three different albino/pale-green plant lines. Using quantitative proteomics, we report a common molecular phenotype that connects the loss of photosynthetic capacity with other chloroplast and cellular functions, such as protein folding and stability, plastid protein import, and the expression of stress-related genes. Surprisingly, we do not find significant differences in the expression of key transcriptional regulators, suggesting that substantial regulation occurs at the posttranscriptional level. We examine the influence of different normalization schemes on the quantitative proteomics data and report all identified proteins along with their fold changes and P values in albino plants in comparison with the wild type. Our analysis provides initial guidance for the distinction between general and specific adaptations of the proteome in photosynthesis-impaired plants.
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Schönberg A, Baginsky S. Signal integration by chloroplast phosphorylation networks: an update. Front Plant Sci 2012; 3:256. [PMID: 23181067 PMCID: PMC3501822 DOI: 10.3389/fpls.2012.00256] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 11/01/2012] [Indexed: 05/20/2023]
Abstract
Forty years after the initial discovery of light-dependent protein phosphorylation at the thylakoid membrane system, we are now beginning to understand the roles of chloroplast phosphorylation networks in their function to decode and mediate information on the metabolic status of the organelle to long-term adaptations in plastid and nuclear gene expression. With the help of genetics and functional genomics tools, chloroplast kinases and several hundred phosphoproteins were identified that now await detailed functional characterization. The regulation and the target protein spectrum of some kinases are understood, but this information is fragmentary with respect to kinase and target protein crosstalk in a changing environment. In this review, we will highlight the most recent advances in the field and discuss approaches that might lead to a comprehensive understanding of plastid signal integration by protein phosphorylation.
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Affiliation(s)
| | - Sacha Baginsky
- *Correspondence: Sacha Baginsky, Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany. e-mail:
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Bischof S, Baerenfaller K, Wildhaber T, Troesch R, Vidi PA, Roschitzki B, Hirsch-Hoffmann M, Hennig L, Kessler F, Gruissem W, Baginsky S. Plastid proteome assembly without Toc159: photosynthetic protein import and accumulation of N-acetylated plastid precursor proteins. Plant Cell 2011; 23:3911-28. [PMID: 22128122 PMCID: PMC3246318 DOI: 10.1105/tpc.111.092882] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 10/19/2011] [Accepted: 11/14/2011] [Indexed: 05/20/2023]
Abstract
Import of nuclear-encoded precursor proteins from the cytosol is an essential step in chloroplast biogenesis that is mediated by protein translocon complexes at the inner and outer envelope membrane (TOC). Toc159 is thought to be the main receptor for photosynthetic proteins, but lacking a large-scale systems approach, this hypothesis has only been tested for a handful of photosynthetic and nonphotosynthetic proteins. To assess Toc159 precursor specificity, we quantitatively analyzed the accumulation of plastid proteins in two mutant lines deficient in this receptor. Parallel genome-wide transcript profiling allowed us to discern the consequences of impaired protein import from systemic transcriptional responses that contribute to the loss of photosynthetic capacity. On this basis, we defined putative Toc159-independent and Toc159-dependent precursor proteins. Many photosynthetic proteins accumulate in Toc159-deficient plastids, and, surprisingly, several distinct metabolic pathways are negatively affected by Toc159 depletion. Lack of Toc159 furthermore affects several proteins that accumulate as unprocessed N-acetylated precursor proteins outside of plastids. Together, our data show an unexpected client protein promiscuity of Toc159 that requires a far more differentiated view of Toc159 receptor function and regulation of plastid protein import, in which cytosolic Met removal followed by N-terminal acetylation of precursors emerges as an additional regulatory step.
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Affiliation(s)
- Sylvain Bischof
- Department of Biology, Eidgenössische Technische Hochschule Zurich, 8092 Zurich, Switzerland
| | - Katja Baerenfaller
- Department of Biology, Eidgenössische Technische Hochschule Zurich, 8092 Zurich, Switzerland
| | - Thomas Wildhaber
- Department of Biology, Eidgenössische Technische Hochschule Zurich, 8092 Zurich, Switzerland
| | - Raphael Troesch
- Department of Biology, Eidgenössische Technische Hochschule Zurich, 8092 Zurich, Switzerland
| | | | | | | | - Lars Hennig
- Department of Biology, Eidgenössische Technische Hochschule Zurich, 8092 Zurich, Switzerland
| | - Felix Kessler
- Laboratoire de Physiologie Végétale, 2007 Neuchâtel, Switzerland
| | - Wilhelm Gruissem
- Department of Biology, Eidgenössische Technische Hochschule Zurich, 8092 Zurich, Switzerland
- Functional Genomics Center Zurich, 8057 Zurich, Switzerland
| | - Sacha Baginsky
- Department of Biology, Eidgenössische Technische Hochschule Zurich, 8092 Zurich, Switzerland
- Address correspondence to
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Gfeller A, Baerenfaller K, Loscos J, Chételat A, Baginsky S, Farmer EE. Jasmonate controls polypeptide patterning in undamaged tissue in wounded Arabidopsis leaves. Plant Physiol 2011; 156:1797-807. [PMID: 21693672 PMCID: PMC3149931 DOI: 10.1104/pp.111.181008] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 06/20/2011] [Indexed: 05/20/2023]
Abstract
Wounding initiates a strong and largely jasmonate-dependent remodelling of the transcriptome in the leaf blades of Arabidopsis (Arabidopsis thaliana). How much control do jasmonates exert on wound-induced protein repatterning in leaves? Replicated shotgun proteomic analyses of 2.5-mm-wide leaf strips adjacent to wounds revealed 106 differentially regulated proteins. Many of these gene products have not emerged as being wound regulated in transcriptomic studies. From experiments using the jasmonic acid (JA)-deficient allene oxide synthase mutant we estimated that approximately 95% of wound-stimulated changes in protein levels were deregulated in the absence of JA. The levels of two tonoplast proteins already implicated in defense response regulation, TWO-PORE CHANNEL1 and the calcium-V-ATPase ACA4 increased on wounding, but their transcripts were not wound inducible. The data suggest new roles for jasmonate in controlling the levels of calcium-regulated pumps and transporters, proteins involved in targeted proteolysis, a putative bacterial virulence factor target, a light-dependent catalyst, and a key redox-controlled enzyme in glutathione synthesis. Extending the latter observation we found that wounding increased the proportion of oxidized glutathione in leaves, but only in plants able to synthesize JA. The oxidizing conditions generated through JA signaling near wounds help to define the cellular environment in which proteome remodelling occurs.
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van Wijk KJ, Baginsky S. Plastid proteomics in higher plants: current state and future goals. Plant Physiol 2011; 155:1578-88. [PMID: 21350036 PMCID: PMC3091083 DOI: 10.1104/pp.111.172932] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 02/21/2011] [Indexed: 05/18/2023]
Affiliation(s)
- Klaas J van Wijk
- Department of Plant Biology, Cornell University, Ithaca, New York 14853, USA.
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Reiland S, Grossmann J, Baerenfaller K, Gehrig P, Nunes-Nesi A, Fernie AR, Gruissem W, Baginsky S. Integrated proteome and metabolite analysis of the de-etiolation process in plastids from rice (Oryza sativa L.). Proteomics 2011; 11:1751-63. [PMID: 21433289 DOI: 10.1002/pmic.201000703] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 12/14/2010] [Accepted: 01/11/2011] [Indexed: 12/16/2022]
Abstract
We have analyzed the dynamics of the rice etioplast membrane proteome during the early phase of de-etiolation using iTRAQ-based relative protein quantification. Several hundred plastid proteins were identified from enriched membranes, including 36 putative transporters. Hierarchical clustering revealed the coordinated light induction of thylakoid membrane proteins with proteins involved in translation and fatty acid metabolism. No other functional category of identified proteins showed a similarly consistent light induction, and no consistent changes were observed for the identified transporters. This suggests that the etioplast metabolism is already primed to accommodate the metabolic changes that occur during the onset of photosynthesis. This hypothesis was further tested in metabolite profiling experiments. Here, the changes upon illumination are mostly restricted to a decrease in the concentration of some amino acids and an increase in the concentrations of aspartic acid, malic acid, fumaric acid, and succinic acid. These changes are consistent with a rapid activation of photosynthesis and subsequent rapid production of storage carbohydrates and proteins. The information at the proteome level and the parallel measurements of metabolite accumulation both support the view that only minor metabolic network reconstruction and modification of enzyme levels occurs during the first 4 h of etioplast to chloroplast differentiation.
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Affiliation(s)
- Sonja Reiland
- Department of Biology, Plant Biotechnology, ETH Zurich, Zurich, Switzerland
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Infanger S, Bischof S, Hiltbrunner A, Agne B, Baginsky S, Kessler F. The chloroplast import receptor Toc90 partially restores the accumulation of Toc159 client proteins in the Arabidopsis thaliana ppi2 mutant. Mol Plant 2011; 4:252-63. [PMID: 21220583 DOI: 10.1093/mp/ssq071] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Successful import of hundreds of nucleus-encoded proteins is essential for chloroplast biogenesis. The import of cytosolic precursor proteins relies on the Toc- (translocon at the outer chloroplast membrane) and Tic- (translocon at the inner chloroplast membrane) complexes. In Arabidopsis thaliana, precursor recognition is mainly mediated by outer membrane receptors belonging to two gene families: Toc34/33 and Toc159/132/120/90. The role in import and precursor selectivity of these receptors has been intensively studied, but the function of Toc90 still remains unclear. Here, we report the ability of Toc90 to support the import of Toc159 client proteins. We show that the overexpression of Toc90 partially complements the albino knockout of Toc159 and restores photoautotrophic growth. Several lines of evidence including proteome profiling demonstrate the import and accumulation of proteins essential for chloroplast biogenesis and functionality.
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Affiliation(s)
- Sibylle Infanger
- Laboratoire de physiologie végétale, Université de Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
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Baerenfaller K, Hirsch-Hoffmann M, Svozil J, Hull R, Russenberger D, Bischof S, Lu Q, Gruissem W, Baginsky S. pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana. Integr Biol (Camb) 2011; 3:225-37. [PMID: 21264403 DOI: 10.1039/c0ib00078g] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
pep2pro is a comprehensive proteome analysis database specifically suitable for flexible proteome data analysis. The pep2pro database schema offers solutions to the various challenges of developing a proteome data analysis database and because data integrated in pep2pro are in relational format, it enables flexible and detailed data analysis. The information provided here will facilitate building proteome data analysis databases for other organisms or applications. The capacity of the pep2pro database for the integration and analysis of large proteome datasets was demonstrated by creating the pep2pro dataset, which is an organ-specific characterisation of the Arabidopsis thaliana proteome containing 14 522 identified proteins based on 2.6 million peptide spectrum assignments. This dataset provides evidence of protein expression and reveals organ-specific processes. The high coverage and density of the dataset are essential for protein quantification by normalised spectral counting and allowed us to extract information that is usually not accessible in low-coverage datasets. With this quantitative protein information we analysed organ- and organelle-specific sub-proteomes. In addition we matched spectra to regions in the genome that were not predicted to have protein coding capacity and provide PCR validation for selected revised gene models. Furthermore, we analysed the peptide features that distinguish detected from non-detected peptides and found substantial disagreement between predicted and detected proteotypic peptides, suggesting that large-scale proteomics data are essential for efficient selection of proteotypic peptides in targeted proteomics surveys. The pep2pro dataset is available as a resource for plant systems biology at www.pep2pro.ethz.ch.
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Affiliation(s)
- Katja Baerenfaller
- Department of Biology, ETH Zurich, Universitaetstrasse 2, 8092 Zurich, Switzerland.
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Joshi HJ, Hirsch-Hoffmann M, Baerenfaller K, Gruissem W, Baginsky S, Schmidt R, Schulze WX, Sun Q, van Wijk KJ, Egelhofer V, Wienkoop S, Weckwerth W, Bruley C, Rolland N, Toyoda T, Nakagami H, Jones AM, Briggs SP, Castleden I, Tanz SK, Millar AH, Heazlewood JL. MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data. Plant Physiol 2011; 155:259-70. [PMID: 21075962 PMCID: PMC3075751 DOI: 10.1104/pp.110.168195] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 11/10/2010] [Indexed: 05/18/2023]
Abstract
Proteomics has become a critical tool in the functional understanding of plant processes at the molecular level. Proteomics-based studies have also contributed to the ever-expanding array of data in modern biology, with many generating Web portals and online resources that contain incrementally expanding and updated information. Many of these resources reflect specialist research areas with significant and novel information that is not currently captured by centralized repositories. The Arabidopsis (Arabidopsis thaliana) community is well served by a number of online proteomics resources that hold an abundance of functional information. These sites can be difficult to locate among a multitude of online resources. Furthermore, they can be difficult to navigate in order to identify specific features of interest without significant technical knowledge. Recently, members of the Arabidopsis proteomics community involved in developing many of these resources decided to develop a summary aggregation portal that is capable of retrieving proteomics data from a series of online resources on the fly. The Web portal is known as the MASCP Gator and can be accessed at the following address: http://gator.masc-proteomics.org/. Significantly, proteomics data displayed at this site retrieve information from the data repositories upon each request. This means that information is always up to date and displays the latest data sets. The site also provides hyperlinks back to the source information hosted at each of the curated databases to facilitate more in-depth analysis of the primary data.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Joshua L. Heazlewood
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (H.J.J., J.L.H.); Department of Biology, Eidgenössisch Technische Hochschule Zurich, CH–8092 Zurich, Switzerland (M.H.-H., K.B., W.G.); Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany (S.B.); Max-Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (R.S., W.X.S.); Department of Plant Biology, Cornell University, Ithaca, New York 14853 (Q.S., K.J.v.W.); Molecular Systems Biology, University of Vienna, 1090 Vienna, Austria (V.E., S.W., W.W.); Institut National de la Santé et de la Recherche Médicale, Laboratoire d’Etude de la Dynamique des Protéomes, U880, F–38000 Grenoble, France (C.B.); Commissariat à l’Énergie Atomique et aux Énergies Alternatives, Direction des Sciences du Vivant, Institut de Recherches en Technologies et Sciences pour le Vivant, F–38000 Grenoble, France (C.B., N.R.); Université Joseph Fourier, F–38000 Grenoble, France (C.B., N.R.); CNRS, Laboratoire de Physiologie Cellulaire Végétale, UMR5168, F–38000 Grenoble, France (N.R.); INRA, UMR1200, F–38000 Grenoble, France (N.R.); RIKEN Plant Science Center and RIKEN Bioinformatics and Systems Engineering Division, Tsurumi-ku, Yokohama 230–0045, Japan (T.T., H.N.); The Sainsbury Laboratory, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (A.M.J.); Division of Biology, University of California San Diego, La Jolla, California 92093 (S.P.B.); Centre of Excellence for Computational Systems Biology (I.C.) and Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks (I.C., S.K.T., A.H.M.), University of Western Australia, Crawley 6009, Western Australia, Australia
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Agne B, Andrès C, Montandon C, Christ B, Ertan A, Jung F, Infanger S, Bischof S, Baginsky S, Kessler F. The acidic A-domain of Arabidopsis TOC159 occurs as a hyperphosphorylated protein. Plant Physiol 2010; 153:1016-30. [PMID: 20457805 PMCID: PMC2899928 DOI: 10.1104/pp.110.158048] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2010] [Accepted: 05/06/2010] [Indexed: 05/17/2023]
Abstract
The translocon at the outer membrane of the chloroplast assists the import of a large class of preproteins with amino-terminal transit sequences. The preprotein receptors Toc159 and Toc33 in Arabidopsis (Arabidopsis thaliana) are specific for the accumulation of abundant photosynthetic proteins. The receptors are homologous GTPases known to be regulated by phosphorylation within their GTP-binding domains. In addition to the central GTP-binding domain, Toc159 has an acidic N-terminal domain (A-domain) and a C-terminal membrane-anchoring domain (M-domain). The A-domain of Toc159 is dispensable for its in vivo activity in Arabidopsis and prone to degradation in pea (Pisum sativum). Therefore, it has been suggested to have a regulatory function. Here, we show that in Arabidopsis, the A-domain is not simply degraded but that it accumulates as a soluble, phosphorylated protein separated from Toc159. However, the physiological relevance of this process is unclear. The data show that the A-domain of Toc159 as well as those of its homologs Toc132 and Toc120 are targets of a casein kinase 2-like activity.
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Baginsky S, Hennig L, Zimmermann P, Gruissem W. Gene expression analysis, proteomics, and network discovery. Plant Physiol 2010; 152:402-10. [PMID: 20018595 PMCID: PMC2815903 DOI: 10.1104/pp.109.150433] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Accepted: 12/06/2009] [Indexed: 05/21/2023]
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Abstract
Protein phosphorylation is one of the most important posttranslational modifications in eukaryotic cells and affects almost all basic cellular processes. The chloroplast as plant-specific cell organelle with important metabolic functions is integrated into the cellular signaling and phosphorylation network. Recent large-scale chloroplast phosphoproteome analyses in Arabidopsis have provided new information about phosphorylation targets and expanded the list of chloroplast metabolic and regulatory functions that are potentially controlled by protein phosphorylation. Phosphorylated peptides identified from chloroplast proteins provide new insights into phosphorylation motifs, protein kinase activities, and substrate utilization. Phosphorylation sites in protein kinases can reveal chloroplast phosphorylation cascades that may network different functions by integrating signaling chains. Our review provides a meta-analysis of currently available chloroplast phosphoproteome information and discusses biological insights from large-scale chloroplast phosphoprotein profiling as well as technological constraints of kinase network analysis.
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Affiliation(s)
- Sacha Baginsky
- Department of Biology, ETH Zurich, Universitätstrasse 2, 8092 Zürich, Switzerland.
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Bischof S, Reiland S, Baerenfaller K, de la Rosa AB, Schläpfer P, Trösch R, Gruissem W, Baginsky S. Functional proteomics: a cornerstone in plant systems biology. N Biotechnol 2009. [DOI: 10.1016/j.nbt.2009.06.870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Reiland S, Messerli G, Baerenfaller K, Gerrits B, Endler A, Grossmann J, Gruissem W, Baginsky S. Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks. Plant Physiol 2009; 150:889-903. [PMID: 19376835 PMCID: PMC2689975 DOI: 10.1104/pp.109.138677] [Citation(s) in RCA: 355] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Accepted: 04/14/2009] [Indexed: 05/17/2023]
Abstract
We have characterized the phosphoproteome of Arabidopsis (Arabidopsis thaliana) seedlings using high-accuracy mass spectrometry and report the identification of 1,429 phosphoproteins and 3,029 unique phosphopeptides. Among these, 174 proteins were chloroplast phosphoproteins. Motif-X (motif extractor) analysis of the phosphorylation sites in chloroplast proteins identified four significantly enriched kinase motifs, which include casein kinase II (CKII) and proline-directed kinase motifs, as well as two new motifs at the carboxyl terminus of ribosomal proteins. Using the phosphorylation motifs as a footprint for the activity of a specific kinase class, we connected the phosphoproteins with their putative kinases and constructed a chloroplast CKII phosphorylation network. The network topology suggests that CKII is a central regulator of different chloroplast functions. To provide insights into the dynamic regulation of protein phosphorylation, we analyzed the phosphoproteome at the end of day and end of night. The results revealed only minor changes in chloroplast kinase activities and phosphorylation site utilization. A notable exception was ATP synthase beta-subunit, which is found phosphorylated at CKII phosphorylation sites preferentially in the dark. We propose that ATP synthase is regulated in cooperation with 14-3-3 proteins by CKII-mediated phosphorylation of ATP synthase beta-subunit in the dark.
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Affiliation(s)
- Sonja Reiland
- Department of Biology, Eidgenössische Technische Hochschule Zurich, 8092 Zurich, Switzerland
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Abstract
Proteomics is an essential source of information about biological systems because it generates knowledge about the concentrations, interactions, functions, and catalytic activities of proteins, which are the major structural and functional determinants of cells. In the last few years significant technology development has taken place both at the level of data analysis software and mass spectrometry hardware. Conceptual progress in proteomics has made possible the analysis of entire proteomes at previously unprecedented density and accuracy. New concepts have emerged that comprise quantitative analyses of full proteomes, database-independent protein identification strategies, targeted quantitative proteomics approaches with proteotypic peptides and the systematic analysis of an increasing number of posttranslational modifications at high temporal and spatial resolution. Although plant proteomics is making progress, there are still several analytical challenges that await experimental and conceptual solutions. With this review I will highlight the current status of plant proteomics and put it into the context of the aforementioned conceptual progress in the field, illustrate some of the plant-specific challenges and present my view on the great opportunities for plant systems biology offered by proteomics.
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Affiliation(s)
- Sacha Baginsky
- Institute of Plant Sciences, Swiss Federal Institute of Technology, Universitätsstrasse 2, 8092 Zurich, Switzerland.
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Endler A, Reiland S, Gerrits B, Schmidt UG, Baginsky S, Martinoia E. In vivo phosphorylation sites of barley tonoplast proteins identified by a phosphoproteomic approach. Proteomics 2009; 9:310-21. [DOI: 10.1002/pmic.200800323] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Weckwerth W, Baginsky S, van Wijk K, Heazlewood JL, Millar H. The multinational Arabidopsis steering subcommittee for proteomics assembles the largest proteome database resource for plant systems biology. J Proteome Res 2008; 7:4209-10. [PMID: 18785769 DOI: 10.1021/pr800480u] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Baerenfaller K, Grossmann J, Grobei MA, Hull R, Hirsch-Hoffmann M, Yalovsky S, Zimmermann P, Grossniklaus U, Gruissem W, Baginsky S. Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics. Science 2008; 320:938-41. [DOI: 10.1126/science.1157956] [Citation(s) in RCA: 425] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Grossmann J, Fischer B, Baerenfaller K, Owiti J, Buhmann JM, Gruissem W, Baginsky S. A workflow to increase the detection rate of proteins from unsequenced organisms in high-throughput proteomics experiments. Proteomics 2007; 7:4245-54. [DOI: 10.1002/pmic.200700474] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Roos FF, Jacob R, Grossmann J, Fischer B, Buhmann JM, Gruissem W, Baginsky S, Widmayer P. PepSplice: cache-efficient search algorithms for comprehensive identification of tandem mass spectra. Bioinformatics 2007; 23:3016-23. [PMID: 17768164 DOI: 10.1093/bioinformatics/btm417] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Tandem mass spectrometry allows for high-throughput identification of complex protein samples. Searching tandem mass spectra against sequence databases is the main analysis method nowadays. Since many peptide variations are possible, including them in the search space seems only logical. However, the search space usually grows exponentially with the number of independent variations and may therefore overwhelm computational resources. RESULTS We provide fast, cache-efficient search algorithms to screen large peptide search spaces including non-tryptic peptides, whole genomes, dozens of posttranslational modifications, unannotated point mutations and even unannotated splice sites. All these search spaces can be screened simultaneously. By optimizing the cache usage, we achieve a calculation speed that closely approaches the limits of the hardware. At the same time, we control the size of the overall search space by limiting the combinations of variations that can co-occur on the same peptide. Using a hypergeometric scoring scheme, we applied these algorithms to a dataset of 1 420 632 spectra. We were able to identify a considerable number of peptide variations within a modest amount of computing time on standard desktop computers.
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Affiliation(s)
- Franz F Roos
- Institute of Theoretical Computer Science, Institute of Plant Science, Institute of Computational Science, ETH Zurich, CH-8092 Zurich, Switzerland
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Schmidt UG, Endler A, Schelbert S, Brunner A, Schnell M, Neuhaus HE, Marty-Mazars D, Marty F, Baginsky S, Martinoia E. Novel tonoplast transporters identified using a proteomic approach with vacuoles isolated from cauliflower buds. Plant Physiol 2007; 145:216-29. [PMID: 17660356 PMCID: PMC1976570 DOI: 10.1104/pp.107.096917] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Young meristematic plant cells contain a large number of small vacuoles, while the largest part of the vacuome in mature cells is composed by a large central vacuole, occupying 80% to 90% of the cell volume. Thus far, only a limited number of vacuolar membrane proteins have been identified and characterized. The proteomic approach is a powerful tool to identify new vacuolar membrane proteins. To analyze vacuoles from growing tissues we isolated vacuoles from cauliflower (Brassica oleracea) buds, which are constituted by a large amount of small cells but also contain cells in expansion as well as fully expanded cells. Here we show that using purified cauliflower vacuoles and different extraction procedures such as saline, NaOH, acetone, and chloroform/methanol and analyzing the data against the Arabidopsis (Arabidopsis thaliana) database 102 cauliflower integral proteins and 214 peripheral proteins could be identified. The vacuolar pyrophosphatase was the most prominent protein. From the 102 identified proteins 45 proteins were already described. Nine of these, corresponding to 46% of peptides detected, are known vacuolar proteins. We identified 57 proteins (55.9%) containing at least one membrane spanning domain with unknown subcellular localization. A comparison of the newly identified proteins with expression profiles from in silico data revealed that most of them are highly expressed in young, developing tissues. To verify whether the newly identified proteins were indeed localized in the vacuole we constructed and expressed green fluorescence protein fusion proteins for five putative vacuolar membrane proteins exhibiting three to 11 transmembrane domains. Four of them, a putative organic cation transporter, a nodulin N21 family protein, a membrane protein of unknown function, and a senescence related membrane protein were localized in the vacuolar membrane, while a white-brown ATP-binding cassette transporter homolog was shown to reside in the plasma membrane. These results demonstrate that proteomic analysis of highly purified vacuoles from specific tissues allows the identification of new vacuolar proteins and provides an additional view of tonoplastic proteins.
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Affiliation(s)
- Ulrike G Schmidt
- University of Zürich, Institute of Plant Biology, CH-8008 Zurich, Switzerland
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Abstract
Chloroplasts have a complex enzymatic machinery to adjust the relative half-life of their mRNAs to environmental signals. Soluble protein extracts from spinach (Spinacia oleracea L.) chloroplasts that correctly reproduce in vitro the differential mRNA stability observed in vivo were analyzed using shotgun proteomics to identify the proteins that are potentially involved in this process. The combination of a novel strategy for the database-independent detection of proteins from MS/MS data with standard database searches allowed us to identify 243 proteins with high confidence, which include several nucleases and RNA binding proteins but also proteins that have no reported function in chloroplast mRNA metabolism. Characterization of enzyme activities that adjust mRNA stability in response to illumination revealed that the dark-induced RNA degradation pathway involves enzymatic activities that differ from those that direct RNA processing and stabilization in the light. Dark-induced mRNA degradation comprises a MgCl2-independent and a MgCl2-dependent step, which releases nucleoside di- and monophosphates from the petD 3'-UTR precursor substrate. RNA degradation can be blocked with RNasin, a potent inhibitor of eukaryotic ribonucleases, suggesting that chloroplast mRNA degradation involves enzymes that are distinct from those found in prokaryotic-type RNA degradation. On the basis of the identified proteins and the in vitro characterization of the RNA degradation activities, we discuss scenarios and components that potentially determine plastid mRNA stability.
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Affiliation(s)
- Sacha Baginsky
- Institute of Plant Sciences, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland.
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Fischer B, Roth V, Roos F, Grossmann J, Baginsky S, Widmayer P, Gruissem W, Buhmann JM. NovoHMM: a hidden Markov model for de novo peptide sequencing. Anal Chem 2007; 77:7265-73. [PMID: 16285674 DOI: 10.1021/ac0508853] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
De novo sequencing of peptides poses one of the most challenging tasks in data analysis for proteome research. In this paper, a generative hidden Markov model (HMM) of mass spectra for de novo peptide sequencing which constitutes a novel view on how to solve this problem in a Bayesian framework is proposed. Further extensions of the model structure to a graphical model and a factorial HMM to substantially improve the peptide identification results are demonstrated. Inference with the graphical model for de novo peptide sequencing estimates posterior probabilities for amino acids rather than scores for single symbols in the sequence. Our model outperforms state-of-the-art methods for de novo peptide sequencing on a large test set of spectra.
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Affiliation(s)
- Bernd Fischer
- Institute of Computational Science, Institute of Plant Sciences, ETH Zurich, Switzerland
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