1
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Chen Y, Vermeersch M, Van Leene J, De Jaeger G, Li Y, Vanhaeren H. A dynamic ubiquitination balance of cell proliferation and endoreduplication regulators determines plant organ size. Sci Adv 2024; 10:eadj2570. [PMID: 38478622 PMCID: PMC10936951 DOI: 10.1126/sciadv.adj2570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 02/08/2024] [Indexed: 03/17/2024]
Abstract
Ubiquitination plays a crucial role throughout plant growth and development. The E3 ligase DA2 has been reported to activate the peptidase DA1 by ubiquitination, hereby limiting cell proliferation. However, the molecular mechanisms that regulate DA2 remain elusive. Here, we demonstrate that DA2 has a very high turnover and auto-ubiquitinates with K48-linkage polyubiquitin chains, which is counteracted by two deubiquitinating enzymes, UBIQUITIN-SPECIFIC PROTEASE 12 (UBP12) and UBP13. Unexpectedly, we found that auto-ubiquitination of DA2 does not influence its stability but determines its E3 ligase activity. We also demonstrate that impairing the protease activity of DA1 abolishes the growth-reducing effect of DA2. Last, we show that synthetic, constitutively activated DA1-ubiquitin fusion proteins overrule this complex balance of ubiquitination and deubiquitination and strongly restrict growth and promote endoreduplication. Our findings highlight a nonproteolytic function of K48-linked polyubiquitination and reveal a mechanism by which DA2 auto-ubiquitination levels, in concert with UBP12 and UBP13, precisely monitor the activity of DA1 and fine-tune plant organ size.
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Affiliation(s)
- Ying Chen
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
| | - Mattias Vermeersch
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
| | - Jelle Van Leene
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
| | - Geert De Jaeger
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hannes Vanhaeren
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Proeftuinstraat 86, 9000 Ghent, Belgium
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2
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Safi A, Smagghe W, Gonçalves A, Wang Q, Xu K, Fernandez AI, Cappe B, Riquet FB, Mylle E, Eeckhout D, De Winne N, Van De Slijke E, Persyn F, Persiau G, Van Damme D, Geelen D, De Jaeger G, Beeckman T, Van Leene J, Vanneste S. Phase separation-based visualization of protein-protein interactions and kinase activities in plants. Plant Cell 2023; 35:3280-3302. [PMID: 37378595 PMCID: PMC10473206 DOI: 10.1093/plcell/koad188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/23/2023] [Accepted: 06/23/2023] [Indexed: 06/29/2023]
Abstract
Protein activities depend heavily on protein complex formation and dynamic posttranslational modifications, such as phosphorylation. The dynamic nature of protein complex formation and posttranslational modifications is notoriously difficult to monitor in planta at cellular resolution, often requiring extensive optimization. Here, we generated and exploited the SYnthetic Multivalency in PLants (SYMPL)-vector set to assay protein-protein interactions (PPIs) (separation of phases-based protein interaction reporter) and kinase activities (separation of phases-based activity reporter of kinase) in planta, based on phase separation. This technology enabled easy detection of inducible, binary and ternary PPIs among cytoplasmic and nuclear proteins in plant cells via a robust image-based readout. Moreover, we applied the SYMPL toolbox to develop an in vivo reporter for SNF1-related kinase 1 activity, allowing us to visualize tissue-specific, dynamic SnRK1 activity in stable transgenic Arabidopsis (Arabidopsis thaliana) plants. The SYMPL cloning toolbox provides a means to explore PPIs, phosphorylation, and other posttranslational modifications with unprecedented ease and sensitivity.
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Affiliation(s)
- Alaeddine Safi
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Wouter Smagghe
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Amanda Gonçalves
- Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
- VIB, Bioimaging Core, B-9052 Ghent, Belgium
| | - Qing Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Ke Xu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Ana Ibis Fernandez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Benjamin Cappe
- Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
| | - Franck B Riquet
- Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
- Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, 59000 Lille, France
| | - Evelien Mylle
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Nancy De Winne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Eveline Van De Slijke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Freya Persyn
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Geert Persiau
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Danny Geelen
- Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Steffen Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium
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3
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Broucke E, Dang TTV, Li Y, Hulsmans S, Van Leene J, De Jaeger G, Hwang I, Wim VDE, Rolland F. SnRK1 inhibits anthocyanin biosynthesis through both transcriptional regulation and direct phosphorylation and dissociation of the MYB/bHLH/TTG1 MBW complex. Plant J 2023; 115:1193-1213. [PMID: 37219821 DOI: 10.1111/tpj.16312] [Citation(s) in RCA: 4] [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: 12/02/2022] [Revised: 04/21/2023] [Accepted: 05/18/2023] [Indexed: 05/24/2023]
Abstract
Plants have evolved an extensive specialized secondary metabolism. The colorful flavonoid anthocyanins, for example, not only stimulate flower pollination and seed dispersal, but also protect different tissues against high light, UV and oxidative stress. Their biosynthesis is highly regulated by environmental and developmental cues and induced by high sucrose levels. Expression of the biosynthetic enzymes involved is controlled by a transcriptional MBW complex, comprising (R2R3) MYB- and bHLH-type transcription factors and the WD40 repeat protein TTG1. Anthocyanin biosynthesis is not only useful, but also carbon- and energy-intensive and non-vital. Consistently, the SnRK1 protein kinase, a metabolic sensor activated in carbon- and energy-depleting stress conditions, represses anthocyanin biosynthesis. Here we show that Arabidopsis SnRK1 represses MBW complex activity both at the transcriptional and post-translational level. In addition to repressing expression of the key transcription factor MYB75/PAP1, SnRK1 activity triggers MBW complex dissociation, associated with loss of target promoter binding, MYB75 protein degradation and nuclear export of TTG1. We also provide evidence for direct interaction with and phosphorylation of multiple MBW complex proteins. These results indicate that repression of expensive anthocyanin biosynthesis is an important strategy to save energy and redirect carbon flow to more essential processes for survival in metabolic stress conditions.
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Affiliation(s)
- Ellen Broucke
- Laboratory of Molecular Plant Biology, Biology Department, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
- KU Leuven Plant Institute (LPI), Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
| | - Thi Tuong Vi Dang
- Laboratory of Molecular Plant Biology, Biology Department, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
- KU Leuven Plant Institute (LPI), Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, 37673, South Korea
| | - Yi Li
- Laboratory of Molecular Plant Biology, Biology Department, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
- KU Leuven Plant Institute (LPI), Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
| | - Sander Hulsmans
- Laboratory of Molecular Plant Biology, Biology Department, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
- KU Leuven Plant Institute (LPI), Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Ildoo Hwang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, 37673, South Korea
| | - Van den Ende Wim
- Laboratory of Molecular Plant Biology, Biology Department, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
- KU Leuven Plant Institute (LPI), Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
| | - Filip Rolland
- Laboratory of Molecular Plant Biology, Biology Department, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
- KU Leuven Plant Institute (LPI), Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
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4
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Cho H, Banf M, Shahzad Z, Van Leene J, Bossi F, Ruffel S, Bouain N, Cao P, Krouk G, De Jaeger G, Lacombe B, Brandizzi F, Rhee SY, Rouached H. ARSK1 activates TORC1 signaling to adjust growth to phosphate availability in Arabidopsis. Curr Biol 2023; 33:1778-1786.e5. [PMID: 36963384 PMCID: PMC10175222 DOI: 10.1016/j.cub.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 02/12/2023] [Accepted: 03/02/2023] [Indexed: 03/26/2023]
Abstract
Nutrient sensing and signaling are essential for adjusting growth and development to available resources. Deprivation of the essential mineral phosphorus (P) inhibits root growth.1 The molecular processes that sense P limitation to trigger early root growth inhibition are not known yet. Target of rapamycin (TOR) kinase is a central regulatory hub in eukaryotes to adapt growth to internal and external nutritional cues.2,3 How nutritional signals are transduced to TOR to control plant growth remains unclear. Here, we identify Arabidopsis-root-specific kinase 1 (ARSK1), which attenuates initial root growth inhibition in response to P limitation. We demonstrate that ARSK1 phosphorylates and stabilizes the regulatory-associated protein of TOR 1B (RAPTOR1B), a component of the TOR complex 1, to adjust root growth to P availability. These findings uncover signaling components acting upstream of TOR to balance growth to P availability.
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Affiliation(s)
- Huikyong Cho
- The Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA; Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Michael Banf
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Zaigham Shahzad
- Department of Life Sciences, Lahore University of Management Sciences, Lahore 54792, Pakistan
| | - Jelle Van Leene
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Flavia Bossi
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Sandrine Ruffel
- Institute for Plant Sciences of Montpellier, University Montpellier, CNRS, INRAE, Montpellier 34060, France
| | - Nadia Bouain
- Institute for Plant Sciences of Montpellier, University Montpellier, CNRS, INRAE, Montpellier 34060, France
| | - Pengfei Cao
- MSU DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Gabiel Krouk
- Institute for Plant Sciences of Montpellier, University Montpellier, CNRS, INRAE, Montpellier 34060, France
| | - Geert De Jaeger
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Benoit Lacombe
- Institute for Plant Sciences of Montpellier, University Montpellier, CNRS, INRAE, Montpellier 34060, France
| | - Federica Brandizzi
- MSU DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.
| | - Hatem Rouached
- The Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA; Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA.
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5
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Wang P, Siao W, Zhao X, Arora D, Wang R, Eeckhout D, Van Leene J, Kumar R, Houbaert A, De Winne N, Mylle E, Vandorpe M, Korver RA, Testerink C, Gevaert K, Vanneste S, De Jaeger G, Van Damme D, Russinova E. Adaptor protein complex interaction map in Arabidopsis identifies P34 as a common stability regulator. Nat Plants 2023; 9:355-371. [PMID: 36635451 PMCID: PMC7615410 DOI: 10.1038/s41477-022-01328-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Adaptor protein (AP) complexes are evolutionarily conserved vesicle transport regulators that recruit coat proteins, membrane cargoes and coated vesicle accessory proteins. As in plants endocytic and post-Golgi trafficking intersect at the trans-Golgi network, unique mechanisms for sorting cargoes of overlapping vesicular routes are anticipated. The plant AP complexes are part of the sorting machinery, but despite some functional information, their cargoes, accessory proteins and regulation remain largely unknown. Here, by means of various proteomics approaches, we generated the overall interactome of the five AP and the TPLATE complexes in Arabidopsis thaliana. The interactome converged on a number of hub proteins, including the thus far unknown adaptin binding-like protein, designated P34. P34 interacted with the clathrin-associated AP complexes, controlled their stability and, subsequently, influenced clathrin-mediated endocytosis and various post-Golgi trafficking routes. Altogether, the AP interactome network offers substantial resources for further discoveries of unknown endomembrane trafficking regulators in plant cells.
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Affiliation(s)
- Peng Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Wei Siao
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Xiuyang Zhao
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Deepanksha Arora
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Ren Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Rahul Kumar
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Anaxi Houbaert
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Nancy De Winne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Evelien Mylle
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Michael Vandorpe
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Ruud A Korver
- Plant Physiology and Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Christa Testerink
- Plant Physiology and Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
- Laboratory of Plant Physiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Steffen Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- Center for Plant Systems Biology, VIB, Ghent, Belgium.
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6
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Singh DK, Gamboa RS, Singh AK, Walkemeier B, Van Leene J, De Jaeger G, Siddiqi I, Guerois R, Crismani W, Mercier R. The FANCC-FANCE-FANCF complex is evolutionarily conserved and regulates meiotic recombination. Nucleic Acids Res 2023; 51:2516-2528. [PMID: 36652992 PMCID: PMC10085685 DOI: 10.1093/nar/gkac1244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/29/2022] [Accepted: 12/14/2022] [Indexed: 01/20/2023] Open
Abstract
At meiosis, programmed meiotic DNA double-strand breaks are repaired via homologous recombination, resulting in crossovers (COs). From a large excess of DNA double-strand breaks that are formed, only a small proportion gets converted into COs because of active mechanisms that restrict CO formation. The Fanconi anemia (FA) complex proteins AtFANCM, MHF1 and MHF2 were previously identified in a genetic screen as anti-CO factors that function during meiosis in Arabidopsis thaliana. Here, pursuing the same screen, we identify FANCC as a new anti-CO gene. FANCC was previously only identified in mammals because of low primary sequence conservation. We show that FANCC, and its physical interaction with FANCE-FANCF, is conserved from vertebrates to plants. Further, we show that FANCC, together with its subcomplex partners FANCE and FANCF, regulates meiotic recombination. Mutations of any of these three genes partially rescues CO-defective mutants, which is particularly marked in female meiosis. Functional loss of FANCC, FANCE, or FANCF results in synthetic meiotic catastrophe with the pro-CO factor MUS81. This work reveals that FANCC is conserved outside mammals and has an anti-CO role during meiosis together with FANCE and FANCF.
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Affiliation(s)
- Dipesh Kumar Singh
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Rigel Salinas Gamboa
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Avinash Kumar Singh
- CSIR-Centre for Cellular & Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Birgit Walkemeier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium.,Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium.,Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Imran Siddiqi
- CSIR-Centre for Cellular & Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Raphael Guerois
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette 91190, France
| | - Wayne Crismani
- The DNA Repair and Recombination Laboratory, St Vincent's Institute of Medical Research, Melbourne 3065, Australia.,The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
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7
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Van Leene J, Eeckhout D, Gadeyne A, Matthijs C, Han C, De Winne N, Persiau G, Van De Slijke E, Persyn F, Mertens T, Smagghe W, Crepin N, Broucke E, Van Damme D, Pleskot R, Rolland F, De Jaeger G. Mapping of the plant SnRK1 kinase signalling network reveals a key regulatory role for the class II T6P synthase-like proteins. Nat Plants 2022; 8:1245-1261. [PMID: 36376753 DOI: 10.1038/s41477-022-01269-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
The central metabolic regulator SnRK1 controls plant growth and survival upon activation by energy depletion, but detailed molecular insight into its regulation and downstream targets is limited. Here we used phosphoproteomics to infer the sucrose-dependent processes targeted upon starvation by kinases as SnRK1, corroborating the relation of SnRK1 with metabolic enzymes and transcriptional regulators, while also pointing to SnRK1 control of intracellular trafficking. Next, we integrated affinity purification, proximity labelling and crosslinking mass spectrometry to map the protein interaction landscape, composition and structure of the SnRK1 heterotrimer, providing insight in its plant-specific regulation. At the intersection of this multi-dimensional interactome, we discovered a strong association of SnRK1 with class II T6P synthase (TPS)-like proteins. Biochemical and cellular assays show that TPS-like proteins function as negative regulators of SnRK1. Next to stable interactions with the TPS-like proteins, similar intricate connections were found with known regulators, suggesting that plants utilize an extended kinase complex to fine-tune SnRK1 activity for optimal responses to metabolic stress.
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Affiliation(s)
- Jelle Van Leene
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dominique Eeckhout
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Astrid Gadeyne
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Caroline Matthijs
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Chao Han
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Nancy De Winne
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Geert Persiau
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Eveline Van De Slijke
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Freya Persyn
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Toon Mertens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Wouter Smagghe
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Nathalie Crepin
- Laboratory for Molecular Plant Biology, Biology Department, KU Leuven, Heverlee-Leuven, Belgium
- KU Leuven Plant Institute-LPI, Heverlee-Leuven, Belgium
| | - Ellen Broucke
- Laboratory for Molecular Plant Biology, Biology Department, KU Leuven, Heverlee-Leuven, Belgium
- KU Leuven Plant Institute-LPI, Heverlee-Leuven, Belgium
| | - Daniël Van Damme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Roman Pleskot
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic
| | - Filip Rolland
- Laboratory for Molecular Plant Biology, Biology Department, KU Leuven, Heverlee-Leuven, Belgium
- KU Leuven Plant Institute-LPI, Heverlee-Leuven, Belgium
| | - Geert De Jaeger
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
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8
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Arora D, Abel NB, Liu C, Van Damme P, Yperman K, Eeckhout D, Vu LD, Wang J, Tornkvist A, Impens F, Korbei B, Van Leene J, Goossens A, De Jaeger G, Ott T, Moschou PN, Van Damme D. Correction to: Establishment of Proximity-Dependent Biotinylation Approaches in Different Plant Model Systems. Plant Cell 2022; 34:2806. [PMID: 35357494 PMCID: PMC9252476 DOI: 10.1093/plcell/koac101] [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] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Deepanksha Arora
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Nikolaj B Abel
- Faculty of Biology, Cell Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Chen Liu
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-75007, Sweden
| | - Petra Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium
| | - Klaas Yperman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jie Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Anna Tornkvist
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-75007, Sweden
| | - Francis Impens
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
- VIB Center for Medical Biotechnology, 9052 Ghent, Belgium
- VIB Proteomics Core, 9052 Ghent, Belgium
| | - Barbara Korbei
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Thomas Ott
- Faculty of Biology, Cell Biology, University of Freiburg, 79104 Freiburg, Germany
- Centre for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Panagiotis Nikolaou Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-75007, Sweden
- Department of Biology, University of Crete, 70013 Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
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9
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Yperman K, Papageorgiou AC, Merceron R, De Munck S, Bloch Y, Eeckhout D, Jiang Q, Tack P, Grigoryan R, Evangelidis T, Van Leene J, Vincze L, Vandenabeele P, Vanhaecke F, Potocký M, De Jaeger G, Savvides SN, Tripsianes K, Pleskot R, Van Damme D. Distinct EH domains of the endocytic TPLATE complex confer lipid and protein binding. Nat Commun 2021; 12:3050. [PMID: 34031427 PMCID: PMC8144573 DOI: 10.1038/s41467-021-23314-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 04/22/2021] [Indexed: 01/07/2023] Open
Abstract
Clathrin-mediated endocytosis (CME) is the gatekeeper of the plasma membrane. In contrast to animals and yeasts, CME in plants depends on the TPLATE complex (TPC), an evolutionary ancient adaptor complex. However, the mechanistic contribution of the individual TPC subunits to plant CME remains elusive. In this study, we used a multidisciplinary approach to elucidate the structural and functional roles of the evolutionary conserved N-terminal Eps15 homology (EH) domains of the TPC subunit AtEH1/Pan1. By integrating high-resolution structural information obtained by X-ray crystallography and NMR spectroscopy with all-atom molecular dynamics simulations, we provide structural insight into the function of both EH domains. Both domains bind phosphatidic acid with a different strength, and only the second domain binds phosphatidylinositol 4,5-bisphosphate. Unbiased peptidome profiling by mass-spectrometry revealed that the first EH domain preferentially interacts with the double N-terminal NPF motif of a previously unidentified TPC interactor, the integral membrane protein Secretory Carrier Membrane Protein 5 (SCAMP5). Furthermore, we show that AtEH/Pan1 proteins control the internalization of SCAMP5 via this double NPF peptide interaction motif. Collectively, our structural and functional studies reveal distinct but complementary roles of the EH domains of AtEH/Pan1 in plant CME and connect the internalization of SCAMP5 to the TPLATE complex.
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Affiliation(s)
- Klaas Yperman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Anna C Papageorgiou
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Romain Merceron
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- VIB Center for Inflammation Research, Ghent, Belgium
| | - Steven De Munck
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- VIB Center for Inflammation Research, Ghent, Belgium
| | - Yehudi Bloch
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- VIB Center for Inflammation Research, Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Qihang Jiang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Pieter Tack
- Department of Chemistry, X-ray Microspectroscopy and Imaging - XMI Research Unit, Ghent University, Ghent, Belgium
| | - Rosa Grigoryan
- Department of Chemistry, Atomic & Mass Spectrometry - A&MS Research Unit, Ghent University, Ghent, Belgium
| | - Thomas Evangelidis
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Laszlo Vincze
- Department of Chemistry, X-ray Microspectroscopy and Imaging - XMI Research Unit, Ghent University, Ghent, Belgium
| | - Peter Vandenabeele
- Department of Chemistry, X-ray Microspectroscopy and Imaging - XMI Research Unit, Ghent University, Ghent, Belgium
- Archaeometry Research Group, Department of Archaeology, Ghent University, Ghent, Belgium
| | - Frank Vanhaecke
- Department of Chemistry, Atomic & Mass Spectrometry - A&MS Research Unit, Ghent University, Ghent, Belgium
| | - Martin Potocký
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague 6, Czech Republic
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Savvas N Savvides
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
- VIB Center for Inflammation Research, Ghent, Belgium.
| | | | - Roman Pleskot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague 6, Czech Republic.
| | - Daniel Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
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10
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Arora D, Abel NB, Liu C, Van Damme P, Yperman K, Eeckhout D, Vu LD, Wang J, Tornkvist A, Impens F, Korbei B, Van Leene J, Goossens A, De Jaeger G, Ott T, Moschou PN, Van Damme D. Establishment of Proximity-Dependent Biotinylation Approaches in Different Plant Model Systems. Plant Cell 2020; 32:3388-3407. [PMID: 32843435 PMCID: PMC7610282 DOI: 10.1105/tpc.20.00235] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/22/2020] [Accepted: 08/21/2020] [Indexed: 05/19/2023]
Abstract
Proximity labeling is a powerful approach for detecting protein-protein interactions. Most proximity labeling techniques use a promiscuous biotin ligase or a peroxidase fused to a protein of interest, enabling the covalent biotin labeling of proteins and subsequent capture and identification of interacting and neighboring proteins without the need for the protein complex to remain intact. To date, only a few studies have reported on the use of proximity labeling in plants. Here, we present the results of a systematic study applying a variety of biotin-based proximity labeling approaches in several plant systems using various conditions and bait proteins. We show that TurboID is the most promiscuous variant in several plant model systems and establish protocols that combine mass spectrometry-based analysis with harsh extraction and washing conditions. We demonstrate the applicability of TurboID in capturing membrane-associated protein interactomes using Lotus japonicus symbiotically active receptor kinases as a test case. We further benchmark the efficiency of various promiscuous biotin ligases in comparison with one-step affinity purification approaches. We identified both known and novel interactors of the endocytic TPLATE complex. We furthermore present a straightforward strategy to identify both nonbiotinylated and biotinylated peptides in a single experimental setup. Finally, we provide initial evidence that our approach has the potential to suggest structural information of protein complexes.
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Affiliation(s)
- Deepanksha Arora
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Nikolaj B Abel
- Faculty of Biology, Cell Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Chen Liu
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-75007, Sweden
| | - Petra Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium
| | - Klaas Yperman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jie Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Anna Tornkvist
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-75007, Sweden
| | - Francis Impens
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
- VIB Center for Medical Biotechnology, 9052 Ghent, Belgium
- VIB Proteomics Core, 9052 Ghent, Belgium
| | - Barbara Korbei
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Thomas Ott
- Faculty of Biology, Cell Biology, University of Freiburg, 79104 Freiburg, Germany
- Centre for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Panagiotis Nikolaou Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-75007, Sweden
- Department of Biology, University of Crete, 70013 Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
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11
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Forzani C, Duarte GT, Van Leene J, Clément G, Huguet S, Paysant-Le-Roux C, Mercier R, De Jaeger G, Leprince AS, Meyer C. Mutations of the AtYAK1 Kinase Suppress TOR Deficiency in Arabidopsis. Cell Rep 2020; 27:3696-3708.e5. [PMID: 31216485 DOI: 10.1016/j.celrep.2019.05.074] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 04/26/2019] [Accepted: 05/20/2019] [Indexed: 11/28/2022] Open
Abstract
The target of rapamycin (TOR) kinase is a conserved energy sensor that regulates growth in response to environmental cues. However, little is known about the TOR signaling pathway in plants. We used Arabidopsis lines affected in the lethal with SEC13 protein 8 (LST8-1) gene, a core element of the TOR complex, to search for suppressor mutations. Two suppressor lines with improved growth were isolated that carried mutations in the Yet Another Kinase 1 (AtYAK1) gene encoding a member of the dual-specificity tyrosine phosphorylation-regulated kinase (DYRK) family. Atyak1 mutations partly rescued the developmental defects of lst8-1-1 mutants and conferred resistance to the TOR inhibitor AZD-8055. Moreover, atyak1 mutations suppressed the transcriptomic and metabolic perturbations as well as the abscisic acid (ABA) hypersensitivity of the lst8-1-1 mutants. AtYAK1 interacted with the regulatory-associated protein of TOR (RAPTOR), a component of the TOR complex, and was phosphorylated by TOR. Thus, our findings reveal that AtYAK1 is a TOR effector that probably needs to be switched off to activate plant growth.
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Affiliation(s)
- Céline Forzani
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Gustavo T Duarte
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Gilles Clément
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Stéphanie Huguet
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Saclay, Bâtiment 630, Plateau de Moulon, 91192 Gif sur Yvette, France; Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, Plateau de Moulon, 91192 Gif sur Yvette, France
| | - Christine Paysant-Le-Roux
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Saclay, Bâtiment 630, Plateau de Moulon, 91192 Gif sur Yvette, France; Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, Plateau de Moulon, 91192 Gif sur Yvette, France
| | - Raphaël Mercier
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Anne-Sophie Leprince
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France; Sorbonne Université, UFR 927, 4 Place Jussieu, F-75252 Paris Cedex 05, France
| | - Christian Meyer
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France.
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12
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Van Leene J, Han C, Gadeyne A, Eeckhout D, Matthijs C, Cannoot B, De Winne N, Persiau G, Van De Slijke E, Van de Cotte B, Stes E, Van Bel M, Storme V, Impens F, Gevaert K, Vandepoele K, De Smet I, De Jaeger G. Capturing the phosphorylation and protein interaction landscape of the plant TOR kinase. Nat Plants 2019; 5:316-327. [PMID: 30833711 DOI: 10.1038/s41477-019-0378-z] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/28/2019] [Indexed: 05/18/2023]
Abstract
The target of rapamycin (TOR) kinase is a conserved regulatory hub that translates environmental and nutritional information into permissive or restrictive growth decisions. Despite the increased appreciation of the essential role of the TOR complex in plants, no large-scale phosphoproteomics or interactomics studies have been performed to map TOR signalling events in plants. To fill this gap, we combined a systematic phosphoproteomics screen with a targeted protein complex analysis in the model plant Arabidopsis thaliana. Integration of the phosphoproteome and protein complex data on the one hand shows that both methods reveal complementary subspaces of the plant TOR signalling network, enabling proteome-wide discovery of both upstream and downstream network components. On the other hand, the overlap between both data sets reveals a set of candidate direct TOR substrates. The integrated network embeds both evolutionarily-conserved and plant-specific TOR signalling components, uncovering an intriguing complex interplay with protein synthesis. Overall, the network provides a rich data set to start addressing fundamental questions about how TOR controls key processes in plants, such as autophagy, auxin signalling, chloroplast development, lipid metabolism, nucleotide biosynthesis, protein translation or senescence.
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Affiliation(s)
- Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Chao Han
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, College of Life Sciences, Shandong University, Jinan, China
| | - Astrid Gadeyne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Caroline Matthijs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Bernard Cannoot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Nancy De Winne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Geert Persiau
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Eveline Van De Slijke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Brigitte Van de Cotte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Elisabeth Stes
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Michiel Van Bel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Veronique Storme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Francis Impens
- Department of Biochemistry, Ghent University, Ghent, Belgium
- VIB Center for Medical Biotechnology, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium
- VIB Center for Medical Biotechnology, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
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13
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Van Dingenen J, Vermeersch M, De Milde L, Hulsmans S, De Winne N, Van Leene J, Gonzalez N, Dhondt S, De Jaeger G, Rolland F, Inzé D. The role of HEXOKINASE1 in Arabidopsis leaf growth. Plant Mol Biol 2019; 99:79-93. [PMID: 30511331 DOI: 10.1007/s11103-018-0803-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
Here, we used a hxk1 mutant in the Col-0 background. We demonstrated that HXK1 regulates cell proliferation and expansion early during leaf development, and that HXK1 is involved in sucrose-induced leaf growth stimulation independent of GPT2. Furthermore, we identified KINγ as a novel HXK1-interacting protein. In the last decade, extensive efforts have been made to unravel the underlying mechanisms of plant growth control through sugar availability. Signaling by the conserved glucose sensor HEXOKINASE1 (HXK1) has been shown to exert both growth-promoting and growth-inhibitory effects depending on the sugar levels, the environmental conditions and the plant species. Here, we used a hxk1 mutant in the Col-0 background to investigate the role of HXK1 during leaf growth in more detail and show that it is affected in both cell proliferation and cell expansion early during leaf development. Furthermore, the hxk1 mutant is less sensitive to sucrose-induced cell proliferation with no significant increase in final leaf growth after transfer to sucrose. Early during leaf development, transfer to sucrose stimulates expression of GLUCOSE-6-PHOSPHATE/PHOSPHATE TRANSPORTER2 (GPT2) and represses chloroplast differentiation. However, in the hxk1 mutant GPT2 expression was still upregulated by transfer to sucrose although chloroplast differentiation was not affected, suggesting that GPT2 is not involved in HXK1-dependent regulation of leaf growth. Finally, using tandem affinity purification of protein complexes from cell cultures, we identified KINγ, a protein containing four cystathionine β-synthase domains, as an interacting protein of HXK1.
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Affiliation(s)
- Judith Van Dingenen
- Center for Plant Systems Biology, VIB-Ghent University, Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Mattias Vermeersch
- Center for Plant Systems Biology, VIB-Ghent University, Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Liesbeth De Milde
- Center for Plant Systems Biology, VIB-Ghent University, Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Sander Hulsmans
- Laboratory of Molecular Plant Biology, KU Leuven Department of Biology, Kasteelpark Arenberg 31, 3001, Leuven, Belgium
| | - Nancy De Winne
- Center for Plant Systems Biology, VIB-Ghent University, Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Jelle Van Leene
- Center for Plant Systems Biology, VIB-Ghent University, Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Nathalie Gonzalez
- Center for Plant Systems Biology, VIB-Ghent University, Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Stijn Dhondt
- Center for Plant Systems Biology, VIB-Ghent University, Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Geert De Jaeger
- Center for Plant Systems Biology, VIB-Ghent University, Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Filip Rolland
- Laboratory of Molecular Plant Biology, KU Leuven Department of Biology, Kasteelpark Arenberg 31, 3001, Leuven, Belgium
| | - Dirk Inzé
- Center for Plant Systems Biology, VIB-Ghent University, Technologiepark 927, 9052, Gent, Belgium.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium.
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14
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Besbrugge N, Van Leene J, Eeckhout D, Cannoot B, Kulkarni SR, De Winne N, Persiau G, Van De Slijke E, Bontinck M, Aesaert S, Impens F, Gevaert K, Van Damme D, Van Lijsebettens M, Inzé D, Vandepoele K, Nelissen H, De Jaeger G. GS yellow, a Multifaceted Tag for Functional Protein Analysis in Monocot and Dicot Plants. Plant Physiol 2018; 177:447-464. [PMID: 29678859 PMCID: PMC6001315 DOI: 10.1104/pp.18.00175] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/01/2018] [Indexed: 05/04/2023]
Abstract
The ability to tag proteins has boosted the emergence of generic molecular methods for protein functional analysis. Fluorescent protein tags are used to visualize protein localization, and affinity tags enable the mapping of molecular interactions by, for example, tandem affinity purification or chromatin immunoprecipitation. To apply these widely used molecular techniques on a single transgenic plant line, we developed a multifunctional tandem affinity purification tag, named GSyellow, which combines the streptavidin-binding peptide tag with citrine yellow fluorescent protein. We demonstrated the versatility of the GSyellow tag in the dicot Arabidopsis (Arabidopsis thaliana) using a set of benchmark proteins. For proof of concept in monocots, we assessed the localization and dynamic interaction profile of the leaf growth regulator ANGUSTIFOLIA3 (AN3), fused to the GSyellow tag, along the growth zone of the maize (Zea mays) leaf. To further explore the function of ZmAN3, we mapped its DNA-binding landscape in the growth zone of the maize leaf through chromatin immunoprecipitation sequencing. Comparison with AN3 target genes mapped in the developing maize tassel or in Arabidopsis cell cultures revealed strong conservation of AN3 target genes between different maize tissues and across monocots and dicots, respectively. In conclusion, the GSyellow tag offers a powerful molecular tool for distinct types of protein functional analyses in dicots and monocots. As this approach involves transforming a single construct, it is likely to accelerate both basic and translational plant research.
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Affiliation(s)
- Nienke Besbrugge
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Bernard Cannoot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Shubhada R Kulkarni
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
| | - Nancy De Winne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Geert Persiau
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Eveline Van De Slijke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Michiel Bontinck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Stijn Aesaert
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Francis Impens
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
- VIB Center for Medical Biotechnology, 9000 Ghent, Belgium
- VIB Proteomics Core, 9000 Ghent, Belgium
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
- VIB Center for Medical Biotechnology, 9000 Ghent, Belgium
| | - Daniel Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Mieke Van Lijsebettens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
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15
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Bontinck M, Van Leene J, Gadeyne A, De Rybel B, Eeckhout D, Nelissen H, De Jaeger G. Recent Trends in Plant Protein Complex Analysis in a Developmental Context. Front Plant Sci 2018; 9:640. [PMID: 29868093 PMCID: PMC5962756 DOI: 10.3389/fpls.2018.00640] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/26/2018] [Indexed: 05/30/2023]
Abstract
Because virtually all proteins interact with other proteins, studying protein-protein interactions (PPIs) is fundamental in understanding protein function. This is especially true when studying specific developmental processes, in which proteins often make developmental stage- or tissue specific interactions. However, studying these specific PPIs in planta can be challenging. One of the most widely adopted methods to study PPIs in planta is affinity purification coupled to mass spectrometry (AP/MS). Recent developments in the field of mass spectrometry have boosted applications of AP/MS in a developmental context. This review covers two main advancements in the field of affinity purification to study plant developmental processes: increasing the developmental resolution of the harvested tissues and moving from affinity purification to affinity enrichment. Furthermore, we discuss some new affinity purification approaches that have recently emerged and could have a profound impact on the future of protein interactome analysis in plants.
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Affiliation(s)
- Michiel Bontinck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Flanders Institute for Biotechnology, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Flanders Institute for Biotechnology, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Astrid Gadeyne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Flanders Institute for Biotechnology, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Flanders Institute for Biotechnology, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Flanders Institute for Biotechnology, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Flanders Institute for Biotechnology, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Flanders Institute for Biotechnology, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
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16
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Vandereyken K, Van Leene J, De Coninck B, Cammue BPA. Hub Protein Controversy: Taking a Closer Look at Plant Stress Response Hubs. Front Plant Sci 2018; 9:694. [PMID: 29922309 PMCID: PMC5996676 DOI: 10.3389/fpls.2018.00694] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 05/07/2018] [Indexed: 05/20/2023]
Abstract
Plant stress responses involve numerous changes at the molecular and cellular level and are regulated by highly complex signaling pathways. Studying protein-protein interactions (PPIs) and the resulting networks is therefore becoming increasingly important in understanding these responses. Crucial in PPI networks are the so-called hubs or hub proteins, commonly defined as the most highly connected central proteins in scale-free PPI networks. However, despite their importance, a growing amount of confusion and controversy seems to exist regarding hub protein identification, characterization and classification. In order to highlight these inconsistencies and stimulate further clarification, this review critically analyses the current knowledge on hub proteins in the plant interactome field. We focus on current hub protein definitions, including the properties generally seen as hub-defining, and the challenges and approaches associated with hub protein identification. Furthermore, we give an overview of the most important large-scale plant PPI studies of the last decade that identified hub proteins, pointing out the lack of overlap between different studies. As such, it appears that although major advances are being made in the plant interactome field, defining hub proteins is still heavily dependent on the quality, origin and interpretation of the acquired PPI data. Nevertheless, many hub proteins seem to have a reported role in the plant stress response, including transcription factors, protein kinases and phosphatases, ubiquitin proteasome system related proteins, (co-)chaperones and redox signaling proteins. A significant number of identified plant stress hubs are however still functionally uncharacterized, making them interesting targets for future research. This review clearly shows the ongoing improvements in the plant interactome field but also calls attention to the need for a more comprehensive and precise identification of hub proteins, allowing a more efficient systems biology driven unraveling of complex processes, including those involved in stress responses.
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Affiliation(s)
- Katy Vandereyken
- Centre of Microbial and Plant Genetics, KU Leuven, Heverlee, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Jelle Van Leene
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Barbara De Coninck
- Centre of Microbial and Plant Genetics, KU Leuven, Heverlee, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Division of Crop Biotechnics, KU Leuven, Heverlee, Belgium
| | - Bruno P. A. Cammue
- Centre of Microbial and Plant Genetics, KU Leuven, Heverlee, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- *Correspondence: Bruno P. A. Cammue
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17
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Blomme J, Van Aken O, Van Leene J, Jégu T, De Rycke R, De Bruyne M, Vercruysse J, Nolf J, Van Daele T, De Milde L, Vermeersch M, des Francs-Small CC, De Jaeger G, Benhamed M, Millar AH, Inzé D, Gonzalez N. The Mitochondrial DNA-Associated Protein SWIB5 Influences mtDNA Architecture and Homologous Recombination. Plant Cell 2017; 29:1137-1156. [PMID: 28420746 PMCID: PMC5466028 DOI: 10.1105/tpc.16.00899] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 04/04/2017] [Accepted: 04/14/2017] [Indexed: 05/08/2023]
Abstract
In addition to the nucleus, mitochondria and chloroplasts in plant cells also contain genomes. Efficient DNA repair pathways are crucial in these organelles to fix damage resulting from endogenous and exogenous factors. Plant organellar genomes are complex compared with their animal counterparts, and although several plant-specific mediators of organelle DNA repair have been reported, many regulators remain to be identified. Here, we show that a mitochondrial SWI/SNF (nucleosome remodeling) complex B protein, SWIB5, is capable of associating with mitochondrial DNA (mtDNA) in Arabidopsis thaliana Gain- and loss-of-function mutants provided evidence for a role of SWIB5 in influencing mtDNA architecture and homologous recombination at specific intermediate-sized repeats both under normal and genotoxic conditions. SWIB5 interacts with other mitochondrial SWIB proteins. Gene expression and mutant phenotypic analysis of SWIB5 and SWIB family members suggests a link between organellar genome maintenance and cell proliferation. Taken together, our work presents a protein family that influences mtDNA architecture and homologous recombination in plants and suggests a link between organelle functioning and plant development.
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Affiliation(s)
- Jonas Blomme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Olivier Van Aken
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
- Department of Biology, Lund University, 226 52 Lund, Sweden
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Teddy Jégu
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, 91400 Orsay, France
- Molecular Biology Department, Simches Research Center, Boston, Massachusetts 02114
| | - Riet De Rycke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Michiel De Bruyne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jasmien Vercruysse
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jonah Nolf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Twiggy Van Daele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Liesbeth De Milde
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Mattias Vermeersch
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | | | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, 91400 Orsay, France
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Nathalie Gonzalez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- INRA, UMR 1332, Biologie du Fruit et Pathologie, CS20032 Villenave d'Ornon, France
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18
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Goossens J, De Geyter N, Walton A, Eeckhout D, Mertens J, Pollier J, Fiallos-Jurado J, De Keyser A, De Clercq R, Van Leene J, Gevaert K, De Jaeger G, Goormachtig S, Goossens A. Isolation of protein complexes from the model legume Medicago truncatula by tandem affinity purification in hairy root cultures. Plant J 2016; 88:476-489. [PMID: 27377668 DOI: 10.1111/tpj.13258] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 06/21/2016] [Accepted: 06/30/2016] [Indexed: 05/26/2023]
Abstract
Tandem affinity purification coupled to mass spectrometry (TAP-MS) is one of the most powerful techniques to isolate protein complexes and elucidate protein interaction networks. Here, we describe the development of a TAP-MS strategy for the model legume Medicago truncatula, which is widely studied for its ability to produce valuable natural products and to engage in endosymbiotic interactions. As biological material, transgenic hairy roots, generated through Agrobacterium rhizogenes-mediated transformation of M. truncatula seedlings, were used. As proof of concept, proteins involved in the cell cycle, transcript processing and jasmonate signalling were chosen as bait proteins, resulting in a list of putative interactors, many of which confirm the interologue concept of protein interactions, and which can contribute to biological information about the functioning of these bait proteins in planta. Subsequently, binary protein-protein interactions among baits and preys, and among preys were confirmed by a systematic yeast two-hybrid screen. Together, by establishing a M. truncatula TAP-MS platform, we extended the molecular toolbox of this model species.
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Affiliation(s)
- Jonas Goossens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Nathan De Geyter
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Alan Walton
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
- Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jan Mertens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jacob Pollier
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jennifer Fiallos-Jurado
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Annick De Keyser
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Rebecca De Clercq
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Sofie Goormachtig
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
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19
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Iñigo S, Durand AN, Ritter A, Le Gall S, Termathe M, Klassen R, Tohge T, De Coninck B, Van Leene J, De Clercq R, Cammue BPA, Fernie AR, Gevaert K, De Jaeger G, Leidel SA, Schaffrath R, Van Lijsebettens M, Pauwels L, Goossens A. Glutaredoxin GRXS17 Associates with the Cytosolic Iron-Sulfur Cluster Assembly Pathway. Plant Physiol 2016; 172:858-873. [PMID: 27503603 PMCID: PMC5047072 DOI: 10.1104/pp.16.00261] [Citation(s) in RCA: 14] [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] [Received: 02/19/2016] [Accepted: 08/03/2016] [Indexed: 05/12/2023]
Abstract
Cytosolic monothiol glutaredoxins (GRXs) are required in iron-sulfur (Fe-S) cluster delivery and iron sensing in yeast and mammals. In plants, it is unclear whether they have similar functions. Arabidopsis (Arabidopsis thaliana) has a sole class II cytosolic monothiol GRX encoded by GRXS17 Here, we used tandem affinity purification to establish that Arabidopsis GRXS17 associates with most known cytosolic Fe-S assembly (CIA) components. Similar to mutant plants with defective CIA components, grxs17 loss-of-function mutants showed some degree of hypersensitivity to DNA damage and elevated expression of DNA damage marker genes. We also found that several putative Fe-S client proteins directly bind to GRXS17, such as XANTHINE DEHYDROGENASE1 (XDH1), involved in the purine salvage pathway, and CYTOSOLIC THIOURIDYLASE SUBUNIT1 and CYTOSOLIC THIOURIDYLASE SUBUNIT2, both essential for the 2-thiolation step of 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) modification of tRNAs. Correspondingly, profiling of the grxs17-1 mutant pointed to a perturbed flux through the purine degradation pathway and revealed that it phenocopied mutants in the elongator subunit ELO3, essential for the mcm5 tRNA modification step, although we did not find XDH1 activity or tRNA thiolation to be markedly reduced in the grxs17-1 mutant. Taken together, our data suggest that plant cytosolic monothiol GRXs associate with the CIA complex, as in other eukaryotes, and contribute to, but are not essential for, the correct functioning of client Fe-S proteins in unchallenged conditions.
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Affiliation(s)
- Sabrina Iñigo
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Astrid Nagels Durand
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Andrés Ritter
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Sabine Le Gall
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Martin Termathe
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Roland Klassen
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Takayuki Tohge
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Barbara De Coninck
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Rebecca De Clercq
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Bruno P A Cammue
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Alisdair R Fernie
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Kris Gevaert
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Sebastian A Leidel
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Raffael Schaffrath
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Mieke Van Lijsebettens
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Laurens Pauwels
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
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Van Leene J, Blomme J, Kulkarni SR, Cannoot B, De Winne N, Eeckhout D, Persiau G, Van De Slijke E, Vercruysse L, Vanden Bossche R, Heyndrickx KS, Vanneste S, Goossens A, Gevaert K, Vandepoele K, Gonzalez N, Inzé D, De Jaeger G. Functional characterization of the Arabidopsis transcription factor bZIP29 reveals its role in leaf and root development. J Exp Bot 2016; 67:5825-5840. [PMID: 27660483 PMCID: PMC5066499 DOI: 10.1093/jxb/erw347] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [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: 05/18/2023]
Abstract
Plant bZIP group I transcription factors have been reported mainly for their role during vascular development and osmosensory responses. Interestingly, bZIP29 has been identified in a cell cycle interactome, indicating additional functions of bZIP29 in plant development. Here, bZIP29 was functionally characterized to study its role during plant development. It is not present in vascular tissue but is specifically expressed in proliferative tissues. Genome-wide mapping of bZIP29 target genes confirmed its role in stress and osmosensory responses, but also identified specific binding to several core cell cycle genes and to genes involved in cell wall organization. bZIP29 protein complex analyses validated interaction with other bZIP group I members and provided insight into regulatory mechanisms acting on bZIP dimers. In agreement with bZIP29 expression in proliferative tissues and with its binding to promoters of cell cycle regulators, dominant-negative repression of bZIP29 altered the cell number in leaves and in the root meristem. A transcriptome analysis on the root meristem, however, indicated that bZIP29 might regulate cell number through control of cell wall organization. Finally, ectopic dominant-negative repression of bZIP29 and redundant factors led to a seedling-lethal phenotype, pointing to essential roles for bZIP group I factors early in plant development.
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Affiliation(s)
- Jelle Van Leene
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Jonas Blomme
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Shubhada R Kulkarni
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Bernard Cannoot
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Nancy De Winne
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Geert Persiau
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Eveline Van De Slijke
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Leen Vercruysse
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Robin Vanden Bossche
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Ken S Heyndrickx
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Steffen Vanneste
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, B-9000 Gent, Belgium Department of Biochemistry, Ghent University, B-9000 Gent, Belgium
| | - Klaas Vandepoele
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Nathalie Gonzalez
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
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21
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Nagels Durand A, Iñigo S, Ritter A, Iniesto E, De Clercq R, Staes A, Van Leene J, Rubio V, Gevaert K, De Jaeger G, Pauwels L, Goossens A. The Arabidopsis Iron-Sulfur Protein GRXS17 is a Target of the Ubiquitin E3 Ligases RGLG3 and RGLG4. Plant Cell Physiol 2016; 57:1801-1813. [PMID: 27497447 DOI: 10.1093/pcp/pcw122] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/05/2016] [Indexed: 06/06/2023]
Abstract
The stability of signaling proteins in eukaryotes is often controlled by post-translational modifiers. For polyubiquitination, specificity is assured by E3 ubiquitin ligases. Although plant genomes encode hundreds of E3 ligases, only few targets are known, even in the model Arabidopsis thaliana. Here, we identified the monothiol glutaredoxin GRXS17 as a substrate of the Arabidopsis E3 ubiquitin ligases RING DOMAIN LIGASE 3 (RGLG3) and RGLG4 using a substrate trapping approach involving tandem affinity purification of RING-dead versions. Simultaneously, we used a ubiquitin-conjugating enzym (UBC) panel screen to pinpoint UBC30 as a cognate E2 UBC capable of interacting with RGLG3 and RGLG4 and mediating auto-ubiquitination of RGLG3 and ubiquitination of GRXS17 in vitro. Accordingly, GRXS17 is ubiquitinated and degraded in an RGLG3- and RGLG4-dependent manner in planta. The truncated hemoglobin GLB3 also interacted with RGLG3 and RGLG4 but appeared to obstruct RGLG3 ubiquitination activity rather than being its substrate. Our results suggest that the RGLG family is intimately linked to the essential element iron.
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Affiliation(s)
- Astrid Nagels Durand
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium These authors contributed equally to this work
| | - Sabrina Iñigo
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium These authors contributed equally to this work
| | - Andrés Ritter
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - Elisa Iniesto
- Plant Molecular Genetics Department, National Centre for Biotechnology (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Campus Universidad Autónoma, Madrid, Spain
| | - Rebecca De Clercq
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - An Staes
- Medical Biotechnology Center, VIB, B-9000 Ghent, Belgium Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - Vicente Rubio
- Plant Molecular Genetics Department, National Centre for Biotechnology (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Campus Universidad Autónoma, Madrid, Spain
| | - Kris Gevaert
- Medical Biotechnology Center, VIB, B-9000 Ghent, Belgium Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - Laurens Pauwels
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium These authors contributed equally to this work
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium These authors contributed equally to this work.
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22
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Dedecker M, Van Leene J, De Winne N, Eeckhout D, Persiau G, Van De Slijke E, Cannoot B, Vercruysse L, Dumoulin L, Wojsznis N, Gevaert K, Vandenabeele S, De Jaeger G. Transferring an optimized TAP-toolbox for the isolation of protein complexes to a portfolio of rice tissues. Plant Mol Biol 2016; 91:341-354. [PMID: 27003905 DOI: 10.1007/s11103-016-0471-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 03/10/2016] [Indexed: 06/05/2023]
Abstract
Proteins are the cell's functional entities. Rather than operating independently, they interact with other proteins. Capturing in vivo protein complexes is therefore crucial to gain understanding of the function of a protein in a cellular context. Affinity purification coupled to mass spectrometry has proven to yield a wealth of information about protein complex constitutions for a broad range of organisms. For Oryza sativa, the technique has been initiated in callus and shoots, but has not been optimized ever since. We translated an optimized tandem affinity purification (TAP) approach from Arabidopsis thaliana toward Oryza sativa, and demonstrate its applicability in a variety of rice tissues. A list of non-specific and false positive interactors is presented, based on re-occurrence over more than 170 independent experiments, to filter bona fide interactors. We demonstrate the sensitivity of our approach by isolating the complexes for the rice ANAPHASE PROMOTING COMPLEX SUBUNIT 10 (APC10) and CYCLIN-DEPENDENT KINASE D (CDKD) proteins from the proliferation zone of the emerging fourth leaf. Next to APC10 and CDKD, we tested several additional baits in the different rice tissues and reproducibly retrieved at least one interactor for 81.4 % of the baits screened for in callus tissue and T1 seedlings. By transferring an optimized TAP tag combined with state-of-the-art mass spectrometry, our TAP protocol enables the discovery of interactors for low abundance proteins in rice and opens the possibility to capture complex dynamics by comparing tissues at different stages of a developing rice organ.
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Affiliation(s)
- Maarten Dedecker
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
- CropDesign N.V., Technologiepark 21, 9052, Ghent, Belgium.
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Nancy De Winne
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Geert Persiau
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Eveline Van De Slijke
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Bernard Cannoot
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Leen Vercruysse
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Lies Dumoulin
- CropDesign N.V., Technologiepark 21, 9052, Ghent, Belgium
| | | | - Kris Gevaert
- Department of Medical Protein Research and Biochemistry, VIB, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
| | | | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
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23
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Pauwels L, Ritter A, Goossens J, Durand AN, Liu H, Gu Y, Geerinck J, Boter M, Vanden Bossche R, De Clercq R, Van Leene J, Gevaert K, De Jaeger G, Solano R, Stone S, Innes RW, Callis J, Goossens A. The RING E3 Ligase KEEP ON GOING Modulates JASMONATE ZIM-DOMAIN12 Stability. Plant Physiol 2015; 169:1405-17. [PMID: 26320228 PMCID: PMC4587444 DOI: 10.1104/pp.15.00479] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 08/27/2015] [Indexed: 05/20/2023]
Abstract
Jasmonate (JA) signaling in plants is mediated by the JASMONATE ZIM-DOMAIN (JAZ) proteins that repress the activity of several transcription factors regulating JA-inducible gene expression. The hormone JA-isoleucine triggers the interaction of JAZ repressor proteins with the F-box protein CORONATINE INSENSITIVE1 (COI1), part of an S-phase kinase-associated protein1/Cullin1/F-box protein COI1 (SCF(COI1)) E3 ubiquitin ligase complex, and their degradation by the 26S proteasome. In Arabidopsis (Arabidopsis thaliana), the JAZ family consists of 13 members. The level of redundancy or specificity among these members is currently not well understood. Here, we characterized JAZ12, encoded by a highly expressed JAZ gene. JAZ12 interacted with the transcription factors MYC2, MYC3, and MYC4 in vivo and repressed MYC2 activity. Using tandem affinity purification, we found JAZ12 to interact with SCF(COI1) components, matching with observed in vivo ubiquitination and with rapid degradation after treatment with JA. In contrast to the other JAZ proteins, JAZ12 also interacted directly with the E3 RING ligase KEEP ON GOING (KEG), a known repressor of the ABSCISIC ACID INSENSITIVE5 transcription factor in abscisic acid signaling. To study the functional role of this interaction, we circumvented the lethality of keg loss-of-function mutants by silencing KEG using an artificial microRNA approach. Abscisic acid treatment promoted JAZ12 degradation, and KEG knockdown led to a decrease in JAZ12 protein levels. Correspondingly, KEG overexpression was capable of partially inhibiting COI1-mediated JAZ12 degradation. Our results provide additional evidence for KEG as an important factor in plant hormone signaling and a positive regulator of JAZ12 stability.
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Affiliation(s)
- Laurens Pauwels
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Molecular and Cellular Biology, University of California, Davis, California 95616 (L.P., J.C.);Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2 (H.L., S.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Y.Gu, R.W.I.);Plant Molecular Genetics Department, National Centre for Biotechnology, Consejo Superior de Investigaciones Científicas, Campus University Autónoma, 28049 Madrid, Spain (M.B., R.S.);Department of Medical Protein Research, Flanders Institute for Biotechnology, 9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, 9000 Ghent, Belgium (K.G.)
| | - Andrés Ritter
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Molecular and Cellular Biology, University of California, Davis, California 95616 (L.P., J.C.);Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2 (H.L., S.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Y.Gu, R.W.I.);Plant Molecular Genetics Department, National Centre for Biotechnology, Consejo Superior de Investigaciones Científicas, Campus University Autónoma, 28049 Madrid, Spain (M.B., R.S.);Department of Medical Protein Research, Flanders Institute for Biotechnology, 9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, 9000 Ghent, Belgium (K.G.)
| | - Jonas Goossens
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Molecular and Cellular Biology, University of California, Davis, California 95616 (L.P., J.C.);Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2 (H.L., S.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Y.Gu, R.W.I.);Plant Molecular Genetics Department, National Centre for Biotechnology, Consejo Superior de Investigaciones Científicas, Campus University Autónoma, 28049 Madrid, Spain (M.B., R.S.);Department of Medical Protein Research, Flanders Institute for Biotechnology, 9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, 9000 Ghent, Belgium (K.G.)
| | - Astrid Nagels Durand
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Molecular and Cellular Biology, University of California, Davis, California 95616 (L.P., J.C.);Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2 (H.L., S.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Y.Gu, R.W.I.);Plant Molecular Genetics Department, National Centre for Biotechnology, Consejo Superior de Investigaciones Científicas, Campus University Autónoma, 28049 Madrid, Spain (M.B., R.S.);Department of Medical Protein Research, Flanders Institute for Biotechnology, 9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, 9000 Ghent, Belgium (K.G.)
| | - Hongxia Liu
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Molecular and Cellular Biology, University of California, Davis, California 95616 (L.P., J.C.);Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2 (H.L., S.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Y.Gu, R.W.I.);Plant Molecular Genetics Department, National Centre for Biotechnology, Consejo Superior de Investigaciones Científicas, Campus University Autónoma, 28049 Madrid, Spain (M.B., R.S.);Department of Medical Protein Research, Flanders Institute for Biotechnology, 9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, 9000 Ghent, Belgium (K.G.)
| | - Yangnan Gu
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Molecular and Cellular Biology, University of California, Davis, California 95616 (L.P., J.C.);Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2 (H.L., S.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Y.Gu, R.W.I.);Plant Molecular Genetics Department, National Centre for Biotechnology, Consejo Superior de Investigaciones Científicas, Campus University Autónoma, 28049 Madrid, Spain (M.B., R.S.);Department of Medical Protein Research, Flanders Institute for Biotechnology, 9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, 9000 Ghent, Belgium (K.G.)
| | - Jan Geerinck
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Molecular and Cellular Biology, University of California, Davis, California 95616 (L.P., J.C.);Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2 (H.L., S.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Y.Gu, R.W.I.);Plant Molecular Genetics Department, National Centre for Biotechnology, Consejo Superior de Investigaciones Científicas, Campus University Autónoma, 28049 Madrid, Spain (M.B., R.S.);Department of Medical Protein Research, Flanders Institute for Biotechnology, 9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, 9000 Ghent, Belgium (K.G.)
| | - Marta Boter
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Molecular and Cellular Biology, University of California, Davis, California 95616 (L.P., J.C.);Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2 (H.L., S.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Y.Gu, R.W.I.);Plant Molecular Genetics Department, National Centre for Biotechnology, Consejo Superior de Investigaciones Científicas, Campus University Autónoma, 28049 Madrid, Spain (M.B., R.S.);Department of Medical Protein Research, Flanders Institute for Biotechnology, 9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, 9000 Ghent, Belgium (K.G.)
| | - Robin Vanden Bossche
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Molecular and Cellular Biology, University of California, Davis, California 95616 (L.P., J.C.);Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2 (H.L., S.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Y.Gu, R.W.I.);Plant Molecular Genetics Department, National Centre for Biotechnology, Consejo Superior de Investigaciones Científicas, Campus University Autónoma, 28049 Madrid, Spain (M.B., R.S.);Department of Medical Protein Research, Flanders Institute for Biotechnology, 9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, 9000 Ghent, Belgium (K.G.)
| | - Rebecca De Clercq
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Molecular and Cellular Biology, University of California, Davis, California 95616 (L.P., J.C.);Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2 (H.L., S.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Y.Gu, R.W.I.);Plant Molecular Genetics Department, National Centre for Biotechnology, Consejo Superior de Investigaciones Científicas, Campus University Autónoma, 28049 Madrid, Spain (M.B., R.S.);Department of Medical Protein Research, Flanders Institute for Biotechnology, 9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, 9000 Ghent, Belgium (K.G.)
| | - Jelle Van Leene
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Molecular and Cellular Biology, University of California, Davis, California 95616 (L.P., J.C.);Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2 (H.L., S.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Y.Gu, R.W.I.);Plant Molecular Genetics Department, National Centre for Biotechnology, Consejo Superior de Investigaciones Científicas, Campus University Autónoma, 28049 Madrid, Spain (M.B., R.S.);Department of Medical Protein Research, Flanders Institute for Biotechnology, 9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, 9000 Ghent, Belgium (K.G.)
| | - Kris Gevaert
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Molecular and Cellular Biology, University of California, Davis, California 95616 (L.P., J.C.);Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2 (H.L., S.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Y.Gu, R.W.I.);Plant Molecular Genetics Department, National Centre for Biotechnology, Consejo Superior de Investigaciones Científicas, Campus University Autónoma, 28049 Madrid, Spain (M.B., R.S.);Department of Medical Protein Research, Flanders Institute for Biotechnology, 9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, 9000 Ghent, Belgium (K.G.)
| | - Geert De Jaeger
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Molecular and Cellular Biology, University of California, Davis, California 95616 (L.P., J.C.);Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2 (H.L., S.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Y.Gu, R.W.I.);Plant Molecular Genetics Department, National Centre for Biotechnology, Consejo Superior de Investigaciones Científicas, Campus University Autónoma, 28049 Madrid, Spain (M.B., R.S.);Department of Medical Protein Research, Flanders Institute for Biotechnology, 9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, 9000 Ghent, Belgium (K.G.)
| | - Roberto Solano
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Molecular and Cellular Biology, University of California, Davis, California 95616 (L.P., J.C.);Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2 (H.L., S.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Y.Gu, R.W.I.);Plant Molecular Genetics Department, National Centre for Biotechnology, Consejo Superior de Investigaciones Científicas, Campus University Autónoma, 28049 Madrid, Spain (M.B., R.S.);Department of Medical Protein Research, Flanders Institute for Biotechnology, 9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, 9000 Ghent, Belgium (K.G.)
| | - Sophia Stone
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Molecular and Cellular Biology, University of California, Davis, California 95616 (L.P., J.C.);Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2 (H.L., S.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Y.Gu, R.W.I.);Plant Molecular Genetics Department, National Centre for Biotechnology, Consejo Superior de Investigaciones Científicas, Campus University Autónoma, 28049 Madrid, Spain (M.B., R.S.);Department of Medical Protein Research, Flanders Institute for Biotechnology, 9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, 9000 Ghent, Belgium (K.G.)
| | - Roger W Innes
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Molecular and Cellular Biology, University of California, Davis, California 95616 (L.P., J.C.);Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2 (H.L., S.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Y.Gu, R.W.I.);Plant Molecular Genetics Department, National Centre for Biotechnology, Consejo Superior de Investigaciones Científicas, Campus University Autónoma, 28049 Madrid, Spain (M.B., R.S.);Department of Medical Protein Research, Flanders Institute for Biotechnology, 9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, 9000 Ghent, Belgium (K.G.)
| | - Judy Callis
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Molecular and Cellular Biology, University of California, Davis, California 95616 (L.P., J.C.);Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2 (H.L., S.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Y.Gu, R.W.I.);Plant Molecular Genetics Department, National Centre for Biotechnology, Consejo Superior de Investigaciones Científicas, Campus University Autónoma, 28049 Madrid, Spain (M.B., R.S.);Department of Medical Protein Research, Flanders Institute for Biotechnology, 9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, 9000 Ghent, Belgium (K.G.)
| | - Alain Goossens
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (L.P., A.R., J.Go., A.N.D., J.Ge., R.V.B., R.D.C., J.V.L., G.D.J., A.G.);Department of Molecular and Cellular Biology, University of California, Davis, California 95616 (L.P., J.C.);Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2 (H.L., S.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Y.Gu, R.W.I.);Plant Molecular Genetics Department, National Centre for Biotechnology, Consejo Superior de Investigaciones Científicas, Campus University Autónoma, 28049 Madrid, Spain (M.B., R.S.);Department of Medical Protein Research, Flanders Institute for Biotechnology, 9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, 9000 Ghent, Belgium (K.G.)
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24
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Gonzalez N, Pauwels L, Baekelandt A, De Milde L, Van Leene J, Besbrugge N, Heyndrickx KS, Cuéllar Pérez A, Durand AN, De Clercq R, Van De Slijke E, Vanden Bossche R, Eeckhout D, Gevaert K, Vandepoele K, De Jaeger G, Goossens A, Inzé D. A Repressor Protein Complex Regulates Leaf Growth in Arabidopsis. Plant Cell 2015; 27:2273-87. [PMID: 26232487 PMCID: PMC4568497 DOI: 10.1105/tpc.15.00006] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 06/15/2015] [Accepted: 07/16/2015] [Indexed: 05/18/2023]
Abstract
Cell number is an important determinant of final organ size. In the leaf, a large proportion of cells are derived from the stomatal lineage. Meristemoids, which are stem cell-like precursor cells, undergo asymmetric divisions, generating several pavement cells adjacent to the two guard cells. However, the mechanism controlling the asymmetric divisions of these stem cells prior to differentiation is not well understood. Here, we characterized PEAPOD (PPD) proteins, the only transcriptional regulators known to negatively regulate meristemoid division. PPD proteins interact with KIX8 and KIX9, which act as adaptor proteins for the corepressor TOPLESS. D3-type cyclin encoding genes were identified among direct targets of PPD2, being negatively regulated by PPDs and KIX8/9. Accordingly, kix8 kix9 mutants phenocopied PPD loss-of-function producing larger leaves resulting from increased meristemoid amplifying divisions. The identified conserved complex might be specific for leaf growth in the second dimension, since it is not present in Poaceae (grasses), which also lack the developmental program it controls.
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Affiliation(s)
- Nathalie Gonzalez
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Laurens Pauwels
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Alexandra Baekelandt
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Liesbeth De Milde
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Jelle Van Leene
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Nienke Besbrugge
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Ken S Heyndrickx
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Amparo Cuéllar Pérez
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Astrid Nagels Durand
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Rebecca De Clercq
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Eveline Van De Slijke
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Robin Vanden Bossche
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research and Biochemistry, VIB, 9000 Ghent, Belgium Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Alain Goossens
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
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25
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Nelissen H, Eeckhout D, Demuynck K, Persiau G, Walton A, van Bel M, Vervoort M, Candaele J, De Block J, Aesaert S, Van Lijsebettens M, Goormachtig S, Vandepoele K, Van Leene J, Muszynski M, Gevaert K, Inzé D, De Jaeger G. Dynamic Changes in ANGUSTIFOLIA3 Complex Composition Reveal a Growth Regulatory Mechanism in the Maize Leaf. Plant Cell 2015; 27:1605-19. [PMID: 26036253 PMCID: PMC4498210 DOI: 10.1105/tpc.15.00269] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/22/2015] [Indexed: 05/16/2023]
Abstract
Most molecular processes during plant development occur with a particular spatio-temporal specificity. Thus far, it has remained technically challenging to capture dynamic protein-protein interactions within a growing organ, where the interplay between cell division and cell expansion is instrumental. Here, we combined high-resolution sampling of the growing maize (Zea mays) leaf with tandem affinity purification followed by mass spectrometry. Our results indicate that the growth-regulating SWI/SNF chromatin remodeling complex associated with ANGUSTIFOLIA3 (AN3) was conserved within growing organs and between dicots and monocots. Moreover, we were able to demonstrate the dynamics of the AN3-interacting proteins within the growing leaf, since copurified GROWTH-REGULATING FACTORs (GRFs) varied throughout the growing leaf. Indeed, GRF1, GRF6, GRF7, GRF12, GRF15, and GRF17 were significantly enriched in the division zone of the growing leaf, while GRF4 and GRF10 levels were comparable between division zone and expansion zone in the growing leaf. These dynamics were also reflected at the mRNA and protein levels, indicating tight developmental regulation of the AN3-associated chromatin remodeling complex. In addition, the phenotypes of maize plants overexpressing miRNA396a-resistant GRF1 support a model proposing that distinct associations of the chromatin remodeling complex with specific GRFs tightly regulate the transition between cell division and cell expansion. Together, our data demonstrate that advancing from static to dynamic protein-protein interaction analysis in a growing organ adds insights in how developmental switches are regulated.
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Affiliation(s)
- Hilde Nelissen
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Kirin Demuynck
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Geert Persiau
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Alan Walton
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium Department of Medical Protein Research, VIB, 9000 Ghent, Belgium Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Michiel van Bel
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Marieke Vervoort
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Jasper Candaele
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Jolien De Block
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Stijn Aesaert
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Mieke Van Lijsebettens
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Sofie Goormachtig
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Klaas Vandepoele
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Michael Muszynski
- Department of Genetics, Development, and Cell Biology, Iowa State University, Iowa 50011-3268
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
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26
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Dedecker M, Van Leene J, De Jaeger G. Unravelling plant molecular machineries through affinity purification coupled to mass spectrometry. Curr Opin Plant Biol 2015; 24:1-9. [PMID: 25603557 DOI: 10.1016/j.pbi.2015.01.001] [Citation(s) in RCA: 14] [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] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/30/2014] [Accepted: 01/04/2015] [Indexed: 05/23/2023]
Abstract
Rather than functioning independently, proteins tend to work in concert with each other and with other macromolecules to form macromolecular complexes. Affinity purification coupled to mass spectrometry (AP-MS) can lead to a better understanding of the cellular functions of these complexes. With the development of easy purification protocols and ultra-sensitive MS, AP-MS is currently widely used for screening co-complex membership in plants. Studying complexes in their developmental context through the isolation of specific organs and tissues has now become feasible. Besides, the tagged protein can be employed for probing other interactions like protein-DNA and protein-RNA interactions. With the tools at hand, protein-centred interaction studies will greatly improve our knowledge of how plant cells wire their functional components in relation to their function.
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Affiliation(s)
- Maarten Dedecker
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; CropDesign N.V., Technologiepark 21, B-9052 Ghent, Belgium
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium.
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27
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Vieira P, De Clercq A, Stals H, Van Leene J, Van De Slijke E, Van Isterdael G, Eeckhout D, Persiau G, Van Damme D, Verkest A, Antonino de Souza JD, Júnior, Glab N, Abad P, Engler G, Inzé D, De Veylder L, De Jaeger G, Engler JDA. The Cyclin-Dependent Kinase Inhibitor KRP6 Induces Mitosis and Impairs Cytokinesis in Giant Cells Induced by Plant-Parasitic Nematodes in Arabidopsis. Plant Cell 2014; 26:2633-2647. [PMID: 24963053 PMCID: PMC4114956 DOI: 10.1105/tpc.114.126425] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 04/09/2014] [Accepted: 05/28/2014] [Indexed: 10/25/2023]
Abstract
In Arabidopsis thaliana, seven cyclin-dependent kinase (CDK) inhibitors have been identified, designated interactors of CDKs or Kip-related proteins (KRPs). Here, the function of KRP6 was investigated during cell cycle progression in roots infected by plant-parasitic root-knot nematodes. Contrary to expectations, analysis of Meloidogyne incognita-induced galls of KRP6-overexpressing lines revealed a role for this particular KRP as an activator of the mitotic cell cycle. In accordance, KRP6-overexpressing suspension cultures displayed accelerated entry into mitosis, but delayed mitotic progression. Likewise, phenotypic analysis of cultured cells and nematode-induced giant cells revealed a failure in mitotic exit, with the appearance of multinucleated cells as a consequence. Strong KRP6 expression upon nematode infection and the phenotypic resemblance between KRP6 overexpression cell cultures and root-knot morphology point toward the involvement of KRP6 in the multinucleate and acytokinetic state of giant cells. Along these lines, the parasite might have evolved to manipulate plant KRP6 transcription to the benefit of gall establishment.
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Affiliation(s)
- Paulo Vieira
- Institut National de la Recherche Agronomique, UMR 1355 ISA/Centre National de la Recherche Scientifique, UMR 7254 ISA/Université de Nice-Sophia Antipolis, UMR ISA, 400 route des Chappes, 06903 Sophia-Antipolis, France
| | - Annelies De Clercq
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Hilde Stals
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Jelle Van Leene
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Eveline Van De Slijke
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Gert Van Isterdael
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Geert Persiau
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Daniël Van Damme
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Aurine Verkest
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - José Dijair Antonino de Souza
- Institut National de la Recherche Agronomique, UMR 1355 ISA/Centre National de la Recherche Scientifique, UMR 7254 ISA/Université de Nice-Sophia Antipolis, UMR ISA, 400 route des Chappes, 06903 Sophia-Antipolis, France Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, Brasília, 70770-900 Distrito Federal, Brazil Institut de Biologie des Plantes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 8618, Université Paris-Sud, Saclay Plant Sciences, 91405 Orsay Cedex, France
| | - Júnior
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, Brasília, 70770-900 Distrito Federal, Brazil
| | - Nathalie Glab
- Institut de Biologie des Plantes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 8618, Université Paris-Sud, Saclay Plant Sciences, 91405 Orsay Cedex, France
| | - Pierre Abad
- Institut National de la Recherche Agronomique, UMR 1355 ISA/Centre National de la Recherche Scientifique, UMR 7254 ISA/Université de Nice-Sophia Antipolis, UMR ISA, 400 route des Chappes, 06903 Sophia-Antipolis, France
| | - Gilbert Engler
- Institut National de la Recherche Agronomique, UMR 1355 ISA/Centre National de la Recherche Scientifique, UMR 7254 ISA/Université de Nice-Sophia Antipolis, UMR ISA, 400 route des Chappes, 06903 Sophia-Antipolis, France
| | - Dirk Inzé
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Lieven De Veylder
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Janice de Almeida Engler
- Institut National de la Recherche Agronomique, UMR 1355 ISA/Centre National de la Recherche Scientifique, UMR 7254 ISA/Université de Nice-Sophia Antipolis, UMR ISA, 400 route des Chappes, 06903 Sophia-Antipolis, France
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28
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Verkest A, Abeel T, Heyndrickx KS, Van Leene J, Lanz C, Van De Slijke E, De Winne N, Eeckhout D, Persiau G, Van Breusegem F, Inzé D, Vandepoele K, De Jaeger G. A generic tool for transcription factor target gene discovery in Arabidopsis cell suspension cultures based on tandem chromatin affinity purification. Plant Physiol 2014; 164:1122-33. [PMID: 24453163 PMCID: PMC3938607 DOI: 10.1104/pp.113.229617] [Citation(s) in RCA: 18] [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] [Received: 10/01/2013] [Accepted: 01/20/2014] [Indexed: 05/20/2023]
Abstract
Genome-wide identification of transcription factor (TF) binding sites is pivotal to our understanding of gene expression regulation. Although much progress has been made in the determination of potential binding regions of proteins by chromatin immunoprecipitation, this method has some inherent limitations regarding DNA enrichment efficiency and antibody necessity. Here, we report an alternative strategy for assaying in vivo TF-DNA binding in Arabidopsis (Arabidopsis thaliana) cells by tandem chromatin affinity purification (TChAP). Evaluation of TChAP using the E2Fa TF and comparison with traditional chromatin immunoprecipitation and single chromatin affinity purification illustrates the suitability of TChAP and provides a resource for exploring the E2Fa transcriptional network. Integration with transcriptome, cis-regulatory element, functional enrichment, and coexpression network analyses demonstrates the quality of the E2Fa TChAP sequencing data and validates the identification of new direct E2Fa targets. TChAP enhances both TF target mapping throughput, by circumventing issues related to antibody availability, and output, by improving DNA enrichment efficiency.
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Affiliation(s)
- Aurine Verkest
- Department of Plant Systems Biology, VIB, B–9052 Ghent, Belgium (A.V., T.A., K.S.H., J.V.L., E.V.D.S., N.D.W., D.E., G.P., F.V.B., D.I., K.V., G.D.J.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B–9052 Ghent, Belgium (A.V., T.A., K.S.H., J.V.L., E.V.D.S., N.D.W., D.E., G.P., F.V.B., D.I., K.V., G.D.J.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | | | - Ken S. Heyndrickx
- Department of Plant Systems Biology, VIB, B–9052 Ghent, Belgium (A.V., T.A., K.S.H., J.V.L., E.V.D.S., N.D.W., D.E., G.P., F.V.B., D.I., K.V., G.D.J.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B–9052 Ghent, Belgium (A.V., T.A., K.S.H., J.V.L., E.V.D.S., N.D.W., D.E., G.P., F.V.B., D.I., K.V., G.D.J.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, B–9052 Ghent, Belgium (A.V., T.A., K.S.H., J.V.L., E.V.D.S., N.D.W., D.E., G.P., F.V.B., D.I., K.V., G.D.J.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B–9052 Ghent, Belgium (A.V., T.A., K.S.H., J.V.L., E.V.D.S., N.D.W., D.E., G.P., F.V.B., D.I., K.V., G.D.J.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Christa Lanz
- Department of Plant Systems Biology, VIB, B–9052 Ghent, Belgium (A.V., T.A., K.S.H., J.V.L., E.V.D.S., N.D.W., D.E., G.P., F.V.B., D.I., K.V., G.D.J.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B–9052 Ghent, Belgium (A.V., T.A., K.S.H., J.V.L., E.V.D.S., N.D.W., D.E., G.P., F.V.B., D.I., K.V., G.D.J.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Eveline Van De Slijke
- Department of Plant Systems Biology, VIB, B–9052 Ghent, Belgium (A.V., T.A., K.S.H., J.V.L., E.V.D.S., N.D.W., D.E., G.P., F.V.B., D.I., K.V., G.D.J.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B–9052 Ghent, Belgium (A.V., T.A., K.S.H., J.V.L., E.V.D.S., N.D.W., D.E., G.P., F.V.B., D.I., K.V., G.D.J.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Nancy De Winne
- Department of Plant Systems Biology, VIB, B–9052 Ghent, Belgium (A.V., T.A., K.S.H., J.V.L., E.V.D.S., N.D.W., D.E., G.P., F.V.B., D.I., K.V., G.D.J.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B–9052 Ghent, Belgium (A.V., T.A., K.S.H., J.V.L., E.V.D.S., N.D.W., D.E., G.P., F.V.B., D.I., K.V., G.D.J.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, B–9052 Ghent, Belgium (A.V., T.A., K.S.H., J.V.L., E.V.D.S., N.D.W., D.E., G.P., F.V.B., D.I., K.V., G.D.J.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B–9052 Ghent, Belgium (A.V., T.A., K.S.H., J.V.L., E.V.D.S., N.D.W., D.E., G.P., F.V.B., D.I., K.V., G.D.J.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Geert Persiau
- Department of Plant Systems Biology, VIB, B–9052 Ghent, Belgium (A.V., T.A., K.S.H., J.V.L., E.V.D.S., N.D.W., D.E., G.P., F.V.B., D.I., K.V., G.D.J.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B–9052 Ghent, Belgium (A.V., T.A., K.S.H., J.V.L., E.V.D.S., N.D.W., D.E., G.P., F.V.B., D.I., K.V., G.D.J.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, B–9052 Ghent, Belgium (A.V., T.A., K.S.H., J.V.L., E.V.D.S., N.D.W., D.E., G.P., F.V.B., D.I., K.V., G.D.J.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B–9052 Ghent, Belgium (A.V., T.A., K.S.H., J.V.L., E.V.D.S., N.D.W., D.E., G.P., F.V.B., D.I., K.V., G.D.J.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, B–9052 Ghent, Belgium (A.V., T.A., K.S.H., J.V.L., E.V.D.S., N.D.W., D.E., G.P., F.V.B., D.I., K.V., G.D.J.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B–9052 Ghent, Belgium (A.V., T.A., K.S.H., J.V.L., E.V.D.S., N.D.W., D.E., G.P., F.V.B., D.I., K.V., G.D.J.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
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Fonseca S, Fernández-Calvo P, Fernández GM, Díez-Díaz M, Gimenez-Ibanez S, López-Vidriero I, Godoy M, Fernández-Barbero G, Van Leene J, De Jaeger G, Franco-Zorrilla JM, Solano R. bHLH003, bHLH013 and bHLH017 are new targets of JAZ repressors negatively regulating JA responses. PLoS One 2014; 9:e86182. [PMID: 24465948 PMCID: PMC3900477 DOI: 10.1371/journal.pone.0086182] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [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: 10/17/2013] [Accepted: 12/06/2013] [Indexed: 11/19/2022] Open
Abstract
Cell reprogramming in response to jasmonates requires a tight control of transcription that is achieved by the activity of JA-related transcription factors (TFs). Among them, MYC2, MYC3 and MYC4 have been described as activators of JA responses. Here we characterized the function of bHLH003, bHLH013 and bHLH017 that conform a phylogenetic clade closely related to MYC2, MYC3 and MYC4. We found that these bHLHs form homo- and heterodimers and also interact with JAZ repressors in vitro and in vivo. Phenotypic analysis of JA-regulated processes, including root and rosette growth, anthocyanin accumulation, chlorophyll loss and resistance to Pseudomonas syringae, on mutants and overexpression lines, suggested that these bHLHs are repressors of JA responses. bHLH003, bHLH013 and bHLH017 are mainly nuclear proteins and bind DNA with similar specificity to that of MYC2, MYC3 and MYC4, but lack a conserved activation domain, suggesting that repression is achieved by competition for the same cis-regulatory elements. Moreover, expression of bHLH017 is induced by JA and depends on MYC2, suggesting a negative feed-back regulation of the activity of positive JA-related TFs. Our results suggest that the competition between positive and negative TFs determines the output of JA-dependent transcriptional activation.
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Affiliation(s)
- Sandra Fonseca
- Departamento de Genetica Molecular de Plantas, Centro Nacional de Biotecnología–Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, Madrid, Spain
| | - Patricia Fernández-Calvo
- Departamento de Genetica Molecular de Plantas, Centro Nacional de Biotecnología–Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, Madrid, Spain
| | - Guillermo M. Fernández
- Departamento de Genetica Molecular de Plantas, Centro Nacional de Biotecnología–Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, Madrid, Spain
| | - Monica Díez-Díaz
- Departamento de Genetica Molecular de Plantas, Centro Nacional de Biotecnología–Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, Madrid, Spain
| | - Selena Gimenez-Ibanez
- Departamento de Genetica Molecular de Plantas, Centro Nacional de Biotecnología–Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, Madrid, Spain
| | - Irene López-Vidriero
- Genomics Unit, Centro Nacional de Biotecnología–Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, Madrid, Spain
| | - Marta Godoy
- Genomics Unit, Centro Nacional de Biotecnología–Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, Madrid, Spain
| | - Gemma Fernández-Barbero
- Departamento de Genetica Molecular de Plantas, Centro Nacional de Biotecnología–Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, Madrid, Spain
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - José Manuel Franco-Zorrilla
- Genomics Unit, Centro Nacional de Biotecnología–Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, Madrid, Spain
| | - Roberto Solano
- Departamento de Genetica Molecular de Plantas, Centro Nacional de Biotecnología–Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, Madrid, Spain
- * E-mail:
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Vercruyssen L, Verkest A, Gonzalez N, Heyndrickx KS, Eeckhout D, Han SK, Jégu T, Archacki R, Van Leene J, Andriankaja M, De Bodt S, Abeel T, Coppens F, Dhondt S, De Milde L, Vermeersch M, Maleux K, Gevaert K, Jerzmanowski A, Benhamed M, Wagner D, Vandepoele K, De Jaeger G, Inzé D. ANGUSTIFOLIA3 binds to SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development. Plant Cell 2014; 26:210-29. [PMID: 24443518 PMCID: PMC3963571 DOI: 10.1105/tpc.113.115907] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 12/16/2013] [Accepted: 12/24/2013] [Indexed: 05/18/2023]
Abstract
The transcriptional coactivator ANGUSTIFOLIA3 (AN3) stimulates cell proliferation during Arabidopsis thaliana leaf development, but the molecular mechanism is largely unknown. Here, we show that inducible nuclear localization of AN3 during initial leaf growth results in differential expression of important transcriptional regulators, including GROWTH REGULATING FACTORs (GRFs). Chromatin purification further revealed the presence of AN3 at the loci of GRF5, GRF6, CYTOKININ RESPONSE FACTOR2, CONSTANS-LIKE5 (COL5), HECATE1 (HEC1), and ARABIDOPSIS RESPONSE REGULATOR4 (ARR4). Tandem affinity purification of protein complexes using AN3 as bait identified plant SWITCH/SUCROSE NONFERMENTING (SWI/SNF) chromatin remodeling complexes formed around the ATPases BRAHMA (BRM) or SPLAYED. Moreover, SWI/SNF ASSOCIATED PROTEIN 73B (SWP73B) is recruited by AN3 to the promoters of GRF5, GRF3, COL5, and ARR4, and both SWP73B and BRM occupy the HEC1 promoter. Furthermore, we show that AN3 and BRM genetically interact. The data indicate that AN3 associates with chromatin remodelers to regulate transcription. In addition, modification of SWI3C expression levels increases leaf size, underlining the importance of chromatin dynamics for growth regulation. Our results place the SWI/SNF-AN3 module as a major player at the transition from cell proliferation to cell differentiation in a developing leaf.
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Affiliation(s)
- Liesbeth Vercruyssen
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Aurine Verkest
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Nathalie Gonzalez
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Ken S. Heyndrickx
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Soon-Ki Han
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Teddy Jégu
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618, Université Paris-Sud XI, 91405 Orsay, France
| | - Rafal Archacki
- Laboratory of Plant Molecular Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Megan Andriankaja
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Stefanie De Bodt
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Thomas Abeel
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Frederik Coppens
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Stijn Dhondt
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Liesbeth De Milde
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Mattias Vermeersch
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Katrien Maleux
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research and Biochemistry, VIB, 90 00 Ghent, Belgium
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Andrzej Jerzmanowski
- Laboratory of Plant Molecular Biology, University of Warsaw, 02-106 Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Moussa Benhamed
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618, Université Paris-Sud XI, 91405 Orsay, France
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Klaas Vandepoele
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Address correspondence to
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Nodzynski T, Feraru MI, Hirsch S, De Rycke R, Niculaes C, Boerjan W, Van Leene J, De Jaeger G, Vanneste S, Friml J. Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. Mol Plant 2013; 6:1849-62. [PMID: 23770835 DOI: 10.1093/mp/sst044] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Intracellular protein routing is mediated by vesicular transport which is tightly regulated in eukaryotes. The protein and lipid homeostasis depends on coordinated delivery of de novo synthesized or recycled cargoes to the plasma membrane by exocytosis and their subsequent removal by rerouting them for recycling or degradation. Here, we report the characterization of protein affected trafficking 3 (pat3) mutant that we identified by an epifluorescence-based forward genetic screen for mutants defective in subcellular distribution of Arabidopsis auxin transporter PIN1-GFP. While pat3 displays largely normal plant morphology and development in nutrient-rich conditions, it shows strong ectopic intracellular accumulations of different plasma membrane cargoes in structures that resemble prevacuolar compartments (PVC) with an aberrant morphology. Genetic mapping revealed that pat3 is defective in vacuolar protein sorting 35A (VPS35A), a putative subunit of the retromer complex that mediates retrograde trafficking between the PVC and trans-Golgi network. Similarly, a mutant defective in another retromer subunit, vps29, shows comparable subcellular defects in PVC morphology and protein accumulation. Thus, our data provide evidence that the retromer components VPS35A and VPS29 are essential for normal PVC morphology and normal trafficking of plasma membrane proteins in plants. In addition, we show that, out of the three VPS35 retromer subunits present in Arabidopsis thaliana genome, the VPS35 homolog A plays a prevailing role in trafficking to the lytic vacuole, presenting another level of complexity in the retromer-dependent vacuolar sorting.
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Affiliation(s)
- Tomasz Nodzynski
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University (MU), Kamenice 5, CZ-625 00, Brno, Czech Republic
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Heyman J, Cools T, Vandenbussche F, Heyndrickx KS, Van Leene J, Vercauteren I, Vanderauwera S, Vandepoele K, De Jaeger G, Van Der Straeten D, De Veylder L. ERF115 controls root quiescent center cell division and stem cell replenishment. Science 2013; 342:860-3. [PMID: 24158907 DOI: 10.1126/science.1240667] [Citation(s) in RCA: 186] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The quiescent center (QC) plays an essential role during root development by creating a microenvironment that preserves the stem cell fate of its surrounding cells. Despite being surrounded by highly mitotic active cells, QC cells self-renew at a low proliferation rate. Here, we identified the ERF115 transcription factor as a rate-limiting factor of QC cell division, acting as a transcriptional activator of the phytosulfokine PSK5 peptide hormone. ERF115 marks QC cell division but is restrained through proteolysis by the APC/C(CCS52A2) ubiquitin ligase, whereas QC proliferation is driven by brassinosteroid-dependent ERF115 expression. Together, these two antagonistic mechanisms delimit ERF115 activity, which is called upon when surrounding stem cells are damaged, revealing a cell cycle regulatory mechanism accounting for stem cell niche longevity.
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Affiliation(s)
- Jefri Heyman
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
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Abstract
Protein-protein interactions are a critical element of biological systems, and the analysis of interaction partners can provide valuable hints about unknown functions of a protein. In recent years, several large-scale protein interaction studies have begun to unravel the complex networks through which plant proteins exert their functions. Two major classes of experimental approaches are used for protein interaction mapping: analysis of direct interactions using binary methods such as yeast two-hybrid or split ubiquitin, and analysis of protein complexes through affinity purification followed by mass spectrometry. In addition, bioinformatics predictions can suggest interactions that have evaded detection by other methods or those of proteins that have not been investigated. Here we review the major approaches to construct, analyze, use, and carry out quality control on plant protein interactome networks. We present experimental and computational approaches for large-scale mapping, methods for validation or smaller-scale functional studies, important bioinformatics resources, and findings from recently published large-scale plant interactome network maps.
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Affiliation(s)
- Pascal Braun
- Department of Plant Systems Biology, Center for Life and Food Sciences Weihenstephan, Technische Universität München (TUM), 85354 Freising-Weihenstephan, Germany.
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Van Leene J, Hollunder J, Eeckhout D, Persiau G, Van De Slijke E, Stals H, Van Isterdael G, Verkest A, Neirynck S, Buffel Y, De Bodt S, Maere S, Laukens K, Pharazyn A, Ferreira PCG, Eloy N, Renne C, Meyer C, Faure JD, Steinbrenner J, Beynon J, Larkin JC, Van de Peer Y, Hilson P, Kuiper M, De Veylder L, Van Onckelen H, Inzé D, Witters E, De Jaeger G. Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Mol Syst Biol 2011; 6:397. [PMID: 20706207 PMCID: PMC2950081 DOI: 10.1038/msb.2010.53] [Citation(s) in RCA: 271] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Accepted: 06/12/2010] [Indexed: 12/27/2022] Open
Abstract
A protein interactome focused towards cell proliferation was mapped comprising 857 interactions among 393 proteins, leading to many new insights in plant cell cycle regulation. A comprehensive view on heterodimeric cyclin-dependent kinase (CDK)/cyclin complexes in plants is obtained, in relation with their regulators. Over 100 new candidate cell cycle proteins were predicted.
The basic underlying mechanisms that govern the cell cycle are conserved among all eukaryotes. Peculiar for plants, however, is that their genome contains a collection of cell cycle regulatory genes that is intriguingly large (Vandepoele et al, 2002; Menges et al, 2005) compared to other eukaryotes. Arabidopsis thaliana (Arabidopsis) encodes 71 genes in five regulatory classes versus only 15 in yeast and 23 in human. Despite the discovery of numerous cell cycle genes, little is known about the protein complex machinery that steers plant cell division. Therefore, we applied tandem affinity purification (TAP) approach coupled with mass spectrometry (MS) on Arabidopsis cell suspension cultures to isolate and analyze protein complexes involved in the cell cycle. This approach allowed us to successfully map a first draft of the basic cell cycle complex machinery of Arabidopsis, providing many new insights into plant cell division. To map the interactome, we relied on a streamlined platform comprising generic Gateway-based vectors with high cloning flexibility, the fast generation of transgenic suspension cultures, TAP adapted for plant cells, and matrix-assisted laser desorption ionization (MALDI) tandem-MS for the identification of purified proteins (Van Leene et al, 2007, 2008Van Leene et al, 2007, 2008). Complexes for 102 cell cycle proteins were analyzed using this approach, leading to a non-redundant data set of 857 interactions among 393 proteins (Figure 1A). Two subspaces were identified in this data set, domain I1, containing interactions confirmed in at least two independent experimental repeats or in the reciprocal purification experiment, and domain I2 consisting of uniquely observed interactions. Several observations underlined the quality of both domains. All tested reverse purifications found the original interaction, and 150 known or predicted interactions were confirmed, meaning that also a huge stack of new interactions was revealed. An in-depth computational analysis revealed enrichment for many cell cycle-related features among the proteins of the network (Figure 1B), and many protein pairs were coregulated at the transcriptional level (Figure 1C). Through integration of known cell cycle-related features, more than 100 new candidate cell cycle proteins were predicted (Figure 1D). Besides common qualities of both interactome domains, their real significance appeared through mutual differences exposing two subspaces in the cell cycle interactome: a central regulatory network of stable complexes that are repeatedly isolated and represent core regulatory units, and a peripheral network comprising transient interactions identified less frequently, which are involved in other aspects of the process, such as crosstalk between core complexes or connections with other pathways. To evaluate the biological relevance of the cell cycle interactome in plants, we validated interactions from both domains by a transient split-luciferase assay in Arabidopsis plants (Marion et al, 2008), further sustaining the hypothesis-generating power of the data set to understand plant growth. With respect to insights into the cell cycle physiology, the interactome was subdivided according to the functional classes of the baits and core protein complexes were extracted, covering cyclin-dependent kinase (CDK)/cyclin core complexes together with their positive and negative regulation networks, DNA replication complexes, the anaphase-promoting complex, and spindle checkpoint complexes. The data imply that mitotic A- and B-type cyclins exclusively form heterodimeric complexes with the plant-specific B-type CDKs and not with CDKA;1, whereas D-type cyclins seem to associate with CDKA;1. Besides the extraction of complexes previously shown in other organisms, our data also suggested many new functional links; for example, the link coupling cell division with the regulation of transcript splicing. The association of negative regulators of CDK/cyclin complexes with transcription factors suggests that their role in reallocation is not solely targeted to CDK/cyclin complexes. New members of the Siamese-related inhibitory proteins were identified, and for the first time potential inhibitors of plant-specific mitotic B-type CDKs have been found in plants. New evidence that the E2F–DP–RBR network is not only active at G1-to-S, but also at the G2-to-M transition is provided and many complexes involved in DNA replication or repair were isolated. For the first time, a plant APC has been isolated biochemically, identifying three potential new plant-specific APC interactors, and finally, complexes involved in the spindle checkpoint were isolated mapping many new but specific interactions. Finally, to get a general view on the complex machinery, modules of interacting cyclins and core cell cycle regulators were ranked along the cell cycle phases according to the transcript expression peak of the cyclins, showing an assorted set of CDK–cyclin complexes with high regulatory differentiation (Figure 4). Even within the same subfamily (e.g. cyclin A3, B1, B2, D3, and D4), cyclins differ not only in their functional time frame but also in the type and number of CDKs, inhibitors, and scaffolding proteins they bind, further indicating their functional diversification. According to our interaction data, at least 92 different variants of CDK–cyclin complexes are found in Arabidopsis. In conclusion, these results reflect how several rounds of gene duplication (Sterck et al, 2007) led to the evolution of a large set of cyclin paralogs and a myriad of regulators, resulting in a significant jump in the complexity of the cell cycle machinery that could accommodate unique plant-specific features such as an indeterminate mode of postembryonic development. Through their extensive regulation and connection with a myriad of up- and downstream pathways, the core cell cycle complexes might offer the plant a flexible toolkit to fine-tune cell proliferation in response to an ever-changing environment. Cell proliferation is the main driving force for plant growth. Although genome sequence analysis revealed a high number of cell cycle genes in plants, little is known about the molecular complexes steering cell division. In a targeted proteomics approach, we mapped the core complex machinery at the heart of the Arabidopsis thaliana cell cycle control. Besides a central regulatory network of core complexes, we distinguished a peripheral network that links the core machinery to up- and downstream pathways. Over 100 new candidate cell cycle proteins were predicted and an in-depth biological interpretation demonstrated the hypothesis-generating power of the interaction data. The data set provided a comprehensive view on heterodimeric cyclin-dependent kinase (CDK)–cyclin complexes in plants. For the first time, inhibitory proteins of plant-specific B-type CDKs were discovered and the anaphase-promoting complex was characterized and extended. Important conclusions were that mitotic A- and B-type cyclins form complexes with the plant-specific B-type CDKs and not with CDKA;1, and that D-type cyclins and S-phase-specific A-type cyclins seem to be associated exclusively with CDKA;1. Furthermore, we could show that plants have evolved a combinatorial toolkit consisting of at least 92 different CDK–cyclin complex variants, which strongly underscores the functional diversification among the large family of cyclins and reflects the pivotal role of cell cycle regulation in the developmental plasticity of plants.
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Van Leene J, Boruc J, De Jaeger G, Russinova E, De Veylder L. A kaleidoscopic view of the Arabidopsis core cell cycle interactome. Trends Plant Sci 2011; 16:141-50. [PMID: 21233003 DOI: 10.1016/j.tplants.2010.12.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 11/24/2010] [Accepted: 12/10/2010] [Indexed: 05/20/2023]
Abstract
Although protein-protein interaction (PPI) networks have been shown to offer a systems-wide view of cellular processes, only a few plant PPI maps are available. Recently, the core cell cycle of Arabidopsis thaliana has been analyzed by three independent PPI technologies, including yeast two-hybrid systems, bimolecular fluorescence complementation and tandem affinity purification. Here, we merge the three interactomes with literature-curated and computationally predicted interactions, paving the way for a comprehensive picture of the plant core cell cycle machinery. Platform-specific interactions unveil the strengths and weaknesses of each detection method and give insights into the nature of the interactions among cell cycle proteins. Moreover, comparison of the obtained data reveals that a complete interactome can only be obtained when multiple techniques are applied in parallel.
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Affiliation(s)
- Jelle Van Leene
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium.
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Van Leene J, Eeckhout D, Persiau G, Van De Slijke E, Geerinck J, Van Isterdael G, Witters E, De Jaeger G. Isolation of transcription factor complexes from Arabidopsis cell suspension cultures by tandem affinity purification. Methods Mol Biol 2011; 754:195-218. [PMID: 21720954 DOI: 10.1007/978-1-61779-154-3_11] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [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: 12/22/2022]
Abstract
Defining protein complexes is critical to virtually all aspects of cell biology because most cellular processes are regulated by stable or more dynamic protein interactions. Elucidation of the protein-protein interaction network around transcription factors is essential to fully understand their function and regulation. In the last decade, new technologies have emerged to study protein-protein interactions under near-physiological conditions. We have developed a high-throughput tandem affinity purification (TAP)/mass spectrometry (MS) platform for cell suspension cultures to analyze protein complexes in Arabidopsis thaliana. This streamlined platform follows an integrated approach comprising generic Gateway-based vectors with high cloning flexibility, the fast generation of transgenic suspension cultures, TAP adapted for plant cells, and tandem matrix-assisted laser desorption ionization MS for the identification of purified proteins. Recently, we evaluated the GS tag, originally developed to study mammalian protein complexes, that combines two IgG-binding domains of protein G with a streptavidin-binding peptide, separated by two tobacco etch virus cleavage sites. We found that this GS tag outperforms the traditional TAP tag in plant cells, regarding both specificity and complex yield. Here, we provide detailed protocols of the GS-based TAP platform that allowed us to characterize transcription factor complexes involved in signaling in response to the plant phytohormone jasmonate.
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Affiliation(s)
- Jelle Van Leene
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, Gent, Belgium.
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Boudolf V, Lammens T, Boruc J, Van Leene J, Van Den Daele H, Maes S, Van Isterdael G, Russinova E, Kondorosi E, Witters E, De Jaeger G, Inzé D, De Veylder L. CDKB1;1 forms a functional complex with CYCA2;3 to suppress endocycle onset. Plant Physiol 2009; 150:1482-93. [PMID: 19458112 PMCID: PMC2705057 DOI: 10.1104/pp.109.140269] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Accepted: 05/15/2009] [Indexed: 05/19/2023]
Abstract
The mitosis-to-endocycle transition requires the controlled inactivation of M phase-associated cyclin-dependent kinase (CDK) activity. Previously, the B-type CDKB1;1 was identified as an important negative regulator of endocycle onset. Here, we demonstrate that CDKB1;1 copurifies and associates with the A2-type cyclin CYCA2;3. Coexpression of CYCA2;3 with CDKB1;1 triggered ectopic cell divisions and inhibited endoreduplication. Moreover, the enhanced endoreduplication phenotype observed after overexpression of a dominant-negative allele of CDKB1;1 could be partially complemented by CYCA2;3 co-overexpression, illustrating that both subunits unite in vivo to form a functional complex. CYCA2;3 protein stability was found to be controlled by CCS52A1, an activator of the anaphase-promoting complex. We conclude that CCS52A1 participates in endocycle onset by down-regulating CDKB1;1 activity through the destruction of CYCA2;3.
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Affiliation(s)
- Véronique Boudolf
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium
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Remmerie N, Roef L, Van De Slijke E, Van Leene J, Persiau G, Eeckhout D, Stals H, Laukens K, Lemière F, Esmans E, Van Onckelen H, Inzé D, De Jaeger G, Witters E. A bioanalytical method for the proteome wide display and analysis of protein complexes from whole plant cell lysates. Proteomics 2009. [DOI: 10.1002/pmic.200990016] [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: 11/06/2022]
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Remmerie N, Roef L, Van De Slijke E, Van Leene J, Persiau G, Eeckhout D, Stals H, Laukens K, Lemière F, Esmans E, Van Onckelen H, Inzé D, De Jaeger G, Witters E. A bioanalytical method for the proteome wide display and analysis of protein complexes from whole plant cell lysates. Proteomics 2009; 9:598-609. [DOI: 10.1002/pmic.200800100] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Wabnik K, Hvidsten TR, Kedzierska A, Van Leene J, De Jaeger G, Beemster GTS, Komorowski J, Kuiper MTR. Gene expression trends and protein features effectively complement each other in gene function prediction. ACTA ACUST UNITED AC 2008; 25:322-30. [PMID: 19050035 DOI: 10.1093/bioinformatics/btn625] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION Genome-scale 'omics' data constitute a potentially rich source of information about biological systems and their function. There is a plethora of tools and methods available to mine omics data. However, the diversity and complexity of different omics data types is a stumbling block for multi-data integration, hence there is a dire need for additional methods to exploit potential synergy from integrated orthogonal data. Rough Sets provide an efficient means to use complex information in classification approaches. Here, we set out to explore the possibilities of Rough Sets to incorporate diverse information sources in a functional classification of unknown genes. RESULTS We explored the use of Rough Sets for a novel data integration strategy where gene expression data, protein features and Gene Ontology (GO) annotations were combined to describe general and biologically relevant patterns represented by If-Then rules. The descriptive rules were used to predict the function of unknown genes in Arabidopsis thaliana and Schizosaccharomyces pombe. The If-Then rule models showed success rates of up to 0.89 (discriminative and predictive power for both modeled organisms); whereas, models built solely of one data type (protein features or gene expression data) yielded success rates varying from 0.68 to 0.78. Our models were applied to generate classifications for many unknown genes, of which a sizeable number were confirmed either by PubMed literature reports or electronically interfered annotations. Finally, we studied cell cycle protein-protein interactions derived from both tandem affinity purification experiments and in silico experiments in the BioGRID interactome database and found strong experimental evidence for the predictions generated by our models. The results show that our approach can be used to build very robust models that create synergy from integrating gene expression data and protein features. AVAILABILITY The Rough Set-based method is implemented in the Rosetta toolkit kernel version 1.0.1 available at: http://rosetta.lcb.uu.se/
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Affiliation(s)
- Krzysztof Wabnik
- Department of Plant Systems Biology, VIB Technologiepark 927, 9052 Gent, Belgium.
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Van Leene J, Witters E, Inzé D, De Jaeger G. Boosting tandem affinity purification of plant protein complexes. Trends Plant Sci 2008; 13:517-20. [PMID: 18771946 DOI: 10.1016/j.tplants.2008.08.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Revised: 08/01/2008] [Accepted: 08/04/2008] [Indexed: 05/05/2023]
Abstract
Protein-interaction mapping based on the tandem affinity purification (TAP) approach has been successfully established for several systems, such as yeast and mammalian cells. However, relatively few protein complex purifications have been reported for plants. Here, we highlight solutions for the pitfalls and propose a major breakthrough in the quest for a better TAP tag in plants.
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Affiliation(s)
- Jelle Van Leene
- Department of Plant Systems Biology, Flanders Institute for Biotechnology and Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
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Van Leene J, Stals H, Eeckhout D, Persiau G, Van De Slijke E, Van Isterdael G, De Clercq A, Bonnet E, Laukens K, Remmerie N, Henderickx K, De Vijlder T, Abdelkrim A, Pharazyn A, Van Onckelen H, Inzé D, Witters E, De Jaeger G. A Tandem Affinity Purification-based Technology Platform to Study the Cell Cycle Interactome in Arabidopsis thaliana. Mol Cell Proteomics 2007; 6:1226-38. [PMID: 17426018 DOI: 10.1074/mcp.m700078-mcp200] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.6] [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: 12/18/2022] Open
Abstract
Defining protein complexes is critical to virtually all aspects of cell biology because many cellular processes are regulated by stable protein complexes, and their identification often provides insights into their function. We describe the development and application of a high throughput tandem affinity purification/mass spectrometry platform for cell suspension cultures to analyze cell cycle-related protein complexes in Arabidopsis thaliana. Elucidation of this protein-protein interaction network is essential to fully understand the functional differences between the highly redundant cyclin-dependent kinase/cyclin modules, which are generally accepted to play a central role in cell cycle control, in all eukaryotes. Cell suspension cultures were chosen because they provide an unlimited supply of protein extracts of actively dividing and undifferentiated cells, which is crucial for a systematic study of the cell cycle interactome in the absence of plant development. Here we report the mapping of a protein interaction network around six known core cell cycle proteins by an integrated approach comprising generic Gateway-based vectors with high cloning flexibility, the fast generation of transgenic suspension cultures, tandem affinity purification adapted for plant cells, matrix-assisted laser desorption ionization tandem mass spectrometry, data analysis, and functional assays. We identified 28 new molecular associations and confirmed 14 previously described interactions. This systemic approach provides new insights into the basic cell cycle control mechanisms and is generally applicable to other pathways in plants.
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Affiliation(s)
- Jelle Van Leene
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Gent, Belgium
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Eeckhout D, De Clercq A, Van De Slijke E, Van Leene J, Stals H, Casteels P, Persiau G, Vercammen D, Van Breusegem F, Zabeau M, Inzé D, Jespers L, Depicker A, De Jaeger G. A technology platform for the fast production of monoclonal recombinant antibodies against plant proteins and peptides. J Immunol Methods 2004; 294:181-7. [PMID: 15604026 DOI: 10.1016/j.jim.2004.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2004] [Revised: 07/12/2004] [Accepted: 08/12/2004] [Indexed: 11/17/2022]
Abstract
The application of recombinant antibodies in plant biology research is limited because plant researchers have minimal access to high-quality phage display libraries. Therefore, we constructed a library of 1.3 x 10(10) clones displaying human single-chain variable fragments (scFvs) that is available to the academic community. The scFvs selected from the library against a diverse set of plant proteins showed moderate to high antigen-binding affinity together with high specificity. Moreover, to optimize an scFv as immunodetection agent, two expression systems that allow efficient production and purification of bivalent scFv-Fc and scFv-CkappaZIP fusion proteins were integrated. We are convinced that this antibody platform will further stimulate applications of recombinant antibodies such as the diagnostic detection or immunomodulation of specific antigens in plants.
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Affiliation(s)
- Dominique Eeckhout
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, Technologiepark 927, B-9052 Gent, Belgium
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