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Iantcheva A, Zhiponova M, Revalska M, Heyman J, Dincheva I, Badjakov I, De Geyter N, Boycheva I, Goormachtig S, De Veylder L. A common F-box gene regulates the leucine homeostasis of Medicago truncatula and Arabidopsis thaliana. PROTOPLASMA 2022; 259:277-290. [PMID: 33973099 DOI: 10.1007/s00709-021-01662-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
The F-box domain is a conserved structural protein motif that most frequently interacts with the SKP1 protein, the core of the SCFs (SKP1-CULLIN-F-box protein ligase) E3 ubiquitin protein ligases. As part of the SCF complexes, the various F-box proteins recruit substrates for degradation through ubiquitination. In this study, we functionally characterized an F-box gene (MtF-box) identified earlier in a population of Tnt1 retrotransposon-tagged mutants of Medicago truncatula and its Arabidopsis thaliana homolog (AtF-box) using gain- and loss-of-function plants. We highlighted the importance of MtF-box in leaf development of M. truncatula. Protein-protein interaction analyses revealed the 2-isopropylmalate synthase (IPMS) protein as a common interactor partner of MtF-box and AtF-box, being a key enzyme in the biosynthesis pathway of the branched-chain amino acid leucine. For further detailed analysis, we focused on AtF-box and its role during the cell division cycle. Based on this work, we suggest a mechanism for the role of the studied F-box gene in regulation of leucine homeostasis, which is important for growth.
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Affiliation(s)
- Anelia Iantcheva
- AgroBioInstitute, Agricultural Academy, Blvd. Dragan Tsankov 8, 1164, Sofia, Bulgaria.
| | - Miroslava Zhiponova
- Department of Plant Physiology, Faculty of Biology, Sofia University "St. Kliment Ohridski", 8 Dragan Tsankov blvd., 1164, Sofia, Bulgaria
| | - Miglena Revalska
- AgroBioInstitute, Agricultural Academy, Blvd. Dragan Tsankov 8, 1164, Sofia, Bulgaria
| | - Jefri Heyman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Ivayla Dincheva
- AgroBioInstitute, Agricultural Academy, Blvd. Dragan Tsankov 8, 1164, Sofia, Bulgaria
| | - Ilian Badjakov
- AgroBioInstitute, Agricultural Academy, Blvd. Dragan Tsankov 8, 1164, Sofia, Bulgaria
| | - Nathan De Geyter
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Irina Boycheva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bl. 21, 1113, Sofia, Bulgaria
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
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2
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Erffelinck ML, Ribeiro B, Gryffroy L, Rai A, Pollier J, Goossens A. The Heat Shock Protein 40-Type Chaperone MASH Supports the Endoplasmic Reticulum-Associated Degradation E3 Ubiquitin Ligase MAKIBISHI1 in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2021; 12:639625. [PMID: 33708234 PMCID: PMC7940691 DOI: 10.3389/fpls.2021.639625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/19/2021] [Indexed: 06/02/2023]
Abstract
Jasmonates (JA) are oxylipin-derived phytohormones that trigger the production of specialized metabolites that often serve in defense against biotic stresses. In Medicago truncatula, a JA-induced endoplasmic reticulum-associated degradation (ERAD)-type machinery manages the production of bioactive triterpenes and thereby secures correct plant metabolism, growth, and development. This machinery involves the conserved RING membrane-anchor (RMA)-type E3 ubiquitin ligase MAKIBISHI1 (MKB1). Here, we discovered two additional members of this protein control apparatus via a yeast-based protein-protein interaction screen and characterized their function. First, a cognate E2 ubiquitin-conjugating enzyme was identified that interacts with MKB1 to deliver activated ubiquitin and to mediate its ubiquitination activity. Second, we identified a heat shock protein 40 (HSP40) that interacts with MKB1 to support its activity and was therefore designated MKB1-supporting HSP40 (MASH). MASH expression was found to be co-regulated with that of MKB1. The presence of MASH is critical for MKB1 and ERAD functioning because the dramatic morphological, transcriptional, and metabolic phenotype of MKB1 knock-down M. truncatula hairy roots was phenocopied by silencing of MASH. Interaction was also observed between the Arabidopsis thaliana (Arabidopsis) homologs of MASH and MKB1, suggesting that MASH represents an essential and plant-specific component of this vital and conserved eukaryotic protein quality control machinery.
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Affiliation(s)
- Marie-Laure Erffelinck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Bianca Ribeiro
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lore Gryffroy
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Avanish Rai
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Jacob Pollier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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3
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A user-friendly platform for yeast two-hybrid library screening using next generation sequencing. PLoS One 2018; 13:e0201270. [PMID: 30576311 PMCID: PMC6303091 DOI: 10.1371/journal.pone.0201270] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/26/2018] [Indexed: 01/19/2023] Open
Abstract
Yeast two-hybrid (Y2H) is a well-established genetics-based system that uses yeast to selectively display binary protein-protein interactions (PPIs). To meet the current need to unravel complex PPI networks, several adaptations have been made to establish medium- to high-throughput Y2H screening platforms, with several having successfully incorporated the use of the next-generation sequencing (NGS) technology to increase the scale and sensitivity of the method. However, these have been to date mainly restricted to the use of fully annotated custom-made open reading frame (ORF) libraries and subject to complex downstream data processing. Here, a streamlined Y2H library screening strategy, based on integration of Y2H with NGS, called Y2H-seq, was developed, which allows efficient and reliable screening of Y2H cDNA libraries. To generate proof of concept, the method was applied to screen for interaction partners of two key components of the jasmonate signaling machinery in the model plant Arabidopsis thaliana, resulting in the identification of several previously reported as well as hitherto unknown interactors. Our Y2H-seq method offers a user-friendly, specific and sensitive screening method that allows identification of PPIs without prior knowledge of the organism’s ORFs, thereby extending the method to organisms of which the genome has not entirely been annotated yet. The quantitative NGS readout allows to increase genome coverage, thereby overcoming some of the bottlenecks of current Y2H technologies, which will further strengthen the value of the Y2H technology as a discovery platform.
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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. FRONTIERS IN PLANT SCIENCE 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] [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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Struk S, Braem L, Walton A, De Keyser A, Boyer FD, Persiau G, De Jaeger G, Gevaert K, Goormachtig S. Quantitative Tandem Affinity Purification, an Effective Tool to Investigate Protein Complex Composition in Plant Hormone Signaling: Strigolactones in the Spotlight. FRONTIERS IN PLANT SCIENCE 2018; 9:528. [PMID: 29755490 PMCID: PMC5932160 DOI: 10.3389/fpls.2018.00528] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/04/2018] [Indexed: 05/13/2023]
Abstract
Phytohormones tightly regulate plant growth by integrating changing environmental and developmental cues. Although the key players have been identified in many plant hormonal pathways, the molecular mechanisms and mode of action of perception and signaling remain incompletely resolved. Characterization of protein partners of known signaling components provides insight into the formed protein complexes, but, unless quantification is involved, does not deliver much, if any, information about the dynamics of the induced or disrupted protein complexes. Therefore, in proteomics research, the discovery of what actually triggers, regulates or interrupts the composition of protein complexes is gaining importance. Here, tandem affinity purification coupled to mass spectrometry (TAP-MS) is combined with label-free quantification (LFQ) to a highly valuable tool to detect physiologically relevant, dynamic protein-protein interactions in Arabidopsis thaliana cell cultures. To demonstrate its potential, we focus on the signaling pathway of one of the most recently discovered phytohormones, strigolactones.
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Affiliation(s)
- Sylwia Struk
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Lukas Braem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Alan Walton
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Annick De Keyser
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - François-Didier Boyer
- UMR 1318, Institut National de la Recherche Agronomique – Institut Jean-Pierre Bourgin, Versailles, France
- Institut de Chimie des Substances Naturelles – UPR 2301, Centre de Recherche de Gif, Centre National de la Recherche Scientifique, Paris, France
| | - Geert Persiau
- 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
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- *Correspondence: Sofie Goormachtig,
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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. FRONTIERS IN PLANT SCIENCE 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] [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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7
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García-León M, Iniesto E, Rubio V. Tandem Affinity Purification of Protein Complexes from Arabidopsis Cell Cultures. Methods Mol Biol 2018; 1794:297-309. [PMID: 29855967 DOI: 10.1007/978-1-4939-7871-7_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Tandem affinity purification (TAP) coupled to mass spectrometry has become a powerful approach to identify protein-protein interactions from different biological systems, including plants, in a proteome-wide manner. By using two sequential affinity purification steps, TAP allows for isolation of high-purity TAP-tagged proteins of interest and their associated proteins. Here we describe optimized procedures to use the GSRhino TAP technology for protein complex isolation from Arabidopsis cell suspension cultures.
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Affiliation(s)
- Marta García-León
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Elisa Iniesto
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Vicente Rubio
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
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Bassard JE, Halkier BA. How to prove the existence of metabolons? PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2018; 17:211-227. [PMID: 29755303 PMCID: PMC5932110 DOI: 10.1007/s11101-017-9509-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/19/2017] [Indexed: 05/21/2023]
Abstract
Sequential enzymes in biosynthetic pathways are organized in metabolons. It is challenging to provide experimental evidence for the existence of metabolons as biosynthetic pathways are composed of highly dynamic protein-protein interactions. Many different methods are being applied, each with strengths and weaknesses. We will present and evaluate several techniques that have been applied in providing evidence for the orchestration of the biosynthetic pathways of cyanogenic glucosides and glucosinolates in metabolons. These evolutionarily related pathways have ER-localized cytochromes P450 that are proposed to function as anchoring site for assembly of the enzymes into metabolons. Additionally, we have included commonly used techniques, even though they have not been used (yet) on these two pathways. In the review, special attention will be given to less-exploited fluorescence-based methods such as FCS and FLIM. Ultimately, understanding the orchestration of biosynthetic pathways may contribute to successful engineering in heterologous hosts.
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Affiliation(s)
- Jean-Etienne Bassard
- Plant Biochemistry Laboratory, Center for Synthetic Biology, VILLUM Research Center “Plant Plasticity”, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Barbara Ann Halkier
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
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