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Fiorucci AS, Bourbousse C, Concia L, Rougée M, Deton-Cabanillas AF, Zabulon G, Layat E, Latrasse D, Kim SK, Chaumont N, Lombard B, Stroebel D, Lemoine S, Mohammad A, Blugeon C, Loew D, Bailly C, Bowler C, Benhamed M, Barneche F. Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in H3K4me3 independently from histone H2B monoubiquitination. Genome Biol 2019; 20:100. [PMID: 31113491 PMCID: PMC6528313 DOI: 10.1186/s13059-019-1705-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/02/2019] [Indexed: 12/19/2022] Open
Abstract
Background The functional determinants of H3K4me3, their potential dependency on histone H2B monoubiquitination, and their contribution to defining transcriptional regimes are poorly defined in plant systems. Unlike in Saccharomyces cerevisiae, where a single SET1 protein catalyzes H3K4me3 as part of COMPlex of proteins ASsociated with Set1 (COMPASS), in Arabidopsis thaliana, this activity involves multiple histone methyltransferases. Among these, the plant-specific SET DOMAIN GROUP 2 (SDG2) has a prominent role. Results We report that SDG2 co-regulates hundreds of genes with SWD2-like b (S2Lb), a plant ortholog of the Swd2 axillary subunit of yeast COMPASS. We show that S2Lb co-purifies with the AtCOMPASS core subunit WDR5, and both S2Lb and SDG2 directly influence H3K4me3 enrichment over highly transcribed genes. S2Lb knockout triggers pleiotropic developmental phenotypes at the vegetative and reproductive stages, including reduced fertility and seed dormancy. However, s2lb seedlings display little transcriptomic defects as compared to the large repertoire of genes targeted by S2Lb, SDG2, or H3K4me3, suggesting that H3K4me3 enrichment is important for optimal gene induction during cellular transitions rather than for determining on/off transcriptional status. Moreover, unlike in budding yeast, most of the S2Lb and H3K4me3 genomic distribution does not rely on a trans-histone crosstalk with histone H2B monoubiquitination. Conclusions Collectively, this study unveils that the evolutionarily conserved COMPASS-like complex has been co-opted by the plant-specific SDG2 histone methyltransferase and mediates H3K4me3 deposition through an H2B monoubiquitination-independent pathway in Arabidopsis. Electronic supplementary material The online version of this article (10.1186/s13059-019-1705-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anne-Sophie Fiorucci
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France.,Present address: Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Clara Bourbousse
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Lorenzo Concia
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405, Orsay, France
| | - Martin Rougée
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Anne-Flore Deton-Cabanillas
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Gérald Zabulon
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Elodie Layat
- Laboratoire de Biologie du Développement, Sorbonne Université, CNRS, 75005, Paris, France
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405, Orsay, France
| | - Soon Kap Kim
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405, Orsay, France
| | - Nicole Chaumont
- Laboratoire de Biologie du Développement, Sorbonne Université, CNRS, 75005, Paris, France
| | - Bérangère Lombard
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie, PSL Research University, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - David Stroebel
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Sophie Lemoine
- Genomic Facility, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, Paris, 75005, France
| | - Ammara Mohammad
- Genomic Facility, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, Paris, 75005, France
| | - Corinne Blugeon
- Genomic Facility, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, Paris, 75005, France
| | - Damarys Loew
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie, PSL Research University, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Christophe Bailly
- Laboratoire de Biologie du Développement, Sorbonne Université, CNRS, 75005, Paris, France
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405, Orsay, France
| | - Fredy Barneche
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France.
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Kuzu G, Keskin O, Nussinov R, Gursoy A. Modeling protein assemblies in the proteome. Mol Cell Proteomics 2014; 13:887-96. [PMID: 24445405 PMCID: PMC3945916 DOI: 10.1074/mcp.m113.031294] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 12/13/2013] [Indexed: 11/06/2022] Open
Abstract
Most (if not all) proteins function when associated in multimolecular assemblies. Attaining the structures of protein assemblies at the atomic scale is an important aim of structural biology. Experimentally, structures are increasingly available, and computations can help bridge the resolution gap between high- and low-resolution scales. Existing computational methods have made substantial progress toward this aim; however, current approaches are still limited. Some involve manual adjustment of experimental data; some are automated docking methods, which are computationally expensive and not applicable to large-scale proteome studies; and still others exploit the symmetry of the complexes and thus are not applicable to nonsymmetrical complexes. Our study aims to take steps toward overcoming these limitations. We have developed a strategy for the construction of protein assemblies computationally based on binary interactions predicted by a motif-based protein interaction prediction tool, PRISM (Protein Interactions by Structural Matching). Previously, we have shown its power in predicting pairwise interactions. Here we take a step toward multimolecular assemblies, reflecting the more prevalent cellular scenarios. With this method we are able to construct homo-/hetero-complexes and symmetric/asymmetric complexes without a limitation on the number of components. The method considers conformational changes and is applicable to large-scale studies. We also exploit electron microscopy density maps to select a solution from among the predictions. Here we present the method, illustrate its results, and highlight its current limitations.
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Affiliation(s)
- Guray Kuzu
- From the ‡Center for Computational Biology and Bioinformatics and College of Engineering, Koc University Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey
| | - Ozlem Keskin
- From the ‡Center for Computational Biology and Bioinformatics and College of Engineering, Koc University Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey
| | - Ruth Nussinov
- §Cancer and Inflammation Program, Leidos Biomedical Research, Inc., National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
- ¶Sackler Institute of Molecular Medicine Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Attila Gursoy
- From the ‡Center for Computational Biology and Bioinformatics and College of Engineering, Koc University Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey
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