1
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Davarinejad H, Arvanitis-Vigneault A, Nygard D, Lavallée-Adam M, Couture JF. Modus operandi: Chromatin recognition by α-helical histone readers. Structure 2024; 32:8-17. [PMID: 37922903 DOI: 10.1016/j.str.2023.10.008] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/25/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023]
Abstract
Histone reader domains provide a mechanism for sensing states of coordinated nuclear processes marked by histone proteins' post-translational modifications (PTMs). Among a growing number of discovered histone readers, the 14-3-3s, ankyrin repeat domains (ARDs), tetratricopeptide repeats (TPRs), bromodomains (BRDs), and HEAT domains are a group of domains using various mechanisms to recognize unmodified or modified histones, yet they all are composed of an α-helical fold. In this review, we compare how these readers fold to create protein domains that are very diverse in their tertiary structures, giving rise to intriguing peptide binding mechanisms resulting in vastly different footprints of their targets.
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Affiliation(s)
- Hossein Davarinejad
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Alexis Arvanitis-Vigneault
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Dallas Nygard
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada.
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2
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Zeghal M, Matte K, Venes A, Patel S, Laroche G, Sarvan S, Joshi M, Rain JC, Couture JF, Giguère PM. Development of a V5-tag-directed nanobody and its implementation as an intracellular biosensor of GPCR signaling. J Biol Chem 2023; 299:105107. [PMID: 37517699 PMCID: PMC10470007 DOI: 10.1016/j.jbc.2023.105107] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 04/20/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/01/2023] Open
Abstract
Protein-protein interactions (PPIs) form the foundation of any cell signaling network. Considering that PPIs are highly dynamic processes, cellular assays are often essential for their study because they closely mimic the biological complexities of cellular environments. However, incongruity may be observed across different PPI assays when investigating a protein partner of interest; these discrepancies can be partially attributed to the fusion of different large functional moieties, such as fluorescent proteins or enzymes, which can yield disparate perturbations to the protein's stability, subcellular localization, and interaction partners depending on the given cellular assay. Owing to their smaller size, epitope tags may exhibit a diminished susceptibility to instigate such perturbations. However, while they have been widely used for detecting or manipulating proteins in vitro, epitope tags lack the in vivo traceability and functionality needed for intracellular biosensors. Herein, we develop NbV5, an intracellular nanobody binding the V5-tag, which is suitable for use in cellular assays commonly used to study PPIs such as BRET, NanoBiT, and Tango. The NbV5:V5 tag system has been applied to interrogate G protein-coupled receptor signaling, specifically by replacing larger functional moieties attached to the protein interactors, such as fluorescent or luminescent proteins (∼30 kDa), by the significantly smaller V5-tag peptide (1.4 kDa), and for microscopy imaging which is successfully detected by NbV5-based biosensors. Therefore, the NbV5:V5 tag system presents itself as a versatile tool for live-cell imaging and a befitting adaptation to existing cellular assays dedicated to probing PPIs.
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Affiliation(s)
- Manel Zeghal
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Kevin Matte
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Angelica Venes
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Shivani Patel
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Geneviève Laroche
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Sabina Sarvan
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Monika Joshi
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Jean-François Couture
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Patrick M Giguère
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Brain and Mind Research Institute, University of Ottawa, Ottawa, Ontario, Canada.
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3
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Farhat D, Rezaei F, Ristovski M, Yang Y, Stancescu A, Dzimkova L, Samnani S, Couture JF, Lee JY. Structural analysis of cholesterol binding and sterol selectivity by ABCG5/G8. J Mol Biol 2022; 434:167795. [PMID: 35988751 DOI: 10.1016/j.jmb.2022.167795] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/30/2022] [Accepted: 08/15/2022] [Indexed: 01/08/2023]
Abstract
The ATP-binding cassette (ABC) sterol transporters are responsible for maintaining cholesterol homeostasis in mammals by participating in reverse cholesterol transport (RCT) or transintestinal cholesterol efflux (TICE). The heterodimeric ABCG5/G8 carries out selective sterol excretion, preventing the abnormal accumulation of plant sterols in human bodies, while homodimeric ABCG1 contributes to the biogenesis and metabolism of high-density lipoproteins. A sterol-binding site on ABCG5/G8 was proposed at the interface of the transmembrane domain and the core of lipid bilayers. In this study, we have determined the crystal structure of ABCG5/G8 in a cholesterol-bound state. The structure combined with amino acid sequence analysis shows that in the proximity of the sterol-binding site, a highly conserved phenylalanine array supports functional implications for ABCG cholesterol/sterol transporters. Lastly, in silico docking analysis of cholesterol and stigmasterol (a plant sterol) suggests sterol-binding selectivity on ABCG5/G8, but not ABCG1. Together, our results provide a structural basis for cholesterol binding on ABCG5/G8 and the sterol selectivity by ABCG transporters.
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Affiliation(s)
- Danny Farhat
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Fatemeh Rezaei
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Milica Ristovski
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Translational and Molecular Medicine Program, Faculty of Medicine, University of Ottawa, Ontario, Ottawa, Canada
| | - Yidai Yang
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Albert Stancescu
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Biochemistry Program, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Lucia Dzimkova
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Biochemistry Program, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Sabrina Samnani
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Biochemistry Program, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Jean-François Couture
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Jyh-Yeuan Lee
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.
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4
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Davarinejad H, Huang YC, Mermaz B, LeBlanc C, Poulet A, Thomson G, Joly V, Muñoz M, Arvanitis-Vigneault A, Valsakumar D, Villarino G, Ross A, Rotstein BH, Alarcon EI, Brunzelle JS, Voigt P, Dong J, Couture JF, Jacob Y. The histone H3.1 variant regulates TONSOKU-mediated DNA repair during replication. Science 2022; 375:1281-1286. [PMID: 35298257 PMCID: PMC9153895 DOI: 10.1126/science.abm5320] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The tail of replication-dependent histone H3.1 varies from that of replication-independent H3.3 at the amino acid located at position 31 in plants and animals, but no function has been assigned to this residue to demonstrate a unique and conserved role for H3.1 during replication. We found that TONSOKU (TSK/TONSL), which rescues broken replication forks, specifically interacts with H3.1 via recognition of alanine 31 by its tetratricopeptide repeat domain. Our results indicate that genomic instability in the absence of ATXR5/ATXR6-catalyzed histone H3 lysine 27 monomethylation in plants depends on H3.1, TSK, and DNA polymerase theta (Pol θ). This work reveals an H3.1-specific function during replication and a common strategy used in multicellular eukaryotes for regulating post-replicative chromatin maturation and TSK, which relies on histone monomethyltransferases and reading of the H3.1 variant.
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Affiliation(s)
- Hossein Davarinejad
- Ottawa Institute of Systems Biology; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa; Ottawa, Ontario K1H 8M5, Canada
| | - Yi-Chun Huang
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; 260 Whitney Avenue, New Haven, Connecticut 06511, USA
| | - Benoit Mermaz
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; 260 Whitney Avenue, New Haven, Connecticut 06511, USA
| | - Chantal LeBlanc
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; 260 Whitney Avenue, New Haven, Connecticut 06511, USA
| | - Axel Poulet
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; 260 Whitney Avenue, New Haven, Connecticut 06511, USA
| | - Geoffrey Thomson
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; 260 Whitney Avenue, New Haven, Connecticut 06511, USA
| | - Valentin Joly
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; 260 Whitney Avenue, New Haven, Connecticut 06511, USA
| | - Marcelo Muñoz
- Ottawa Institute of Systems Biology; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa; Ottawa, Ontario K1H 8M5, Canada
| | - Alexis Arvanitis-Vigneault
- Ottawa Institute of Systems Biology; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa; Ottawa, Ontario K1H 8M5, Canada
| | - Devisree Valsakumar
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh; Edinburgh, EH9 3BF, United Kingdom
- Epigenetics Programme, Babraham Institute; Cambridge, CB22 3AT, United Kingdom
| | - Gonzalo Villarino
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; 260 Whitney Avenue, New Haven, Connecticut 06511, USA
| | - Alex Ross
- BEaTS Research Laboratory, Division of Cardiac Surgery, University of Ottawa Heart Institute; Ottawa, ON K1Y4W7, Canada
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa; Ottawa, ON K1H 8M5, Canada
| | - Benjamin H. Rotstein
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa; Ottawa, ON K1H 8M5, Canada
- University of Ottawa Heart Institute; Ottawa, ON K1Y4W7, Canada
| | - Emilio I. Alarcon
- BEaTS Research Laboratory, Division of Cardiac Surgery, University of Ottawa Heart Institute; Ottawa, ON K1Y4W7, Canada
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa; Ottawa, ON K1H 8M5, Canada
| | - Joseph S. Brunzelle
- Feinberg School of Medicine, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University; Chicago, Illinois 60611, USA
| | - Philipp Voigt
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh; Edinburgh, EH9 3BF, United Kingdom
- Epigenetics Programme, Babraham Institute; Cambridge, CB22 3AT, United Kingdom
| | - Jie Dong
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; 260 Whitney Avenue, New Haven, Connecticut 06511, USA
- Institute of Crop Science, Zhejiang University; Hangzhou 310058, China
| | - Jean-François Couture
- Ottawa Institute of Systems Biology; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa; Ottawa, Ontario K1H 8M5, Canada
| | - Yannick Jacob
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; 260 Whitney Avenue, New Haven, Connecticut 06511, USA
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5
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Karunakaran G, Yang Y, Tremblay V, Ning Z, Martin J, Belaouad A, Figeys D, Brunzelle J, Giguere PM, Stintzi A, Couture JF. Structural analysis of Atopobium parvulum SufS cysteine desulfurase linked to Crohn's disease. FEBS Lett 2022; 596:898-909. [PMID: 35122247 DOI: 10.1002/1873-3468.14295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 08/23/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/09/2022]
Abstract
Crohn's Disease (CD) is characterized by the chronic inflammation of the gastrointestinal tract. A dysbiotic microbiome and a defective immune system are linked to CD, where hydrogen sulfide (H2 S) microbial producers positively correlate with the severity of the disease. Atopobium parvulum is a key H2 S producer from the microbiome of CD patients. In this study, the biochemical characterization of two Atopobium parvulum cysteine desulfurases, ApSufS and ApCsdB, show that the enzymes are allosterically regulated. Structural analyses reveal that ApSufS forms a dimer with conserved characteristics observed in type II cysteine desulfurases. Four residues surrounding the active site are essential to catalyze cysteine desulfurylation, and a segment of short-chain residues grant access for substrate binding. A better understanding of ApSufS will help future avenues for CD treatment.
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Affiliation(s)
- Gapisha Karunakaran
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Yidai Yang
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Véronique Tremblay
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Zhibin Ning
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Jade Martin
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Amine Belaouad
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Joseph Brunzelle
- Feinberg School of Medicine, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois, 60611, USA
| | - Patrick M Giguere
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Alain Stintzi
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Jean-François Couture
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
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6
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Narayanan C, Bernard DN, Létourneau M, Gagnon J, Gagné D, Bafna K, Calmettes C, Couture JF, Agarwal PK, Doucet N. Insights into Structural and Dynamical Changes Experienced by Human RNase 6 upon Ligand Binding. Biochemistry 2020; 59:755-765. [PMID: 31909602 DOI: 10.1021/acs.biochem.9b00888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Ribonuclease 6 (RNase 6) is one of eight catalytically active human pancreatic-type RNases that belong to a superfamily of rapidly evolving enzymes. Like some of its human homologues, RNase 6 exhibits host defense properties such as antiviral and antibacterial activities. Recently solved crystal structures of this enzyme in its nucleotide-free form show the conservation of the prototypical kidney-shaped fold preserved among vertebrate RNases, in addition to revealing the presence of a unique secondary active site. In this study, we determine the structural and conformational properties experienced by RNase 6 upon binding to substrate and product analogues. We present the first crystal structures of RNase 6 bound to a nucleotide ligand (adenosine 5'-monophosphate), in addition to RNase 6 bound to phosphate ions. While the enzyme preserves B2 subsite ligand preferences, our results show a lack of typical B2 subsite interactions normally observed in homologous ligand-bound RNases. A comparison of the dynamical properties of RNase 6 in its apo-, substrate-, and product-bound states highlight the unique dynamical properties experienced on time scales ranging from nano- to milliseconds. Overall, our results confirm the specific evolutionary adaptation of RNase 6 relative to its unique catalytic and biological activities.
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Affiliation(s)
- Chitra Narayanan
- Centre Armand-Frappier Santé Biotechnologie , Institut National de la Recherche Scientifique (INRS), Université du Québec , 531 Boulevard des Prairies , Laval , Quebec City H7V 1B7 , Canada
| | - David N Bernard
- Centre Armand-Frappier Santé Biotechnologie , Institut National de la Recherche Scientifique (INRS), Université du Québec , 531 Boulevard des Prairies , Laval , Quebec City H7V 1B7 , Canada
| | - Myriam Létourneau
- Centre Armand-Frappier Santé Biotechnologie , Institut National de la Recherche Scientifique (INRS), Université du Québec , 531 Boulevard des Prairies , Laval , Quebec City H7V 1B7 , Canada
| | - Jacinthe Gagnon
- Centre Armand-Frappier Santé Biotechnologie , Institut National de la Recherche Scientifique (INRS), Université du Québec , 531 Boulevard des Prairies , Laval , Quebec City H7V 1B7 , Canada
| | - Donald Gagné
- Centre Armand-Frappier Santé Biotechnologie , Institut National de la Recherche Scientifique (INRS), Université du Québec , 531 Boulevard des Prairies , Laval , Quebec City H7V 1B7 , Canada
| | - Khushboo Bafna
- Genome Science and Technology , University of Tennesse , Knoxville , Tennessee 37996 , United States
| | - Charles Calmettes
- Centre Armand-Frappier Santé Biotechnologie , Institut National de la Recherche Scientifique (INRS), Université du Québec , 531 Boulevard des Prairies , Laval , Quebec City H7V 1B7 , Canada.,PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications , Université Laval , 1045 Avenue de la Médecine , Quebec , Quebec G1V 0A6 , Canada
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology , University of Ottawa , 451 Smyth Road , Ottawa , Ontario K1H 8M5 , Canada
| | - Pratul K Agarwal
- Department of Biochemistry, Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie , Institut National de la Recherche Scientifique (INRS), Université du Québec , 531 Boulevard des Prairies , Laval , Quebec City H7V 1B7 , Canada.,PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications , Université Laval , 1045 Avenue de la Médecine , Quebec , Quebec G1V 0A6 , Canada
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7
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Yang Y, Joshi M, Takahashi YH, Ning Z, Qu Q, Brunzelle JS, Skiniotis G, Figeys D, Shilatifard A, Couture JF. A non-canonical monovalent zinc finger stabilizes the integration of Cfp1 into the H3K4 methyltransferase complex COMPASS. Nucleic Acids Res 2020; 48:421-431. [PMID: 31724694 PMCID: PMC7145517 DOI: 10.1093/nar/gkz1037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 07/16/2019] [Revised: 10/16/2019] [Accepted: 10/24/2019] [Indexed: 12/28/2022] Open
Abstract
COMPlex ASsociating with SET1 (COMPASS) is a histone H3 Lys-4 methyltransferase that typically marks the promoter region of actively transcribed genes. COMPASS is a multi-subunit complex in which the catalytic unit, SET1, is required for H3K4 methylation. An important subunit known to regulate SET1 methyltransferase activity is the CxxC zinc finger protein 1 (Cfp1). Cfp1 binds to COMPASS and is critical to maintain high level of H3K4me3 in cells but the mechanisms underlying its stimulatory activity is poorly understood. In this study, we show that Cfp1 only modestly activates COMPASS methyltransferase activity in vitro. Binding of Cfp1 to COMPASS is in part mediated by a new type of monovalent zinc finger (ZnF). This ZnF interacts with the COMPASS's subunits RbBP5 and disruption of this interaction blunts its methyltransferase activity in cells and in vivo. Collectively, our studies reveal that a novel form of ZnF on Cfp1 enables its integration into COMPASS and contributes to epigenetic signaling.
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Affiliation(s)
- Yidai Yang
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology , University of Ottawa, Ottawa , ON K1H 8M5 , Canada
| | - Monika Joshi
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology , University of Ottawa, Ottawa , ON K1H 8M5 , Canada
| | - Yoh-hei Takahashi
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Zhibin Ning
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology , University of Ottawa, Ottawa , ON K1H 8M5 , Canada
| | - Qianhui Qu
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph S Brunzelle
- Northwestern Synchrotron Research Centers, Life Science Collaborative Access Team, Northwestern University, Evanston, IL, USA
| | - Georgios Skiniotis
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daniel Figeys
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology , University of Ottawa, Ottawa , ON K1H 8M5 , Canada
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Jean-François Couture
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology , University of Ottawa, Ottawa , ON K1H 8M5 , Canada
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8
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Goel K, Zuñiga-Bustos M, Lazurko C, Jacques E, Galaz-Araya C, Valenzuela-Henriquez F, Pacioni NL, Couture JF, Poblete H, Alarcon EI. Nanoparticle Concentration vs Surface Area in the Interaction of Thiol-Containing Molecules: Toward a Rational Nanoarchitectural Design of Hybrid Materials. ACS Appl Mater Interfaces 2019; 11:17697-17705. [PMID: 31013043 DOI: 10.1021/acsami.9b03942] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The effect of accounting for the total surface in the association of thiol-containing molecules to nanosilver was assessed using isothermal titration calorimetry, along with a new open access algorithm that calculates the total surface area for samples of different polydispersity. Further, we used advanced molecular dynamic calculations to explore the underlying mechanisms for the interaction of the studied molecules in the presence of a nanosilver surface in the form of flat surfaces or as three-dimensional pseudospherical nanostructures. Our data indicate that not only is the total surface area available for binding but also the supramolecular arrangements of the molecules in the near proximity of the nanosilver surface strongly affects the affinity of thiol-containing molecules to nanosilver surfaces.
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Affiliation(s)
- Keshav Goel
- Division of Cardiac Surgery , University of Ottawa Heart Institute , 40 Ruskin Street , Ottawa , Ontario , Canada K1Y 4W7
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine , University of Ottawa , 451 Smyth Road , Ottawa , Ontario , Canada K1H 8M5
| | - Matias Zuñiga-Bustos
- Center for Bioinformatics and Molecular Simulations, Facultad de Ingeniería , Universidad de Talca , Campus Lircay s/n , Talca 3460000 , Chile
| | - Caitlin Lazurko
- Division of Cardiac Surgery , University of Ottawa Heart Institute , 40 Ruskin Street , Ottawa , Ontario , Canada K1Y 4W7
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine , University of Ottawa , 451 Smyth Road , Ottawa , Ontario , Canada K1H 8M5
| | - Erik Jacques
- Division of Cardiac Surgery , University of Ottawa Heart Institute , 40 Ruskin Street , Ottawa , Ontario , Canada K1Y 4W7
| | - Constanza Galaz-Araya
- Center for Bioinformatics and Molecular Simulations, Facultad de Ingeniería , Universidad de Talca , Campus Lircay s/n , Talca 3460000 , Chile
| | - Francisco Valenzuela-Henriquez
- Instituto de Matemática , Pontificia Universidad Católica de Valparaíso , Blanco Viel 596, Cerro Barón , Valparaíso 2350026 , Chile
| | - Natalia L Pacioni
- Facultad de Ciencias Químicas, Departamento de Química Orgánica , Universidad Nacional de Córdoba , Haya de la Torre y Medina Allende s/n, Ciudad Universitaria , Córdoba X5000HUA , Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), INFIQC , Buenos Aires 1418 , Córdoba X5000IND , Argentina
| | - Jean-François Couture
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine , University of Ottawa , 451 Smyth Road , Ottawa , Ontario , Canada K1H 8M5
| | - Horacio Poblete
- Center for Bioinformatics and Molecular Simulations, Facultad de Ingeniería , Universidad de Talca , Campus Lircay s/n , Talca 3460000 , Chile
- Núcleo Científico Multidisciplinario, Dirección de Investigación , Universidad de Talca , Talca 3460000 , Chile
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD) , Talca 3460000 , Chile
| | - Emilio I Alarcon
- Division of Cardiac Surgery , University of Ottawa Heart Institute , 40 Ruskin Street , Ottawa , Ontario , Canada K1Y 4W7
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine , University of Ottawa , 451 Smyth Road , Ottawa , Ontario , Canada K1H 8M5
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9
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Sarvan S, Yeung A, Charih F, Stintzi A, Couture JF. Purification and characterization of Campylobacter jejuni ferric uptake regulator. Biometals 2019; 32:491-500. [PMID: 30706282 DOI: 10.1007/s10534-019-00177-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 01/16/2019] [Accepted: 01/24/2019] [Indexed: 02/06/2023]
Abstract
The ferric uptake regulator (Fur) is a superfamily of transcription factors found in bacteria which control the expression of a myriad of genes. In this study, we report a simple protocol for the purification of recombinant untagged Campylobacter jejuni Fur (CjFur). CjFur was isolated using a combination of three ion exchange chromatography steps followed by size exclusion chromatography on a Superdex 75. ESI-MS analysis shows that our method yields pure CjFur and that this tag-free version incorporates metal more efficiently than recombinant CjFur harboring a tag or tag remnants. Finally, electrophoretic mobility shift assays show that this new purification method yields a CjFur preparation that binds DNA more efficiently. These results suggest that adding a N-terminus tag onto CjFur is detrimental to its activity. Overall, the approaches detailed in this study offer an alternative strategy for the purification of CjFur, and likely other metalloregulators, for future biochemical and biophysical studies.
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Affiliation(s)
- Sabina Sarvan
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON, K1H 8M5, Canada
| | - Allison Yeung
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON, K1H 8M5, Canada
| | - François Charih
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON, K1H 8M5, Canada
| | - Alain Stintzi
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON, K1H 8M5, Canada
| | - Jean-François Couture
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON, K1H 8M5, Canada.
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10
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Haddad JF, Yang Y, Takahashi YH, Joshi M, Chaudhary N, Woodfin AR, Benyoucef A, Yeung S, Brunzelle JS, Skiniotis G, Brand M, Shilatifard A, Couture JF. Structural Analysis of the Ash2L/Dpy-30 Complex Reveals a Heterogeneity in H3K4 Methylation. Structure 2018; 26:1594-1603.e4. [PMID: 30270175 DOI: 10.1016/j.str.2018.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 05/02/2018] [Revised: 06/28/2018] [Accepted: 08/08/2018] [Indexed: 01/09/2023]
Abstract
Dpy-30 is a regulatory subunit controlling the histone methyltransferase activity of the KMT2 enzymes in vivo. Paradoxically, in vitro methyltransferase assays revealed that Dpy-30 only modestly participates in the positive heterotypic allosteric regulation of these methyltransferases. Detailed genome-wide, molecular and structural studies reveal that an extensive network of interactions taking place at the interface between Dpy-30 and Ash2L are critical for the correct placement, genome-wide, of H3K4me2 and H3K4me3 but marginally contribute to the methyltransferase activity of KMT2 enzymes in vitro. Moreover, we show that H3K4me2 peaks persisting following the loss of Dpy-30 are found in regions of highly transcribed genes, highlighting an interplay between Complex of Proteins Associated with SET1 (COMPASS) kinetics and the cycling of RNA polymerase to control H3K4 methylation. Overall, our data suggest that Dpy-30 couples its modest positive heterotypic allosteric regulation of KMT2 methyltransferase activity with its ability to help the positioning of SET1/COMPASS to control epigenetic signaling.
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Affiliation(s)
- John Faissal Haddad
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada
| | - Yidai Yang
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada
| | - Yoh-Hei Takahashi
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Monika Joshi
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada
| | - Nidhi Chaudhary
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada
| | - Ashley R Woodfin
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Aissa Benyoucef
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Sylvain Yeung
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada
| | - Joseph S Brunzelle
- Northwestern Synchrotron Research Centers, Life Science Collaborative Access Team, Northwestern University, Evanston, IL, USA
| | - Georgios Skiniotis
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marjorie Brand
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8L6, Canada
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada.
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11
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Walton CJW, Thiebaut F, Brunzelle JS, Couture JF, Chica RA. Structural Determinants of the Stereoinverting Activity of Pseudomonas stutzeri d-Phenylglycine Aminotransferase. Biochemistry 2018; 57:5437-5446. [PMID: 30153007 DOI: 10.1021/acs.biochem.8b00767] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aromatic d-amino acids are key precursors for the production of many small molecule therapeutics. Therefore, the development of biocatalytic methods for their synthesis is of great interest. An enzyme that has great potential as a biocatalyst for the synthesis of d-amino acids is the stereoinverting d-phenylglycine aminotransferase (DPAT) from Pseudomonas stutzeri ST-201. This enzyme catalyzes a unique l to d transamination reaction that produces d-phenylglycine and α-ketoglutarate from benzoylformate and l-glutamate, via a mechanism that is poorly understood. Here, we present the crystal structure of DPAT, which shows that the enzyme folds into a two-domain structure representative of class III aminotransferases. Guided by the crystal structure, we performed saturation mutagenesis to probe the substrate binding pockets of the enzyme. These experiments helped us identify two arginine residues (R34 and R407), one in each binding pocket, that are essential to catalysis. Together with kinetic analyses using a library of amino acid substrates, our mutagenesis and structural studies allow us to propose a binding model that explains the dual l/d specificity of DPAT. Our kinetic analyses also demonstrate that DPAT can catalyze the transamination of β- and γ-amino acids, reclassifying this enzyme as an ω-aminotransferase. Collectively, our studies highlight that the DPAT active site is amenable to protein engineering for expansion of its substrate scope, which offers the opportunity to generate new biocatalysts for the synthesis of a variety of valuable optically pure d-amino acids from inexpensive and abundant l-amino acids.
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Affiliation(s)
- Curtis J W Walton
- Department of Chemistry and Biomolecular Sciences , University of Ottawa , Ottawa , Ontario , Canada K1N 6N5.,Centre for Catalysis Research and Innovation , University of Ottawa , Ottawa , Ontario , Canada K1N 6N5
| | - Frédéric Thiebaut
- Department of Chemistry and Biomolecular Sciences , University of Ottawa , Ottawa , Ontario , Canada K1N 6N5.,Centre for Catalysis Research and Innovation , University of Ottawa , Ottawa , Ontario , Canada K1N 6N5
| | - Joseph S Brunzelle
- Life Science Collaborative Access Team, Northwestern Synchrotron Research Centers , Northwestern University , Argonne , Illinois 60439 , United States
| | - Jean-François Couture
- Centre for Catalysis Research and Innovation , University of Ottawa , Ottawa , Ontario , Canada K1N 6N5.,Department of Biochemistry, Microbiology and Immunology, and Ottawa Institute of Systems Biology , University of Ottawa , Ottawa , Ontario , Canada K1H 8M5
| | - Roberto A Chica
- Department of Chemistry and Biomolecular Sciences , University of Ottawa , Ottawa , Ontario , Canada K1N 6N5.,Centre for Catalysis Research and Innovation , University of Ottawa , Ottawa , Ontario , Canada K1N 6N5
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12
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Yang Y, Joshi M, Couture JF. Cfp1/Cps40 stabilizes MLL complex formation through multi-valent interactions. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s010876731809863x] [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: 11/10/2022] Open
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13
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Davarinejad H, Joshi M, Hamou NA, Couture JF. Characterization of the dual function of ATXR5 PIP motif in PCNA and nucleosome binding. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s0108767318097398] [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: 11/11/2022] Open
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14
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Chitiprolu M, Jagow C, Tremblay V, Bondy-Chorney E, Paris G, Savard A, Palidwor G, Barry FA, Zinman L, Keith J, Rogaeva E, Robertson J, Lavallée-Adam M, Woulfe J, Couture JF, Côté J, Gibbings D. A complex of C9ORF72 and p62 uses arginine methylation to eliminate stress granules by autophagy. Nat Commun 2018; 9:2794. [PMID: 30022074 PMCID: PMC6052026 DOI: 10.1038/s41467-018-05273-7] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [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: 05/15/2017] [Accepted: 06/21/2018] [Indexed: 12/12/2022] Open
Abstract
Mutations in proteins like FUS which cause Amyotrophic Lateral Sclerosis (ALS) result in the aberrant formation of stress granules while ALS-linked mutations in other proteins impede elimination of stress granules. Repeat expansions in C9ORF72, the major cause of ALS, reduce C9ORF72 levels but how this impacts stress granules is uncertain. Here, we demonstrate that C9ORF72 associates with the autophagy receptor p62 and controls elimination of stress granules by autophagy. This requires p62 to associate via the Tudor protein SMN with proteins, including FUS, that are symmetrically methylated on arginines. Mice lacking p62 accumulate arginine-methylated proteins and alterations in FUS-dependent splicing. Patients with C9ORF72 repeat expansions accumulate symmetric arginine dimethylated proteins which co-localize with p62. This suggests that C9ORF72 initiates a cascade of ALS-linked proteins (C9ORF72, p62, SMN, FUS) to recognize stress granules for degradation by autophagy and hallmarks of a defect in this process are observable in ALS patients. Many Amyotrophic Lateral Sclerosis (ALS)-linked mutations cause accumulation of stress granules, and most ALS cases are caused by repeat expansions in C9ORF72. Here the authors show that C9ORF72 and the autophagy receptor p62 interact to associate with proteins symmetrically dimethylated on arginines such as FUS, to eliminate stress granules by autophagy.
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Affiliation(s)
- Maneka Chitiprolu
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Chantal Jagow
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Veronique Tremblay
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Emma Bondy-Chorney
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Geneviève Paris
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Alexandre Savard
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Gareth Palidwor
- Ottawa Bioinformatics Core Facility, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, Ontario, K1H 8L6, Canada
| | - Francesca A Barry
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Lorne Zinman
- Sunnybrook Health Sciences Centre, 2075 Bayview Avenue, Toronto, Ontario, M4N 3M5, Canada
| | - Julia Keith
- Sunnybrook Health Sciences Centre, 2075 Bayview Avenue, Toronto, Ontario, M4N 3M5, Canada
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Disease, University of Toronto, Krembil Discovery Tower, 60 Leonard Avenue, Toronto, Ontario, M5T 2S8, Canada
| | - Janice Robertson
- Tanz Centre for Research in Neurodegenerative Disease, University of Toronto, Krembil Discovery Tower, 60 Leonard Avenue, Toronto, Ontario, M5T 2S8, Canada
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - John Woulfe
- Department of Pathology and Laboratory Medicine, University of Ottawa, 501 Smyth Road, Ottawa, Ontario, K1H 8L6, Canada
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Jocelyn Côté
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Derrick Gibbings
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada. .,Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.
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15
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Sarvan S, Butcher J, Stintzi A, Couture JF. Variation on a theme: investigating the structural repertoires used by ferric uptake regulators to control gene expression. Biometals 2018; 31:681-704. [DOI: 10.1007/s10534-018-0120-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 06/12/2018] [Indexed: 11/29/2022]
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16
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Sarvan S, Charih F, Butcher J, Brunzelle JS, Stintzi A, Couture JF. Crystal structure of Campylobacter jejuni peroxide regulator. FEBS Lett 2018; 592:2351-2360. [PMID: 29856899 DOI: 10.1002/1873-3468.13120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 05/10/2018] [Revised: 05/28/2018] [Accepted: 05/30/2018] [Indexed: 11/08/2022]
Abstract
In Campylobacter jejuni (Cj), the metal-cofactored peroxide response regulator (PerR) transcription factor allows C. jejuni to respond to oxidative stresses. The crystal structure of the metalated form of CjPerR shows that the protein folds as an asymmetric dimer displaying structural differences in the orientation of its DNA-binding domain. Comparative analysis shows that such asymmetry is a conserved feature among crystallized PerR proteins, and mutational analysis reveals that residues found in the first α-helix of CjPerR contribute to DNA binding. These studies present the structure of CjPerR protein and highlight structural heterogeneity in the orientation of the metalated PerR DNA-binding domain which may underlie the ability of PerR to recognize DNA, control gene expression, and contribute to bacterial pathogenesis.
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Affiliation(s)
- Sabina Sarvan
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Canada
| | - François Charih
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Canada
| | - James Butcher
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Canada
| | - Joseph S Brunzelle
- Life Science Collaborative Access Team, Northwestern Synchrotron Research Centers, Northwestern University, Evanston, IL, USA
| | - Alain Stintzi
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Canada
| | - Jean-François Couture
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Canada
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17
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Sarvan S, Charih F, Askoura M, Butcher J, Brunzelle JS, Stintzi A, Couture JF. Functional insights into the interplay between DNA interaction and metal coordination in ferric uptake regulators. Sci Rep 2018; 8:7140. [PMID: 29739988 PMCID: PMC5940780 DOI: 10.1038/s41598-018-25157-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 01/05/2018] [Accepted: 04/11/2018] [Indexed: 12/19/2022] Open
Abstract
Ferric uptake regulators (Fur) are a family of transcription factors coupling gene regulatory events to metal concentration. Recent evidence has expanded the mechanistic repertoires employed by Fur to activate or repress gene expression in the presence or absence of regulatory metals. However, the mechanistic basis underlying this extended repertoire has remained largely unexplored. In this study, we used an extensive set of mutations to demonstrate that Campylobacter jejuni Fur (CjFur) employs the same surface to positively and negatively control gene expression regardless of the presence or absence of metals. Moreover, the crystal structure determination of a CjFur devoid of any regulatory metals shows that subtle reorientation of the transcription factor DNA binding domain negatively impacts DNA binding, gene expression and gut colonization in chickens. Overall, these results highlight the versatility of the CjFur DNA binding domain in mediating all gene regulatory events controlled by the metalloregulator and that the full metalation of CjFur is critical to the Campylobacter jejuni life cycle in vivo.
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Affiliation(s)
- Sabina Sarvan
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - François Charih
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Momen Askoura
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.,Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - James Butcher
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Joseph S Brunzelle
- Feinberg School of Medicine, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois, 60611, USA
| | - Alain Stintzi
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.
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18
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Gagnon J, Sarvan S, Gagne D, Couture JF, Doucet N. Human ribonuclease 6 crystal structure and conformational analysis. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317091732] [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: 11/10/2022] Open
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19
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Bergamin E, Sarvan S, Malette J, Eram MS, Yeung S, Mongeon V, Joshi M, Brunzelle JS, Michaels SD, Blais A, Vedadi M, Couture JF. Molecular basis for the methylation specificity of ATXR5 for histone H3. Nucleic Acids Res 2017; 45:6375-6387. [PMID: 28383693 PMCID: PMC5499861 DOI: 10.1093/nar/gkx224] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [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: 10/12/2015] [Accepted: 03/23/2017] [Indexed: 12/30/2022] Open
Abstract
In plants, the histone H3.1 lysine 27 (H3K27) mono-methyltransferases ARABIDOPSIS TRITHORAX RELATED PROTEIN 5 and 6 (ATXR5/6) regulate heterochromatic DNA replication and genome stability. Our initial studies showed that ATXR5/6 discriminate between histone H3 variants and preferentially methylate K27 on H3.1. In this study, we report three regulatory mechanisms contributing to the specificity of ATXR5/6. First, we show that ATXR5 preferentially methylates the R/F-K*-S/C-G/A-P/C motif with striking preference for hydrophobic and aromatic residues in positions flanking this core of five amino acids. Second, we demonstrate that post-transcriptional modifications of residues neighboring K27 that are typically associated with actively transcribed chromatin are detrimental to ATXR5 activity. Third, we show that ATXR5 PHD domain employs a narrow binding pocket to selectively recognize unmethylated K4 of histone H3. Finally, we demonstrate that deletion or mutation of the PHD domain reduces the catalytic efficiency (kcat/Km of AdoMet) of ATXR5 up to 58-fold, highlighting the multifunctional nature of ATXR5 PHD domain. Overall, our results suggest that several molecular determinants regulate ATXR5/6 methyltransferase activity and epigenetic inheritance of H3.1 K27me1 mark in plants.
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Affiliation(s)
- Elisa Bergamin
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Sabina Sarvan
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Josée Malette
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Mohammad S Eram
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5J 1L7, Canada
| | - Sylvain Yeung
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Vanessa Mongeon
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Monika Joshi
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Joseph S Brunzelle
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, IL 60439, USA
| | - Scott D Michaels
- Department of Biology, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA
| | - Alexandre Blais
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5J 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
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20
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Alarcon EI, Poblete H, Roh H, Couture JF, Comer J, Kochevar IE. Rose Bengal Binding to Collagen and Tissue Photobonding. ACS Omega 2017; 2:6646-6657. [PMID: 31457260 PMCID: PMC6644953 DOI: 10.1021/acsomega.7b00675] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/11/2017] [Indexed: 05/19/2023]
Abstract
We investigated two critical aspects of rose Bengal (RB) photosensitized protein cross-linking that may underlie recently developed medical applications. Our studies focused on the binding of RB to collagen by physical interaction and the effect of this binding and certain amino acids on RB photochemistry. Molecular dynamics simulations and free-energy calculation techniques, complemented with isothermal titration calorimetry, provided insight into the binding between RB and a collagen-like peptide (CLP) at the atomic level. Electrostatic interactions dominated, which is consistent with the finding that RB bound equally well to triple helical and single chain collagen. The binding free energy ranged from -5.7 to -3 kcal/mol and was strongest near the positively charged amino groups at the N-terminus and on lysine side chains. At high RB concentration, a maximum of 16 ± 3 bound dye molecules per peptide was found, which is consistent with spectroscopic evidence for aggregated RB bound to collagen or the CLP. Within a tissue-mimetic collagen matrix, RB photobleached rapidly, probably due to electron transfer to certain protein amino acids, as was demonstrated in solutions of free RB and arginine. In the presence of arginine and low oxygen concentrations, a product absorbing at 510 nm formed, presumably due to dehalogenation after electron transfer to RB. In the collagen matrix without arginine, the dye generated singlet oxygen as well as the 510 nm product. These results provide the first evidence of the effects of a tissue-like environment on the photochemical mechanisms of rose Bengal.
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Affiliation(s)
- Emilio I. Alarcon
- Division
of Cardiac Surgery, University of Ottawa
Heart Institute, 40 Ruskin
Street, K1Y 4W7 Ottawa, ON, Canada
- Department
of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, K1H 8M5 Ottawa, ON, Canada
| | - Horacio Poblete
- Center
for Bioinformatics and Molecular Simulation, Universidad de Talca, 2 Norte 685, Casilla 721, Talca 3460000, Chile
- Institute
of Computational Comparative Medicine, Nanotechnology Innovation Center
of Kansas State, and Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66503, United States
| | - HeeGwang Roh
- Wellman
Center for Photomedicine, Massachusetts
General Hospital and Harvard Medical School, 40 Blossom Street, Boston, Massachusetts 02114, United States
| | - Jean-François Couture
- Department
of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, K1H 8M5 Ottawa, ON, Canada
| | - Jeffrey Comer
- Institute
of Computational Comparative Medicine, Nanotechnology Innovation Center
of Kansas State, and Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66503, United States
| | - Irene E. Kochevar
- Wellman
Center for Photomedicine, Massachusetts
General Hospital and Harvard Medical School, 40 Blossom Street, Boston, Massachusetts 02114, United States
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21
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Thandapani P, Couturier AM, Yu Z, Li X, Couture JF, Li S, Masson JY, Richard S. Lysine methylation of FEN1 by SET7 is essential for its cellular response to replicative stress. Oncotarget 2017; 8:64918-64931. [PMID: 29029401 PMCID: PMC5630301 DOI: 10.18632/oncotarget.18070] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 04/18/2017] [Indexed: 12/17/2022] Open
Abstract
The DNA damage response (DDR) is central to the cell survival and it requires post-translational modifications, in part, to sense the damage, amplify the signaling response and recruit and regulate DNA repair enzymes. Lysine methylation of histones such as H4K20 and non-histone proteins including p53 has been shown to be essential for the mounting of the DDR. It is well-known that the lysine methyltransferase SET7 regulates the DDR, as cells lacking this enzyme are hypersensitive to chemotherapeutic drugs. To define addition substrates of SET7 involved in the DDR, we screened a peptide array encompassing potential lysine methylation sites from >100 key DDR proteins and identified peptides from 58 proteins to be lysine methylated defining a methylation consensus sequence of [S>K-2; S>R-1; K0] consistent with previous findings. We focused on K377 methylation of the Flap endonuclease 1 (FEN1), a structure specific endonuclease with important functions in Okazaki fragment processing during DNA replication as a substrate of SET7. FEN1 was monomethylated by SET7 in vivo in a cell cycle dependent manner with levels increasing as cells progressed through S phase and decreasing as they exited S phase, as detected using K377me1 specific antibodies. Although K377me1 did not affect the enzymatic activity of FEN1, it was required for the cellular response to replicative stress by FEN1. These finding define FEN1 as a new substrate of SET7 required for the DDR.
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Affiliation(s)
- Palaniraja Thandapani
- Terry Fox Molecular Oncology Group and Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Departments of Oncology and Medicine, McGill University, Montréal, Québec, Canada
| | - Anthony M. Couturier
- Genome Stability Laboratory, Laval University Cancer Research Center, CRCHU de Québec, Québec, Canada
| | - Zhenbao Yu
- Terry Fox Molecular Oncology Group and Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Departments of Oncology and Medicine, McGill University, Montréal, Québec, Canada
| | - Xing Li
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Shawn Li
- Genome Stability Laboratory, Laval University Cancer Research Center, CRCHU de Québec, Québec, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, Laval University Cancer Research Center, CRCHU de Québec, Québec, Canada
| | - Stéphane Richard
- Terry Fox Molecular Oncology Group and Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Departments of Oncology and Medicine, McGill University, Montréal, Québec, Canada
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22
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Haddad JF, Yang Y, Yeung S, Couture JF. Recognizing asymmetry in pseudo-symmetry; structural insights into the interaction between amphipathic α-helices and X-bundle proteins. Biochim Biophys Acta Proteins Proteom 2017; 1865:1605-1612. [PMID: 28652208 DOI: 10.1016/j.bbapap.2017.06.017] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 05/14/2017] [Accepted: 06/21/2017] [Indexed: 11/27/2022]
Abstract
An α-helix bundle is a small and compact protein fold always composed of more than 2 α-helices that typically run nearly parallel or antiparallel to each other. The repertoire of arrangements of α-helix bundle is such that these domains bind to a myriad of molecular entities including DNA, RNA, proteins and small molecules. A special instance of α-helical bundle is the X-type in which the arrangement of two α-helices interact at 45° to form an X. Among those, some X-helix bundle proteins bind to the hydrophobic section of an amphipathic α-helix in a seemingly orientation and sequence specific manner. In this review, we will compare the binding mode of amphipathic α-helices to X-helix bundle and α-helical bundle proteins. From these structures, we will highlight potential regulatory paradigms that may control the specific interactions of X-helix bundle proteins to amphipathic α-helices. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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Affiliation(s)
- John Faissal Haddad
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Yidai Yang
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Sylvain Yeung
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada.
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23
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Abstract
The Ferric Uptake Regulator (FUR) is a transcription factor (TF) regulating the expression of several genes to control iron levels in prokaryotes. Members of this family of TFs share a common structural scaffold that typically comprises two regions that include a DNA binding and dimerization domains. While this structural organization is conserved, FUR proteins employ different mechanisms to bind divergent DNA binding elements and regulate gene expression in the absence or presence of regulatory metals. These findings, combined with the observations that FUR proteins display different geometries in regard to the relative orientation of the DNA binding and dimerization domains, have highlighted an expanding repertoire of molecular mechanisms controlling the activity of this family of TFs. In this chapter, we present an overview of the methods to purify, crystallize, and solve the structure of Campylobacter jejuni FUR.
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Affiliation(s)
- Sabina Sarvan
- Ottawa Institute of Systems Biology, University of Ottawa, Roger Guindon Hall, 451 Smyth Road, Ottawa, ON, Canada, K1H 8M5
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Roger Guindon Hall, 451 Smyth Road, Ottawa, ON, Canada, K1H 8M5
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, University of Ottawa, Roger Guindon Hall, 451 Smyth Road, Ottawa, ON, Canada, K1H 8M5
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Roger Guindon Hall, 451 Smyth Road, Ottawa, ON, Canada, K1H 8M5
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24
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Gagnon J, Sarvan S, Gagné D, Couture JF, Simonović M, Doucet N. Crystal structure and biophysical characterization of ligand-free and -bound RNases 4 and 6, members of the human RNase A superfamily. Acta Crystallogr A Found Adv 2016. [DOI: 10.1107/s2053273316096753] [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: 11/10/2022] Open
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25
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Gagné D, Narayanan C, Nguyen-Thi N, Roux LD, Bernard DN, Brunzelle JS, Couture JF, Agarwal PK, Doucet N. Ligand Binding Enhances Millisecond Conformational Exchange in Xylanase B2 from Streptomyces lividans. Biochemistry 2016; 55:4184-96. [PMID: 27387012 DOI: 10.1021/acs.biochem.6b00130] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Xylanases catalyze the hydrolysis of xylan, an abundant carbon and energy source with important commercial ramifications. Despite tremendous efforts devoted to the catalytic improvement of xylanases, success remains limited because of our relatively poor understanding of their molecular properties. Previous reports suggested the potential role of atomic-scale residue dynamics in modulating the catalytic activity of GH11 xylanases; however, dynamics in these studies was probed on time scales orders of magnitude faster than the catalytic time frame. Here, we used nuclear magnetic resonance titration and relaxation dispersion experiments ((15)N-CPMG) in combination with X-ray crystallography and computational simulations to probe conformational motions occurring on the catalytically relevant millisecond time frame in xylanase B2 (XlnB2) and its catalytically impaired mutant E87A from Streptomyces lividans 66. Our results show distinct dynamical properties for the apo and ligand-bound states of the enzymes. The apo form of XlnB2 experiences conformational exchange for residues in the fingers and palm regions of the catalytic cleft, while the catalytically impaired E87A variant displays millisecond dynamics only in the fingers, demonstrating the long-range effect of the mutation on flexibility. Ligand binding induces enhanced conformational exchange of residues interacting with the ligand in the fingers and thumb loop regions, emphasizing the potential role of residue motions in the fingers and thumb loop regions for recognition, positioning, processivity, and/or stabilization of ligands in XlnB2. To the best of our knowledge, this work represents the first experimental characterization of millisecond dynamics in a GH11 xylanase family member. These results offer new insights into the potential role of conformational exchange in GH11 enzymes, providing essential dynamic information to help improve protein engineering and design applications.
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Affiliation(s)
- Donald Gagné
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - Chitra Narayanan
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - Nhung Nguyen-Thi
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - Louise D Roux
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - David N Bernard
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - Joseph S Brunzelle
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University , 320 East Superior Street, Chicago, Illinois 60611, United States
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada.,PROTEO, Québec Network for Research on Protein Function, Engineering, and Applications, Université Laval , 1045 Avenue de la Médecine, Québec, Québec G1V 0A6, Canada.,GRASP, Groupe de Recherche Axé sur la Structure des Protéines, McGill University , 3649 Promenade Sir William Osler, Montréal, Québec H3G 0B1, Canada
| | - Pratul K Agarwal
- Computational Biology Institute and Computer Science and Mathematics Division, Oak Ridge National Laboratory , 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States.,Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Nicolas Doucet
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada.,PROTEO, Québec Network for Research on Protein Function, Engineering, and Applications, Université Laval , 1045 Avenue de la Médecine, Québec, Québec G1V 0A6, Canada.,GRASP, Groupe de Recherche Axé sur la Structure des Protéines, McGill University , 3649 Promenade Sir William Osler, Montréal, Québec H3G 0B1, Canada
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26
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Zhang P, Bergamin E, Couture JF. The many facets of MLL1 regulation. Biopolymers 2016; 99:136-45. [PMID: 23175388 DOI: 10.1002/bip.22126] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 07/04/2012] [Accepted: 07/06/2012] [Indexed: 01/07/2023]
Abstract
In the last 20 years, we have witnessed an exponential number of evidences linking the human mixed lineage leukemia-1 (MLL1) gene to several acute and myelogenous leukemias. MLL1 is one of the founding members of the SET1 family of lysine methyltransferases and is key for the proper control of developmentally regulated gene expression. MLL1 is a structurally complex protein composed of several functional domains. These domains play pivotal roles for the recruitment of regulatory proteins. These MLL1 regulatory proteins (MRPs) dynamically interact with MLL1 and consequently control gene expression. In this review, we summarize recent structural and functional studies of MRPs and discuss emergent structural paradigms for the control of MLL1 activity.
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Affiliation(s)
- Pamela Zhang
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H8M5
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27
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Abstract
In eukaryotes, several lysine residues on histone proteins are methylated. This posttranslational modification is linked to a myriad of nuclear-based transactions such as epigenetic inheritance of heterochromatin, regulation of gene expression, DNA damage repair, and DNA replication. The majority of the enzymes responsible for writing these marks onto chromatin belong to the SET domain family of histone lysine methyltransferases. Although they often share important structural features, including a conserved catalytic domain, SET domain enzymes use different mechanisms to achieve substrate recognition, mono-, di-, or trimethylate lysine residues and some require other proteins to achieve maximal methyltransferase activity. In this chapter, we summarize our efforts to purify, crystallize, and enzymatically characterize SET domain enzymes with a specific focus on the histone H3K27 monomethyltransferase ATXR5.
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Affiliation(s)
- E Bergamin
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - J F Couture
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.
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28
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Pandelieva AT, Baran MJ, Calderini GF, McCann JL, Tremblay V, Sarvan S, Davey JA, Couture JF, Chica RA. Brighter Red Fluorescent Proteins by Rational Design of Triple-Decker Motif. ACS Chem Biol 2016; 11:508-17. [PMID: 26697759 DOI: 10.1021/acschembio.5b00774] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Red fluorescent proteins (RFPs) are used extensively in chemical biology research as fluorophores for live cell imaging, as partners in FRET pairs, and as signal transducers in biosensors. For all of these applications, brighter RFP variants are desired. Here, we used rational design to increase the quantum yield of monomeric RFPs in order to improve their brightness. We postulated that we could increase quantum yield by restricting the conformational degrees of freedom of the RFP chromophore. To test our hypothesis, we introduced aromatic residues above the chromophore of mRojoA, a dim RFP containing a π-stacked Tyr residue directly beneath the chromophore, in order to reduce chromophore conformational flexibility via improved packing and steric complementarity. The best mutant identified displayed an absolute quantum yield increase of 0.07, representing an over 3-fold improvement relative to mRojoA. Remarkably, this variant was isolated following the screening of only 48 mutants, a library size that is several orders of magnitude smaller than those previously used to achieve equivalent gains in quantum yield in other RFPs. The crystal structure of the highest quantum yield mutant showed that the chromophore is sandwiched between two Tyr residues in a triple-decker motif of aromatic rings. Presence of this motif increases chromophore rigidity, as evidenced by the significantly reduced temperature factors compared to dim RFPs. Overall, the approach presented here paves the way for the rapid development of fluorescent proteins with higher quantum yield and overall brightness.
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Affiliation(s)
- Antonia T Pandelieva
- Department of Chemistry and Biomolecular Sciences, University of Ottawa , 10 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Miranda J Baran
- Department of Chemistry and Biomolecular Sciences, University of Ottawa , 10 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Guido F Calderini
- Department of Chemistry and Biomolecular Sciences, University of Ottawa , 10 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Jenna L McCann
- Department of Chemistry and Biomolecular Sciences, University of Ottawa , 10 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Véronique Tremblay
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Sabina Sarvan
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - James A Davey
- Department of Chemistry and Biomolecular Sciences, University of Ottawa , 10 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Centre for Catalysis Research and Innovation, University of Ottawa , 30 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Roberto A Chica
- Department of Chemistry and Biomolecular Sciences, University of Ottawa , 10 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
- Centre for Catalysis Research and Innovation, University of Ottawa , 30 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
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29
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Tan Y, AlKhamees B, Jia D, Li L, Couture JF, Figeys D, Jinushi M, Wang L. MFG-E8 Is Critical for Embryonic Stem Cell-Mediated T Cell Immunomodulation. Stem Cell Reports 2015; 5:741-752. [PMID: 26455415 PMCID: PMC4649138 DOI: 10.1016/j.stemcr.2015.09.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 09/08/2015] [Accepted: 09/09/2015] [Indexed: 02/03/2023] Open
Abstract
The molecules and mechanisms pertinent to the low immunogenicity of undifferentiated embryonic stem cells (ESCs) remain poorly understood. Here, we provide evidence that milk fat globule epidermal growth factor 8 (MFG-E8) is a vital mediator in this phenomenon and directly suppresses T cell immune responses. MFG-E8 is enriched in undifferentiated ESCs but diminished in differentiated ESCs. Upregulation of MFG-E8 in ESCs increases the successful engraftment of both undifferentiated and differentiated ESCs across major histocompatibility complex barriers. MFG-E8 suppresses T cell activation/proliferation and inhibits Th1, Th2, and Th17 subpopulations while increasing regulatory T cell subsets. Neutralizing MFG-E8 substantially abrogates these effects, whereas addition of recombinant MFG-E8 to differentiated ESCs restores immunosuppression. Furthermore, we provide the evidence that MFG-E8 suppresses T cell activation and regulates T cell polarization by inhibiting PKCθ phosphorylation through the α3/5βV integrin receptor. Our findings offer an approach to facilitate transplantation acceptance. MFG-E8 is enriched in undifferentiated but diminished in differentiated ESCs MFG-E8 promotes allogeneic engraftment of ESC-derived tissues across the MHC barrier ESC-produced MFG-E8 inhibits Th1/Th2/Th17 while promoting regulatory T cells MFG-E8 modulates T cell polarization via inhibiting PKCθ phosphorylation
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Affiliation(s)
- Yuan Tan
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Bodour AlKhamees
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Deyong Jia
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Li Li
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Jean-François Couture
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Masahisa Jinushi
- Institute for Advanced Medical Research, Keio University School of Medicine, 35 Shinanomachi, Shinjiku-ku, Tokyo 160-8582, Japan.
| | - Lisheng Wang
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.
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30
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Zhang P, Chaturvedi CP, Tremblay V, Cramet M, Brunzelle JS, Skiniotis G, Brand M, Shilatifard A, Couture JF. A phosphorylation switch on RbBP5 regulates histone H3 Lys4 methylation. Genes Dev 2015; 29:123-8. [PMID: 25593305 PMCID: PMC4298132 DOI: 10.1101/gad.254870.114] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The methyltransferase activity of MLL1 is allosterically regulated by a four-subunit complex composed of WDR5, RbBP5, Ash2L, and DPY30 (also referred to as WRAD). Zhang et al. show that in WRAD, a concave surface of the Ash2L SPRY domain binds to RbBP5. This Ash2L/RbBP5 interface is important for heterodimer formation, stimulation of MLL1 catalytic activity, and erythroid cell terminal differentiation. A phosphorylation switch on RbBP5 stimulates WRAD complex formation and significantly increases KMT2 enzyme methylation rates. The methyltransferase activity of the trithorax group (TrxG) protein MLL1 found within its COMPASS (complex associated with SET1)-like complex is allosterically regulated by a four-subunit complex composed of WDR5, RbBP5, Ash2L, and DPY30 (also referred to as WRAD). We report structural evidence showing that in WRAD, a concave surface of the Ash2L SPIa and ryanodine receptor (SPRY) domain binds to a cluster of acidic residues, referred to as the D/E box, in RbBP5. Mutational analysis shows that residues forming the Ash2L/RbBP5 interface are important for heterodimer formation, stimulation of MLL1 catalytic activity, and erythroid cell terminal differentiation. We also demonstrate that a phosphorylation switch on RbBP5 stimulates WRAD complex formation and significantly increases KMT2 (lysine [K] methyltransferase 2) enzyme methylation rates. Overall, our findings provide structural insights into the assembly of the WRAD complex and point to a novel regulatory mechanism controlling the activity of the KMT2/COMPASS family of lysine methyltransferases.
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Affiliation(s)
- Pamela Zhang
- Department of Biochemistry, Microbiology, and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Chandra-Prakash Chaturvedi
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ontario K1H 8L6, Canada
| | - Veronique Tremblay
- Department of Biochemistry, Microbiology, and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Myriam Cramet
- Department of Biochemistry, Microbiology, and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Joseph S Brunzelle
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Georgios Skiniotis
- Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Marjorie Brand
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ontario K1H 8L6, Canada
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois 60611, USA
| | - Jean-François Couture
- Department of Biochemistry, Microbiology, and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada;
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Lanouette S, Davey JA, Elisma F, Ning Z, Figeys D, Chica RA, Couture JF. Discovery of substrates for a SET domain lysine methyltransferase predicted by multistate computational protein design. Structure 2014; 23:206-215. [PMID: 25533488 DOI: 10.1016/j.str.2014.11.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [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: 08/29/2014] [Revised: 11/04/2014] [Accepted: 11/05/2014] [Indexed: 01/01/2023]
Abstract
Characterization of lysine methylation has proven challenging despite its importance in biological processes such as gene transcription, protein turnover, and cytoskeletal organization. In contrast to other key posttranslational modifications, current proteomics techniques have thus far shown limited success at characterizing methyl-lysine residues across the cellular landscape. To complement current biochemical characterization methods, we developed a multistate computational protein design procedure to probe the substrate specificity of the protein lysine methyltransferase SMYD2. Modeling of substrate-bound SMYD2 identified residues important for substrate recognition and predicted amino acids necessary for methylation. Peptide- and protein- based substrate libraries confirmed that SMYD2 activity is dictated by the motif [LFM]-1-K(∗)-[AFYMSHRK]+1-[LYK]+2 around the target lysine K(∗). Comprehensive motif-based searches and mutational analysis further established four additional substrates of SMYD2. Our methodology paves the way to systematically predict and validate posttranslational modification sites while simultaneously pairing them with their associated enzymes.
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Affiliation(s)
- Sylvain Lanouette
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - James A Davey
- Department of Chemistry, University of Ottawa, Ottawa, ON, K1N 6N5, Canada; Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Fred Elisma
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Department of Chemistry, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Roberto A Chica
- Department of Chemistry, University of Ottawa, Ottawa, ON, K1N 6N5, Canada; Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
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32
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Tremblay V, Zhang P, Chaturvedi CP, Thornton J, Brunzelle JS, Skiniotis G, Shilatifard A, Brand M, Couture JF. Molecular basis for DPY-30 association to COMPASS-like and NURF complexes. Structure 2014; 22:1821-1830. [PMID: 25456412 DOI: 10.1016/j.str.2014.10.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 09/15/2014] [Accepted: 10/06/2014] [Indexed: 01/31/2023]
Abstract
DPY-30 is a subunit of mammalian COMPASS-like complexes (complex of proteins associated with Set1) and regulates global histone H3 Lys-4 trimethylation. Here we report structural evidence showing that the incorporation of DPY-30 into COMPASS-like complexes is mediated by several hydrophobic interactions between an amphipathic α helix located on the C terminus of COMPASS subunit ASH2L and the inner surface of the DPY-30 dimerization/docking (D/D) module. Mutations impairing the interaction between ASH2L and DPY-30 result in a loss of histone H3K4me3 at the β locus control region and cause a delay in erythroid cell terminal differentiation. Using overlay assays, we defined a consensus sequence for DPY-30 binding proteins and found that DPY-30 interacts with BAP18, a subunit of the nucleosome remodeling factor complex. Overall, our results indicate that the ASH2L/DPY-30 complex is important for cell differentiation and provide insights into the ability of DPY-30 to associate with functionally divergent multisubunit complexes.
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Affiliation(s)
- Véronique Tremblay
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Pamela Zhang
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Chandra-Prakash Chaturvedi
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8L6, Canada
| | - Janet Thornton
- Department of Biochemistry and Molecular Genetics, Northwestern University, Searle Building, 320 East Superior Street, Chicago, IL 60611, USA
| | - Joseph S Brunzelle
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Georgios Skiniotis
- Life Sciences Institute and Department of Biological Chemistry, Medical School, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University, Searle Building, 320 East Superior Street, Chicago, IL 60611, USA
| | - Marjorie Brand
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8L6, Canada
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada.
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Gagné D, Couture JF, Simonović M, Doucet N. Structural and biophysical characterization of human RNase 6. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314083569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Human members of the RNase A superfamily include eight rapidly evolving homologous enzymes with varying ribonucleolytic activity. All eight canonical members are characterized by the presence of two histidines and a lysine forming the catalytic triad, in addition to strictly conserved cysteines involved in the formation of 3 or 4 disulfide bridges essential for structural integrity. Despite these architectural and catalytic similarities, human RNases are functionally diverse and their biological activities remain elusive. Apart from degrading RNA with varying degrees of efficiency, these structural homologues have acquired a variety of distinct biological functions, including anti-bactericidal, cytotoxic, angiogenic, immunosuppressive, anti-tumoral and/or anti-viral activities. Among human members of this vertebrate-specific family, RNase 6 and RNase 8 have never been structurally resolved. To better understand its biological function and to characterize its molecular interactions with RNA and/or potential unknown ligands, we present the three-dimensional structure of human RNase 6 in its apo form. While the enzyme shares similar structural features with other members of the RNase A superfamily, we emphasize interesting differences unique to RNase 6 that may be pertaining to its unique biological function. Additional NMR, CD and ITC biophysical characterization in presence of RNA ligands will also be presented.
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Bergamin E, Blais A, Couture JF. Keeping them all together: β-propeller domains in histone methyltransferase complexes. J Mol Biol 2014; 426:3363-75. [PMID: 24853063 DOI: 10.1016/j.jmb.2014.05.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 05/05/2014] [Accepted: 05/07/2014] [Indexed: 12/28/2022]
Abstract
Histone methyltransferases (HKMTs) residing in multi-subunit protein complexes frequently require the presence of β-propeller proteins to achieve their biological functions. Recent biochemical studies have highlighted the functional diversity of these scaffolding proteins in maintaining the integrity of the complexes, allosterically regulating HKMT enzymatic activity and acting as "histone tethering devices" to facilitate the interaction between HKMTs and their substrates. Structural studies have revealed that, while β-propeller domain proteins share structural similarity, they employ divergent mechanisms to achieve their functions. This review focuses on the progress made in the last decade to identify the biochemical determinants underlying the functions of these important proteins.
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Affiliation(s)
- Elisa Bergamin
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Alexandre Blais
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.
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35
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Abstract
Large‐scale characterization of post‐translational modifications (PTMs), such as phosphorylation, acetylation and ubiquitination, has highlighted their importance in the regulation of a myriad of signaling events. While high‐throughput technologies have tremendously helped cataloguing the proteins modified by these PTMs, the identification of lysine‐methylated proteins, a PTM involving the transfer of one, two or three methyl groups to the ε‐amine of a lysine side chain, has lagged behind. While the initial findings were focused on the methylation of histone proteins, several studies have recently identified novel non‐histone lysine‐methylated proteins. This review provides a compilation of all lysine methylation sites reported to date. We also present key examples showing the impact of lysine methylation and discuss the circuitries wired by this important PTM.
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Affiliation(s)
- Sylvain Lanouette
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
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Jacob Y, Bergamin E, Donoghue MTA, Mongeon V, LeBlanc C, Voigt P, Underwood CJ, Brunzelle JS, Michaels SD, Reinberg D, Couture JF, Martienssen RA. Selective methylation of histone H3 variant H3.1 regulates heterochromatin replication. Science 2014; 343:1249-53. [PMID: 24626927 DOI: 10.1126/science.1248357] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Histone variants have been proposed to act as determinants for posttranslational modifications with widespread regulatory functions. We identify a histone-modifying enzyme that selectively methylates the replication-dependent histone H3 variant H3.1. The crystal structure of the SET domain of the histone H3 lysine-27 (H3K27) methyltransferase ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5 (ATXR5) in complex with a H3.1 peptide shows that ATXR5 contains a bipartite catalytic domain that specifically "reads" alanine-31 of H3.1. Variation at position 31 between H3.1 and replication-independent H3.3 is conserved in plants and animals, and threonine-31 in H3.3 is responsible for inhibiting the activity of ATXR5 and its paralog, ATXR6. Our results suggest a simple model for the mitotic inheritance of the heterochromatic mark H3K27me1 and the protection of H3.3-enriched genes against heterochromatization during DNA replication.
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Affiliation(s)
- Yannick Jacob
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
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Bélanger K, Savoie M, Rosales Gerpe MC, Couture JF, Langlois MA. Binding of RNA by APOBEC3G controls deamination-independent restriction of retroviruses. Nucleic Acids Res 2013; 41:7438-52. [PMID: 23761443 PMCID: PMC3753645 DOI: 10.1093/nar/gkt527] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [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: 01/24/2013] [Revised: 05/19/2013] [Accepted: 05/21/2013] [Indexed: 11/19/2022] Open
Abstract
APOBEC3G (A3G) is a host-encoded protein that potently restricts the infectivity of a broad range of retroviruses. This can occur by mechanisms dependent on catalytic activity, resulting in the mutagenic deamination of nascent viral cDNA, and/or by other means that are independent of its catalytic activity. It is not yet known to what extent deamination-independent processes contribute to the overall restriction, how they exactly work or how they are regulated. Here, we show that alanine substitution of either tryptophan 94 (W94A) or 127 (W127A) in the non-catalytic N-terminal domain of A3G severely impedes RNA binding and alleviates deamination-independent restriction while still maintaining DNA mutator activity. Substitution of both tryptophans (W94A/W127A) produces a more severe phenotype in which RNA binding and RNA-dependent protein oligomerization are completely abrogated. We further demonstrate that RNA binding is specifically required for crippling late reverse transcript accumulation, preventing proviral DNA integration and, consequently, restricting viral particle release. We did not find that deaminase activity made a significant contribution to the restriction of any of these processes. In summary, this work reveals that there is a direct correlation between A3G's capacity to bind RNA and its ability to inhibit retroviral infectivity in a deamination-independent manner.
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Affiliation(s)
- Kasandra Bélanger
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5, Emerging Pathogens Research Centre, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5 and Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Mathieu Savoie
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5, Emerging Pathogens Research Centre, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5 and Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - María Carla Rosales Gerpe
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5, Emerging Pathogens Research Centre, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5 and Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Jean-François Couture
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5, Emerging Pathogens Research Centre, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5 and Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Marc-André Langlois
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5, Emerging Pathogens Research Centre, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5 and Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
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38
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Mitchell L, Lau A, Lambert JP, Zhou H, Fong Y, Couture JF, Figeys D, Baetz K. Regulation of septin dynamics by the Saccharomyces cerevisiae lysine acetyltransferase NuA4. PLoS One 2011; 6:e25336. [PMID: 21984913 PMCID: PMC3184947 DOI: 10.1371/journal.pone.0025336] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 09/01/2011] [Indexed: 01/08/2023] Open
Abstract
In the budding yeast Saccharomyces cerevisiae, the lysine acetyltransferase NuA4 has been linked to a host of cellular processes through the acetylation of histone and non-histone targets. To discover proteins regulated by NuA4-dependent acetylation, we performed genome-wide synthetic dosage lethal screens to identify genes whose overexpression is toxic to non-essential NuA4 deletion mutants. The resulting genetic network identified a novel link between NuA4 and septin proteins, a group of highly conserved GTP-binding proteins that function in cytokinesis. We show that acetyltransferase-deficient NuA4 mutants have defects in septin collar formation resulting in the development of elongated buds through the Swe1-dependent morphogenesis checkpoint. We have discovered multiple sites of acetylation on four of the five yeast mitotic septins, Cdc3, Cdc10, Cdc12 and Shs1, and determined that NuA4 can acetylate three of the four in vitro. In vivo we find that acetylation levels of both Shs1 and Cdc10 are reduced in a catalytically inactive esa1 mutant. Finally, we determine that cells expressing a Shs1 protein with decreased acetylation in vivo have defects in septin localization that are similar to those observed in NuA4 mutants. These findings provide the first evidence that yeast septin proteins are acetylated and that NuA4 impacts septin dynamics.
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Affiliation(s)
- Leslie Mitchell
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Andrea Lau
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Jean-Philippe Lambert
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Hu Zhou
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Ying Fong
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Kristin Baetz
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
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Abu-Farha M, Lanouette S, Elisma F, Tremblay V, Butson J, Figeys D, Couture JF. Proteomic analyses of the SMYD family interactomes identify HSP90 as a novel target for SMYD2. J Mol Cell Biol 2011; 3:301-8. [DOI: 10.1093/jmcb/mjr025] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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40
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Sarvan S, Avdic V, Tremblay V, Chaturvedi CP, Zhang P, Lanouette S, Blais A, Brunzelle JS, Brand M, Couture JF. Crystal structure of the trithorax group protein ASH2L reveals a forkhead-like DNA binding domain. Nat Struct Mol Biol 2011; 18:857-9. [PMID: 21642971 PMCID: PMC3983046 DOI: 10.1038/nsmb.2093] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 05/30/2011] [Indexed: 01/15/2023]
Abstract
Absent, small or homeotic discs-like 2 (ASH2L) is a trithorax group (TrxG) protein and a regulatory subunit of the SET1 family of lysine methyltransferases. Here we report that ASH2L binds DNA using a forkhead-like helix-wing-helix (HWH) domain. In vivo, the ASH2L HWH domain is required for binding to the β-globin locus control region, histone H3 Lys4 (H3K4) trimethylation and maximal expression of the β-globin gene (Hbb-1), validating the functional importance of the ASH2L DNA binding domain.
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Affiliation(s)
- Sabina Sarvan
- Ottawa Institute of Systems Biology, Department of Biochemistry, University of Ottawa, Ottawa, Ontario, Canada
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41
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Avdic V, Zhang P, Lanouette S, Groulx A, Tremblay V, Brunzelle J, Couture JF. Structural and biochemical insights into MLL1 core complex assembly. Structure 2011; 19:101-8. [PMID: 21220120 DOI: 10.1016/j.str.2010.09.022] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 08/31/2010] [Accepted: 09/30/2010] [Indexed: 12/31/2022]
Abstract
Histone H3 Lys-4 methylation is predominantly catalyzed by a family of methyltransferases whose enzymatic activity depends on their interaction with a three-subunit complex composed of WDR5, RbBP5, and Ash2L. Here, we report that a segment of 50 residues of RbBP5 bridges the Ash2L C-terminal domain to WDR5. The crystal structure of WDR5 in ternary complex with RbBP5 and MLL1 reveals that both proteins binds peptide-binding clefts located on opposite sides of WDR5's β-propeller domain. RbBP5 engages in several hydrogen bonds and van der Waals contacts within a V-shaped cleft formed by the junction of two blades on WDR5. Mutational analyses of both the WDR5 V-shaped cleft and RbBP5 residues reveal that the interactions between RbBP5 and WDR5 are important for the stimulation of MLL1 methyltransferase activity. Overall, this study provides the structural basis underlying the formation of the WDR5-RbBP5 subcomplex and further highlight the crucial role of WDR5 in scaffolding the MLL1 core complex.
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Affiliation(s)
- Vanja Avdic
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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42
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Del Rizzo PA, Couture JF, Dirk LMA, Strunk BS, Roiko MS, Brunzelle JS, Houtz RL, Trievel RC. SET7/9 catalytic mutants reveal the role of active site water molecules in lysine multiple methylation. J Biol Chem 2010; 285:31849-58. [PMID: 20675860 DOI: 10.1074/jbc.m110.114587] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
SET domain lysine methyltransferases (KMTs) methylate specific lysine residues in histone and non-histone substrates. These enzymes also display product specificity by catalyzing distinct degrees of methylation of the lysine ε-amino group. To elucidate the molecular mechanism underlying this specificity, we have characterized the Y245A and Y305F mutants of the human KMT SET7/9 (also known as KMT7) that alter its product specificity from a monomethyltransferase to a di- and a trimethyltransferase, respectively. Crystal structures of these mutants in complex with peptides bearing unmodified, mono-, di-, and trimethylated lysines illustrate the roles of active site water molecules in aligning the lysine ε-amino group for methyl transfer with S-adenosylmethionine. Displacement or dissociation of these solvent molecules enlarges the diameter of the active site, accommodating the increasing size of the methylated ε-amino group during successive methyl transfer reactions. Together, these results furnish new insights into the roles of active site water molecules in modulating lysine multiple methylation by SET domain KMTs and provide the first molecular snapshots of the mono-, di-, and trimethyl transfer reactions catalyzed by these enzymes.
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Affiliation(s)
- Paul A Del Rizzo
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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43
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Bulfer SL, Scott EM, Couture JF, Pillus L, Trievel RC. Crystal structure and functional analysis of homocitrate synthase, an essential enzyme in lysine biosynthesis. J Biol Chem 2009; 284:35769-80. [PMID: 19776021 PMCID: PMC2791007 DOI: 10.1074/jbc.m109.046821] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 09/10/2009] [Indexed: 11/06/2022] Open
Abstract
Homocitrate synthase (HCS) catalyzes the first and committed step in lysine biosynthesis in many fungi and certain Archaea and is a potential target for antifungal drugs. Here we report the crystal structure of the HCS apoenzyme from Schizosaccharomyces pombe and two distinct structures of the enzyme in complex with the substrate 2-oxoglutarate (2-OG). The structures reveal that HCS forms an intertwined homodimer stabilized by domain-swapping between the N- and C-terminal domains of each monomer. The N-terminal catalytic domain is composed of a TIM barrel fold in which 2-OG binds via hydrogen bonds and coordination to the active site divalent metal ion, whereas the C-terminal domain is composed of mixed alpha/beta topology. In the structures of the HCS apoenzyme and one of the 2-OG binary complexes, a lid motif from the C-terminal domain occludes the entrance to the active site of the neighboring monomer, whereas in the second 2-OG complex the lid is disordered, suggesting that it regulates substrate access to the active site through its apparent flexibility. Mutations of the active site residues involved in 2-OG binding or implicated in acid-base catalysis impair or abolish activity in vitro and in vivo. Together, these results yield new insights into the structure and catalytic mechanism of HCSs and furnish a platform for developing HCS-selective inhibitors.
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Affiliation(s)
- Stacie L. Bulfer
- From the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109 and
| | - Erin M. Scott
- the Division of Biological Sciences and UCSD Moores Cancer Center, University of California, San Diego, California 92093
| | - Jean-François Couture
- From the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109 and
| | - Lorraine Pillus
- the Division of Biological Sciences and UCSD Moores Cancer Center, University of California, San Diego, California 92093
| | - Raymond C. Trievel
- From the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109 and
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Cantin L, Faucher F, Couture JF, de Jésus-Tran KP, Legrand P, Ciobanu LC, Fréchette Y, Labrecque R, Singh SM, Labrie F, Breton R. Structural characterization of the human androgen receptor ligand-binding domain complexed with EM5744, a rationally designed steroidal ligand bearing a bulky chain directed toward helix 12. J Biol Chem 2007; 282:30910-9. [PMID: 17711855 DOI: 10.1074/jbc.m705524200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [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: 01/09/2023] Open
Abstract
Antiandrogens are commonly used to treat androgen-dependent disorders. The currently used drugs unfortunately possess very weak affinity for the human AR (hAR), thus indicating the need to develop new high-affinity steroidal antiandrogens. Our compounds are specially designed to impede repositioning of the mobile carboxyl-terminal helix 12, which blocks the ligand-dependent transactivation function (AF-2) located in the AR ligand-binding domain (ARLBD). Using crystal structures of the hARLBD, we first found that H12 could be directly reached from the ligand-binding pocket (LBP) by a chain positioned on the C18 atom of an androgen steroid nucleus. A set of 5alpha-dihydrotestosterone-derived molecules bearing various C18 chains were thus synthesized and tested for their capacity to bind hAR and act as antagonists. Although most of those having very high affinity for hAR were agonists, several very potent antagonists were obtained, confirming the structural importance of the C18 chain. To understand the role of the C18 chain in their agonistic/antagonistic properties, the structure of the hARLBD complexed with one of these agonists, EM5744, was determined at a 1.65-A resolution. We have identified new interactions involving Gln(738), Met(742), and His(874) that explain both the high affinity of this compound and the inability of its bulky chain to prevent the repositioning of H12. This structural information will be helpful to refine the structure of the chains placed on the C18 atom to obtain efficient H12-directed steroidal antiandrogens.
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Affiliation(s)
- Line Cantin
- Oncology and Molecular Endocrinology Research Center, Laval University Medical Center (CHUL) and Laval University, Québec G1V 4G2, Canada
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Couture JF, Collazo E, Ortiz-Tello PA, Brunzelle JS, Trievel RC. Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase. Nat Struct Mol Biol 2007; 14:689-95. [PMID: 17589523 DOI: 10.1038/nsmb1273] [Citation(s) in RCA: 219] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2007] [Accepted: 06/15/2007] [Indexed: 12/25/2022]
Abstract
JMJD2A is a JmjC histone demethylase (HDM) that catalyzes the demethylation of di- and trimethylated Lys9 and Lys36 in histone H3 (H3K9me2/3 and H3K36me2/3). Here we present the crystal structures of the JMJD2A catalytic domain in complex with H3K9me3, H3K36me2 and H3K36me3 peptides. The structures reveal that histone substrates are recognized through a network of backbone hydrogen bonds and hydrophobic interactions that deposit the trimethyllysine into the active site. The trimethylated epsilon-ammonium cation is coordinated within a methylammonium-binding pocket through carbon-oxygen (CH...O) hydrogen bonds that position one of the zeta-methyl groups adjacent to the Fe(II) center for hydroxylation and demethylation. Mutations of the residues comprising this pocket abrogate demethylation by JMJD2A, with the exception of an S288A substitution, which augments activity, particularly toward H3K9me2. We propose that this residue modulates the methylation-state specificities of JMJD2 enzymes and other trimethyllysine-specific JmjC HDMs.
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Affiliation(s)
- Jean-François Couture
- Department of Biological Chemistry, University of Michigan, 1150 West Medical Center Drive, Ann Arbor, Michigan 48109-0606, USA
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Dirk LMA, Flynn EM, Dietzel K, Couture JF, Trievel RC, Houtz RL. Kinetic manifestation of processivity during multiple methylations catalyzed by SET domain protein methyltransferases. Biochemistry 2007; 46:3905-15. [PMID: 17338551 DOI: 10.1021/bi6023644] [Citation(s) in RCA: 39] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Processive versus distributive methyl group transfer was assessed for pea Rubisco large subunit methyltransferase, a SET domain protein lysine methyltransferase catalyzing the formation of trimethyllysine-14 in the large subunit of Rubisco. Catalytically competent complexes between an immobilized form of des(methyl) Rubisco and Rubisco large subunit methyltransferase were used to demonstrate enzyme release that was co-incident with and dependent on formation of trimethyllysine. Catalytic rate constants determined for formation of trimethyllysine were considerably lower ( approximately 10-fold) than rate constants determined for total radiolabel incorporation from [3H-methyl]-S-adenosylmethionine. Double-reciprocal velocity plots under catalytic conditions favoring monomethyllysine indicated a random or ordered reaction mechanism, while conditions favoring trimethyllysine suggested a hybrid ping-pong mechanism. These results were compared with double-reciprocal velocity plots and product analyses obtained for HsSET7/9 (a monomethyltransferase) and SpCLR4 (a dimethyltransferase) and suggest a predictive ability of double-reciprocal velocity plots for single versus multiple methyl group transfers by SET domain protein lysine methyltransferases. A model is proposed for SET domain protein lysine methyltransferases in which initial binding of polypeptide substrate and S-adenosylmethionine is random, with polypeptide binding followed by deprotonation of the epsilon-amine of the target lysyl residue and subsequent methylation. Following methyl group transfer, S-adenosylhomocysteine and monomethylated polypeptide dissociate from monomethyltransferases, but di- and trimethyltransferases begin a successive and catalytically obligatory deprotonation of enzyme-bound methylated lysyl intermediates, which along with binding and release of S-adenosylmethionine and S-adenosylhomocysteine is manifested as a hybrid ping-pong-like reaction mechanism.
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Affiliation(s)
- Lynnette M A Dirk
- Department of Horticulture, Plant Physiology/Biochemistry/Molecular Biology Program, 401D Plant Science Building, University of Kentucky, Lexington, Kentucky 40546-0312, USA
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Couture JF, Trievel RC. Histone-modifying enzymes: encrypting an enigmatic epigenetic code. Curr Opin Struct Biol 2006; 16:753-60. [PMID: 17070031 DOI: 10.1016/j.sbi.2006.10.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Revised: 09/14/2006] [Accepted: 10/13/2006] [Indexed: 10/24/2022]
Abstract
Histone-modifying enzymes catalyze a diverse array of post-translational modifications of core and linker histones within chromatin. These modifications govern a multitude of genomic functions, particularly gene expression, and are believed to constitute an epigenetic code. Histone-modifying enzymes inscribe this code by catalyzing site-selective modifications, which are subsequently interpreted by effector proteins that recognize specific covalent marks. The substrate specificity of these enzymes is of fundamental biological importance because it underpins this epigenetic code. Recently, the structural basis of this specificity has been examined with regards to recently determined structures of GCN5 acetyltransferases and SET domain methyltransferases in complex with their cognate histone substrates.
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Affiliation(s)
- Jean-François Couture
- Department of Biological Chemistry, University of Michigan, 1150 West Medical Center Drive, Ann Arbor, MI 48109-0606, USA
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Couture JF, Collazo E, Trievel RC. Molecular recognition of histone H3 by the WD40 protein WDR5. Nat Struct Mol Biol 2006; 13:698-703. [PMID: 16829960 DOI: 10.1038/nsmb1116] [Citation(s) in RCA: 191] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2006] [Accepted: 05/31/2006] [Indexed: 11/09/2022]
Abstract
The WD40-repeat protein WDR5 is a conserved subunit of Trithorax (TRX) histone methyltransferase complexes. WDR5 has been reported to selectively bind dimethylated Lys4 (K4me2) in histone H3 to promote K4 trimethylation by TRX. To elucidate the basis of this binding specificity, we have determined the crystal structure of WDR5 bound to a histone H3 peptide bearing K4me2. The structure reveals that the N terminus of histone H3 binds as a 3(10)-helix in the central depression formed by the WD40 repeats. R2 in histone H3 is bound in the acidic channel in the protein's core, whereas K4me2 is solvent exposed and does not engage in direct interactions with WDR5. Functional studies confirm that WDR5 recognizes A1, R2 and T3 in histone H3 but has virtually identical affinities for the unmodified and mono-, di- and trimethylated forms of K4, demonstrating that it does not discriminate among different degrees of methylation of this residue.
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Affiliation(s)
- Jean-François Couture
- Department of Biological Chemistry, University of Michigan, 1301 Catherine Road, Ann Arbor, Michigan 48109-0606, USA
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Couture JF, Hauk G, Thompson MJ, Blackburn GM, Trievel RC. Catalytic roles for carbon-oxygen hydrogen bonding in SET domain lysine methyltransferases. J Biol Chem 2006; 281:19280-7. [PMID: 16682405 DOI: 10.1074/jbc.m602257200] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SET domain enzymes represent a distinct family of protein lysine methyltransferases in eukaryotes. Recent studies have yielded significant insights into the structural basis of substrate recognition and the product specificities of these enzymes. However, the mechanism by which SET domain methyltransferases catalyze the transfer of the methyl group from S-adenosyl-L-methionine to the lysine epsilon-amine has remained unresolved. To elucidate this mechanism, we have determined the structures of the plant SET domain enzyme, pea ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit methyltransferase, bound to S-adenosyl-L-methionine, and its non-reactive analogs Aza-adenosyl-L-methionine and Sinefungin, and characterized the binding of these ligands to a homolog of the enzyme. The structural and biochemical data collectively reveal that S-adenosyl-L-methionine is selectively recognized through carbon-oxygen hydrogen bonds between the cofactor's methyl group and an array of structurally conserved oxygens that comprise the methyl transfer pore in the active site. Furthermore, the structure of the enzyme co-crystallized with the product epsilon-N-trimethyllysine reveals a trigonal array of carbon-oxygen interactions between the epsilon-ammonium methyl groups and the oxygens in the pore. Taken together, these results establish a central role for carbon-oxygen hydrogen bonding in aligning the cofactor's methyl group for transfer to the lysine epsilon-amine and in coordinating the methyl groups after transfer to facilitate multiple rounds of lysine methylation.
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Affiliation(s)
- Jean-François Couture
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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Couture JF, Collazo E, Hauk G, Trievel RC. Structural basis for the methylation site specificity of SET7/9. Nat Struct Mol Biol 2006; 13:140-6. [PMID: 16415881 DOI: 10.1038/nsmb1045] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2005] [Accepted: 12/05/2005] [Indexed: 11/09/2022]
Abstract
Human SET7/9 is a protein lysine methyltransferase (PKMT) that methylates histone H3, the tumor suppressor p53 and the TBP-associated factor TAF10. To elucidate the determinants of its substrate specificity, we have solved the enzyme's structure bound to a TAF10 peptide and examined its ability to methylate histone H3, TAF10 and p53 substrates bearing either mutations or covalent modifications within their respective methylation sites. Collectively, our data reveal that SET7/9 recognizes a conserved K/R-S/T/A motif preceding the lysine substrate and has a propensity to bind aspartates and asparagines on the C-terminal side of the lysine target. We then used a sequence-based approach with this motif to identify novel substrates for this PKMT. Among the putative targets is TAF7, which is methylated at Lys5 by the enzyme in vitro. These results demonstrate the predictive value of the consensus motif in identifying novel substrates for SET7/9.
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Affiliation(s)
- Jean-François Couture
- Department of Biological Chemistry, University of Michigan, 1301 Catherine Road, Ann Arbor, Michigan 48109-0606, USA
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