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Mihalič F, Benz C, Kassa E, Lindqvist R, Simonetti L, Inturi R, Aronsson H, Andersson E, Chi CN, Davey NE, Överby AK, Jemth P, Ivarsson Y. Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets. Nat Commun 2023; 14:5636. [PMID: 37704626 PMCID: PMC10499821 DOI: 10.1038/s41467-023-41312-8] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 08/30/2023] [Indexed: 09/15/2023] Open
Abstract
The virus life cycle depends on host-virus protein-protein interactions, which often involve a disordered protein region binding to a folded protein domain. Here, we used proteomic peptide phage display (ProP-PD) to identify peptides from the intrinsically disordered regions of the human proteome that bind to folded protein domains encoded by the SARS-CoV-2 genome. Eleven folded domains of SARS-CoV-2 proteins were found to bind 281 peptides from human proteins, and affinities of 31 interactions involving eight SARS-CoV-2 protein domains were determined (KD ∼ 7-300 μM). Key specificity residues of the peptides were established for six of the interactions. Two of the peptides, binding Nsp9 and Nsp16, respectively, inhibited viral replication. Our findings demonstrate how high-throughput peptide binding screens simultaneously identify potential host-virus interactions and peptides with antiviral properties. Furthermore, the high number of low-affinity interactions suggest that overexpression of viral proteins during infection may perturb multiple cellular pathways.
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Affiliation(s)
- Filip Mihalič
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Caroline Benz
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Eszter Kassa
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Richard Lindqvist
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187, Umeå, Sweden
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Raviteja Inturi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Hanna Aronsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Celestine N Chi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Anna K Överby
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187, Umeå, Sweden
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden.
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
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2
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Mészáros B, Hatos A, Palopoli N, Quaglia F, Salladini E, Van Roey K, Arthanari H, Dosztányi Z, Felli IC, Fischer PD, Hoch JC, Jeffries CM, Longhi S, Maiani E, Orchard S, Pancsa R, Papaleo E, Pierattelli R, Piovesan D, Pritisanac I, Tenorio L, Viennet T, Tompa P, Vranken W, Tosatto SCE, Davey NE. Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions. Nat Methods 2023; 20:1291-1303. [PMID: 37400558 DOI: 10.1038/s41592-023-01915-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 05/18/2023] [Indexed: 07/05/2023]
Abstract
An unambiguous description of an experiment, and the subsequent biological observation, is vital for accurate data interpretation. Minimum information guidelines define the fundamental complement of data that can support an unambiguous conclusion based on experimental observations. We present the Minimum Information About Disorder Experiments (MIADE) guidelines to define the parameters required for the wider scientific community to understand the findings of an experiment studying the structural properties of intrinsically disordered regions (IDRs). MIADE guidelines provide recommendations for data producers to describe the results of their experiments at source, for curators to annotate experimental data to community resources and for database developers maintaining community resources to disseminate the data. The MIADE guidelines will improve the interpretability of experimental results for data consumers, facilitate direct data submission, simplify data curation, improve data exchange among repositories and standardize the dissemination of the key metadata on an IDR experiment by IDR data sources.
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Affiliation(s)
- Bálint Mészáros
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Structural Biology and Center for Data Driven Discovery, St Jude Children's Research Hospital, Memphis, TN, USA
| | - András Hatos
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
| | - Nicolas Palopoli
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Bernal, Buenos Aires, Argentina
| | - Federica Quaglia
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR-IBIOM), Bari, Italy
| | - Edoardo Salladini
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Kim Van Roey
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Haribabu Arthanari
- Harvard Medical School (HMS), Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA
| | | | - Isabella C Felli
- Department of Chemistry 'Ugo Schiff' and Magnetic Resonance Center, University of Florence, Sesto Fiorentino (Florence), Italy
| | - Patrick D Fischer
- Harvard Medical School (HMS), Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA
| | - Jeffrey C Hoch
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, USA
| | - Cy M Jeffries
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, c/o Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - Sonia Longhi
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), Marseille, France
| | - Emiliano Maiani
- Cancer Structural Biology, Danish Cancer Society Research Center, Copenhagen, Denmark
- UniCamillus - Saint Camillus International University of Health and Medical Sciences, Rome, Italy
| | - Sandra Orchard
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, UK
| | - Rita Pancsa
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Elena Papaleo
- Cancer Structural Biology, Danish Cancer Society Research Center, Copenhagen, Denmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, Lyngby, Denmark
| | - Roberta Pierattelli
- Department of Chemistry 'Ugo Schiff' and Magnetic Resonance Center, University of Florence, Sesto Fiorentino (Florence), Italy
| | - Damiano Piovesan
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Iva Pritisanac
- Hospital for Sick Children, Toronto, Ontario, Canada
- Medical University of Graz, Graz, Austria
| | - Luiggi Tenorio
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Thibault Viennet
- Harvard Medical School (HMS), Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA
| | - Peter Tompa
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- VIB-VUB Center for Structural Biology, Brussels, Belgium
- Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Wim Vranken
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Norman E Davey
- Division Of Cancer Biology, Institute of Cancer Research, Chester Beatty Laboratories, Chelsea, London, UK.
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Kliche J, Garvanska DH, Simonetti L, Badgujar D, Dobritzsch D, Nilsson J, Davey NE, Ivarsson Y. Large-scale phosphomimetic screening identifies phospho-modulated motif-based protein interactions. Mol Syst Biol 2023; 19:e11164. [PMID: 37219487 PMCID: PMC10333884 DOI: 10.15252/msb.202211164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
Phosphorylation is a ubiquitous post-translation modification that regulates protein function by promoting, inhibiting or modulating protein-protein interactions. Hundreds of thousands of phosphosites have been identified but the vast majority have not been functionally characterised and it remains a challenge to decipher phosphorylation events modulating interactions. We generated a phosphomimetic proteomic peptide-phage display library to screen for phosphosites that modulate short linear motif-based interactions. The peptidome covers ~13,500 phospho-serine/threonine sites found in the intrinsically disordered regions of the human proteome. Each phosphosite is represented as wild-type and phosphomimetic variant. We screened 71 protein domains to identify 248 phosphosites that modulate motif-mediated interactions. Affinity measurements confirmed the phospho-modulation of 14 out of 18 tested interactions. We performed a detailed follow-up on a phospho-dependent interaction between clathrin and the mitotic spindle protein hepatoma-upregulated protein (HURP), demonstrating the essentiality of the phospho-dependency to the mitotic function of HURP. Structural characterisation of the clathrin-HURP complex elucidated the molecular basis for the phospho-dependency. Our work showcases the power of phosphomimetic ProP-PD to discover novel phospho-modulated interactions required for cellular function.
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Affiliation(s)
- Johanna Kliche
- Department of Chemistry, BMCUppsala UniversityUppsalaSweden
| | - Dimitriya Hristoforova Garvanska
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | | | - Dilip Badgujar
- Department of Chemistry, BMCUppsala UniversityUppsalaSweden
| | | | - Jakob Nilsson
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Norman E Davey
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
| | - Ylva Ivarsson
- Department of Chemistry, BMCUppsala UniversityUppsalaSweden
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4
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Davey NE, Simonetti L, Ivarsson Y. The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome. Curr Opin Struct Biol 2023; 80:102593. [PMID: 37099901 DOI: 10.1016/j.sbi.2023.102593] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/09/2023] [Accepted: 03/17/2023] [Indexed: 04/28/2023]
Abstract
Short linear motifs (SLiMs) are a unique and ubiquitous class of protein interaction modules that perform key regulatory functions and drive dynamic complex formation. For decades, interactions mediated by SLiMs have accumulated through detailed low-throughput experiments. Recent methodological advances have opened this previously underexplored area of the human interactome to high-throughput protein-protein interaction discovery. In this article, we discuss that SLiM-based interactions represent a significant blind spot in the current interactomics data, introduce the key methods that are illuminating the elusive SLiM-mediated interactome of the human cell on a large scale, and discuss the implications for the field.
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Affiliation(s)
- Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK.
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
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5
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Kotb HM, Davey NE. xProtCAS: A Toolkit for Extracting Conserved Accessible Surfaces from Protein Structures. Biomolecules 2023; 13:906. [PMID: 37371487 DOI: 10.3390/biom13060906] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
The identification of protein surfaces required for interaction with other biomolecules broadens our understanding of protein function, their regulation by post-translational modification, and the deleterious effect of disease mutations. Protein interaction interfaces are often identifiable as patches of conserved residues on a protein's surface. However, finding conserved accessible surfaces on folded regions requires an understanding of the protein structure to discriminate between functional and structural constraints on residue conservation. With the emergence of deep learning methods for protein structure prediction, high-quality structural models are now available for any protein. In this study, we introduce tools to identify conserved surfaces on AlphaFold2 structural models. We define autonomous structural modules from the structural models and convert these modules to a graph encoding residue topology, accessibility, and conservation. Conserved surfaces are then extracted using a novel eigenvector centrality-based approach. We apply the tool to the human proteome identifying hundreds of uncharacterised yet highly conserved surfaces, many of which contain clinically significant mutations. The xProtCAS tool is available as open-source Python software and an interactive web server.
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Affiliation(s)
- Hazem M Kotb
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
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6
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Simonetti L, Nilsson J, McInerney G, Ivarsson Y, Davey NE. SLiM-binding pockets: an attractive target for broad-spectrum antivirals. Trends Biochem Sci 2023; 48:420-427. [PMID: 36623987 DOI: 10.1016/j.tibs.2022.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 12/09/2022] [Accepted: 12/15/2022] [Indexed: 01/08/2023]
Abstract
Short linear motif (SLiM)-mediated interactions offer a unique strategy for viral intervention due to their compact interfaces, ease of convergent evolution, and key functional roles. Consequently, many viruses extensively mimic host SLiMs to hijack or deregulate cellular pathways and the same motif-binding pocket is often targeted by numerous unrelated viruses. A toolkit of therapeutics targeting commonly mimicked SLiMs could provide prophylactic and therapeutic broad-spectrum antivirals and vastly improve our ability to treat ongoing and future viral outbreaks. In this opinion article, we discuss the therapeutic relevance of SLiMs, advocating their suitability as targets for broad-spectrum antiviral inhibitors.
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Affiliation(s)
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Husargatan 3, 751 23 Uppsala, Sweden
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
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7
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Mihalič F, Simonetti L, Giudice G, Sander MR, Lindqvist R, Peters MBA, Benz C, Kassa E, Badgujar D, Inturi R, Ali M, Krystkowiak I, Sayadi A, Andersson E, Aronsson H, Söderberg O, Dobritzsch D, Petsalaki E, Överby AK, Jemth P, Davey NE, Ivarsson Y. Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs. Nat Commun 2023; 14:2409. [PMID: 37100772 PMCID: PMC10132805 DOI: 10.1038/s41467-023-38015-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
Viruses mimic host short linear motifs (SLiMs) to hijack and deregulate cellular functions. Studies of motif-mediated interactions therefore provide insight into virus-host dependencies, and reveal targets for therapeutic intervention. Here, we describe the pan-viral discovery of 1712 SLiM-based virus-host interactions using a phage peptidome tiling the intrinsically disordered protein regions of 229 RNA viruses. We find mimicry of host SLiMs to be a ubiquitous viral strategy, reveal novel host proteins hijacked by viruses, and identify cellular pathways frequently deregulated by viral motif mimicry. Using structural and biophysical analyses, we show that viral mimicry-based interactions have similar binding strength and bound conformations as endogenous interactions. Finally, we establish polyadenylate-binding protein 1 as a potential target for broad-spectrum antiviral agent development. Our platform enables rapid discovery of mechanisms of viral interference and the identification of potential therapeutic targets which can aid in combating future epidemics and pandemics.
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Affiliation(s)
- Filip Mihalič
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Girolamo Giudice
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Marie Rubin Sander
- Department of Pharmaceutical Biosciences, Uppsala University, Husargatan 3, Box 591, SE-751 24, Uppsala, Sweden
| | - Richard Lindqvist
- Department of Clinical Microbiology, Umeå University, 90187, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90186, Umeå, Sweden
| | - Marie Berit Akpiroro Peters
- Department of Clinical Microbiology, Umeå University, 90187, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90186, Umeå, Sweden
| | - Caroline Benz
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Eszter Kassa
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Dilip Badgujar
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Raviteja Inturi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Muhammad Ali
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Izabella Krystkowiak
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Ahmed Sayadi
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Hanna Aronsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ola Söderberg
- Department of Pharmaceutical Biosciences, Uppsala University, Husargatan 3, Box 591, SE-751 24, Uppsala, Sweden
| | - Doreen Dobritzsch
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Evangelia Petsalaki
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Anna K Överby
- Department of Clinical Microbiology, Umeå University, 90187, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90186, Umeå, Sweden
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden.
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK.
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
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8
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Madhu P, Davey NE, Ivarsson Y. How viral proteins bind short linear motifs and intrinsically disordered domains. Essays Biochem 2022; 66:EBC20220047. [PMID: 36504386 DOI: 10.1042/ebc20220047] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 02/11/2024]
Abstract
Viruses are the obligate intracellular parasites that exploit the host cellular machinery to replicate their genome. During the viral life cycle viruses manipulate the host cell through interactions with host proteins. Many of these protein-protein interactions are mediated through the recognition of host globular domains by short linear motifs (SLiMs), or longer intrinsically disordered domains (IDD), in the disordered regions of viral proteins. However, viruses also employ their own globular domains for binding to SLiMs and IDDs present in host proteins or virus proteins. In this review, we focus on the different strategies adopted by viruses to utilize proteins or protein domains for binding to the disordered regions of human or/and viral ligands. With a set of examples, we describe viral domains that bind human SLiMs. We also provide examples of viral proteins that bind to SLiMs, or IDDs, of viral proteins as a part of complex assembly and regulation of protein functions. The protein-protein interactions are often crucial for viral replication, and may thus offer possibilities for innovative inhibitor design.
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Affiliation(s)
- Priyanka Madhu
- Department of Chemistry, BMC, Uppsala University, Uppsala, Sweden
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, London, U.K
| | - Ylva Ivarsson
- Department of Chemistry, BMC, Uppsala University, Uppsala, Sweden
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9
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Akdel M, Pires DEV, Pardo EP, Jänes J, Zalevsky AO, Mészáros B, Bryant P, Good LL, Laskowski RA, Pozzati G, Shenoy A, Zhu W, Kundrotas P, Serra VR, Rodrigues CHM, Dunham AS, Burke D, Borkakoti N, Velankar S, Frost A, Basquin J, Lindorff-Larsen K, Bateman A, Kajava AV, Valencia A, Ovchinnikov S, Durairaj J, Ascher DB, Thornton JM, Davey NE, Stein A, Elofsson A, Croll TI, Beltrao P. A structural biology community assessment of AlphaFold2 applications. Nat Struct Mol Biol 2022; 29:1056-1067. [PMID: 36344848 PMCID: PMC9663297 DOI: 10.1038/s41594-022-00849-w] [Citation(s) in RCA: 176] [Impact Index Per Article: 88.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 09/20/2022] [Indexed: 11/09/2022]
Abstract
Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of the cell. Recent developments in computational methods for protein structure predictions have reached the accuracy of experimentally determined models. Although this has been independently verified, the implementation of these methods across structural-biology applications remains to be tested. Here, we evaluate the use of AlphaFold2 (AF2) predictions in the study of characteristic structural elements; the impact of missense variants; function and ligand binding site predictions; modeling of interactions; and modeling of experimental structural data. For 11 proteomes, an average of 25% additional residues can be confidently modeled when compared with homology modeling, identifying structural features rarely seen in the Protein Data Bank. AF2-based predictions of protein disorder and complexes surpass dedicated tools, and AF2 models can be used across diverse applications equally well compared with experimentally determined structures, when the confidence metrics are critically considered. In summary, we find that these advances are likely to have a transformative impact in structural biology and broader life-science research.
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Affiliation(s)
- Mehmet Akdel
- Bioinformatics Group, Department of Plant Sciences, Wageningen University and Research, Wageningen, the Netherlands
| | - Douglas E V Pires
- School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia
| | - Eduard Porta Pardo
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Jürgen Jänes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Arthur O Zalevsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | | | - Patrick Bryant
- Dep of Biochemistry and Biophysics and Science for Life Laboratory, Solna, Sweden
| | - Lydia L Good
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Roman A Laskowski
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Gabriele Pozzati
- Dep of Biochemistry and Biophysics and Science for Life Laboratory, Solna, Sweden
| | - Aditi Shenoy
- Dep of Biochemistry and Biophysics and Science for Life Laboratory, Solna, Sweden
| | - Wensi Zhu
- Dep of Biochemistry and Biophysics and Science for Life Laboratory, Solna, Sweden
| | - Petras Kundrotas
- Dep of Biochemistry and Biophysics and Science for Life Laboratory, Solna, Sweden
| | | | - Carlos H M Rodrigues
- School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia
| | - Alistair S Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - David Burke
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Neera Borkakoti
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Sameer Velankar
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Adam Frost
- Department of Biochemistry and Biophysics University of California, San Francisco, CA, USA
| | - Jérôme Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Andrey V Kajava
- Université de Montpellier, Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM) CNRS, Montpellier, France
| | | | - Sergey Ovchinnikov
- Faculty of Arts and Sciences, Division of Science, Harvard University, Cambridge, MA, USA.
| | | | - David B Ascher
- School of Chemistry and Molecular Biology, University of Queensland, Brisbane, Queensland, Australia.
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.
| | | | - Amelie Stein
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Arne Elofsson
- Dep of Biochemistry and Biophysics and Science for Life Laboratory, Solna, Sweden.
| | - Tristan I Croll
- Cambridge Institute for Medical Research, Department of Haematology, The University of Cambridge, Cambridge, UK.
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland.
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10
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Ripamonti M, Lamarca A, Davey NE, Tonoli D, Surini S, de Curtis I. A functional interaction between liprin-α1 and B56γ regulatory subunit of protein phosphatase 2A supports tumor cell motility. Commun Biol 2022; 5:1025. [PMID: 36171301 PMCID: PMC9519923 DOI: 10.1038/s42003-022-03989-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 09/13/2022] [Indexed: 11/25/2022] Open
Abstract
Scaffold liprin-α1 is required to assemble dynamic plasma membrane-associated platforms (PMAPs) at the front of migrating breast cancer cells, to promote protrusion and invasion. We show that the N-terminal region of liprin-α1 contains an LxxIxE motif interacting with B56 regulatory subunits of serine/threonine protein phosphatase 2A (PP2A). The specific interaction of B56γ with liprin-α1 requires an intact motif, since two point mutations strongly reduce the interaction. B56γ mediates the interaction of liprin-α1 with the heterotrimeric PP2A holoenzyme. Most B56γ protein is recovered in the cytosolic fraction of invasive MDA-MB-231 breast cancer cells, where B56γ is complexed with liprin-α1. While mutation of the short linear motif (SLiM) does not affect localization of liprin-α1 to PMAPs, localization of B56γ at these sites specifically requires liprin-α1. Silencing of B56γ or liprin-α1 inhibits to similar extent cell spreading on extracellular matrix, invasion, motility and lamellipodia dynamics in migrating MDA-MB-231 cells, suggesting that B56γ/PP2A is a novel component of the PMAPs machinery regulating tumor cell motility. In this direction, inhibition of cell spreading by silencing liprin-α1 is not rescued by expression of B56γ binding-defective liprin-α1 mutant. We propose that liprin-α1-mediated recruitment of PP2A via B56γ regulates cell motility by controlling protrusion in migrating MDA-MB-231 cells.
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Affiliation(s)
- Marta Ripamonti
- San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milano, Italy
| | - Andrea Lamarca
- San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milano, Italy
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Diletta Tonoli
- San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milano, Italy
| | - Sara Surini
- San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milano, Italy
| | - Ivan de Curtis
- San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milano, Italy.
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11
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Davey NE, Simonetti L, Ivarsson Y. ProP-PD for proteome-wide motif-mediated interaction discovery. Trends Biochem Sci 2022; 47:547-548. [PMID: 35168834 DOI: 10.1016/j.tibs.2022.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 12/22/2022]
Affiliation(s)
- Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
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12
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Benz C, Ali M, Krystkowiak I, Simonetti L, Sayadi A, Mihalic F, Kliche J, Andersson E, Jemth P, Davey NE, Ivarsson Y. Proteome-scale mapping of binding sites in the unstructured regions of the human proteome. Mol Syst Biol 2022; 18:e10584. [PMID: 35044719 PMCID: PMC8769072 DOI: 10.15252/msb.202110584] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 12/18/2022] Open
Abstract
Specific protein-protein interactions are central to all processes that underlie cell physiology. Numerous studies have together identified hundreds of thousands of human protein-protein interactions. However, many interactions remain to be discovered, and low affinity, conditional, and cell type-specific interactions are likely to be disproportionately underrepresented. Here, we describe an optimized proteomic peptide-phage display library that tiles all disordered regions of the human proteome and allows the screening of ~ 1,000,000 overlapping peptides in a single binding assay. We define guidelines for processing, filtering, and ranking the results and provide PepTools, a toolkit to annotate the identified hits. We uncovered >2,000 interaction pairs for 35 known short linear motif (SLiM)-binding domains and confirmed the quality of the produced data by complementary biophysical or cell-based assays. Finally, we show how the amino acid resolution-binding site information can be used to pinpoint functionally important disease mutations and phosphorylation events in intrinsically disordered regions of the proteome. The optimized human disorderome library paired with PepTools represents a powerful pipeline for unbiased proteome-wide discovery of SLiM-based interactions.
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Affiliation(s)
- Caroline Benz
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
| | - Muhammad Ali
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
| | | | | | - Ahmed Sayadi
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
| | - Filip Mihalic
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Johanna Kliche
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
| | - Eva Andersson
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Per Jemth
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Norman E Davey
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
| | - Ylva Ivarsson
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
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13
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Kruse T, Benz C, Garvanska DH, Lindqvist R, Mihalic F, Coscia F, Inturi R, Sayadi A, Simonetti L, Nilsson E, Ali M, Kliche J, Moliner Morro A, Mund A, Andersson E, McInerney G, Mann M, Jemth P, Davey NE, Överby AK, Nilsson J, Ivarsson Y. Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities. Nat Commun 2021; 12:6761. [PMID: 34799561 PMCID: PMC8605023 DOI: 10.1038/s41467-021-26498-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/06/2021] [Indexed: 12/13/2022] Open
Abstract
Viral proteins make extensive use of short peptide interaction motifs to hijack cellular host factors. However, most current large-scale methods do not identify this important class of protein-protein interactions. Uncovering peptide mediated interactions provides both a molecular understanding of viral interactions with their host and the foundation for developing novel antiviral reagents. Here we describe a viral peptide discovery approach covering 23 coronavirus strains that provides high resolution information on direct virus-host interactions. We identify 269 peptide-based interactions for 18 coronaviruses including a specific interaction between the human G3BP1/2 proteins and an ΦxFG peptide motif in the SARS-CoV-2 nucleocapsid (N) protein. This interaction supports viral replication and through its ΦxFG motif N rewires the G3BP1/2 interactome to disrupt stress granules. A peptide-based inhibitor disrupting the G3BP1/2-N interaction dampened SARS-CoV-2 infection showing that our results can be directly translated into novel specific antiviral reagents.
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Affiliation(s)
- Thomas Kruse
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Caroline Benz
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Dimitriya H Garvanska
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Richard Lindqvist
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90186, Umeå, Sweden
| | - Filip Mihalic
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Fabian Coscia
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200, Copenhagen, Denmark
- Spatial Proteomics Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Raviteja Inturi
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ahmed Sayadi
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Emma Nilsson
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90186, Umeå, Sweden
| | - Muhammad Ali
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Johanna Kliche
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ainhoa Moliner Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Andreas Mund
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Matthias Mann
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Anna K Överby
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden.
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90186, Umeå, Sweden.
| | - Jakob Nilsson
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
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14
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Bandyopadhyay S, Bhaduri S, Örd M, Davey NE, Loog M, Pryciak PM. Comprehensive Analysis of G1 Cyclin Docking Motif Sequences that Control CDK Regulatory Potency In Vivo. Curr Biol 2020; 30:4454-4466.e5. [PMID: 32976810 PMCID: PMC8009629 DOI: 10.1016/j.cub.2020.08.099] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 11/17/2022]
Abstract
Many protein-modifying enzymes recognize their substrates via docking motifs, but the range of functionally permissible motif sequences is often poorly defined. During eukaryotic cell division, cyclin-specific docking motifs help cyclin-dependent kinases (CDKs) phosphorylate different substrates at different stages, thus enforcing a temporally ordered series of events. In budding yeast, CDK substrates with Leu/Pro-rich (LP) docking motifs are recognized by Cln1/2 cyclins in late G1 phase, yet the key sequence features of these motifs were unknown. Here, we comprehensively analyze LP motif requirements in vivo by combining a competitive growth assay with deep mutational scanning. We quantified the effect of all single-residue replacements in five different LP motifs by using six distinct G1 cyclins from diverse fungi including medical and agricultural pathogens. The results uncover substantial tolerance for deviations from the consensus sequence, plus requirements at some positions that are contingent on the favorability of other motif residues. They also reveal the basis for variations in functional potency among wild-type motifs, and allow derivation of a quantitative matrix that predicts the strength of other candidate motif sequences. Finally, we find that variation in docking motif potency can advance or delay the time at which CDK substrate phosphorylation occurs, and thereby control the temporal ordering of cell cycle regulation. The overall results provide a general method for surveying viable docking motif sequences and quantifying their potency in vivo, and they reveal how variations in docking strength can tune the degree and timing of regulatory modifications.
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Affiliation(s)
- Sushobhana Bandyopadhyay
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Samyabrata Bhaduri
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Mihkel Örd
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Mart Loog
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Peter M Pryciak
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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15
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Wigington CP, Roy J, Damle NP, Yadav VK, Blikstad C, Resch E, Wong CJ, Mackay DR, Wang JT, Krystkowiak I, Bradburn DA, Tsekitsidou E, Hong SH, Kaderali MA, Xu SL, Stearns T, Gingras AC, Ullman KS, Ivarsson Y, Davey NE, Cyert MS. Systematic Discovery of Short Linear Motifs Decodes Calcineurin Phosphatase Signaling. Mol Cell 2020; 79:342-358.e12. [PMID: 32645368 DOI: 10.1016/j.molcel.2020.06.029] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [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: 07/10/2019] [Revised: 03/24/2020] [Accepted: 05/26/2020] [Indexed: 12/17/2022]
Abstract
Short linear motifs (SLiMs) drive dynamic protein-protein interactions essential for signaling, but sequence degeneracy and low binding affinities make them difficult to identify. We harnessed unbiased systematic approaches for SLiM discovery to elucidate the regulatory network of calcineurin (CN)/PP2B, the Ca2+-activated phosphatase that recognizes LxVP and PxIxIT motifs. In vitro proteome-wide detection of CN-binding peptides, in vivo SLiM-dependent proximity labeling, and in silico modeling of motif determinants uncovered unanticipated CN interactors, including NOTCH1, which we establish as a CN substrate. Unexpectedly, CN shows SLiM-dependent proximity to centrosomal and nuclear pore complex (NPC) proteins-structures where Ca2+ signaling is largely uncharacterized. CN dephosphorylates human and yeast NPC proteins and promotes accumulation of a nuclear transport reporter, suggesting conserved NPC regulation by CN. The CN network assembled here provides a resource to investigate Ca2+ and CN signaling and demonstrates synergy between experimental and computational methods, establishing a blueprint for examining SLiM-based networks.
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Affiliation(s)
| | - Jagoree Roy
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Nikhil P Damle
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Vikash K Yadav
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Cecilia Blikstad
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Eduard Resch
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology TMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Cassandra J Wong
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Douglas R Mackay
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jennifer T Wang
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Izabella Krystkowiak
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | | | | | - Su Hyun Hong
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Malika Amyn Kaderali
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Shou-Ling Xu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Tim Stearns
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, M5S 3H7 ON, Canada
| | - Katharine S Ullman
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fullham Road, London SW3 6JB, UK
| | - Martha S Cyert
- Department of Biology, Stanford University, Stanford, CA, USA.
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16
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Kumar M, Gouw M, Michael S, Sámano-Sánchez H, Pancsa R, Glavina J, Diakogianni A, Valverde JA, Bukirova D, Čalyševa J, Palopoli N, Davey NE, Chemes LB, Gibson TJ. ELM-the eukaryotic linear motif resource in 2020. Nucleic Acids Res 2020; 48:D296-D306. [PMID: 31680160 PMCID: PMC7145657 DOI: 10.1093/nar/gkz1030] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [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: 09/25/2019] [Revised: 10/18/2019] [Accepted: 10/23/2019] [Indexed: 12/20/2022] Open
Abstract
The eukaryotic linear motif (ELM) resource is a repository of manually curated experimentally validated short linear motifs (SLiMs). Since the initial release almost 20 years ago, ELM has become an indispensable resource for the molecular biology community for investigating functional regions in many proteins. In this update, we have added 21 novel motif classes, made major revisions to 12 motif classes and added >400 new instances mostly focused on DNA damage, the cytoskeleton, SH2-binding phosphotyrosine motifs and motif mimicry by pathogenic bacterial effector proteins. The current release of the ELM database contains 289 motif classes and 3523 individual protein motif instances manually curated from 3467 scientific publications. ELM is available at: http://elm.eu.org.
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Affiliation(s)
- Manjeet Kumar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Marc Gouw
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Sushama Michael
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hugo Sámano-Sánchez
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.,Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Rita Pancsa
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Juliana Glavina
- Instituto de Investigaciones Biotecnológicas (IIBio) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de San Martín. Av. 25 de Mayo y Francia, CP1650, Buenos Aires, Argentina
| | - Athina Diakogianni
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Jesús Alvarado Valverde
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Dayana Bukirova
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.,Nazarbayev University, Nur-Sultan 010000, Kazakhstan
| | - Jelena Čalyševa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.,Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Nicolas Palopoli
- Department of Science and Technology, Universidad Nacional de Quilmes - CONICET, Bernal B1876BXD, Buenos Aires, Argentina
| | - Norman E Davey
- The Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Rd, Chelsea, London SW3 6JB, UK
| | - Lucía B Chemes
- Instituto de Investigaciones Biotecnológicas (IIBio) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de San Martín. Av. 25 de Mayo y Francia, CP1650, Buenos Aires, Argentina
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
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17
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Hatos A, Hajdu-Soltész B, Monzon AM, Palopoli N, Álvarez L, Aykac-Fas B, Bassot C, Benítez GI, Bevilacqua M, Chasapi A, Chemes L, Davey NE, Davidović R, Dunker AK, Elofsson A, Gobeill J, Foutel NSG, Sudha G, Guharoy M, Horvath T, Iglesias V, Kajava AV, Kovacs OP, Lamb J, Lambrughi M, Lazar T, Leclercq JY, Leonardi E, Macedo-Ribeiro S, Macossay-Castillo M, Maiani E, Manso JA, Marino-Buslje C, Martínez-Pérez E, Mészáros B, Mičetić I, Minervini G, Murvai N, Necci M, Ouzounis CA, Pajkos M, Paladin L, Pancsa R, Papaleo E, Parisi G, Pasche E, Barbosa Pereira PJ, Promponas VJ, Pujols J, Quaglia F, Ruch P, Salvatore M, Schad E, Szabo B, Szaniszló T, Tamana S, Tantos A, Veljkovic N, Ventura S, Vranken W, Dosztányi Z, Tompa P, Tosatto SCE, Piovesan D. DisProt: intrinsic protein disorder annotation in 2020. Nucleic Acids Res 2020; 48:D269-D276. [PMID: 31713636 PMCID: PMC7145575 DOI: 10.1093/nar/gkz975] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [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: 09/15/2019] [Revised: 10/11/2019] [Accepted: 10/12/2019] [Indexed: 11/29/2022] Open
Abstract
The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. The website includes a redesigned graphical interface, a better search engine, a clearer API for programmatic access and a new annotation interface that integrates text mining technologies. The new entry format provides a greater flexibility, simplifies maintenance and allows the capture of more information from the literature. The new disorder ontology has been formalized and made interoperable by adopting the OWL format, as well as its structure and term definitions have been improved. The new annotation interface has made the curation process faster and more effective. We recently showed that new DisProt annotations can be effectively used to train and validate disorder predictors. We believe the growth of DisProt will accelerate, contributing to the improvement of function and disorder predictors and therefore to illuminate the ‘dark’ proteome.
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Affiliation(s)
- András Hatos
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy
| | - Borbála Hajdu-Soltész
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest 1117, Hungary
| | - Alexander M Monzon
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy
| | - Nicolas Palopoli
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Bernal, Buenos Aires B1876BXD, Argentina
| | - Lucía Álvarez
- Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas IIBIO, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Burcu Aykac-Fas
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark
| | - Claudio Bassot
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, Solna 17121, Sweden
| | - Guillermo I Benítez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Bernal, Buenos Aires B1876BXD, Argentina
| | - Martina Bevilacqua
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy
| | - Anastasia Chasapi
- Biological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica GR-57500, Greece
| | - Lucia Chemes
- Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas IIBIO, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina.,Departamento de Fisiología y Biología Molecular y Celular (DFBMC), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, Chelsea, London SW3 6BJ, UK
| | - Radoslav Davidović
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences Vinca, University of Belgrade, Belgrade 11001, Serbia
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, IN 46202, USA
| | - Arne Elofsson
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, Solna 17121, Sweden
| | - Julien Gobeill
- Swiss Institute of Bioinformatics and HES-SO \ HEG, Geneva 1200, Switzerland
| | - Nicolás S González Foutel
- Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas IIBIO, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Govindarajan Sudha
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, Solna 17121, Sweden
| | - Mainak Guharoy
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium
| | - Tamas Horvath
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Valentin Iglesias
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, Montpellier 34293, France.,Institut de Biologie Computationnelle(IBC), Montpellier 34095, France
| | - Orsolya P Kovacs
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - John Lamb
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, Solna 17121, Sweden
| | - Matteo Lambrughi
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark
| | - Tamas Lazar
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium
| | - Jeremy Y Leclercq
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, Montpellier 34293, France
| | - Emanuela Leonardi
- Department of Woman and Child Health, University of Padova, Padova 35127, Italy.,Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova 35127, Italy
| | - Sandra Macedo-Ribeiro
- Instituto de Biologia Molecular e Celular (IBMC) and Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal
| | - Mauricio Macossay-Castillo
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium
| | - Emiliano Maiani
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark
| | - José A Manso
- Instituto de Biologia Molecular e Celular (IBMC) and Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal
| | - Cristina Marino-Buslje
- Bioinformatics Unit. Fundación Instituto Leloir, Ciudad de Buenos Aires C1405BWE, Argentina
| | | | - Bálint Mészáros
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest 1117, Hungary
| | - Ivan Mičetić
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy
| | - Giovanni Minervini
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy
| | - Nikoletta Murvai
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Marco Necci
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy
| | - Christos A Ouzounis
- Biological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica GR-57500, Greece
| | - Mátyás Pajkos
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest 1117, Hungary
| | - Lisanna Paladin
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy
| | - Rita Pancsa
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark.,Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Bernal, Buenos Aires B1876BXD, Argentina
| | - Emilie Pasche
- Swiss Institute of Bioinformatics and HES-SO \ HEG, Geneva 1200, Switzerland
| | - Pedro J Barbosa Pereira
- Instituto de Biologia Molecular e Celular (IBMC) and Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal
| | - Vasilis J Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, CY 1678, Cyprus
| | - Jordi Pujols
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Federica Quaglia
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy
| | - Patrick Ruch
- Swiss Institute of Bioinformatics and HES-SO \ HEG, Geneva 1200, Switzerland
| | - Marco Salvatore
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, Solna 17121, Sweden
| | - Eva Schad
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Beata Szabo
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Tamás Szaniszló
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest 1117, Hungary
| | - Stella Tamana
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, CY 1678, Cyprus
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Nevena Veljkovic
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences Vinca, University of Belgrade, Belgrade 11001, Serbia
| | - Salvador Ventura
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Wim Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium.,Interuniversity Institute of Bioinformatics in Brussels (IB2), ULB-VUB, Brussels 1050, Belgium
| | - Zsuzsanna Dosztányi
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest 1117, Hungary
| | - Peter Tompa
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy.,CNR Institute of Neurosceince, Padova 35121, Italy
| | - Damiano Piovesan
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy
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18
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Balasuriya N, Davey NE, Johnson JL, Liu H, Biggar KK, Cantley LC, Li SSC, O'Donoghue P. Phosphorylation-dependent substrate selectivity of protein kinase B (AKT1). J Biol Chem 2020; 295:8120-8134. [PMID: 32350110 DOI: 10.1074/jbc.ra119.012425] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [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: 12/20/2019] [Revised: 04/22/2020] [Indexed: 12/31/2022] Open
Abstract
Protein kinase B (AKT1) is a central node in a signaling pathway that regulates cell survival. The diverse pathways regulated by AKT1 are communicated in the cell via the phosphorylation of perhaps more than 100 cellular substrates. AKT1 is itself activated by phosphorylation at Thr-308 and Ser-473. Despite the fact that these phosphorylation sites are biomarkers for cancers and tumor biology, their individual roles in shaping AKT1 substrate selectivity are unknown. We recently developed a method to produce AKT1 with programmed phosphorylation at either or both of its key regulatory sites. Here, we used both defined and randomized peptide libraries to map the substrate selectivity of site-specific, singly and doubly phosphorylated AKT1 variants. To globally quantitate AKT1 substrate preferences, we synthesized three AKT1 substrate peptide libraries: one based on 84 "known" substrates and two independent and larger oriented peptide array libraries (OPALs) of ∼1011 peptides each. We found that each phospho-form of AKT1 has common and distinct substrate requirements. Compared with pAKT1T308, the addition of Ser-473 phosphorylation increased AKT1 activities on some, but not all of its substrates. This is the first report that Ser-473 phosphorylation can positively or negatively regulate kinase activity in a substrate-dependent fashion. Bioinformatics analysis indicated that the OPAL-activity data effectively discriminate known AKT1 substrates from closely related kinase substrates. Our results also enabled predictions of novel AKT1 substrates that suggest new and expanded roles for AKT1 signaling in regulating cellular processes.
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Affiliation(s)
- Nileeka Balasuriya
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, London, United Kingdom
| | - Jared L Johnson
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, New York, United States
| | - Huadong Liu
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada.,Center for Mitochondrial Biology and Medicine, Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Kyle K Biggar
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada.,Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Lewis C Cantley
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, New York, United States
| | - Shawn Shun-Cheng Li
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Patrick O'Donoghue
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada .,Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
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19
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Palopoli N, Iserte JA, Chemes LB, Marino-Buslje C, Parisi G, Gibson TJ, Davey NE. The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification. Database (Oxford) 2020; 2020:baaa040. [PMID: 32507889 PMCID: PMC7276420 DOI: 10.1093/database/baaa040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 04/24/2020] [Accepted: 05/06/2020] [Indexed: 11/12/2022]
Abstract
Modern biology produces data at a staggering rate. Yet, much of these biological data is still isolated in the text, figures, tables and supplementary materials of articles. As a result, biological information created at great expense is significantly underutilised. The protein motif biology field does not have sufficient resources to curate the corpus of motif-related literature and, to date, only a fraction of the available articles have been curated. In this study, we develop a set of tools and a web resource, 'articles.ELM', to rapidly identify the motif literature articles pertinent to a researcher's interest. At the core of the resource is a manually curated set of about 8000 motif-related articles. These articles are automatically annotated with a range of relevant biological data allowing in-depth search functionality. Machine-learning article classification is used to group articles based on their similarity to manually curated motif classes in the Eukaryotic Linear Motif resource. Articles can also be manually classified within the resource. The 'articles.ELM' resource permits the rapid and accurate discovery of relevant motif articles thereby improving the visibility of motif literature and simplifying the recovery of valuable biological insights sequestered within scientific articles. Consequently, this web resource removes a critical bottleneck in scientific productivity for the motif biology field. Database URL: http://slim.icr.ac.uk/articles/.
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Affiliation(s)
- N Palopoli
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Roque Saenz Peña 352, Bernal, Buenos Aires B1876BXD, Argentina
| | - J A Iserte
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, Av. Patricias Argentinas 435, Ciudad de Buenos Aires C1405BWE, Argentina
| | - L B Chemes
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de General San Martín, IIB-INTECH-CONICET, Av. 25 de Mayo y Francia, San Martín, Buenos Aires B1650, Argentina
| | - C Marino-Buslje
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, Av. Patricias Argentinas 435, Ciudad de Buenos Aires C1405BWE, Argentina
| | - G Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Roque Saenz Peña 352, Bernal, Buenos Aires B1876BXD, Argentina
| | - T J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, Heidelberg 69117, Germany
| | - N E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
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20
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Davey NE, Babu MM, Blackledge M, Bridge A, Capella-Gutierrez S, Dosztanyi Z, Drysdale R, Edwards RJ, Elofsson A, Felli IC, Gibson TJ, Gutmanas A, Hancock JM, Harrow J, Higgins D, Jeffries CM, Le Mercier P, Mészáros B, Necci M, Notredame C, Orchard S, Ouzounis CA, Pancsa R, Papaleo E, Pierattelli R, Piovesan D, Promponas VJ, Ruch P, Rustici G, Romero P, Sarntivijai S, Saunders G, Schuler B, Sharan M, Shields DC, Sussman JL, Tedds JA, Tompa P, Turewicz M, Vondrasek J, Vranken WF, Wallace BA, Wichapong K, Tosatto SCE. An intrinsically disordered proteins community for ELIXIR. F1000Res 2019; 8. [PMID: 31824649 PMCID: PMC6880265 DOI: 10.12688/f1000research.20136.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/18/2019] [Indexed: 01/20/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The goal of these developments is to drive the creation of high-quality tools and resources to support the identification, analysis and functional characterisation of IDPs. The roadmap is the result of a workshop titled “An intrinsically disordered protein user community proposal for ELIXIR” held at the University of Padua. The workshop, and further consultation with the members of the wider IDP community, identified the key priority areas for the roadmap including the development of standards for data annotation, storage and dissemination; integration of IDP data into the ELIXIR Core Data Resources; and the creation of benchmarking criteria for IDP-related software. Here, we discuss these areas of priority, how they can be implemented in cooperation with the ELIXIR platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for an IDP Community in ELIXIR and is an appeal to identify and involve new stakeholders.
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Affiliation(s)
- Norman E Davey
- Division of Cancer Biology, Institute of Cancer Research, UK, London, SW3 6JB, UK
| | - M Madan Babu
- MRC Laboratory of Molecular Biology,, Cambridge, CB2 0QH, UK
| | - Martin Blackledge
- Institut de Biologie Structurale, Université Grenoble Alpes, Grenoble, 38000, France
| | - Alan Bridge
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | | | - Zsuzsanna Dosztanyi
- Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | | | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Arne Elofsson
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Isabella C Felli
- Department of Chemistry and CERM "Ugo Schiff", University of Florence, Florence, Italy
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Aleksandras Gutmanas
- Protein Data Bank in Europe, European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Cambridge, CB10 1SD, UK
| | - John M Hancock
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Jen Harrow
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Desmond Higgins
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin, D4, Ireland
| | - Cy M Jeffries
- European Molecular Biology Laboratory, Hamburg, Germany
| | - Philippe Le Mercier
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Balint Mészáros
- Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Marco Necci
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Cedric Notredame
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sandra Orchard
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Cambridge, CB10 1SD, UK
| | - Christos A Ouzounis
- BCPL-CPERI, Centre for Research & Technology Hellas (CERTH), Thessalonica, 57001, Greece
| | - Rita Pancsa
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
| | - Roberta Pierattelli
- Department of Chemistry and CERM "Ugo Schiff", University of Florence, Florence, Italy
| | - Damiano Piovesan
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Vasilis J Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, CY-1678, Cyprus
| | - Patrick Ruch
- HES-SO/HEG and SIB Text Mining, Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Gabriella Rustici
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Pedro Romero
- University of Wisconsin-Madison, Madison, WI, 53706-1544, USA
| | | | - Gary Saunders
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Malvika Sharan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Denis C Shields
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin, D4, Ireland
| | - Joel L Sussman
- Department of Structural Biology and the Israel Structural Proteomics, Center (ISPC), Weizmann Institute of Science, Reḥovot, 7610001, Israel
| | | | - Peter Tompa
- VIB Center for Structural Biology (CSB), VIB Flemish Institute for Biotechnology, Brussels, 1050, Belgium
| | - Michael Turewicz
- Faculty of Medicine, Medizinisches Proteom-Center, Ruhr University Bochum, GesundheitsCampus 4, Bochum, 44801, Germany
| | - Jiri Vondrasek
- Institute of Organic Chemistry and Biochemistry, CAS, Prague, Czech Republic
| | - Wim F Vranken
- VUB/ULB Interuniversity Institute of Bioinformatics in Brussels and Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, B-1050, Belgium
| | - Bonnie Ann Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1H 0HA, UK
| | - Kanin Wichapong
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
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21
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Smith RJ, Cordeiro MH, Davey NE, Vallardi G, Ciliberto A, Gross F, Saurin AT. PP1 and PP2A Use Opposite Phospho-dependencies to Control Distinct Processes at the Kinetochore. Cell Rep 2019; 28:2206-2219.e8. [PMID: 31433993 PMCID: PMC6715587 DOI: 10.1016/j.celrep.2019.07.067] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/18/2019] [Accepted: 07/18/2019] [Indexed: 12/12/2022] Open
Abstract
PP1 and PP2A-B56 are major serine/threonine phosphatase families that achieve specificity by colocalizing with substrates. At the kinetochore, however, both phosphatases localize to an almost identical molecular space and yet they still manage to regulate unique pathways and processes. By switching or modulating the positions of PP1/PP2A-B56 at kinetochores, we show that their unique downstream effects are not due to either the identity of the phosphatase or its precise location. Instead, these phosphatases signal differently because their kinetochore recruitment can be either inhibited (PP1) or enhanced (PP2A) by phosphorylation inputs. Mathematical modeling explains how these inverse phospho-dependencies elicit unique forms of cross-regulation and feedback, which allows otherwise indistinguishable phosphatases to produce distinct network behaviors and control different mitotic processes. Furthermore, our genome-wide analysis suggests that these major phosphatase families may have evolved to respond to phosphorylation inputs in opposite ways because many other PP1 and PP2A-B56-binding motifs are also phospho-regulated.
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Affiliation(s)
- Richard J Smith
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Marilia H Cordeiro
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Norman E Davey
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Giulia Vallardi
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | | | - Fridolin Gross
- Istituto Firc di Oncologia Molecolare, IFOM, Milano, Italy
| | - Adrian T Saurin
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK.
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22
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Jespersen N, Estelle A, Waugh N, Davey NE, Blikstad C, Ammon YC, Akhmanova A, Ivarsson Y, Hendrix DA, Barbar E. Systematic identification of recognition motifs for the hub protein LC8. Life Sci Alliance 2019; 2:2/4/e201900366. [PMID: 31266884 PMCID: PMC6607443 DOI: 10.26508/lsa.201900366] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 03/05/2019] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 01/17/2023] Open
Abstract
LC8 is a eukaryotic hub protein that interacts with multifarious partners; analysis of more than 100 binding/nonbinding sequences led to an algorithm that predicts LC8 partners with 78% accuracy. Hub proteins participate in cellular regulation by dynamic binding of multiple proteins within interaction networks. The hub protein LC8 reversibly interacts with more than 100 partners through a flexible pocket at its dimer interface. To explore the diversity of the LC8 partner pool, we screened for LC8 binding partners using a proteomic phage display library composed of peptides from the human proteome, which had no bias toward a known LC8 motif. Of the identified hits, we validated binding of 29 peptides using isothermal titration calorimetry. Of the 29 peptides, 19 were entirely novel, and all had the canonical TQT motif anchor. A striking observation is that numerous peptides containing the TQT anchor do not bind LC8, indicating that residues outside of the anchor facilitate LC8 interactions. Using both LC8-binding and nonbinding peptides containing the motif anchor, we developed the “LC8Pred” algorithm that identifies critical residues flanking the anchor and parses random sequences to predict LC8-binding motifs with ∼78% accuracy. Our findings significantly expand the scope of the LC8 hub interactome.
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Affiliation(s)
- Nathan Jespersen
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Aidan Estelle
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Nathan Waugh
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Ireland
| | - Cecilia Blikstad
- Department of Chemistry - Biomedical Centre, Uppsala University, Uppsala, Sweden
| | | | - Anna Akhmanova
- Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Ylva Ivarsson
- Department of Chemistry - Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - David A Hendrix
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA.,School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA
| | - Elisar Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
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23
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Sebaa R, Johnson J, Pileggi C, Norgren M, Xuan J, Sai Y, Tong Q, Krystkowiak I, Bondy-Chorney E, Davey NE, Krogan N, Downey M, Harper ME. SIRT3 controls brown fat thermogenesis by deacetylation regulation of pathways upstream of UCP1. Mol Metab 2019; 25:35-49. [PMID: 31060926 PMCID: PMC6601363 DOI: 10.1016/j.molmet.2019.04.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 03/27/2019] [Accepted: 04/11/2019] [Indexed: 01/14/2023] Open
Abstract
OBJECTIVE Brown adipose tissue (BAT) is important for thermoregulation in many mammals. Uncoupling protein 1 (UCP1) is the critical regulator of thermogenesis in BAT. Here we aimed to investigate the deacetylation control of BAT and to investigate a possible functional connection between UCP1 and sirtuin 3 (SIRT3), the master mitochondrial lysine deacetylase. METHODS We carried out physiological, molecular, and proteomic analyses of BAT from wild-type and Sirt3KO mice when BAT is activated. Mice were either cold exposed for 2 days or were injected with the β3-adrenergic agonist, CL316,243 (1 mg/kg; i.p.). Mutagenesis studies were conducted in a cellular model to assess the impact of acetylation lysine sites on UCP1 function. Cardiac punctures were collected for proteomic analysis of blood acylcarnitines. Isolated mitochondria were used for functional analysis of OXPHOS proteins. RESULTS Our findings showed that SIRT3 absence in mice resulted in impaired BAT lipid use, whole body thermoregulation, and respiration in BAT mitochondria, without affecting UCP1 expression. Acetylome profiling of BAT mitochondria revealed that SIRT3 regulates acetylation status of many BAT mitochondrial proteins including UCP1 and crucial upstream proteins. Mutagenesis work in cells suggested that UCP1 activity was independent of direct SIRT3-regulated lysine acetylation. However, SIRT3 impacted BAT mitochondrial proteins activities of acylcarnitine metabolism and specific electron transport chain complexes, CI and CII. CONCLUSIONS Our data highlight that SIRT3 likely controls BAT thermogenesis indirectly by targeting pathways upstream of UCP1.
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Affiliation(s)
- Rajaa Sebaa
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada; Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada; Department of Medical Laboratories, College of Applied Medical Sciences, University of Shaqra, Duwadimi, Saudi Arabia
| | - Jeff Johnson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Chantal Pileggi
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Michaela Norgren
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Jian Xuan
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Yuka Sai
- Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada; Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Qiang Tong
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Izabella Krystkowiak
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Emma Bondy-Chorney
- Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada; Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Norman E Davey
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland; Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Nevan Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Michael Downey
- Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada; Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
| | - Mary-Ellen Harper
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada; Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
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24
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Krystkowiak I, Davey NE. SLiMSearch: a framework for proteome-wide discovery and annotation of functional modules in intrinsically disordered regions. Nucleic Acids Res 2019; 45:W464-W469. [PMID: 28387819 PMCID: PMC5570202 DOI: 10.1093/nar/gkx238] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [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: 01/28/2017] [Accepted: 04/05/2017] [Indexed: 12/12/2022] Open
Abstract
The extensive intrinsically disordered regions of higher eukaryotic proteomes contain vast numbers of functional interaction modules known as short linear motifs (SLiMs). Here, we present SLiMSearch, a motif discovery tool that scans a motif consensus, representing the specificity determinants of a motif-binding domain, against a proteome to discover putative novel motif instances. SLiMSearch applies several distinct and complementary approaches exploiting the common properties of SLiMs to predict novel motifs. Consensus matches are annotated with overlapping sequence annotation, including feature information describing protein modular architecture, post-translational modification, structure, sequence variation and experimental characterisation of functional regions. Discriminatory motif attributes such as conservation and accessibility are also calculated. In addition, SLiMSearch provides functional enrichment and evolutionary analysis tools. The enrichment tool analyses GO terms, keywords and interacting partner enrichment to indicate possible motif function. The evolutionary tool evaluates motif taxonomic range and the conservation of motif sequence context. Consensus matches can be filtered based on motif attributes such as accessibility and taxonomic range; or by the localisation, interacting partners or ontology annotation of the peptide-containing protein. SLiMSearch supports a range of species of experimental and therapeutic relevance and is available online at http://slim.ucd.ie/slimsearch/.
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Affiliation(s)
- Izabella Krystkowiak
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.,UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Norman E Davey
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.,UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
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25
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Davey NE. The functional importance of structure in unstructured protein regions. Curr Opin Struct Biol 2019; 56:155-163. [DOI: 10.1016/j.sbi.2019.03.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/01/2019] [Accepted: 03/07/2019] [Indexed: 12/15/2022]
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26
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Krystkowiak I, Manguy J, Davey NE. PSSMSearch: a server for modeling, visualization, proteome-wide discovery and annotation of protein motif specificity determinants. Nucleic Acids Res 2018; 46:W235-W241. [PMID: 29873773 PMCID: PMC6030969 DOI: 10.1093/nar/gky426] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [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: 02/05/2018] [Revised: 04/11/2018] [Accepted: 05/15/2018] [Indexed: 11/29/2022] Open
Abstract
There is a pressing need for in silico tools that can aid in the identification of the complete repertoire of protein binding (SLiMs, MoRFs, miniMotifs) and modification (moiety attachment/removal, isomerization, cleavage) motifs. We have created PSSMSearch, an interactive web-based tool for rapid statistical modeling, visualization, discovery and annotation of protein motif specificity determinants to discover novel motifs in a proteome-wide manner. PSSMSearch analyses proteomes for regions with significant similarity to a motif specificity determinant model built from a set of aligned motif-containing peptides. Multiple scoring methods are available to build a position-specific scoring matrix (PSSM) describing the motif specificity determinant model. This model can then be modified by a user to add prior knowledge of specificity determinants through an interactive PSSM heatmap. PSSMSearch includes a statistical framework to calculate the significance of specificity determinant model matches against a proteome of interest. PSSMSearch also includes the SLiMSearch framework's annotation, motif functional analysis and filtering tools to highlight relevant discriminatory information. Additional tools to annotate statistically significant shared keywords and GO terms, or experimental evidence of interaction with a motif-recognizing protein have been added. Finally, PSSM-based conservation metrics have been created for taxonomic range analyses. The PSSMSearch web server is available at http://slim.ucd.ie/pssmsearch/.
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Affiliation(s)
- Izabella Krystkowiak
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
- UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Jean Manguy
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
- UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
- Food for Health Ireland, University College Dublin, Belfield, Dublin 4, Ireland
| | - Norman E Davey
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
- UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
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27
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Gouw M, Michael S, Sámano-Sánchez H, Kumar M, Zeke A, Lang B, Bely B, Chemes LB, Davey NE, Deng Z, Diella F, Gürth CM, Huber AK, Kleinsorg S, Schlegel LS, Palopoli N, Roey KV, Altenberg B, Reményi A, Dinkel H, Gibson TJ. The eukaryotic linear motif resource - 2018 update. Nucleic Acids Res 2018; 46:D428-D434. [PMID: 29136216 PMCID: PMC5753338 DOI: 10.1093/nar/gkx1077] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [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: 10/01/2017] [Revised: 10/17/2017] [Accepted: 10/23/2017] [Indexed: 11/14/2022] Open
Abstract
Short linear motifs (SLiMs) are protein binding modules that play major roles in almost all cellular processes. SLiMs are short, often highly degenerate, difficult to characterize and hard to detect. The eukaryotic linear motif (ELM) resource (elm.eu.org) is dedicated to SLiMs, consisting of a manually curated database of over 275 motif classes and over 3000 motif instances, and a pipeline to discover candidate SLiMs in protein sequences. For 15 years, ELM has been one of the major resources for motif research. In this database update, we present the latest additions to the database including 32 new motif classes, and new features including Uniprot and Reactome integration. Finally, to help provide cellular context, we present some biological insights about SLiMs in the cell cycle, as targets for bacterial pathogenicity and their functionality in the human kinome.
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Affiliation(s)
- Marc Gouw
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Sushama Michael
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hugo Sámano-Sánchez
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Manjeet Kumar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - András Zeke
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Benjamin Lang
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Benoit Bely
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Lucía B Chemes
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires CP 1405, Argentina
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires CP 2160, Argentina
- Instituto de Investigaciones Biotecnoltógicas, Universidad Nacional de General San Martín, IIB-INTECH-CONICET, San Martín, Buenos Aires CP 1650, Argentina
| | - Norman E Davey
- UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ziqi Deng
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Francesca Diella
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | | | | | | | | | - Nicolás Palopoli
- Department of Science and Technology, Universidad Nacional de Quilmes, CONICET, Bernal B1876BXD, Buenos Aires, Argentina
| | - Kim V Roey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Brigitte Altenberg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Attila Reményi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Holger Dinkel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Leibniz-Institute on Aging, Fritz Lipmann Institute (FLI), Jena D-07745, Germany
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
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28
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Kruse T, Biedenkopf N, Hertz EPT, Dietzel E, Stalmann G, López-Méndez B, Davey NE, Nilsson J, Becker S. The Ebola Virus Nucleoprotein Recruits the Host PP2A-B56 Phosphatase to Activate Transcriptional Support Activity of VP30. Mol Cell 2017; 69:136-145.e6. [PMID: 29290611 DOI: 10.1016/j.molcel.2017.11.034] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [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: 08/31/2017] [Revised: 11/01/2017] [Accepted: 11/27/2017] [Indexed: 10/18/2022]
Abstract
Transcription of the Ebola virus genome depends on the viral transcription factor VP30 in its unphosphorylated form, but the underlying molecular mechanism of VP30 dephosphorylation is unknown. Here we show that the Ebola virus nucleoprotein (NP) recruits the host PP2A-B56 protein phosphatase through a B56-binding LxxIxE motif and that this motif is essential for VP30 dephosphorylation and viral transcription. The LxxIxE motif and the binding site of VP30 in NP are in close proximity, and both binding sites are required for the dephosphorylation of VP30. We generate a specific inhibitor of PP2A-B56 and show that it suppresses Ebola virus transcription and infection. This work dissects the molecular mechanism of VP30 dephosphorylation by PP2A-B56, and it pinpoints this phosphatase as a potential target for therapeutic intervention.
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Affiliation(s)
- Thomas Kruse
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Nadine Biedenkopf
- Institute of Virology, Philipps Universität Marburg, Marburg, Germany; German Center of Infection Research (DZIF), Giessen-Marburg-Langen, Marburg, Germany
| | - Emil Peter Thrane Hertz
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Erik Dietzel
- Institute of Virology, Philipps Universität Marburg, Marburg, Germany; German Center of Infection Research (DZIF), Giessen-Marburg-Langen, Marburg, Germany
| | - Gertrud Stalmann
- Institute of Virology, Philipps Universität Marburg, Marburg, Germany; German Center of Infection Research (DZIF), Giessen-Marburg-Langen, Marburg, Germany
| | - Blanca López-Méndez
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland
| | - Jakob Nilsson
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
| | - Stephan Becker
- Institute of Virology, Philipps Universität Marburg, Marburg, Germany; German Center of Infection Research (DZIF), Giessen-Marburg-Langen, Marburg, Germany.
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29
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Abstract
The anaphase-promoting complex or cyclosome (APC/C) is a ubiquitin ligase that polyubiquitinates specific substrates at precise times in the cell cycle, thereby triggering the events of late mitosis in a strict order. The robust substrate specificity of the APC/C prevents the potentially deleterious degradation of non-APC/C substrates and also averts the cell-cycle errors and genomic instability that could result from mistimed degradation of APC/C targets. The APC/C recognizes short linear sequence motifs, or degrons, on its substrates. The specific and timely modification and degradation of APC/C substrates is likely to be modulated by variations in degron sequence and context. We discuss the extensive affinity, specificity, and selectivity determinants encoded in APC/C degrons, and we describe some of the extrinsic mechanisms that control APC/C-substrate recognition. As an archetype for protein motif-driven regulation of cell function, the APC/C-substrate interaction provides insights into the general properties of post-translational regulatory systems.
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Affiliation(s)
- Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland.
| | - David O Morgan
- Departments of Physiology and Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA.
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30
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Davey NE, Seo MH, Yadav VK, Jeon J, Nim S, Krystkowiak I, Blikstad C, Dong D, Markova N, Kim PM, Ivarsson Y. Discovery of short linear motif-mediated interactions through phage display of intrinsically disordered regions of the human proteome. FEBS J 2017; 284:485-498. [PMID: 28002650 DOI: 10.1111/febs.13995] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [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: 08/26/2016] [Revised: 12/04/2016] [Accepted: 12/19/2016] [Indexed: 12/29/2022]
Abstract
The intrinsically disordered regions of eukaryotic proteomes are enriched in short linear motifs (SLiMs), which are of crucial relevance for cellular signaling and protein regulation; many mediate interactions by providing binding sites for peptide-binding domains. The vast majority of SLiMs remain to be discovered highlighting the need for experimental methods for their large-scale identification. We present a novel proteomic peptide phage display (ProP-PD) library that displays peptides representing the disordered regions of the human proteome, allowing direct large-scale interrogation of most potential binding SLiMs in the proteome. The performance of the ProP-PD library was validated through selections against SLiM-binding bait domains with distinct folds and binding preferences. The vast majority of identified binding peptides contained sequences that matched the known SLiM-binding specificities of the bait proteins. For SHANK1 PDZ, we establish a novel consensus TxF motif for its non-C-terminal ligands. The binding peptides mostly represented novel target proteins, however, several previously validated protein-protein interactions (PPIs) were also discovered. We determined the affinities between the VHS domain of GGA1 and three identified ligands to 40-130 μm through isothermal titration calorimetry, and confirmed interactions through coimmunoprecipitation using full-length proteins. Taken together, we outline a general pipeline for the design and construction of ProP-PD libraries and the analysis of ProP-PD-derived, SLiM-based PPIs. We demonstrated the methods potential to identify low affinity motif-mediated interactions for modular domains with distinct binding preferences. The approach is a highly useful complement to the current toolbox of methods for PPI discovery.
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Affiliation(s)
- Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Ireland
| | - Moon-Hyeong Seo
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada
| | | | - Jouhyun Jeon
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada
| | - Satra Nim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada
| | - Izabella Krystkowiak
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Ireland
| | | | - Debbie Dong
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada
| | | | - Philip M Kim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada.,Department of Molecular Genetics and Department of Computer Science, University of Toronto, Canada
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Sweden
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31
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Abstract
Tandem mass spectrometry (MS/MS) techniques, developed for protein identification, are increasingly being applied in the field of peptidomics. Using this approach, the set of protein fragments observed in a sample of interest can be determined to gain insights into important biological processes such as signaling and other bioactivities. As the peptidomics era progresses, there is a need for robust and convenient methods to inspect and analyze MS/MS derived data. Here, we present Peptigram, a novel tool dedicated to the visualization and comparison of peptides detected by MS/MS. The principal advantage of Peptigram is that it provides visualizations at both the protein and peptide level, allowing users to simultaneously visualize the peptide distributions of one or more samples of interest, mapped to their parent proteins. In this way rapid comparisons between samples can be made in terms of their peptide coverage and abundance. Moreover, Peptigram integrates and displays key sequence features from external databases and links with peptide analysis tools to offer the user a comprehensive peptide discovery resource. Here, we illustrate the use of Peptigram on a data set of milk hydrolysates. For convenience, Peptigram is implemented as a web application, and is freely available for academic use at http://bioware.ucd.ie/peptigram .
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Affiliation(s)
- Jean Manguy
- Food for Health Ireland, ‡UCD Conway Institute of Biomolecular and Biomedical Research, §School of Medicine, ∥School of Biomolecular and Biomedical Science, University College Dublin , Belfield, Dublin 4, Ireland
| | - Peter Jehl
- Food for Health Ireland, ‡UCD Conway Institute of Biomolecular and Biomedical Research, §School of Medicine, ∥School of Biomolecular and Biomedical Science, University College Dublin , Belfield, Dublin 4, Ireland
| | - Eugène T Dillon
- Food for Health Ireland, ‡UCD Conway Institute of Biomolecular and Biomedical Research, §School of Medicine, ∥School of Biomolecular and Biomedical Science, University College Dublin , Belfield, Dublin 4, Ireland
| | - Norman E Davey
- Food for Health Ireland, ‡UCD Conway Institute of Biomolecular and Biomedical Research, §School of Medicine, ∥School of Biomolecular and Biomedical Science, University College Dublin , Belfield, Dublin 4, Ireland
| | - Denis C Shields
- Food for Health Ireland, ‡UCD Conway Institute of Biomolecular and Biomedical Research, §School of Medicine, ∥School of Biomolecular and Biomedical Science, University College Dublin , Belfield, Dublin 4, Ireland
| | - Thérèse A Holton
- Food for Health Ireland, ‡UCD Conway Institute of Biomolecular and Biomedical Research, §School of Medicine, ∥School of Biomolecular and Biomedical Science, University College Dublin , Belfield, Dublin 4, Ireland
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32
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Di Fiore B, Wurzenberger C, Davey NE, Pines J. The Mitotic Checkpoint Complex Requires an Evolutionary Conserved Cassette to Bind and Inhibit Active APC/C. Mol Cell 2016; 64:1144-1153. [PMID: 27939943 PMCID: PMC5179498 DOI: 10.1016/j.molcel.2016.11.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/12/2016] [Accepted: 10/31/2016] [Indexed: 12/26/2022]
Abstract
The Spindle Assembly Checkpoint (SAC) ensures genomic stability by preventing sister chromatid separation until all chromosomes are attached to the spindle. It catalyzes the production of the Mitotic Checkpoint Complex (MCC), which inhibits Cdc20 to inactivate the Anaphase Promoting Complex/Cyclosome (APC/C). Here we show that two Cdc20-binding motifs in BubR1 of the recently identified ABBA motif class are crucial for the MCC to recognize active APC/C-Cdc20. Mutating these motifs eliminates MCC binding to the APC/C, thereby abolishing the SAC and preventing cells from arresting in response to microtubule poisons. These ABBA motifs flank a KEN box to form a cassette that is highly conserved through evolution, both in the arrangement and spacing of the ABBA-KEN-ABBA motifs, and association with the amino-terminal KEN box required to form the MCC. We propose that the ABBA-KEN-ABBA cassette holds the MCC onto the APC/C by binding the two Cdc20 molecules in the MCC-APC/C complex.
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Affiliation(s)
- Barbara Di Fiore
- The Gurdon Institute and Department of Zoology, University of Cambridge, Cambridge CB2 1QN, UK
| | - Claudia Wurzenberger
- The Gurdon Institute and Department of Zoology, University of Cambridge, Cambridge CB2 1QN, UK
| | - Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland
| | - Jonathon Pines
- The Gurdon Institute and Department of Zoology, University of Cambridge, Cambridge CB2 1QN, UK; Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
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33
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Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, Minervini G, Murvai N, Pujols J, Roche DB, Salladini E, Schad E, Schramm A, Szabo B, Tantos A, Tonello F, Tsirigos KD, Veljković N, Ventura S, Vranken W, Warholm P, Uversky VN, Dunker AK, Longhi S, Tompa P, Tosatto SCE. Corrigendum: DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Res 2016; 45:D1123-D1124. [PMID: 27965415 PMCID: PMC5210598 DOI: 10.1093/nar/gkw1279] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Damiano Piovesan
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Francesco Tabaro
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy.,Institute of Biosciences and Medical Technology, University of Tampere, Finland
| | - Ivan Mičetić
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Marco Necci
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Federica Quaglia
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Christopher J Oldfield
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 46202 Indianapolis, IN, USA
| | | | - Norman E Davey
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.,Ireland UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Radoslav Davidović
- Centre for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, 11001 Belgrade, Serbia
| | - Zsuzsanna Dosztányi
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, 1/c Pázmány Péter sétány, 1117 Budapest, Hungary.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary
| | - Arne Elofsson
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Alessandra Gasparini
- Department of Woman and Child Health, University of Padova, I-35128 Padova, Italy
| | - András Hatos
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier 1919 Route de Mende, Cedex 5, Montpellier 34293, France.,Institut de Biologie Computationnelle (IBC), Montpellier 34095, France.,University ITMO, Institute of Bioengineering, St. Petersburg 197101, Russia
| | - Lajos Kalmar
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary.,Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Emanuela Leonardi
- Department of Woman and Child Health, University of Padova, I-35128 Padova, Italy
| | - Tamas Lazar
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,Structural Biology Research Center (SBRC), Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium
| | - Sandra Macedo-Ribeiro
- Biomolecular Structure and Function Group, Instituto de Biologia Molecular e Celular (IBMC) and Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal
| | - Mauricio Macossay-Castillo
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,Structural Biology Research Center (SBRC), Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium
| | - Attila Meszaros
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary
| | - Giovanni Minervini
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Nikoletta Murvai
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary
| | - Jordi Pujols
- Departament de Bioquimica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Daniel B Roche
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier 1919 Route de Mende, Cedex 5, Montpellier 34293, France.,Institut de Biologie Computationnelle (IBC), Montpellier 34095, France
| | | | - Eva Schad
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary
| | | | - Beata Szabo
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary
| | - Fiorella Tonello
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy.,CNR Institute of Neurosceince, I-35121 Padova, Italy
| | - Konstantinos D Tsirigos
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Nevena Veljković
- Centre for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, 11001 Belgrade, Serbia
| | - Salvador Ventura
- Departament de Bioquimica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Wim Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,Structural Biology Research Center (SBRC), Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium.,Interuniversity Institute of Bioinformatics in Brussels (IB2), ULB-VUB, Brussels 1050, Belgium
| | - Per Warholm
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Vladimir N Uversky
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia.,Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 46202 Indianapolis, IN, USA
| | - Sonia Longhi
- Aix-Marseille Univ, CNRS, AFMB, UMR 7257, Marseille, France
| | - Peter Tompa
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary .,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,Structural Biology Research Center (SBRC), Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy .,CNR Institute of Neurosceince, I-35121 Padova, Italy
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Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, Minervini G, Murvai N, Pujols J, Roche DB, Salladini E, Schad E, Schramm A, Szabo B, Tantos A, Tonello F, Tsirigos KD, Veljković N, Ventura S, Vranken W, Warholm P, Uversky VN, Dunker AK, Longhi S, Tompa P, Tosatto SCE. DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Res 2016; 45:D219-D227. [PMID: 27899601 PMCID: PMC5210544 DOI: 10.1093/nar/gkw1056] [Citation(s) in RCA: 193] [Impact Index Per Article: 24.1] [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: 09/27/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 01/16/2023] Open
Abstract
The Database of Protein Disorder (DisProt, URL: www.disprot.org) has been significantly updated and upgraded since its last major renewal in 2007. The current release holds information on more than 800 entries of IDPs/IDRs, i.e. intrinsically disordered proteins or regions that exist and function without a well-defined three-dimensional structure. We have re-curated previous entries to purge DisProt from conflicting cases, and also upgraded the functional classification scheme to reflect continuous advance in the field in the past 10 years or so. We define IDPs as proteins that are disordered along their entire sequence, i.e. entirely lack structural elements, and IDRs as regions that are at least five consecutive residues without well-defined structure. We base our assessment of disorder strictly on experimental evidence, such as X-ray crystallography and nuclear magnetic resonance (primary techniques) and a broad range of other experimental approaches (secondary techniques). Confident and ambiguous annotations are highlighted separately. DisProt 7.0 presents classified knowledge regarding the experimental characterization and functional annotations of IDPs/IDRs, and is intended to provide an invaluable resource for the research community for a better understanding structural disorder and for developing better computational tools for studying disordered proteins.
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Affiliation(s)
- Damiano Piovesan
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Francesco Tabaro
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy.,Institute of Biosciences and Medical Technology, University of Tampere, Finland
| | - Ivan Mičetić
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Marco Necci
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Federica Quaglia
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Christopher J Oldfield
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 46202 Indianapolis, IN, USA
| | | | - Norman E Davey
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.,Ireland UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Radoslav Davidović
- Centre for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, 11001 Belgrade, Serbia
| | - Zsuzsanna Dosztányi
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, 1/c Pázmány Péter sétány, 1117 Budapest, Hungary.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary
| | - Arne Elofsson
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Alessandra Gasparini
- Department of Woman and Child Health, University of Padova, I-35128 Padova, Italy
| | - András Hatos
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier 1919 Route de Mende, Cedex 5, Montpellier 34293, France.,Institut de Biologie Computationnelle (IBC), Montpellier 34095, France.,University ITMO, Institute of Bioengineering, St. Petersburg 197101, Russia
| | - Lajos Kalmar
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary.,Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Emanuela Leonardi
- Department of Woman and Child Health, University of Padova, I-35128 Padova, Italy
| | - Tamas Lazar
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,Structural Biology Research Center (SBRC), Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium
| | - Sandra Macedo-Ribeiro
- Biomolecular Structure and Function Group, Instituto de Biologia Molecular e Celular (IBMC) and Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal
| | - Mauricio Macossay-Castillo
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,Structural Biology Research Center (SBRC), Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium
| | - Attila Meszaros
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary
| | - Giovanni Minervini
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Nikoletta Murvai
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary
| | - Jordi Pujols
- Departament de Bioquimica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Daniel B Roche
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier 1919 Route de Mende, Cedex 5, Montpellier 34293, France.,Institut de Biologie Computationnelle (IBC), Montpellier 34095, France
| | | | - Eva Schad
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary
| | | | - Beata Szabo
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary
| | - Fiorella Tonello
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy.,CNR Institute of Neurosceince, I-35121 Padova, Italy
| | - Konstantinos D Tsirigos
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Nevena Veljković
- Centre for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, 11001 Belgrade, Serbia
| | - Salvador Ventura
- Departament de Bioquimica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Wim Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,Structural Biology Research Center (SBRC), Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium.,Interuniversity Institute of Bioinformatics in Brussels (IB2), ULB-VUB, Brussels 1050, Belgium
| | - Per Warholm
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Vladimir N Uversky
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia.,Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 46202 Indianapolis, IN, USA
| | - Sonia Longhi
- Aix-Marseille Univ, CNRS, AFMB, UMR 7257, Marseille, France
| | - Peter Tompa
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary .,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,Structural Biology Research Center (SBRC), Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy .,CNR Institute of Neurosceince, I-35121 Padova, Italy
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Hertz EPT, Kruse T, Davey NE, López-Méndez B, Sigurðsson JO, Montoya G, Olsen JV, Nilsson J. A Conserved Motif Provides Binding Specificity to the PP2A-B56 Phosphatase. Mol Cell 2016; 63:686-695. [PMID: 27453045 DOI: 10.1016/j.molcel.2016.06.024] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 06/05/2016] [Accepted: 06/15/2016] [Indexed: 01/17/2023]
Abstract
Dynamic protein phosphorylation is a fundamental mechanism regulating biological processes in all organisms. Protein phosphatase 2A (PP2A) is the main source of phosphatase activity in the cell, but the molecular details of substrate recognition are unknown. Here, we report that a conserved surface-exposed pocket on PP2A regulatory B56 subunits binds to a consensus sequence on interacting proteins, which we term the LxxIxE motif. The composition of the motif modulates the affinity for B56, which in turn determines the phosphorylation status of associated substrates. Phosphorylation of amino acid residues within the motif increases B56 binding, allowing integration of kinase and phosphatase activity. We identify conserved LxxIxE motifs in essential proteins throughout the eukaryotic domain of life and in human viruses, suggesting that the motifs are required for basic cellular function. Our study provides a molecular description of PP2A binding specificity with broad implications for understanding signaling in eukaryotes.
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Affiliation(s)
- Emil Peter Thrane Hertz
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Thomas Kruse
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland
| | - Blanca López-Méndez
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Jón Otti Sigurðsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Guillermo Montoya
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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Jehl P, Manguy J, Shields DC, Higgins DG, Davey NE. ProViz-a web-based visualization tool to investigate the functional and evolutionary features of protein sequences. Nucleic Acids Res 2016; 44:W11-5. [PMID: 27085803 PMCID: PMC4987877 DOI: 10.1093/nar/gkw265] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [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: 01/31/2016] [Accepted: 04/04/2016] [Indexed: 11/26/2022] Open
Abstract
Low-throughput experiments and high-throughput proteomic and genomic analyses have created enormous quantities of data that can be used to explore protein function and evolution. The ability to consolidate these data into an informative and intuitive format is vital to our capacity to comprehend these distinct but complementary sources of information. However, existing tools to visualize protein-related data are restricted by their presentation, sources of information, functionality or accessibility. We introduce ProViz, a powerful browser-based tool to aid biologists in building hypotheses and designing experiments by simplifying the analysis of functional and evolutionary features of proteins. Feature information is retrieved in an automated manner from resources describing protein modular architecture, post-translational modification, structure, sequence variation and experimental characterization of functional regions. These features are mapped to evolutionary information from precomputed multiple sequence alignments. Data are displayed in an interactive and information-rich yet intuitive visualization, accessible through a simple protein search interface. This allows users with limited bioinformatic skills to rapidly access data pertinent to their research. Visualizations can be further customized with user-defined data either manually or using a REST API. ProViz is available at http://proviz.ucd.ie/.
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Affiliation(s)
- Peter Jehl
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Jean Manguy
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Denis C Shields
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Desmond G Higgins
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Norman E Davey
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
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37
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Dinkel H, Van Roey K, Michael S, Kumar M, Uyar B, Altenberg B, Milchevskaya V, Schneider M, Kühn H, Behrendt A, Dahl SL, Damerell V, Diebel S, Kalman S, Klein S, Knudsen AC, Mäder C, Merrill S, Staudt A, Thiel V, Welti L, Davey NE, Diella F, Gibson TJ. ELM 2016--data update and new functionality of the eukaryotic linear motif resource. Nucleic Acids Res 2016; 44:D294-300. [PMID: 26615199 PMCID: PMC4702912 DOI: 10.1093/nar/gkv1291] [Citation(s) in RCA: 223] [Impact Index Per Article: 27.9] [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: 10/11/2015] [Revised: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 01/18/2023] Open
Abstract
The Eukaryotic Linear Motif (ELM) resource (http://elm.eu.org) is a manually curated database of short linear motifs (SLiMs). In this update, we present the latest additions to this resource, along with more improvements to the web interface. ELM 2016 contains more than 240 different motif classes with over 2700 experimentally validated instances, manually curated from more than 2400 scientific publications. In addition, more data have been made available as individually searchable pages and are downloadable in various formats.
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Affiliation(s)
- Holger Dinkel
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Kim Van Roey
- Health Services Research Unit, Operational Direction Public Health and Surveillance, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Sushama Michael
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Manjeet Kumar
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Bora Uyar
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Brigitte Altenberg
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Vladislava Milchevskaya
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Helen Kühn
- Ruprecht-Karls-Universität, Heidelberg, Germany
| | | | | | | | | | - Sara Kalman
- Ruprecht-Karls-Universität, Heidelberg, Germany
| | | | | | | | | | | | - Vera Thiel
- Ruprecht-Karls-Universität, Heidelberg, Germany
| | - Lukas Welti
- Ruprecht-Karls-Universität, Heidelberg, Germany
| | - Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland
| | - Francesca Diella
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Toby J Gibson
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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38
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Van Roey K, Davey NE. Motif co-regulation and co-operativity are common mechanisms in transcriptional, post-transcriptional and post-translational regulation. Cell Commun Signal 2015; 13:45. [PMID: 26626130 PMCID: PMC4666095 DOI: 10.1186/s12964-015-0123-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/24/2015] [Indexed: 01/01/2023] Open
Abstract
A substantial portion of the regulatory interactions in the higher eukaryotic cell are mediated by simple sequence motifs in the regulatory segments of genes and (pre-)mRNAs, and in the intrinsically disordered regions of proteins. Although these regulatory modules are physicochemically distinct, they share an evolutionary plasticity that has facilitated a rapid growth of their use and resulted in their ubiquity in complex organisms. The ease of motif acquisition simplifies access to basal housekeeping functions, facilitates the co-regulation of multiple biomolecules allowing them to respond in a coordinated manner to changes in the cell state, and supports the integration of multiple signals for combinatorial decision-making. Consequently, motifs are indispensable for temporal, spatial, conditional and basal regulation at the transcriptional, post-transcriptional and post-translational level. In this review, we highlight that many of the key regulatory pathways of the cell are recruited by motifs and that the ease of motif acquisition has resulted in large networks of co-regulated biomolecules. We discuss how co-operativity allows simple static motifs to perform the conditional regulation that underlies decision-making in higher eukaryotic biological systems. We observe that each gene and its products have a unique set of DNA, RNA or protein motifs that encode a regulatory program to define the logical circuitry that guides the life cycle of these biomolecules, from transcription to degradation. Finally, we contrast the regulatory properties of protein motifs and the regulatory elements of DNA and (pre-)mRNAs, advocating that co-regulation, co-operativity, and motif-driven regulatory programs are common mechanisms that emerge from the use of simple, evolutionarily plastic regulatory modules.
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Affiliation(s)
- Kim Van Roey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany. .,Health Services Research Unit, Operational Direction Public Health and Surveillance, Scientific Institute of Public Health (WIV-ISP), 1050, Brussels, Belgium.
| | - Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland.
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39
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Abstract
Short sequence motifs are ubiquitous across the three major types of biomolecules: hundreds of classes and thousands of instances of DNA regulatory elements, RNA motifs and protein short linear motifs (SLiMs) have been characterised. The increase in complexity of transcriptional, post-transcriptional and post-translational regulation in higher Eukaryotes has coincided with a significant expansion of motif use. But how did the eukaryotic cell acquire such a vast repertoire of motifs? In this review, we curate the available literature on protein motif evolution and discuss the evidence that suggests SLiMs can be acquired by mutations, insertions and deletions in disordered regions. We propose a mechanism of ex nihilo SLiM evolution – the evolution of a novel SLiM from “nothing” – adding a functional module to a previously non-functional region of protein sequence. In our model, hundreds of motif-binding domains in higher eukaryotic proteins connect simple motif specificities with useful functions to create a large functional motif space. Accessible peptides that match the specificity of these motif-binding domains are continuously created and destroyed by mutations in rapidly evolving disordered regions, creating a dynamic supply of new interactions that may have advantageous phenotypic novelty. This provides a reservoir of diversity to modify existing interaction networks. Evolutionary pressures will act on these motifs to retain beneficial instances. However, most will be lost on an evolutionary timescale as negative selection and genetic drift act on deleterious and neutral motifs respectively. In light of the parallels between the presented model and the evolution of motifs in the regulatory segments of genes and (pre-)mRNAs, we suggest our understanding of regulatory networks would benefit from the creation of a shared model describing the evolution of transcriptional, post-transcriptional and post-translational regulation.
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Affiliation(s)
- Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland.
| | - Martha S Cyert
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
| | - Alan M Moses
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada. .,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada.
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40
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Uyar B, Weatheritt RJ, Dinkel H, Davey NE, Gibson TJ. Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer? Mol Biosyst 2015; 10:2626-42. [PMID: 25057855 PMCID: PMC4306509 DOI: 10.1039/c4mb00290c] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Mutations in short linear motifs impair the functions of intrinsically disordered proteins in cellular signaling/regulation and contribute substantially to human diseases.
Disease mutations are traditionally thought to impair protein functionality by disrupting the folded globular structure of proteins. However, 22% of human disease mutations occur in natively unstructured segments of proteins known as intrinsically disordered regions (IDRs). This therefore implicates defective IDR functionality in various human diseases including cancer. The functionality of IDRs is partly attributable to short linear motifs (SLiMs), but it remains an open question how much defects in SLiMs contribute to human diseases. A proteome-wide comparison of the distribution of missense mutations from disease and non-disease mutation datasets revealed that, in IDRs, disease mutations are more likely to occur within SLiMs than neutral missense mutations. Moreover, compared to neutral missense mutations, disease mutations more frequently impact functionally important residues of SLiMs, cause changes in the physicochemical properties of SLiMs, and disrupt more SLiM-mediated interactions. Analysis of these mutations resulted in a comprehensive list of experimentally validated or predicted SLiMs disrupted in disease. Furthermore, this in-depth analysis suggests that ‘prostate cancer pathway’ is particularly enriched for proteins with disease-related SLiMs. The contribution of mutations in SLiMs to disease may currently appear small when compared to mutations in globular domains. However, our analysis of mutations in predicted SLiMs suggests that this contribution might be more substantial. Therefore, when analysing the functional impact of mutations on proteins, SLiMs in proteins should not be neglected. Our results suggest that an increased focus on SLiMs in the coming decades will improve our understanding of human diseases and aid in the development of targeted treatments.
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Affiliation(s)
- Bora Uyar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
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41
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Di Fiore B, Davey NE, Hagting A, Izawa D, Mansfeld J, Gibson TJ, Pines J. The ABBA motif binds APC/C activators and is shared by APC/C substrates and regulators. Dev Cell 2015; 32:358-372. [PMID: 25669885 PMCID: PMC4713905 DOI: 10.1016/j.devcel.2015.01.003] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [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: 03/21/2014] [Revised: 09/03/2014] [Accepted: 01/05/2015] [Indexed: 11/30/2022]
Abstract
The anaphase-promoting complex or cyclosome (APC/C) is the ubiquitin ligase that regulates mitosis by targeting specific proteins for degradation at specific times under the control of the spindle assembly checkpoint (SAC). How the APC/C recognizes its different substrates is a key problem in the control of cell division. Here, we have identified the ABBA motif in cyclin A, BUBR1, BUB1, and Acm1, and we show that it binds to the APC/C coactivator CDC20. The ABBA motif in cyclin A is required for its proper degradation in prometaphase through competing with BUBR1 for the same site on CDC20. Moreover, the ABBA motifs in BUBR1 and BUB1 are necessary for the SAC to work at full strength and to recruit CDC20 to kinetochores. Thus, we have identified a conserved motif integral to the proper control of mitosis that connects APC/C substrate recognition with the SAC.
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Affiliation(s)
- Barbara Di Fiore
- The Gurdon Institute and Department of Zoology, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Norman E. Davey
- Department of Physiology and Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Baden-Württemberg 69117, Germany
| | - Anja Hagting
- The Gurdon Institute and Department of Zoology, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Daisuke Izawa
- The Gurdon Institute and Department of Zoology, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Jörg Mansfeld
- Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Toby J. Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Baden-Württemberg 69117, Germany
| | - Jonathon Pines
- The Gurdon Institute and Department of Zoology, University of Cambridge, Cambridge, CB2 1QN, UK
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42
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Downey M, Johnson JR, Davey NE, Newton BW, Johnson TL, Galaang S, Seller CA, Krogan N, Toczyski DP. Acetylome profiling reveals overlap in the regulation of diverse processes by sirtuins, gcn5, and esa1. Mol Cell Proteomics 2014; 14:162-76. [PMID: 25381059 DOI: 10.1074/mcp.m114.043141] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Although histone acetylation and deacetylation machineries (HATs and HDACs) regulate important aspects of cell function by targeting histone tails, recent work highlights that non-histone protein acetylation is also pervasive in eukaryotes. Here, we use quantitative mass-spectrometry to define acetylations targeted by the sirtuin family, previously implicated in the regulation of non-histone protein acetylation. To identify HATs that promote acetylation of these sites, we also performed this analysis in gcn5 (SAGA) and esa1 (NuA4) mutants. We observed strong sequence specificity for the sirtuins and for each of these HATs. Although the Gcn5 and Esa1 consensus sequences are entirely distinct, the sirtuin consensus overlaps almost entirely with that of Gcn5, suggesting a strong coordination between these two regulatory enzymes. Furthermore, by examining global acetylation in an ada2 mutant, which dissociates Gcn5 from the SAGA complex, we found that a subset of Gcn5 targets did not depend on an intact SAGA complex for targeting. Our work provides a framework for understanding how HAT and HDAC enzymes collaborate to regulate critical cellular processes related to growth and division.
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Affiliation(s)
- Michael Downey
- From the ‡Department of Biochemistry and Biophysics, University of California, San Francisco, 1450 3rd Street, San Francisco, CA, 94158;
| | - Jeffrey R Johnson
- §Cellular and Molecular Pharmacology, University of California, San Francisco, 1700 4th Street, QB3, San Francisco, CA, 94158
| | - Norman E Davey
- ¶Department of Physiology and Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Billy W Newton
- §Cellular and Molecular Pharmacology, University of California, San Francisco, 1700 4th Street, QB3, San Francisco, CA, 94158
| | - Tasha L Johnson
- §Cellular and Molecular Pharmacology, University of California, San Francisco, 1700 4th Street, QB3, San Francisco, CA, 94158
| | - Shastyn Galaang
- From the ‡Department of Biochemistry and Biophysics, University of California, San Francisco, 1450 3rd Street, San Francisco, CA, 94158
| | - Charles A Seller
- From the ‡Department of Biochemistry and Biophysics, University of California, San Francisco, 1450 3rd Street, San Francisco, CA, 94158
| | - Nevan Krogan
- §Cellular and Molecular Pharmacology, University of California, San Francisco, 1700 4th Street, QB3, San Francisco, CA, 94158
| | - David P Toczyski
- From the ‡Department of Biochemistry and Biophysics, University of California, San Francisco, 1450 3rd Street, San Francisco, CA, 94158
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43
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Lu D, Hsiao JY, Davey NE, Van Voorhis VA, Foster SA, Tang C, Morgan DO. Multiple mechanisms determine the order of APC/C substrate degradation in mitosis. ACTA ACUST UNITED AC 2014; 207:23-39. [PMID: 25287299 PMCID: PMC4195823 DOI: 10.1083/jcb.201402041] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [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] [Indexed: 12/23/2022]
Abstract
To ensure proper mitotic progression, robust ordering of the destruction of APC/CCdc20 substrates is driven by the integration of molecular mechanisms ranging from phosphorylation-dependent interaction with substrates to sensing of the status of the spindle assembly checkpoint. The ubiquitin protein ligase anaphase-promoting complex or cyclosome (APC/C) controls mitosis by promoting ordered degradation of securin, cyclins, and other proteins. The mechanisms underlying the timing of APC/C substrate degradation are poorly understood. We explored these mechanisms using quantitative fluorescence microscopy of GFP-tagged APC/CCdc20 substrates in living budding yeast cells. Degradation of the S cyclin, Clb5, begins early in mitosis, followed 6 min later by the degradation of securin and Dbf4. Anaphase begins when less than half of securin is degraded. The spindle assembly checkpoint delays the onset of Clb5 degradation but does not influence securin degradation. Early Clb5 degradation depends on its interaction with the Cdk1–Cks1 complex and the presence of a Cdc20-binding “ABBA motif” in its N-terminal region. The degradation of securin and Dbf4 is delayed by Cdk1-dependent phosphorylation near their Cdc20-binding sites. Thus, a remarkably diverse array of mechanisms generates robust ordering of APC/CCdc20 substrate destruction.
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Affiliation(s)
- Dan Lu
- Department of Physiology and Department of Biochemistry and Biophysics and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
| | - Jennifer Y Hsiao
- Department of Physiology and Department of Biochemistry and Biophysics and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
| | - Norman E Davey
- Department of Physiology and Department of Biochemistry and Biophysics and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
| | - Vanessa A Van Voorhis
- Department of Physiology and Department of Biochemistry and Biophysics and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
| | - Scott A Foster
- Department of Physiology and Department of Biochemistry and Biophysics and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
| | - Chao Tang
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - David O Morgan
- Department of Physiology and Department of Biochemistry and Biophysics and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
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44
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Van Roey K, Uyar B, Weatheritt RJ, Dinkel H, Seiler M, Budd A, Gibson TJ, Davey NE. Short Linear Motifs: Ubiquitous and Functionally Diverse Protein Interaction Modules Directing Cell Regulation. Chem Rev 2014; 114:6733-78. [DOI: 10.1021/cr400585q] [Citation(s) in RCA: 293] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Kim Van Roey
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Bora Uyar
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Robert J. Weatheritt
- MRC
Laboratory of Molecular Biology (LMB), Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Holger Dinkel
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Markus Seiler
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Aidan Budd
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Toby J. Gibson
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Norman E. Davey
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department
of Physiology, University of California, San Francisco, San Francisco, California 94143, United States
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45
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Dinkel H, Van Roey K, Michael S, Davey NE, Weatheritt RJ, Born D, Speck T, Krüger D, Grebnev G, Kuban M, Strumillo M, Uyar B, Budd A, Altenberg B, Seiler M, Chemes LB, Glavina J, Sánchez IE, Diella F, Gibson TJ. The eukaryotic linear motif resource ELM: 10 years and counting. Nucleic Acids Res 2013; 42:D259-66. [PMID: 24214962 PMCID: PMC3964949 DOI: 10.1093/nar/gkt1047] [Citation(s) in RCA: 229] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The eukaryotic linear motif (ELM http://elm.eu.org) resource is a hub for collecting, classifying and curating information about short linear motifs (SLiMs). For >10 years, this resource has provided the scientific community with a freely accessible guide to the biology and function of linear motifs. The current version of ELM contains ∼200 different motif classes with over 2400 experimentally validated instances manually curated from >2000 scientific publications. Furthermore, detailed information about motif-mediated interactions has been annotated and made available in standard exchange formats. Where appropriate, links are provided to resources such as switches.elm.eu.org and KEGG pathways.
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Affiliation(s)
- Holger Dinkel
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, Department of Physiology, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA, Structural Studies Division, MRC, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK, Ruprecht-Karls-Universität, 69117 Heidelberg, Germany, School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Co. Dublin, Republic of Ireland, Laboratory of Bioinformatics and Biostatistics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, WK Roentgena 5, 02-781 Warsaw, Poland, Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas Avenida Patricias Argentinas 435 CP 1405 Buenos Aires, Argentina and Departamento de Química Biológica and IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Gúiraldes 2160 CP 1428, Argentina
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46
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Pushker R, Mooney C, Davey NE, Jacqué JM, Shields DC. Marked variability in the extent of protein disorder within and between viral families. PLoS One 2013; 8:e60724. [PMID: 23620725 PMCID: PMC3631256 DOI: 10.1371/journal.pone.0060724] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 03/01/2013] [Indexed: 12/28/2022] Open
Abstract
Intrinsically disordered regions in eukaryotic proteomes contain key signaling and regulatory modules and mediate interactions with many proteins. Many viral proteomes encode disordered proteins and modulate host factors through the use of short linear motifs (SLiMs) embedded within disordered regions. However, the degree of viral protein disorder across different viruses is not well understood, so we set out to establish the constraints acting on viruses, in terms of their use of disordered protein regions. We surveyed predicted disorder across 2,278 available viral genomes in 41 families, and correlated the extent of disorder with genome size and other factors. Protein disorder varies strikingly between viral families (from 2.9% to 23.1% of residues), and also within families. However, this substantial variation did not follow the established trend among their hosts, with increasing disorder seen across eubacterial, archaebacterial, protists, and multicellular eukaryotes. For example, among large mammalian viruses, poxviruses and herpesviruses showed markedly differing disorder (5.6% and 17.9%, respectively). Viral families with smaller genome sizes have more disorder within each of five main viral types (ssDNA, dsDNA, ssRNA+, dsRNA, retroviruses), except for negative single-stranded RNA viruses, where disorder increased with genome size. However, surveying over all viruses, which compares tiny and enormous viruses over a much bigger range of genome sizes, there is no strong association of genome size with protein disorder. We conclude that there is extensive variation in the disorder content of viral proteomes. While a proportion of this may relate to base composition, to extent of gene overlap, and to genome size within viral types, there remain important additional family and virus-specific effects. Differing disorder strategies are likely to impact on how different viruses modulate host factors, and on how rapidly viruses can evolve novel instances of SLiMs subverting host functions, such as innate and acquired immunity.
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Affiliation(s)
- Ravindra Pushker
- UCD Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Catherine Mooney
- UCD Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Norman E. Davey
- EMBL Structural and Computational Biology Unit, Heidelberg, Germany
| | - Jean-Marc Jacqué
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland
- Centre for Research in Infectious Diseases, University College Dublin, Belfield, Dublin, Ireland
| | - Denis C. Shields
- UCD Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland
- * E-mail:
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47
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Van Roey K, Dinkel H, Weatheritt RJ, Gibson TJ, Davey NE. The switches.ELM resource: a compendium of conditional regulatory interaction interfaces. Sci Signal 2013; 6:rs7. [PMID: 23550212 DOI: 10.1126/scisignal.2003345] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Short linear motifs (SLiMs) are protein interaction sites that play an important role in cell regulation by controlling protein activity, localization, and local abundance. The functionality of a SLiM can be modulated in a context-dependent manner to induce a gain, loss, or exchange of binding partners, which will affect the function of the SLiM-containing protein. As such, these conditional interactions underlie molecular decision-making in cell signaling. We identified multiple types of pre- and posttranslational switch mechanisms that can regulate the function of a SLiM and thereby control its interactions. The collected examples of experimentally characterized SLiM-based switch mechanisms were curated in the freely accessible switches.ELM resource (http://switches.elm.eu.org). On the basis of these examples, we defined and integrated rules to analyze SLiMs for putative regulatory switch mechanisms. We applied these rules to known validated SLiMs, providing evidence that more than half of these are likely to be pre- or posttranslationally regulated. In addition, we showed that posttranslationally modified sites are enriched around SLiMs, which enables cooperative and integrative regulation of protein interaction interfaces. We foresee switches.ELM complementing available resources to extend our knowledge of the molecular mechanisms underlying cell signaling.
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Affiliation(s)
- Kim Van Roey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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48
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Davey NE, Cowan JL, Shields DC, Gibson TJ, Coldwell MJ, Edwards RJ. SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions. Nucleic Acids Res 2012; 40:10628-41. [PMID: 22977176 PMCID: PMC3510515 DOI: 10.1093/nar/gks854] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [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] [Indexed: 12/21/2022] Open
Abstract
Large portions of higher eukaryotic proteomes are intrinsically disordered, and abundant evidence suggests that these unstructured regions of proteins are rich in regulatory interaction interfaces. A major class of disordered interaction interfaces are the compact and degenerate modules known as short linear motifs (SLiMs). As a result of the difficulties associated with the experimental identification and validation of SLiMs, our understanding of these modules is limited, advocating the use of computational methods to focus experimental discovery. This article evaluates the use of evolutionary conservation as a discriminatory technique for motif discovery. A statistical framework is introduced to assess the significance of relatively conserved residues, quantifying the likelihood a residue will have a particular level of conservation given the conservation of the surrounding residues. The framework is expanded to assess the significance of groupings of conserved residues, a metric that forms the basis of SLiMPrints (short linear motif fingerprints), a de novo motif discovery tool. SLiMPrints identifies relatively overconstrained proximal groupings of residues within intrinsically disordered regions, indicative of putatively functional motifs. Finally, the human proteome is analysed to create a set of highly conserved putative motif instances, including a novel site on translation initiation factor eIF2A that may regulate translation through binding of eIF4E.
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Affiliation(s)
- Norman E Davey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Baden-Württemberg 69117, Germany.
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49
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Stavropoulos I, Khaldi N, Davey NE, O’Brien K, Martin F, Shields DC. Protein disorder and short conserved motifs in disordered regions are enriched near the cytoplasmic side of single-pass transmembrane proteins. PLoS One 2012; 7:e44389. [PMID: 22962613 PMCID: PMC3433447 DOI: 10.1371/journal.pone.0044389] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 08/06/2012] [Indexed: 01/07/2023] Open
Abstract
Intracellular juxtamembrane regions of transmembrane proteins play pivotal roles in cell signalling, mediated by protein-protein interactions. Disordered protein regions, and short conserved motifs within them, are emerging as key determinants of many such interactions. Here, we investigated whether disorder and conserved motifs are enriched in the juxtamembrane area of human single-pass transmembrane proteins. Conserved motifs were defined as short disordered regions that were much more conserved than the adjacent disordered residues. Human single-pass proteins had higher mean disorder in their cytoplasmic segments than their extracellular parts. Some, but not all, of this effect reflected the shorter length of the cytoplasmic tail. A peak of cytoplasmic disorder was seen at around 30 residues from the membrane. We noted a significant increase in the incidence of conserved motifs within the disordered regions at the same location, even after correcting for the extent of disorder. We conclude that elevated disorder within the cytoplasmic tail of many transmembrane proteins is likely to be associated with enrichment for signalling interactions mediated by conserved short motifs.
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Affiliation(s)
- Ilias Stavropoulos
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
- Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
- Conway Institute, University College Dublin, Dublin, Ireland
| | - Nora Khaldi
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
- Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
- Conway Institute, University College Dublin, Dublin, Ireland
- Department of Food Science and Technology, University of California Davis, Davis, California, United States of America
| | - Norman E. Davey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Kevin O’Brien
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
- Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
- Conway Institute, University College Dublin, Dublin, Ireland
| | - Finian Martin
- Conway Institute, University College Dublin, Dublin, Ireland
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Denis C. Shields
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
- Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
- Conway Institute, University College Dublin, Dublin, Ireland
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50
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Bharat TAM, Davey NE, Ulbrich P, Riches JD, de Marco A, Rumlova M, Sachse C, Ruml T, Briggs JAG. Structure of the immature retroviral capsid at 8 Å resolution by cryo-electron microscopy. Nature 2012; 487:385-9. [PMID: 22722831 DOI: 10.1038/nature11169] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 04/27/2012] [Indexed: 12/27/2022]
Abstract
The assembly of retroviruses such as HIV-1 is driven by oligomerization of their major structural protein, Gag. Gag is a multidomain polyprotein including three conserved folded domains: MA (matrix), CA (capsid) and NC (nucleocapsid). Assembly of an infectious virion proceeds in two stages. In the first stage, Gag oligomerization into a hexameric protein lattice leads to the formation of an incomplete, roughly spherical protein shell that buds through the plasma membrane of the infected cell to release an enveloped immature virus particle. In the second stage, cleavage of Gag by the viral protease leads to rearrangement of the particle interior, converting the non-infectious immature virus particle into a mature infectious virion. The immature Gag shell acts as the pivotal intermediate in assembly and is a potential target for anti-retroviral drugs both in inhibiting virus assembly and in disrupting virus maturation. However, detailed structural information on the immature Gag shell has not previously been available. For this reason it is unclear what protein conformations and interfaces mediate the interactions between domains and therefore the assembly of retrovirus particles, and what structural transitions are associated with retrovirus maturation. Here we solve the structure of the immature retroviral Gag shell from Mason-Pfizer monkey virus by combining cryo-electron microscopy and tomography. The 8-Å resolution structure permits the derivation of a pseudo-atomic model of CA in the immature retrovirus, which defines the protein interfaces mediating retrovirus assembly. We show that transition of an immature retrovirus into its mature infectious form involves marked rotations and translations of CA domains, that the roles of the amino-terminal and carboxy-terminal domains of CA in assembling the immature and mature hexameric lattices are exchanged, and that the CA interactions that stabilize the immature and mature viruses are almost completely distinct.
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Affiliation(s)
- Tanmay A M Bharat
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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