|
1
|
Jeong A, Auger SA, Maity S, Fredriksen K, Zhong R, Li L, Distefano MD. In Vivo Prenylomic Profiling in the Brain of a Transgenic Mouse Model of Alzheimer's Disease Reveals Increased Prenylation of a Key Set of Proteins. ACS Chem Biol 2022; 17:2863-2876. [PMID: 36109170 PMCID: PMC9799064 DOI: 10.1021/acschembio.2c00486] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Dysregulation of protein prenylation has been implicated in many diseases, including Alzheimer's disease (AD). Prenylomic analysis, the combination of metabolic incorporation of an isoprenoid analogue (C15AlkOPP) into prenylated proteins with a bottom-up proteomic analysis, has allowed the identification of prenylated proteins in various cellular models. Here, transgenic AD mice were administered with C15AlkOPP through intracerebroventricular (ICV) infusion over 13 days. Using prenylomic analysis, 36 prenylated proteins were enriched in the brains of AD mice. Importantly, the prenylated forms of 15 proteins were consistently upregulated in AD mice compared to nontransgenic wild-type controls. These results highlight the power of this in vivo metabolic labeling approach to identify multiple post-translationally modified proteins that may serve as potential therapeutic targets for a disease that has proved refractory to treatment thus far. Moreover, this method should be applicable to many other types of protein modifications, significantly broadening its scope.
Collapse
Affiliation(s)
- Angela Jeong
- University of Minnesota, Minneapolis, MN, 55455 USA
| | | | - Sanjay Maity
- University of Minnesota, Minneapolis, MN, 55455 USA
| | | | - Rui Zhong
- University of Minnesota, Minneapolis, MN, 55455 USA
| | - Ling Li
- University of Minnesota, Minneapolis, MN, 55455 USA
| | | |
Collapse
|
|
2
|
Del Toro N, Shrivastava A, Ragueneau E, Meldal B, Combe C, Barrera E, Perfetto L, How K, Ratan P, Shirodkar G, Lu O, Mészáros B, Watkins X, Pundir S, Licata L, Iannuccelli M, Pellegrini M, Martin MJ, Panni S, Duesbury M, Vallet SD, Rappsilber J, Ricard-Blum S, Cesareni G, Salwinski L, Orchard S, Porras P, Panneerselvam K, Hermjakob H. The IntAct database: efficient access to fine-grained molecular interaction data. Nucleic Acids Res 2021; 50:D648-D653. [PMID: 34761267 PMCID: PMC8728211 DOI: 10.1093/nar/gkab1006] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/06/2021] [Accepted: 10/21/2021] [Indexed: 01/18/2023] Open
Abstract
The IntAct molecular interaction database (https://www.ebi.ac.uk/intact) is a curated resource of molecular interactions, derived from the scientific literature and from direct data depositions. As of August 2021, IntAct provides more than one million binary interactions, curated by twelve global partners of the International Molecular Exchange consortium, for which the IntAct database provides a shared curation and dissemination platform. The IMEx curation policy has always emphasised a fine-grained data and curation model, aiming to capture the relevant experimental detail essential for the interpretation of the provided molecular interaction data. Here, we present recent curation focus and progress, as well as a completely redeveloped website which presents IntAct data in a much more user-friendly and detailed way.
Collapse
Affiliation(s)
- Noemi Del Toro
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Anjali Shrivastava
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Eliot Ragueneau
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Birgit Meldal
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Colin Combe
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Elisabet Barrera
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Livia Perfetto
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK.,Fondazione Human Technopole, Milan 20157, Italy
| | - Karyn How
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Prashansa Ratan
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Gautam Shirodkar
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Odilia Lu
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Bálint Mészáros
- Gibson Group, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Xavier Watkins
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Sangya Pundir
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Luana Licata
- Bioinformatics and Computational Biology Unit, Dept. of Molecular Biology, University of Rome Tor Vergata, Rome, Italy
| | - Marta Iannuccelli
- Bioinformatics and Computational Biology Unit, Dept. of Molecular Biology, University of Rome Tor Vergata, Rome, Italy
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Maria Jesus Martin
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Simona Panni
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Rende, Italy
| | - Margaret Duesbury
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK.,UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Sylvain D Vallet
- ICBMS UMR CNRS 5246, University Lyon 1, Lyon, Villeurbanne 69622, France
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.,Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany
| | - Sylvie Ricard-Blum
- ICBMS UMR CNRS 5246, University Lyon 1, Lyon, Villeurbanne 69622, France
| | - Gianni Cesareni
- Bioinformatics and Computational Biology Unit, Dept. of Molecular Biology, University of Rome Tor Vergata, Rome, Italy
| | - Lukasz Salwinski
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Sandra Orchard
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Pablo Porras
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Kalpana Panneerselvam
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Henning Hermjakob
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK
| |
Collapse
|
|
4
|
Bateman A, Martin MJ, Orchard S, Magrane M, Agivetova R, Ahmad S, Alpi E, Bowler-Barnett EH, Britto R, Bursteinas B, Bye-A-Jee H, Coetzee R, Cukura A, Da Silva A, Denny P, Dogan T, Ebenezer T, Fan J, Castro LG, Garmiri P, Georghiou G, Gonzales L, Hatton-Ellis E, Hussein A, Ignatchenko A, Insana G, Ishtiaq R, Jokinen P, Joshi V, Jyothi D, Lock A, Lopez R, Luciani A, Luo J, Lussi Y, MacDougall A, Madeira F, Mahmoudy M, Menchi M, Mishra A, Moulang K, Nightingale A, Oliveira CS, Pundir S, Qi G, Raj S, Rice D, Lopez MR, Saidi R, Sampson J, Sawford T, Speretta E, Turner E, Tyagi N, Vasudev P, Volynkin V, Warner K, Watkins X, Zaru R, Zellner H, Bridge A, Poux S, Redaschi N, Aimo L, Argoud-Puy G, Auchincloss A, Axelsen K, Bansal P, Baratin D, Blatter MC, Bolleman J, Boutet E, Breuza L, Casals-Casas C, de Castro E, Echioukh KC, Coudert E, Cuche B, Doche M, Dornevil D, Estreicher A, Famiglietti ML, Feuermann M, Gasteiger E, Gehant S, Gerritsen V, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, Hyka-Nouspikel N, Jungo F, Keller G, Kerhornou A, Lara V, Le Mercier P, Lieberherr D, Lombardot T, Martin X, Masson P, Morgat A, Neto TB, Paesano S, Pedruzzi I, Pilbout S, Pourcel L, Pozzato M, Pruess M, Rivoire C, Sigrist C, Sonesson K, Stutz A, Sundaram S, Tognolli M, Verbregue L, Wu CH, Arighi CN, Arminski L, Chen C, Chen Y, Garavelli JS, Huang H, Laiho K, McGarvey P, Natale DA, Ross K, Vinayaka CR, Wang Q, Wang Y, Yeh LS, Zhang J, Ruch P, Teodoro D. UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res 2021; 49:D480-D489. [PMID: 33237286 PMCID: PMC7778908 DOI: 10.1093/nar/gkaa1100] [Citation(s) in RCA: 3581] [Impact Index Per Article: 1193.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/21/2020] [Accepted: 11/02/2020] [Indexed: 02/07/2023] Open
Abstract
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately 190 million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome completeness and quality. We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented Association-Rule-Based Annotator (ARBA). We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries. We describe how UniProtKB responded to the COVID-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.
Collapse
|