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Cabral G, Moss WJ, Brown KM. Proteomic approaches for protein kinase substrate identification in Apicomplexa. Mol Biochem Parasitol 2024; 259:111633. [PMID: 38821187 PMCID: PMC11194964 DOI: 10.1016/j.molbiopara.2024.111633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/10/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
Apicomplexa is a phylum of protist parasites, notable for causing life-threatening diseases including malaria, toxoplasmosis, cryptosporidiosis, and babesiosis. Apicomplexan pathogenesis is generally a function of lytic replication, dissemination, persistence, host cell modification, and immune subversion. Decades of research have revealed essential roles for apicomplexan protein kinases in establishing infections and promoting pathogenesis. Protein kinases modify their substrates by phosphorylating serine, threonine, tyrosine, or other residues, resulting in rapid functional changes in the target protein. Post-translational modification by phosphorylation can activate or inhibit a substrate, alter its localization, or promote interactions with other proteins or ligands. Deciphering direct kinase substrates is crucial to understand mechanisms of kinase signaling, yet can be challenging due to the transient nature of kinase phosphorylation and potential for downstream indirect phosphorylation events. However, with recent advances in proteomic approaches, our understanding of kinase function in Apicomplexa has improved dramatically. Here, we discuss methods that have been used to identify kinase substrates in apicomplexan parasites, classifying them into three main categories: i) kinase interactome, ii) indirect phosphoproteomics and iii) direct labeling. We briefly discuss each approach, including their advantages and limitations, and highlight representative examples from the Apicomplexa literature. Finally, we conclude each main category by introducing prospective approaches from other fields that would benefit kinase substrate identification in Apicomplexa.
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Affiliation(s)
- Gabriel Cabral
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - William J Moss
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kevin M Brown
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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2
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Xiao Y, Yuan Y, Liu Y, Lin Z, Zheng G, Zhou D, Lv D. Targeted Protein Degradation: Current and Emerging Approaches for E3 Ligase Deconvolution. J Med Chem 2024. [PMID: 38981094 DOI: 10.1021/acs.jmedchem.4c00723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Targeted protein degradation (TPD), including the use of proteolysis-targeting chimeras (PROTACs) and molecular glue degraders (MGDs) to degrade proteins, is an emerging strategy to develop novel therapies for cancer and beyond. PROTACs or MGDs function by inducing the proximity between an E3 ligase and a protein of interest (POI), leading to ubiquitination and consequent proteasomal degradation of the POI. Notably, one major issue in TPD is the lack of ligandable E3 ligases, as current studies predominantly use CUL4CRBN and CUL2VHL. The TPD community is seeking to expand the landscape of ligandable E3 ligases, but most discoveries rely on phenotypic screens or serendipity, necessitating systematic target deconvolution. Here, we examine and discuss both current and emerging E3 ligase deconvolution approaches for degraders discovered from phenotypic screens or monovalent glue chemistry campaigns, highlighting future prospects for identifying more ligandable E3 ligases.
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Affiliation(s)
- Yufeng Xiao
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Yaxia Yuan
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
| | - Yi Liu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, Missouri 63110, United States
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Daohong Zhou
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
| | - Dongwen Lv
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
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3
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Surana S, Villarroel-Campos D, Rhymes ER, Kalyukina M, Panzi C, Novoselov SS, Fabris F, Richter S, Pirazzini M, Zanotti G, Sleigh JN, Schiavo G. The tyrosine phosphatases LAR and PTPRδ act as receptors of the nidogen-tetanus toxin complex. EMBO J 2024:10.1038/s44318-024-00164-8. [PMID: 38977849 DOI: 10.1038/s44318-024-00164-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/14/2024] [Accepted: 06/19/2024] [Indexed: 07/10/2024] Open
Abstract
Tetanus neurotoxin (TeNT) causes spastic paralysis by inhibiting neurotransmission in spinal inhibitory interneurons. TeNT binds to the neuromuscular junction, leading to its internalisation into motor neurons and subsequent transcytosis into interneurons. While the extracellular matrix proteins nidogens are essential for TeNT binding, the molecular composition of its receptor complex remains unclear. Here, we show that the receptor-type protein tyrosine phosphatases LAR and PTPRδ interact with the nidogen-TeNT complex, enabling its neuronal uptake. Binding of LAR and PTPRδ to the toxin complex is mediated by their immunoglobulin and fibronectin III domains, which we harnessed to inhibit TeNT entry into motor neurons and protect mice from TeNT-induced paralysis. This function of LAR is independent of its role in regulating TrkB receptor activity, which augments axonal transport of TeNT. These findings reveal a multi-subunit receptor complex for TeNT and demonstrate a novel trafficking route for extracellular matrix proteins. Our study offers potential new avenues for developing therapeutics to prevent tetanus and dissecting the mechanisms controlling the targeting of physiological ligands to long-distance axonal transport in the nervous system.
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Affiliation(s)
- Sunaina Surana
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.
- UCL Queen Square Motor Neuron Disease Centre, University College London, London, WC1N 3BG, UK.
- UK Dementia Research Institute, University College London, London, WC1E 6BT, UK.
| | - David Villarroel-Campos
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
- UCL Queen Square Motor Neuron Disease Centre, University College London, London, WC1N 3BG, UK
- UK Dementia Research Institute, University College London, London, WC1E 6BT, UK
| | - Elena R Rhymes
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
- UCL Queen Square Motor Neuron Disease Centre, University College London, London, WC1N 3BG, UK
| | - Maria Kalyukina
- Department of Clinical and Experimental Epilepsy, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Chiara Panzi
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
- UCL Queen Square Motor Neuron Disease Centre, University College London, London, WC1N 3BG, UK
- UK Dementia Research Institute, University College London, London, WC1E 6BT, UK
| | - Sergey S Novoselov
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
- UCL Queen Square Motor Neuron Disease Centre, University College London, London, WC1N 3BG, UK
| | - Federico Fabris
- Department of Biomedical Sciences, University of Padova, Padova, 35131, Italy
| | - Sandy Richter
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
- Department of Biomedical Sciences, University of Padova, Padova, 35131, Italy
| | - Marco Pirazzini
- Department of Biomedical Sciences, University of Padova, Padova, 35131, Italy
| | - Giuseppe Zanotti
- Department of Biomedical Sciences, University of Padova, Padova, 35131, Italy
| | - James N Sleigh
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
- UCL Queen Square Motor Neuron Disease Centre, University College London, London, WC1N 3BG, UK
- UK Dementia Research Institute, University College London, London, WC1E 6BT, UK
| | - Giampietro Schiavo
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.
- UCL Queen Square Motor Neuron Disease Centre, University College London, London, WC1N 3BG, UK.
- UK Dementia Research Institute, University College London, London, WC1E 6BT, UK.
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4
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Costacurta M, Sandow JJ, Maher B, Susanto O, Vervoort SJ, Devlin JR, Garama D, Condina MR, Steele JR, Kahrood HV, Gough D, Johnstone RW, Shortt J. Mapping the IMiD-dependent cereblon interactome using BioID-proximity labelling. FEBS J 2024. [PMID: 38975872 DOI: 10.1111/febs.17196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 04/17/2024] [Accepted: 05/24/2024] [Indexed: 07/09/2024]
Abstract
Immunomodulatory imide drugs (IMiDs) are central components of therapy for multiple myeloma (MM). IMiDs bind cereblon (CRBN), an adaptor for the CUL4-DDB1-RBX1 E3 ligase to change its substrate specificity and induce degradation of 'neosubstrate' transcription factors that are essential to MM cells. Mechanistic studies to date have largely focussed on mediators of therapeutic activity and insight into clinical IMiD toxicities is less developed. We adopted BioID2-dependent proximity labelling (BioID2-CRBN) to characterise the CRBN interactome in the presence and absence of various IMiDs and the proteasome inhibitor, bortezomib. We aimed to leverage this technology to further map CRBN interactions beyond what has been achieved by conventional proteomic techniques. In support of this approach, analysis of cells expressing BioID2-CRBN following IMiD treatment displayed biotinylation of known CRBN interactors and neosubstrates. We observed that bortezomib alone significantly modifies the CRBN interactome. Proximity labelling also suggested that IMiDs augment the interaction between CRBN and proteins that are not degraded, thus designating 'neointeractors' distinct from previously disclosed 'neosubstrates'. Here we identify Non-Muscle Myosin Heavy Chain IIA (MYH9) as a putative CRBN neointeractor that may contribute to the haematological toxicity of IMiDs. These studies provide proof of concept for proximity labelling technologies in the mechanistic profiling of IMiDs and related E3-ligase-modulating drugs.
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Affiliation(s)
- Matteo Costacurta
- Monash Haematology, Monash Health, Clayton, Australia
- Blood Cancer Therapeutics Laboratory, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Jarrod J Sandow
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Belinda Maher
- Monash Haematology, Monash Health, Clayton, Australia
- Blood Cancer Therapeutics Laboratory, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Olivia Susanto
- Monash Haematology, Monash Health, Clayton, Australia
- Blood Cancer Therapeutics Laboratory, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Stephin J Vervoort
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Jennifer R Devlin
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia
| | - Daniel Garama
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Australia
| | - Mark R Condina
- Mass Dynamics, Melbourne, Australia
- Clinical & Health Sciences, University of South Australia, Adelaide, Australia
| | - Joel R Steele
- Monash Proteomics and Metabolomics Platform, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia
- Monash Bioinformatics Platform, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Hossein V Kahrood
- Monash Proteomics and Metabolomics Platform, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Daniel Gough
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Australia
| | - Ricky W Johnstone
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia
| | - Jake Shortt
- Monash Haematology, Monash Health, Clayton, Australia
- Blood Cancer Therapeutics Laboratory, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia
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5
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Nie DY, Tabor JR, Li J, Kutera M, St-Germain J, Hanley RP, Wolf E, Paulakonis E, Kenney TMG, Duan S, Shrestha S, Owens DDG, Maitland MER, Pon A, Szewczyk M, Lamberto AJ, Menes M, Li F, Penn LZ, Barsyte-Lovejoy D, Brown NG, Barsotti AM, Stamford AW, Collins JL, Wilson DJ, Raught B, Licht JD, James LI, Arrowsmith CH. Recruitment of FBXO22 for targeted degradation of NSD2. Nat Chem Biol 2024:10.1038/s41589-024-01660-y. [PMID: 38965384 DOI: 10.1038/s41589-024-01660-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 05/31/2024] [Indexed: 07/06/2024]
Abstract
Targeted protein degradation (TPD) is an emerging therapeutic strategy that would benefit from new chemical entities with which to recruit a wider variety of ubiquitin E3 ligases to target proteins for proteasomal degradation. Here we describe a TPD strategy involving the recruitment of FBXO22 to induce degradation of the histone methyltransferase and oncogene NSD2. UNC8732 facilitates FBXO22-mediated degradation of NSD2 in acute lymphoblastic leukemia cells harboring the NSD2 gain-of-function mutation p.E1099K, resulting in growth suppression, apoptosis and reversal of drug resistance. The primary amine of UNC8732 is metabolized to an aldehyde species, which engages C326 of FBXO22 to recruit the SCFFBXO22 Cullin complex. We further demonstrate that a previously reported alkyl amine-containing degrader targeting XIAP is similarly dependent on SCFFBXO22. Overall, we present a potent NSD2 degrader for the exploration of NSD2 disease phenotypes and a new FBXO22-recruitment strategy for TPD.
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Affiliation(s)
- David Y Nie
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John R Tabor
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jianping Li
- University of Florida Health Cancer Center, Gainesville, FL, USA
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Maria Kutera
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan St-Germain
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ronan P Hanley
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- C4 Therapeutics, Watertown, MA, USA
| | - Esther Wolf
- Department of Chemistry, York University, Toronto, Ontario, Canada
| | - Ethan Paulakonis
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Tristan M G Kenney
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Shili Duan
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Suman Shrestha
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Dominic D G Owens
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Amphista Therapeutics, Cambridge, UK
| | | | - Ailing Pon
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Magdalena Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | - Michael Menes
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Linda Z Penn
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas G Brown
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anthony M Barsotti
- Deerfield Discovery and Development, Deerfield Management, New York, NY, USA
| | - Andrew W Stamford
- Deerfield Discovery and Development, Deerfield Management, New York, NY, USA
| | - Jon L Collins
- Office of the Vice Chancellor for Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, Ontario, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan D Licht
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Lindsey I James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
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6
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Delhaye L, Moschonas GD, Fijalkowska D, Verhee A, De Sutter D, Van de Steene T, De Meyer M, Grzesik H, Van Moortel L, De Bosscher K, Jacobs T, Eyckerman S. Leveraging a self-cleaving peptide for tailored control in proximity labeling proteomics. CELL REPORTS METHODS 2024:100818. [PMID: 38986614 DOI: 10.1016/j.crmeth.2024.100818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 05/15/2024] [Accepted: 06/17/2024] [Indexed: 07/12/2024]
Abstract
Protein-protein interactions play an important biological role in every aspect of cellular homeostasis and functioning. Proximity labeling mass spectrometry-based proteomics overcomes challenges typically associated with other methods and has quickly become the current state of the art in the field. Nevertheless, tight control of proximity-labeling enzymatic activity and expression levels is crucial to accurately identify protein interactors. Here, we leverage a T2A self-cleaving peptide and a non-cleaving mutant to accommodate the protein of interest in the experimental and control TurboID setup. To allow easy and streamlined plasmid assembly, we built a Golden Gate modular cloning system to generate plasmids for transient expression and stable integration. To highlight our T2A Split/link design, we applied it to identify protein interactions of the glucocorticoid receptor and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid and non-structural protein 7 (NSP7) proteins by TurboID proximity labeling. Our results demonstrate that our T2A split/link provides an opportune control that builds upon previously established control requirements in the field.
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Affiliation(s)
- Louis Delhaye
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium; OncoRNALab, Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium
| | - George D Moschonas
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Daria Fijalkowska
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Annick Verhee
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Delphine De Sutter
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Tessa Van de Steene
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Margaux De Meyer
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Hanna Grzesik
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Laura Van Moortel
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Karolien De Bosscher
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Thomas Jacobs
- VIB-UGent Center for Plant Systems Biology, VIB, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium.
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7
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Pirayeshfard L, Luo S, Githaka JM, Saini A, Touret N, Goping IS, Julien O. Comparing the BAD Protein Interactomes in 2D and 3D Cell Culture Using Proximity Labeling. J Proteome Res 2024. [PMID: 38959414 DOI: 10.1021/acs.jproteome.4c00111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Protein-protein interaction studies using proximity labeling techniques, such as biotin ligase-based BioID, have become integral in understanding cellular processes. Most studies utilize conventional 2D cell culture systems, potentially missing important differences in protein behavior found in 3D tissues. In this study, we investigated the protein-protein interactions of a protein, Bcl-2 Agonist of cell death (BAD), and compared conventional 2D culture conditions to a 3D system, wherein cells were embedded within a 3D extracellular matrix (ECM) mimic. Using BAD fused to the engineered biotin ligase miniTurbo (BirA*), we identified both overlapping and distinct BAD interactomes under 2D and 3D conditions. The known BAD binding proteins 14-3-3 isoforms and Bcl-XL interacted with BAD in both 2D and 3D. Of the 131 BAD-interactors identified, 56% were specific to 2D, 14% were specific to 3D, and 30% were common to both conditions. Interaction network analysis demonstrated differential associations between 2D and 3D interactomes, emphasizing the impact of the culture conditions on protein interactions. The 2D-3D overlap interactome encapsulated the apoptotic program, which is a well-known role of BAD. The 3D unique pathways were enriched in ECM signaling, suggestive of hitherto unknown functions for BAD. Thus, exploring protein-protein interactions in 3D provides novel clues into cell behavior. This exciting approach has the potential to bridge the knowledge gap between tractable 2D cell culture and organoid-like 3D systems.
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Affiliation(s)
- Leila Pirayeshfard
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Shu Luo
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | | | - Arashdeep Saini
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Nicolas Touret
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Ing Swie Goping
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Department of Oncology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Olivier Julien
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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8
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Quan J, Fan Q, Simons LM, Smukowski SN, Pegg C, Longnecker R, Savas JN, Hultquist JF, Smith GA. Leveraging biotin-based proximity labeling to identify cellular factors governing early alphaherpesvirus infection. mBio 2024:e0144524. [PMID: 38953638 DOI: 10.1128/mbio.01445-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 07/04/2024] Open
Abstract
Neurotropic alphaherpesviruses, including herpes simplex virus type 1 and pseudorabies virus, establish a lifelong presence within the peripheral nervous system of their mammalian hosts. Upon entering cells, two conserved tegument proteins, pUL36 and pUL37, traffic DNA-containing capsids to nuclei. These proteins support long-distance retrograde axonal transport and invasion of the nervous system in vivo. To better understand how pUL36 and pUL37 function, recombinant viral particles carrying BioID2 fused to these proteins were produced to biotinylate cellular proteins in their proximity (<10 nm) during infection. Eighty-six high-confidence host proteins were identified by mass spectrometry and subsequently targeted by CRISPR-Cas9 gene editing to assess their contributions to early infection. Proteins were identified that both supported and antagonized infection in immortalized human epithelial cells. The latter included zyxin, a protein that localizes to focal adhesions and regulates actin cytoskeletal dynamics. Zyxin knockout cells were hyper-permissive to infection and could be rescued with even modest expression of GFP-zyxin. These results provide a resource for studies of the virus-cell interface and identify zyxin as a novel deterrent to alphaherpesvirus infection.IMPORTANCENeuroinvasive alphaherpesviruses are highly prevalent with many members found across mammals [e.g., herpes simplex virus type 1 (HSV-1) in humans and pseudorabies virus in pigs]. HSV-1 causes a range of clinical manifestations from cold sores to blindness and encephalitis. There are no vaccines or curative therapies available for HSV-1. A fundamental feature of these viruses is their establishment of lifelong infection of the nervous system in their respective hosts. This outcome is possible due to a potent neuroinvasive property that is coordinated by two proteins: pUL36 and pUL37. In this study, we explore the cellular protein network in proximity to pUL36 and pUL37 during infection and examine the impact of knocking down the expression of these proteins upon infection.
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Affiliation(s)
- Jenai Quan
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Qing Fan
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Lacy M Simons
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Samuel N Smukowski
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Caitlin Pegg
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Richard Longnecker
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jeffrey N Savas
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Judd F Hultquist
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Gregory A Smith
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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9
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Zhong X, Li Q, Polacco BJ, Patil T, Marley A, Foussard H, Khare P, Vartak R, Xu J, DiBerto JF, Roth BL, Eckhardt M, von Zastrow M, Krogan NJ, Hüttenhain R. A proximity proteomics pipeline with improved reproducibility and throughput. Mol Syst Biol 2024:10.1038/s44320-024-00049-2. [PMID: 38951684 DOI: 10.1038/s44320-024-00049-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/09/2024] [Accepted: 06/11/2024] [Indexed: 07/03/2024] Open
Abstract
Proximity labeling (PL) via biotinylation coupled with mass spectrometry (MS) captures spatial proteomes in cells. Large-scale processing requires a workflow minimizing hands-on time and enhancing quantitative reproducibility. We introduced a scalable PL pipeline integrating automated enrichment of biotinylated proteins in a 96-well plate format. Combining this with optimized quantitative MS based on data-independent acquisition (DIA), we increased sample throughput and improved protein identification and quantification reproducibility. We applied this pipeline to delineate subcellular proteomes across various compartments. Using the 5HT2A serotonin receptor as a model, we studied temporal changes of proximal interaction networks induced by receptor activation. In addition, we modified the pipeline for reduced sample input to accommodate CRISPR-based gene knockout, assessing dynamics of the 5HT2A network in response to perturbation of selected interactors. This PL approach is universally applicable to PL proteomics using biotinylation-based PL enzymes, enhancing throughput and reproducibility of standard protocols.
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Affiliation(s)
- Xiaofang Zhong
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Qiongyu Li
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Benjamin J Polacco
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Trupti Patil
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Aaron Marley
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, 94158, USA
| | - Helene Foussard
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Prachi Khare
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Rasika Vartak
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Jiewei Xu
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Jeffrey F DiBerto
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Bryan L Roth
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Manon Eckhardt
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Mark von Zastrow
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, 94158, USA
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Ruth Hüttenhain
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA.
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA.
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA.
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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10
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Wang C, Huang Y, Yang Y, Li R, Li Y, Qiu H, Wu J, Shi G, Ma W, Songyang Z. ILF3 safeguards telomeres from aberrant homologous recombination as a telomeric R-loop reader. Protein Cell 2024; 15:493-511. [PMID: 37991243 PMCID: PMC11214836 DOI: 10.1093/procel/pwad054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 10/09/2023] [Indexed: 11/23/2023] Open
Abstract
Telomeres are specialized structures at the ends of linear chromosomes that protect genome stability. The telomeric repeat-containing RNA (TERRA) that is transcribed from subtelomeric regions can invade into double-stranded DNA regions and form RNA:DNA hybrid-containing structure called R-loop. In tumor cells, R-loop formation is closely linked to gene expression and the alternative lengthening of telomeres (ALT) pathway. Dysregulated R-loops can cause stalled replication forks and telomere instability. However, how R-loops are recognized and regulated, particularly at telomeres, is not well understood. We discovered that ILF3 selectively associates with telomeric R-loops and safeguards telomeres from abnormal homologous recombination. Knocking out ILF3 results in excessive R-loops at telomeres and triggers telomeric DNA damage responses. In addition, ILF3 deficiency disrupts telomere homeostasis and causes abnormalities in the ALT pathway. Using the proximity-dependent biotin identification (BioID) technology, we mapped the ILF3 interactome and discovered that ILF3 could interact with several DNA/RNA helicases, including DHX9. Importantly, ILF3 may aid in the resolution of telomeric R-loops through its interaction with DHX9. Our findings suggest that ILF3 may function as a reader of telomeric R-loops, helping to prevent abnormal homologous recombination and maintain telomere homeostasis.
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Affiliation(s)
- Chuanle Wang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangzhou Key Laboratory of Healthy Aging, School of Lifesciences, Sun Yat-sen University, Guangzhou 510275, China
- Department of Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Yan Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangzhou Key Laboratory of Healthy Aging, School of Lifesciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yue Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangzhou Key Laboratory of Healthy Aging, School of Lifesciences, Sun Yat-sen University, Guangzhou 510275, China
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Ruofei Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangzhou Key Laboratory of Healthy Aging, School of Lifesciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yingying Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangzhou Key Laboratory of Healthy Aging, School of Lifesciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Hongxin Qiu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangzhou Key Laboratory of Healthy Aging, School of Lifesciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jiali Wu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangzhou Key Laboratory of Healthy Aging, School of Lifesciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Guang Shi
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangzhou Key Laboratory of Healthy Aging, School of Lifesciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wenbin Ma
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangzhou Key Laboratory of Healthy Aging, School of Lifesciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhou Songyang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangzhou Key Laboratory of Healthy Aging, School of Lifesciences, Sun Yat-sen University, Guangzhou 510275, China
- Department of Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
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11
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Kim JW, Yong AJH, Aisenberg EE, Lobel JH, Wang W, Dawson TM, Dawson VL, Gao R, Jan YN, Bateup HS, Ingolia NT. Molecular recording of calcium signals via calcium-dependent proximity labeling. Nat Chem Biol 2024; 20:894-905. [PMID: 38658655 DOI: 10.1038/s41589-024-01603-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 03/08/2024] [Indexed: 04/26/2024]
Abstract
Calcium ions serve as key intracellular signals. Local, transient increases in calcium concentrations can activate calcium sensor proteins that in turn trigger downstream effectors. In neurons, calcium transients play a central role in regulating neurotransmitter release and synaptic plasticity. However, it is challenging to capture the molecular events associated with these localized and ephemeral calcium signals. Here we present an engineered biotin ligase that generates permanent molecular traces in a calcium-dependent manner. The enzyme, calcium-dependent BioID (Cal-ID), biotinylates nearby proteins within minutes in response to elevated local calcium levels. The biotinylated proteins can be identified via mass spectrometry and visualized using microscopy. In neurons, Cal-ID labeling is triggered by neuronal activity, leading to prominent protein biotinylation that enables transcription-independent activity labeling in the brain. In summary, Cal-ID produces a biochemical record of calcium signals and neuronal activity with high spatial resolution and molecular specificity.
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Affiliation(s)
- J Wren Kim
- Department of Molecular and Cell Biology at the University of California, Berkeley, Berkeley, CA, USA
| | - Adeline J H Yong
- Department of Physiology at the University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute at the University of California, San Francisco, San Francisco, CA, USA
| | - Erin E Aisenberg
- Helen Wills Neuroscience Institute at the University of California, Berkeley, Berkeley, CA, USA
| | - Joseph H Lobel
- Department of Molecular and Cell Biology at the University of California, Berkeley, Berkeley, CA, USA
| | - Wei Wang
- Department of Chemistry at the University of Illinois, Chicago, Chicago, IL, USA
| | - Ted M Dawson
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valina L Dawson
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ruixuan Gao
- Department of Chemistry at the University of Illinois, Chicago, Chicago, IL, USA
| | - Yuh Nung Jan
- Department of Physiology at the University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute at the University of California, San Francisco, San Francisco, CA, USA
| | - Helen S Bateup
- Department of Molecular and Cell Biology at the University of California, Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute at the University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology at the University of California, Berkeley, Berkeley, CA, USA.
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12
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Bedir M, Outwin E, Colnaghi R, Bassett L, Abramowicz I, O'Driscoll M. A novel role for the peptidyl-prolyl cis-trans isomerase Cyclophilin A in DNA-repair following replication fork stalling via the MRE11-RAD50-NBS1 complex. EMBO Rep 2024:10.1038/s44319-024-00184-9. [PMID: 38943005 DOI: 10.1038/s44319-024-00184-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/28/2024] [Accepted: 06/05/2024] [Indexed: 06/30/2024] Open
Abstract
Cyclosporin A (CsA) induces DNA double-strand breaks in LIG4 syndrome fibroblasts, specifically upon transit through S-phase. The basis underlying this has not been described. CsA-induced genomic instability may reflect a direct role of Cyclophilin A (CYPA) in DNA repair. CYPA is a peptidyl-prolyl cis-trans isomerase (PPI). CsA inhibits the PPI activity of CYPA. Using an integrated approach involving CRISPR/Cas9-engineering, siRNA, BioID, co-immunoprecipitation, pathway-specific DNA repair investigations as well as protein expression interaction analysis, we describe novel impacts of CYPA loss and inhibition on DNA repair. We characterise a direct CYPA interaction with the NBS1 component of the MRE11-RAD50-NBS1 complex, providing evidence that CYPA influences DNA repair at the level of DNA end resection. We define a set of genetic vulnerabilities associated with CYPA loss and inhibition, identifying DNA replication fork protection as an important determinant of viability. We explore examples of how CYPA inhibition may be exploited to selectively kill cancers sharing characteristic genomic instability profiles, including MYCN-driven Neuroblastoma, Multiple Myeloma and Chronic Myelogenous Leukaemia. These findings propose a repurposing strategy for Cyclophilin inhibitors.
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Affiliation(s)
- Marisa Bedir
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK
| | - Emily Outwin
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK
| | - Rita Colnaghi
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK
| | - Lydia Bassett
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK
| | - Iga Abramowicz
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK
| | - Mark O'Driscoll
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK.
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13
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Wang B, Yang F, Wang W, Zhao F, Sun X. TurboID-mediated proximity labeling technologies to identify virus co-receptors. Front Cell Infect Microbiol 2024; 14:1371837. [PMID: 38994005 PMCID: PMC11236563 DOI: 10.3389/fcimb.2024.1371837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/12/2024] [Indexed: 07/13/2024] Open
Abstract
Virus receptors determine the tissue tropism of viruses and have a certain relationship with the clinical outcomes caused by viral infection, which is of great importance for the identification of virus receptors to understand the infection mechanism of viruses and to develop entry inhibitor. Proximity labeling (PL) is a new technique for studying protein-protein interactions, but it has not yet been applied to the identification of virus receptors or co-receptors. Here, we attempt to identify co-receptor of SARS-CoV-2 by employing TurboID-catalyzed PL. The membrane protein angiotensin-converting enzyme 2 (ACE2) was employed as a bait and conjugated to TurboID, and a A549 cell line with stable expression of ACE2-TurboID was constructed. SARS-CoV-2 pseudovirus were incubated with ACE2-TurboID stably expressed cell lines in the presence of biotin and ATP, which could initiate the catalytic activity of TurboID and tag adjacent endogenous proteins with biotin. Subsequently, the biotinylated proteins were harvested and identified by mass spectrometry. We identified a membrane protein, AXL, that has been functionally shown to mediate SARS-CoV-2 entry into host cells. Our data suggest that PL could be used to identify co-receptors for virus entry.
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Affiliation(s)
- Bo Wang
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Fan Yang
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
| | - Wuqian Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
- Jiaxing Maternity and Children Health Care Hospital, Affiliated Women and Children Hospital Jiaxing University, Jiaxing, Zhejiang, China
| | - Fei Zhao
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
| | - Xiaofang Sun
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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14
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Fujimoto T, Okamura T, Itoh K. Extraction method combining saponin and trehalose useful for analyzing fragile intermolecular association. Biochem Biophys Res Commun 2024; 727:150323. [PMID: 38945065 DOI: 10.1016/j.bbrc.2024.150323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/02/2024]
Abstract
Immunoprecipitation (IP) and co-immunoprecipitation (co-IP) are well-established methodologies to analyze protein expression and intermolecular interaction. Composition of extraction and washing buffer for preparing protein is important to accomplish experimental purpose. Various kinds of detergents are included in buffer to adjust extraction efficiency and washing effect. Among them, Triton X-100 (Tx-100), Nonidet P-40 (NP40), deoxycholic acid (DOC) and SDS are generally used according to experimental purpose and characteristic features of protein of interest. In some cases, general detergents disrupt intermolecular interaction and make it impossible to analyze molecular relation of protein of interest with its binding partners. In this study, we propose saponin, a natural detergent, is useful for co-immunoprecipitation when analyzing fragile intermolecular interactions, in which dystrophin and dystroglycan are used as a representative interaction. One of the most notable findings in this report is that intermolecular association between dystrophin and dystroglycan is maintained in saponin buffer whereas general detergents, such as Tx-100, NP40 and DOC, dissociate its binding. Furthermore, supplementation of trehalose, which has been shown to act as a molecular chaperone, facilitates efficient detection of dystrophin-dystroglycan macromolecular complex in co-IP assay. Importantly, the extraction buffer comprising 3 % saponin, 0.5 M trehalose and 0.05 % Tx-100 (we named it STX buffer) is applicable to co-IP for another molecular interaction, N-cadherin and β-catenin, indicating that this methodology can be used for versatile proteins of interest. Thus, STX buffer emerges as an alternative extraction method useful for analyzing fragile intermolecular associations and provides opportunity to identify complex interactomes, which may facilitate proteome-research and functional analysis of proteins of interest.
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Affiliation(s)
- Takahiro Fujimoto
- Department of Pathology and Applied Neurobiology, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, 465 Kajii-cho, Kawaramachi Hirokoji, Kamigyo-ku, Kyoto, 602-8566, Japan.
| | - Tadashi Okamura
- Department of Laboratory Animal Medicine, Research Institute, National Center for Global Health and Medicine (NCGM), Tokyo, 162-8655, Japan
| | - Kyoko Itoh
- Department of Pathology and Applied Neurobiology, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, 465 Kajii-cho, Kawaramachi Hirokoji, Kamigyo-ku, Kyoto, 602-8566, Japan
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15
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Zhang S, Tang Q, Zhang X, Chen X. Proximitomics by Reactive Species. ACS CENTRAL SCIENCE 2024; 10:1135-1147. [PMID: 38947200 PMCID: PMC11212136 DOI: 10.1021/acscentsci.4c00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 07/02/2024]
Abstract
The proximitome is defined as the entire collection of biomolecules spatially in the proximity of a biomolecule of interest. More broadly, the concept of the proximitome can be extended to the totality of cells proximal to a specific cell type. Since the spatial organization of biomolecules and cells is essential for almost all biological processes, proximitomics has recently emerged as an active area of scientific research. One of the growing strategies for proximitomics leverages reactive species-which are generated in situ and spatially confined, to chemically tag and capture proximal biomolecules and cells for systematic analysis. In this Outlook, we summarize different types of reactive species that have been exploited for proximitomics and discuss their pros and cons for specific applications. In addition, we discuss the current challenges and future directions of this exciting field.
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Affiliation(s)
- Shaoran Zhang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Qi Tang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Beijing
National Laboratory for Molecular Sciences, Peking University, Beijing 100871, People’s
Republic of China
| | - Xu Zhang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Xing Chen
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
- Beijing
National Laboratory for Molecular Sciences, Peking University, Beijing 100871, People’s
Republic of China
- Synthetic
and Functional Biomolecules Center, Peking
University, Beijing 100871, People’s
Republic of China
- Key
Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry
of Education, Peking University, Beijing 100871, People’s Republic of China
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16
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Bachiri K, Kantar D, Laurent EM, Gaboriaud P, Durand L, Drouin A, Chollot M, Schrama D, Houben R, Kervarrec T, Trapp-Fragnet L, Touzé A, Coyaud E. DNA damage stress control is a tLT- and EHMT2-dependent central feature of Merkel Cell Carcinoma. J Invest Dermatol 2024:S0022-202X(24)01860-8. [PMID: 38908781 DOI: 10.1016/j.jid.2024.04.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 06/24/2024]
Abstract
Merkel cell carcinoma (MCC) is an aggressive skin cancer with a high mortality rate. MC polyomavirus (MCPyV) causes 80% of MCCs, encoding the viral oncogenes small T (sT) and truncated large T antigens (tLT). These proteins impair the Rb1-dependent G1/S checkpoint blockade and subvert the host cell epigenome to promote cancer. Whole proteome analysis and proximal interactomics identified a tLT-dependent deregulation of DNA damage response (DDR). Our investigation revealed a previously unreported interaction between tLT and the histone methyltransferase EHMT2, to our knowledge. T Antigens knockdown reduced DDR protein levels and increased levels of the DNA damage marker γH2Ax. EHMT2 normally promotes H3K9 methylation and DDR signaling. Given that inhibition of EHMT2 did not significantly change the MCC cells proteome, tLT-EHMT2 interaction could affect the DDR. With tLT, we report that EHMT2 gained DNA damage repair proximal interactors. EHMT2 inhibition rescued proliferation in MCC cells depleted for their T antigens, suggesting impaired DDR and/or lack of checkpoint efficiency. Combined tLT and EHMT2 inhibition led to altered DDR, evidenced by multiple signaling alterations. Here we show that tLT hijacks multiple components of the DNA damage machinery to enhance tolerance to DNA damage in MCC cells, which could explain the genetic stability of these cancers.
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Affiliation(s)
- Kamel Bachiri
- Univ.Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France
| | - Diala Kantar
- Univ.Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France
| | - Estelle Mn Laurent
- Univ.Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France
| | - Pauline Gaboriaud
- "Biologie des infections à Polyomavirus" team, UMR INRA ISP1282, University of Tours, Tours, France
| | - Laurine Durand
- "Biologie des infections à Polyomavirus" team, UMR INRA ISP1282, University of Tours, Tours, France
| | - Aurélie Drouin
- "Biologie des infections à Polyomavirus" team, UMR INRA ISP1282, University of Tours, Tours, France
| | | | - David Schrama
- Department of Dermatology, Venereology und Allergology, University Hospital, Würzburg, Germany
| | - Roland Houben
- Department of Dermatology, Venereology und Allergology, University Hospital, Würzburg, Germany
| | - Thibault Kervarrec
- "Biologie des infections à Polyomavirus" team, UMR INRA ISP1282, University of Tours, Tours, France; Department of Pathology, University Hospital Center of Tours, Tours, France
| | | | - Antoine Touzé
- "Biologie des infections à Polyomavirus" team, UMR INRA ISP1282, University of Tours, Tours, France
| | - Etienne Coyaud
- Univ.Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France.
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17
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Knutson SD, Buksh BF, Huth SW, Morgan DC, MacMillan DWC. Current advances in photocatalytic proximity labeling. Cell Chem Biol 2024; 31:1145-1161. [PMID: 38663396 PMCID: PMC11193652 DOI: 10.1016/j.chembiol.2024.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/31/2024] [Accepted: 03/29/2024] [Indexed: 06/23/2024]
Abstract
Understanding the intricate network of biomolecular interactions that govern cellular processes is a fundamental pursuit in biology. Over the past decade, photocatalytic proximity labeling has emerged as one of the most powerful and versatile techniques for studying these interactions as well as uncovering subcellular trafficking patterns, drug mechanisms of action, and basic cellular physiology. In this article, we review the basic principles, methodologies, and applications of photocatalytic proximity labeling as well as examine its modern development into currently available platforms. We also discuss recent key studies that have successfully leveraged these technologies and importantly highlight current challenges faced by the field. Together, this review seeks to underscore the potential of photocatalysis in proximity labeling for enhancing our understanding of cell biology while also providing perspective on technological advances needed for future discovery.
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Affiliation(s)
- Steve D Knutson
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Benito F Buksh
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Sean W Huth
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Danielle C Morgan
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - David W C MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.
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18
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Zhou C, Wagner S, Liang FS. Induced proximity labeling and editing for epigenetic research. Cell Chem Biol 2024; 31:1118-1131. [PMID: 38866004 PMCID: PMC11193966 DOI: 10.1016/j.chembiol.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/12/2024] [Accepted: 05/21/2024] [Indexed: 06/14/2024]
Abstract
Epigenetic regulation plays a pivotal role in various biological and disease processes. Two key lines of investigation have been pursued that aim to unravel endogenous epigenetic events at particular genes (probing) and artificially manipulate the epigenetic landscape (editing). The concept of induced proximity has inspired the development of powerful tools for epigenetic research. Induced proximity strategies involve bringing molecular effectors into spatial proximity with specific genomic regions to achieve the probing or manipulation of local epigenetic environments with increased proximity. In this review, we detail the development of induced proximity methods and applications in shedding light on the intricacies of epigenetic regulation.
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Affiliation(s)
- Chenwei Zhou
- Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH 44106, USA
| | - Sarah Wagner
- Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH 44106, USA
| | - Fu-Sen Liang
- Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH 44106, USA.
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19
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Kageler L, Perr J, Flynn RA. Tools to investigate the cell surface: Proximity as a central concept in glycoRNA biology. Cell Chem Biol 2024; 31:1132-1144. [PMID: 38772372 PMCID: PMC11193615 DOI: 10.1016/j.chembiol.2024.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/02/2024] [Accepted: 04/25/2024] [Indexed: 05/23/2024]
Abstract
Proximity is a fundamental concept in chemistry and biology, referring to the convergence of molecules to facilitate new molecular interactions or reactions. Hybrid biopolymers like glycosylphosphatidylinositol (GPI)-anchored proteins, ubiquitinated proteins, glycosylated RNAs (glycoRNAs), and RNAylated proteins exemplify this by covalent bonding of moieties that are often orthogonally active. Hybrid molecules like glycoRNAs are localized to new physical spaces, generating new interfaces for biological functions. To fully investigate the compositional and spatial features of molecules like glycoRNAs, flexible genetic and chemical tools that encompass different encoding and targeting biopolymers are required. Here we discuss concepts of molecular proximity and explore newer proximity labeling technologies that facilitate applications in RNA biology, cell surface biology, and the interface therein with a particular focus on glycoRNA biology. We review the advantages and disadvantages of methods pertaining to cell surface RNA identification and provide insights into the vast opportunities for method development in this area.
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Affiliation(s)
- Lauren Kageler
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Jonathan Perr
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
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20
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Lambert GS, Rice BL, Maldonado RJK, Chang J, Parent LJ. Comparative analysis of retroviral Gag-host cell interactions: focus on the nuclear interactome. Retrovirology 2024; 21:13. [PMID: 38898526 PMCID: PMC11186191 DOI: 10.1186/s12977-024-00645-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 06/21/2024] Open
Abstract
Retroviruses exploit host proteins to assemble and release virions from infected cells. Previously, most studies focused on interacting partners of retroviral Gag proteins that localize to the cytoplasm or plasma membrane. Given that several full-length Gag proteins have been found in the nucleus, identifying the Gag-nuclear interactome has high potential for novel findings involving previously unknown host processes. Here we systematically compared nuclear factors identified in published HIV-1 proteomic studies and performed our own mass spectrometry analysis using affinity-tagged HIV-1 and RSV Gag proteins mixed with nuclear extracts. We identified 57 nuclear proteins in common between HIV-1 and RSV Gag, and a set of nuclear proteins present in our analysis and ≥ 1 of the published HIV-1 datasets. Many proteins were associated with nuclear processes which could have functional consequences for viral replication, including transcription initiation/elongation/termination, RNA processing, splicing, and chromatin remodeling. Examples include facilitating chromatin remodeling to expose the integrated provirus, promoting expression of viral genes, repressing the transcription of antagonistic cellular genes, preventing splicing of viral RNA, altering splicing of cellular RNAs, or influencing viral or host RNA folding or RNA nuclear export. Many proteins in our pulldowns common to RSV and HIV-1 Gag are critical for transcription, including PolR2B, the second largest subunit of RNA polymerase II (RNAPII), and LEO1, a PAF1C complex member that regulates transcriptional elongation, supporting the possibility that Gag influences the host transcription profile to aid the virus. Through the interaction of RSV and HIV-1 Gag with splicing-related proteins CBLL1, HNRNPH3, TRA2B, PTBP1 and U2AF1, we speculate that Gag could enhance unspliced viral RNA production for translation and packaging. To validate one putative hit, we demonstrated an interaction of RSV Gag with Mediator complex member Med26, required for RNA polymerase II-mediated transcription. Although 57 host proteins interacted with both Gag proteins, unique host proteins belonging to each interactome dataset were identified. These results provide a strong premise for future functional studies to investigate roles for these nuclear host factors that may have shared functions in the biology of both retroviruses, as well as functions specific to RSV and HIV-1, given their distinctive hosts and molecular pathology.
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Affiliation(s)
- Gregory S Lambert
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Breanna L Rice
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Rebecca J Kaddis Maldonado
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
- Department of Microbiology and Immunology, Penn State College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Jordan Chang
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Leslie J Parent
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA, 17033, USA.
- Department of Microbiology and Immunology, Penn State College of Medicine, 500 University Drive, Hershey, PA, 17033, USA.
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21
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Zhang H, Zhang D, Li L, Willard B, Runge KW. In Vivo Proximity Labeling Identifies a New Function for the Lifespan and Autophagy-regulating Kinase Pef1, an Ortholog of Human Cdk5. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598664. [PMID: 38915521 PMCID: PMC11195251 DOI: 10.1101/2024.06.12.598664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Cdk5 is a highly-conserved, noncanonical cell division kinase important to the terminal differentiation of mammalian cells in multiple organ systems. We previously identified Pef1, the Schizosaccharomyces pombe ortholog of cdk5, as regulator of chronological lifespan. To reveal the processes impacted by Pef1, we developed APEX2-biotin phenol-mediated proximity labeling in S. pombe. Efficient labeling required a short period of cell wall digestion and eliminating glucose and nitrogen sources from the medium. We identified 255 high-confidence Pef1 neighbors in growing cells and a novel Pef1-interacting partner, the DNA damage response protein Rad24. The Pef1-Rad24 interaction was validated by reciprocal proximity labeling and co-immunoprecipitation. Eliminating Pef1 partially rescued the DNA damage sensitivity of cells lacking Rad24. To monitor how Pef1 neighbors change under different conditions, cells induced for autophagy were labeled and 177 high-confidence Pef1 neighbors were identified. Gene ontology (GO) analysis of the Pef1 neighbors identified proteins participating in processes required for autophagosome expansion including regulation of actin dynamics and vesicle-mediated transport. Some of these proteins were identified in both exponentially growing and autophagic cells. Pef1-APEX2 proximity labeling therefore identified a new Pef1 function in modulating the DNA damage response and candidate processes that Pef1 and other cdk5 orthologs may regulate.
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Affiliation(s)
- Haitao Zhang
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine at CWRU
| | - Dongmei Zhang
- Lerner Research Institute Proteomics Core and Case Comprehensive Cancer Center Cleveland Clinic Lerner College of Medicine at CWRU
| | - Ling Li
- Lerner Research Institute Proteomics Core and Case Comprehensive Cancer Center Cleveland Clinic Lerner College of Medicine at CWRU
| | - Belinda Willard
- Lerner Research Institute Proteomics Core and Case Comprehensive Cancer Center Cleveland Clinic Lerner College of Medicine at CWRU
| | - Kurt W. Runge
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine at CWRU
- Department of Genomics and Genome Sciences, Case Western Reserve University School of Medicine
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22
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Chen X, Li Y, Xu J, Cui Y, Wu Q, Yin H, Li Y, Gao C, Jiang L, Wang H, Wen Z, Yao Z, Wu Z. Styxl2 regulates de novo sarcomere assembly by binding to non-muscle myosin IIs and promoting their degradation. eLife 2024; 12:RP87434. [PMID: 38829202 PMCID: PMC11147509 DOI: 10.7554/elife.87434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024] Open
Abstract
Styxl2, a poorly characterized pseudophosphatase, was identified as a transcriptional target of the Jak1-Stat1 pathway during myoblast differentiation in culture. Styxl2 is specifically expressed in vertebrate striated muscles. By gene knockdown in zebrafish or genetic knockout in mice, we found that Styxl2 plays an essential role in maintaining sarcomere integrity in developing muscles. To further reveal the functions of Styxl2 in adult muscles, we generated two inducible knockout mouse models: one with Styxl2 being deleted in mature myofibers to assess its role in sarcomere maintenance, and the other in adult muscle satellite cells (MuSCs) to assess its role in de novo sarcomere assembly. We find that Styxl2 is not required for sarcomere maintenance but functions in de novo sarcomere assembly during injury-induced muscle regeneration. Mechanistically, Styxl2 interacts with non-muscle myosin IIs, enhances their ubiquitination, and targets them for autophagy-dependent degradation. Without Styxl2, the degradation of non-muscle myosin IIs is delayed, which leads to defective sarcomere assembly and force generation. Thus, Styxl2 promotes de novo sarcomere assembly by interacting with non-muscle myosin IIs and facilitating their autophagic degradation.
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Affiliation(s)
- Xianwei Chen
- Division of Life Science, Hong Kong University of Science & TechnologyHong KongChina
| | - Yanfeng Li
- Division of Life Science, Hong Kong University of Science & TechnologyHong KongChina
| | - Jin Xu
- Division of Life Science, Hong Kong University of Science & TechnologyHong KongChina
| | - Yong Cui
- School of Life Sciences, Chinese University of Hong KongHong KongChina
| | - Qian Wu
- Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic UniversityHong KongChina
| | - Haidi Yin
- Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic UniversityHong KongChina
| | - Yuying Li
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong KongHong KongChina
| | - Chuan Gao
- Division of Life Science, Hong Kong University of Science & TechnologyHong KongChina
| | - Liwen Jiang
- School of Life Sciences, Chinese University of Hong KongHong KongChina
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong KongHong KongChina
| | - Zilong Wen
- Division of Life Science, Hong Kong University of Science & TechnologyHong KongChina
| | - Zhongping Yao
- Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic UniversityHong KongChina
| | - Zhenguo Wu
- Division of Life Science, Hong Kong University of Science & TechnologyHong KongChina
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23
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Chamrád I, Simerský R, Lenobel R, Novák O. Exploring affinity chromatography in proteomics: A comprehensive review. Anal Chim Acta 2024; 1306:342513. [PMID: 38692783 DOI: 10.1016/j.aca.2024.342513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 05/03/2024]
Abstract
Over the past decades, the proteomics field has undergone rapid growth. Progress in mass spectrometry and bioinformatics, together with separation methods, has brought many innovative approaches to the study of the molecular biology of the cell. The potential of affinity chromatography was recognized immediately after its first application in proteomics, and since that time, it has become one of the cornerstones of many proteomic protocols. Indeed, this chromatographic technique exploiting the specific binding between two molecules has been employed for numerous purposes, from selective removal of interfering (over)abundant proteins or enrichment of scarce biomarkers in complex biological samples to mapping the post-translational modifications and protein interactions with other proteins, nucleic acids or biologically active small molecules. This review presents a comprehensive survey of this versatile analytical tool in current proteomics. To navigate the reader, the haphazard space of affinity separations is classified according to the experiment's aims and the separated molecule's nature. Different types of available ligands and experimental strategies are discussed in further detail for each of the mentioned procedures.
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Affiliation(s)
- Ivo Chamrád
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic.
| | - Radim Simerský
- Department of Chemical Biology, Faculty of Science, Palacký University, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - René Lenobel
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
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24
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Holfeld A, Schuster D, Sesterhenn F, Gillingham AK, Stalder P, Haenseler W, Barrio-Hernandez I, Ghosh D, Vowles J, Cowley SA, Nagel L, Khanppnavar B, Serdiuk T, Beltrao P, Korkhov VM, Munro S, Riek R, de Souza N, Picotti P. Systematic identification of structure-specific protein-protein interactions. Mol Syst Biol 2024; 20:651-675. [PMID: 38702390 PMCID: PMC11148107 DOI: 10.1038/s44320-024-00037-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/06/2024] Open
Abstract
The physical interactome of a protein can be altered upon perturbation, modulating cell physiology and contributing to disease. Identifying interactome differences of normal and disease states of proteins could help understand disease mechanisms, but current methods do not pinpoint structure-specific PPIs and interaction interfaces proteome-wide. We used limited proteolysis-mass spectrometry (LiP-MS) to screen for structure-specific PPIs by probing for protease susceptibility changes of proteins in cellular extracts upon treatment with specific structural states of a protein. We first demonstrated that LiP-MS detects well-characterized PPIs, including antibody-target protein interactions and interactions with membrane proteins, and that it pinpoints interfaces, including epitopes. We then applied the approach to study conformation-specific interactors of the Parkinson's disease hallmark protein alpha-synuclein (aSyn). We identified known interactors of aSyn monomer and amyloid fibrils and provide a resource of novel putative conformation-specific aSyn interactors for validation in further studies. We also used our approach on GDP- and GTP-bound forms of two Rab GTPases, showing detection of differential candidate interactors of conformationally similar proteins. This approach is applicable to screen for structure-specific interactomes of any protein, including posttranslationally modified and unmodified, or metabolite-bound and unbound protein states.
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Affiliation(s)
- Aleš Holfeld
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Dina Schuster
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Fabian Sesterhenn
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | | | - Patrick Stalder
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Walther Haenseler
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- University Research Priority Program AdaBD (Adaptive Brain Circuits in Development and Learning), University of Zurich, Zurich, Switzerland
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Dhiman Ghosh
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Jane Vowles
- James and Lillian Martin Centre for Stem Cell Research, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Sally A Cowley
- James and Lillian Martin Centre for Stem Cell Research, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Luise Nagel
- Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Basavraj Khanppnavar
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Tetiana Serdiuk
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Pedro Beltrao
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Volodymyr M Korkhov
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Natalie de Souza
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Paola Picotti
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland.
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25
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McAlary L, Nan JR, Shyu C, Sher M, Plotkin SS, Cashman NR. Amyloidogenic regions in beta-strands II and III modulate the aggregation and toxicity of SOD1 in living cells. Open Biol 2024; 14:230418. [PMID: 38835240 DOI: 10.1098/rsob.230418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/16/2024] [Indexed: 06/06/2024] Open
Abstract
Mutations in the protein superoxide dismutase-1 (SOD1) promote its misfolding and aggregation, ultimately causing familial forms of the debilitating neurodegenerative disease amyotrophic lateral sclerosis (ALS). Currently, over 220 (mostly missense) ALS-causing mutations in the SOD1 protein have been identified, indicating that common structural features are responsible for aggregation and toxicity. Using in silico tools, we predicted amyloidogenic regions in the ALS-associated SOD1-G85R mutant, finding seven regions throughout the structure. Introduction of proline residues into β-strands II (I18P) or III (I35P) reduced the aggregation propensity and toxicity of SOD1-G85R in cells, significantly more so than proline mutations in other amyloidogenic regions. The I18P and I35P mutations also reduced the capability of SOD1-G85R to template onto previously formed non-proline mutant SOD1 aggregates as measured by fluorescence recovery after photobleaching. Finally, we found that, while the I18P and I35P mutants are less structurally stable than SOD1-G85R, the proline mutants are less aggregation-prone during proteasome inhibition, and less toxic to cells overall. Our research highlights the importance of a previously underappreciated SOD1 amyloidogenic region in β-strand II (15QGIINF20) to the aggregation and toxicity of SOD1 in ALS mutants, and suggests that β-strands II and III may be good targets for the development of SOD1-associated ALS therapies.
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Affiliation(s)
- Luke McAlary
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada
| | - Jeremy R Nan
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Clay Shyu
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Mine Sher
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Steven S Plotkin
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada
- Genome Sciences and Technology Program, University of British Columbia, Vancouver, BC, Canada
| | - Neil R Cashman
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
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26
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Kunitomi A, Chiba S, Higashitani N, Higashitani A, Sato S, Mizuno K, Ohashi K. Solo regulates the localization and activity of PDZ-RhoGEF for actin cytoskeletal remodeling in response to substrate stiffness. Mol Biol Cell 2024; 35:ar87. [PMID: 38656797 DOI: 10.1091/mbc.e23-11-0421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024] Open
Abstract
Recent findings indicate that Solo, a RhoGEF, is involved in cellular mechanical stress responses. However, the mechanism of actin cytoskeletal remodeling via Solo remains unclear. Therefore, this study aimed to identify Solo-interacting proteins using the BioID, a proximal-dependent labeling method, and elucidate the molecular mechanisms of function of Solo. We identified PDZ-RhoGEF (PRG) as a Solo-interacting protein. PRG colocalized with Solo in the basal area of cells, depending on Solo localization, and enhanced actin polymerization at the Solo accumulation sites. Additionally, Solo and PRG interaction was necessary for actin cytoskeletal remodeling. Furthermore, the purified Solo itself had little or negligible GEF activity, even its GEF-inactive mutant directly activated the GEF activity of PRG through interaction. Moreover, overexpression of the Solo and PRG binding domains, respectively, had a dominant-negative effect on actin polymerization and actin stress fiber formation in response to substrate stiffness. Therefore, Solo restricts the localization of PRG and regulates actin cytoskeletal remodeling in synergy with PRG in response to the surrounding mechanical environment.
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Affiliation(s)
- Aoi Kunitomi
- Laboratory of Molecular and Cellular Biology, Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 6-3 Aramaki-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Shuhei Chiba
- Laboratory of Molecular and Cellular Biology, Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 6-3 Aramaki-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Nahoko Higashitani
- Laboratory of Molecular Genetics and Physiology, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Atsushi Higashitani
- Laboratory of Molecular Genetics and Physiology, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Shinichi Sato
- Laboratory of Bioactive Molecules, Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Kensaku Mizuno
- Laboratory of Molecular and Cellular Biology, Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 6-3 Aramaki-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Kazumasa Ohashi
- Laboratory of Molecular and Cellular Biology, Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 6-3 Aramaki-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
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27
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Chandrasekharan G, Unnikrishnan M. High throughput methods to study protein-protein interactions during host-pathogen interactions. Eur J Cell Biol 2024; 103:151393. [PMID: 38306772 DOI: 10.1016/j.ejcb.2024.151393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/18/2024] [Accepted: 01/21/2024] [Indexed: 02/04/2024] Open
Abstract
The ability of a pathogen to survive and cause an infection is often determined by specific interactions between the host and pathogen proteins. Such interactions can be both intra- and extracellular and may define the outcome of an infection. There are a range of innovative biochemical, biophysical and bioinformatic techniques currently available to identify protein-protein interactions (PPI) between the host and the pathogen. However, the complexity and the diversity of host-pathogen PPIs has led to the development of several high throughput (HT) techniques that enable the study of multiple interactions at once and/or screen multiple samples at the same time, in an unbiased manner. We review here the major HT laboratory-based technologies employed for host-bacterial interaction studies.
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Affiliation(s)
| | - Meera Unnikrishnan
- Division of Biomedical Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom.
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28
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Lü Y, Cho T, Mukherjee S, Suarez CF, Gonzalez-Foutel NS, Malik A, Martinez S, Dervovic D, Oh RH, Langille E, Al-Zahrani KN, Hoeg L, Lin ZY, Tsai R, Mbamalu G, Rotter V, Ashton-Prolla P, Moffat J, Chemes LB, Gingras AC, Oren M, Durocher D, Schramek D. Genome-wide CRISPR screens identify novel regulators of wild-type and mutant p53 stability. Mol Syst Biol 2024; 20:719-740. [PMID: 38580884 PMCID: PMC11148184 DOI: 10.1038/s44320-024-00032-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 03/06/2024] [Accepted: 03/12/2024] [Indexed: 04/07/2024] Open
Abstract
Tumor suppressor p53 (TP53) is frequently mutated in cancer, often resulting not only in loss of its tumor-suppressive function but also acquisition of dominant-negative and even oncogenic gain-of-function traits. While wild-type p53 levels are tightly regulated, mutants are typically stabilized in tumors, which is crucial for their oncogenic properties. Here, we systematically profiled the factors that regulate protein stability of wild-type and mutant p53 using marker-based genome-wide CRISPR screens. Most regulators of wild-type p53 also regulate p53 mutants, except for p53 R337H regulators, which are largely private to this mutant. Mechanistically, FBXO42 emerged as a positive regulator for a subset of p53 mutants, working with CCDC6 to control USP28-mediated mutant p53 stabilization. Additionally, C16orf72/HAPSTR1 negatively regulates both wild-type p53 and all tested mutants. C16orf72/HAPSTR1 is commonly amplified in breast cancer, and its overexpression reduces p53 levels in mouse mammary epithelium leading to accelerated breast cancer. This study offers a network perspective on p53 stability regulation, potentially guiding strategies to reinforce wild-type p53 or target mutant p53 in cancer.
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Affiliation(s)
- YiQing Lü
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- Department of Biology, Suffolk University, Boston, MA, 02108, USA
| | - Tiffany Cho
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Saptaparna Mukherjee
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Carmen Florencia Suarez
- Instituto de Investigaciones Biotecnológicas (IIBiO-CONICET), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Nicolas S Gonzalez-Foutel
- Instituto de Investigaciones Biotecnológicas (IIBiO-CONICET), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Ahmad Malik
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Sebastien Martinez
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
| | - Dzana Dervovic
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
| | - Robin Hyunseo Oh
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Ellen Langille
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Khalid N Al-Zahrani
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
| | - Lisa Hoeg
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
| | - Zhen Yuan Lin
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
| | - Ricky Tsai
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
| | - Geraldine Mbamalu
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
| | - Varda Rotter
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Patricia Ashton-Prolla
- Departamento de Genética, Universidade Federal do Rio Grande do Sul and Serviço de Genetica Médica HCPA, Porto Alegre, Brasil
| | - Jason Moffat
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, M5S3G9, Canada
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada
| | - Lucia Beatriz Chemes
- Instituto de Investigaciones Biotecnológicas (IIBiO-CONICET), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Anne-Claude Gingras
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Moshe Oren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Daniel Durocher
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.
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29
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Androniciuc AM, Tate EW, Vincent JP. Engineering of TurboID-Wingless for the identification of Wingless interactors through in vivo proximity labelling. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001210. [PMID: 38872844 PMCID: PMC11170289 DOI: 10.17912/micropub.biology.001210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/17/2024] [Accepted: 05/28/2024] [Indexed: 06/15/2024]
Abstract
Wnt signalling coordinates growth and cell fate decisions during development and mis-regulation of Wnt signalling in adults is associated with a range of conditions, including cancer and neurodegenerative diseases. Therefore, means of modulating Wnt proteins and/or cofactors could have significant therapeutic potential. As a first step towards enumerating the Wnt interactome, we devised an in vivo proximity labelling strategy to identify proteins that interact with Wingless (Wg), the main Drosophila Wnt. We engineered the wingless locus to express a functional TurboID-Wg fusion at endogenous levels and identified in vivo interactors by streptavidin pull-down from embryos, followed by mass spectrometry. Further analysis may in future extend the screen coverage and deliver functional validation of the newly identified interactors.
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Affiliation(s)
- Ana-Miruna Androniciuc
- The Francis Crick Institute, London, England, United Kingdom
- Department of Chemistry, Imperial College London, London, England, United Kingdom
| | - Edward W. Tate
- The Francis Crick Institute, London, England, United Kingdom
- Department of Chemistry, Imperial College London, London, England, United Kingdom
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30
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Kourtis S, Cianferoni D, Serrano L, Sdelci S. Detection of differential bait proteoforms through immunoprecipitation-mass spectrometry data analysis. Sci Data 2024; 11:551. [PMID: 38811611 PMCID: PMC11137132 DOI: 10.1038/s41597-024-03394-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024] Open
Abstract
Proteins are often referred to as the workhorses of cells, and their interactions are necessary to facilitate specific cellular functions. Despite the recognition that protein-protein interactions, and thus protein functions, are determined by proteoform states, such as mutations and post-translational modifications (PTMs), methods for determining the differential abundance of proteoforms across conditions are very limited. Classically, immunoprecipitation coupled with mass spectrometry (IP-MS) has been used to understand how the interactome (preys) of a given protein (bait) changes between conditions to elicit specific cellular functions. Reversing this concept, we present here a new workflow for IP-MS data analysis that focuses on identifying the differential peptidoforms of the bait protein between conditions. This method can provide detailed information about specific bait proteoforms, potentially revealing pathogenic protein states that can be exploited for the development of targeted therapies.
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Affiliation(s)
- Savvas Kourtis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Damiano Cianferoni
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sara Sdelci
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
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31
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Brock K, Alpha KM, Brennan G, De Jong EP, Luke E, Turner CE. A comparative analysis of paxillin and Hic-5 proximity interactomes. Cytoskeleton (Hoboken) 2024. [PMID: 38801098 DOI: 10.1002/cm.21878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/18/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024]
Abstract
Focal adhesions serve as structural and signaling hubs, facilitating bidirectional communication at the cell-extracellular matrix interface. Paxillin and the related Hic-5 (TGFβ1i1) are adaptor/scaffold proteins that recruit numerous structural and regulatory proteins to focal adhesions, where they perform both overlapping and discrete functions. In this study, paxillin and Hic-5 were expressed in U2OS osteosarcoma cells as biotin ligase (BioID2) fusion proteins and used as bait proteins for proximity-dependent biotinylation in order to directly compare their respective interactomes. The fusion proteins localized to both focal adhesions and the centrosome, resulting in biotinylation of components of each of these structures. Biotinylated proteins were purified and analyzed by mass spectrometry. The list of proximity interactors for paxillin and Hic-5 comprised numerous shared core focal adhesion proteins that likely contribute to their similar functions in cell adhesion and migration, as well as proteins unique to paxillin and Hic-5 that have been previously localized to focal adhesions, the centrosome, or the nucleus. Western blotting confirmed biotinylation and enrichment of FAK and vinculin, known interactors of Hic-5 and paxillin, as well as several potentially unique proximity interactors of Hic-5 and paxillin, including septin 7 and ponsin, respectively. Further investigation into the functional relationship between the unique interactors and Hic-5 or paxillin may yield novel insights into their distinct roles in cell migration.
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Affiliation(s)
- Katia Brock
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Kyle M Alpha
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Grant Brennan
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Ebbing P De Jong
- Proteomics Core Facility, State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Elizabeth Luke
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Christopher E Turner
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, New York, USA
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32
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Segovia D, Adams DW, Hoffman N, Safaric Tepes P, Wee TL, Cifani P, Joshua-Tor L, Krainer AR. SRSF1 interactome determined by proximity labeling reveals direct interaction with spliceosomal RNA helicase DDX23. Proc Natl Acad Sci U S A 2024; 121:e2322974121. [PMID: 38743621 PMCID: PMC11126954 DOI: 10.1073/pnas.2322974121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
SRSF1 is the founding member of the SR protein family. It is required-interchangeably with other SR proteins-for pre-mRNA splicing in vitro, and it regulates various alternative splicing events. Dysregulation of SRSF1 expression contributes to cancer and other pathologies. Here, we characterized SRSF1's interactome using proximity labeling and mass spectrometry. This approach yielded 190 proteins enriched in the SRSF1 samples, independently of the N- or C-terminal location of the biotin-labeling domain. The detected proteins reflect established functions of SRSF1 in pre-mRNA splicing and reveal additional connections to spliceosome proteins, in addition to other recently identified functions. We validated a robust interaction with the spliceosomal RNA helicase DDX23/PRP28 using bimolecular fluorescence complementation and in vitro binding assays. The interaction is mediated by the N-terminal RS-like domain of DDX23 and both RRM1 and the RS domain of SRSF1. During pre-mRNA splicing, DDX23's ATPase activity is essential for the pre-B to B spliceosome complex transition and for release of U1 snRNP from the 5' splice site. We show that the RS-like region of DDX23's N-terminal domain is important for spliceosome incorporation, while larger deletions in this domain alter subnuclear localization. We discuss how the identified interaction of DDX23 with SRSF1 and other SR proteins may be involved in the regulation of these processes.
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Affiliation(s)
- Danilo Segovia
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
- Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, NY11794
| | - Dexter W. Adams
- HHMI, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY11794
| | | | | | - Tse-Luen Wee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
| | - Paolo Cifani
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
| | - Leemor Joshua-Tor
- HHMI, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
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33
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Goyal P, Tao AJ, Mumby EJ, English JG, Ferguson FM. Measuring Ligand-bound Protein Complexes with Proximity Labeling: A Practical Guide. Chembiochem 2024; 25:e202400073. [PMID: 38457625 DOI: 10.1002/cbic.202400073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 03/10/2024]
Abstract
Identifying the drug-target interactome of small molecule therapeutics is essential for understanding the full pharmacological effects of a compound. These therapies often induce changes within the cellular proteome, leading to unexpected consequences such as changes in the targets complexation state or off-target interactions between the compound and additional proteins. Currently, unbiased target-ID approaches are being used to embark on this task. Here we provide an overview of the strengths and limitations of these methods, and a practical step-by-step protocol for using the BioTAC system to assist with drug target and interactome ID.
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Affiliation(s)
- Pavitra Goyal
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Andrew J Tao
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Elizabeth J Mumby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Justin G English
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Fleur M Ferguson
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
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34
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Charneau S, de Oliveira LS, Zenonos Z, Hopp CS, Bastos IMD, Loew D, Lombard B, Pandolfo Silveira A, de Carvalho Nardeli Basílio Lobo G, Bao SN, Grellier P, Rayner JC. APEX2-based proximity proteomic analysis identifies candidate interactors for Plasmodium falciparum knob-associated histidine-rich protein in infected erythrocytes. Sci Rep 2024; 14:11242. [PMID: 38755230 PMCID: PMC11099048 DOI: 10.1038/s41598-024-61295-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 05/03/2024] [Indexed: 05/18/2024] Open
Abstract
The interaction of Plasmodium falciparum-infected red blood cells (iRBCs) with the vascular endothelium plays a crucial role in malaria pathology and disease. KAHRP is an exported P. falciparum protein involved in iRBC remodelling, which is essential for the formation of protrusions or "knobs" on the iRBC surface. These knobs and the proteins that are concentrated within them allow the parasites to escape the immune response and host spleen clearance by mediating cytoadherence of the iRBC to the endothelial wall, but this also slows down blood circulation, leading in some cases to severe cerebral and placental complications. In this work, we have applied genetic and biochemical tools to identify proteins that interact with P. falciparum KAHRP using enhanced ascorbate peroxidase 2 (APEX2) proximity-dependent biotinylation and label-free shotgun proteomics. A total of 30 potential KAHRP-interacting candidates were identified, based on the assigned fragmented biotinylated ions. Several identified proteins have been previously reported to be part of the Maurer's clefts and knobs, where KAHRP resides. This study may contribute to a broader understanding of P. falciparum protein trafficking and knob architecture and shows for the first time the feasibility of using APEX2-proximity labelling in iRBCs.
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Affiliation(s)
- Sébastien Charneau
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, 70910-900, Brazil.
| | - Lucas Silva de Oliveira
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, 70910-900, Brazil
- UMR 7245 MCAM Molecules of Communication and Adaptation of Microorganisms, Muséum National d'Histoire Naturelle, CNRS, 75231, Paris Cedex 05, France
| | - Zenon Zenonos
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
- Biologics Engineering, Oncology R&D, AstraZenecaGranta Park, Cambridge, UK
| | - Christine S Hopp
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Izabela M D Bastos
- Laboratory of Host Pathogen Interaction, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, 70910-900, Brazil
| | - Damarys Loew
- Institut Curie, Centre de Recherche, PSL Research University, CurieCoreTech Mass Spectrometry Proteomics, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Bérangère Lombard
- Institut Curie, Centre de Recherche, PSL Research University, CurieCoreTech Mass Spectrometry Proteomics, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Ariane Pandolfo Silveira
- Laboratory of Microscopy and Microanalysis, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, 70910-900, Brazil
| | | | - Sônia Nair Bao
- Laboratory of Microscopy and Microanalysis, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, 70910-900, Brazil
| | - Philippe Grellier
- UMR 7245 MCAM Molecules of Communication and Adaptation of Microorganisms, Muséum National d'Histoire Naturelle, CNRS, 75231, Paris Cedex 05, France
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK
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35
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Shang Z, Zhang S, Wang J, Zhou L, Zhang X, Billadeau DD, Yang P, Zhang L, Zhou F, Bai P, Jia D. TRIM25 predominately associates with anti-viral stress granules. Nat Commun 2024; 15:4127. [PMID: 38750080 PMCID: PMC11096359 DOI: 10.1038/s41467-024-48596-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 05/07/2024] [Indexed: 05/18/2024] Open
Abstract
Stress granules (SGs) are induced by various environmental stressors, resulting in their compositional and functional heterogeneity. SGs play a crucial role in the antiviral process, owing to their potent translational repressive effects and ability to trigger signal transduction; however, it is poorly understood how these antiviral SGs differ from SGs induced by other environmental stressors. Here we identify that TRIM25, a known driver of the ubiquitination-dependent antiviral innate immune response, is a potent and critical marker of the antiviral SGs. TRIM25 undergoes liquid-liquid phase separation (LLPS) and co-condenses with the SG core protein G3BP1 in a dsRNA-dependent manner. The co-condensation of TRIM25 and G3BP1 results in a significant enhancement of TRIM25's ubiquitination activity towards multiple antiviral proteins, which are mainly located in SGs. This co-condensation is critical in activating the RIG-I signaling pathway, thus restraining RNA virus infection. Our studies provide a conceptual framework for better understanding the heterogeneity of stress granule components and their response to distinct environmental stressors.
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Affiliation(s)
- Zehua Shang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Sitao Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Jinrui Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Lili Zhou
- Institutes of Biology and Medical Science, Soochow University, Suzhou, 215000, China
| | - Xinyue Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Daniel D Billadeau
- Division of Oncology Research and Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Peiguo Yang
- School of Life Sciences, Westlake University, Hangzhou, 310024, 310030, China
| | - Lingqiang Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 100850, Beijing, China
| | - Fangfang Zhou
- Institutes of Biology and Medical Science, Soochow University, Suzhou, 215000, China
| | - Peng Bai
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China.
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China.
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36
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Zhang R, Anguiano M, Aarrestad IK, Lin S, Chandra J, Vadde SS, Olson DE, Kim CK. Rapid, biochemical tagging of cellular activity history in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.06.556431. [PMID: 38798353 PMCID: PMC11118534 DOI: 10.1101/2023.09.06.556431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Intracellular calcium (Ca2+) is ubiquitous to cell signaling across all biology. While existing fluorescent sensors and reporters can detect activated cells with elevated Ca2+ levels, these approaches require implants to deliver light to deep tissue, precluding their noninvasive use in freely-behaving animals. Here we engineered an enzyme-catalyzed approach that rapidly and biochemically tags cells with elevated Ca2+ in vivo. Ca2+-activated Split-TurboID (CaST) labels activated cells within 10 minutes with an exogenously-delivered biotin molecule. The enzymatic signal increases with Ca2+ concentration and biotin labeling time, demonstrating that CaST is a time-gated integrator of total Ca2+ activity. Furthermore, the CaST read-out can be performed immediately after activity labeling, in contrast to transcriptional reporters that require hours to produce signal. These capabilities allowed us to apply CaST to tag prefrontal cortex neurons activated by psilocybin, and to correlate the CaST signal with psilocybin-induced head-twitch responses in untethered mice.
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Affiliation(s)
- Run Zhang
- Biomedical Engineering Graduate Group, University of California, Davis, Davis, CA 95616
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
| | - Maribel Anguiano
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
- Neuroscience Graduate Group, University of California, Davis, Davis, CA 95618
| | - Isak K. Aarrestad
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
- Neuroscience Graduate Group, University of California, Davis, Davis, CA 95618
- Institute for Psychedelics and Neurotherapeutics, University of California, Davis, Davis, CA 95616
| | - Sophia Lin
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
- Department of Neurology, University of California, Davis, Sacramento, CA 95817
| | - Joshua Chandra
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
- Neuroscience Graduate Group, University of California, Davis, Davis, CA 95618
| | - Sruti S. Vadde
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
- Department of Neurology, University of California, Davis, Sacramento, CA 95817
| | - David E. Olson
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
- Institute for Psychedelics and Neurotherapeutics, University of California, Davis, Davis, CA 95616
- Department of Chemistry, University of California, Davis, Davis, CA 95616
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, CA 95817
| | - Christina K. Kim
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
- Institute for Psychedelics and Neurotherapeutics, University of California, Davis, Davis, CA 95616
- Department of Neurology, University of California, Davis, Sacramento, CA 95817
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37
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Liu X, Abad L, Chatterjee L, Cristea IM, Varjosalo M. Mapping protein-protein interactions by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38742660 DOI: 10.1002/mas.21887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Protein-protein interactions (PPIs) are essential for numerous biological activities, including signal transduction, transcription control, and metabolism. They play a pivotal role in the organization and function of the proteome, and their perturbation is associated with various diseases, such as cancer, neurodegeneration, and infectious diseases. Recent advances in mass spectrometry (MS)-based protein interactomics have significantly expanded our understanding of the PPIs in cells, with techniques that continue to improve in terms of sensitivity, and specificity providing new opportunities for the study of PPIs in diverse biological systems. These techniques differ depending on the type of interaction being studied, with each approach having its set of advantages, disadvantages, and applicability. This review highlights recent advances in enrichment methodologies for interactomes before MS analysis and compares their unique features and specifications. It emphasizes prospects for further improvement and their potential applications in advancing our knowledge of PPIs in various biological contexts.
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Affiliation(s)
- Xiaonan Liu
- Department of Physiology, Faculty of Medical Sciences in Katowice, Medical University of Silesia in Katowice, Katowice, Poland
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Lawrence Abad
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Lopamudra Chatterjee
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Markku Varjosalo
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
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Choudhury R, Venkateswaran Venkatasubramani A, Hua J, Borsò M, Franconi C, Kinkley S, Forné I, Imhof A. The role of RNA in the maintenance of chromatin domains as revealed by antibody-mediated proximity labelling coupled to mass spectrometry. eLife 2024; 13:e95718. [PMID: 38717135 PMCID: PMC11147508 DOI: 10.7554/elife.95718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 04/26/2024] [Indexed: 06/04/2024] Open
Abstract
Eukaryotic chromatin is organized into functional domains, that are characterized by distinct proteomic compositions and specific nuclear positions. In contrast to cellular organelles surrounded by lipid membranes, the composition of distinct chromatin domains is rather ill described and highly dynamic. To gain molecular insight into these domains and explore their composition, we developed an antibody-based proximity biotinylation method targeting the RNA and proteins constituents. The method that we termed antibody-mediated proximity labelling coupled to mass spectrometry (AMPL-MS) does not require the expression of fusion proteins and therefore constitutes a versatile and very sensitive method to characterize the composition of chromatin domains based on specific signature proteins or histone modifications. To demonstrate the utility of our approach we used AMPL-MS to characterize the molecular features of the chromocenter as well as the chromosome territory containing the hyperactive X chromosome in Drosophila. This analysis identified a number of known RNA-binding proteins in proximity of the hyperactive X and the centromere, supporting the accuracy of our method. In addition, it enabled us to characterize the role of RNA in the formation of these nuclear bodies. Furthermore, our method identified a new set of RNA molecules associated with the Drosophila centromere. Characterization of these novel molecules suggested the formation of R-loops in centromeres, which we validated using a novel probe for R-loops in Drosophila. Taken together, AMPL-MS improves the selectivity and specificity of proximity ligation allowing for novel discoveries of weak protein-RNA interactions in biologically diverse domains.
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Affiliation(s)
- Rupam Choudhury
- Department of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians UniversityPlanegg-MartinsriedGermany
| | - Anuroop Venkateswaran Venkatasubramani
- Department of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians UniversityPlanegg-MartinsriedGermany
- Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Jie Hua
- Department of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians UniversityPlanegg-MartinsriedGermany
| | - Marco Borsò
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians, University (LMU) MunichPlanegg-MartinsriedGermany
| | - Celeste Franconi
- Chromatin Structure and Function group, Department of Computational Molecular Biology, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Sarah Kinkley
- Chromatin Structure and Function group, Department of Computational Molecular Biology, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Ignasi Forné
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians, University (LMU) MunichPlanegg-MartinsriedGermany
| | - Axel Imhof
- Department of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians UniversityPlanegg-MartinsriedGermany
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians, University (LMU) MunichPlanegg-MartinsriedGermany
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39
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Gurung P, McGee JP, Dvorin JD. PfCAP-H is essential for assembly of condensin I complex and karyokinesis during asexual proliferation of Plasmodium falciparum. mBio 2024; 15:e0285023. [PMID: 38564676 PMCID: PMC11078010 DOI: 10.1128/mbio.02850-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
Condensin I is a pentameric complex that regulates the mitotic chromosome assembly in eukaryotes. The kleisin subunit CAP-H of the condensin I complex acts as a linchpin to maintain the structural integrity and loading of this complex on mitotic chromosomes. This complex is present in all eukaryotes and has recently been identified in Plasmodium spp. However, how this complex is assembled and whether the kleisin subunit is critical for this complex in these parasites are yet to be explored. To examine the role of PfCAP-H during cell division within erythrocytes, we generated an inducible PfCAP-H knockout parasite. We find that PfCAP-H is dynamically expressed during mitosis with the peak expression at the metaphase plate. PfCAP-H interacts with PfCAP-G and is a non-SMC member of the condensin I complex. Notably, the absence of PfCAP-H does not alter the expression of PfCAP-G but affects its localization at the mitotic chromosomes. While mitotic spindle assembly is intact in PfCAP-H-deficient parasites, duplicated centrosomes remain clustered over the mass of unsegmented nuclei with failed karyokinesis. This failure leads to the formation of an abnormal nuclear mass, while cytokinesis occurs normally. Altogether, our data suggest that PfCAP-H plays a crucial role in maintaining the structural integrity of the condensin I complex on the mitotic chromosomes and is essential for the asexual development of malarial parasites. IMPORTANCE Mitosis is a fundamental process for Plasmodium parasites, which plays a vital role in their survival within two distinct hosts-human and Anopheles mosquitoes. Despite its great significance, our comprehension of mitosis and its regulation remains limited. In eukaryotes, mitosis is regulated by one of the pivotal complexes known as condensin complexes. The condensin complexes are responsible for chromosome condensation, ensuring the faithful distribution of genetic material to daughter cells. While condensin complexes have recently been identified in Plasmodium spp., our understanding of how this complex is assembled and its precise functions during the blood stage development of Plasmodium falciparum remains largely unexplored. In this study, we investigate the role of a central protein, PfCAP-H, during the blood stage development of P. falciparum. Our findings reveal that PfCAP-H is essential and plays a pivotal role in upholding the structure of condensin I and facilitating karyokinesis.
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Affiliation(s)
- Pratima Gurung
- Division of Infectious Diseases, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - James P. McGee
- Division of Infectious Diseases, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Jeffrey D. Dvorin
- Division of Infectious Diseases, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
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40
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Guo S, Hu X, Cotton JL, Ma L, Li Q, Cui J, Wang Y, Thakare RP, Tao Z, Ip YT, Wu X, Wang J, Mao J. VGLL2 and TEAD1 fusion proteins drive YAP/TAZ-independent transcription and tumorigenesis by engaging p300. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592016. [PMID: 38746415 PMCID: PMC11092657 DOI: 10.1101/2024.05.01.592016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Studies on Hippo pathway regulation of tumorigenesis largely center on YAP and TAZ, the transcriptional co-regulators of TEAD. Here, we present an oncogenic mechanism involving VGLL and TEAD fusions that is Hippo pathway-related but YAP/TAZ-independent. We characterize two recurrent fusions, VGLL2-NCOA2 and TEAD1-NCOA2, recently identified in spindle cell rhabdomyosarcoma. We demonstrate that, in contrast to VGLL2 and TEAD1, the fusion proteins are strong activators of TEAD-dependent transcription, and their function does not require YAP/TAZ. Furthermore, we identify that VGLL2 and TEAD1 fusions engage specific epigenetic regulation by recruiting histone acetyltransferase p300 to control TEAD-mediated transcriptional and epigenetic landscapes. We showed that small molecule p300 inhibition can suppress fusion proteins-induced oncogenic transformation both in vitro and in vivo. Overall, our study reveals a molecular basis for VGLL involvement in cancer and provides a framework for targeting tumors carrying VGLL, TEAD, or NCOA translocations.
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Affiliation(s)
- Susu Guo
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No 241, West Huaihai Road, Shanghai, P. R., 200030, China
| | - Xiaodi Hu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Jennifer L. Cotton
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Lifang Ma
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No 241, West Huaihai Road, Shanghai, P. R., 200030, China
| | - Qi Li
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Jiangtao Cui
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No 241, West Huaihai Road, Shanghai, P. R., 200030, China
| | - Yongjie Wang
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No 241, West Huaihai Road, Shanghai, P. R., 200030, China
| | - Ritesh P. Thakare
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Zhipeng Tao
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, 01605, USA
| | - Y. Tony Ip
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Xu Wu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, 01605, USA
| | - Jiayi Wang
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No 241, West Huaihai Road, Shanghai, P. R., 200030, China
| | - Junhao Mao
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
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41
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Bergeron JJM. Proteomics Impact on Cell Biology to Resolve Cell Structure and Function. Mol Cell Proteomics 2024; 23:100758. [PMID: 38574860 PMCID: PMC11070594 DOI: 10.1016/j.mcpro.2024.100758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
The acceleration of advances in proteomics has enabled integration with imaging at the EM and light microscopy levels, cryo-EM of protein structures, and artificial intelligence with proteins comprehensively and accurately resolved for cell structures at nanometer to subnanometer resolution. Proteomics continues to outpace experimentally based structural imaging, but their ultimate integration is a path toward the goal of a compendium of all proteins to understand mechanistically cell structure and function.
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Affiliation(s)
- John J M Bergeron
- Department of Medicine, McGill University Hospital Research Institute, Montreal, Quebec, Canada.
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42
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John A, Krämer M, Lehmann M, Kunz HH, Aarabi F, Alseekh S, Fernie A, Sommer F, Schroda M, Zimmer D, Mühlhaus T, Peisker H, Gutbrod K, Dörmann P, Neunzig J, Philippar K, Neuhaus HE. Degradation of FATTY ACID EXPORT PROTEIN1 by RHOMBOID-LIKE PROTEASE11 contributes to cold tolerance in Arabidopsis. THE PLANT CELL 2024; 36:1937-1962. [PMID: 38242838 PMCID: PMC11062452 DOI: 10.1093/plcell/koae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/21/2024]
Abstract
Plants need to acclimate to different stresses to optimize growth under unfavorable conditions. In Arabidopsis (Arabidopsis thaliana), the abundance of the chloroplast envelope protein FATTY ACID EXPORT PROTEIN1 (FAX1) decreases after the onset of low temperatures. However, how FAX1 degradation occurs and whether altered FAX1 abundance contributes to cold tolerance in plants remains unclear. The rapid cold-induced increase in RHOMBOID-LIKE PROTEASE11 (RBL11) transcript levels, the physical interaction of RBL11 with FAX1, the specific FAX1 degradation after RBL11 expression, and the absence of cold-induced FAX1 degradation in rbl11 loss-of-function mutants suggest that this enzyme is responsible for FAX1 degradation. Proteomic analyses showed that rbl11 mutants have higher levels of FAX1 and other proteins involved in membrane lipid homeostasis, suggesting that RBL11 is a key element in the remodeling of membrane properties during cold conditions. Consequently, in the cold, rbl11 mutants show a shift in lipid biosynthesis toward the eukaryotic pathway, which coincides with impaired cold tolerance. To test whether cold sensitivity is due to increased FAX1 levels, we analyzed FAX1 overexpressors. The rbl11 mutants and FAX1 overexpressor lines show superimposable phenotypic defects upon exposure to cold temperatures. Our re-sults show that the cold-induced degradation of FAX1 by RBL11 is critical for Arabidop-sis to survive cold and freezing periods.
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Affiliation(s)
- Annalisa John
- Plant Physiology, University of Kaiserslautern, Kaiserslautern D-67653, Germany
| | - Moritz Krämer
- Plant Biochemistry, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried 82152, Germany
| | - Martin Lehmann
- Plant Biochemistry, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried 82152, Germany
| | - Hans-Henning Kunz
- Plant Biochemistry, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried 82152, Germany
| | - Fayezeh Aarabi
- Max Planck Institut for Molecular Plant Physiology, Central Metabolism, Potsdam D-14476, Germany
| | - Saleh Alseekh
- Max Planck Institut for Molecular Plant Physiology, Central Metabolism, Potsdam D-14476, Germany
| | - Alisdair Fernie
- Max Planck Institut for Molecular Plant Physiology, Central Metabolism, Potsdam D-14476, Germany
| | - Frederik Sommer
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern, Kaiserslautern D-67653, Germany
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern, Kaiserslautern D-67653, Germany
| | - David Zimmer
- Computational Systems Biology, University of Kaiserslautern, Kaiserslautern D-67653, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, University of Kaiserslautern, Kaiserslautern D-67653, Germany
| | - Helga Peisker
- Institute for Molecular Physiology and Biotechnology of Plants, IMBIO, University of Bonn, Bonn D-53115, Germany
| | - Katharina Gutbrod
- Institute for Molecular Physiology and Biotechnology of Plants, IMBIO, University of Bonn, Bonn D-53115, Germany
| | - Peter Dörmann
- Institute for Molecular Physiology and Biotechnology of Plants, IMBIO, University of Bonn, Bonn D-53115, Germany
| | - Jens Neunzig
- Plant Biology, Center for Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken D-66123, Germany
| | - Katrin Philippar
- Plant Biology, Center for Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken D-66123, Germany
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43
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Nelson ZM, Kadiri O, Fehl C. GlycoID Proximity Labeling to Identify O-GlcNAcylated Protein Interactomes in Live Cells. Curr Protoc 2024; 4:e1052. [PMID: 38752278 PMCID: PMC11101149 DOI: 10.1002/cpz1.1052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2024]
Abstract
Cells continuously remodel their intracellular proteins with the monosaccharide O-linked N-acetylglucosamine (O-GlcNAc) to regulate metabolism, signaling, and stress. This protocol describes the use of GlycoID tools to capture O-GlcNAc dynamics in live cells. GlycoID constructs contain an O-GlcNAc binding domain linked to a proximity labeling domain and a subcellular localization sequence. When expressed in mammalian cells, GlycoID tracks changes in O-GlcNAc-modified proteins and their interactomes in response to chemical induction with biotin over time. Pairing the subcellular localization of GlycoID with the chemical induction of activity enables spatiotemporal studies of O-GlcNAc biology during cellular events such as insulin signaling. However, optimizing intracellular labeling experiments requires attention to several variables. Here, we describe two protocols to adapt GlycoID methods to a cell line and biological process of interest. Next, we describe how to conduct a semiquantitative proteomic analysis of O-GlcNAcylated proteins and their interactomes using insulin versus glucagon signaling as a sample application. This articles aims to establish baseline GlycoID protocols for new users and set the stage for widespread use over diverse cellular applications for the functional study of O-GlcNAc glycobiology. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Expression of targeted GlycoID constructs to verify subcellular location and labeling activity in mammalian cells Basic Protocol 2: GlycoID labeling in live HeLa cells for O-GlcNAc proteomic comparisons.
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Affiliation(s)
- Zachary M. Nelson
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI, United States
| | - Oseni Kadiri
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI, United States
| | - Charlie Fehl
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI, United States
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44
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Pani S, Qiu T, Kentala K, Azizi SA, Dickinson BC. Bioorthogonal masked acylating agents for proximity-dependent RNA labelling. Nat Chem 2024; 16:717-726. [PMID: 38594368 DOI: 10.1038/s41557-024-01493-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 02/28/2024] [Indexed: 04/11/2024]
Abstract
RNA localization is highly regulated, with subcellular organization driving context-dependent cell physiology. Although proximity-based labelling technologies that use highly reactive radicals or carbenes provide a powerful method for unbiased mapping of protein organization within a cell, methods for unbiased RNA mapping are scarce and comparably less robust. Here we develop α-alkoxy thioenol and chloroenol esters that function as potent acylating agents upon controlled ester unmasking. We pair these probes with subcellular-localized expression of a bioorthogonal esterase to establish a platform for spatial analysis of RNA: bioorthogonal acylating agents for proximity labelling and sequencing (BAP-seq). We demonstrate that, by selectively unmasking the enol probe in a locale of interest, we can map RNA distribution in membrane-bound and membrane-less organelles. The controlled-release acylating agent chemistry and corresponding BAP-seq method expand the scope of proximity labelling technologies and provide a powerful approach to interrogate the cellular organization of RNAs.
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Affiliation(s)
- Shubhashree Pani
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Tian Qiu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Kaitlin Kentala
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Saara-Anne Azizi
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Medical Scientist Training Program, Pritzker School of Medicine, The University of Chicago, Chicago, IL, USA
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
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45
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Gutiérrez LK, Moreno-Manuel AI, Jalife J. Kir2.1-Na V1.5 channelosome and its role in arrhythmias in inheritable cardiac diseases. Heart Rhythm 2024; 21:630-646. [PMID: 38244712 DOI: 10.1016/j.hrthm.2024.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/10/2024] [Accepted: 01/13/2024] [Indexed: 01/22/2024]
Abstract
Sudden cardiac death in children and young adults is a relatively rare but tragic event whose pathophysiology is unknown at the molecular level. Evidence indicates that the main cardiac sodium channel (NaV1.5) and the strong inward rectifier potassium channel (Kir2.1) physically interact and form macromolecular complexes (channelosomes) with common partners, including adapter, scaffolding, and regulatory proteins that help them traffic together to their eventual membrane microdomains. Most important, dysfunction of either or both ion channels has direct links to hereditary human diseases. For example, certain mutations in the KCNJ2 gene encoding the Kir2.1 protein result in Andersen-Tawil syndrome type 1 and alter both inward rectifier potassium and sodium inward currents. Similarly, trafficking-deficient mutations in the gene encoding the NaV1.5 protein (SCN5A) result in Brugada syndrome and may also disturb both inward rectifier potassium and sodium inward currents. Moreover, gain-of-function mutations in KCNJ2 result in short QT syndrome type 3, which is extremely rare but highly arrhythmogenic, and can modify Kir2.1-NaV1.5 interactions in a mutation-specific way, further highlighting the relevance of channelosomes in ion channel diseases. By expressing mutant proteins that interrupt or modify Kir2.1 or NaV1.5 function in animal models and patient-specific pluripotent stem cell-derived cardiomyocytes, investigators are defining for the first time the mechanistic framework of how mutation-induced dysregulation of the Kir2.1-NaV1.5 channelosome affects cardiac excitability, resulting in arrhythmias and sudden death in different cardiac diseases.
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Affiliation(s)
- Lilian K Gutiérrez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | | | - José Jalife
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain; CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain; Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan.
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46
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Quirion L, Robert A, Boulais J, Huang S, Bernal Astrain G, Strakhova R, Jo CH, Kherdjemil Y, Faubert D, Thibault MP, Kmita M, Baskin JM, Gingras AC, Smith MJ, Côté JF. Mapping the global interactome of the ARF family reveals spatial organization in cellular signaling pathways. J Cell Sci 2024; 137:jcs262140. [PMID: 38606629 PMCID: PMC11166204 DOI: 10.1242/jcs.262140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024] Open
Abstract
The ADP-ribosylation factors (ARFs) and ARF-like (ARL) GTPases serve as essential molecular switches governing a wide array of cellular processes. In this study, we used proximity-dependent biotin identification (BioID) to comprehensively map the interactome of 28 out of 29 ARF and ARL proteins in two cellular models. Through this approach, we identified ∼3000 high-confidence proximal interactors, enabling us to assign subcellular localizations to the family members. Notably, we uncovered previously undefined localizations for ARL4D and ARL10. Clustering analyses further exposed the distinctiveness of the interactors identified with these two GTPases. We also reveal that the expression of the understudied member ARL14 is confined to the stomach and intestines. We identified phospholipase D1 (PLD1) and the ESCPE-1 complex, more precisely, SNX1, as proximity interactors. Functional assays demonstrated that ARL14 can activate PLD1 in cellulo and is involved in cargo trafficking via the ESCPE-1 complex. Overall, the BioID data generated in this study provide a valuable resource for dissecting the complexities of ARF and ARL spatial organization and signaling.
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Affiliation(s)
- Laura Quirion
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Amélie Robert
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | - Jonathan Boulais
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | - Shiying Huang
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Gabriela Bernal Astrain
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Regina Strakhova
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Chang Hwa Jo
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Yacine Kherdjemil
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | - Denis Faubert
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | | | - Marie Kmita
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Department of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Department of Experimental Medicine, McGill University, Montréal, QC H3G 2M1, Canada
| | - Jeremy M. Baskin
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Matthew J. Smith
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Jean-François Côté
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Department of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Department of Anatomy and Cell Biology, McGill University, Montréal, QC H3A 0C7, Canada
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47
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Yan B, Zeng T, Liu X, Guo Y, Chen H, Guo S, Liu W. Study on the interaction protein of transcription factor Smad3 based on TurboID proximity labeling technology. Genomics 2024; 116:110839. [PMID: 38537808 DOI: 10.1016/j.ygeno.2024.110839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/27/2024] [Accepted: 03/24/2024] [Indexed: 05/27/2024]
Abstract
TurboID is a highly efficient biotin-labelling enzyme, which can be used to explore a number of new intercalating proteins due to the very transient binding and catalytic functions of many proteins. TGF-β/Smad3 signaling pathway is involved in many diseases, especially in diabetic nephropathy and inflammation. In this paper, a stably cell line transfected with Smad3 were constructed by using lentiviral infection. To further investigate the function of TGF-β/Smad3, the protein labeling experiment was conducted to find the interacting protein with Smad3 gene. Label-free mass spectrometry analysis was performed to obtain 491 interacting proteins, and the interacting protein hnRNPM was selected for IP and immunofluorescence verification, and it was verified that the Smad3 gene had a certain promoting effect on the expression of hnRNPM gene, and then had an inhibitory effect on IL-6. It lays a foundation for further study of the function of Smad3 gene and its involved regulatory network.
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Affiliation(s)
- Biao Yan
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning 437000, Hubei, China
| | - Ting Zeng
- Medicine Research Institute, Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning 437000, Hubei, China
| | - Xiaoshan Liu
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning 437000, Hubei, China; School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning 437000, Hubei, China
| | - Yuanyuan Guo
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning 437000, Hubei, China
| | - Hongguang Chen
- Medicine Research Institute, Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning 437000, Hubei, China.
| | - Shuang Guo
- Medicine Research Institute, Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning 437000, Hubei, China.
| | - Wu Liu
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning 437000, Hubei, China.
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48
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Zhong X, Li Q, Polacco BJ, Patil T, Marley A, Foussard H, Khare P, Vartak R, Xu J, DiBerto JF, Roth BL, Eckhardt M, Zastrow MV, Krogan NJ, Hüttenhain R. A proximity proteomics pipeline with improved reproducibility and throughput. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.11.536358. [PMID: 37090610 PMCID: PMC10120663 DOI: 10.1101/2023.04.11.536358] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Proximity labeling (PL) through biotinylation coupled with mass spectrometry (MS) has emerged as a powerful technique for capturing spatial proteomes within living cells. Large-scale sample processing for proximity proteomics requires a workflow that minimizes hands-on time while enhancing quantitative reproducibility. Here, we present a scalable PL pipeline integrating automated enrichment of biotinylated proteins in a 96-well plate format. By combining this pipeline with an optimized quantitative MS acquisition method based on data-independent acquisition (DIA), we not only significantly increased sample throughput but also improved the reproducibility of protein identification and quantification. We applied this pipeline to delineate subcellular proteomes across various cellular compartments, including endosomes, late endosomes/lysosomes, the Golgi apparatus, and the plasma membrane. Moreover, employing 5HT2A serotonin receptor as a model, we investigated temporal changes of proximal interaction networks induced by the receptor's activation with serotonin. Finally, to demonstrate the applicability of our PL pipeline across multiple experimental conditions, we further modified the PL pipeline for reduced sample input amounts to accommodate CRISPR-based gene knockout, and assessed the dynamics of the 5HT2A network in response to the perturbation of selected proximal interactors. Importantly, the presented PL approach is universally applicable to PL proteomics using biotinylation-based PL enzymes, increasing both throughput and reproducibility of standard protocols.
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Affiliation(s)
- Xiaofang Zhong
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Qiongyu Li
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Benjamin J Polacco
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Trupti Patil
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Aaron Marley
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA 94158, USA
| | - Helene Foussard
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Prachi Khare
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Rasika Vartak
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jiewei Xu
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jeffrey F DiBerto
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bryan L Roth
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Manon Eckhardt
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mark Von Zastrow
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA 94158, USA
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ruth Hüttenhain
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
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49
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Ito Y, Nagamoto S, Takano T. Synaptic proteomics decode novel molecular landscape in the brain. Front Mol Neurosci 2024; 17:1361956. [PMID: 38726307 PMCID: PMC11079194 DOI: 10.3389/fnmol.2024.1361956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 04/12/2024] [Indexed: 05/12/2024] Open
Abstract
Synapses play a pivotal role in forming neural circuits, with critical implications for brain functions such as learning, memory, and emotions. Several advances in synaptic research have demonstrated the diversity of synaptic structure and function, which can form thousands of connections depending on the neuronal cell types. Moreover, synapses not only interconnect neurons but also establish connections with glial cells such as astrocytes, which play a key role in the architecture and function of neuronal circuits in the brain. Emerging evidence suggests that dysfunction of synaptic proteins contributes to a variety of neurological and psychiatric disorders. Therefore, it is crucial to determine the molecular networks within synapses in various neuronal cell types to gain a deeper understanding of how the nervous system regulates brain function. Recent advances in synaptic proteome approaches, such as fluorescence-activated synaptosome sorting (FASS) and proximity labeling, have allowed for a detailed and spatial analysis of many cell-type-specific synaptic molecules in vivo. In this brief review, we highlight these novel spatial proteomic approaches and discuss the regulation of synaptic formation and function in the brain. This knowledge of molecular networks provides new insight into the understanding of many neurological and psychiatric disorders.
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Affiliation(s)
- Yuki Ito
- Division of Molecular Systems for Brain Function, Institute for Advanced Study, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Division of Integrated Omics, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Sayaka Nagamoto
- Division of Molecular Systems for Brain Function, Institute for Advanced Study, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Tetsuya Takano
- Division of Molecular Systems for Brain Function, Institute for Advanced Study, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Department of Neurophysiology, Keio University School of Medicine, Tokyo, Japan
- PRESTO, Japan Science and Technology Agency, Saitama, Japan
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50
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Liu X, Yam PT, Schlienger S, Cai E, Zhang J, Chen WJ, Torres Gutierrez O, Jimenez Amilburu V, Ramamurthy V, Ting AY, Branon TC, Cayouette M, Gen R, Marks T, Kong JH, Charron F, Ge X. Numb positively regulates Hedgehog signaling at the ciliary pocket. Nat Commun 2024; 15:3365. [PMID: 38664376 PMCID: PMC11045789 DOI: 10.1038/s41467-024-47244-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Hedgehog (Hh) signaling relies on the primary cilium, a cell surface organelle that serves as a signaling hub for the cell. Using proximity labeling and quantitative proteomics, we identify Numb as a ciliary protein that positively regulates Hh signaling. Numb localizes to the ciliary pocket and acts as an endocytic adaptor to incorporate Ptch1 into clathrin-coated vesicles, thereby promoting Ptch1 exit from the cilium, a key step in Hh signaling activation. Numb loss impedes Sonic hedgehog (Shh)-induced Ptch1 exit from the cilium, resulting in reduced Hh signaling. Numb loss in spinal neural progenitors reduces Shh-induced differentiation into cell fates reliant on high Hh activity. Genetic ablation of Numb in the developing cerebellum impairs the proliferation of granule cell precursors, a Hh-dependent process, resulting in reduced cerebellar size. This study highlights Numb as a regulator of ciliary Ptch1 levels during Hh signal activation and demonstrates the key role of ciliary pocket-mediated endocytosis in cell signaling.
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Affiliation(s)
- Xiaoliang Liu
- Department of Molecular and Cell Biology, University of California, Merced, Merced, CA, 95340, USA
| | - Patricia T Yam
- Montreal Clinical Research Institute (IRCM), Montreal, QC, H2W 1R7, Canada
| | - Sabrina Schlienger
- Montreal Clinical Research Institute (IRCM), Montreal, QC, H2W 1R7, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, H3A 0G4, Canada
| | - Eva Cai
- Department of Molecular and Cell Biology, University of California, Merced, Merced, CA, 95340, USA
| | - Jingyi Zhang
- Department of Molecular and Cell Biology, University of California, Merced, Merced, CA, 95340, USA
| | - Wei-Ju Chen
- Montreal Clinical Research Institute (IRCM), Montreal, QC, H2W 1R7, Canada
- Department of Biology, McGill University, Montreal, QC, H3A 0G4, Canada
| | - Oscar Torres Gutierrez
- Department of Molecular and Cell Biology, University of California, Merced, Merced, CA, 95340, USA
| | | | - Vasanth Ramamurthy
- Montreal Clinical Research Institute (IRCM), Montreal, QC, H2W 1R7, Canada
| | - Alice Y Ting
- Departments of Genetics, of Biology, and by courtesy, of Chemistry, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Tess C Branon
- Departments of Genetics, of Biology, and by courtesy, of Chemistry, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Interline Therapeutics, South San Francisco, CA, USA
| | - Michel Cayouette
- Montreal Clinical Research Institute (IRCM), Montreal, QC, H2W 1R7, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, H3A 0G4, Canada
- Department of Medicine, University of Montreal, Montreal, QC, H3T 1J4, Canada
| | - Risako Gen
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Tessa Marks
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Jennifer H Kong
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Frédéric Charron
- Montreal Clinical Research Institute (IRCM), Montreal, QC, H2W 1R7, Canada.
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, H3A 0G4, Canada.
- Department of Medicine, University of Montreal, Montreal, QC, H3T 1J4, Canada.
| | - Xuecai Ge
- Department of Molecular and Cell Biology, University of California, Merced, Merced, CA, 95340, USA.
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