1
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Li Z, Fei J. NDF/GLYR1 Promotes RNA Polymerase II Processivity via Pol II Binding and Nucleosome Destabilization. Int J Mol Sci 2025; 26:4874. [PMID: 40430013 PMCID: PMC12112590 DOI: 10.3390/ijms26104874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2025] [Revised: 05/06/2025] [Accepted: 05/14/2025] [Indexed: 05/29/2025] Open
Abstract
The Nucleosome Destabilizing Factor (NDF) facilitates transcription through chromatin, but its precise mechanism remains incompletely understood. Here, we identify a critical region (amino acids 140-160) within NDF that specifically interacts with phosphorylated RPB1, the largest subunit of elongating RNA Polymerase II (Pol II). Mutations in this region disrupt Pol II interaction and impair Pol II elongation both in vitro and in cells, yet do not affect NDF's ability to destabilize nucleosomes, establishing a functional separation between these two activities. Cellular studies reveal that NDF knockout cells display faster Pol II elongation rates but produce fewer nascent transcripts, demonstrating NDF's primary role in maintaining transcriptional processivity throughout gene bodies. Our findings demonstrate that NDF uses distinct mechanisms to ensure productive transcription elongation rather than simply enhancing elongation speed, offering new insights into how transcription efficiency is maintained in chromatin.
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Affiliation(s)
- Ziwei Li
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA;
| | - Jia Fei
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA;
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
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2
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Song J, Wang B, Zou M, Zhou H, Ding Y, Ren W, Fang L, Zhang J. Mapping the Interactome of KRAS and Its G12C/D/V Mutants by Integrating TurboID Proximity Labeling with Quantitative Proteomics. BIOLOGY 2025; 14:477. [PMID: 40427667 PMCID: PMC12109396 DOI: 10.3390/biology14050477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2025] [Revised: 04/20/2025] [Accepted: 04/24/2025] [Indexed: 05/29/2025]
Abstract
KRAS mutations are major drivers of human cancers, yet how distinct mutations rewire protein interactions and metabolic pathways to promote tumorigenesis remains poorly understood. To address this, we systematically mapped the protein interaction networks of wild-type KRAS and three high-frequency oncogenic mutants (G12C, G12D, and G12V) using TurboID proximity labeling coupled with quantitative proteomics. Bioinformatic analysis revealed mutant-specific binding partners and metabolic pathway alterations, including significant enrichment in insulin signaling, reactive oxygen species regulation, and glucose/lipid metabolism. These changes collectively drive tumor proliferation and immune evasion. Comparative analysis identified shared interactome shifts across all mutants: reduced binding to LZTR1, an adaptor for KRAS degradation, and enhanced recruitment of LAMTOR1, a regulator of mTORC1-mediated growth signaling. Our multi-dimensional profiling establishes the first comprehensive map of KRAS-mutant interactomes and links specific mutations to metabolic reprogramming. These findings provide mechanistic insights into KRAS-driven malignancy and highlight LZTR1 and LAMTOR1 as potential therapeutic targets. The study further lays a foundation for developing mutation-specific strategies to counteract KRAS oncogenic signaling.
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Affiliation(s)
- Jiangwei Song
- Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210093, China; (J.S.); (J.Z.)
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210029, China; (B.W.); (M.Z.); (H.Z.); (Y.D.)
| | - Busong Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210029, China; (B.W.); (M.Z.); (H.Z.); (Y.D.)
| | - Mingjie Zou
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210029, China; (B.W.); (M.Z.); (H.Z.); (Y.D.)
| | - Haiyuan Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210029, China; (B.W.); (M.Z.); (H.Z.); (Y.D.)
| | - Yibing Ding
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210029, China; (B.W.); (M.Z.); (H.Z.); (Y.D.)
| | - Wei Ren
- Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210093, China; (J.S.); (J.Z.)
| | - Lei Fang
- Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210093, China; (J.S.); (J.Z.)
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210029, China; (B.W.); (M.Z.); (H.Z.); (Y.D.)
| | - Jingzi Zhang
- Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210093, China; (J.S.); (J.Z.)
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210029, China; (B.W.); (M.Z.); (H.Z.); (Y.D.)
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3
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Leung K, Schaefer K, Lin Z, Yao Z, Wells JA. Engineered Proteins and Chemical Tools to Probe the Cell Surface Proteome. Chem Rev 2025; 125:4069-4110. [PMID: 40178992 PMCID: PMC12022999 DOI: 10.1021/acs.chemrev.4c00554] [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: 07/25/2024] [Revised: 02/05/2025] [Accepted: 03/07/2025] [Indexed: 04/05/2025]
Abstract
The cell surface proteome, or surfaceome, is the hub for cells to interact and communicate with the outside world. Many disease-associated changes are hard-wired within the surfaceome, yet approved drugs target less than 50 cell surface proteins. In the past decade, the proteomics community has made significant strides in developing new technologies tailored for studying the surfaceome in all its complexity. In this review, we first dive into the unique characteristics and functions of the surfaceome, emphasizing the necessity for specialized labeling, enrichment, and proteomic approaches. An overview of surfaceomics methods is provided, detailing techniques to measure changes in protein expression and how this leads to novel target discovery. Next, we highlight advances in proximity labeling proteomics (PLP), showcasing how various enzymatic and photoaffinity proximity labeling techniques can map protein-protein interactions and membrane protein complexes on the cell surface. We then review the role of extracellular post-translational modifications, focusing on cell surface glycosylation, proteolytic remodeling, and the secretome. Finally, we discuss methods for identifying tumor-specific peptide MHC complexes and how they have shaped therapeutic development. This emerging field of neo-protein epitopes is constantly evolving, where targets are identified at the proteome level and encompass defined disease-associated PTMs, complexes, and dysregulated cellular and tissue locations. Given the functional importance of the surfaceome for biology and therapy, we view surfaceomics as a critical piece of this quest for neo-epitope target discovery.
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Affiliation(s)
- Kevin
K. Leung
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Kaitlin Schaefer
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Zhi Lin
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Zi Yao
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - James A. Wells
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
- Department
of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
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4
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Gericke N, Beqaj D, Kronenberger T, Kulik A, Gavriilidou A, Franz-Wachtel M, Schoppmeier U, Harbig T, Rapp J, Grin I, Ziemert N, Link H, Nieselt K, Macek B, Wohlleben W, Stegmann E, Wagner S. Unveiling the substrate specificity of the ABC transporter Tba and its role in glycopeptide biosynthesis. iScience 2025; 28:112135. [PMID: 40171492 PMCID: PMC11960670 DOI: 10.1016/j.isci.2025.112135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Revised: 01/16/2025] [Accepted: 02/26/2025] [Indexed: 04/03/2025] Open
Abstract
Glycopeptide antibiotics (GPA) such as vancomycin are essential last-resort antibiotics produced by actinomycetes. Their biosynthesis is encoded within biosynthetic gene clusters, also harboring genes for regulation, and transport. Diverse types of GPAs have been characterized that differ in peptide backbone composition and modification patterns. However, little is known about the ATP-binding cassette (ABC) transporters facilitating GPA export. Employing a multifaceted approach, we investigated the substrate specificity of GPA ABC-transporters toward the type-I GPA balhimycin. Phylogenetic analysis suggested and trans-complementation experiments confirmed that balhimycin is exported only by the related type I GPA transporters Tba and Tva (transporter of vancomycin). Molecular dynamics simulations and mutagenesis experiments showed that Tba exhibits specificity toward the peptide backbone rather than the modifications. Unexpectedly, deletion or functional inactivation of Tba halted balhimycin biosynthesis. Combined with proximity biotinylation experiments, this suggested that the interaction of the active transporter with the biosynthetic machinery is required for biosynthesis.
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Affiliation(s)
- Nicola Gericke
- Cellular and Molecular Microbiology, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Elfriede-Aulhorn-Str. 6, 72076 Tübingen, Germany
| | - Dardan Beqaj
- Microbial Active Compounds, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Thales Kronenberger
- Cellular and Molecular Microbiology, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Elfriede-Aulhorn-Str. 6, 72076 Tübingen, Germany
- Partner-Site: DZIF Tübingen, Elfriede-Aulhorn-Str. 6/Auf der Morgenstelle 28, 72076 Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Yliopistonrinne 3, 70211 Kuopio, Finland
| | - Andreas Kulik
- Microbial Active Compounds, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Athina Gavriilidou
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 24, 72076 Tübingen, Germany
| | - Mirita Franz-Wachtel
- Proteome Center Tübingen, Institute of Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Ulrich Schoppmeier
- Cellular and Molecular Microbiology, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Elfriede-Aulhorn-Str. 6, 72076 Tübingen, Germany
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), University of Tübingen, 72076 Tübingen, Germany
| | - Theresa Harbig
- Interfaculty Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - Johanna Rapp
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), University of Tübingen, 72076 Tübingen, Germany
- Bacterial Metabolomics, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Iwan Grin
- Cellular and Molecular Microbiology, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Elfriede-Aulhorn-Str. 6, 72076 Tübingen, Germany
| | - Nadine Ziemert
- Partner-Site: DZIF Tübingen, Elfriede-Aulhorn-Str. 6/Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 24, 72076 Tübingen, Germany
| | - Hannes Link
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), University of Tübingen, 72076 Tübingen, Germany
- Bacterial Metabolomics, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Kay Nieselt
- Interfaculty Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - Boris Macek
- Proteome Center Tübingen, Institute of Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Wolfgang Wohlleben
- Partner-Site: DZIF Tübingen, Elfriede-Aulhorn-Str. 6/Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), University of Tübingen, 72076 Tübingen, Germany
- Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Evi Stegmann
- Microbial Active Compounds, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Partner-Site: DZIF Tübingen, Elfriede-Aulhorn-Str. 6/Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), University of Tübingen, 72076 Tübingen, Germany
| | - Samuel Wagner
- Cellular and Molecular Microbiology, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Elfriede-Aulhorn-Str. 6, 72076 Tübingen, Germany
- Partner-Site: DZIF Tübingen, Elfriede-Aulhorn-Str. 6/Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), University of Tübingen, 72076 Tübingen, Germany
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5
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Mocăniță M, Martz K, D'Costa VM. Characterizing host-microbe interactions with bacterial effector proteins using proximity-dependent biotin identification (BioID). Commun Biol 2025; 8:597. [PMID: 40210669 PMCID: PMC11985969 DOI: 10.1038/s42003-025-07950-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: 09/25/2024] [Accepted: 03/18/2025] [Indexed: 04/12/2025] Open
Abstract
Bacterial pathogens have evolved diverse strategies to manipulate host cells to establish infection. At a molecular level, this is often mediated by virulence factors that are secreted into host cells (herein referred to as effectors), which target host cellular pathways by initiating host-pathogen protein-protein interactions that alter cellular function in the host. By establishing this network of host-pathogen protein-protein interactions, pathogenic bacteria modulate and hijack host cell processes for the benefit of the pathogen, ultimately promoting survival, replication, and cell-to-cell spread within the host. Effector proteins also mediate diverse host-microbe interactions in nature, contributing to symbiotic relationships spanning from mutualism to commensalism to parasitism. While effector proteins play crucial roles in nature, molecular properties such as the transient nature of the underlying protein-protein interactions and their affinity for targeting host biological membranes often presents challenges to elucidating host targets and mechanism of action. Proximity-dependent biotin identification (termed BioID) has proven to be a valuable tool in the field of cell biology to identify candidate protein-protein interactions in eukaryotic cells, yet has remained relatively underexploited by bacterial pathogenesis researchers. Here, we discuss bacterial effector function at a molecular level, and challenges presented by traditional approaches to host target identification. We highlight the BioID approach and its potential strengths in the context of identifying host-pathogen protein-protein interactions, and explore BioID's implementation to study host-microbe interactions mediated by bacteria. Collectively, BioID represents a powerful tool for the study of bacterial effector proteins, providing new insight into our understanding of pathogenesis and other symbiotic relationships, and opportunities to identify new factors that contribute to host response to infection.
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Affiliation(s)
- Mădălina Mocăniță
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Kailey Martz
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Vanessa M D'Costa
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.
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6
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Simonian TL, Meyer AS, Guo J, Sha J, Wohlschlegel JA, Droujinine IA, Perrimon N, McMahon AP. Sex and Depot Specific Adipocyte Proteome Profiling In Vivo via Intracellular Proximity Labeling. Compr Physiol 2025; 15:e70007. [PMID: 40181252 PMCID: PMC11969033 DOI: 10.1002/cph4.70007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Revised: 02/22/2025] [Accepted: 02/27/2025] [Indexed: 04/05/2025]
Abstract
Adipose tissue has varying distributions and metabolic properties between the sexes. Inherent sex-specific differences in adipocytes may heighten the risk of metabolic disease in males. Analysis of the adipocyte proteome can potentially provide important insight. To enable cell-type specific proteomic profiling in vivo, we genetically engineered a mouse line for cell-type specific production of a promiscuous biotin ligase (BirA*G3) facilitating the rapid isolation of biotinylated cell-type specific proteomes. Adipocyte-specific activation of cytoplasmic BirA*G3 led to robust biotinylation of adipocyte proteins across all major fat depots. Comparison of brown adipose tissue (BAT) and subcutaneous white adipose tissue (SAT) proteomes identified 229 brown adipose-enriched and 35 white adipose-enriched proteins. Regional comparison of white fat depots revealed additional differences across depots. Comparison of male and female depots identified sexually dimorphic adipose proteins: AHNAK predominating in the male and ACOT2 in the female. These findings validate the genetic model and highlight insights to be gained through targeted profiling of adipocytes. The genetic tool adds to existing approaches for in vivo proximity profiling of cell-type specific proteome programs.
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Affiliation(s)
- Taylor L. Simonian
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Amanda S. Meyer
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Jinjin Guo
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Jihui Sha
- Department of Biological Chemistry, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - James A. Wohlschlegel
- Department of Biological Chemistry, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Ilia A. Droujinine
- Department of Molecular MedicineScripps Research InstituteLa JollaCaliforniaUSA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik InstituteHarvard Medical SchoolCambridgeMassachusettsUSA
- Howard Hughes Medical InstituteChevy ChaseMarylandUSA
| | - Andrew P. McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
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7
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Dugied G, Laurent EM, Attia M, Gimeno JP, Bachiri K, Samavarchi-Tehrani P, Donati F, Rahou Y, Munier S, Amara F, Dos Santos M, Soler N, Volant S, Pietrosemoli N, Gingras AC, Pavlopoulos GA, van der Werf S, Falter-Braun P, Aloy P, Jacob Y, Komarova A, Sofianatos Y, Coyaud E, Demeret C. Multimodal SARS-CoV-2 interactome sketches the virus-host spatial organization. Commun Biol 2025; 8:501. [PMID: 40140549 PMCID: PMC11947133 DOI: 10.1038/s42003-025-07933-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Accepted: 03/12/2025] [Indexed: 03/28/2025] Open
Abstract
An accurate spatial representation of protein-protein interaction networks is needed to achieve a realistic and biologically relevant representation of interactomes. Here, we leveraged the spatial information included in Proximity-Dependent Biotin Identification (BioID) interactomes of SARS-CoV-2 proteins to calculate weighted distances and model the organization of the SARS-CoV-2-human interactome in three dimensions (3D) within a cell-like volume. Cell regions with viral occupancy were highlighted, along with the coordination of viral proteins exploiting the cellular machinery. Profiling physical intra-virus and virus-host contacts enabled us to demonstrate both the accuracy and the predictive value of our 3D map for direct interactions, meaning that proteins in closer proximity tend to interact physically. Several functionally important virus-host complexes were detected, and robust structural models were obtained, opening the way to structure-directed drug discovery screens. This PPI discovery pipeline approach brings us closer to a realistic spatial representation of interactomes, which, when applied to viruses or other pathogens, can provide significant information for infection. Thus, it represents a promising tool for coping with emerging infectious diseases.
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Affiliation(s)
- Guillaume Dugied
- Institut Pasteur, Université Paris Cité, UMR 3569, Centre National de la Recherche Scientifique, Molecular Genetics of RNA Viruses, 28 rue du Docteur Roux, F-75015, Paris, France
- Institut Pasteur, Université Paris Cité, Interactomics, RNA and Immunity, 28 rue du Docteur Roux, F-75015, Paris, France
| | - Estelle Mn Laurent
- Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
| | - Mikaël Attia
- Institut Pasteur, Université Paris Cité, UMR 3569, Centre National de la Recherche Scientifique, Molecular Genetics of RNA Viruses, 28 rue du Docteur Roux, F-75015, Paris, France
- Institut Pasteur, Université Paris Cité, Interactomics, RNA and Immunity, 28 rue du Docteur Roux, F-75015, Paris, France
| | - Jean-Pascal Gimeno
- Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
| | - Kamel Bachiri
- Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
| | | | - Flora Donati
- Institut Pasteur, Université Paris Cité, National Reference Center for respiratory viruses, 28 rue du Docteur Roux, F-75015, Paris, France
| | - Yannis Rahou
- Institut Pasteur, Université Paris Cité, UMR 3569, Centre National de la Recherche Scientifique, Molecular Genetics of RNA Viruses, 28 rue du Docteur Roux, F-75015, Paris, France
- Institut Pasteur, Université Paris Cité, National Reference Center for respiratory viruses, 28 rue du Docteur Roux, F-75015, Paris, France
| | - Sandie Munier
- Institut Pasteur, Université Paris Cité, UMR 3569, Centre National de la Recherche Scientifique, Molecular Genetics of RNA Viruses, 28 rue du Docteur Roux, F-75015, Paris, France
| | - Faustine Amara
- Institut Pasteur, Université Paris Cité, UMR 3569, Centre National de la Recherche Scientifique, Molecular Genetics of RNA Viruses, 28 rue du Docteur Roux, F-75015, Paris, France
| | - Mélanie Dos Santos
- Institut Pasteur, Université Paris Cité, UMR 3569, Centre National de la Recherche Scientifique, Molecular Genetics of RNA Viruses, 28 rue du Docteur Roux, F-75015, Paris, France
| | - Nicolas Soler
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10 -12, 08020, Barcelona, Spain
| | - Stevenn Volant
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, F-75015, Paris, France
| | - Natalia Pietrosemoli
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, F-75015, Paris, France
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - Georgios A Pavlopoulos
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", 34 Fleming Street, 16672, Vari, Greece
| | - Sylvie van der Werf
- Institut Pasteur, Université Paris Cité, UMR 3569, Centre National de la Recherche Scientifique, Molecular Genetics of RNA Viruses, 28 rue du Docteur Roux, F-75015, Paris, France
- Institut Pasteur, Université Paris Cité, National Reference Center for respiratory viruses, 28 rue du Docteur Roux, F-75015, Paris, France
| | - Pascal Falter-Braun
- Institute of Network Biology (INET), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Center Munich, German Research Center for Environmental Health, Munich-Neuherberg, Munich, Germany
- Microbe-Host Interactions, Faculty of Biology, Ludwig-Maximilians-Universität (LMU) München, Planegg-Martinsried, Munich, Germany
| | - Patrick Aloy
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10 -12, 08020, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançat (ICREA), Pg. Lluís Companys, 23, 08010, Barcelona, Spain
| | - Yves Jacob
- Institut Pasteur, Université Paris Cité, UMR 3569, Centre National de la Recherche Scientifique, Molecular Genetics of RNA Viruses, 28 rue du Docteur Roux, F-75015, Paris, France
| | - Anastassia Komarova
- Institut Pasteur, Université Paris Cité, UMR 3569, Centre National de la Recherche Scientifique, Molecular Genetics of RNA Viruses, 28 rue du Docteur Roux, F-75015, Paris, France
- Institut Pasteur, Université Paris Cité, Interactomics, RNA and Immunity, 28 rue du Docteur Roux, F-75015, Paris, France
| | - Yorgos Sofianatos
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", 34 Fleming Street, 16672, Vari, Greece.
| | - Etienne Coyaud
- Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France.
| | - Caroline Demeret
- Institut Pasteur, Université Paris Cité, UMR 3569, Centre National de la Recherche Scientifique, Molecular Genetics of RNA Viruses, 28 rue du Docteur Roux, F-75015, Paris, France.
- Institut Pasteur, Université Paris Cité, Interactomics, RNA and Immunity, 28 rue du Docteur Roux, F-75015, Paris, France.
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8
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Ward JS, Schreiber KJ, Tam J, Youn JY, Melnyk RA. Mapping C. difficile TcdB interactions with host cell-surface and intracellular factors using proximity-dependent biotinylation labeling. mBio 2025; 16:e0333624. [PMID: 39818874 PMCID: PMC11796423 DOI: 10.1128/mbio.03336-24] [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: 10/24/2024] [Accepted: 12/17/2024] [Indexed: 01/19/2025] Open
Abstract
Many bacterial toxins exert their cytotoxic effects by enzymatically inactivating one or more cytosolic targets in host cells. To reach their intracellular targets, these toxins possess functional domains or subdomains that interact with and exploit various host factors and biological processes. Despite great progress in identifying many of the key host factors involved in the uptake of toxins, significant knowledge gaps remain as to how partially characterized and newly discovered microbial toxins exploit host factors or processes to intoxicate target cells. Proximity-dependent biotinylation (e.g., BioID) is a powerful method to identify nearby host factors in living cells, offering the potential to identify host targets of microbial toxins. Here, we used BioID to interrogate proximal interactors of the multi-domain Clostridioides difficile TcdB toxin. Expressed fusions of TurboID to different fragments of TcdB identified several high-confidence proteins in the cytosol, including members of the Rho GTPase signaling network and the actin cytoskeletal network. Additionally, we developed an extracellular proximity labeling method using recombinant TurboID-toxin chimeras, which uncovered a limited number of cell-surface targets including LRP1, which was previously identified as a cell-surface receptor of TcdB. Our work reveals surface receptors and intracellular components exploited by bacterial toxins, highlighting key vulnerabilities in host cells.IMPORTANCEBacterial toxins are the causative agents of many human diseases. Further characterizing the intoxication mechanisms of these proteins is important for the development of vaccines and treatments for toxin-mediated disease. Proximity-dependent biotinylation approaches offer an orthogonal approach to complement genetic screens. Here, we evaluate the potential of this method to identify host-toxin interactions on the cell surface and in the cytosol, where the toxin modifies essential host targets. Critically, we have highlighted several limitations of this method as applied to protein toxins, which are important for researchers to weigh when considering this technique for exotoxin studies.
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Affiliation(s)
- Jennifer S. Ward
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Karl J. Schreiber
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - John Tam
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Ji-Young Youn
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Roman A. Melnyk
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
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9
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Critcher M, Pang JM, Huang ML. Mapping the FGF2 Interactome Identifies a Functional Proteoglycan Coreceptor. ACS Chem Biol 2025; 20:105-116. [PMID: 39704408 PMCID: PMC11858877 DOI: 10.1021/acschembio.4c00475] [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] [Indexed: 12/21/2024]
Abstract
Fibroblast growth factor 2 (FGF2) is a multipotent growth factor and signaling protein that exhibits broad functions across multiple cell types. These functions are often initiated by binding to growth factor receptors and fine-tuned by glycosaminoglycan (GAG)-modified proteins called proteoglycans. The various outputs of FGF2 signaling and functions arise from a dynamic and cell type-specific set of binding partners. However, the interactome of FGF2 has yet to be comprehensively determined. Moreover, the identity of the proteoglycan proteins carrying GAG chains is often overlooked and remains unknown in most cell contexts. Here, we perform peroxidase-catalyzed live cell proximity labeling using an engineered APEX2-FGF2 fusion protein to map the interactome of FGF2. Across two cell lines with established and distinct FGF2-driven functions, we greatly expand upon the known FGF2 interactome, identifying >600 new putative FGF2 interactors. Notably, our results demonstrate a key role for the GAG binding capacity of FGF2 in modulating its interactome.
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Affiliation(s)
- Meg Critcher
- Department of Chemistry, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, California 92037, United States
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N Torrey Pines Rd, La Jolla California 92037, United States
| | - Jia Meng Pang
- Department of Chemistry, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, California 92037, United States
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N Torrey Pines Rd, La Jolla California 92037, United States
| | - Mia L Huang
- Department of Chemistry, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, California 92037, United States
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N Torrey Pines Rd, La Jolla California 92037, United States
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10
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Rahmati S, Emili A. Proximity Labeling: Precise Proteomics Technology for Mapping Receptor Protein Neighborhoods at the Cancer Cell Surface. Cancers (Basel) 2025; 17:179. [PMID: 39857961 PMCID: PMC11763998 DOI: 10.3390/cancers17020179] [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: 12/19/2024] [Revised: 01/05/2025] [Accepted: 01/06/2025] [Indexed: 01/27/2025] Open
Abstract
Cell surface receptors are pivotal to cancer cell transformation, disease progression, metastasis, early detection, targeted therapy, drug responses, and clinical outcomes. Since they coordinate complex signaling communication networks in the tumor microenvironment, mapping the physical interaction partners of cell surface receptors in vivo is vital for understanding their roles, functional states, and suitability as therapeutic targets. Yet traditional methods like immunoprecipitation and affinity purification-mass spectrometry often fail to detect key but weak or transient receptor-protein interactions. Proximity labeling, a cutting-edge proteomics technology, addresses these technical challenges by enabling precise mapping of protein neighborhoods around a receptor target on the cell surface of cancer cells. This technique has been successfully applied in vitro and in vivo for proteomic mapping across various model systems. This review explores the fundamental principles, technologies, advantages, limitations, and applications of proximity labeling in cancer biology, focusing on mapping receptor microenvironments. By advancing mechanistic insights into cancer cell receptor signaling mechanisms, proximity labeling is poised to transform cancer research, improve targeted therapies, and illuminate avenues to overcome drug resistance.
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Affiliation(s)
| | - Andrew Emili
- Department of Biomedical Engineering, Division of Oncological Sciences, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA;
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11
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Tang Y, Gu Y. Unraveling Plant Nuclear Envelope Composition Using Proximity Labeling Proteomics. Methods Mol Biol 2025; 2873:145-165. [PMID: 39576601 DOI: 10.1007/978-1-0716-4228-3_9] [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] [Indexed: 11/24/2024]
Abstract
The nuclear envelope (NE) defines the eukaryotic cell and functions in a myriad of fundamental cellular processes including but not limited to signal transduction, lipid metabolism, chromatin organization, and nucleocytoplasmic transportation. Although the general structure of the NE is well-conserved across eukaryotic kingdoms, its composition and functions vary substantially between species and remain largely unknown in plants. In this chapter, we describe a proximity-labeling-based proteomic approach to profile novel NE components in the model organism Arabidopsis. This method is generally suitable for the identification of protein components in subcellular compartments or protein complexes that are poorly accessible to traditional mass spectrometry approaches and can be easily applied to other plant species. In addition to giving a step-by-step detailed description of the proximity labeling proteomics procedure in plant samples, we also provide guidelines on the appropriate use of controls and statistical analysis to achieve a highly specific selection of probed candidates.
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Affiliation(s)
- Yu Tang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Yangnan Gu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
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12
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Rich JA, Gurung S, Coates-Park S, Liu Y, Govil A, Stetler-Stevenson WG, Peeney D. Protocol to study secretome interactions using extracellular proximity labeling. STAR Protoc 2024; 5:103509. [PMID: 39673706 PMCID: PMC11699400 DOI: 10.1016/j.xpro.2024.103509] [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: 09/06/2024] [Revised: 10/17/2024] [Accepted: 11/15/2024] [Indexed: 12/16/2024] Open
Abstract
Biotin ligase-based proximity ligation is a widely used, highly effective technique for the study of in vivo protein-protein interactions. However, there are few reports and little consensus on the most effective methods for studying the proximal interactomes of secreted factors. Here, we present a protocol for studying extracellular proximal interactomes using an adaptation of TurboID/BioID2-based proximity ligation. We describe steps for cell preparation, sample collection, and initial processing. We then detail procedures for biotinylated protein enrichment, on-bead digestion, and post-pull-down processing. For complete details on the use and execution of this protocol, please refer to Peeney et al.1.
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Affiliation(s)
- Joshua A Rich
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sadeechya Gurung
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sasha Coates-Park
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Yueqin Liu
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Anshika Govil
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - David Peeney
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
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13
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Ali A, Hussain S, Bedekovics T, Jeon RH, May DG, Roux KJ, Galardy PJ. Proximity Proteomics Reveals USP44 Forms a Complex with BRCA2 in Neuroblastoma Cells and Is Required to Prevent Chromosome Breakage. Biomedicines 2024; 12:2901. [PMID: 39767807 PMCID: PMC11727000 DOI: 10.3390/biomedicines12122901] [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: 11/25/2024] [Revised: 12/13/2024] [Accepted: 12/17/2024] [Indexed: 01/16/2025] Open
Abstract
BACKGROUND/OBJECTIVES The enzyme ubiquitin-specific protease 44 (USP44) is a deubiquitinating enzyme with identified physiological roles as a tumor suppressor and an oncogene. While some binding partners and substrates are known for USP44, the identification of other interactions may improve our understanding of its role in cancer. We therefore performed a proximity biotinylation study that identified products of several known cancer genes that are associated with USP44, including a novel interaction between BRCA2 and USP44. METHODS We expressed a fusion protein that linked USP44 and mutant Escherichia coli biotin ligase BioID in SH-SY5Y neuroblastoma cells. Control experiments were performed using BioID alone. In duplicate experiments, cells were pulsed with biotin and biotinylated proteins were isolated under denaturing conditions and the proteins were identified by mass spectrometry. The resulting list of proteins were analyzed using Enrichr and cross-referenced with the COSMIC Cancer Gene Census. We validated the association with BRCA2 using immunoprecipitation. The role of USP44 in the Fanconi anemia DNA repair pathway was investigated using chromosome analysis of wild-type or Usp44-knockout cells after exposure to mitomycin C. RESULTS We identified 146 proteins that were selectively retrieved by the USP44 construct and compared with cells expressing the BioID ligase alone, including 15 gene products encoded by genes on tier 1 of the COSMIC Cancer Gene Census, including BRCA2. The association between USP44 and BRCA2 was validated through immunoprecipitation. We tested the functional role of USP44 in the Fanconi anemia DNA repair pathway through chromosome breakage analysis and found that cells lacking USP44 had a significant increase in chromosome breaks and radial chromosomes. We found that high BRCA2 transcript was correlated with poor survival in neuroblastoma, likely due to its tight association with proliferation in these tumors. CONCLUSIONS Our results identified novel potential binding partners and potential substrates for USP44, including several with direct roles in cancer pathogenesis. Our results identified a novel association between BRCA2 and USP44, and a previously unknown role for USP44 in the Fanconi anemia DNA repair pathway that may contribute to its role in cancer.
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Affiliation(s)
- Asma Ali
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA; (A.A.); (S.H.); (T.B.); (R.H.J.)
| | - Sajjad Hussain
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA; (A.A.); (S.H.); (T.B.); (R.H.J.)
- Department of Family Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Tibor Bedekovics
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA; (A.A.); (S.H.); (T.B.); (R.H.J.)
| | - Raymond H. Jeon
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA; (A.A.); (S.H.); (T.B.); (R.H.J.)
| | - Danielle G. May
- Enabling Technology Group, Sanford Research, Sioux Falls, SD 57104, USA; (D.G.M.); (K.J.R.)
| | - Kyle J. Roux
- Enabling Technology Group, Sanford Research, Sioux Falls, SD 57104, USA; (D.G.M.); (K.J.R.)
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105, USA
| | - Paul J. Galardy
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA; (A.A.); (S.H.); (T.B.); (R.H.J.)
- Division of Pediatric Hematology-Oncology, Mayo Clinic, Rochester, MN 55905, USA
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14
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Cenik BK, Aoi Y, Iwanaszko M, Howard BC, Morgan MA, Andersen GD, Bartom ET, Shilatifard A. TurboCas: A method for locus-specific labeling of genomic regions and isolating their associated protein interactome. Mol Cell 2024; 84:4929-4944.e8. [PMID: 39706164 DOI: 10.1016/j.molcel.2024.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 08/19/2024] [Accepted: 11/07/2024] [Indexed: 12/23/2024]
Abstract
Regulation of gene expression during development and stress response requires the concerted action of transcription factors and chromatin-binding proteins. Because this process is cell-type specific and varies with cellular conditions, mapping of chromatin factors at individual regulatory loci is crucial for understanding cis-regulatory control. Previous methods only characterize static protein binding. We present "TurboCas," a method combining a proximity-labeling (PL) enzyme, miniTurbo, with CRISPR-dCas9 that allows for efficient and site-specific labeling of chromatin factors in mammalian cells. Validating TurboCas at the FOS promoter, we identify proteins recruited upon heat shock, cross-validated via RNA polymerase II and P-TEFb immunoprecipitation. These methodologies reveal canonical and uncharacterized factors that function to activate expression of heat-shock-responsive genes. Applying TurboCas to the MYC promoter, we identify two P-TEFb coactivators, the super elongation complex (SEC) and BRD4, as MYC co-regulators. TurboCas provides a genome-specific targeting PL, with the potential to deepen our molecular understanding of transcriptional regulatory pathways in development and stress response.
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Affiliation(s)
- Bercin K Cenik
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA
| | - Yuki Aoi
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA
| | - Marta Iwanaszko
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA
| | - Benjamin C Howard
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA
| | - Marc A Morgan
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA
| | - Grant D Andersen
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA
| | - Elizabeth T Bartom
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA; Robert H. Lurie NCI Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA.
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15
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Wilson ER, Nunes GDF, Shen S, Moore S, Gawron J, Maxwell J, Syed U, Hurley E, Lanka M, Qu J, Désaubry L, Wrabetz L, Poitelon Y, Feltri ML. Loss of prohibitin 2 in Schwann cells dysregulates key transcription factors controlling developmental myelination. Glia 2024; 72:2247-2267. [PMID: 39215540 PMCID: PMC11577967 DOI: 10.1002/glia.24610] [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: 03/21/2024] [Revised: 07/18/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024]
Abstract
Schwann cells are critical for the proper development and function of the peripheral nervous system (PNS), where they form a collaborative relationship with axons. Past studies highlighted that a pair of proteins called the prohibitins play major roles in Schwann cell biology. Prohibitins are ubiquitously expressed and versatile proteins. We have previously shown that while prohibitins play a crucial role in Schwann cell mitochondria for long-term myelin maintenance and axon health, they may also be present at the Schwann cell-axon interface during development. Here, we expand on this, showing that drug-mediated modulation of prohibitins in vitro disrupts myelination and confirming that Schwann cell-specific ablation of prohibitin 2 (Phb2) in vivo results in severe defects in radial sorting and myelination. We show in vivo that Phb2-null Schwann cells cannot effectively proliferate and the transcription factors EGR2 (KROX20), POU3F1 (OCT6), and POU3F2 (BRN2), necessary for proper Schwann cell maturation, are dysregulated. Schwann cell-specific deletion of Jun, a transcription factor associated with negative regulation of myelination, confers partial rescue of the developmental defect seen in mice lacking Schwann cell Phb2. Finally, we identify a pool of candidate PHB2 interactors that change their interaction with PHB2 depending on neuronal signals, and thus are potential mediators of PHB2-associated developmental defects. This work develops our understanding of Schwann cell biology, revealing that Phb2 may modulate the timely expression of transcription factors necessary for proper PNS development, and proposing candidates that may play a role in PHB2-mediated integration of axon signals in the Schwann cell.
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Affiliation(s)
- Emma R Wilson
- Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, England, UK
| | - Gustavo Della-Flora Nunes
- Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Shichen Shen
- Department of Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
| | - Seth Moore
- Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
| | - Joseph Gawron
- Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
| | - Jessica Maxwell
- Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
| | - Umair Syed
- Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
| | - Edward Hurley
- Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
| | - Meghana Lanka
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, New York, USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
| | - Laurent Désaubry
- Center of Research in Biomedicine of Strasbourg, Regenerative Nanomedicine (UMR 1260), INSERM, University of Strasbourg, Strasbourg, France
| | - Lawrence Wrabetz
- Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
- Department of Neurology, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
| | - Yannick Poitelon
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, New York, USA
| | - M Laura Feltri
- Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
- Department of Neurology, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
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16
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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; 20:1597-1607. [PMID: 38965384 PMCID: PMC11581931 DOI: 10.1038/s41589-024-01660-y] [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: 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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17
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Haidar-Ahmad N, Tomaro K, Lavallée-Adam M, Campbell-Valois FX. The promiscuous biotin ligase TurboID reveals the proxisome of the T3SS chaperone IpgC in Shigella flexneri. mSphere 2024; 9:e0055324. [PMID: 39480076 PMCID: PMC11580435 DOI: 10.1128/msphere.00553-24] [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: 07/06/2024] [Accepted: 10/01/2024] [Indexed: 11/02/2024] Open
Abstract
Promiscuous biotin ligases derived from the bacterial enzyme BirA are used to identify proteins vicinal to a bait protein, thereby defining its proxisome. Despite the popularity of this approach, surprisingly little is known about its use in prokaryotes. Here, we compared the activity of four widely used promiscuous biotin ligases in the cytoplasm of Shigella flexneri, a pathogenic subgroup of Escherichia coli. Our data indicate that the kinetics of TurboID's biotinylating activity is the highest of those tested. In addition, TurboID showed reduced interaction with the natural BirA binding partners, BccP and the biotin operator, when compared to its ancestor BioID. We therefore evaluated the ability of TurboID to probe the proxisome of the type III secretion system (T3SS) chaperone IpgC and the transcriptional activator MxiE. When the T3SS is inactive (off-state), these proteins are inhibited by forming complexes with the T3SS substrates OspD1 and IpaBC, respectively. In contrast, when the T3SS is active (on-state), OspD1 and IpaBC are secreted allowing MxiE and IpgC to interact together and activate their target genes. The results obtained with the IpgC and TurboID fusions capture a good fraction of these known interactions. It also suggests that the availability of IpgC increases in the on-state, resulting in a greater number of proteins detected in its vicinity. Among these is the T3SS ATPase SpaL (also known as Spa47 or SctN), further supporting the notion that chaperones escort their substrate to the T3SS. Interestingly, a specific subset of proteins conserved in E. coli completes the IpgC proxisome in the on-state.IMPORTANCEPromiscuous biotin ligases are widely used to study protein function in eukaryotes. Strikingly, their use in prokaryotes has been rare. Indeed, the small volume and the cytoplasmic location of the biotin ligase's natural binding partners in these organisms pose unique challenges that can interfere with the study of the proxisome of proteins of interest. Here, we evaluated four of the most common promiscuous biotin ligases and found TurboID was best suited for use in the cytoplasm of Shigella flexneri. Using this method, we extended the proxisome of IpgC beyond its known direct binding partners involved in the regulation of the type III secretion system (T3SS) signaling cascade. Of particular interest for further study are transcription factors and housekeeping proteins that are enriched around IpgC when the T3SS is active. We propose a model in which the increased availability of IpgC in the on-state may allow cross-talk of the T3SS with other cellular processes.
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Affiliation(s)
- Nathaline Haidar-Ahmad
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, Host-Microbe Interactions Laboratory, University of Ottawa, Ottawa, Ontario, Canada
| | - Kyle Tomaro
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, Host-Microbe Interactions Laboratory, University of Ottawa, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology and Immunology, Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Mathieu Lavallée-Adam
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - François-Xavier Campbell-Valois
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, Host-Microbe Interactions Laboratory, University of Ottawa, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology and Immunology, Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
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18
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Al Mismar R, Samavarchi-Tehrani P, Seale B, Kasmaeifar V, Martin CE, Gingras AC. Extracellular proximal interaction profiling by cell surface-targeted TurboID reveals LDLR as a partner of liganded EGFR. Sci Signal 2024; 17:eadl6164. [PMID: 39499777 DOI: 10.1126/scisignal.adl6164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 05/25/2024] [Accepted: 10/01/2024] [Indexed: 11/07/2024]
Abstract
Plasma membrane proteins play pivotal roles in receiving and transducing signals from other cells and from the environment and are vital for cellular functionality. Enzyme-based, proximity-dependent approaches, such as biotin identification (BioID), combined with mass spectrometry have begun to illuminate the landscape of proximal protein interactions within intracellular compartments. To extend the potential of these approaches to study the extracellular environment, we developed extracellular TurboID (ecTurboID), a method designed to profile the interactions between proteins on the surfaces of living cells over short timescales using the fast-acting biotin ligase TurboID. After optimizing our experimental and data analysis strategies to capture extracellular proximity interactions, we used ecTurboID to reveal the proximal interactomes of several plasma membrane proteins, including the epidermal growth factor receptor (EGFR). We found that EGF stimulation induced an association between EGFR and the low-density lipoprotein receptor (LDLR) and changed the interactome of LDLR by increasing its proximity with proteins that regulate EGFR signaling. The identification of this interaction between two well-studied and clinically relevant receptors illustrates the utility of our modified proximity labeling methodology for identifying dynamic extracellular associations between plasma membrane proteins.
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Affiliation(s)
- Rasha Al Mismar
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | | | - Brendon Seale
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, Canada
| | - Vesal Kasmaeifar
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Claire E Martin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
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19
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Suzuki Y, Tsubota S, Kadomatsu K, Sakamoto K. Identification of APBB1 as a substrate for anaplastic lymphoma kinase. J Biochem 2024; 176:395-403. [PMID: 39115278 PMCID: PMC11954158 DOI: 10.1093/jb/mvae055] [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: 03/19/2024] [Accepted: 07/15/2024] [Indexed: 11/05/2024] Open
Abstract
Anaplastic lymphoma kinase (ALK) is a well-known oncogene involved in various malignancies such as anaplastic large cell lymphoma, lung cancer and neuroblastoma. Several substrates for fused ALK have been identified and their biological functions have been described. However, the lack of a comprehensive identification of ALK substrates limits our understanding of the biological roles of receptor ALK. Thus, this study aimed to identify novel ALK substrates and characterize their biological functions. We screened the interactors of the kinase domain of receptor ALK using proximity-dependent biotin identification and identified 43 interactors. We narrowed down the candidates by evaluating whether these interactors were downstream of ALK in a neuroblastoma cell line, NB-1. Amongst these, we identified amyloid beta precursor protein-binding family B member 1 (APBB1) as an ALK downstream molecule involved in NB-1 cell viability. Finally, we assessed the kinase-substrate relationship between ALK and APBB1 and found that ALK phosphorylated multiple tyrosine residues in APBB1 both in-cell and in-tube assays, with tyrosine 269 as a major target. In conclusion, we successfully identified a new substrate for receptor ALK. Our results may help further elucidate the molecular mechanism of ALK downstream signalling in neuroblastoma.
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Affiliation(s)
- Yuji Suzuki
- Department of Integrative Physiology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
- Department of Biochemistry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
| | - Shoma Tsubota
- Department of Biochemistry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
| | - Kenji Kadomatsu
- Institute for Glyco-core Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Kazuma Sakamoto
- Department of Biochemistry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
- Institute for Glyco-core Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
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20
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Kim D, Bhargava R, Wang SC, Lee D, Patel R, Oh S, Bowman RW, Na CH, O'Sullivan RJ, Miller KM. TRIM24 directs replicative stress responses to maintain ALT telomeres via chromatin signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.18.618947. [PMID: 39463989 PMCID: PMC11507842 DOI: 10.1101/2024.10.18.618947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
Abstract
An inability to replicate the genome can cause replication stress and genome instability. Here, we develop BLOCK-ID, a proteomic method to identify and visualize proteins at stressed replication forks. This approach successfully identified novel mediators of the replication stress response, including the chromatin acetylation reader protein TRIM24. In validating TRIM24 function, we uncovered its crucial role in coordinating Alternative Lengthening of Telomeres (ALT), a cancer-specific telomere extension pathway involving replication stress. Our data reveal that TRIM24 is directed to telomeres via a p300/CBP-dependent acetylation chromatin signaling cascade, where it organizes ALT-associated PML bodies (APBs) to promote telomere DNA synthesis. Strikingly, we demonstrate that when artificially tethered at telomeres, TRIM24 can stimulate new telomere DNA synthesis in a SUMO-dependent manner, independently of p300/CBP or PML-dependent APBs. Thus, this study identifies a TRIM24 chromatin signaling pathway required for ALT telomere maintenance.
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21
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Zheng X, Zhu H, Zhao X, Wang J, Li Q, Zhao X. Emerging affinity methods for protein-drug interaction analysis. J Pharm Biomed Anal 2024; 249:116371. [PMID: 39047466 DOI: 10.1016/j.jpba.2024.116371] [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: 05/30/2024] [Revised: 07/15/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024]
Abstract
The study of protein-drug interaction plays a crucial role in understanding drug mechanisms, identifying new drug targets and biomarkers, and facilitating drug development and disease treatment. In recent years, significant progress has been made in various protein-drug interaction research methods due to the rapid development and in-depth application of mass spectrometry, nuclear magnetic resonance, Raman spectroscopy, and other technologies. The progress has enhanced the sensitivity, precision, accuracy, and applicability of analytical methods, enabling the establishment of drug-protein interaction networks. This review discusses various emerging research methods, such as native mass spectrometry, infrared spectroscopy, nuclear magnetic resonance and spectrum, biosensor technologies employing surface enhanced Raman, electrochemistry, and magneto resistive signals, as well as affinity magnetic levitation and affinity chromatography. The article also delves into the principles, applications, advantages, and limitations of these technologies.
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Affiliation(s)
- Xinxin Zheng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Huiting Zhu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Xue Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Jing Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Qian Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Xinfeng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China.
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22
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Baek K, Metivier RJ, Roy Burman SS, Bushman JW, Yoon H, Lumpkin RJ, Abeja DM, Lakshminarayan M, Yue H, Ojeda S, Verano AL, Gray NS, Donovan KA, Fischer ES. Unveiling the hidden interactome of CRBN molecular glues with chemoproteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.11.612438. [PMID: 39314457 PMCID: PMC11419069 DOI: 10.1101/2024.09.11.612438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Targeted protein degradation and induced proximity refer to strategies that leverage the recruitment of proteins to facilitate their modification, regulation or degradation. As prospective design of glues remains challenging, unbiased discovery methods are needed to unveil hidden chemical targets. Here we establish a high throughput affinity purification mass spectrometry workflow in cell lysates for the unbiased identification of molecular glue targets. By mapping the targets of 20 CRBN-binding molecular glues, we identify 298 protein targets and demonstrate the utility of enrichment methods for identifying novel targets overlooked using established methods. We use a computational workflow to estimate target confidence and perform a biochemical screen to identify a lead compound for the new non-ZF target PPIL4. Our study provides a comprehensive inventory of targets chemically recruited to CRBN and delivers a robust and scalable workflow for identifying new drug-induced protein interactions in cell lysates.
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Affiliation(s)
- Kheewoong Baek
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Rebecca J. Metivier
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Shourya S. Roy Burman
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jonathan W. Bushman
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hojong Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ryan J. Lumpkin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Dinah M. Abeja
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Megha Lakshminarayan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Hong Yue
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Samuel Ojeda
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Alyssa L. Verano
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nathanael S. Gray
- Department of Chemical and Systems Biology, ChEM-H and Stanford Cancer Institute, Stanford Medical School, Stanford University, Stanford, CA, 94305, USA
| | - Katherine A. Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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23
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Cuadrado AF, Van Damme D. Unlocking protein-protein interactions in plants: a comprehensive review of established and emerging techniques. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5220-5236. [PMID: 38437582 DOI: 10.1093/jxb/erae088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/29/2024] [Indexed: 03/06/2024]
Abstract
Protein-protein interactions orchestrate plant development and serve as crucial elements for cellular and environmental communication. Understanding these interactions offers a gateway to unravel complex protein networks that will allow a better understanding of nature. Methods for the characterization of protein-protein interactions have been around over 30 years, yet the complexity of some of these interactions has fueled the development of new techniques that provide a better understanding of the underlying dynamics. In many cases, the application of these techniques is limited by the nature of the available sample. While some methods require an in vivo set-up, others solely depend on protein sequences to study protein-protein interactions via an in silico set-up. The vast number of techniques available to date calls for a way to select the appropriate tools for the study of specific interactions. Here, we classify widely spread tools and new emerging techniques for the characterization of protein-protein interactions based on sample requirements while providing insights into the information that they can potentially deliver. We provide a comprehensive overview of commonly used techniques and elaborate on the most recent developments, showcasing their implementation in plant research.
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Affiliation(s)
- Alvaro Furones Cuadrado
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
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24
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Serafin DS, Harris NR, Bálint L, Douglas ES, Caron KM. Proximity interactome of lymphatic VE-cadherin reveals mechanisms of junctional remodeling and reelin secretion. Nat Commun 2024; 15:7734. [PMID: 39232006 PMCID: PMC11374903 DOI: 10.1038/s41467-024-51918-1] [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: 03/30/2023] [Accepted: 08/20/2024] [Indexed: 09/06/2024] Open
Abstract
The adhesion receptor vascular endothelial (VE)-cadherin transduces an array of signals that modulate crucial lymphatic cell behaviors including permeability and cytoskeletal remodeling. Consequently, VE-cadherin must interact with a multitude of intracellular proteins to exert these functions. Yet, the full protein interactome of VE-cadherin in endothelial cells remains a mystery. Here, we use proximity proteomics to illuminate how the VE-cadherin interactome changes during junctional reorganization from dis-continuous to continuous junctions, triggered by the lymphangiogenic factor adrenomedullin. These analyses identified interactors that reveal roles for ADP ribosylation factor 6 (ARF6) and the exocyst complex in VE-cadherin trafficking and recycling. We also identify a requisite role for VE-cadherin in the in vitro and in vivo control of secretion of reelin-a lymphangiocrine glycoprotein with recently appreciated roles in governing heart development and injury repair. This VE-cadherin protein interactome shines light on mechanisms that control adherens junction remodeling and secretion from lymphatic endothelial cells.
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Affiliation(s)
- D Stephen Serafin
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, 111 Mason Farm Road, Chapel Hill, 27599, NC, USA
| | - Natalie R Harris
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, 111 Mason Farm Road, Chapel Hill, 27599, NC, USA
| | - László Bálint
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, 111 Mason Farm Road, Chapel Hill, 27599, NC, USA
| | - Elizabeth S Douglas
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, 111 Mason Farm Road, Chapel Hill, 27599, NC, USA
| | - Kathleen M Caron
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, 111 Mason Farm Road, Chapel Hill, 27599, NC, USA.
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25
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Owens DDG, Maitland MER, Khalili Yazdi A, Song X, Reber V, Schwalm MP, Machado RAC, Bauer N, Wang X, Szewczyk MM, Dong C, Dong A, Loppnau P, Calabrese MF, Dowling MS, Lee J, Montgomery JI, O'Connell TN, Subramanyam C, Wang F, Adamson EC, Schapira M, Gstaiger M, Knapp S, Vedadi M, Min J, Lajoie GA, Barsyte-Lovejoy D, Owen DR, Schild-Poulter C, Arrowsmith CH. A chemical probe to modulate human GID4 Pro/N-degron interactions. Nat Chem Biol 2024; 20:1164-1175. [PMID: 38773330 DOI: 10.1038/s41589-024-01618-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/12/2024] [Indexed: 05/23/2024]
Abstract
The C-terminal to LisH (CTLH) complex is a ubiquitin ligase complex that recognizes substrates with Pro/N-degrons via its substrate receptor Glucose-Induced Degradation 4 (GID4), but its function and substrates in humans remain unclear. Here, we report PFI-7, a potent, selective and cell-active chemical probe that antagonizes Pro/N-degron binding to human GID4. Use of PFI-7 in proximity-dependent biotinylation and quantitative proteomics enabled the identification of GID4 interactors and GID4-regulated proteins. GID4 interactors are enriched for nucleolar proteins, including the Pro/N-degron-containing RNA helicases DDX21 and DDX50. We also identified a distinct subset of proteins whose cellular levels are regulated by GID4 including HMGCS1, a Pro/N-degron-containing metabolic enzyme. These data reveal human GID4 Pro/N-degron targets regulated through a combination of degradative and nondegradative functions. Going forward, PFI-7 will be a valuable research tool for investigating CTLH complex biology and facilitating development of targeted protein degradation strategies that highjack CTLH E3 ligase activity.
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Affiliation(s)
- Dominic D G Owens
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Matthew E R Maitland
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Don Rix Protein Identification Facility, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | | | - Xiaosheng Song
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Viviane Reber
- Institute of Molecular Systems Biology at ETH Zurich, Zurich, Switzerland
| | - Martin P Schwalm
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Frankfurt am Main, Germany
- Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Raquel A C Machado
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Nicolas Bauer
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Frankfurt am Main, Germany
- Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Xu Wang
- Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | | | - Cheng Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Jisun Lee
- Development and Medical, Pfizer Worldwide Research, Groton, CT, USA
| | | | | | | | - Feng Wang
- Development and Medical, Pfizer Worldwide Research, Groton, CT, USA
| | - Ella C Adamson
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Matthias Gstaiger
- Institute of Molecular Systems Biology at ETH Zurich, Zurich, Switzerland
| | - Stefan Knapp
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Frankfurt am Main, Germany
- Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Gilles A Lajoie
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Don Rix Protein Identification Facility, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Dafydd R Owen
- Development and Medical, Pfizer Worldwide Research, Groton, CT, USA
| | - Caroline Schild-Poulter
- Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
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26
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Odenwald J, Gabiatti B, Braune S, Shen S, Zoltner M, Kramer S. Detection of TurboID fusion proteins by fluorescent streptavidin outcompetes antibody signals and visualises targets not accessible to antibodies. eLife 2024; 13:RP95028. [PMID: 39206942 PMCID: PMC11361705 DOI: 10.7554/elife.95028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
Immunofluorescence localises proteins via fluorophore-labelled antibodies. However, some proteins evade detection due to antibody-accessibility issues or because they are naturally low abundant or antigen density is reduced by the imaging method. Here, we show that the fusion of the target protein to the biotin ligase TurboID and subsequent detection of biotinylation by fluorescent streptavidin offers an 'all in one' solution to these restrictions. For all proteins tested, the streptavidin signal was significantly stronger than an antibody signal, markedly improving the sensitivity of expansion microscopy and correlative light and electron microscopy. Importantly, proteins within phase-separated regions, such as the central channel of the nuclear pores, the nucleolus, or RNA granules, were readily detected with streptavidin, while most antibodies failed. When TurboID is used in tandem with an HA epitope tag, co-probing with streptavidin and anti-HA can map antibody-accessibility and we created such a map for the trypanosome nuclear pore. Lastly, we show that streptavidin imaging resolves dynamic, temporally, and spatially distinct sub-complexes and, in specific cases, reveals a history of dynamic protein interaction. In conclusion, streptavidin imaging has major advantages for the detection of lowly abundant or inaccessible proteins and in addition, provides information on protein interactions and biophysical environment.
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Affiliation(s)
| | | | - Silke Braune
- Biocenter, University of WürzburgWürzburgGermany
| | - Siqi Shen
- Department of Parasitology, Faculty of Science, Charles University in PraguePragueCzech Republic
| | - Martin Zoltner
- Department of Parasitology, Faculty of Science, Charles University in PraguePragueCzech Republic
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27
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Becker AP, Biletch E, Kennelly JP, Julio AR, Villaneuva M, Nagari RT, Turner DW, Burton NR, Fukuta T, Cui L, Xiao X, Hong SG, Mack JJ, Tontonoz P, Backus KM. Lipid- and protein-directed photosensitizer proximity labeling captures the cholesterol interactome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.20.608660. [PMID: 39229057 PMCID: PMC11370482 DOI: 10.1101/2024.08.20.608660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
The physical properties of cellular membranes, including fluidity and function, are influenced by protein and lipid interactions. In situ labeling chemistries, most notably proximity-labeling interactomics are well suited to characterize these dynamic and often fleeting interactions. Established methods require distinct chemistries for proteins and lipids, which limits the scope of such studies. Here we establish a singlet-oxygen-based photocatalytic proximity labeling platform (POCA) that reports intracellular interactomes for both proteins and lipids with tight spatiotemporal resolution using cell-penetrant photosensitizer reagents. Using both physiologically relevant lipoprotein-complexed probe delivery and genetic manipulation of cellular cholesterol handling machinery, cholesterol-directed POCA captured established and unprecedented cholesterol binding proteins, including protein complexes sensitive to intracellular cholesterol levels and proteins uniquely captured by lipoprotein uptake. Protein-directed POCA accurately mapped known intracellular membrane complexes, defined sterol-dependent changes to the non-vesicular cholesterol transport protein interactome, and captured state-dependent changes in the interactome of the cholesterol transport protein Aster-B. More broadly, we find that POCA is a versatile interactomics platform that is straightforward to implement, using the readily available HaloTag system, and fulfills unmet needs in intracellular singlet oxygen-based proximity labeling proteomics. Thus, we expect widespread utility for POCA across a range of interactome applications, spanning imaging to proteomics.
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Affiliation(s)
- Andrew P. Becker
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
| | - Elijah Biletch
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
| | - John Paul Kennelly
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, Los Angeles, California 90095, USA
| | - Ashley R. Julio
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
| | - Miranda Villaneuva
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, USA
| | - Rohith T. Nagari
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, Los Angeles, California 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, USA
| | - Daniel W. Turner
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
| | - Nikolas R. Burton
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
| | - Tomoyuki Fukuta
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, USA
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Liujuan Cui
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, Los Angeles, California 90095, USA
| | - Xu Xiao
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, Los Angeles, California 90095, USA
| | - Soon-Gook Hong
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, USA
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, USA
| | - Julia J. Mack
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, USA
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, USA
| | - Peter Tontonoz
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, Los Angeles, California 90095, USA
| | - Keriann M. Backus
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, California 90095, USA
- Jonsson Cancer Center, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, USA
- UCLA-DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095, USA
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Kociemba J, Jørgensen ACS, Tadić N, Harris A, Sideri T, Chan WY, Ibrahim F, Ünal E, Skehel M, Shahrezaei V, Argüello-Miranda O, van Werven FJ. Multi-signal regulation of the GSK-3β homolog Rim11 controls meiosis entry in budding yeast. EMBO J 2024; 43:3256-3286. [PMID: 38886580 PMCID: PMC11294583 DOI: 10.1038/s44318-024-00149-7] [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: 09/28/2023] [Revised: 04/22/2024] [Accepted: 05/27/2024] [Indexed: 06/20/2024] Open
Abstract
Starvation in diploid budding yeast cells triggers a cell-fate program culminating in meiosis and spore formation. Transcriptional activation of early meiotic genes (EMGs) hinges on the master regulator Ime1, its DNA-binding partner Ume6, and GSK-3β kinase Rim11. Phosphorylation of Ume6 by Rim11 is required for EMG activation. We report here that Rim11 functions as the central signal integrator for controlling Ume6 phosphorylation and EMG transcription. In nutrient-rich conditions, PKA suppresses Rim11 levels, while TORC1 retains Rim11 in the cytoplasm. Inhibition of PKA and TORC1 induces Rim11 expression and nuclear localization. Remarkably, nuclear Rim11 is required, but not sufficient, for Rim11-dependent Ume6 phosphorylation. In addition, Ime1 is an anchor protein enabling Ume6 phosphorylation by Rim11. Subsequently, Ume6-Ime1 coactivator complexes form and induce EMG transcription. Our results demonstrate how various signaling inputs (PKA/TORC1/Ime1) converge through Rim11 to regulate EMG expression and meiosis initiation. We posit that the signaling-regulatory network elucidated here generates robustness in cell-fate control.
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Affiliation(s)
- Johanna Kociemba
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Andreas Christ Sølvsten Jørgensen
- Department of Mathematics, Imperial College London, London, SW7 2BX, UK
- I-X Centre for AI In Science, Imperial College London, White City Campus, 84 Wood Lane, London, W12 0BZ, UK
| | - Nika Tadić
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695-7612, USA
| | - Anthony Harris
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Theodora Sideri
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Wei Yee Chan
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Fairouz Ibrahim
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Mark Skehel
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Vahid Shahrezaei
- Department of Mathematics, Imperial College London, London, SW7 2BX, UK.
| | - Orlando Argüello-Miranda
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695-7612, USA.
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29
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Boulanger C, Haidara N, Yague-Sanz C, Larochelle M, Jacques PÉ, Hermand D, Bachand F. Repression of pervasive antisense transcription is the primary role of fission yeast RNA polymerase II CTD serine 2 phosphorylation. Nucleic Acids Res 2024; 52:7572-7589. [PMID: 38801067 PMCID: PMC11260464 DOI: 10.1093/nar/gkae436] [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: 03/23/2024] [Revised: 05/03/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
The RNA polymerase II carboxy-terminal domain (CTD) consists of conserved heptapeptide repeats that can be phosphorylated to influence distinct stages of the transcription cycle, including RNA processing. Although CTD-associated proteins have been identified, phospho-dependent CTD interactions have remained elusive. Proximity-dependent biotinylation (PDB) has recently emerged as an alternative approach to identify protein-protein associations in the native cellular environment. In this study, we present a PDB-based map of the fission yeast RNAPII CTD interactome in living cells and identify phospho-dependent CTD interactions by using a mutant in which Ser2 was replaced by alanine in every repeat of the fission yeast CTD. This approach revealed that CTD Ser2 phosphorylation is critical for the association between RNAPII and the histone methyltransferase Set2 during transcription elongation, but is not required for 3' end processing and transcription termination. Accordingly, loss of CTD Ser2 phosphorylation causes a global increase in antisense transcription, correlating with elevated histone acetylation in gene bodies. Our findings reveal that the fundamental role of CTD Ser2 phosphorylation is to establish a chromatin-based repressive state that prevents cryptic intragenic transcription initiation.
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Affiliation(s)
- Cédric Boulanger
- RNA Group, Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Nouhou Haidara
- RNA Group, Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Carlo Yague-Sanz
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur 5000, Belgium
| | - Marc Larochelle
- RNA Group, Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | | | - Damien Hermand
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur 5000, Belgium
- The Francis Crick Institute, 1 Midland Road London NW1 1AT, UK
| | - Francois Bachand
- RNA Group, Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
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30
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Heimdörfer D, Vorleuter A, Eschlböck A, Spathopoulou A, Suarez-Cubero M, Farhan H, Reiterer V, Spanjaard M, Schaaf CP, Huber LA, Kremser L, Sarg B, Edenhofer F, Geley S, de Araujo MEG, Huettenhofer A. Truncated variants of MAGEL2 are involved in the etiologies of the Schaaf-Yang and Prader-Willi syndromes. Am J Hum Genet 2024; 111:1383-1404. [PMID: 38908375 PMCID: PMC11267527 DOI: 10.1016/j.ajhg.2024.05.023] [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: 04/16/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/24/2024] Open
Abstract
The neurodevelopmental disorders Prader-Willi syndrome (PWS) and Schaaf-Yang syndrome (SYS) both arise from genomic alterations within human chromosome 15q11-q13. A deletion of the SNORD116 cluster, encoding small nucleolar RNAs, or frameshift mutations within MAGEL2 result in closely related phenotypes in individuals with PWS or SYS, respectively. By investigation of their subcellular localization, we observed that in contrast to a predominant cytoplasmic localization of wild-type (WT) MAGEL2, a truncated MAGEL2 mutant was evenly distributed between the cytoplasm and the nucleus. To elucidate regulatory pathways that may underlie both diseases, we identified protein interaction partners for WT or mutant MAGEL2, in particular the survival motor neuron protein (SMN), involved in spinal muscular atrophy, and the fragile-X-messenger ribonucleoprotein (FMRP), involved in autism spectrum disorders. The interactome of the non-coding RNA SNORD116 was also investigated by RNA-CoIP. We show that WT and truncated MAGEL2 were both involved in RNA metabolism, while regulation of transcription was mainly observed for WT MAGEL2. Hence, we investigated the influence of MAGEL2 mutations on the expression of genes from the PWS locus, including the SNORD116 cluster. Thereby, we provide evidence for MAGEL2 mutants decreasing the expression of SNORD116, SNORD115, and SNORD109A, as well as protein-coding genes MKRN3 and SNRPN, thus bridging the gap between PWS and SYS.
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Affiliation(s)
- David Heimdörfer
- Institute of Genomics and RNomics, Biocenter Innsbruck, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria.
| | - Alexander Vorleuter
- Institute of Genomics and RNomics, Biocenter Innsbruck, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Alexander Eschlböck
- Institute for Molecular Biology, Genomics, Stem Cell Biology & Regenerative Medicine Group, University of Innsbruck and CMBI, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Angeliki Spathopoulou
- Institute for Molecular Biology, Genomics, Stem Cell Biology & Regenerative Medicine Group, University of Innsbruck and CMBI, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Marta Suarez-Cubero
- Institute for Molecular Biology, Genomics, Stem Cell Biology & Regenerative Medicine Group, University of Innsbruck and CMBI, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Hesso Farhan
- Institute of Pathophysiology, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Veronika Reiterer
- Institute of Pathophysiology, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Melanie Spanjaard
- Institute of Human Genetics, Heidelberg University, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Christian P Schaaf
- Institute of Human Genetics, Heidelberg University, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Lukas A Huber
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innrain 80/82, Innsbruck 6020, Austria
| | - Leopold Kremser
- Institute of Medical Biochemistry, Protein Core Facility, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Bettina Sarg
- Institute of Medical Biochemistry, Protein Core Facility, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Frank Edenhofer
- Institute for Molecular Biology, Genomics, Stem Cell Biology & Regenerative Medicine Group, University of Innsbruck and CMBI, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Stephan Geley
- Institute of Pathophysiology, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Mariana E G de Araujo
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innrain 80/82, Innsbruck 6020, Austria
| | - Alexander Huettenhofer
- Institute of Genomics and RNomics, Biocenter Innsbruck, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria.
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31
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Carpanese V, Festa M, Prosdocimi E, Bachmann M, Sadeghi S, Bertelli S, Stein F, Velle A, Abdel-Salam MAL, Romualdi C, Pusch M, Checchetto V. Interactomic exploration of LRRC8A in volume-regulated anion channels. Cell Death Discov 2024; 10:299. [PMID: 38909013 PMCID: PMC11193767 DOI: 10.1038/s41420-024-02032-0] [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: 11/27/2023] [Revised: 05/08/2024] [Accepted: 05/16/2024] [Indexed: 06/24/2024] Open
Abstract
Ion channels are critical in enabling ion movement into and within cells and are important targets for pharmacological interventions in different human diseases. In addition to their ion transport abilities, ion channels interact with signalling and scaffolding proteins, which affects their function, cellular positioning, and links to intracellular signalling pathways. The study of "channelosomes" within cells has the potential to uncover their involvement in human diseases, although this field of research is still emerging. LRRC8A is the gene that encodes a crucial protein involved in the formation of volume-regulated anion channels (VRACs). Some studies suggest that LRRC8A could be a valuable prognostic tool in different types of cancer, serving as a biomarker for predicting patients' outcomes. LRRC8A expression levels might be linked to tumour progression, metastasis, and treatment response, although its implications in different cancer types can be varied. Here, publicly accessible databases of cancer patients were systematically analysed to determine if a correlation between VRAC channel expression and survival rate exists across distinct cancer types. Moreover, we re-evaluated the impact of LRRC8A on cellular proliferation and migration in colon cancer via HCT116 LRRC8A-KO cells, which is a current topic of debate in the literature. In addition, to investigate the role of LRRC8A in cellular signalling, we conducted biotin proximity-dependent identification (BioID) analysis, revealing a correlation between VRAC channels and cell-cell junctions, mechanisms that govern cellular calcium homeostasis, kinases, and GTPase signalling. Overall, this dataset improves our understanding of LRRC8A/VRAC and explores new research avenues while identifying promising therapeutic targets and promoting inventive methods for disease treatment.
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Affiliation(s)
| | - Margherita Festa
- DiBio, Unipd, via Ugo Bassi 58/B, 35131, Padova, Italy
- Institute of Biophysics, CNR, Via De Marini, 6 16149, Genova, Italy
| | | | - Magdalena Bachmann
- DiBio, Unipd, via Ugo Bassi 58/B, 35131, Padova, Italy
- Daba Farber Cancer Research Institute, Boston, MA, USA
| | - Soha Sadeghi
- DiBio, Unipd, via Ugo Bassi 58/B, 35131, Padova, Italy
| | - Sara Bertelli
- Institute of Biophysics, CNR, Via De Marini, 6, 16149, Genova, Italy
- Humboldt Universität Berlin, AG Zelluläre Biophysik, Dorotheenstr, 19-21 10099, Berlin, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Angelo Velle
- DiBio, Unipd, via Ugo Bassi 58/B, 35131, Padova, Italy
| | - Mostafa A L Abdel-Salam
- DiBio, Unipd, via Ugo Bassi 58/B, 35131, Padova, Italy
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Chiara Romualdi
- DiBio, Unipd, via Ugo Bassi 58/B, 35131, Padova, Italy
- Padua Center for Network Medicine, University of Padua, Via F. Marzolo 8, 315126, Padova, Italy
| | - Michael Pusch
- Institute of Biophysics, CNR, Via De Marini, 6, 16149, Genova, Italy
- RAISE Ecosystem, Genova, Italy
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32
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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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33
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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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34
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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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35
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Haddad R, Sadeh O, Ziv T, Erlich I, Haimovich-Caspi L, Shemesh A, van der Velden J, Kehat I. Localized translation and sarcomere maintenance requires ribosomal protein SA in mice. J Clin Invest 2024; 134:e174527. [PMID: 38743494 PMCID: PMC11213506 DOI: 10.1172/jci174527] [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: 08/11/2023] [Accepted: 05/07/2024] [Indexed: 05/16/2024] Open
Abstract
Cardiomyocyte sarcomeres contain localized ribosomes, but the factors responsible for their localization and the significance of localized translation are unknown. Using proximity labeling, we identified ribosomal protein SA (RPSA) as a Z-line protein. In cultured cardiomyocytes, the loss of RPSA led to impaired local protein translation and reduced sarcomere integrity. By employing CAS9-expressing mice, along with adeno-associated viruses expressing CRE recombinase and single-guide RNAs targeting Rpsa, we knocked out Rpsa in vivo and observed mislocalization of ribosomes and diminished local translation. These genetic mosaic mice with Rpsa knockout in a subset of cardiomyocytes developed dilated cardiomyopathy, featuring atrophy of RPSA-deficient cardiomyocytes, compensatory hypertrophy of unaffected cardiomyocytes, left ventricular dilation, and impaired contractile function. We demonstrated that RPSA C-terminal domain is sufficient for localization to the Z-lines and that if the microtubule network is disrupted RPSA loses its sarcomeric localization. These findings highlight RPSA as a ribosomal factor essential for ribosome localization to the Z-line, facilitating local translation and sarcomere maintenance.
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Affiliation(s)
- Rami Haddad
- Rappaport Family Institute for Research in the Medical Sciences and The Ruth and Bruce Rappaport Faculty of Medicine
| | - Omer Sadeh
- Rappaport Family Institute for Research in the Medical Sciences and The Ruth and Bruce Rappaport Faculty of Medicine
| | - Tamar Ziv
- Smoler Proteomics Center, Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, and
| | - Itai Erlich
- Rappaport Family Institute for Research in the Medical Sciences and The Ruth and Bruce Rappaport Faculty of Medicine
| | - Lilac Haimovich-Caspi
- Rappaport Family Institute for Research in the Medical Sciences and The Ruth and Bruce Rappaport Faculty of Medicine
| | - Ariel Shemesh
- Biomedical Core Facility at the Faculty of Medicine, Technion – Israel Institute of Technology, Haifa, Israel
| | - Jolanda van der Velden
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands
| | - Izhak Kehat
- Rappaport Family Institute for Research in the Medical Sciences and The Ruth and Bruce Rappaport Faculty of Medicine
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36
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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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37
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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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38
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Hanswillemenke A, Hofacker DT, Sorgenfrei M, Fruhner C, Franz-Wachtel M, Schwarzer D, Maček B, Stafforst T. Profiling the interactome of oligonucleotide drugs by proximity biotinylation. Nat Chem Biol 2024; 20:555-565. [PMID: 38233583 PMCID: PMC11062921 DOI: 10.1038/s41589-023-01530-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 12/17/2023] [Indexed: 01/19/2024]
Abstract
Drug-ID is a novel method applying proximity biotinylation to identify drug-protein interactions inside living cells. The covalent conjugation of a drug with a biotin ligase enables targeted biotinylation and identification of the drug-bound proteome. We established Drug-ID for two small-molecule drugs, JQ1 and SAHA, and applied it for RNaseH-recruiting antisense oligonucleotides (ASOs). Drug-ID profiles the drug-protein interactome de novo under native conditions, directly inside living cells and at pharmacologically effective drug concentrations. It requires minimal amounts of cell material and might even become applicable in vivo. We studied the dose-dependent aggregation of ASOs and the effect of different wing chemistries (locked nucleic acid, 2'-methoxyethyl and 2'-Fluoro) and ASO lengths on the interactome. Finally, we demonstrate the detection of stress-induced, intracellular interactome changes (actinomycin D treatment) with an in situ variant of the approach, which uses a recombinant biotin ligase and does not require genetic manipulation of the target cell.
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Affiliation(s)
| | | | - Michèle Sorgenfrei
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Carolin Fruhner
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Mirita Franz-Wachtel
- Interfaculty Institute of Cell Biology, University of Tübingen, Tübingen, Germany
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Boris Maček
- Interfaculty Institute of Cell Biology, University of Tübingen, Tübingen, Germany
| | - Thorsten Stafforst
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.
- Gene and RNA Therapy Center (GRTC), Faculty of Medicine, University of Tübingen, Tübingen, Germany.
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39
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Reina J, Vallmajo-Martin Q, Ning J, Michi AN, Yeung K, Wahl GM, Hunter T. LHPP expression in triple-negative breast cancer promotes tumor growth and metastasis by modulating the tumor microenvironment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590151. [PMID: 38712081 PMCID: PMC11071390 DOI: 10.1101/2024.04.19.590151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Triple-negative breast cancer (TNBC) is a highly aggressive and metastatic form of breast cancer that lacks an effective targeted therapy. To identify new therapeutic targets, we investigated the phosphohistidine phosphatase, LHPP, which has been implicated in the development of several types of cancer. However, the full significance of LHPP in cancer progression remains unclear due to our limited understanding of its molecular mechanism. We found that levels of the LHPP phosphohistidine phosphatase were significantly increased in human breast cancer patients compared to normal adjacent tissues, with the highest levels in the TNBC subtype. When LHPP was knocked out in the MDA-MB-231 human TNBC cell line, cell proliferation, wound healing capacity, and invasion were significantly reduced. However, LHPP knockout in TNBC cells did not affect the phosphohistidine protein levels. Interestingly, LHPP knockout in MDA-MB-231 cells delayed tumor growth and reduced metastasis when orthotopically transplanted into mouse mammary glands. To investigate LHPP's role in breast cancer progression, we used next-generation sequencing and proximity-labeling proteomics, and found that LHPP regulates gene expression in chemokine-mediated signaling and actin cytoskeleton organization. Depletion of LHPP reduced the presence of tumor-infiltrating macrophages in mouse xenografts. Our results uncover a new tumor promoter role for LHPP phosphohistidine phosphatase in TNBC and suggest that targeting LHPP phosphatase could be a potential therapeutic strategy for TNBC.
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Affiliation(s)
- Jeffrey Reina
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Jia Ning
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Aubrey N Michi
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Kay Yeung
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Geoffrey M Wahl
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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40
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Zhu Y, Akkaya KC, Ruta J, Yokoyama N, Wang C, Ruwolt M, Lima DB, Lehmann M, Liu F. Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topologies. Nat Commun 2024; 15:3290. [PMID: 38632225 PMCID: PMC11024108 DOI: 10.1038/s41467-024-47569-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: 03/04/2023] [Accepted: 04/05/2024] [Indexed: 04/19/2024] Open
Abstract
The functions of cellular organelles and sub-compartments depend on their protein content, which can be characterized by spatial proteomics approaches. However, many spatial proteomics methods are limited in their ability to resolve organellar sub-compartments, profile multiple sub-compartments in parallel, and/or characterize membrane-associated proteomes. Here, we develop a cross-link assisted spatial proteomics (CLASP) strategy that addresses these shortcomings. Using human mitochondria as a model system, we show that CLASP can elucidate spatial proteomes of all mitochondrial sub-compartments and provide topological insight into the mitochondrial membrane proteome. Biochemical and imaging-based follow-up studies confirm that CLASP allows discovering mitochondria-associated proteins and revising previous protein sub-compartment localization and membrane topology data. We also validate the CLASP concept in synaptic vesicles, demonstrating its applicability to different sub-cellular compartments. This study extends the scope of cross-linking mass spectrometry beyond protein structure and interaction analysis towards spatial proteomics, and establishes a method for concomitant profiling of sub-organelle and membrane proteomes.
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Affiliation(s)
- Ying Zhu
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Kerem Can Akkaya
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
- Department of Molecular Physiology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Julia Ruta
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Nanako Yokoyama
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Cong Wang
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Max Ruwolt
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Diogo Borges Lima
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Martin Lehmann
- Department of Molecular Physiology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Fan Liu
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany.
- Charité - Universitätsmedizin Berlin, Charitépl. 1, 10117, Berlin, Germany.
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41
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Shrestha HK, Lee D, Wu Z, Wang Z, Fu Y, Wang X, Serrano GE, Beach TG, Peng J. Profiling Protein-Protein Interactions in the Human Brain by Refined Cofractionation Mass Spectrometry. J Proteome Res 2024; 23:1221-1231. [PMID: 38507900 PMCID: PMC11065482 DOI: 10.1021/acs.jproteome.3c00685] [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: 03/22/2024]
Abstract
Proteins usually execute their biological functions through interactions with other proteins and by forming macromolecular complexes, but global profiling of protein complexes directly from human tissue samples has been limited. In this study, we utilized cofractionation mass spectrometry (CF-MS) to map protein complexes within the postmortem human brain with experimental replicates. First, we used concatenated anion and cation Ion Exchange Chromatography (IEX) to separate native protein complexes in 192 fractions and then proceeded with Data-Independent Acquisition (DIA) mass spectrometry to analyze the proteins in each fraction, quantifying a total of 4,804 proteins with 3,260 overlapping in both replicates. We improved the DIA's quantitative accuracy by implementing a constant amount of bovine serum albumin (BSA) in each fraction as an internal standard. Next, advanced computational pipelines, which integrate both a database-based complex analysis and an unbiased protein-protein interaction (PPI) search, were applied to identify protein complexes and construct protein-protein interaction networks in the human brain. Our study led to the identification of 486 protein complexes and 10054 binary protein-protein interactions, which represents the first global profiling of human brain PPIs using CF-MS. Overall, this study offers a resource and tool for a wide range of human brain research, including the identification of disease-specific protein complexes in the future.
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Affiliation(s)
- Him K. Shrestha
- Departments of Structural Biology and Developmental Neurobiology
| | - DongGeun Lee
- Departments of Structural Biology and Developmental Neurobiology
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology
| | - Zhen Wang
- Departments of Structural Biology and Developmental Neurobiology
| | - Yingxue Fu
- Departments of Structural Biology and Developmental Neurobiology
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, Tennessee, 38105, USA
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, Tennessee, 38105, USA
| | | | - Thomas G. Beach
- Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology
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42
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Schreiber KJ, Kadijk E, Youn JY. Exploring Options for Proximity-Dependent Biotinylation Experiments: Comparative Analysis of Labeling Enzymes and Affinity Purification Resins. J Proteome Res 2024; 23:1531-1543. [PMID: 38507741 PMCID: PMC11002925 DOI: 10.1021/acs.jproteome.3c00908] [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: 12/21/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
Proximity-dependent biotinylation (PDB) techniques provide information about the molecular neighborhood of a protein of interest, yielding insights into its function and localization. Here, we assessed how different labeling enzymes and streptavidin resins influence PDB results. We compared the high-confidence interactors of the DNA/RNA-binding protein transactive response DNA-binding protein 43 kDa (TDP-43) identified using either miniTurbo (biotin ligase) or APEX2 (peroxidase) enzymes. We also evaluated two commercial affinity resins for purification of biotinylated proteins: conventional streptavidin sepharose versus a new trypsin-resistant streptavidin conjugated to magnetic resin, which significantly reduces the level of contamination by streptavidin peptides following on-bead trypsin digestion. Downstream analyses involved liquid chromatography coupled to mass spectrometry in data-dependent acquisition mode, database searching, and statistical analysis of high-confidence interactors using SAINTexpress. The APEX2-TDP-43 experiment identified more interactors than miniTurbo-TDP-43, although miniTurbo provided greater overlap with previously documented TDP-43 interactors. Purifications on sepharose resin yielded more interactors than magnetic resin in small-scale experiments using a range of magnetic resin volumes. We suggest that resin-specific background protein binding profiles and different lysate-to-resin ratios cumulatively affect the distributions of prey protein abundance in experimental and control samples, which impact statistical confidence scores. Overall, we highlight key experimental variables to consider for the empirical optimization of PDB experiments.
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Affiliation(s)
- Karl J. Schreiber
- Program
in Molecular Medicine, The Hospital for
Sick Children, Toronto, ON M5G 0A4, Canada
| | - Eileigh Kadijk
- Program
in Molecular Medicine, The Hospital for
Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ji-Young Youn
- Program
in Molecular Medicine, The Hospital for
Sick Children, Toronto, ON M5G 0A4, Canada
- Department
of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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43
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Zhang ZW, Wang M, Sun LX, Elsheikha HM, Lei CL, Wang JL, Fu BQ, Luo JX, Zhu XQ, Li TT. Trx4, a novel thioredoxin protein, is important for Toxoplasma gondii fitness. Parasit Vectors 2024; 17:178. [PMID: 38576040 PMCID: PMC10996207 DOI: 10.1186/s13071-024-06259-9] [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: 02/26/2024] [Accepted: 03/21/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND To successfully replicate within the host cell, Toxoplasma gondii employs several mechanisms to overcome the host cell defenses and mitigate the harmful effects of the free radicals resulting from its own metabolic processes using effectors such as thioredoxin proteins. In this study, we characterize the location and functions of a newly identified thioredoxin in T. gondii, which was named Trx4. METHODS We characterized the functional role of Trx4 in T. gondii Type I RH and Type II Pru strains by gene knockout and studied its subcellular localization by endogenous protein HA tagging using CRISPR-Cas9 gene editing. The enzyme-catalyzed proximity labeling technique, the TurboID system, was employed to identify the proteins in proximity to Trx4. RESULTS Trx4 was identified as a dense granule protein of T. gondii predominantly expressed in the parasitophorous vacuole (PV) and was partially co-localized with GRA1 and GRA5. Functional analysis showed that deletion of trx4 markedly influenced the parasite lytic cycle, resulting in impaired host cell invasion capacity in both RH and Pru strains. Mutation of Trx domains in Trx4 in RH strain revealed that two Trx domains were important for the parasite invasion. By utilizing the TurboID system to biotinylate proteins in proximity to Trx4, we identified a substantial number of proteins, some of which are novel, and others are previously characterized, predominantly distributed in the dense granules. In addition, we uncovered three novel proteins co-localized with Trx4. Intriguingly, deletion of trx4 did not affect the localization of these three proteins. Finally, a virulence assay demonstrated that knockout of trx4 resulted in a significant attenuation of virulence and a significant reduction in brain cyst loads in mice. CONCLUSIONS Trx4 plays an important role in T. gondii invasion and virulence in Type I RH strain and Type II Pru strain. Combining the TurboID system with CRISPR-Cas9 technique revealed many PV-localized proximity proteins associated with Trx4. These findings suggest a versatile role of Trx4 in mediating the processes that occur in this distinctive intracellular membrane-bound vacuolar compartment.
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Affiliation(s)
- Zhi-Wei Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People's Republic of China
| | - Meng Wang
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People's Republic of China
| | - Li-Xiu Sun
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People's Republic of China
| | - Hany M Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Cheng-Lin Lei
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People's Republic of China
| | - Jin-Lei Wang
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People's Republic of China
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, Sichuan Province, 610213, People's Republic of China
| | - Bao-Quan Fu
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People's Republic of China
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, Sichuan Province, 610213, People's Republic of China
| | - Jian-Xun Luo
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People's Republic of China
| | - Xing-Quan Zhu
- Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi Province, 030801, People's Republic of China.
| | - Ting-Ting Li
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People's Republic of China.
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, Sichuan Province, 610213, People's Republic of China.
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44
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Peng Q, Weerapana E. Profiling nuclear cysteine ligandability and effects on nuclear localization using proximity labeling-coupled chemoproteomics. Cell Chem Biol 2024; 31:550-564.e9. [PMID: 38086369 PMCID: PMC10960692 DOI: 10.1016/j.chembiol.2023.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/11/2023] [Accepted: 11/17/2023] [Indexed: 03/24/2024]
Abstract
The nucleus controls cell growth and division through coordinated interactions between nuclear proteins and chromatin. Mutations that impair nuclear protein association with chromatin are implicated in numerous diseases. Covalent ligands are a promising strategy to pharmacologically target nuclear proteins, such as transcription factors, which lack ordered small-molecule binding pockets. To identify nuclear cysteines that are susceptible to covalent liganding, we couple proximity labeling (PL), using a histone H3.3-TurboID (His-TID) construct, with chemoproteomics. Using covalent scout fragments, KB02 and KB05, we identified ligandable cysteines on proteins involved in spindle assembly, DNA repair, and transcriptional regulation, such as Cys101 of histone acetyltransferase 1 (HAT1). Furthermore, we show that covalent fragments can affect the abundance, localization, and chromatin association of nuclear proteins. Notably, the Parkinson disease protein 7 (PARK7) showed increased nuclear localization and chromatin association upon KB02 modification at Cys106. Together, this platform provides insights into targeting nuclear cysteines with covalent ligands.
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Affiliation(s)
- Qianni Peng
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
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45
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Wilson ER, Nunes GDF, Shen S, Moore S, Gawron J, Maxwell J, Syed U, Hurley E, Lanka M, Qu J, Desaubry L, Wrabetz L, Poitelon Y, Feltri ML. Loss of prohibitin 2 in Schwann cells dysregulates key transcription factors controlling developmental myelination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585915. [PMID: 38562812 PMCID: PMC10983910 DOI: 10.1101/2024.03.20.585915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Schwann cells are critical for the proper development and function of the peripheral nervous system, where they form a mutually beneficial relationship with axons. Past studies have highlighted that a pair of proteins called the prohibitins play major roles in Schwann cell biology. Prohibitins are ubiquitously expressed and versatile proteins. We have previously shown that while prohibitins play a crucial role in Schwann cell mitochondria for long-term myelin maintenance and axon health, they may also be present at the Schwann cell-axon interface during development. Here, we expand on this work, showing that drug-mediated modulation of prohibitins in vitro disrupts myelination and confirming that Schwann cell-specific ablation of prohibitin 2 (Phb2) in vivo results in early and severe defects in peripheral nerve development. Using a proteomic approach in vitro, we identify a pool of candidate PHB2 interactors that change their interaction with PHB2 depending on the presence of axonal signals. Furthermore, we show in vivo that loss of Phb2 in mouse Schwann cells causes ineffective proliferation and dysregulation of transcription factors EGR2 (KROX20), POU3F1 (OCT6) and POU3F2 (BRN2) that are necessary for proper Schwann cell maturation. Schwann cell-specific deletion of Jun, a transcription factor associated with negative regulation of myelination, confers partial rescue of the development defect seen in mice lacking Schwann cell Phb2. This work develops our understanding of Schwann cell biology, revealing that Phb2 may directly or indirectly modulate the timely expression of transcription factors necessary for proper peripheral nervous system development, and proposing candidates that may play a role in PHB2-mediated integration of axon signals in the Schwann cell.
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Affiliation(s)
- Emma R Wilson
- Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
- Department of Clinical Neurosciences, Cambridge University, Cambridge, UK
| | - Gustavo Della-Flora Nunes
- Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Shichen Shen
- Department of Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Seth Moore
- Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Joseph Gawron
- Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Jessica Maxwell
- Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Umair Syed
- Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Edward Hurley
- Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Meghana Lanka
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, New York, USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Laurent Desaubry
- Center of Research in Biomedicine of Strasbourg, Regenerative Nanomedicine (UMR 1260), INSERM, University of Strasbourg, 67000 Strasbourg, France
| | - Lawrence Wrabetz
- Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
- Department of Neurology, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Yannick Poitelon
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, New York, USA
| | - M Laura Feltri
- Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
- Department of Neurology, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
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46
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Shi Y, Bashian EE, Hou Y, Wu P. Chemical immunology: Recent advances in tool development and applications. Cell Chem Biol 2024; 31:S2451-9456(24)00080-1. [PMID: 38508196 PMCID: PMC11393185 DOI: 10.1016/j.chembiol.2024.02.006] [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: 09/01/2023] [Revised: 02/01/2024] [Accepted: 02/22/2024] [Indexed: 03/22/2024]
Abstract
Immunology was one of the first biological fields to embrace chemical approaches. The development of new chemical approaches and techniques has provided immunologists with an impressive arsenal of tools to address challenges once considered insurmountable. This review focuses on advances at the interface of chemistry and immunobiology over the past two decades that have not only opened new avenues in basic immunological research, but also revolutionized drug development for the treatment of cancer and autoimmune diseases. These include chemical approaches to understand and manipulate antigen presentation and the T cell priming process, to facilitate immune cell trafficking and regulate immune cell functions, and therapeutic applications of chemical approaches to disease control and treatment.
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Affiliation(s)
- Yujie Shi
- Department of Molecular and Cellular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Eleanor E Bashian
- Department of Molecular and Cellular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yingqin Hou
- Department of Molecular and Cellular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Peng Wu
- Department of Molecular and Cellular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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47
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Lambert GS, Rice BL, Kaddis Maldonado RJ, Chang J, Parent LJ. Comparative analysis of retroviral Gag-host cell interactions: focus on the nuclear interactome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.575255. [PMID: 38293010 PMCID: PMC10827203 DOI: 10.1101/2024.01.18.575255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Retroviruses exploit a variety of host proteins to assemble and release virions from infected cells. To date, most studies that examined possible interacting partners of retroviral Gag proteins focused on host proteins that localize primarily to the cytoplasm or plasma membrane. Given the recent findings that several full-length Gag proteins localize to the nucleus, identifying the Gag-nuclear interactome has high potential for novel findings that reveal previously unknown host processes. In this study, we systematically compared nuclear factors identified in published HIV-1 proteomic studies which had used a variety of experimental approaches. In addition, to contribute to this body of knowledge, we report results from a mass spectrometry approach using affinity-tagged (His6) HIV-1 and RSV Gag proteins mixed with nuclear extracts. Taken together, the previous studies-as well as our own-identified potential binding partners of HIV-1 and RSV Gag involved in several nuclear processes, including transcription, splicing, RNA modification, and chromatin remodeling. Although a subset of host proteins interacted with both Gag proteins, there were also unique host proteins belonging to each interactome dataset. To validate one of the novel findings, we demonstrated the interaction of RSV Gag with a member of the Mediator complex, Med26, which is required for RNA polymerase II-mediated transcription. 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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48
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Holdgate GA, Bardelle C, Berry SK, Lanne A, Cuomo ME. Screening for molecular glues - Challenges and opportunities. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100136. [PMID: 38104659 DOI: 10.1016/j.slasd.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/03/2023] [Accepted: 12/14/2023] [Indexed: 12/19/2023]
Abstract
Molecular glues are small molecules, typically smaller than PROTACs, and usually with improved physicochemical properties that aim to stabilise the interaction between two proteins. Most often this approach is used to improve or induce an interaction between the target and an E3 ligase, but other interactions which stabilise interactions to increase activity or to inhibit binding to a natural effector have also been demonstrated. This review will describe the effects of induced proximity, discuss current methods used to identify molecular glues and introduce approaches that could be adapted for molecular glue screening.
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Affiliation(s)
| | - Catherine Bardelle
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Sophia K Berry
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Alice Lanne
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
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49
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Yang N, Ren J, Dai S, Wang K, Leung M, Lu Y, An Y, Burlingame A, Xu S, Wang Z, Yu W, Li N. The Quantitative Biotinylproteomics Studies Reveal a WInd-Related Kinase 1 (Raf-Like Kinase 36) Functioning as an Early Signaling Component in Wind-Induced Thigmomorphogenesis and Gravitropism. Mol Cell Proteomics 2024; 23:100738. [PMID: 38364992 PMCID: PMC10951710 DOI: 10.1016/j.mcpro.2024.100738] [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: 08/04/2023] [Revised: 01/31/2024] [Accepted: 02/08/2024] [Indexed: 02/18/2024] Open
Abstract
Wind is one of the most prevalent environmental forces entraining plants to develop various mechano-responses, collectively called thigmomorphogenesis. Largely unknown is how plants transduce these versatile wind force signals downstream to nuclear events and to the development of thigmomorphogenic phenotype or anemotropic response. To identify molecular components at the early steps of the wind force signaling, two mechanical signaling-related phosphoproteins, identified from our previous phosphoproteomic study of Arabidopsis touch response, mitogen-activated protein kinase kinase 1 (MKK1) and 2 (MKK2), were selected for performing in planta TurboID (ID)-based quantitative proximity-labeling (PL) proteomics. This quantitative biotinylproteomics was separately performed on MKK1-ID and MKK2-ID transgenic plants, respectively, using the genetically engineered TurboID biotin ligase expression transgenics as a universal control. This unique PTM proteomics successfully identified 11 and 71 MKK1 and MKK2 putative interactors, respectively. Biotin occupancy ratio (BOR) was found to be an alternative parameter to measure the extent of proximity and specificity between the proximal target proteins and the bait fusion protein. Bioinformatics analysis of these biotinylprotein data also found that TurboID biotin ligase favorably labels the loop region of target proteins. A WInd-Related Kinase 1 (WIRK1), previously known as rapidly accelerated fibrosarcoma (Raf)-like kinase 36 (RAF36), was found to be a putative common interactor for both MKK1 and MKK2 and preferentially interacts with MKK2. Further molecular biology studies of the Arabidopsis RAF36 kinase found that it plays a role in wind regulation of the touch-responsive TCH3 and CML38 gene expression and the phosphorylation of a touch-regulated PATL3 phosphoprotein. Measurement of leaf morphology and shoot gravitropic response of wirk1 (raf36) mutant revealed that the WIRK1 gene is involved in both wind-triggered rosette thigmomorphogenesis and gravitropism of Arabidopsis stems, suggesting that the WIRK1 (RAF36) protein probably functioning upstream of both MKK1 and MKK2 and that it may serve as the crosstalk point among multiple mechano-signal transduction pathways mediating both wind mechano-response and gravitropism.
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Affiliation(s)
- Nan Yang
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Jia Ren
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Shuaijian Dai
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Kai Wang
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Manhin Leung
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Yinglin Lu
- Institute of Nanfan and Seed Industry, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Yuxing An
- Institute of Nanfan and Seed Industry, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Al Burlingame
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Shouling Xu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA
| | - Zhiyong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA
| | - Weichuan Yu
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China.
| | - Ning Li
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China; Shenzhen Research Institute, The Hong Kong University of Science and Technology, Shenzhen, Guangdong, China.
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50
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Wang Y, Qin W. Revealing protein trafficking by proximity labeling-based proteomics. Bioorg Chem 2024; 143:107041. [PMID: 38134520 DOI: 10.1016/j.bioorg.2023.107041] [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: 10/26/2023] [Revised: 11/22/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023]
Abstract
Protein trafficking is a fundamental process with profound implications for both intracellular and intercellular functions. Proximity labeling (PL) technology has emerged as a powerful tool for capturing precise snapshots of subcellular proteomes by directing promiscuous enzymes to specific cellular locations. These enzymes generate reactive species that tag endogenous proteins, enabling their identification through mass spectrometry-based proteomics. In this comprehensive review, we delve into recent advancements in PL-based methodologies, placing particular emphasis on the label-and-fractionation approach and TransitID, for mapping proteome trafficking. These methodologies not only facilitate the exploration of dynamic intracellular protein trafficking between organelles but also illuminate the intricate web of intercellular and inter-organ protein communications.
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Affiliation(s)
- Yankun Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Wei Qin
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China; MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China; The State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, China.
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