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Sandeep P, Sharma P, Luhach K, Dhiman N, Kharkwal H, Sharma B. Neuron navigators: A novel frontier with physiological and pathological implications. Mol Cell Neurosci 2023; 127:103905. [PMID: 37972804 DOI: 10.1016/j.mcn.2023.103905] [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: 09/12/2023] [Revised: 10/31/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023] Open
Abstract
Neuron navigators are microtubule plus-end tracking proteins containing basic and serine rich regions which are encoded by neuron navigator genes (NAVs). Neuron navigator proteins are essential for neurite outgrowth, neuronal migration, and overall neurodevelopment along with some other functions as well. The navigator proteins are substantially expressed in the developing brain and have been reported to be differentially expressed in various tissues at different ages. Over the years, the research has found neuron navigators to be implicated in a spectrum of pathological conditions such as developmental anomalies, neurodegenerative disorders, neuropathic pain, anxiety, cancers, and certain inflammatory conditions. The existing knowledge about neuron navigators remains sparse owing to their differential functions, undiscovered modulators, and unknown molecular mechanisms. Investigating the possible role of neuron navigators in various physiological processes and pathological conditions pose as a novel field that requires extensive research and might provide novel mechanistic insights and understanding of these aspects.
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Affiliation(s)
- Parth Sandeep
- Department of Pharmacology, Amity Institute of Pharmacy, Amity University, Uttar Pradesh, Noida, India
| | - Poonam Sharma
- Department of Pharmacology, Amity Institute of Pharmacy, Amity University, Uttar Pradesh, Noida, India
| | - Kanishk Luhach
- Department of Pharmacology, Amity Institute of Pharmacy, Amity University, Uttar Pradesh, Noida, India
| | - Neerupma Dhiman
- Amity Institute of Pharmacy, Amity University, Uttar Pradesh, Noida, India
| | - Harsha Kharkwal
- Amity Natural and Herbal Product Research, Amity Institute of Phytochemistry and Phytomedicine, Amity University, Uttar Pradesh, India
| | - Bhupesh Sharma
- Department of Pharmacology, Amity Institute of Pharmacy, Amity University, Uttar Pradesh, Noida, India.
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2
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Bogaert A, Fijalkowska D, Staes A, Van de Steene T, Vuylsteke M, Stadler C, Eyckerman S, Spirohn K, Hao T, Calderwood MA, Gevaert K. N-terminal proteoforms may engage in different protein complexes. Life Sci Alliance 2023; 6:e202301972. [PMID: 37316325 PMCID: PMC10267514 DOI: 10.26508/lsa.202301972] [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: 02/06/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023] Open
Abstract
Alternative translation initiation and alternative splicing may give rise to N-terminal proteoforms, proteins that differ at their N-terminus compared with their canonical counterparts. Such proteoforms can have altered localizations, stabilities, and functions. Although proteoforms generated from splice variants can be engaged in different protein complexes, it remained to be studied to what extent this applies to N-terminal proteoforms. To address this, we mapped the interactomes of several pairs of N-terminal proteoforms and their canonical counterparts. First, we generated a catalogue of N-terminal proteoforms found in the HEK293T cellular cytosol from which 22 pairs were selected for interactome profiling. In addition, we provide evidence for the expression of several N-terminal proteoforms, identified in our catalogue, across different human tissues, as well as tissue-specific expression, highlighting their biological relevance. Protein-protein interaction profiling revealed that the overlap of the interactomes for both proteoforms is generally high, showing their functional relation. We also showed that N-terminal proteoforms can be engaged in new interactions and/or lose several interactions compared with their canonical counterparts, thus further expanding the functional diversity of proteomes.
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Affiliation(s)
- Annelies Bogaert
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Daria Fijalkowska
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - An Staes
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Tessa Van de Steene
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Charlotte Stadler
- Department of Protein Science, KTH Royal Institute of Technology and Science for Life Laboratories, Stockholm, Sweden
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kerstin Spirohn
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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3
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Moschonas GD, De Meyer M, De Sutter D, Timmerman E, Van Damme P, Eyckerman S. Virotrap: Trapping Protein Complexes in Virus-Like Particles. Methods Mol Biol 2023; 2718:53-71. [PMID: 37665454 DOI: 10.1007/978-1-0716-3457-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The discovery of protein-protein interactions can provide crucial information on protein function by linking proteins into known pathways or complexes within the cell. Mass spectrometry (MS)-based methods, such as affinity purification (AP)-MS and proximity-dependent biotin identification (BioID), allowed for a vast increase in the number of reported protein complexes. As a more recent addition to the arsenal of MS-based methods, Virotrap represents a unique technology that benefits from the specific properties of the human immunodeficiency virus-1 (HIV-1) Gag polyprotein. More specifically, Virotrap captures protein complexes in virus-like particles budded from human embryonic kidney (HEK293T) cells, bypassing the need for cell lysis and thus supporting identification of their content using MS. Being intrinsically different to its two main predecessors, affinity purification MS (AP-MS) and biotin-dependent identification (BioID), Virotrap was shown to complement data obtained with the existing MS-based toolkit. The proven complementarity of these MS-based strategies underlines the importance of using different techniques to enable comprehensive mapping of protein-protein interactions (PPIs). In this chapter, we provide a detailed overview of the Virotrap protocol to screen for PPIs using a bait protein of interest.
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Affiliation(s)
- George D Moschonas
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Margaux De Meyer
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- iRIP Unit, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Delphine De Sutter
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Evy Timmerman
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Petra Van Damme
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- iRIP Unit, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
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4
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Studying the ubiquitin code through biotin-based labelling methods. Semin Cell Dev Biol 2022; 132:109-119. [PMID: 35181195 DOI: 10.1016/j.semcdb.2022.02.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 12/15/2022]
Abstract
Post-translational modifications of cellular substrates by members of the ubiquitin (Ub) and ubiquitin-like (UbL) family are crucial for regulating protein homeostasis in organisms. The term "ubiquitin code" encapsulates how this diverse family of modifications, via adding single UbLs or different types of UbL chains, leads to specific fates for substrates. Cancer, neurodegeneration and other conditions are sometimes linked to underlying errors in this code. Studying these modifications in cells is particularly challenging since they are usually transient, scarce, and compartment-specific. Advances in the use of biotin-based methods to label modified proteins, as well as their proximally-located interactors, facilitate isolation and identification of substrates, modification sites, and the enzymes responsible for writing and erasing these modifications, as well as factors recruited as a consequence of the substrate being modified. In this review, we discuss site-specific and proximity biotinylation approaches being currently applied for studying modifications by UbLs, highlighting the pros and cons, with mention of complementary methods when possible. Future improvements may come from bioengineering and chemical biology but even now, biotin-based technology is uncovering new substrates and regulators, expanding potential therapeutic targets to manipulate the Ub code.
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Delhaye L, De Bruycker E, Volders PJ, Fijalkowska D, De Sutter D, Degroeve S, Martens L, Mestdagh P, Eyckerman S. Orthogonal proteomics methods to unravel the HOTAIR interactome. Sci Rep 2022; 12:1513. [PMID: 35087108 PMCID: PMC8795419 DOI: 10.1038/s41598-022-05405-6] [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: 10/22/2021] [Accepted: 01/11/2022] [Indexed: 11/17/2022] Open
Abstract
Accumulating evidence highlights the role of long non-coding RNAs (lncRNAs) in cellular homeostasis, and their dysregulation in disease settings. Most lncRNAs function by interacting with proteins or protein complexes. While several orthogonal methods have been developed to identify these proteins, each method has its inherent strengths and limitations. Here, we combine two RNA-centric methods ChIRP-MS and RNA-BioID to obtain a comprehensive list of proteins that interact with the well-known lncRNA HOTAIR. Overexpression of HOTAIR has been associated with a metastasis-promoting phenotype in various cancers. Although HOTAIR is known to bind with PRC2 and LSD1 protein complexes, only very limited unbiased comprehensive approaches to map its interactome have been performed. Both ChIRP-MS and RNA-BioID data sets show an association of HOTAIR with mitoribosomes, suggesting that HOTAIR has functions independent of its (post-)transcriptional mode-of-action.
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Affiliation(s)
- Louis Delhaye
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
- OncoRNALab, Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Edith De Bruycker
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Pieter-Jan Volders
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
- OncoRNALab, Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | | | - Delphine De Sutter
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
| | - Sven Degroeve
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
| | - Lennart Martens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
| | - Pieter Mestdagh
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- OncoRNALab, Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium.
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6
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De Meyer M, Fijalkowski I, Jonckheere V, De Sutter D, Eyckerman S, Van Damme P. Capturing Salmonella SspH2 Host Targets in Virus-Like Particles. Front Med (Lausanne) 2021; 8:725072. [PMID: 34568381 PMCID: PMC8455821 DOI: 10.3389/fmed.2021.725072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/19/2021] [Indexed: 01/09/2023] Open
Abstract
In the context of host-pathogen interactions, gram-negative bacterial virulence factors, such as effectors, may be transferred from bacterial to eukaryotic host cytoplasm by multicomponent Type III protein secretion systems (T3SSs). Central to Salmonella enterica serovar Typhimurium (S. Typhimurium) pathogenesis is the secretion of over 40 effectors by two T3SSs encoded within pathogenicity islands SPI-1 and SPI-2. These effectors manipulate miscellaneous host cellular processes, such as cytoskeleton organization and immune signaling pathways, thereby permitting host colonization and bacterial dissemination. Recent research on effector biology provided mechanistic insights for some effectors. However, for many effectors, clearly defined roles and host target repertoires-further clarifying effector interconnectivity and virulence networks-are yet to be uncovered. Here we demonstrate the utility of the recently described viral-like particle trapping technology Virotrap as an effective approach to catalog S. Typhimurium effector-host protein complexes (EH-PCs). Mass spectrometry-based Virotrap analysis of the novel E3 ubiquitin ligase SspH2 previously shown to be implicated in modulating actin dynamics and immune signaling, exposed known host interactors PFN1 and-2 besides several putative novel, interconnected host targets. Network analysis revealed an actin (-binding) cluster among the significantly enriched hits for SspH2, consistent with the known localization of the S-palmitoylated effector with actin cytoskeleton components in the host. We show that Virotrap complements the current state-of-the-art toolkit to study protein complexes and represents a valuable means to screen for effector host targets in a high-throughput manner, thereby bridging the knowledge gap between effector-host interplay and pathogenesis.
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Affiliation(s)
- Margaux De Meyer
- iRIP Unit, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Vlaams Instituut voor Biotechnologie Center for Medical Biotechnology, Vlaams Instituut voor Biotechnologie, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Igor Fijalkowski
- iRIP Unit, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Veronique Jonckheere
- iRIP Unit, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Delphine De Sutter
- Vlaams Instituut voor Biotechnologie Center for Medical Biotechnology, Vlaams Instituut voor Biotechnologie, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- Vlaams Instituut voor Biotechnologie Center for Medical Biotechnology, Vlaams Instituut voor Biotechnologie, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Petra Van Damme
- iRIP Unit, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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7
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Tullett KM, Tan PS, Park HY, Schittenhelm RB, Michael N, Li R, Policheni AN, Gruber E, Huang C, Fulcher AJ, Danne JC, Czabotar PE, Wakim LM, Mintern JD, Ramm G, Radford KJ, Caminschi I, O'Keeffe M, Villadangos JA, Wright MD, Blewitt ME, Heath WR, Shortman K, Purcell AW, Nicola NA, Zhang JG, Lahoud MH. RNF41 regulates the damage recognition receptor Clec9A and antigen cross-presentation in mouse dendritic cells. eLife 2020; 9:63452. [PMID: 33264090 PMCID: PMC7710356 DOI: 10.7554/elife.63452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/18/2020] [Indexed: 11/22/2022] Open
Abstract
The dendritic cell receptor Clec9A facilitates processing of dead cell-derived antigens for cross-presentation and the induction of effective CD8+ T cell immune responses. Here, we show that this process is regulated by E3 ubiquitin ligase RNF41 and define a new ubiquitin-mediated mechanism for regulation of Clec9A, reflecting the unique properties of Clec9A as a receptor specialized for delivery of antigens for cross-presentation. We reveal RNF41 is a negative regulator of Clec9A and the cross-presentation of dead cell-derived antigens by mouse dendritic cells. Intriguingly, RNF41 regulates the downstream fate of Clec9A by directly binding and ubiquitinating the extracellular domains of Clec9A. At steady-state, RNF41 ubiquitination of Clec9A facilitates interactions with ER-associated proteins and degradation machinery to control Clec9A levels. However, Clec9A interactions are altered following dead cell uptake to favor antigen presentation. These findings provide important insights into antigen cross-presentation and have implications for development of approaches to modulate immune responses.
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Affiliation(s)
- Kirsteen M Tullett
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Peck Szee Tan
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Hae-Young Park
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Facility, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Nicole Michael
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Rong Li
- Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
| | - Antonia N Policheni
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Emily Gruber
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Cheng Huang
- Monash Proteomics and Metabolomics Facility, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Alex J Fulcher
- Monash Micro Imaging Facility, Monash University, Clayton, Australia
| | - Jillian C Danne
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Australia
| | - Peter E Czabotar
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Linda M Wakim
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Justine D Mintern
- Department of Biochemistry and Molecular Biology at the Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Australia
| | - Georg Ramm
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.,Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Australia
| | - Kristen J Radford
- Mater Research Institute - University of Queensland, Translational Research Institute, Brisbane, Australia
| | - Irina Caminschi
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.,Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Meredith O'Keeffe
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Jose A Villadangos
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia.,Department of Biochemistry and Molecular Biology at the Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Australia
| | - Mark D Wright
- Department of Immunology, Monash University, Melbourne, Australia
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - William R Heath
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Ken Shortman
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Anthony W Purcell
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Nicos A Nicola
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Jian-Guo Zhang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Mireille H Lahoud
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
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8
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Meyer MD, Ryck JD, Goormachtig S, Van Damme P. Keeping in Touch with Type-III Secretion System Effectors: Mass Spectrometry-Based Proteomics to Study Effector-Host Protein-Protein Interactions. Int J Mol Sci 2020; 21:E6891. [PMID: 32961832 PMCID: PMC7555288 DOI: 10.3390/ijms21186891] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 01/03/2023] Open
Abstract
Manipulation of host cellular processes by translocated bacterial effectors is key to the success of bacterial pathogens and some symbionts. Therefore, a comprehensive understanding of effectors is of critical importance to understand infection biology. It has become increasingly clear that the identification of host protein targets contributes invaluable knowledge to the characterization of effector function during pathogenesis. Recent advances in mapping protein-protein interaction networks by means of mass spectrometry-based interactomics have enabled the identification of host targets at large-scale. In this review, we highlight mass spectrometry-driven proteomics strategies and recent advances to elucidate type-III secretion system effector-host protein-protein interactions. Furthermore, we highlight approaches for defining spatial and temporal effector-host interactions, and discuss possible avenues for studying natively delivered effectors in the context of infection. Overall, the knowledge gained when unravelling effector complexation with host factors will provide novel opportunities to control infectious disease outcomes.
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Affiliation(s)
- Margaux De Meyer
- Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium; (M.D.M.); (J.D.R.)
- VIB Center for Medical Biotechnology, Technologiepark 75, 9052 Zwijnaarde, Belgium
| | - Joren De Ryck
- Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium; (M.D.M.); (J.D.R.)
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Zwijnaarde, Belgium;
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Zwijnaarde, Belgium
| | - Sofie Goormachtig
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Zwijnaarde, Belgium;
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Zwijnaarde, Belgium
| | - Petra Van Damme
- Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium; (M.D.M.); (J.D.R.)
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9
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Pick a Tag and Explore the Functions of Your Pet Protein. Trends Biotechnol 2019; 37:1078-1090. [PMID: 31036349 DOI: 10.1016/j.tibtech.2019.03.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 01/01/2023]
Abstract
Protein tags have been essential for advancing our knowledge of the function of proteins, their localization, and the mapping of their interaction partners. Expressing epitope-tagged proteins has become a standard practice in every life science laboratory and, thus, continues to enable new studies. In recent years, several new tagging moieties have entered the limelight, many of them bringing new functionalities, such as targeted protein degradation, accurate quantification, and proximity labeling. Other novel tags aim at tackling research questions in challenging niches. In this review, we elaborate on recently introduced tags and the opportunities they provide for future research endeavors. In addition, we highlight how the genome-engineering revolution may boost the field of protein tags.
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10
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Early girl is a novel component of the Fat signaling pathway. PLoS Genet 2019; 15:e1007955. [PMID: 30699121 PMCID: PMC6370246 DOI: 10.1371/journal.pgen.1007955] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 02/11/2019] [Accepted: 01/11/2019] [Indexed: 01/05/2023] Open
Abstract
The Drosophila protocadherins Dachsous and Fat regulate growth and tissue polarity by modulating the levels, membrane localization and polarity of the atypical myosin Dachs. Localization to the apical junctional membrane is critical for Dachs function, and the adapter protein Vamana/Dlish and palmitoyl transferase Approximated are required for Dachs membrane localization. However, how Dachs levels are regulated is poorly understood. Here we identify the early girl gene as playing an essential role in Fat signaling by limiting the levels of Dachs protein. early girl mutants display overgrowth of the wings and reduced cross vein spacing, hallmark features of mutations affecting Fat signaling. Genetic experiments reveal that it functions in parallel with Fat to regulate Dachs. early girl encodes an E3 ubiquitin ligase, physically interacts with Dachs, and regulates its protein stability. Concomitant loss of early girl and approximated results in accumulation of Dachs and Vamana in cytoplasmic punctae, suggesting that it also regulates their trafficking to the apical membrane. Our findings establish a crucial role for early girl in Fat signaling, involving regulation of Dachs and Vamana, two key downstream effectors of this pathway. During development, organs grow to achieve a consistent final size. The evolutionarily conserved Hippo signaling network plays a central role in organ size control, and when dysregulated can be associated with cancer and other diseases. Fat signaling is one of several upstream pathways that impinge on Hippo signaling to regulate organ growth. We describe here identification of the Drosophila early girl gene as a new component of the Fat signaling pathway. We show that Early girl controls Fat signaling by regulating the levels of the Dachs protein. However Early girl differs from other Fat signaling regulators in that it doesn’t influence planar cell polarity or control the polarity of Dachs localization. early girl encodes a conserved protein that is predicted to influence protein stability, and it can physically associate with Dachs. We also discovered that Early girl acts together with another protein, called Approximated, to regulate the sub-cellular localization of Dachs and a Dachs-interacting protein called Vamana. Altogether, our observations establish Early girl as an essential component of Fat signaling that acts to regulate the levels and localization of Dachs and Vamana.
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Van Quickelberghe E, De Sutter D, van Loo G, Eyckerman S, Gevaert K. A protein-protein interaction map of the TNF-induced NF-κB signal transduction pathway. Sci Data 2018; 5:180289. [PMID: 30561431 PMCID: PMC6298254 DOI: 10.1038/sdata.2018.289] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 10/26/2018] [Indexed: 12/12/2022] Open
Abstract
Tumor Necrosis Factor (TNF) has a crucial role in inflammation, cell proliferation and cell death. Dysregulation of TNF receptor 1 (TNFR1)-induced Nuclear Factor-kappa B (NF-κB) signaling leads to chronic inflammation and is associated with several human inflammatory pathologies. Hence, TNF neutralization suppresses inflammation and attenuates inflammatory pathology. However, despite its beneficial effects, anti-TNF therapy suffers from efficacy issues and severe immune side effects. There is thus an urging need to identify novel targets for pharmaceutical intervention in the NF-κB signaling pathway. Here, we present a protein-protein interaction dataset of the TNFR1-induced signaling pathway. For this, we used Virotrap, a novel method for studying protein complexes without disrupting the cellular integrity, on 12 central proteins controlling NF-κB and cell death signaling, both under resting conditions as well as upon TNF stimulation. Our dataset reveals dynamic interactions in TNFR1-induced NF-κB signaling and identifies both known as well as novel interactors that may help to further unravel the molecular mechanisms steering TNF-induced inflammatory signaling and pathology.
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Affiliation(s)
- Emmy Van Quickelberghe
- VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium
| | - Delphine De Sutter
- VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium
| | - Geert van Loo
- VIB Center for Inflammation Research, B-9052 Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium
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