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Rattray DG, Foster LJ. Dynamics of protein complex components. Curr Opin Chem Biol 2019; 48:81-85. [DOI: 10.1016/j.cbpa.2018.11.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 08/31/2018] [Accepted: 11/01/2018] [Indexed: 11/28/2022]
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Titeca K, Lemmens I, Tavernier J, Eyckerman S. Discovering cellular protein-protein interactions: Technological strategies and opportunities. MASS SPECTROMETRY REVIEWS 2019; 38:79-111. [PMID: 29957823 DOI: 10.1002/mas.21574] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 01/03/2018] [Accepted: 06/04/2018] [Indexed: 05/09/2023]
Abstract
The analysis of protein interaction networks is one of the key challenges in the study of biology. It connects genotypes to phenotypes, and disruption often leads to diseases. Hence, many technologies have been developed to study protein-protein interactions (PPIs) in a cellular context. The expansion of the PPI technology toolbox however complicates the selection of optimal approaches for diverse biological questions. This review gives an overview of the binary and co-complex technologies, with the former evaluating the interaction of two co-expressed genetically tagged proteins, and the latter only needing the expression of a single tagged protein or no tagged proteins at all. Mass spectrometry is crucial for some binary and all co-complex technologies. After the detailed description of the different technologies, the review compares their unique specifications, advantages, disadvantages, and applicability, while highlighting opportunities for further advancements.
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Affiliation(s)
- Kevin Titeca
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Irma Lemmens
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Jan Tavernier
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
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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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Argentini A, Staes A, Grüning B, Mehta S, Easterly C, Griffin TJ, Jagtap P, Impens F, Martens L. Update on the moFF Algorithm for Label-Free Quantitative Proteomics. J Proteome Res 2018; 18:728-731. [DOI: 10.1021/acs.jproteome.8b00708] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrea Argentini
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - An Staes
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Björn Grüning
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Baden-Württemberg 79110, Germany
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis 55455, United States
| | - Caleb Easterly
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis 55455, United States
| | - Timothy J. Griffin
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis 55455, United States
| | - Pratik Jagtap
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis 55455, United States
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
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Sala S, Catillon M, Hadzic E, Schaffner-Reckinger E, Van Troys M, Ampe C. The PET and LIM1-2 domains of testin contribute to intramolecular and homodimeric interactions. PLoS One 2017; 12:e0177879. [PMID: 28542564 PMCID: PMC5436826 DOI: 10.1371/journal.pone.0177879] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 05/04/2017] [Indexed: 12/18/2022] Open
Abstract
The focal adhesion protein testin is a modular scaffold and tumour suppressor that consists of an N-terminal cysteine rich (CR) domain, a PET domain of unknown function and three C-terminal LIM domains. Testin has been proposed to have an open and a closed conformation based on the observation that its N-terminal half and C-terminal half directly interact. Here we extend the testin conformational model by demonstrating that testin can also form an antiparallel homodimer. In support of this extended model we determined that the testin region (amino acids 52–233) harbouring the PET domain interacts with the C-terminal LIM1-2 domains in vitro and in cells, and assign a critical role to tyrosine 288 in this interaction.
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Affiliation(s)
- Stefano Sala
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Marie Catillon
- Cytoskeleton and Cell Plasticity Lab, Life Sciences Research Unit - FSTC, University of Luxembourg, Luxembourg, Luxembourg
| | - Ermin Hadzic
- Cytoskeleton and Cell Plasticity Lab, Life Sciences Research Unit - FSTC, University of Luxembourg, Luxembourg, Luxembourg
| | - Elisabeth Schaffner-Reckinger
- Cytoskeleton and Cell Plasticity Lab, Life Sciences Research Unit - FSTC, University of Luxembourg, Luxembourg, Luxembourg
| | | | - Christophe Ampe
- Department of Biochemistry, Ghent University, Ghent, Belgium
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Sala S, Van Troys M, Medves S, Catillon M, Timmerman E, Staes A, Schaffner-Reckinger E, Gevaert K, Ampe C. Expanding the Interactome of TES by Exploiting TES Modules with Different Subcellular Localizations. J Proteome Res 2017; 16:2054-2071. [DOI: 10.1021/acs.jproteome.7b00034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stefano Sala
- Department of Biochemistry, Ghent University, 9000 Gent, Belgium
| | | | - Sandrine Medves
- Cytoskeleton
and Cell Plasticity Lab, Life Sciences Research Unit − FSTC, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
- Laboratory of Experimental Cancer Research, LIH, 1445 Strassen, Luxembourg
| | - Marie Catillon
- Cytoskeleton
and Cell Plasticity Lab, Life Sciences Research Unit − FSTC, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Evy Timmerman
- Department of Biochemistry, Ghent University, 9000 Gent, Belgium
- VIB Medical Biotechnology Center, 9000 Gent, Belgium
| | - An Staes
- Department of Biochemistry, Ghent University, 9000 Gent, Belgium
- VIB Medical Biotechnology Center, 9000 Gent, Belgium
| | - Elisabeth Schaffner-Reckinger
- Cytoskeleton
and Cell Plasticity Lab, Life Sciences Research Unit − FSTC, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, 9000 Gent, Belgium
- VIB Medical Biotechnology Center, 9000 Gent, Belgium
| | - Christophe Ampe
- Department of Biochemistry, Ghent University, 9000 Gent, Belgium
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Vandemoortele G, De Sutter D, Eyckerman S. Robust Generation of Knock-in Cell Lines Using CRISPR-Cas9 and rAAV-assisted Repair Template Delivery. Bio Protoc 2017; 7:e2211. [PMID: 34541219 DOI: 10.21769/bioprotoc.2211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/27/2016] [Accepted: 03/14/2017] [Indexed: 11/02/2022] Open
Abstract
The programmable Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated nuclease 9 (Cas9) technology revolutionized genome editing by providing an efficient way to cut the genome at a desired location (Ledford, 2015). In mammalian cells, DNA lesions trigger the error-prone non-homologous end joining (NHEJ) DNA repair mechanism. However, in presence of a DNA repair template, Homology-Directed Repair (HDR) can occur leading to precise repair of the lesion site. This last process can be exploited to enable precise knock-in changes by introducing the desired genomic alteration on the repair template. In this protocol, we describe the delivery of long repair templates (> 200 nucleotides) using recombinant Adeno Associated Virus (rAAV) for CRISPR-Cas9-based knock-in of a C-terminal tag sequence in a human cell line.
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Affiliation(s)
- Giel Vandemoortele
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Delphine De Sutter
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
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