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Emslander Q, Krey K, Hamad S, Maidl S, Oubraham L, Hesse J, Henrici A, Austen K, Mergner J, Grass V, Pichlmair A. MDM2 Influences ACE2 Stability and SARS-CoV-2 Uptake. Viruses 2023; 15:1763. [PMID: 37632105 PMCID: PMC10459000 DOI: 10.3390/v15081763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/20/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Angiotensin-converting enzyme 2 (ACE2) is the central entry receptor for SARS-CoV-2. However, surprisingly little is known about the effects of host regulators on ACE2 localization, expression, and the associated influence on SARS-CoV-2 infection. Here we identify that ACE2 expression levels are regulated by the E3 ligase MDM2 and that MDM2 levels indirectly influence infection with SARS-CoV-2. Genetic depletion of MDM2 elevated ACE2 expression levels, which strongly promoted infection with all SARS-CoV-2 isolates tested. SARS-CoV-2 spike-pseudotyped viruses and the uptake of non-replication-competent virus-like particles showed that MDM2 affects the viral uptake process. MDM2 ubiquitinates Lysine 788 of ACE2 to induce proteasomal degradation, and degradation of this residue led to higher ACE2 expression levels and superior virus particle uptake. Our study illustrates that cellular regulators of ACE2 stability, such as MDM2, play an important role in defining the infection capabilities of SARS-CoV-2.
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Affiliation(s)
- Quirin Emslander
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Karsten Krey
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Sabri Hamad
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Susanne Maidl
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Lila Oubraham
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Joshua Hesse
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Alexander Henrici
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Katharina Austen
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Julia Mergner
- BayBioMS@MRI—Bavarian Center for Biomolecular Mass Spectrometry at Klinikum Rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Vincent Grass
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Andreas Pichlmair
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
- German Centre for Infection Research (DZIF), Partner site Munich, 81675 Munich, Germany
- Center of Immunology of Viral Infection (CiViA), Aarhus University, 8000 Aarhus, Denmark
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Falgenhauer E, von Schönberg S, Meng C, Mückl A, Vogele K, Emslander Q, Ludwig C, Simmel FC. Evaluation of an E. coli Cell Extract Prepared by Lysozyme-Assisted Sonication via Gene Expression, Phage Assembly and Proteomics. Chembiochem 2021; 22:2805-2813. [PMID: 34240805 PMCID: PMC8518995 DOI: 10.1002/cbic.202100257] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/08/2021] [Indexed: 11/08/2022]
Abstract
Over the past decades, starting from crude cell extracts, a variety of successful preparation protocols and optimized reaction conditions have been established for the production of cell-free gene expression systems. One of the crucial steps during the preparation of cell extract-based expression systems is the cell lysis procedure itself, which largely determines the quality of the active components of the extract. Here we evaluate the utility of an E. coli cell extract, which was prepared using a combination of lysozyme incubation and a gentle sonication step. As quality measure, we demonstrate the cell-free expression of YFP at concentrations up to 0.6 mg/mL. In addition, we produced and assembled T7 bacteriophages up to a titer of 108 PFU/mL. State-of-the-art quantitative proteomics was used to compare the produced extracts with each other and with a commercial extract. The differences in protein composition were surprisingly small between lysozyme-assisted sonication (LAS) extracts, but we observed an increase in the release of DNA-binding proteins for increasing numbers of sonication cycles. Proteins taking part in carbohydrate metabolism, glycolysis, amino acid and nucleotide related pathways were found to be more abundant in the LAS extract, while proteins related to RNA modification and processing, DNA modification and replication, transcription regulation, initiation, termination and the TCA cycle were found enriched in the commercial extract.
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Affiliation(s)
- Elisabeth Falgenhauer
- Physics of Synthetic Biological Systems, Physics Department E14Technical University of MunichAm Coulombwall 4a85748GarchingGermany
| | - Sophie von Schönberg
- Physics of Synthetic Biological Systems, Physics Department E14Technical University of MunichAm Coulombwall 4a85748GarchingGermany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS)Technical University of MunichGregor-Mendel-Strasse 485354FreisingGermany
| | - Andrea Mückl
- Physics of Synthetic Biological Systems, Physics Department E14Technical University of MunichAm Coulombwall 4a85748GarchingGermany
| | - Kilian Vogele
- Physics of Synthetic Biological Systems, Physics Department E14Technical University of MunichAm Coulombwall 4a85748GarchingGermany
| | - Quirin Emslander
- Physics of Synthetic Biological Systems, Physics Department E14Technical University of MunichAm Coulombwall 4a85748GarchingGermany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS)Technical University of MunichGregor-Mendel-Strasse 485354FreisingGermany
| | - Friedrich C. Simmel
- Physics of Synthetic Biological Systems, Physics Department E14Technical University of MunichAm Coulombwall 4a85748GarchingGermany
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Joppich M, Olenchuk M, Mayer JM, Emslander Q, Jimenez-Soto LF, Zimmer R. SEQU-INTO: Early detection of impurities, contamination and off-targets (ICOs) in long read/MinION sequencing. Comput Struct Biotechnol J 2020; 18:1342-1351. [PMID: 32612757 PMCID: PMC7306586 DOI: 10.1016/j.csbj.2020.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 05/04/2020] [Accepted: 05/09/2020] [Indexed: 11/15/2022] Open
Abstract
The MinION sequencer by Oxford Nanopore Technologies turns DNA and RNA sequencing into a routine task in biology laboratories or in field research. For downstream analysis it is required to have a sufficient amount of target reads. Especially prokaryotic or bacteriophagic sequencing samples can contain a significant amount of off-target sequences in the processed sample, stemming from human DNA/RNA contamination, insufficient rRNA depletion, or remaining DNA/RNA from other organisms (e.g. host organism from bacteriophage cultivation). Such impurity, contamination and off-targets (ICOs) block read capacity, requiring to sequence deeper. In comparison to second-generation sequencing, MinION sequencing allows to reuse its chip after a (partial) run. This allows further usage of the same chip with more sample, even after adjusting the library preparation to reduce ICOs. The earlier a sample's ICOs are detected, the better the sequencing chip can be conserved for future use. Here we present sequ-into, a low-resource and user-friendly cross-platform tool to detect ICO sequences from a predefined ICO database in samples early during a MinION sequencing run. The data provided by sequ-into empowers the user to quickly take action to preserve sample material and chip capacity. sequ-into is available from https://github.com/mjoppich/sequ-into.
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Affiliation(s)
- Markus Joppich
- LFE Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, 80333 München, Germany
| | - Margaryta Olenchuk
- LFE Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, 80333 München, Germany
| | - Julia M. Mayer
- LFE Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, 80333 München, Germany
| | - Quirin Emslander
- Physics of Synthetic Biological Systems, Physics Department, Technische Universität München, 85748 Garching, Germany
| | - Luisa F. Jimenez-Soto
- Walther Straub Institute for Pharmacology and Toxicology, Ludwig-Maximilians-Universität München, Goethestrasse 33, 80336 München, Germany
| | - Ralf Zimmer
- LFE Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, 80333 München, Germany
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