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Neumann-Staubitz P, Kitsberg D, Buxboim A, Neumann H. A method to map the interaction network of the nuclear lamina with genetically encoded photo-crosslinkers in vivo. Front Chem 2022; 10:905794. [PMID: 36110135 PMCID: PMC9468544 DOI: 10.3389/fchem.2022.905794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 07/29/2022] [Indexed: 11/23/2022] Open
Abstract
Lamins are intermediate filaments that assemble in a meshwork at the inner nuclear periphery of metazoan cells. The nuclear periphery fulfils important functions by providing stability to the nuclear membrane, connecting the cytoskeleton with chromatin, and participating in signal transduction. Mutations in lamins interfere with these functions and cause severe, phenotypically diverse diseases collectively referred to as laminopathies. The molecular consequences of these mutations are largely unclear but likely include alterations in lamin-protein and lamin-chromatin interactions. These interactions are challenging to study biochemically mainly because the lamina is resistant to high salt and detergent concentrations and co-immunoprecipitation are susceptible to artefacts. Here, we used genetic code expansion to install photo-activated crosslinkers to capture direct lamin-protein interactions in vivo. Mapping the Ig-fold of laminC for interactions, we identified laminC-crosslink products with laminB1, LAP2, and TRIM28. We observed significant changes in the crosslink intensities between laminC mutants mimicking different phosphorylation states. Similarly, we found variations in laminC crosslink product intensities comparing asynchronous cells and cells synchronized in prophase. This method can be extended to other laminC domains or other lamins to reveal changes in their interactome as a result of mutations or cell cycle stages.
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Affiliation(s)
| | - Daniel Kitsberg
- Institute of Life Science, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amnon Buxboim
- Institute of Life Science, Hebrew University of Jerusalem, Jerusalem, Israel
- Rachel and Selim Benin School of Computer Science and Engineering, Hebrew University of Jerusalem, Jerusalem, Israel
- Alexander Grass Center for Bioengineering, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Heinz Neumann
- University of Applied Sciences Darmstadt, Darmstadt, Germany
- *Correspondence: Heinz Neumann,
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Peschel A, Diepold A, Fuchs TM, Ast J, Lemoine M, Schink B, Turgay K, Stecher B, Thormann K, Colin R, Sander J, Neumann-Staubitz P, Aichane K, Kruck D. Journal Club. Biospektrum 2022; 28:50-57. [PMID: 35194334 PMCID: PMC8853319 DOI: 10.1007/s12268-022-1708-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Neumann-Staubitz P, Lammers M, Neumann H. Genetic Code Expansion Tools to Study Lysine Acylation. Adv Biol (Weinh) 2021; 5:e2100926. [PMID: 34713630 DOI: 10.1002/adbi.202100926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 05/06/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 12/17/2022]
Abstract
Lysine acylation is a ubiquitous protein modification that controls various aspects of protein function, such as the activity, localization, and stability of enzymes. Mass spectrometric identification of lysine acylations has witnessed tremendous improvements in sensitivity over the last decade, facilitating the discovery of thousands of lysine acylation sites in proteins involved in all essential cellular functions across organisms of all domains of life. However, the vast majority of currently known acylation sites are of unknown function. Semi-synthetic methods for installing lysine derivatives are ideally suited for in vitro experiments, while genetic code expansion (GCE) allows the installation and study of such lysine modifications, especially their dynamic properties, in vivo. An overview of the current state of the art is provided, and its potential is illustrated with case studies from recent literature. These include the application of engineered enzymes and GCE to install lysine modifications or photoactivatable crosslinker amino acids. Their use in the context of central metabolism, bacterial and viral pathogenicity, the cytoskeleton and chromatin dynamics, is investigated.
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Affiliation(s)
- Petra Neumann-Staubitz
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Stephanstrasse 7, 64295, Darmstadt, Germany
| | - Michael Lammers
- Institute for Biochemistry, Department Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Heinz Neumann
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Stephanstrasse 7, 64295, Darmstadt, Germany
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Schübel M, Hantke K, Garcia Varo J, Seiffert-Störiko A, Schulz S, Neumann-Staubitz P, Gewering T, Kruck D, Schnell S, Steinert M. Journal Club. Biospektrum 2020; 26:748-752. [PMID: 33250578 PMCID: PMC7686443 DOI: 10.1007/s12268-020-1502-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
- Marisa Schübel
- Fakultät für Biologie, LMU München, Großhaderner Straße 2, Planegg-Martinsried, D-82152 München, Deutschland
| | - Klaus Hantke
- Fakultät für Biologie, Universität Tübingen, Auf der Morgenstelle 28, D-72076 Tübingen, Deutschland
| | - Javier Garcia Varo
- Karlsruhe Institut für Technologie (KIT), Postfach 6980, D-76049 Karlsruhe, Deutschland
| | | | | | - Petra Neumann-Staubitz
- Institut für Mikrobiologie und Genetik, Universität Göttingen, Grisebachstraße 8, D-37077 Göttingen, Deutschland
| | - Theresa Gewering
- Max Planck Institut für Biophysik, Max-von-Laue-Straße 3, D-60438 Frankfurt a. M., Deutschland
| | - Daniela Kruck
- Fakultät Chemie, Universität Duisburg-Essen, Universitätsstraße 5, D-45141 Essen, Deutschland
| | - Sylvia Schnell
- Institut für Angewandte Mikrobiologie, Universität Gießen, IFZ, Heinrich-Buff-Ring 26-32, D-35392 Gießen, Deutschland
| | - Michael Steinert
- Institut für Mikrobiologie, TU Braunschweig, Spielmannstraße 7, D-38106 Braunschweig, Deutschland
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Abstract
The installation of unnatural amino acids into proteins of living cells is an enabling technology that facilitates an enormous number of applications. UV-activatable crosslinker amino acids allow the formation of a covalent bond between interaction partners in living cells with nearly perfect spatial and temporal control. Here, we describe how this method can be employed to map chromatin interactions and to follow these interactions across the cell cycle in synchronized yeast populations. This method thereby provides unprecedented insights into the molecular events controlling chromatin reorganization in mitosis. As similar tools are available for other organisms, it should be possible to derive similar strategies for these and for other synchronizable processes.
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Affiliation(s)
- Christian Hoffmann
- Georg August University Göttingen, Göttingen, Germany
- Accurion GmbH, Stresemannstr. 30, 37079, Göttingen, Germany
| | - Heinz Neumann
- Georg August University Göttingen, Göttingen, Germany.
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany.
| | - Petra Neumann-Staubitz
- Georg August University Göttingen, Göttingen, Germany.
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany.
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Neumann-Staubitz P, Neumann H. The use of unnatural amino acids to study and engineer protein function. Curr Opin Struct Biol 2016; 38:119-28. [DOI: 10.1016/j.sbi.2016.06.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/02/2016] [Accepted: 06/04/2016] [Indexed: 12/21/2022]
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Rakebrandt N, Lentes S, Neumann H, James LC, Neumann-Staubitz P. Antibody- and TRIM21-dependent intracellular restriction of Salmonella enterica. Pathog Dis 2014; 72:131-7. [PMID: 24920099 DOI: 10.1111/2049-632x.12192] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 05/17/2014] [Accepted: 05/28/2014] [Indexed: 11/27/2022] Open
Abstract
TRIM21 ('tripartite motif-containing protein 21', Ro52) is a ubiquitously expressed cytosolic Fc receptor, which has a potent role in protective immunity against nonenveloped viruses. TRIM21 mediates intracellular neutralisation of antibody-coated viruses, a process called ADIN (antibody-dependent intracellular neutralisation). Our results reveal a similar mechanism to fight bacterial infections. TRIM21 is recruited to the intracellular pathogen Salmonella enterica in epithelial cells early in infection. TRIM21 does not bind directly to S. enterica, but to antibodies opsonising it. Most importantly, bacterial restriction is dependent on TRIM21 as well as on the opsonisation state of the bacteria. Finally, Salmonella and TRIM21 colocalise with the autophagosomal marker LC3, and intracellular defence is enhanced in starved cells suggesting an involvement of the autophagocytic pathway. Our data extend the protective role of TRIM21 from viruses to bacteria and thereby strengthening the general role of ADIN in cellular immunity.
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Affiliation(s)
- Nikolas Rakebrandt
- Institute for Microbiology and Genetics, Georg-August-University Goettingen, Goettingen, Germany
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Baumbach J, Hoeke H, Weege F, Schmeisky AG, Neumann-Staubitz P. Salmonella enterica Modulates Its Infectivity in Response to Intestinal Stimuli. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/ojmm.2012.22006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Neumann-Staubitz P, Hall SL, Kuo J, Jackson AP. Characterization of a temperature-sensitive vertebrate clathrin heavy chain mutant as a tool to study clathrin-dependent events in vivo. PLoS One 2010; 5:e12017. [PMID: 20700507 PMCID: PMC2917355 DOI: 10.1371/journal.pone.0012017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2008] [Accepted: 07/15/2010] [Indexed: 01/27/2023] Open
Abstract
Clathrin and clathrin-dependent events are evolutionary conserved although it is believed that there are differences in the requirement for clathrin in yeast and higher vertebrates. Clathrin is a long-lived protein and thus, with clathrin knockdowns only long-term consequences of clathrin depletion can be studied. Here, we characterize the first vertebrate temperature-sensitive clathrin heavy chain mutant as a tool to investigate responses to rapid clathrin inactivation in higher eukaryotes. Although we created this mutant using a clathrin cryo-electron microscopy model and a yeast temperature-sensitive mutant as a guide, the resulting temperature-sensitive clathrin showed an altered phenotype compared to the corresponding yeast temperature-sensitive clathrin. First, it seemed to form stable triskelions at the non-permissive temperature although endocytosis was impaired under these conditions. Secondly, as a likely consequence of the stable triskelions at the non-permissive temperature, clathrin also localized correctly to its target membranes. Thirdly, we did not observe missorting of the lysosomal enzyme beta-glucuronidase which could indicate that the temperature-sensitive clathrin is still operating at the non-permissive temperature at the Golgi or, that, like in yeast, more than one TGN trafficking pathway exists. Fourthly, in contrast to yeast, actin does not appear to actively compensate in general endocytosis. Thus, there seem to be differences between vertebrates and yeast which can be studied in further detail with this newly created tool.
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Neumann H, Neumann-Staubitz P. Synthetic biology approaches in drug discovery and pharmaceutical biotechnology. Appl Microbiol Biotechnol 2010; 87:75-86. [PMID: 20396881 PMCID: PMC2872025 DOI: 10.1007/s00253-010-2578-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 03/21/2010] [Accepted: 03/22/2010] [Indexed: 12/17/2022]
Abstract
Synthetic biology is the attempt to apply the concepts of engineering to biological systems with the aim to create organisms with new emergent properties. These organisms might have desirable novel biosynthetic capabilities, act as biosensors or help us to understand the intricacies of living systems. This approach has the potential to assist the discovery and production of pharmaceutical compounds at various stages. New sources of bioactive compounds can be created in the form of genetically encoded small molecule libraries. The recombination of individual parts has been employed to design proteins that act as biosensors, which could be used to identify and quantify molecules of interest. New biosynthetic pathways may be designed by stitching together enzymes with desired activities, and genetic code expansion can be used to introduce new functionalities into peptides and proteins to increase their chemical scope and biological stability. This review aims to give an insight into recently developed individual components and modules that might serve as parts in a synthetic biology approach to pharmaceutical biotechnology.
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Affiliation(s)
- Heinz Neumann
- Free Floater (Junior) Research Group “Applied Synthetic Biology”, Institute for Microbiology and Genetics, Georg-August University Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
| | - Petra Neumann-Staubitz
- General Microbiology, Institute for Microbiology and Genetics, Georg-August University Göttingen, Grisebachstrasse 8, 37077 Göttingen, Germany
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