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Schwanke H, Gonçalves Magalhães V, Schmelz S, Wyler E, Hennig T, Günther T, Grundhoff A, Dölken L, Landthaler M, van Ham M, Jänsch L, Büssow K, van den Heuvel J, Blankenfeldt W, Friedel CC, Erhard F, Brinkmann MM. The Cytomegalovirus M35 Protein Directly Binds to the Interferon-β Enhancer and Modulates Transcription of Ifnb1 and Other IRF3-Driven Genes. J Virol 2023; 97:e0040023. [PMID: 37289084 PMCID: PMC10308904 DOI: 10.1128/jvi.00400-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/04/2023] [Indexed: 06/09/2023] Open
Abstract
Induction of type I interferon (IFN) gene expression is among the first lines of cellular defense a virus encounters during primary infection. We previously identified the tegument protein M35 of murine cytomegalovirus (MCMV) as an essential antagonist of this antiviral system, showing that M35 interferes with type I IFN induction downstream of pattern-recognition receptor (PRR) activation. Here, we report structural and mechanistic details of M35's function. Determination of M35's crystal structure combined with reverse genetics revealed that homodimerization is a key feature for M35's immunomodulatory activity. In electrophoretic mobility shift assays (EMSAs), purified M35 protein specifically bound to the regulatory DNA element that governs transcription of the first type I IFN gene induced in nonimmune cells, Ifnb1. DNA-binding sites of M35 overlapped with the recognition elements of interferon regulatory factor 3 (IRF3), a key transcription factor activated by PRR signaling. Chromatin immunoprecipitation (ChIP) showed reduced binding of IRF3 to the host Ifnb1 promoter in the presence of M35. We furthermore defined the IRF3-dependent and the type I IFN signaling-responsive genes in murine fibroblasts by RNA sequencing of metabolically labeled transcripts (SLAM-seq) and assessed M35's global effect on gene expression. Stable expression of M35 broadly influenced the transcriptome in untreated cells and specifically downregulated basal expression of IRF3-dependent genes. During MCMV infection, M35 impaired expression of IRF3-responsive genes aside of Ifnb1. Our results suggest that M35-DNA binding directly antagonizes gene induction mediated by IRF3 and impairs the antiviral response more broadly than formerly recognized. IMPORTANCE Replication of the ubiquitous human cytomegalovirus (HCMV) in healthy individuals mostly goes unnoticed but can impair fetal development or cause life-threatening symptoms in immunosuppressed or -deficient patients. Like other herpesviruses, CMV extensively manipulates its hosts and establishes lifelong latent infections. Murine CMV (MCMV) presents an important model system as it allows the study of CMV infection in the host organism. We previously showed that during entry into host cells, MCMV virions release the evolutionary conserved protein M35 protein to immediately dampen the antiviral type I interferon (IFN) response induced by pathogen detection. Here, we show that M35 dimers bind to regulatory DNA elements and interfere with recruitment of interferon regulatory factor 3 (IRF3), a key cellular factor for antiviral gene expression. Thereby, M35 interferes with expression of type I IFNs and other IRF3-dependent genes, reflecting the importance for herpesviruses to avoid IRF3-mediated gene induction.
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Affiliation(s)
- Hella Schwanke
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
- Virology and Innate Immunity Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Stefan Schmelz
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Helmholtz Association, Berlin, Germany
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | | | | | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Helmholtz Association, Berlin, Germany
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marco van Ham
- Cellular Proteome Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lothar Jänsch
- Cellular Proteome Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Konrad Büssow
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Joop van den Heuvel
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Wulf Blankenfeldt
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Caroline C. Friedel
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Melanie M. Brinkmann
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
- Virology and Innate Immunity Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
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Chen F, Yalcin I, Zhao M, Chen C, Blankenfeldt W, Pessler F, Büssow K. Amino acid positions near the active site determine the reduced activity of human ACOD1 compared to murine ACOD1. Sci Rep 2023; 13:10360. [PMID: 37365251 DOI: 10.1038/s41598-023-37373-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/20/2023] [Indexed: 06/28/2023] Open
Abstract
cis-Aconitate decarboxylase (ACOD1, IRG1) converts cis-aconitate to the immunomodulatory and antibacterial metabolite itaconate. Although the active site residues of human and mouse ACOD1 are identical, the mouse enzyme is about fivefold more active. Aiming to identify the cause of this difference, we mutated positions near the active site in human ACOD1 to the corresponding residues of mouse ACOD1 and measured resulting activities in vitro and in transfected cells. Interestingly, Homo sapiens is the only species with methionine instead of isoleucine at residue 154 and introduction of isoleucine at this position increased the activity of human ACOD1 1.5-fold in transfected cells and 3.5-fold in vitro. Enzyme activity of gorilla ACOD1, which is almost identical to the human enzyme but has isoleucine at residue 154, was similar to the mouse enzyme in vitro. Met154 in human ACOD1 forms a sulfur-π bond to Phe381, which is positioned to impede access of the substrate to the active site. It appears that the ACOD1 sequence has changed at position 154 during human evolution, resulting in a pronounced decrease in activity. This change might have offered a selective advantage in diseases such as cancer.
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Affiliation(s)
- Fangfang Chen
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Research Group Biomarkers for Infectious Diseases, TWINCORE Centre for Experimental and Clinical Infection Research, a Joint Venture Between Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Israfil Yalcin
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Mingming Zhao
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Chutao Chen
- Research Group Biomarkers for Infectious Diseases, TWINCORE Centre for Experimental and Clinical Infection Research, a Joint Venture Between Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Wulf Blankenfeldt
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Frank Pessler
- Research Group Biomarkers for Infectious Diseases, TWINCORE Centre for Experimental and Clinical Infection Research, a Joint Venture Between Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Centre for Individualised Infection Medicine, Hannover, Germany
| | - Konrad Büssow
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany.
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Chen F, Elgaher WAM, Winterhoff M, Büssow K, Waqas FH, Graner E, Pires-Afonso Y, Casares Perez L, de la Vega L, Sahini N, Czichon L, Zobl W, Zillinger T, Shehata M, Pleschka S, Bähre H, Falk C, Michelucci A, Schuchardt S, Blankenfeldt W, Hirsch AKH, Pessler F. Citraconate inhibits ACOD1 (IRG1) catalysis, reduces interferon responses and oxidative stress, and modulates inflammation and cell metabolism. Nat Metab 2022; 4:534-546. [PMID: 35655026 PMCID: PMC9170585 DOI: 10.1038/s42255-022-00577-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 04/20/2022] [Indexed: 01/08/2023]
Abstract
Although the immunomodulatory and cytoprotective properties of itaconate have been studied extensively, it is not known whether its naturally occurring isomers mesaconate and citraconate have similar properties. Here, we show that itaconate is partially converted to mesaconate intracellularly and that mesaconate accumulation in macrophage activation depends on prior itaconate synthesis. When added to human cells in supraphysiological concentrations, all three isomers reduce lactate levels, whereas itaconate is the strongest succinate dehydrogenase (SDH) inhibitor. In cells infected with influenza A virus (IAV), all three isomers profoundly alter amino acid metabolism, modulate cytokine/chemokine release and reduce interferon signalling, oxidative stress and the release of viral particles. Of the three isomers, citraconate is the strongest electrophile and nuclear factor-erythroid 2-related factor 2 (NRF2) agonist. Only citraconate inhibits catalysis of itaconate by cis-aconitate decarboxylase (ACOD1), probably by competitive binding to the substrate-binding site. These results reveal mesaconate and citraconate as immunomodulatory, anti-oxidative and antiviral compounds, and citraconate as the first naturally occurring ACOD1 inhibitor.
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Affiliation(s)
- F Chen
- Research Group Biomarkers for Infectious Diseases, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Research Group Biomarkers for Infectious Diseases, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - W A M Elgaher
- Helmholtz Institute for Pharmaceutical Research Saarland - Helmholtz Centre for Infection Research, Saarbrücken, Germany
| | - M Winterhoff
- Research Group Biomarkers for Infectious Diseases, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Research Group Biomarkers for Infectious Diseases, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - K Büssow
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - F H Waqas
- Research Group Biomarkers for Infectious Diseases, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Research Group Biomarkers for Infectious Diseases, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - E Graner
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Y Pires-Afonso
- Neuro-Immunology Group, Department of Cancer Research, LIH Luxembourg Institute of Health, Luxembourg, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-Belval, Luxembourg
| | - L Casares Perez
- Division of Molecular Medicine, University of Dundee, Dundee, UK
| | - L de la Vega
- Division of Molecular Medicine, University of Dundee, Dundee, UK
| | - N Sahini
- Research Group Biomarkers for Infectious Diseases, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Research Group Biomarkers for Infectious Diseases, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - L Czichon
- Research Group Biomarkers for Infectious Diseases, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Research Group Biomarkers for Infectious Diseases, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - W Zobl
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Hannover, Germany
| | - T Zillinger
- Institute of Clinical Chemistry and Clinical Pharmacology, University Medical Centre Bonn, Bonn, Germany
- Institute of Immunology, Philipps-University Marburg, Marburg, Germany
| | - M Shehata
- Institute of Medical Virology, Justus-Liebig-University Giessen, Giessen, Germany
- National Research Centre, Giza, Egypt
| | - S Pleschka
- Institute of Medical Virology, Justus-Liebig-University Giessen, Giessen, Germany
- German Center for Infection Research partner site Giessen, Giessen, Germany
| | - H Bähre
- Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - C Falk
- Department of Transplantation Immunology, Hannover Medical School, Hannover, Germany
| | - A Michelucci
- Neuro-Immunology Group, Department of Cancer Research, LIH Luxembourg Institute of Health, Luxembourg, Luxembourg
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg
| | - S Schuchardt
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Hannover, Germany
| | - W Blankenfeldt
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - A K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland - Helmholtz Centre for Infection Research, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - F Pessler
- Research Group Biomarkers for Infectious Diseases, Helmholtz Centre for Infection Research, Braunschweig, Germany.
- Research Group Biomarkers for Infectious Diseases, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany.
- Centre for Individualised Infection Medicine, Hannover, Germany.
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Scheithauer L, Thiem S, Schmelz S, Dellmann A, Büssow K, Brouwer RMHJ, Ünal CM, Blankenfeldt W, Steinert M. Zinc metalloprotease ProA of Legionella pneumophila increases alveolar septal thickness in human lung tissue explants by collagen IV degradation. Cell Microbiol 2021; 23:e13313. [PMID: 33491325 DOI: 10.1111/cmi.13313] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 06/18/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 01/25/2023]
Abstract
ProA is a secreted zinc metalloprotease of Legionella pneumophila causing lung damage in animal models of Legionnaires' disease. Here we demonstrate that ProA promotes infection of human lung tissue explants (HLTEs) and dissect the contribution to cell type specific replication and extracellular virulence mechanisms. For the first time, we reveal that co-incubation of HLTEs with purified ProA causes a significant increase of the alveolar septal thickness. This destruction of connective tissue fibres was further substantiated by collagen IV degradation assays. The moderate attenuation of a proA-negative mutant in A549 epithelial cells and THP-1 macrophages suggests that effects of ProA in tissue mainly result from extracellular activity. Correspondingly, ProA contributes to dissemination and serum resistance of the pathogen, which further expands the versatile substrate spectrum of this thermolysin-like protease. The crystal structure of ProA at 1.48 Å resolution showed high congruence to pseudolysin of Pseudomonas aeruginosa, but revealed deviations in flexible loops, the substrate binding pocket S1 ' and the repertoire of cofactors, by which ProA can be distinguished from respective homologues. In sum, this work specified virulence features of ProA at different organisational levels by zooming in from histopathological effects in human lung tissue to atomic details of the protease substrate determination.
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Affiliation(s)
- Lina Scheithauer
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Stefanie Thiem
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Stefan Schmelz
- Structure and Function of Proteins, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Ansgar Dellmann
- Institut für Pathologie, Städtisches Klinikum Braunschweig gGmbH, Braunschweig, Germany
| | - Konrad Büssow
- Structure and Function of Proteins, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - René M H J Brouwer
- Herz-, Thorax-, Gefäßchirurgie, Städtisches Klinikum Braunschweig gGmbH, Braunschweig, Germany.,Institut für Psychologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Can M Ünal
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany.,Fen Fakültesi, Turkish-German University, Istanbul, Turkey
| | - Wulf Blankenfeldt
- Structure and Function of Proteins, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael Steinert
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
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Muthukumar Y, Münkemer J, Mathieu D, Richter C, Schwalbe H, Steinmetz H, Kessler W, Reichelt J, Beutling U, Frank R, Büssow K, van den Heuvel J, Brönstrup M, Taylor RE, Laschat S, Sasse F. Investigations on the mode of action of gephyronic acid, an inhibitor of eukaryotic protein translation from myxobacteria. PLoS One 2018; 13:e0201605. [PMID: 30063768 PMCID: PMC6067752 DOI: 10.1371/journal.pone.0201605] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 05/13/2018] [Accepted: 07/18/2018] [Indexed: 11/19/2022] Open
Abstract
The identification of inhibitors of eukaryotic protein biosynthesis, which are targeting single translation factors, is highly demanded. Here we report on a small molecule inhibitor, gephyronic acid, isolated from the myxobacterium Archangium gephyra that inhibits growth of transformed mammalian cell lines in the nM range. In direct comparison, primary human fibroblasts were shown to be less sensitive to toxic effects of gephyronic acid than cancer-derived cells. Gephyronic acid is targeting the protein translation system. Experiments with IRES dual luciferase reporter assays identified it as an inhibitor of the translation initiation. DARTs approaches, co-localization studies and pull-down assays indicate that the binding partner could be the eukaryotic initiation factor 2 subunit alpha (eIF2α). Gephyronic acid seems to have a different mode of action than the structurally related polyketides tedanolide, myriaporone, and pederin and is a valuable tool for investigating the eukaryotic translation system. Because cancer derived cells were found to be especially sensitive, gephyronic acid could potentially find use as a drug candidate.
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Affiliation(s)
- Yazh Muthukumar
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Johanna Münkemer
- Institut für Organische Chemie, Universität Stuttgart, Stuttgart, Germany
| | - Daniel Mathieu
- Zentrum für Biomolekulare Magnetische Resonanz, Universität Frankfurt, Frankfurt, Germany
| | - Christian Richter
- Zentrum für Biomolekulare Magnetische Resonanz, Universität Frankfurt, Frankfurt, Germany
| | - Harald Schwalbe
- Zentrum für Biomolekulare Magnetische Resonanz, Universität Frankfurt, Frankfurt, Germany
| | - Heinrich Steinmetz
- Department of Microbial Drugs, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Wolfgang Kessler
- Department of Microbial Drugs, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Joachim Reichelt
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ulrike Beutling
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ronald Frank
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Konrad Büssow
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Joop van den Heuvel
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Richard E. Taylor
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Sabine Laschat
- Institut für Organische Chemie, Universität Stuttgart, Stuttgart, Germany
- * E-mail: (FS); (SL)
| | - Florenz Sasse
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- * E-mail: (FS); (SL)
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Baser B, Spehr J, Büssow K, van den Heuvel J. A method for specifically targeting two independent genomic integration sites for co-expression of genes in CHO cells. Methods 2016; 95:3-12. [DOI: 10.1016/j.ymeth.2015.11.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 11/24/2015] [Accepted: 11/26/2015] [Indexed: 11/30/2022] Open
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Büssow K. Stable mammalian producer cell lines for structural biology. Curr Opin Struct Biol 2015; 32:81-90. [DOI: 10.1016/j.sbi.2015.03.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 02/11/2015] [Accepted: 03/03/2015] [Indexed: 11/28/2022]
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Jäger V, Büssow K, Wagner A, Weber S, Hust M, Frenzel A, Schirrmann T. High level transient production of recombinant antibodies and antibody fusion proteins in HEK293 cells. BMC Biotechnol 2013; 13:52. [PMID: 23802841 PMCID: PMC3699382 DOI: 10.1186/1472-6750-13-52] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 05/24/2013] [Indexed: 12/02/2022] Open
Abstract
Background The demand of monospecific high affinity binding reagents, particularly monoclonal antibodies, has been steadily increasing over the last years. Enhanced throughput of antibody generation has been addressed by optimizing in vitro selection using phage display which moved the major bottleneck to the production and purification of recombinant antibodies in an end-user friendly format. Single chain (sc)Fv antibody fragments require additional tags for detection and are not as suitable as immunoglobulins (Ig)G in many immunoassays. In contrast, the bivalent scFv-Fc antibody format shares many properties with IgG and has a very high application compatibility. Results In this study transient expression of scFv-Fc antibodies in human embryonic kidney (HEK) 293 cells was optimized. Production levels of 10-20 mg/L scFv-Fc antibody were achieved in adherent HEK293T cells. Employment of HEK293-6E suspension cells expressing a truncated variant of the Epstein Barr virus (EBV) nuclear antigen (EBNA) 1 in combination with production under serum free conditions increased the volumetric yield up to 10-fold to more than 140 mg/L scFv-Fc antibody. After vector optimization and process optimization the yield of an scFv-Fc antibody and a cytotoxic antibody-RNase fusion protein further increased 3-4-fold to more than 450 mg/L. Finally, an entirely new mammalian expression vector was constructed for single step in frame cloning of scFv genes from antibody phage display libraries. Transient expression of more than 20 different scFv-Fc antibodies resulted in volumetric yields of up to 600 mg/L and 400 mg/L in average. Conclusion Transient production of recombinant scFv-Fc antibodies in HEK293-6E in combination with optimized vectors and fed batch shake flasks cultivation is efficient and robust, and integrates well into a high-throughput recombinant antibody generation pipeline.
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de Groot JC, Weidner C, Krausze J, Kawamoto K, Schroeder FC, Sauer S, Büssow K. Structural Characterization of Amorfrutins Bound to the Peroxisome Proliferator-Activated Receptor γ. J Med Chem 2013; 56:1535-43. [DOI: 10.1021/jm3013272] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jens C. de Groot
- Department of Molecular Structural
Biology, Helmholtz Centre for Infection Research, 38214 Braunschweig, Germany
| | - Christopher Weidner
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Joern Krausze
- Department of Molecular Structural
Biology, Helmholtz Centre for Infection Research, 38214 Braunschweig, Germany
| | - Ken Kawamoto
- Boyce Thompson Institute and Department of Chemistry
and Chemical Biology, Cornell University, Ithaca, New York, United States
| | - Frank C. Schroeder
- Boyce Thompson Institute and Department of Chemistry
and Chemical Biology, Cornell University, Ithaca, New York, United States
| | - Sascha Sauer
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Konrad Büssow
- Department of Molecular Structural
Biology, Helmholtz Centre for Infection Research, 38214 Braunschweig, Germany
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Wilke S, Krausze J, Büssow K. Crystal structure of human lysosome-associated membrane protein 3 (LAMP-3). Acta Crystallogr A 2012. [DOI: 10.1107/s0108767312099333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Wilke S, Krausze J, Büssow K. Crystal structure of the conserved domain of the DC lysosomal associated membrane protein: implications for the lysosomal glycocalyx. BMC Biol 2012; 10:62. [PMID: 22809326 PMCID: PMC3409847 DOI: 10.1186/1741-7007-10-62] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 07/19/2012] [Indexed: 01/09/2023] Open
Abstract
Background The family of lysosome-associated membrane proteins (LAMP) comprises the multifunctional, ubiquitous LAMP-1 and LAMP-2, and the cell type-specific proteins DC-LAMP (LAMP-3), BAD-LAMP (UNC-46, C20orf103) and macrosialin (CD68). LAMPs have been implicated in a multitude of cellular processes, including phagocytosis, autophagy, lipid transport and aging. LAMP-2 isoform A acts as a receptor in chaperone-mediated autophagy. LAMP-2 deficiency causes the fatal Danon disease. The abundant proteins LAMP-1 and LAMP-2 are major constituents of the glycoconjugate coat present on the inside of the lysosomal membrane, the 'lysosomal glycocalyx'. The LAMP family is characterized by a conserved domain of 150 to 200 amino acids with two disulfide bonds. Results The crystal structure of the conserved domain of human DC-LAMP was solved. It is the first high-resolution structure of a heavily glycosylated lysosomal membrane protein. The structure represents a novel β-prism fold formed by two β-sheets bent by β-bulges and connected by a disulfide bond. Flexible loops and a hydrophobic pocket represent possible sites of molecular interaction. Computational models of the glycosylated luminal regions of LAMP-1 and LAMP-2 indicate that the proteins adopt a compact conformation in close proximity to the lysosomal membrane. The models correspond to the thickness of the lysosomal glycoprotein coat of only 5 to 12 nm, according to electron microscopy. Conclusion The conserved luminal domain of lysosome-associated membrane proteins forms a previously unknown β-prism fold. Insights into the structure of the lysosomal glycoprotein coat were obtained by computational models of the LAMP-1 and LAMP-2 luminal regions.
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Affiliation(s)
- Sonja Wilke
- Department of Molecular Structural Biology, Helmholtz Centre for Infection Research, Inhoffenstr, 7, 38124 Braunschweig, Germany
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12
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de Groot JC, Schlüter K, Carius Y, Quedenau C, Vingadassalom D, Faix J, Weiss SM, Reichelt J, Standfuss-Gabisch C, Lesser CF, Leong JM, Heinz DW, Büssow K, Stradal TEB. Structural basis for complex formation between human IRSp53 and the translocated intimin receptor Tir of enterohemorrhagic E. coli. Structure 2011; 19:1294-306. [PMID: 21893288 DOI: 10.1016/j.str.2011.06.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 06/09/2011] [Accepted: 06/13/2011] [Indexed: 10/17/2022]
Abstract
Actin assembly beneath enterohemorrhagic E. coli (EHEC) attached to its host cell is triggered by the intracellular interaction of its translocated effector proteins Tir and EspF(U) with human IRSp53 family proteins and N-WASP. Here, we report the structure of the N-terminal I-BAR domain of IRSp53 in complex with a Tir-derived peptide, in which the homodimeric I-BAR domain binds two Tir molecules aligned in parallel. This arrangement provides a protein scaffold linking the bacterium to the host cell's actin polymerization machinery. The structure uncovers a specific peptide-binding site on the I-BAR surface, conserved between IRSp53 and IRTKS. The Tir Asn-Pro-Tyr (NPY) motif, essential for pedestal formation, is specifically recognized by this binding site. The site was confirmed by mutagenesis and in vivo-binding assays. It is possible that IRSp53 utilizes the NPY-binding site for additional interactions with as yet unknown partners within the host cell.
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Affiliation(s)
- Jens C de Groot
- Division of Structural Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
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13
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Wilke S, Groebe L, Maffenbeier V, Jäger V, Gossen M, Josewski J, Duda A, Polle L, Owens RJ, Wirth D, Heinz DW, van den Heuvel J, Büssow K. Streamlining homogeneous glycoprotein production for biophysical and structural applications by targeted cell line development. PLoS One 2011; 6:e27829. [PMID: 22174749 PMCID: PMC3235087 DOI: 10.1371/journal.pone.0027829] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [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: 07/15/2011] [Accepted: 10/26/2011] [Indexed: 11/19/2022] Open
Abstract
Studying the biophysical characteristics of glycosylated proteins and solving their three-dimensional structures requires homogeneous recombinant protein of high quality.We introduce here a new approach to produce glycoproteins in homogenous form with the well-established, glycosylation mutant CHO Lec3.2.8.1 cells. Using preparative cell sorting, stable, high-expressing GFP 'master' cell lines were generated that can be converted fast and reliably by targeted integration via Flp recombinase-mediated cassette exchange (RMCE) to produce any glycoprotein. Small-scale transient transfection of HEK293 cells was used to identify genetically engineered constructs suitable for constructing stable cell lines. Stable cell lines expressing 10 different proteins were established. The system was validated by expression, purification, deglycosylation and crystallization of the heavily glycosylated luminal domains of lysosome-associated membrane proteins (LAMP).
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Affiliation(s)
- Sonja Wilke
- Department of Molecular Structural Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lothar Groebe
- Department of Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Vitali Maffenbeier
- Department of Molecular Structural Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Volker Jäger
- Department of Molecular Structural Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Manfred Gossen
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
- Berlin-Brandenburg Centre for Regenerative Therapies (BCRT), Berlin, Germany
| | - Jörn Josewski
- Department of Molecular Structural Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Agathe Duda
- Department of Molecular Structural Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lilia Polle
- Department of Molecular Structural Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Raymond J. Owens
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford, United Kingdom
- Oxford Protein Production Facility UK, The Research Complex at Harwell, Rutherford Appleton Laboratory Harwell Science and Innovation Campus, Oxfordshire, United Kingdom
| | - Dagmar Wirth
- Department of Gene Regulation and Differentiation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Dirk W. Heinz
- Department of Molecular Structural Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Joop van den Heuvel
- Department of Molecular Structural Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Konrad Büssow
- Department of Molecular Structural Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
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14
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Wilke S, Krausze J, Gossen M, Groebe L, Jäger V, Gherardi E, van den Heuvel J, Büssow K. Glycoprotein production for structure analysis with stable, glycosylation mutant CHO cell lines established by fluorescence-activated cell sorting. Protein Sci 2010; 19:1264-71. [PMID: 20512979 DOI: 10.1002/pro.390] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Stable mammalian cell lines are excellent tools for the expression of secreted and membrane glycoproteins. However, structural analysis of these molecules is generally hampered by the complexity of N-linked carbohydrate side chains. Cell lines with mutations are available that result in shorter and more homogenous carbohydrate chains. Here, we use preparative fluorescence-activated cell sorting (FACS) and site-specific gene excision to establish high-yield glycoprotein expression for structural studies with stable clones derived from the well-established Lec3.2.8.1 glycosylation mutant of the Chinese hamster ovary (CHO) cell line. We exemplify the strategy by describing novel clones expressing single-chain hepatocyte growth factor/scatter factor (HGF/SF, a secreted glycoprotein) and a domain of lysosome-associated membrane protein 3 (LAMP3d). In both cases, stable GFP-expressing cell lines were established by transfection with a genetic construct including a GFP marker and two rounds of cell sorting after 1 and 2 weeks. The GFP marker was subsequently removed by heterologous expression of Flp recombinase. Production of HGF/SF and LAMP3d was stable over several months. 1.2 mg HGF/SF and 0.9 mg LAMP3d were purified per litre of culture, respectively. Homogenous glycoprotein preparations were amenable to enzymatic deglycosylation under native conditions. Purified and deglycosylated LAMP3d protein was readily crystallized. The combination of FACS and gene excision described here constitutes a robust and fast procedure for maximizing the yield of glycoproteins for structural analysis from glycosylation mutant cell lines.
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Affiliation(s)
- Sonja Wilke
- Division of Structural Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
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15
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Schütz A, van den Heuvel J, Jäger V, Büssow K, Heinz D, Heinemann U. PSPF - a protein sample production facility for structural biologists. Acta Crystallogr A 2010. [DOI: 10.1107/s0108767310097382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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16
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Ergin A, Adam T, Büssow K, Thiel A, Sieper J, Duchmann R. Identification of the predominant antigenic epitopes in intestinal flora in IBD. Mucosal Immunol 2008; 1 Suppl 1:S19-23. [PMID: 19079222 DOI: 10.1038/mi.2008.44] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The normal intestinal flora is required for the development of intestinal inflammation in animal models of inflammatory bowel disease (IBD). In humans, several studies indicated a potential association of Escherichia coli (E. coli) with IBD. In addition, we have shown that T-cell clones of IBD patients cross react toward different enteric bacterial species and thus likely respond to conserved bacterial antigens. Therefore, we hypothesized that highly conserved E. coli proteins might be a reasonable candidate to screen for abnormal T-cell responses in IBD. We used high-throughput techniques for cloning, expression, and purification under native conditions of a set of 271 conserved proteins of E. coli, of which 196 were used for whole blood stimulations to assess peripheral T helper (T(H))-cell responses. In addition, because of the association of an adherent-invasive E. coli with Crohn's disease (CD), we included 13 pathogenicity factors of E. coli in the study. We observed that pools of these conserved E. coli proteins less frequently induced interferon-gamma (IFNgamma) production in peripheral T(H) cells in patients with CD and ankylosing spondylitis (AS) compared with healthy controls. In addition, lower percentage of patients with CD and AS responded toward single proteins. The reason for the decreased frequency of an in vitro T(H)-cell IFNgamma response toward E. coli proteins in peripheral blood of CD and AS patients, e.g., increased suppression needs to be clarified.
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Affiliation(s)
- A Ergin
- Medizinische Klinik I, Universitätsmedizin Berlin, Charité, Campus Benjamin Franklin, Hindenburgdamm, Berlin, Germany
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17
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Schulze JO, Quedenau C, Roske Y, Adam T, Schüler H, Behlke J, Turnbull AP, Sievert V, Scheich C, Mueller U, Heinemann U, Büssow K. Structural and functional characterization of human Iba proteins. FEBS J 2008; 275:4627-40. [DOI: 10.1111/j.1742-4658.2008.06605.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Manjasetty BA, Turnbull AP, Panjikar S, Büssow K, Chance MR. Automated technologies and novel techniques to accelerate protein crystallography for structural genomics. Proteomics 2008; 8:612-25. [PMID: 18210369 DOI: 10.1002/pmic.200700687] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The sequence infrastructure that has arisen through large-scale genomic projects dedicated to protein analysis, has provided a wealth of information and brought together scientists and institutions from all over the world. As a consequence, the development of novel technologies and methodologies in proteomics research is helping to unravel the biochemical and physiological mechanisms of complex multivariate diseases at both a functional and molecular level. In the late sixties, when X-ray crystallography had just been established, the idea of determining protein structure on an almost universal basis was akin to an impossible dream or a miracle. Yet only forty years after, automated protein structure determination platforms have been established. The widespread use of robotics in protein crystallography has had a huge impact at every stage of the pipeline from protein cloning, over-expression, purification, crystallization, data collection, structure solution, refinement, validation and data management- all of which have become more or less automated with minimal human intervention necessary. Here, recent advances in protein crystal structure analysis in the context of structural genomics will be discussed. In addition, this review aims to give an overview of recent developments in high throughput instrumentation, and technologies and strategies to accelerate protein structure/function analysis.
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Affiliation(s)
- Babu A Manjasetty
- Case Center for Synchrotron Biosciences, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY11973, USA.
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19
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Gräslund S, Nordlund P, Weigelt J, Hallberg BM, Bray J, Gileadi O, Knapp S, Oppermann U, Arrowsmith C, Hui R, Ming J, dhe-Paganon S, Park HW, Savchenko A, Yee A, Edwards A, Vincentelli R, Cambillau C, Kim R, Kim SH, Rao Z, Shi Y, Terwilliger TC, Kim CY, Hung LW, Waldo GS, Peleg Y, Albeck S, Unger T, Dym O, Prilusky J, Sussman JL, Stevens RC, Lesley SA, Wilson IA, Joachimiak A, Collart F, Dementieva I, Donnelly MI, Eschenfeldt WH, Kim Y, Stols L, Wu R, Zhou M, Burley SK, Emtage JS, Sauder JM, Thompson D, Bain K, Luz J, Gheyi T, Zhang F, Atwell S, Almo SC, Bonanno JB, Fiser A, Swaminathan S, Studier FW, Chance MR, Sali A, Acton TB, Xiao R, Zhao L, Ma LC, Hunt JF, Tong L, Cunningham K, Inouye M, Anderson S, Janjua H, Shastry R, Ho CK, Wang D, Wang H, Jiang M, Montelione GT, Stuart DI, Owens RJ, Daenke S, Schütz A, Heinemann U, Yokoyama S, Büssow K, Gunsalus KC. Protein production and purification. Nat Methods 2008; 5:135-46. [PMID: 18235434 PMCID: PMC3178102 DOI: 10.1038/nmeth.f.202] [Citation(s) in RCA: 612] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In selecting a method to produce a recombinant protein, a researcher is faced with a bewildering array of choices as to where to start. To facilitate decision-making, we describe a consensus 'what to try first' strategy based on our collective analysis of the expression and purification of over 10,000 different proteins. This review presents methods that could be applied at the outset of any project, a prioritized list of alternate strategies and a list of pitfalls that trip many new investigators.
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20
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Abstract
The systematic structural analysis of many target proteins involves generating expression clones in high throughput. This requires robust laboratory procedures and benefits from laboratory automation and data management systems. This chapter gives an overview of the Protein Structure Factory, a structural genomics project focusing on human proteins, and presents the authors' method for cloning bacterial expression clones with the restriction enzymes BamHI and NotI and compatible enzymes. PCR amplification, product purification and digestion and vector ligation were adapted to the 96-well microtiter plate format.
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Affiliation(s)
- Volker Sievert
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Protein Structure Factory, Berlin, Germany
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21
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Ergin A, Büssow K, Sieper J, Thiel A, Duchmann R, Adam T. Homologous high-throughput expression and purification of highly conserved E coli proteins. Microb Cell Fact 2007; 6:18. [PMID: 17553160 PMCID: PMC1914363 DOI: 10.1186/1475-2859-6-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2007] [Accepted: 06/06/2007] [Indexed: 01/12/2023] Open
Abstract
Background Genetic factors and a dysregulated immune response towards commensal bacteria contribute to the pathogenesis of Inflammatory Bowel Disease (IBD). Animal models demonstrated that the normal intestinal flora is crucial for the development of intestinal inflammation. However, due to the complexity of the intestinal flora, it has been difficult to design experiments for detection of proinflammatory bacterial antigen(s) involved in the pathogenesis of the disease. Several studies indicated a potential association of E. coli with IBD. In addition, T cell clones of IBD patients were shown to cross react towards antigens from different enteric bacterial species and thus likely responded to conserved bacterial antigens. We therefore chose highly conserved E. coli proteins as candidate antigens for abnormal T cell responses in IBD and used high-throughput techniques for cloning, expression and purification under native conditions of a set of 271 conserved E. coli proteins for downstream immunologic studies. Results As a standardized procedure, genes were PCR amplified and cloned into the expression vector pQTEV2 in order to express proteins N-terminally fused to a seven-histidine-tag. Initial small-scale expression and purification under native conditions by metal chelate affinity chromatography indicated that the vast majority of target proteins were purified in high yields. Targets that revealed low yields after purification probably due to weak solubility were shuttled into Gateway (Invitrogen) destination vectors in order to enhance solubility by N-terminal fusion of maltose binding protein (MBP), N-utilizing substance A (NusA), or glutathione S-transferase (GST) to the target protein. In addition, recombinant proteins were treated with polymyxin B coated magnetic beads in order to remove lipopolysaccharide (LPS). Thus, 73% of the targeted proteins could be expressed and purified in large-scale to give soluble proteins in the range of 500 μg. Conclusion Here, we report a cost-efficient procedure to produce around 200 soluble recombinant E. coli proteins in large-scale, including removal of LPS by polymyxin B coated beads for subsequent use of the proteins in downstream immunological studies.
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Affiliation(s)
- Asgar Ergin
- Universitätsmedizin Berlin, Charité, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Konrad Büssow
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
| | - Joachim Sieper
- Universitätsmedizin Berlin, Charité, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Andreas Thiel
- Deutsches Rheuma-Forschungszentrum, Charitéplatz 1, 10117 Berlin, Germany
| | - Rainer Duchmann
- Universitätsmedizin Berlin, Charité, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Thomas Adam
- Universitätsmedizin Berlin, Charité, Campus Charité Mitte, Dorotheenstr. 96, 10117 Berlin, Germany
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22
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Abstract
A vector system is presented that allows generation of E. coli co-expression clones by a standardized, robust cloning procedure. The number of co-expressed proteins is not limited. Five ‘pQLink’ vectors for expression of His-tag and GST-tag fusion proteins as well as untagged proteins and for cloning by restriction enzymes or Gateway cloning were generated. The vectors allow proteins to be expressed individually; to achieve co-expression, two pQLink plasmids are combined by ligation-independent cloning. pQLink co-expression plasmids can accept an unrestricted number of genes. As an example, the co-expression of a heterotetrameric human transport protein particle (TRAPP) complex from a single plasmid, its isolation and analysis of its stoichiometry are shown. pQLink clones can be used directly for pull-down experiments if the proteins are expressed with different tags. We demonstrate pull-down experiments of human valosin-containing protein (VCP) with fragments of the autocrine motility factor receptor (AMFR). The cloning method avoids PCR or gel isolation of restriction fragments, and a single resistance marker and origin of replication are used, allowing over-expression of rare tRNAs from a second plasmid. It is expected that applications are not restricted to bacteria, but could include co-expression in other hosts such as Bacluovirus/insect cells.
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Affiliation(s)
- Christoph Scheich
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestr. 63-73, 14195 Berlin, Germany, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany and Free University of Berlin, Institute of Chemistry and Biochemistry, Takustraße 6, 14195 Berlin, Germany
| | - Daniel Kümmel
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestr. 63-73, 14195 Berlin, Germany, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany and Free University of Berlin, Institute of Chemistry and Biochemistry, Takustraße 6, 14195 Berlin, Germany
| | - Dimitri Soumailakakis
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestr. 63-73, 14195 Berlin, Germany, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany and Free University of Berlin, Institute of Chemistry and Biochemistry, Takustraße 6, 14195 Berlin, Germany
| | - Udo Heinemann
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestr. 63-73, 14195 Berlin, Germany, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany and Free University of Berlin, Institute of Chemistry and Biochemistry, Takustraße 6, 14195 Berlin, Germany
| | - Konrad Büssow
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestr. 63-73, 14195 Berlin, Germany, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany and Free University of Berlin, Institute of Chemistry and Biochemistry, Takustraße 6, 14195 Berlin, Germany
- *To whom correspondence should be addressed. +49 30 9406 2983+49 30 9406 2925
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Berrow NS, Büssow K, Coutard B, Diprose J, Ekberg M, Folkers GE, Levy N, Lieu V, Owens RJ, Peleg Y, Pinaglia C, Quevillon-Cheruel S, Salim L, Scheich C, Vincentelli R, Busso D. Recombinant protein expression and solubility screening in Escherichia coli: a comparative study. Acta Crystallogr D Biol Crystallogr 2006; 62:1218-26. [PMID: 17001098 DOI: 10.1107/s0907444906031337] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2006] [Accepted: 08/09/2006] [Indexed: 11/10/2022]
Abstract
Producing soluble proteins in Escherichia coli is still a major bottleneck for structural proteomics. Therefore, screening for soluble expression on a small scale is an attractive way of identifying constructs that are likely to be amenable to structural analysis. A variety of expression-screening methods have been developed within the Structural Proteomics In Europe (SPINE) consortium and to assist the further refinement of such approaches, eight laboratories participating in the network have benchmarked their protocols. For this study, the solubility profiles of a common set of 96 His(6)-tagged proteins were assessed by expression screening in E. coli. The level of soluble expression for each target was scored according to estimated protein yield. By reference to a subset of the proteins, it is demonstrated that the small-scale result can provide a useful indicator of the amount of soluble protein likely to be produced on a large scale (i.e. sufficient for structural studies). In general, there was agreement between the different groups as to which targets were not soluble and which were the most soluble. However, for a large number of the targets there were wide discrepancies in the results reported from the different screening methods, which is correlated with variations in the procedures and the range of parameters explored. Given finite resources, it appears that the question of how to most effectively explore ;expression space' is similar to several other multi-parameter problems faced by crystallographers, such as crystallization.
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Affiliation(s)
- Nick S Berrow
- Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, Oxford, England
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24
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Manjasetty BA, Büssow K, Fieber-Erdmann M, Roske Y, Gobom J, Scheich C, Götz F, Niesen FH, Heinemann U. Crystal structure of Homo sapiens PTD012 reveals a zinc-containing hydrolase fold. Protein Sci 2006; 15:914-20. [PMID: 16522806 PMCID: PMC2242484 DOI: 10.1110/ps.052037006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The human protein PTD012 is the longer product of an alternatively spliced gene and was described to be localized in the nucleus. The X-ray structure analysis at 1.7 A resolution of PTD012 through SAD phasing reveals a monomeric protein and a novel fold. The shorter splice form was also studied and appears to be unfolded and non-functional. The structure of PTD012 displays an alphabetabetaalpha four-layer topology. A metal ion residing between the central beta-sheets is partially coordinated by three histidine residues. X-ray absorption near-edge structure (XANES) analysis identifies the PTD012-bound ion as Zn(2+). Tetrahedral coordination of the ion is completed by the carboxylate oxygen atom of an acetate molecule taken up from the crystallization buffer. The binding of Zn(2+) to PTD012 is reminiscent of zinc-containing enzymes such as carboxypeptidase, carbonic anhydrase, and beta-lactamase. Biochemical assays failed to demonstrate any of these enzyme activities in PTD012. However, PTD012 exhibits ester hydrolase activity on the substrate p-nitrophenyl acetate.
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25
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Kümmel D, Müller JJ, Roske Y, Misselwitz R, Büssow K, Heinemann U. The structure of the TRAPP subunit TPC6 suggests a model for a TRAPP subcomplex. EMBO Rep 2006; 6:787-93. [PMID: 16025134 PMCID: PMC1369139 DOI: 10.1038/sj.embor.7400463] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2005] [Revised: 05/17/2005] [Accepted: 05/25/2005] [Indexed: 11/08/2022] Open
Abstract
The TRAPP (transport protein particle) complexes are tethering complexes that have an important role at the different steps of vesicle transport. Recently, the crystal structures of the TRAPP subunits SEDL and BET3 have been determined, and we present here the 1.7 Angstroms crystal structure of human TPC6, a third TRAPP subunit. The protein adopts an alpha/beta-plait topology and forms a dimer. In spite of low sequence similarity, the structure of TPC6 strikingly resembles that of BET3. The similarity is especially prominent at the dimerization interfaces of the proteins. This suggests heterodimerization of TPC6 and BET3, which is shown by in vitro and in vivo association studies. Together with TPC5, another TRAPP subunit, TPC6 and BET3 are supposed to constitute a family of paralogous proteins with closely similar three-dimensional structures but little sequence similarity among its members.
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Affiliation(s)
- Daniel Kümmel
- Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13092 Berlin, Germany
- Chemistry Institute, Free University, Takustrasse 6, 14195 Berlin, Germany
| | - Jürgen J Müller
- Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13092 Berlin, Germany
| | - Yvette Roske
- Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13092 Berlin, Germany
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
| | - Rolf Misselwitz
- Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13092 Berlin, Germany
| | - Konrad Büssow
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Udo Heinemann
- Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13092 Berlin, Germany
- Chemistry Institute, Free University, Takustrasse 6, 14195 Berlin, Germany
- Tel: +49 30 9406 3420; Fax: +49 30 9406 2548; E-mail:
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Hultschig C, Kreutzberger J, Seitz H, Konthur Z, Büssow K, Lehrach H. Recent advances of protein microarrays. Curr Opin Chem Biol 2005; 10:4-10. [PMID: 16376134 PMCID: PMC7108394 DOI: 10.1016/j.cbpa.2005.12.011] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2005] [Accepted: 12/07/2005] [Indexed: 11/28/2022]
Abstract
Technological innovations and novel applications have greatly advanced the field of protein microarrays. Over the past two years, different types of protein microarrays have been used for serum profiling, protein abundance determinations, and identification of proteins that bind DNA or small compounds. However, considerable development is still required to ensure common quality standards and to establish large content repertoires. Here, we summarize applications available to date and discuss recent technological achievements and efforts on standardization.
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Manjasetty BA, Niesen FH, Scheich C, Roske Y, Goetz F, Behlke J, Sievert V, Heinemann U, Büssow K. X-ray structure of engineered human Aortic Preferentially Expressed Protein-1 (APEG-1). BMC Struct Biol 2005; 5:21. [PMID: 16354304 PMCID: PMC1352370 DOI: 10.1186/1472-6807-5-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2005] [Accepted: 12/14/2005] [Indexed: 11/26/2022]
Abstract
Background Human Aortic Preferentially Expressed Protein-1 (APEG-1) is a novel specific smooth muscle differentiation marker thought to play a role in the growth and differentiation of arterial smooth muscle cells (SMCs). Results Good quality crystals that were suitable for X-ray crystallographic studies were obtained following the truncation of the 14 N-terminal amino acids of APEG-1, a region predicted to be disordered. The truncated protein (termed ΔAPEG-1) consists of a single immunoglobulin (Ig) like domain which includes an Arg-Gly-Asp (RGD) adhesion recognition motif. The RGD motif is crucial for the interaction of extracellular proteins and plays a role in cell adhesion. The X-ray structure of ΔAPEG-1 was determined and was refined to sub-atomic resolution (0.96 Å). This is the best resolution for an immunoglobulin domain structure so far. The structure adopts a Greek-key β-sandwich fold and belongs to the I (intermediate) set of the immunoglobulin superfamily. The residues lying between the β-sheets form a hydrophobic core. The RGD motif folds into a 310 helix that is involved in the formation of a homodimer in the crystal which is mainly stabilized by salt bridges. Analytical ultracentrifugation studies revealed a moderate dissociation constant of 20 μM at physiological ionic strength, suggesting that APEG-1 dimerisation is only transient in the cell. The binding constant is strongly dependent on ionic strength. Conclusion Our data suggests that the RGD motif might play a role not only in the adhesion of extracellular proteins but also in intracellular protein-protein interactions. However, it remains to be established whether the rather weak dimerisation of APEG-1 involving this motif is physiogically relevant.
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Affiliation(s)
- Babu A Manjasetty
- Protein Structure Factory, c/o BESSY GmbH, Albert-Einstein-Str. 15, 12489 Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13092 Berlin, Germany
- Case Centre for Proteomics, Case Western Reserve University, Upton, New York 11973, USA
| | - Frank H Niesen
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Charité Universitätsmedizin Berlin, Institut für Medizinische Physik & Biophysik, Ziegelstr. 5-9, 10098 Berlin, Germany
- Structural Genomics Consortium, University of Oxford, Botnar Research Centre, Oxford, OX3 7LD, UK
| | - Christoph Scheich
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
| | - Yvette Roske
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13092 Berlin, Germany
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
| | - Frank Goetz
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13092 Berlin, Germany
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
| | - Joachim Behlke
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Volker Sievert
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
| | - Udo Heinemann
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13092 Berlin, Germany
- Institut für Chemie/Kristallographie, Freie Universität, Takustr. 6, 14195 Berlin, Germany
| | - Konrad Büssow
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
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Büssow K, Scheich C, Sievert V, Harttig U, Schultz J, Simon B, Bork P, Lehrach H, Heinemann U. Structural genomics of human proteins--target selection and generation of a public catalogue of expression clones. Microb Cell Fact 2005; 4:21. [PMID: 15998469 PMCID: PMC1250228 DOI: 10.1186/1475-2859-4-21] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2005] [Accepted: 07/05/2005] [Indexed: 11/12/2022] Open
Abstract
Background The availability of suitable recombinant protein is still a major bottleneck in protein structure analysis. The Protein Structure Factory, part of the international structural genomics initiative, targets human proteins for structure determination. It has implemented high throughput procedures for all steps from cloning to structure calculation. This article describes the selection of human target proteins for structure analysis, our high throughput cloning strategy, and the expression of human proteins in Escherichia coli host cells. Results and Conclusion Protein expression and sequence data of 1414 E. coli expression clones representing 537 different proteins are presented. 139 human proteins (18%) could be expressed and purified in soluble form and with the expected size. All E. coli expression clones are publicly available to facilitate further functional characterisation of this set of human proteins.
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Affiliation(s)
- Konrad Büssow
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
| | - Christoph Scheich
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
| | - Volker Sievert
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
| | - Ulrich Harttig
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- RZPD German Resource Center for Genome Research GmbH, Heubnerweg 6, 14059 Berlin, Germany
- DIFE, Arthur-Scheunert-Allee 114–116, 14558 Nuthetal, Germany
| | - Jörg Schultz
- EMBL Heidelberg, Meyerhofstr. 1, 69117 Heidelberg, Germany
- Department of Bioinformatics, University of Würzburg, Biocenter, Am Hubland, 97074 Würzburg, Germany
| | - Bernd Simon
- EMBL Heidelberg, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Peer Bork
- EMBL Heidelberg, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Hans Lehrach
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
| | - Udo Heinemann
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13092 Berlin, Germany
- Institut für Chemie/Kristallographie, Freie Universität, Takustr. 6, 14195 Berlin, Germany
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Cepok S, Zhou D, Srivastava R, Nessler S, Stei S, Büssow K, Sommer N, Hemmer B. Identification of Epstein-Barr virus proteins as putative targets of the immune response in multiple sclerosis. J Clin Invest 2005; 115:1352-60. [PMID: 15841210 PMCID: PMC1077174 DOI: 10.1172/jci23661] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2004] [Accepted: 02/15/2005] [Indexed: 11/17/2022] Open
Abstract
MS is a chronic inflammatory and demyelinating disease of the CNS with as yet unknown etiology. A hallmark of this disease is the occurrence of oligoclonal IgG antibodies in the cerebrospinal fluid (CSF). To assess the specificity of these antibodies, we screened protein expression arrays containing 37,000 tagged proteins. The 2 most frequent MS-specific reactivities were further mapped to identify the underlying high-affinity epitopes. In both cases, we identified peptide sequences derived from EBV proteins expressed in latently infected cells. Immunoreactivities to these EBV proteins, BRRF2 and EBNA-1, were significantly higher in the serum and CSF of MS patients than in those of control donors. Oligoclonal CSF IgG from MS patients specifically bound both EBV proteins. Also, CD8(+) T cell responses to latent EBV proteins were higher in MS patients than in controls. In summary, these findings demonstrate an increased immune response to EBV in MS patients, which suggests that the virus plays an important role in the pathogenesis of disease.
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Affiliation(s)
- Sabine Cepok
- Department of Neurology, Heinrich Heine University, Duesseldorf, Germany
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Cepok S, Zhou D, Srivastava R, Nessler S, Stei S, Büssow K, Sommer N, Hemmer B. Identification of Epstein-Barr virus proteins as putative targets of the immune response in multiple sclerosis. J Clin Invest 2005. [DOI: 10.1172/jci200523661] [Citation(s) in RCA: 217] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Manjasetty BA, Niesen FH, Delbrück H, Götz F, Sievert V, Büssow K, Behlke J, Heinemann U. X-ray structure of fumarylacetoacetate hydrolase family member Homo sapiens FLJ36880. Biol Chem 2005; 385:935-42. [PMID: 15551868 DOI: 10.1515/bc.2004.122] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The human protein FLJ36880 belongs to the fumarylacetoacetate hydrolase family. The X-ray structure of FLJ36880 has been determined to 2.2 A resolution employing the semi-automated high-throughput structural genomics approach of the Protein Structure Factory. FLJ36880 adopts a mixed beta-sandwich roll fold and forms homodimers in crystals as well as in solution. One Mg2+ ion is bound to each subunit of the dimeric protein by coordination to three carboxylate oxygens and three water molecules. These metal binding sites are accessible from the same surface of the dimer, partly due to the disorder of the undecapeptide stretch D29 to L39. The overall structure and metal binding site of FLJ36880 bear clear similarities to the C-terminal domain of the bifunctional enzyme HpcE from Escherichia coli C, fumarylacetoacetate hydrolase from Mus musculus and to YcgM (Apc5008) from E. coli 1262. These similarities provide a framework for suggesting biochemical functions and evolutionary relationships of FLJ36880. It appears highly probable that the metal binding sites are involved in an enzymatic activity related to the catabolism of aromatic amino acids. Two point mutations in the active-site of FAH, responsible for the metabolic disease hereditary tyrosinemia type I (HTI) in humans, affect residues that are structurally conserved in FLJ36880 and located in the putative catalytic site.
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Affiliation(s)
- Babu A Manjasetty
- Protein Structure Factory, c/o BESSY GmbH, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
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Mueller U, Büssow K, Diehl A, Bartl FJ, Niesen FH, Nyarsik L, Heinemann U. Rapid purification and crystal structure analysis of a small protein carrying two terminal affinity tags. ACTA ACUST UNITED AC 2005; 4:217-25. [PMID: 15185962 DOI: 10.1023/b:jsfg.0000016119.50040.a3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Small peptide tags are often fused to proteins to allow their affinity purification in high-throughput structure analysis schemes. To assess the compatibility of small peptide tags with protein crystallization and to examine if the tags alter the three-dimensional structure, the N-terminus of the chicken alpha-spectrin SH3 domain was labeled with a His6 tag and the C-terminus with a StrepII tag. The resulting protein, His6-SH3-StrepII, consists of 83 amino-acid residues, 23 of which originate from the tags. His6-SH3-StrepII is readily purified by dual affinity chromatography, has very similar biophysical characteristics as the untagged protein domain and crystallizes readily from a number of sparse-matrix screen conditions. The crystal structure analysis at 2.3 A resolution proves native-like structure of His6-SH3-StrepII and shows the entire His6 tag and part of the StrepII tag to be disordered in the crystal. Obviously, the fused affinity tags did not interfere with crystallization and structure analysis and did not change the protein structure. From the extreme case of His6-SH3-StrepII, where affinity tags represent 27% of the total fusion protein mass, we extrapolate that protein constructs with N- and C-terminal peptide tags may lend themselves to biophysical and structural investigations in high-throughput regimes.
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Affiliation(s)
- Uwe Mueller
- Institut für Chemie/Kristallographie, Freie Universität Berlin, Takustr. 6, D-14195 Berlin, Germany
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Soukenik M, Diehl A, Leidert M, Sievert V, Büssow K, Leitner D, Labudde D, Ball LJ, Lechner A, Nägler DK, Oschkinat H. The SEP domain of p47 acts as a reversible competitive inhibitor of cathepsin L. FEBS Lett 2004; 576:358-62. [PMID: 15498563 DOI: 10.1016/j.febslet.2004.09.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2004] [Revised: 09/13/2004] [Accepted: 09/13/2004] [Indexed: 11/25/2022]
Abstract
The solution structure of the human p47 SEP domain in a construct comprising residues G1-S2-p47(171-270) was determined by NMR spectroscopy. A structure-derived hypothesis about the domains' function was formulated and pursued in binding experiments with cysteine proteases. The SEP domain was found to be a reversible competitive inhibitor of cathepsin L with a Ki of 1.5 microM. The binding of G1-S2-p47(171-270) to cathepsin L was mapped by biochemical assays and the binding interface was investigated by NMR chemical shift perturbation experiments.
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Affiliation(s)
- Michael Soukenik
- Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle Str. 10, D-13125 Berlin, Germany
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Goehler H, Lalowski M, Stelzl U, Waelter S, Stroedicke M, Worm U, Droege A, Lindenberg KS, Knoblich M, Haenig C, Herbst M, Suopanki J, Scherzinger E, Abraham C, Bauer B, Hasenbank R, Fritzsche A, Ludewig AH, Büssow K, Buessow K, Coleman SH, Gutekunst CA, Landwehrmeyer BG, Lehrach H, Wanker EE. A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington's disease. Mol Cell 2004; 15:853-65. [PMID: 15383276 DOI: 10.1016/j.molcel.2004.09.016] [Citation(s) in RCA: 341] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2003] [Revised: 06/28/2004] [Accepted: 07/09/2004] [Indexed: 01/18/2023]
Abstract
Analysis of protein-protein interactions (PPIs) is a valuable approach for characterizing proteins of unknown function. Here, we have developed a strategy combining library and matrix yeast two-hybrid screens to generate a highly connected PPI network for Huntington's disease (HD). The network contains 186 PPIs among 35 bait and 51 prey proteins. It revealed 165 new potential interactions, 32 of which were confirmed by independent binding experiments. The network also permitted the functional annotation of 16 uncharacterized proteins and facilitated the discovery of GIT1, a G protein-coupled receptor kinase-interacting protein, which enhances huntingtin aggregation by recruitment of the protein into membranous vesicles. Coimmunoprecipitations and immunofluorescence studies revealed that GIT1 and huntingtin associate in mammalian cells under physiological conditions. Moreover, GIT1 localizes to neuronal inclusions, and is selectively cleaved in HD brains, indicating that its distribution and function is altered during disease pathogenesis.
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Affiliation(s)
- Heike Goehler
- Max-Delbrueck-Center for Molecular Medicine, 13125 Berlin-Buch, Germany
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Abstract
The preparation of proteins for structural and functional analysis using the Escherichia coli expression system is often hampered by the formation of insoluble intracellular protein aggregates (inclusion bodies). Transferring those proteins into their native states by in vitro protein folding requires screening for the best buffer conditions and suitable additives. However, it is difficult to assess the success of such a screen if no biological assay is available. We established a fully automated folding screen and a system to detect folded protein that is based on analytical hydrophobic interaction chromatography and tryptophan fluorescence spectroscopy. The system was evaluated with two model enzymes (carbonic anhydrase II and malate dehydrogenase), and was successfully applied to the folding of the p22 subunit of human dynactin, which is expressed in inclusion bodies in E. coli. The described screen allows for high-throughput folding analysis of inclusion body proteins for structural and functional analyses.
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36
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Büssow K, Quedenau C, Sievert V, Tischer J, Scheich C, Seitz H, Hieke B, Niesen FH, Götz F, Harttig U, Lehrach H. A catalog of human cDNA expression clones and its application to structural genomics. Genome Biol 2004; 5:R71. [PMID: 15345055 PMCID: PMC522878 DOI: 10.1186/gb-2004-5-9-r71] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [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: 04/16/2004] [Revised: 07/21/2004] [Accepted: 07/23/2004] [Indexed: 11/10/2022] Open
Abstract
We describe here a systematic approach to the identification of human proteins and protein fragments that can be expressed as soluble proteins in Escherichia coli. A cDNA expression library of 10,825 clones was screened by small-scale expression and purification and 2,746 clones were identified. Sequence and protein-expression data were entered into a public database. A set of 163 clones was selected for structural analysis and 17 proteins were prepared for crystallization, leading to three new structures.
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Affiliation(s)
- Konrad Büssow
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max Planck Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin, Germany
| | - Claudia Quedenau
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max Planck Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin, Germany
| | - Volker Sievert
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max Planck Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin, Germany
| | - Janett Tischer
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max Planck Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin, Germany
| | - Christoph Scheich
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max Planck Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin, Germany
| | - Harald Seitz
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max Planck Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin, Germany
| | - Brigitte Hieke
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max Planck Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin, Germany
| | - Frank H Niesen
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Institute of Medical Physics and Biophysics, Charité Medical School, Ziegelstraße 5/9, 10117 Berlin, Germany
| | - Frank Götz
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Alpha Bioverfahrenstechnik GmbH, Heinrich-Hertz-Straße 1b, 14532 Kleinmachnow, Germany
| | - Ulrich Harttig
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- RZPD German Resource Center for Genome Research GmbH, Heubnerweg 6, 14059 Berlin, Germany
| | - Hans Lehrach
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max Planck Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin, Germany
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Abstract
This chapter describes the production of a cDNA expression library from human fetal brain, the construction of a high-density protein array from such a library, and two applications to screen the array for binding proteins. After producing the library and decollating the expression clones, one can pick thousands of expression clones with a laboratory robot and can deposit them into microtiter plates in an ordered manner. Such ordered clone libraries are the starting material for the construction of a high-density protein array. This array is constructed by spotting the expression clones onto a protein-binding membrane. Following cell growth and induction of protein expression on the membrane, the cell spots are lysed and their recombinant protein immobilized on the membrane. The so-constructed array carries thousands of proteins without the need to clone, express, and spot individual proteins. Such arrays allow one to screen for numerous protein functions in a high-throughput manner.
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Affiliation(s)
- Hendrik Weiner
- Department of Vertebrate Genomics, Max Planck Institute of Molecular Genetics, Berlin, Germany
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Holz C, Prinz B, Bolotina N, Sievert V, Büssow K, Simon B, Stahl U, Lang C. Establishing the yeast Saccharomyces cerevisiae as a system for expression of human proteins on a proteome-scale. ACTA ACUST UNITED AC 2004; 4:97-108. [PMID: 14649293 DOI: 10.1023/a:1026226429429] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Structural genomics requires the application of a standardised process for overexpression of soluble proteins that allows high-throughput purification and analysis of protein products. We have developed a highly parallel approach to protein expression, including the simultaneous expression screening of a large number of cDNA clones in an appropriate vector system and the use of a protease-deficient host strain. A set of 221 human genes coding for proteins of various sizes with unknown structures was selected to evaluate the system. We transferred the cDNAs from an E. coli vector to the yeast expression vector by recombinational cloning, avoiding time-consuming recloning steps and the use of restriction enzymes in the cloning process. The subcloning yield was 95%, provided that a PCR fragment of the correct size could be obtained. Sixty percent of these proteins were expressed as soluble products at detectable levels and 48% were successfully purified under native conditions using the His6 tag fusion. The advantages of the developed yeast-based expression system are the ease of manipulation and cultivation of S. cerevisiae in the same way as with prokaryotic hosts and the ability to introduce post-translational modifications of proteins if required, thus being an attractive system for heterologous expression of mammalian proteins. The expression clones selected in this screening process are passed on to the fermentation process in order to provide milligram amounts of proteins for structure analysis within the 'Berlin Protein Structure Factory'. All data generated is stored in a relational database and is available on our website (http://www.proteinstrukturfabrik.de).
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Affiliation(s)
- Caterina Holz
- Berlin University of Technology, Institute for Biotechnology, Dept. Microbiology and Genetics, Gustav-Meyer-Allee 25, D-13355 Berlin, Germany
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Manjasetty BA, Delbrück H, Pham DT, Mueller U, Fieber-Erdmann M, Scheich C, Sievert V, Büssow K, Niesen FH, Weihofen W, Loll B, Saenger W, Heinemann U, Neisen FH. Crystal structure of Homo sapiens protein hp14.5. Proteins 2004; 54:797-800. [PMID: 14997576 DOI: 10.1002/prot.10619] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Manjasetty BA, Quedenau C, Sievert V, Büssow K, Niesen F, Delbrück H, Heinemann U. X-ray structure of human gankyrin, the product of a gene linked to hepatocellular carcinoma. Proteins 2004; 55:214-7. [PMID: 14997555 DOI: 10.1002/prot.20028] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Babu A Manjasetty
- Protein Structure Factory, c/o BESSY GmbH, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
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Manjasetty BA, Delbrück H, Pham DT, Mueller U, Fieber-Erdmann M, Scheich C, Sievert V, Büssow K, Niesen FH, Weihofen W, Loll B, Saenger W, Heinemann U. Crystal structure of Homo sapiens protein hp14.5. Proteins 2004. [DOI: 10.1002/prot.20188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Scheich C, Leitner D, Sievert V, Leidert M, Schlegel B, Simon B, Letunic I, Büssow K, Diehl A. Fast identification of folded human protein domains expressed in E. coli suitable for structural analysis. BMC Struct Biol 2004; 4:4. [PMID: 15113422 PMCID: PMC516802 DOI: 10.1186/1472-6807-4-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2004] [Accepted: 03/08/2004] [Indexed: 11/30/2022]
Abstract
Background High-throughput protein structure analysis of individual protein domains requires analysis of large numbers of expression clones to identify suitable constructs for structure determination. For this purpose, methods need to be implemented for fast and reliable screening of the expressed proteins as early as possible in the overall process from cloning to structure determination. Results 88 different E. coli expression constructs for 17 human protein domains were analysed using high-throughput cloning, purification and folding analysis to obtain candidates suitable for structural analysis. After 96 deep-well microplate expression and automated protein purification, protein domains were directly analysed using 1D 1H-NMR spectroscopy. In addition, analytical hydrophobic interaction chromatography (HIC) was used to detect natively folded protein. With these two analytical methods, six constructs (representing two domains) were quickly identified as being well folded and suitable for structural analysis. Conclusion The described approach facilitates high-throughput structural analysis. Clones expressing natively folded proteins suitable for NMR structure determination were quickly identified upon small scale expression screening using 1D 1H-NMR and/or analytical HIC. This procedure is especially effective as a fast and inexpensive screen for the 'low hanging fruits' in structural genomics.
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Affiliation(s)
- Christoph Scheich
- Proteinstrukturfabrik, Heubnerweg 6, 14059 Berlin, Germany
- Max Planck Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, Germany
| | - Dietmar Leitner
- Proteinstrukturfabrik, Heubnerweg 6, 14059 Berlin, Germany
- Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Volker Sievert
- Proteinstrukturfabrik, Heubnerweg 6, 14059 Berlin, Germany
- Max Planck Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, Germany
| | - Martina Leidert
- Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Brigitte Schlegel
- Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Bernd Simon
- Proteinstrukturfabrik, Heubnerweg 6, 14059 Berlin, Germany
- European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Ivica Letunic
- European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Konrad Büssow
- Proteinstrukturfabrik, Heubnerweg 6, 14059 Berlin, Germany
- Max Planck Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, Germany
| | - Anne Diehl
- Proteinstrukturfabrik, Heubnerweg 6, 14059 Berlin, Germany
- Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
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de Graaf K, Hekerman P, Spelten O, Herrmann A, Packman LC, Büssow K, Müller-Newen G, Becker W. Characterization of cyclin L2, a novel cyclin with an arginine/serine-rich domain: phosphorylation by DYRK1A and colocalization with splicing factors. J Biol Chem 2004; 279:4612-24. [PMID: 14623875 DOI: 10.1074/jbc.m310794200] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A novel method employing filter arrays of a cDNA expression library for the identification of substrates for protein kinases was developed. With this technique, we identified a new member of the cyclin family, cyclin L2, as a substrate of the nuclear protein kinase DYRK1A. Cyclin L2 contains an N-terminal cyclin domain and a C-terminal arginine/serine-rich domain (RS domain), which is a hallmark of many proteins involved in pre-mRNA processing. The gene for cyclin L2 encodes the full-length cyclin L2, which is predominantly expressed in testis, as well as a truncated splicing variant (cyclin L2S) that lacks the RS domain and is ubiquitously expressed in human tissues. Full-length cyclin L2, but not cyclin L2S, was associated with the cyclin-dependent kinase PITSLRE. Cyclin L2 interacted with splicing factor 2 in vitro and was co-localized with the splicing factor SC35 in the nuclear speckle compartment. Photobleaching experiments showed that a fusion protein of green fluorescent protein and cyclin L2 in nuclear speckles rapidly exchanged with unbleached molecules in the nucleus, similar to other RS domain-containing proteins. In striking contrast, the closely related green fluorescent protein-cyclin L1 was immobile in the speckle compartment. DYRK1A interacted with cyclin L2 in pull-down assays, and overexpression of DYRK1A stimulated phosphorylation of cyclin L2 in COS-7 cells. These data characterize cyclin L2 as a highly mobile component of nuclear speckles and suggest that DYRK1A may regulate splicing by phosphorylation of cyclin L2.
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Affiliation(s)
- Katrin de Graaf
- Institut für Pharmakologie und Toxikologie, Medizinische Fakultät der RWTH Aachen, Wendlingweg 2, 52074 Aachen, Germany, Institut für Biochemie, Medizinische Fakultät der RWTH Aachen, Pauwelstrasse 30, 52074 Aachen, Germany
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Brockmann C, Leitner D, Labudde D, Diehl A, Sievert V, Büssow K, Kühne R, Oschkinat H. The solution structure of the SODD BAG domain reveals additional electrostatic interactions in the HSP70 complexes of SODD subfamily BAG domains. FEBS Lett 2004; 558:101-6. [PMID: 14759524 DOI: 10.1016/s0014-5793(03)01490-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2003] [Revised: 12/08/2003] [Accepted: 12/10/2003] [Indexed: 10/26/2022]
Abstract
The solution structure of an N-terminally extended construct of the SODD BAG domain was determined by nuclear magnetic resonance spectroscopy. A homology model of the SODD-BAG/HSP70 complex reveals additional possible interactions that are specific for the SODD subfamily of BAG domains while the overall geometry of the complex remains the same. Relaxation rate measurements show that amino acids N358-S375 of SODD which were previously assigned to its BAG domain are not structured in our construct. The SODD BAG domain is thus indeed smaller than the homologous domain in Bag1 defining a new subfamily of BAG domains.
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Affiliation(s)
- Christoph Brockmann
- Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, D-13125 Berlin, Germany
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Scheich C, Sievert V, Büssow K. An automated method for high-throughput protein purification applied to a comparison of His-tag and GST-tag affinity chromatography. BMC Biotechnol 2003; 3:12. [PMID: 12885298 PMCID: PMC183854 DOI: 10.1186/1472-6750-3-12] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [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: 03/26/2003] [Accepted: 07/28/2003] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Functional Genomics, the systematic characterisation of the functions of an organism's genes, includes the study of the gene products, the proteins. Such studies require methods to express and purify these proteins in a parallel, time and cost effective manner. RESULTS We developed a method for parallel expression and purification of recombinant proteins with a hexahistidine tag (His-tag) or glutathione S-transferase (GST)-tag from bacterial expression systems. Proteins are expressed in 96-well microplates and are purified by a fully automated procedure on a pipetting robot. Up to 90 microgram purified protein can be obtained from 1 ml microplate cultures. The procedure is readily reproducible and 96 proteins can be purified in approximately three hours. It avoids clearing of crude cellular lysates and the use of magnetic affinity beads and is therefore less expensive than comparable commercial systems. We have used this method to compare purification of a set of human proteins via His-tag or GST-tag. Proteins were expressed as fusions to an N-terminal tandem His- and GST-tag and were purified by metal chelating or glutathione affinity chromatography. The purity of the obtained protein samples was similar, yet His-tag purification resulted in higher yields for some proteins. CONCLUSION A fully automated, robust and cost effective method was developed for the purification of proteins that can be used to quickly characterise expression clones in high throughput and to produce large numbers of proteins for functional studies.His-tag affinity purification was found to be more efficient than purification via GST-tag for some proteins.
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Affiliation(s)
- Christoph Scheich
- Protein Structure Factory, Max Planck Institute of Molecular Genetics, Heubnerweg 6, 14059 Berlin, Germany
| | - Volker Sievert
- Protein Structure Factory, Max Planck Institute of Molecular Genetics, Heubnerweg 6, 14059 Berlin, Germany
| | - Konrad Büssow
- Protein Structure Factory, Max Planck Institute of Molecular Genetics, Heubnerweg 6, 14059 Berlin, Germany
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Abstract
Facilities and methods for the high-throughput crystal structure analysis of human proteins are described as recently established in the Protein Structure Factory, a Berlin-area structural genomics project. Genes encoding human proteins are expressed in either recombinant Escherichia coli or yeast (Saccharomyces cerevisiae or Pichia pastoris). To facilitate and standardize protein purification, the target proteins are produced with various tags for affinity chromatography. For high-throughput crystallization, a robotic station is being set up that has the capacity to handle 960 000 experiments simultaneously. The resulting protein crystals will be subjected to X-ray diffraction experiments at the third-generation synchrotron storage ring BESSY where protein crystallography beamlines are currently under construction. The Protein Structure Factory's strategy for high-throughput production and structure analysis of human proteins is evaluated based on first results.
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Affiliation(s)
- Udo Heinemann
- Forschungsgruppe Kristallographie, Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, D-13125 Berlin, Germany.
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Büssow K, Hoffmann S, Sievert V. ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files. BMC Bioinformatics 2002; 3:40. [PMID: 12493080 PMCID: PMC139979 DOI: 10.1186/1471-2105-3-40] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [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: 09/20/2002] [Accepted: 12/19/2002] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Functional genomics involves the parallel experimentation with large sets of proteins. This requires management of large sets of open reading frames as a prerequisite of the cloning and recombinant expression of these proteins. RESULTS A Java program was developed for retrieval of protein and nucleic acid sequences and annotations from NCBI GenBank, using the XML sequence format. Annotations retrieved by ORFer include sequence name, organism and also the completeness of the sequence. The program has a graphical user interface, although it can be used in a non-interactive mode. For protein sequences, the program also extracts the open reading frame sequence, if available, and checks its correct translation. ORFer accepts user input in the form of single or lists of GenBank GI identifiers or accession numbers. It can be used to extract complete sets of open reading frames and protein sequences from any kind of GenBank sequence entry, including complete genomes or chromosomes. Sequences are either stored with their features in a relational database or can be exported as text files in Fasta or tabulator delimited format. The ORFer program is freely available at http://www.proteinstrukturfabrik.de/orfer. CONCLUSION The ORFer program allows for fast retrieval of DNA sequences, protein sequences and their open reading frames and sequence annotations from GenBank. Furthermore, storage of sequences and features in a relational database is supported. Such a database can supplement a laboratory information system (LIMS) with appropriate sequence information.
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Affiliation(s)
- Konrad Büssow
- Protein Structure Factory, Max Planck Institute of Molecular Genetics, Heubnerweg 6, 14059 Berlin, Germany
| | - Steve Hoffmann
- Protein Structure Factory, Max Planck Institute of Molecular Genetics, Heubnerweg 6, 14059 Berlin, Germany
| | - Volker Sievert
- Protein Structure Factory, Max Planck Institute of Molecular Genetics, Heubnerweg 6, 14059 Berlin, Germany
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Eickhoff H, Konthur Z, Lueking A, Lehrach H, Walter G, Nordhoff E, Nyarsik L, Büssow K. Protein array technology: the tool to bridge genomics and proteomics. Adv Biochem Eng Biotechnol 2002; 77:103-12. [PMID: 12227733 DOI: 10.1007/3-540-45713-5_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The generation of protein chips requires much more efforts than DNA microchips. While DNA is DNA and a variety of different DNA molecules behave stable in a hybridisation experiment, proteins are much more difficult to produce and to handle. Outside of a narrow range of environmental conditions, proteins will denature, lose their three-dimensional structure and a lot of their specificity and activity. The chapter describes the pitfalls and challenges in Protein Microarray technology to produce native and functional proteins and store them in a native and special environment for every single spot on an array, making applications like antibody profiling and serum screening possible not only on denatured arrays but also on native protein arrays.
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Abstract
The human genome is sequenced, but only a minority of genes have been assigned a function. Whole-genome expression profiling is an important tool for functional genomic studies. Automated technology allows high-throughput gene activity monitoring by analysis of complex expression patterns, resulting in fingerprints of diseased versus normal or developmentally distinct tissues. Differential gene expression can be most efficiently monitored by DNA hybridization on arrays of oligonucleotides or cDNA clones. Starting from high-density filter membranes, cDNA microarrays have recently been devised in chip format. We have shown that the same cDNA libraries can be used for high-throughput protein expression and antibody screening on high-density filters and microarrays. These libraries connect recombinant proteins to clones identified by DNA hybridization or sequencing, hence creating a direct link between gene catalogs and functional catalogs. Microarrays can now be used to go from an individual clone to a specific gene and its protein product. Clone libraries become amenable to database integration including all steps from DNA sequencing to functional assays of gene products.
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Affiliation(s)
- K Büssow
- Max Planck Institute of Molecular Genetics, Berlin, Germany.
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Abstract
High-throughput protein arrays allow the miniaturized and parallel analysis of large numbers of diagnostic markers in complex samples. Using automated colony picking and gridding, cDNA or antibody libraries can be expressed and screened as clone arrays. Protein microarrays are constructed from recombinantly expressed, purified, and yet functional proteins, entailing a range of optimized expression systems. Antibody microarrays are becoming a robust format for expression profiling of whole genomes. Alternative systems, such as aptamer, PROfusion, nano- and microfluidic arrays are all at proof-of-concept stage. Differential protein profiles have been used as molecular diagnostics for cancer and autoimmune diseases and might ultimately be applied to screening of high-risk and general populations.
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Affiliation(s)
- Gerald Walter
- Biorchard Ltd., c/o Cornupia Capital Ltd., 27 Old Gloucester Street, London, UK WC1N 3XX.
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