1
|
Golm SK, Hübner W, Müller KM. Fluorescence Microscopy in Adeno-Associated Virus Research. Viruses 2023; 15:v15051174. [PMID: 37243260 DOI: 10.3390/v15051174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/02/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Research on adeno-associated virus (AAV) and its recombinant vectors as well as on fluorescence microscopy imaging is rapidly progressing driven by clinical applications and new technologies, respectively. The topics converge, since high and super-resolution microscopes facilitate the study of spatial and temporal aspects of cellular virus biology. Labeling methods also evolve and diversify. We review these interdisciplinary developments and provide information on the technologies used and the biological knowledge gained. The emphasis lies on the visualization of AAV proteins by chemical fluorophores, protein fusions and antibodies as well as on methods for the detection of adeno-associated viral DNA. We add a short overview of fluorescent microscope techniques and their advantages and challenges in detecting AAV.
Collapse
Affiliation(s)
- Susanne K Golm
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Wolfgang Hübner
- Biomolecular Photonics, Faculty of Physics, Bielefeld University, 33615 Bielefeld, Germany
| | - Kristian M Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| |
Collapse
|
2
|
Le DT, Radukic MT, Teschner K, Becker L, Müller KM. Synthesis and Concomitant Assembly of Adeno-Associated Virus-like Particles in Escherichia coli. ACS Synth Biol 2022; 11:3601-3607. [PMID: 36279242 DOI: 10.1021/acssynbio.2c00451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Virus-like particles (VLPs) have been used for numerous pharmaceutical applications, particularly vaccination and drug delivery. Recombinant adeno-associated virus (rAAV), a leading candidate in gene therapy, has been proposed as a vaccine scaffold, but high production costs limit its use. Here we establish intracellular production of AAV VLPs in Escherichia coli. VP3 capsid proteins of AAV serotype 5 (AAV5) were expressed, and VLPs were readily purified. The correct assembly was confirmed by ELISA with an intact-capsid AAV5 antibody and an AAVR domain as well as by atomic force microscopy. Biological functionality was demonstrated with a HeLa cell internalization assay. Coexpression of the assembly-activating protein (AAP) of AAV5 in E. coli improved capsid yield. This work provides the first evidence that AAV VLPs form in E. coli, opening new opportunities for production and exploration of AAV VLPs for biomedical applications.
Collapse
Affiliation(s)
- Dinh To Le
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Marco T Radukic
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Kathrin Teschner
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Lukas Becker
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Kristian M Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| |
Collapse
|
3
|
Karsten L, Goett-Zink L, Schmitz J, Hoffrogge R, Grünberger A, Kottke T, Müller KM. Genetically Encoded Ratiometric pH Sensors for the Measurement of Intra- and Extracellular pH and Internalization Rates. Biosensors 2022; 12:bios12050271. [PMID: 35624572 PMCID: PMC9138566 DOI: 10.3390/bios12050271] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 03/15/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 12/13/2022]
Abstract
pH-sensitive fluorescent proteins as genetically encoded pH sensors are promising tools for monitoring intra- and extracellular pH. However, there is a lack of ratiometric pH sensors, which offer a good dynamic range and can be purified and applied extracellularly to investigate uptake. In our study, the bright fluorescent protein CoGFP_V0 was C-terminally fused to the ligand epidermal growth factor (EGF) and retained its dual-excitation and dual-emission properties as a purified protein. The tandem fluorescent variants EGF-CoGFP-mTagBFP2 (pK′ = 6.6) and EGF-CoGFP-mCRISPRed (pK′ = 6.1) revealed high dynamic ranges between pH 4.0 and 7.5. Using live-cell fluorescence microscopy, both pH sensor molecules permitted the conversion of fluorescence intensity ratios to detailed intracellular pH maps, which revealed pH gradients within endocytic vesicles. Additionally, extracellular binding of the pH sensors to cells expressing the EGF receptor (EGFR) enabled the tracking of pH shifts inside cultivation chambers of a microfluidic device. Furthermore, the dual-emission properties of EGF-CoGFP-mCRISPRed upon 488 nm excitation make this pH sensor a valuable tool for ratiometric flow cytometry. This high-throughput method allowed for the determination of internalization rates, which represents a promising kinetic parameter for the in vitro characterization of protein–drug conjugates in cancer therapy.
Collapse
Affiliation(s)
- Lennard Karsten
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany;
| | - Lukas Goett-Zink
- Biophysical Chemistry and Diagnostics, Medical School OWL, Faculty of Chemistry, Bielefeld University, 33615 Bielefeld, Germany; (L.G.-Z.); (T.K.)
| | - Julian Schmitz
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany; (J.S.); (A.G.)
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Raimund Hoffrogge
- Cell Culture Technology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany;
| | - Alexander Grünberger
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany; (J.S.); (A.G.)
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Tilman Kottke
- Biophysical Chemistry and Diagnostics, Medical School OWL, Faculty of Chemistry, Bielefeld University, 33615 Bielefeld, Germany; (L.G.-Z.); (T.K.)
| | - Kristian M. Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany;
- Correspondence:
| |
Collapse
|
4
|
Gruß H, Feiner RC, Mseya R, Schröder DC, Jewgiński M, Müller KM, Latajka R, Marion A, Sewald N. Peptide stapling by late-stage Suzuki–Miyaura cross-coupling. Beilstein J Org Chem 2022; 18:1-12. [PMID: 35047078 PMCID: PMC8744458 DOI: 10.3762/bjoc.18.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 12/09/2021] [Indexed: 12/19/2022] Open
Abstract
The development of peptide stapling techniques to stabilise α-helical secondary structure motifs of peptides led to the design of modulators of protein–protein interactions, which had been considered undruggable for a long time. We disclose a novel approach towards peptide stapling utilising macrocyclisation by late-stage Suzuki–Miyaura cross-coupling of bromotryptophan-containing peptides of the catenin-binding domain of axin. Optimisation of the linker length in order to find a compromise between both sufficient linker rigidity and flexibility resulted in a peptide with an increased α-helicity and enhanced binding affinity to its native binding partner β-catenin. An increased proteolytic stability against proteinase K has been demonstrated.
Collapse
Affiliation(s)
- Hendrik Gruß
- Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Rebecca C Feiner
- Department of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Ridhiwan Mseya
- Department of Chemistry, Middle East Technical University, 06800, Ankara, Turkey
| | - David C Schröder
- Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Michał Jewgiński
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wrocław, Poland
| | - Kristian M Müller
- Department of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Rafał Latajka
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wrocław, Poland
| | - Antoine Marion
- Department of Chemistry, Middle East Technical University, 06800, Ankara, Turkey
| | - Norbert Sewald
- Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| |
Collapse
|
5
|
Boschanski M, Krüger T, Karsten L, Falck G, Alam S, Gerlach M, Müller B, Müller KM, Sewald N, Dierks T. Site-Specific Conjugation Strategy for Dual Antibody-Drug Conjugates Using Aerobic Formylglycine-Generating Enzymes. Bioconjug Chem 2021; 32:1167-1174. [PMID: 34060308 DOI: 10.1021/acs.bioconjchem.1c00246] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Multiple, site-specific protein conjugation is increasingly attractive for the generation of antibody-drug conjugates (ADCs). As it is important to control the number and position of cargoes in an ADC, position-selective generation of reactive sites in the protein of interest is required. Formylglycine (FGly) residues are generated by enzymatic conversion of cysteine residues embedded in a certain amino acid sequence motif with a formylglycine-generating enzyme (FGE). The addition of copper ions increases FGE activity leading to the conversion of cysteines within less readily accepted sequences. With this tuned enzyme activity, it is possible to address two different recognition sequences using two aerobic formylglycine-generating enzymes. We demonstrate an improved and facile strategy for the functionalization of a DARPin (designed ankyrin repeat protein) and the single-chain antibody scFv425-Fc, both directed against the epidermal growth factor receptor (EGFR). The single-chain antibody was conjugated with monomethyl auristatin E (MMAE) and carboxyfluorescein (CF) and successfully tested for receptor binding, internalization, and cytotoxicity in cell culture, respectively.
Collapse
Affiliation(s)
- Mareile Boschanski
- Biochemistry, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Tobias Krüger
- Organic and Bioorganic Chemistry, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Lennard Karsten
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Georg Falck
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Sarfaraz Alam
- Biochemistry, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Marcus Gerlach
- Organic and Bioorganic Chemistry, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | | | - Kristian M Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Thomas Dierks
- Biochemistry, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| |
Collapse
|
6
|
Radukic MT, Brandt D, Haak M, Müller KM, Kalinowski J. Erratum: Nanopore sequencing of native adeno-associated virus (AAV) single-stranded DNA using a transposase-based rapid protocol. NAR Genom Bioinform 2021; 3:lqab029. [PMID: 33884370 PMCID: PMC8046012 DOI: 10.1093/nargab/lqab029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Marco T Radukic
- Faculty of Technology, Bielefeld University, D-33501 Bielefeld, Germany
| | - David Brandt
- Center for Biotechnology (CeBiTec), Bielefeld University, D-33501 Bielefeld, Germany
| | - Markus Haak
- Center for Biotechnology (CeBiTec), Bielefeld University, D-33501 Bielefeld, Germany
| | - Kristian M Müller
- Faculty of Technology, Bielefeld University, D-33501 Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, D-33501 Bielefeld, Germany
| |
Collapse
|
7
|
Abstract
Virus-like particles (VLPs) are increasingly used for vaccine development and drug delivery. Assembly of VLPs from purified monomers in a chemically defined reaction is advantageous compared to in vivo assembly, because it avoids encapsidation of host-derived components and enables loading with added cargoes. This review provides an overview of ex cella VLP production methods focusing on capsid protein production, factors that impact the in vitro assembly, and approaches to characterize in vitro VLPs. The uses of in vitro produced VLPs as vaccines and for therapeutic delivery are also reported.
Collapse
Affiliation(s)
| | - Kristian M. Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany;
| |
Collapse
|
8
|
Abstract
An array of l- and d-halotryptophans with different substituents at the indole moiety was synthesized employing either enzymatic halogenation by halogenases or incorporation of haloindoles using tryptophan synthase. Introduction of these Trp derivatives into RGD peptides as a benchmark system was performed to investigate their influence on bioactivity. Halotryptophan-containing RGD peptides display increased affinity toward integrin αvβ3 and enhanced selectivity over integrin α5β1. In addition, bromotryptophan was exploited as a platform for late-stage diversification by Suzuki-Miyaura cross-coupling (SMC), resulting in new-to-nature biaryl motifs. These peptides show enhanced affinity toward αvβ3, good affinity to αvβ8, and remarkable selectivity over α5β1 and αIIbβ3 while featuring fluorogenic properties. Their feasibility as a probe was demonstrated in vitro. Extensive molecular dynamics simulations were undertaken to elucidate NMR and high-performance liquid chromatography (HPLC) data for these late-stage diversified cyclic RGD peptides and to further characterize their conformational preferences.
Collapse
Affiliation(s)
- Isabell Kemker
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - David C Schröder
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Rebecca C Feiner
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Kristian M Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Antoine Marion
- Department of Chemistry, Middle East Technical University, Kimya Bölümü Üniversiteler Mah., Çankaya, 06800 Ankara, Turkey
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany.,Department of Chemistry, Middle East Technical University, Kimya Bölümü Üniversiteler Mah., Çankaya, 06800 Ankara, Turkey
| |
Collapse
|
9
|
Janson N, Krüger T, Karsten L, Boschanski M, Dierks T, Müller KM, Sewald N. Bifunctional Reagents for Formylglycine Conjugation: Pitfalls and Breakthroughs. Chembiochem 2020; 21:3580-3593. [PMID: 32767537 PMCID: PMC7756428 DOI: 10.1002/cbic.202000416] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/05/2020] [Indexed: 12/28/2022]
Abstract
Formylglycine-generating enzymes specifically oxidize cysteine within the consensus sequence CxPxR to Cα -formylglycine (FGly). This noncanonical electrophilic amino acid can subsequently be addressed selectively by bioorthogonal hydrazino-iso-Pictet-Spengler (HIPS) or Knoevenagel ligation to attach payloads like fluorophores or drugs to proteins to obtain a defined payload-to-protein ratio. However, the disadvantages of these conjugation techniques include the need for a large excess of conjugation building block, comparably low reaction rates and limited stability of FGly-containing proteins. Therefore, functionalized clickable HIPS and tandem Knoevenagel building blocks were synthesized, conjugated to small proteins (DARPins) and subsequently linked to strained alkyne-containing payloads for protein labeling. This procedure allowed the selective bioconjugation of one or two DBCO-carrying payloads with nearly stoichiometric amounts at low concentrations. Furthermore, an azide-modified tandem Knoevenagel building block enabled the synthesis of branched PEG linkers and the conjugation of two fluorophores, resulting in an improved signal-to-noise ratio in live-cell fluorescence-imaging experiments targeting the EGF receptor.
Collapse
Affiliation(s)
- Nils Janson
- Faculty of ChemistryOrganic and Bioorganic ChemistryBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
| | - Tobias Krüger
- Faculty of ChemistryOrganic and Bioorganic ChemistryBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
| | - Lennard Karsten
- Cellular and Molecular BiotechnologyBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
| | - Mareile Boschanski
- Faculty of ChemistryBiochemistryBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
| | - Thomas Dierks
- Faculty of ChemistryBiochemistryBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
| | - Kristian M. Müller
- Cellular and Molecular BiotechnologyBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
| | - Norbert Sewald
- Faculty of ChemistryOrganic and Bioorganic ChemistryBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
| |
Collapse
|
10
|
Greimelmaier K, Wohlschläger J, Probst A, Hager T, Wardelmann E, Werlein C, Jonigk D, Müller KM. [Mesothelial proliferation of the tunica vaginalis testis]. Pathologe 2020; 41:406-410. [PMID: 32472158 DOI: 10.1007/s00292-020-00797-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proliferative changes seen in reactive mesothelial hyperplasia of a hydrocele sac may mimic malignant mesothelioma. There is no immunohistochemical staining that reliably separates benign from malignant mesothelial proliferations. However, the combined analysis of BAP1 by immunohistochemistry and CDKN2A by FISH has been reported to yield both a high specificity and sensitivity in this differential diagnosis. In addition, the evaluation of risk factors such as asbestos exposure or prior traumata may be helpful for the correct diagnosis. Exclusion of stromal invasion, which is diagnostic for malign mesothelioma, is of utmost importance. Therefore, extended histological workup is essential.
Collapse
Affiliation(s)
- K Greimelmaier
- Institut für Pathologie, Diakonissenkrankenhaus Flensburg, Knuthstr. 1, 24939, Flensburg, Deutschland.
| | - J Wohlschläger
- Institut für Pathologie, Diakonissenkrankenhaus Flensburg, Knuthstr. 1, 24939, Flensburg, Deutschland
- Institut für Pathologie, Universitätsklinikum Essen, Essen, Deutschland
| | - A Probst
- Urologische Klinik, Diakonissenkrankenhaus Flensburg, Flensburg, Deutschland
| | - T Hager
- Institut für Pathologie, Universitätsklinikum Essen, Essen, Deutschland
| | - E Wardelmann
- Gerhard-Domagk-Institut für Pathologie, Universitätsklinikum Münster, Münster, Deutschland
| | - C Werlein
- Institut für Pathologie, Medizinische Hochschule Hannover, Hannover, Deutschland
| | - D Jonigk
- Institut für Pathologie, Medizinische Hochschule Hannover, Hannover, Deutschland
- Deutsches Zentrum für Lungenforschung (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Deutschland
| | - K M Müller
- Gerhard-Domagk-Institut für Pathologie, Universitätsklinikum Münster, Münster, Deutschland
| |
Collapse
|
11
|
Radukic MT, Brandt D, Haak M, Müller KM, Kalinowski J. Nanopore sequencing of native adeno-associated virus (AAV) single-stranded DNA using a transposase-based rapid protocol. NAR Genom Bioinform 2020; 2:lqaa074. [PMID: 33575623 PMCID: PMC7671332 DOI: 10.1093/nargab/lqaa074] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 04/22/2020] [Revised: 08/06/2020] [Accepted: 09/21/2020] [Indexed: 12/14/2022] Open
Abstract
Next-generation sequencing of single-stranded DNA (ssDNA) enables transgene characterization of gene therapy vectors such as adeno-associated virus (AAV), but current library generation uses complicated and potentially biased second-strand synthesis. We report that libraries for nanopore sequencing of ssDNA can be conveniently created without second-strand synthesis using a transposase-based protocol. We show for bacteriophage M13 ssDNA that the MuA transposase has unexpected residual activity on ssDNA, explained in part by transposase action on transient double-stranded hairpins. In case of AAV, library creation is additionally aided by genome hybridization. We demonstrate the power of direct sequencing combined with nanopore long reads by characterizing AAV vector transgenes. Sequencing yielded reads up to full genome length, including GC-rich inverted terminal repeats. Unlike short-read techniques, single reads covered genome-genome and genome-contaminant fusions and other recombination events, whilst additionally providing information on epigenetic methylation. Single-nucleotide variants across the transgene cassette were revealed and secondary genome packaging signals were readily identified. Moreover, comparison of sequence abundance with quantitative polymerase chain reaction results demonstrated the technique's future potential for quantification of DNA impurities in AAV vector stocks. The findings promote direct nanopore sequencing as a fast and versatile platform for ssDNA characterization, such as AAV ssDNA in research and clinical settings.
Collapse
Affiliation(s)
- Marco T Radukic
- Faculty of Technology, Bielefeld University, D-33501 Bielefeld, Germany
| | - David Brandt
- Center for Biotechnology (CeBiTec), Bielefeld University, D-33501 Bielefeld, Germany
| | - Markus Haak
- Center for Biotechnology (CeBiTec), Bielefeld University, D-33501 Bielefeld, Germany
| | - Kristian M Müller
- Faculty of Technology, Bielefeld University, D-33501 Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, D-33501 Bielefeld, Germany
| |
Collapse
|
12
|
Abstract
Monomeric RGD peptides show unspecific fluid-phase uptake in cells, whereas multimeric RGD peptides are thought to be internalized by integrin-mediated endocytosis. However, a potential correlation between uptake mechanism and molecular mass has been neglected so far. A dual derivatization of peptide c(RGDw(7Br)K) was performed to investigate this. A fluorescent probe was installed by chemoselective Suzuki-Miyaura cross-coupling of the 7-bromotryptophan and a poly(ethylene glycol) (PEG) linker was attached to the lysine residue. Flow cytometry and live cell imaging confirmed unspecific uptake of the small, non-PEGylated peptide, whereas the PEG5000 peptide conjugate unveiled a selective internalization by M21 cells overexpressing αv β3 and no uptake in αv -deficient M21L cells.
Collapse
Affiliation(s)
- Isabell Kemker
- Organische und Bioorganische ChemieFakultät für ChemieUniversität BielefeldUniversitätsstrasse 2533615BielefeldGermany
| | - Rebecca C. Feiner
- Zelluläre und Molekulare BiotechnologieTechnische FakultätUniversität BielefeldUniversitätsstrasse 2533615BielefeldGermany
| | - Kristian M. Müller
- Zelluläre und Molekulare BiotechnologieTechnische FakultätUniversität BielefeldUniversitätsstrasse 2533615BielefeldGermany
| | - Norbert Sewald
- Organische und Bioorganische ChemieFakultät für ChemieUniversität BielefeldUniversitätsstrasse 2533615BielefeldGermany
| |
Collapse
|
13
|
Le DT, Radukic MT, Müller KM. Adeno-associated virus capsid protein expression in Escherichia coli and chemically defined capsid assembly. Sci Rep 2019; 9:18631. [PMID: 31819093 PMCID: PMC6901487 DOI: 10.1038/s41598-019-54928-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 07/04/2019] [Accepted: 11/20/2019] [Indexed: 01/17/2023] Open
Abstract
Research and clinical applications of recombinant adeno-associated virus (rAAV) significantly increased in recent years alongside regulatory approvals of rAAV gene therapy products. To date, all rAAV vectors as well as AAV empty capsids are produced in eukaryotic cells. We explored a new route to generate AAV capsids with the aim to analyze capsid assembly in a chemically defined setting and pave the way for new production methods and applications based on AAV virus-like particles (VLPs). We generated these empty capsids by bacterial expression and subsequent concomitant protein refolding and VLP formation. AAV serotype 2 structural protein VP3 was expressed in Escherichia coli. VLPs formed as demonstrated by dynamic light scattering, atomic force microscopy, and ELISA. Furthermore, VLPs internalized into human HeLa cells. To extend the application range of the VLPs, we tested peptide insertions, at the genetic level, in a surface loop (amino acid position 587) or at the C-terminus of VP3 and these variants also formed VLPs. VLPs developed without assembly-activating protein (AAP), but adding purified recombinant AAP to the refolding process increased capsid yield. Our findings offer a new route to understand AAV assembly biology and open a toolbox for AAV production strategies that might enable capsid display for vaccination and matching of capsids with cargoes at large scale and low cost.
Collapse
Affiliation(s)
- Dinh To Le
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Marco T Radukic
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Kristian M Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Bielefeld, Germany.
| |
Collapse
|
14
|
Feiner RC, Teschner J, Teschner KE, Radukic MT, Baumann T, Hagen S, Hannappel Y, Biere N, Anselmetti D, Arndt KM, Müller KM. rAAV Engineering for Capsid-Protein Enzyme Insertions and Mosaicism Reveals Resilience to Mutational, Structural and Thermal Perturbations. Int J Mol Sci 2019; 20:ijms20225702. [PMID: 31739438 PMCID: PMC6887778 DOI: 10.3390/ijms20225702] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/08/2019] [Accepted: 11/11/2019] [Indexed: 12/22/2022] Open
Abstract
Recombinant adeno-associated viruses (rAAV) provide outstanding options for customization and superior capabilities for gene therapy. To access their full potential, facile genetic manipulation is pivotal, including capsid loop modifications. Therefore, we assessed capsid tolerance to modifications of the structural VP proteins in terms of stability and plasticity. Flexible glycine-serine linkers of increasing sizes were, at the genetic level, introduced into the 587 loop region of the VP proteins of serotype 2, the best studied AAV representative. Analyses of biological function and thermal stability with respect to genome release of viral particles revealed structural plasticity. In addition, insertion of the 29 kDa enzyme β-lactamase into the loop region was tested with a complete or a mosaic modification setting. For the mosaic approach, investigation of VP2 trans expression revealed that a Kozak sequence was required to prevent leaky scanning. Surprisingly, even the full capsid modification with β-lactamase allowed for the assembly of capsids with a concomitant increase in size. Enzyme activity assays revealed lactamase functionality for both rAAV variants, which demonstrates the structural robustness of this platform technology.
Collapse
Affiliation(s)
- Rebecca C. Feiner
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany; (R.C.F.); (J.T.); (K.E.T.); (M.T.R.)
| | - Julian Teschner
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany; (R.C.F.); (J.T.); (K.E.T.); (M.T.R.)
| | - Kathrin E. Teschner
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany; (R.C.F.); (J.T.); (K.E.T.); (M.T.R.)
| | - Marco T. Radukic
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany; (R.C.F.); (J.T.); (K.E.T.); (M.T.R.)
| | - Tobias Baumann
- Biocatalysis group, Department of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany;
| | | | - Yvonne Hannappel
- Physical and Biophysical Chemistry (PCIII), Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany;
| | - Niklas Biere
- Experimental Biophysics and Applied Nanoscience, Physics Department, Bielefeld University, 33615 Bielefeld, Germany; (N.B.); (D.A.)
| | - Dario Anselmetti
- Experimental Biophysics and Applied Nanoscience, Physics Department, Bielefeld University, 33615 Bielefeld, Germany; (N.B.); (D.A.)
| | - Katja M. Arndt
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany;
| | - Kristian M. Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany; (R.C.F.); (J.T.); (K.E.T.); (M.T.R.)
- Correspondence: ; Tel.: +49-521-106-6323
| |
Collapse
|
15
|
Krüger T, Weiland S, Boschanski M, Sinha PK, Falck G, Müller KM, Dierks T, Sewald N. Conversion of Serine‐Type Aldehyde Tags by the Radical SAM Protein AtsB from
Methanosarcina mazei. Chembiochem 2019; 20:2074-2078. [DOI: 10.1002/cbic.201900322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Tobias Krüger
- Organische und Bioorganische ChemieFakultät für ChemieUniversität Bielefeld Universitätsstrasse 25 33615 Bielefeld Germany
| | - Stefanie Weiland
- Biochemie IFakultät für ChemieUniversität Bielefeld Universitätsstrasse 25 33615 Bielefeld Germany
| | - Mareile Boschanski
- Biochemie IFakultät für ChemieUniversität Bielefeld Universitätsstrasse 25 33615 Bielefeld Germany
| | - Prem Kumar Sinha
- Biochemie IFakultät für ChemieUniversität Bielefeld Universitätsstrasse 25 33615 Bielefeld Germany
| | - Georg Falck
- Zelluläre und Molekulare BiotechnologieTechnische FakultätUniversität Bielefeld Universitätsstrasse 25 33615 Bielefeld Germany
| | - Kristian M. Müller
- Zelluläre und Molekulare BiotechnologieTechnische FakultätUniversität Bielefeld Universitätsstrasse 25 33615 Bielefeld Germany
| | - Thomas Dierks
- Biochemie IFakultät für ChemieUniversität Bielefeld Universitätsstrasse 25 33615 Bielefeld Germany
| | - Norbert Sewald
- Organische und Bioorganische ChemieFakultät für ChemieUniversität Bielefeld Universitätsstrasse 25 33615 Bielefeld Germany
| |
Collapse
|
16
|
Feiner RC, Pennè I, Müller B, Müller KM. EGF-mCherry Fusion Protein Expressed in E. coli Shows Product Heterogeneity but a High Biological Activity. Biochemistry 2019; 58:1043-1047. [PMID: 30735360 DOI: 10.1021/acs.biochem.9b00021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The epidermal growth factor receptor (EGFR) is a transmembrane protein involved in cell signaling processes, and dysregulation of its activity often drives tumor growth. EGFR is a clinically validated tumor marker and target for antibodies and tyrosine kinase inhibitors. We demonstrate that a fusion protein of the natural ligand epidermal growth factor (EGF) with the fluorescent reporter mCherry can be expressed in the cytosol of E. coli in high yields and with a high biological activity. Biophysical characterization by mass spectrometry analysis confirmed three disulfide bonds that are crucial for protein structure. Biolayer interferometry data of the protein-protein interaction of EGF-mCherry with the soluble EGFR are comparable to that of unmodified EGF. Cell culture experiments demonstrated that this fusion replicates all important features of the natural ligand. Finally, fluorescent assays based on EGF-mCherry provided a simple and convenient method to compare EGFR levels on cells and to determine competition of EGFR-binding molecules. These assays will help to rank competitive properties of EGFR inhibitors.
Collapse
Affiliation(s)
- Rebecca C Feiner
- Cellular and Molecular Biotechnology, Faculty of Technology , Bielefeld University , Bielefeld 33613 , Germany
| | - Ina Pennè
- Cellular and Molecular Biotechnology, Faculty of Technology , Bielefeld University , Bielefeld 33613 , Germany
| | - Benjamin Müller
- Biofidus AG , Hainteichstrasse 78 , Bielefeld 33613 , Germany
| | - Kristian M Müller
- Cellular and Molecular Biotechnology, Faculty of Technology , Bielefeld University , Bielefeld 33613 , Germany
| |
Collapse
|
17
|
Baier T, Kros D, Feiner RC, Lauersen KJ, Müller KM, Kruse O. Engineered Fusion Proteins for Efficient Protein Secretion and Purification of a Human Growth Factor from the Green Microalga Chlamydomonas reinhardtii. ACS Synth Biol 2018; 7:2547-2557. [PMID: 30296377 DOI: 10.1021/acssynbio.8b00226] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Light-driven recombinant protein (RP) production in eukaryotic microalgae offers a sustainable alternative to other established cell-culture systems. RP production via secretion into the culture medium enables simple product separation from the cells adding a layer of process value in addition to the algal biomass, which can be separately harvested. For the model microalga Chlamydomonas reinhardtii, a broad range of molecular tools have been established to enable heterologous gene expression; however, low RP production levels and unreliable purification from secretion concepts have been reported. Domesticated C. reinhardtii strains used for genetic engineering are often cell-wall deficient. These strains nevertheless secrete cell-wall components such as insoluble (hydroxy)proline-rich glycoproteins into the culture media, which hinder downstream purification processes. Here, we attempted to overcome limitations in secretion titers and improve protein purification by combining fusion partners that enhance RP secretion and enable alternative aqueous two-phase (ATPS) RP extraction from the culture medium. Protein fusions were strategically designed to contain a stably folded peptide, which enhanced secretion capacities and gave insights into (some) regulatory mechanisms responsible for this process in the algal host. The elevated protein titers mediated by this fusion were then successfully applied in combination with a fungal hydrophobin tag, which enabled protein purification from the complex microalgal extracellular environment by ATPS, to yield functional recombinant human epidermal growth factor (hEGF) from the algal host.
Collapse
Affiliation(s)
- Thomas Baier
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Dana Kros
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Rebecca C. Feiner
- Bielefeld University, Faculty of Technology, Cellular and Molecular Biotechnology, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Kyle J. Lauersen
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Kristian M. Müller
- Bielefeld University, Faculty of Technology, Cellular and Molecular Biotechnology, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Olaf Kruse
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615 Bielefeld, Germany
| |
Collapse
|
18
|
Krüger T, Weiland S, Falck G, Gerlach M, Boschanski M, Alam S, Müller KM, Dierks T, Sewald N. Zweifach-bioorthogonale Derivatisierung durch verschiedene Formylglycin-generierende Enzyme. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803183] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Tobias Krüger
- Organische und Bioorganische Chemie; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Deutschland
| | - Stefanie Weiland
- Biochemie I; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Deutschland
| | - Georg Falck
- Zelluläre und Molekulare Biotechnologie, Technische Fakultät; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Deutschland
| | - Marcus Gerlach
- Organische und Bioorganische Chemie; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Deutschland
| | - Mareile Boschanski
- Biochemie I; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Deutschland
| | - Sarfaraz Alam
- Biochemie I; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Deutschland
| | - Kristian M. Müller
- Zelluläre und Molekulare Biotechnologie, Technische Fakultät; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Deutschland
| | - Thomas Dierks
- Biochemie I; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Deutschland
| | - Norbert Sewald
- Organische und Bioorganische Chemie; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Deutschland
| |
Collapse
|
19
|
Krüger T, Weiland S, Falck G, Gerlach M, Boschanski M, Alam S, Müller KM, Dierks T, Sewald N. Two-fold Bioorthogonal Derivatization by Different Formylglycine-Generating Enzymes. Angew Chem Int Ed Engl 2018; 57:7245-7249. [DOI: 10.1002/anie.201803183] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Tobias Krüger
- Organische und Bioorganische Chemie; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Germany
| | - Stefanie Weiland
- Biochemie I; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Germany
| | - Georg Falck
- Zelluläre und Molekulare Biotechnologie, Technische Fakultät; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Germany
| | - Marcus Gerlach
- Organische und Bioorganische Chemie; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Germany
| | - Mareile Boschanski
- Biochemie I; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Germany
| | - Sarfaraz Alam
- Biochemie I; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Germany
| | - Kristian M. Müller
- Zelluläre und Molekulare Biotechnologie, Technische Fakultät; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Germany
| | - Thomas Dierks
- Biochemie I; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Germany
| | - Norbert Sewald
- Organische und Bioorganische Chemie; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Germany
| |
Collapse
|
20
|
Hoffmann SA, Wohltat C, Müller KM, Arndt KM. A user-friendly, low-cost turbidostat with versatile growth rate estimation based on an extended Kalman filter. PLoS One 2017; 12:e0181923. [PMID: 28746418 PMCID: PMC5529016 DOI: 10.1371/journal.pone.0181923] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 04/13/2017] [Accepted: 06/28/2017] [Indexed: 01/22/2023] Open
Abstract
For various experimental applications, microbial cultures at defined, constant densities are highly advantageous over simple batch cultures. Due to high costs, however, devices for continuous culture at freely defined densities still experience limited use. We have developed a small-scale turbidostat for research purposes, which is manufactured from inexpensive components and 3D printed parts. A high degree of spatial system integration and a graphical user interface provide user-friendly operability. The used optical density feedback control allows for constant continuous culture at a wide range of densities and offers to vary culture volume and dilution rates without additional parametrization. Further, a recursive algorithm for on-line growth rate estimation has been implemented. The employed Kalman filtering approach based on a very general state model retains the flexibility of the used control type and can be easily adapted to other bioreactor designs. Within several minutes it can converge to robust, accurate growth rate estimates. This is particularly useful for directed evolution experiments or studies on metabolic challenges, as it allows direct monitoring of the population fitness.
Collapse
Affiliation(s)
- Stefan A. Hoffmann
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Christian Wohltat
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Kristian M. Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Katja M. Arndt
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
- * E-mail:
| |
Collapse
|
21
|
Kükenshöner T, Hagemann UB, Wohlwend D, Räuber C, Baumann T, Keller S, Einsle O, Müller KM, Arndt KM. Analysis of selected and designed chimeric D- and L-α-helix assemblies. Biomacromolecules 2014; 15:3296-305. [PMID: 25072521 DOI: 10.1021/bm5006883] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
D-peptides have been attributed pharmacological advantages over regular L-peptides, yet design rules are largely unknown. Based on a designed coiled coil-like D/L heterotetramer, named L-Base/D-Acid, we generated a library offering alternative residues for interaction with the D-peptide. Phage display selection yielded one predominant peptide, named HelixA, that differed at 13 positions from the scaffold helix. In addition to the observed D-/L-heterotetramers, ratio-dependent intermediate states were detected by isothermal titration calorimetry. Importantly, the formation of the selected HelixA/D-Acid bundle passes through fewer intermediate states than L-Base/D-Acid. Back mutation of HelixA core residues to L-Base (HelixLL) revealed that the residues at e/g-positions are responsible for the different intermediates. Furthermore, a Val-core variant (PeptideVV) was completely devoid of binding D-Acid, whereas an Ile-core helix (HelixII) interacted with D-Acid in a significantly more specific complex than L-Base.
Collapse
Affiliation(s)
- Tim Kükenshöner
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam , 14476 Potsdam, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Hagen S, Mattay D, Räuber C, Müller KM, Arndt KM. Characterization and inhibition of AF10-mediated interaction. J Pept Sci 2014; 20:385-97. [PMID: 24692230 DOI: 10.1002/psc.2626] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [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: 10/14/2013] [Revised: 02/13/2014] [Accepted: 02/14/2014] [Indexed: 12/24/2022]
Abstract
The non-random chromosomal translocations t(10;11)(p13;q23) and t(10;11)(p13;q14-21) result in leukemogenic fusion proteins comprising the coiled coil domain of the transcription factor AF10 and the proteins MLL or CALM, respectively, and subsequently cause certain types of acute leukemia. The AF10 coiled-coil domain, which is crucial for the leukemogenic effect, has been shown to interact with GAS41, a protein previously identified as the product of an amplified gene in glioblastoma. Using sequential synthetic peptides, we mapped the potential AF10/GAS41 interaction site, which was subsequently be used as scaffold for a library targeting the AF10 coiled-coil domain. Using phage display, we selected a peptide that binds the AF10 coiled-coil domain with higher affinity than the respective coiled-coil region of wild-type GAS41, as demonstrated by phage ELISA, CD, and PCAs. Furthermore, we were able to successfully deploy the inhibitory peptide in a mammalian cell line to lower the expression of Hoxa genes that have been described to be overexpressed in these leukemias. This work dissects molecular determinants mediating AF10-directed interactions in leukemic fusions comprising the N-terminal parts of the proteins MLL or CALM and the C-terminal coiled-coil domain of AF10. Furthermore, it outlines the first steps in recognizing and blocking the leukemia-associated AF10 interaction in histiocytic lymphoma cells and therefore, may have significant implications in future diagnostics and therapeutics.
Collapse
Affiliation(s)
- Sven Hagen
- Molecular Biotechnology, University of Potsdam, Potsdam/Golm, Germany; Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany; Institute for Biology III, University of Freiburg, Freiburg, Germany
| | | | | | | | | |
Collapse
|
23
|
Kükenshöner T, Wohlwend D, Niemöller C, Dondapati P, Speck J, Adeniran AV, Nieth A, Gerhardt S, Einsle O, Müller KM, Arndt KM. Improving coiled coil stability while maintaining specificity by a bacterial hitchhiker selection system. J Struct Biol 2014; 186:335-48. [PMID: 24631970 DOI: 10.1016/j.jsb.2014.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [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: 11/19/2013] [Revised: 02/28/2014] [Accepted: 03/01/2014] [Indexed: 12/12/2022]
Abstract
The design and selection of peptides targeting cellular proteins is challenging and often yields candidates with undesired properties. Therefore we deployed a new selection system based on the twin-arginine translocase (TAT) pathway of Escherichia coli, named hitchhiker translocation (HiT) selection. A pool of α-helix encoding sequences was designed and selected for interference with the coiled coil domain (CC) of a melanoma-associated basic-helix-loop-helix-leucine-zipper (bHLHLZ) protein, the microphthalmia associated transcription factor (MITF). One predominant sequence (iM10) was enriched during selection and showed remarkable protease resistance, high solubility and thermal stability while maintaining its specificity. Furthermore, it exhibited nanomolar range affinity towards the target peptide. A mutation screen indicated that target-binding helices of increased homodimer stability and improved expression rates were preferred in the selection process. The crystal structure of the iM10/MITF-CC heterodimer (2.1Å) provided important structural insights and validated our design predictions. Importantly, iM10 did not only bind to the MITF coiled coil, but also to the markedly more stable HLHLZ domain of MITF. Characterizing the selected variants of the semi-rational library demonstrated the potential of the innovative bacterial selection approach.
Collapse
Affiliation(s)
- Tim Kükenshöner
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany
| | - Daniel Wohlwend
- Institute for Biochemistry, University of Freiburg, Freiburg im Breisgau, Germany
| | - Christoph Niemöller
- Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany
| | - Padmarupa Dondapati
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany
| | - Janina Speck
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany
| | - Adebola V Adeniran
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany
| | - Anita Nieth
- Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany; Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg im Breisgau, Germany; Freiburg Institute for Advanced Studies, University of Freiburg, Freiburg im Breisgau, Germany
| | - Stefan Gerhardt
- Institute for Biochemistry, University of Freiburg, Freiburg im Breisgau, Germany
| | - Oliver Einsle
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg im Breisgau, Germany; Freiburg Institute for Advanced Studies, University of Freiburg, Freiburg im Breisgau, Germany; Institute for Biochemistry, University of Freiburg, Freiburg im Breisgau, Germany
| | - Kristian M Müller
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany; Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Germany
| | - Katja M Arndt
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany; Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg im Breisgau, Germany; Freiburg Institute for Advanced Studies, University of Freiburg, Freiburg im Breisgau, Germany.
| |
Collapse
|
24
|
Weiz AR, Ishida K, Quitterer F, Meyer S, Kehr JC, Müller KM, Groll M, Hertweck C, Dittmann E. Harnessing the Evolvability of Tricyclic Microviridins To Dissect Protease-Inhibitor Interactions. Angew Chem Int Ed Engl 2014; 53:3735-8. [DOI: 10.1002/anie.201309721] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 01/03/2014] [Indexed: 11/11/2022]
|
25
|
Weiz AR, Ishida K, Quitterer F, Meyer S, Kehr JC, Müller KM, Groll M, Hertweck C, Dittmann E. Analyse von Protease-Inhibitor-Interaktionen unter Nutzung evolvierbarer tricyclischer Microviridine. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309721] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
26
|
Redwan B, Schmidt J, Müller KM, Schmitz R, Sandkötter J, Werner C, Wiebe K. Respiratorische Insuffizienz bei massivem Pleuraerguss durch einen Lungensequester – intrauterine Intervention und postnatale chirurgische Resektion. Pneumologie 2014. [DOI: 10.1055/s-0034-1367765] [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: 10/25/2022]
|
27
|
Bedetti B, Redwan B, Kösek V, Mohr M, Wiewrodt R, Wiebe K, Müller KM. Diagnose einer ausgeprägten Sideroelastose in einer Schweißerlunge bei unklarer interstitieller Lungenerkrankung mit Hämoptysen. Pneumologie 2014. [DOI: 10.1055/s-0034-1367966] [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: 10/25/2022]
|
28
|
Hagen S, Baumann T, Wagner HJ, Morath V, Kaufmann B, Fischer A, Bergmann S, Schindler P, Arndt KM, Müller KM. Modular adeno-associated virus (rAAV) vectors used for cellular virus-directed enzyme prodrug therapy. Sci Rep 2014; 4:3759. [PMID: 24457557 PMCID: PMC3901000 DOI: 10.1038/srep03759] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [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: 10/24/2013] [Accepted: 12/23/2013] [Indexed: 12/26/2022] Open
Abstract
The pre-clinical and clinical development of viral vehicles for gene transfer increased in recent years, and a recombinant adeno-associated virus (rAAV) drug took center stage upon approval in the European Union. However, lack of standardization, inefficient purification methods and complicated retargeting limit general usability. We address these obstacles by fusing rAAV-2 capsids with two modular targeting molecules (DARPin or Affibody) specific for a cancer cell-surface marker (EGFR) while simultaneously including an affinity tag (His-tag) in a surface-exposed loop. Equipping these particles with genes coding for prodrug converting enzymes (thymidine kinase or cytosine deaminase) we demonstrate tumor marker specific transduction and prodrug-dependent apoptosis of cancer cells. Coding terminal and loop modifications in one gene enabled specific and scalable purification. Our genetic parts for viral production adhere to a standardized cloning strategy facilitating rapid prototyping of virus directed enzyme prodrug therapy (VDEPT).
Collapse
Affiliation(s)
- Sven Hagen
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany
- BIOSS Centre for Biological Signalling Studies, Albert Ludwig University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
| | - Tobias Baumann
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany
- BIOSS Centre for Biological Signalling Studies, Albert Ludwig University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
| | - Hanna J. Wagner
- BIOSS Centre for Biological Signalling Studies, Albert Ludwig University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
- Institut für Biologie III, Albert-Ludwigs Universität Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Volker Morath
- BIOSS Centre for Biological Signalling Studies, Albert Ludwig University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
- Institut für Biologie III, Albert-Ludwigs Universität Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Beate Kaufmann
- BIOSS Centre for Biological Signalling Studies, Albert Ludwig University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
- Institut für Biologie III, Albert-Ludwigs Universität Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Adrian Fischer
- BIOSS Centre for Biological Signalling Studies, Albert Ludwig University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
- Institut für Biologie III, Albert-Ludwigs Universität Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Stefan Bergmann
- BIOSS Centre for Biological Signalling Studies, Albert Ludwig University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
- Institut für Biologie III, Albert-Ludwigs Universität Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Patrick Schindler
- BIOSS Centre for Biological Signalling Studies, Albert Ludwig University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
- Institut für Biologie III, Albert-Ludwigs Universität Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Katja M. Arndt
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany
- BIOSS Centre for Biological Signalling Studies, Albert Ludwig University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
| | - Kristian M. Müller
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany
- BIOSS Centre for Biological Signalling Studies, Albert Ludwig University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
- Zelluläre und Molekulare Biotechnologie, Technische Fakultät, Universität Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
| |
Collapse
|
29
|
Baumann T, Arndt KM, Müller KM. Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V. BMC Biotechnol 2013; 13:81. [PMID: 24090222 PMCID: PMC3856533 DOI: 10.1186/1472-6750-13-81] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 09/25/2013] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND DNA fragments carrying internal recognition sites for the restriction endonucleases intended for cloning into a target plasmid pose a challenge for conventional cloning. RESULTS A method for directional insertion of DNA fragments into plasmid vectors has been developed. The target sequence is amplified from a template DNA sample by PCR using two oligonucleotides each containing a single deoxyinosine base at the third position from the 5' end. Treatment of such PCR products with endonuclease V generates 3' protruding ends suitable for ligation with vector fragments created by conventional restriction endonuclease reactions. CONCLUSIONS The developed approach generates terminal cohesive ends without the use of Type II restriction endonucleases, and is thus independent from the DNA sequence. Due to PCR amplification, minimal amounts of template DNA are required. Using the robust Taq enzyme or a proofreading Pfu DNA polymerase mutant, the method is applicable to a broad range of insert sequences. Appropriate primer design enables direct incorporation of terminal DNA sequence modifications such as tag addition, insertions, deletions and mutations into the cloning strategy. Further, the restriction sites of the target plasmid can be either retained or removed.
Collapse
Affiliation(s)
- Tobias Baumann
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Room UHG E2-143 Universitätsstr, 25, Bielefeld 33615, Germany.
| | | | | |
Collapse
|
30
|
Jedrusik-Bode M, Studencka M, Smolka C, Baumann T, Schmidt H, Kampf J, Paap F, Martin S, Tazi J, Müller KM, Krüger M, Braun T, Bober E. The sirtuin SIRT6 regulates stress granule formation in C. elegans and mammals. J Cell Sci 2013; 126:5166-77. [PMID: 24013546 DOI: 10.1242/jcs.130708] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
SIRT6 is a NAD(+)-dependent deacetylase that modulates chromatin structure and safeguards genomic stability. Until now, SIRT6 has been assigned to the nucleus and only nuclear targets of SIRT6 are known. Here, we demonstrate that in response to stress, C. elegans SIR-2.4 and its mammalian orthologue SIRT6 localize to cytoplasmic stress granules, interact with various stress granule components and induce their assembly. Loss of SIRT6 or inhibition of its catalytic activity in mouse embryonic fibroblasts impairs stress granule formation and delays disassembly during recovery, whereas deficiency of SIR-2.4 diminishes maintenance of P granules and decreases survival of C. elegans under stress conditions. Our findings uncover a novel, evolutionary conserved function of SIRT6 in the maintenance of stress granules in response to stress.
Collapse
Affiliation(s)
- Monika Jedrusik-Bode
- Max Planck Institute for Biophysical Chemistry, Epigenetics in C. elegans group, Am Faßberg 11, 37077 Göttingen, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Bedetti B, Redwan B, Schmidt J, Kösek V, Heitplatz B, Müller KM, Mohr M, Wiewrodt R, Wiebe K. Tumor durchwächst biologische dezelluläre Kollagenmatrixmaterialien. Pneumologie 2013. [DOI: 10.1055/s-0033-1334651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
32
|
Müller KM, Kenter M. Tabak-assoziierte siderophile und conchoide Speicherphänomene in Rauchermakrophagen mit Riesenzellen. Pneumologie 2013. [DOI: 10.1055/s-0033-1334697] [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: 10/27/2022]
|
33
|
Kossakowski CA, Müller KM, Otterbach F. Bronchozentrische Granulomatose in Assoziation mit diffuser neuroendokriner Zellhyperplasie (DIPNECH). Pneumologie 2013. [DOI: 10.1055/s-0033-1334625] [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: 10/27/2022]
|
34
|
Speck J, Räuber C, Kükenshöner T, Niemöller C, Mueller KJ, Schleberger P, Dondapati P, Hecky J, Arndt KM, Müller KM. TAT hitchhiker selection expanded to folding helpers, multimeric interactions and combinations with protein fragment complementation. Protein Eng Des Sel 2012; 26:225-42. [PMID: 23223941 DOI: 10.1093/protein/gzs098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Janina Speck
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Speck J, Hecky J, Tam HK, Arndt KM, Einsle O, Müller KM. Exploring the molecular linkage of protein stability traits for enzyme optimization by iterative truncation and evolution. Biochemistry 2012; 51:4850-67. [PMID: 22545913 DOI: 10.1021/bi2018738] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The stability of proteins is paramount for their therapeutic and industrial use and, thus, is a major task for protein engineering. Several types of chemical and physical stabilities are desired, and discussion revolves around whether each stability trait needs to be addressed separately and how specific and compatible stabilizing mutations act. We demonstrate a stepwise perturbation-compensation strategy, which identifies mutations rescuing the activity of a truncated TEM β-lactamase. Analyses relating structural stress with the external stresses of heat, denaturants, and proteases reveal our second-site suppressors as general stability centers that also improve the full-length enzyme. A library of lactamase variants truncated by 15 N-terminal and three C-terminal residues (Bla-NΔ15CΔ3) was subjected to activity selection and DNA shuffling. The resulting clone with the best in vivo performance harbored eight mutations, surpassed the full-length wild-type protein by 5.3 °C in T(m), displayed significantly higher catalytic activity at elevated temperatures, and showed delayed guanidine-induced denaturation. The crystal structure of this mutant was determined and provided insights into its stability determinants. Stepwise reconstitution of the N- and C-termini increased its thermal, denaturant, and proteolytic resistance successively, leading to a full-length enzyme with a T(m) increased by 15.3 °C and a half-denaturation concentration shifted from 0.53 to 1.75 M guanidinium relative to that of the wild type. These improvements demonstrate that iterative truncation-optimization cycles can exploit stability-trait linkages in proteins and are exceptionally suited for the creation of progressively stabilized variants and/or downsized proteins without the need for detailed structural or mechanistic information.
Collapse
Affiliation(s)
- Janina Speck
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | | | | | | | | |
Collapse
|
36
|
Klingström T, Soldatova L, Stevens R, Roos TE, Swertz MA, Müller KM, Kalaš M, Lambrix P, Taussig MJ, Litton JE, Landegren U, Bongcam-Rudloff E. Workshop on laboratory protocol standards for the Molecular Methods Database. N Biotechnol 2012; 30:109-13. [PMID: 22687389 DOI: 10.1016/j.nbt.2012.05.019] [Citation(s) in RCA: 5] [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] [Received: 05/18/2012] [Revised: 05/26/2012] [Accepted: 05/26/2012] [Indexed: 10/28/2022]
Abstract
Management of data to produce scientific knowledge is a key challenge for biological research in the 21st century. Emerging high-throughput technologies allow life science researchers to produce big data at speeds and in amounts that were unthinkable just a few years ago. This places high demands on all aspects of the workflow: from data capture (including the experimental constraints of the experiment), analysis and preservation, to peer-reviewed publication of results. Failure to recognise the issues at each level can lead to serious conflicts and mistakes; research may then be compromised as a result of the publication of non-coherent protocols, or the misinterpretation of published data. In this report, we present the results from a workshop that was organised to create an ontological data-modelling framework for Laboratory Protocol Standards for the Molecular Methods Database (MolMeth). The workshop provided a set of short- and long-term goals for the MolMeth database, the most important being the decision to use the established EXACT description of biomedical ontologies as a starting point.
Collapse
Affiliation(s)
- Tomas Klingström
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Kösek V, Schmidt J, Redwan B, Rukosujew A, Müller KM, Köhler G, Scheld HH, Wiebe K. Interferenz von DIPNECH (diffuse idiopathic pulmonary neuroendocrine cell hyperplasia) mit pulmonalen Metastasen eines Osteosarkoms. Pneumologie 2012. [DOI: 10.1055/s-0032-1302642] [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: 10/28/2022]
|
38
|
Abstract
Synthetic Biology is founded on the idea that complex biological systems are built most effectively when the task is divided in abstracted layers and all required components are readily available and well-described. This requires interdisciplinary collaboration at several levels and a common understanding of the functioning of each component. Standardization of the physical composition and the description of each part is required as well as a controlled vocabulary to aid design and ensure interoperability. Here, we describe standardization initiatives from several disciplines, which can contribute to Synthetic Biology. We provide examples of the concerted standardization efforts of the BioBricks Foundation comprising the request for comments (RFC) and the Registry of Standardized Biological parts as well as the international Genetically Engineered Machine (iGEM) competition.
Collapse
Affiliation(s)
- Kristian M Müller
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
| | | |
Collapse
|
39
|
Wohlschläger J, Sommerwerck U, Jonigk D, Rische J, Baba HA, Müller KM. [Lung transplantation and rejection. Basic principles, clinical aspects and histomorphology]. Pathologe 2011; 32:104-12. [PMID: 21424408 DOI: 10.1007/s00292-010-1403-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Lung transplantation is the ultimate therapeutical approach for the treatment of both children and adults with terminal congenital or acquired lung disease. In contrast to survival rates during the first year following transplantation, the long-term survival for patients after lung transplantation has not significantly improved in the past. In addition to other complications, acute cellular rejection constitutes a major cause for diminished function of pulmonary grafts, and can, among other factors, be causative for chronic rejection (bronchiolitis obliterans syndrome, BOS). In 2006, the International Society for Heart and Lung Transplantation (ISHLT) provided a revised version of the grading system for acute and chronic rejection of pulmonary grafts.
Collapse
Affiliation(s)
- J Wohlschläger
- Institut für Pathologie und Neuropathologie, Universitätsklinikum Essen, Hufelandstr. 55, 45147, Essen, Deutschland.
| | | | | | | | | | | |
Collapse
|
40
|
Abstract
Phage display with filamentous phages is widely applied and well developed, yet proteins requiring a cytoplasmic environment for correct folding still defy attempts at functional display. To extend applicability of phage display, we employed the twin-arginine translocation (TAT) pathway to incorporate proteins fused to the C-terminal domain of the geneIII protein into phage particles. We investigated functionality and display level of fluorescent proteins depending on the translocation pathway, which was the TAT, general secretory (SEC) or signal recognition particle (SRP) pathway mediated by the TorA, PelB or DsbA signal sequences, respectively. Importantly, for green fluorescent protein, yellow fluorescent protein and cyan fluorescent protein, only TAT, but not SEC or SRP, translocation led to fluorescence of purified phage particles, although all three proteins could be displayed regardless of the translocation pathway. In contrast, the monomeric red fluorescent protein mCherry was functionally displayed regardless of the translocation pathway. Hence, correct folding and fluorophor formation of mCherry is not limited to the cytosol. Furthermore, we successfully displayed firefly luciferase as well as an 83 kDa argonaute protein, both containing free cysteines. This demonstrates broad applicability of the TAT-mediated phagemid system for the display of proteins requiring cytoplasmic factors for correct folding and should prove useful for the display of proteins requiring incorporation of co-factors or oligomerization to gain function.
Collapse
Affiliation(s)
- Janina Speck
- Department of Biology, Albert-Ludwigs-University, Freiburg, Germany
| | | | | |
Collapse
|
41
|
Schmidt J, Redwan B, Rukosujew A, Müller KM, Köhler G, Scheld HH, Wiebe K. Development of DIPNECH (Diffuse idiopathic pulmonary neuroendocrine cell hyperplasia) complicating multiple pulmonary metastases of a pelvic osteosarcoma. Thorac Cardiovasc Surg 2011. [DOI: 10.1055/s-0030-1269246] [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: 10/18/2022]
|
42
|
Staab PR, Walossek J, Nellessen D, Grünberg R, Arndt KM, Müller KM. SynBioWave--a real-time communication platform for molecular and synthetic biology. ACTA ACUST UNITED AC 2010; 26:2782-3. [PMID: 20841324 DOI: 10.1093/bioinformatics/btq518] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
SUMMARY Synthetic Biology is advanced by many users and relies on the assembly of genetic elements to devices, systems and finally genomes. SynBioWave is a software suite that enables multiple distributed users to analyze and construct genetic parts in real-time collaboration. It builds on Google Wave and provides an extensible robot-robot-user communication framework, a menu driven user interface, biological data handling including DAS and an internal database communication. We demonstrate its use by implementing robots for gene-data retrieval, manipulation and display. The initial development of SynBioWave demonstrates the power of the underlying Google Wave protocol for Synthetic Biology and lays the foundation for continuous and user-friendly extensions. Specialized wave-robots with a manageable set of capabilities will divide and conquer the complex task of creating a genome in silico. AVAILABILITY The robot is available at SynBioWave@appspot.com, the source code at http://synbiowave.sourceforge.net
Collapse
Affiliation(s)
- Paul R Staab
- Department of Mathematics, University of Freiburg
| | | | | | | | | | | |
Collapse
|
43
|
Morresi-Hauf A, Müller KM, Oelker J, Tannapfel A, Heidrich G, Häußinger K. Akzelerierte Silikose als Differenzialdiagnose eines Lungengerüstprozesses. Pneumologie 2010. [DOI: 10.1055/s-0030-1251193] [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: 10/19/2022]
|
44
|
Schäffer U, Schlosser A, Müller KM, Schäfer A, Katava N, Baumeister R, Schulze E. SnAvi--a new tandem tag for high-affinity protein-complex purification. Nucleic Acids Res 2010; 38:e91. [PMID: 20047968 PMCID: PMC2847239 DOI: 10.1093/nar/gkp1178] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [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] [Indexed: 11/13/2022] Open
Abstract
Systematic tandem-affinity-purification (TAP) of protein complexes was tremendously successful in yeast and has changed the general concept of how we understand protein function in eukaryotic cells. The transfer of this method to other model organisms has been difficult and may require specific adaptations. We were especially interested to establish a cell-type-specific TAP system for Caenorhabditis elegans, a model animal well suited to high-throughput analysis, proteomics and systems biology. By combining the high-affinity interaction between in vivo biotinylated target-proteins and streptavidin with the usage of a newly identified epitope of the publicly shared SB1 monoclonal antibody we created a novel in vivo fluorescent tag, the SnAvi-Tag. We show the versatile application of the SnAvi-Tag in Escherichia coli, vertebrate cells and in C. elegans for tandem affinity purification of protein complexes, western blotting and also for the in vivo sub-cellular localization of labelled proteins.
Collapse
Affiliation(s)
- Ursula Schäffer
- Bioinformatics and Molecular Genetics, ZBMZ, Institute for Biology, ZBSA-Center for Systems Biology, Albert-Ludwigs-Universitaet Freiburg, 79104 Freiburg, Germany
| | | | | | | | | | | | | |
Collapse
|
45
|
Gaisser S, Reiss T, Lunkes A, Müller KM, Bernauer H. Making the most of synthetic biology. Strategies for synthetic biology development in Europe. EMBO Rep 2009; 10 Suppl 1:S5-8. [PMID: 19636305 DOI: 10.1038/embor.2009.118] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Sibylle Gaisser
- Fraunhofer Institute Systems and Innovation Research, Karlsruhe, Germany.
| | | | | | | | | |
Collapse
|
46
|
Schmuecking M, Baum R, Prasad V, Schneider CP, Bank P, Marx C, Wendt TG, Kloetzer KH, Presselt N, Leonhardi J, Müller KM, Bonnet R. Das Will Rogers Phänomen: Beeinflussen die PET als Stagingmethode und die Etablierung eines Referenz-Zentrums Nuklearmedizin/Radiologie das Überleben von Patienten mit nicht-kleinzelligem Lungenkarzinom, die multimodal in Phase III Studien behandelt werden? Pneumologie 2009. [DOI: 10.1055/s-0029-1213936] [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: 10/21/2022]
|
47
|
Müller KM. [Methods in pathology: clinical relevance--CUP syndrome]. Pathologe 2009; 30:89. [PMID: 19221756 DOI: 10.1007/s00292-009-1125-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
48
|
Abstract
Cell physiology depends on a fine-tuned network of protein-protein interactions, and misguided interactions are often associated with various diseases. Consequently, peptides, which are able to specifically interfere with such adventitious interactions, are of high interest for analytical as well as medical purposes. One of the most abundant protein interaction domains is the coiled-coil motif, and thus provides a premier target. Coiled coils, which consist of two or more alpha-helices wrapped around each other, have one of the simplest interaction interfaces, yet they are able to confer highly specific homo- and heterotypic interactions involved in virtually any cellular process. While there are several ways to generate interfering peptides, the combination of library design with a powerful selection system seems to be one of the most effective and promising approaches. This chapter guides through all steps of such a process, starting with library options and cloning, detailing suitable selection techniques and ending with purification for further down-stream characterization. Such generated peptides will function as versatile tools to interfere with the natural function of their targets thereby illuminating their down-stream signaling and, in general, promoting understanding of factors leading to specificity and stability in protein-protein interactions. Furthermore, peptides interfering with medically relevant proteins might become important diagnostics and therapeutics.
Collapse
Affiliation(s)
- Annette Gaida
- Albert-Ludwigs-University of Freiburg, Institute of Biology III, Freiburg, Germany
| | | | | | | | | | | |
Collapse
|
49
|
Abstract
c-Myc is one of the most frequently deregulated oncogenes in human cancers, and recent studies showed that even brief inactivation of Myc can be sufficient to induce tumor regression or loss. Consequently, inactivation of Myc provides a novel therapeutic opportunity and challenge, as the dimerization of Myc with Max is crucial for its function. We applied two strategies to specifically target this coiled coil mediated interaction with interfering peptides: a dominant-negative human Max sequence (Max) and a peptide selected from a genetic library (Mip). Both peptides form coiled coils and were fused to an acidic extension interacting with the basic DNA-binding region of human Myc. The genetic library was obtained by semi-rational design randomizing residues important for interaction, and selection was carried out using a protein-fragment complementation assay. The peptides Max and Mip easily outcompeted the human Myc:Max interaction and successfully interfered with the DNA binding of the complex. Both interfering peptides exhibited higher T(m) (DeltaT(m) = 13 and 15 degrees C) upon interaction with Myc compared to wt Max. The inhibitory effect of the two interfering peptides on human Myc:Max activity makes them promising molecules for analytical and therapeutic Myc-directed research.
Collapse
Affiliation(s)
- Eva M Jouaux
- Institute for Biology III, Albert-Ludwigs University of Freiburg, Schaenzlestrasse 1, Freiburg, Germany
| | | | | | | |
Collapse
|
50
|
MESH Headings
- Antibodies, Monoclonal/analysis
- Antibodies, Monoclonal, Murine-Derived
- Antigens, CD34/analysis
- Biomarkers, Tumor
- Fluorescent Antibody Technique, Direct
- Hemangioma, Capillary/chemistry
- Hemangioma, Capillary/pathology
- Hemangioma, Cavernous/chemistry
- Hemangioma, Cavernous/pathology
- Humans
- Lung/blood supply
- Lung/chemistry
- Lung/pathology
- Lung Neoplasms/chemistry
- Lung Neoplasms/pathology
- Lymphangioma/chemistry
- Lymphangioma/pathology
Collapse
|