1
|
Kramm K, Schröder T, Vera AM, Grabenhorst L, Tinnefeld P, Grohmann D. DNA Origami-Based Single-Molecule Force Spectroscopy and Applications. Methods Mol Biol 2024; 2694:479-507. [PMID: 37824019 DOI: 10.1007/978-1-0716-3377-9_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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Over the last years, single-molecule force spectroscopy provided insights into the intricate connection between mechanical stimuli and biochemical signaling. The underlying molecular mechanisms were uncovered and explored using techniques such as atomic force microscopy and force spectroscopy using optical or magnetic tweezers. These experimental approaches are limited by thermal noise resulting from a physical connection of the studied biological system to the macroscopic world. To overcome this limitation, we recently introduced the DNA origami force clamp (FC) which is a freely diffusing nanodevice that generates piconewton forces on a DNA sequence of interest. Binding of a protein to the DNA under tension can be detected employing fluorescence resonance energy transfer (FRET) as a sensitive readout.This protocol introduces the reader to the working principles of the FC and provides instructions to design and generate a DNA origami FC customized for a protein of interest. Molecular cloning techniques are employed to modify, produce, and purify a custom DNA scaffold. A fluorescently labeled DNA suitable to detect protein binding via FRET is generated via enzymatic ligation of commercial DNA oligonucleotides. After thermal annealing of all components, the DNA origami FC is purified using agarose gel electrophoresis. The final section covers the interrogation of the FC using confocal single-molecule FRET measurements and subsequent data analysis to quantify the binding of a DNA-binding protein to its cognate recognition site under a range of forces. Using this approach, force-dependent DNA-protein interactions can be studied on the single-molecule level on thousands of molecules in a parallelized fashion.
Collapse
Affiliation(s)
- Kevin Kramm
- University of Regensburg, Department of Microbiology and Archaea Centre, Regensburg, Germany
| | - Tim Schröder
- Ludwig-Maximilians-Universität München, Department of Chemistry and Center for NanoScience (CeNS), Munich, Germany
| | - Andrés Manuel Vera
- Ludwig-Maximilians-Universität München, Department of Chemistry and Center for NanoScience (CeNS), Munich, Germany
| | - Lennart Grabenhorst
- Ludwig-Maximilians-Universität München, Department of Chemistry and Center for NanoScience (CeNS), Munich, Germany
| | - Philip Tinnefeld
- Ludwig-Maximilians-Universität München, Department of Chemistry and Center for NanoScience (CeNS), Munich, Germany
| | - Dina Grohmann
- University of Regensburg, Department of Microbiology and Archaea Centre, Regensburg, Germany.
| |
Collapse
|
2
|
Agam G, Gebhardt C, Popara M, Mächtel R, Folz J, Ambrose B, Chamachi N, Chung SY, Craggs TD, de Boer M, Grohmann D, Ha T, Hartmann A, Hendrix J, Hirschfeld V, Hübner CG, Hugel T, Kammerer D, Kang HS, Kapanidis AN, Krainer G, Kramm K, Lemke EA, Lerner E, Margeat E, Martens K, Michaelis J, Mitra J, Moya Muñoz GG, Quast RB, Robb NC, Sattler M, Schlierf M, Schneider J, Schröder T, Sefer A, Tan PS, Thurn J, Tinnefeld P, van Noort J, Weiss S, Wendler N, Zijlstra N, Barth A, Seidel CAM, Lamb DC, Cordes T. Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins. Nat Methods 2023; 20:523-535. [PMID: 36973549 PMCID: PMC10089922 DOI: 10.1038/s41592-023-01807-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [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: 08/02/2022] [Accepted: 01/31/2023] [Indexed: 03/29/2023]
Abstract
Single-molecule Förster-resonance energy transfer (smFRET) experiments allow the study of biomolecular structure and dynamics in vitro and in vivo. We performed an international blind study involving 19 laboratories to assess the uncertainty of FRET experiments for proteins with respect to the measured FRET efficiency histograms, determination of distances, and the detection and quantification of structural dynamics. Using two protein systems with distinct conformational changes and dynamics, we obtained an uncertainty of the FRET efficiency ≤0.06, corresponding to an interdye distance precision of ≤2 Å and accuracy of ≤5 Å. We further discuss the limits for detecting fluctuations in this distance range and how to identify dye perturbations. Our work demonstrates the ability of smFRET experiments to simultaneously measure distances and avoid the averaging of conformational dynamics for realistic protein systems, highlighting its importance in the expanding toolbox of integrative structural biology.
Collapse
Affiliation(s)
- Ganesh Agam
- Department of Chemistry, Ludwig-Maximilians University München, München, Germany
| | - Christian Gebhardt
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians University München, Planegg-Martinsried, Germany
| | - Milana Popara
- Molecular Physical Chemistry, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Rebecca Mächtel
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians University München, Planegg-Martinsried, Germany
| | - Julian Folz
- Molecular Physical Chemistry, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Neharika Chamachi
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Sang Yoon Chung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | | | - Marijn de Boer
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, AG Groningen, the Netherlands
| | - Dina Grohmann
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, Single-Molecule Biochemistry Laboratory, University of Regensburg, Regensburg, Germany
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine and Howard Hughes Medical Institute, Baltimore, MD, USA
| | - Andreas Hartmann
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Jelle Hendrix
- Dynamic Bioimaging Laboratory, Advanced Optical Microscopy Center and Biomedical Research Institute, Hasselt University, Agoralaan C (BIOMED), Hasselt, Belgium
- Department of Chemistry, KU Leuven, Leuven, Belgium
| | | | | | - Thorsten Hugel
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Dominik Kammerer
- Department of Physics, Clarendon Laboratory, University of Oxford, Oxford, UK
- Kavli Institute of Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Hyun-Seo Kang
- Bayerisches NMR Zentrum, Department of Bioscience, School of Natural Sciences, Technical University of München, Garching, Germany
| | - Achillefs N Kapanidis
- Department of Physics, Clarendon Laboratory, University of Oxford, Oxford, UK
- Kavli Institute of Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Georg Krainer
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Kevin Kramm
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, Single-Molecule Biochemistry Laboratory, University of Regensburg, Regensburg, Germany
| | - Edward A Lemke
- Biocenter, Johannes Gutenberg University Mainz, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics and Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Emmanuel Margeat
- Centre de Biologie Structurale (CBS), University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Kirsten Martens
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, the Netherlands
| | | | - Jaba Mitra
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine and Howard Hughes Medical Institute, Baltimore, MD, USA
- Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Gabriel G Moya Muñoz
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians University München, Planegg-Martinsried, Germany
| | - Robert B Quast
- Centre de Biologie Structurale (CBS), University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Nicole C Robb
- Department of Physics, Clarendon Laboratory, University of Oxford, Oxford, UK
- Kavli Institute of Nanoscience Discovery, University of Oxford, Oxford, UK
- Warwick Medical School, The University of Warwick, Coventry, UK
| | - Michael Sattler
- Bayerisches NMR Zentrum, Department of Bioscience, School of Natural Sciences, Technical University of München, Garching, Germany
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Center Munich, Munich, Germany
| | - Michael Schlierf
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden, Germany
| | - Jonathan Schneider
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians University München, Planegg-Martinsried, Germany
| | - Tim Schröder
- Department of Chemistry, Ludwig-Maximilians University München, München, Germany
| | - Anna Sefer
- Institute for Biophysics, Ulm University, Ulm, Germany
| | - Piau Siong Tan
- Biocenter, Johannes Gutenberg University Mainz, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
| | - Johann Thurn
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
- Institute of Technical Physics, German Aerospace Center (DLR), Stuttgart, Germany
| | - Philip Tinnefeld
- Department of Chemistry, Ludwig-Maximilians University München, München, Germany
| | - John van Noort
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, the Netherlands
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Nicolas Wendler
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians University München, Planegg-Martinsried, Germany
| | - Niels Zijlstra
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians University München, Planegg-Martinsried, Germany
| | - Anders Barth
- Molecular Physical Chemistry, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany.
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
| | - Claus A M Seidel
- Molecular Physical Chemistry, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany.
| | - Don C Lamb
- Department of Chemistry, Ludwig-Maximilians University München, München, Germany.
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians University München, Planegg-Martinsried, Germany.
| |
Collapse
|
3
|
Kramm K, Schröder T, Gouge J, Vera AM, Gupta K, Heiss FB, Liedl T, Engel C, Berger I, Vannini A, Tinnefeld P, Grohmann D. DNA origami-based single-molecule force spectroscopy elucidates RNA Polymerase III pre-initiation complex stability. Nat Commun 2020; 11:2828. [PMID: 32504003 PMCID: PMC7275037 DOI: 10.1038/s41467-020-16702-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 09/23/2019] [Accepted: 05/13/2020] [Indexed: 01/03/2023] Open
Abstract
The TATA-binding protein (TBP) and a transcription factor (TF) IIB-like factor are important constituents of all eukaryotic initiation complexes. The reason for the emergence and strict requirement of the additional initiation factor Bdp1 in the RNA polymerase (RNAP) III system, however, remained elusive. A poorly studied aspect in this context is the effect of DNA strain arising from DNA compaction and transcriptional activity on initiation complex formation. We made use of a DNA origami-based force clamp to follow the assembly of human initiation complexes in the RNAP II and RNAP III systems at the single-molecule level under piconewton forces. We demonstrate that TBP-DNA complexes are force-sensitive and TFIIB is sufficient to stabilise TBP on a strained promoter. In contrast, Bdp1 is the pivotal component that ensures stable anchoring of initiation factors, and thus the polymerase itself, in the RNAP III system. Thereby, we offer an explanation for the crucial role of Bdp1 for the high transcriptional output of RNAP III.
Collapse
Affiliation(s)
- Kevin Kramm
- Single-Molecule Biochemistry Lab, Institute of Microbiology and Archaea Centre, University of Regensburg, 93053, Regensburg, Germany
| | - Tim Schröder
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 80539, München, Germany
| | - Jerome Gouge
- Division of Structural Biology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Andrés Manuel Vera
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 80539, München, Germany
| | - Kapil Gupta
- Bristol Synthetic Biology Centre BrisSynBio, Biomedical Sciences, University of Bristol, 1 Tankard's Close, Clifton, BS8 1TD, UK
| | - Florian B Heiss
- Regensburg Center of Biochemistry (RCB), University of Regensburg, 93053, Regensburg, Germany
| | - Tim Liedl
- Faculty of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München, 80539, Munich, Germany
| | - Christoph Engel
- Regensburg Center of Biochemistry (RCB), University of Regensburg, 93053, Regensburg, Germany
| | - Imre Berger
- Bristol Synthetic Biology Centre BrisSynBio, Biomedical Sciences, University of Bristol, 1 Tankard's Close, Clifton, BS8 1TD, UK
| | - Alessandro Vannini
- Division of Structural Biology, The Institute of Cancer Research, London, SW7 3RP, UK
- Human Technopole Foundation, Centre of Structural Biology, 20157, Milan, Italy
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 80539, München, Germany
| | - Dina Grohmann
- Single-Molecule Biochemistry Lab, Institute of Microbiology and Archaea Centre, University of Regensburg, 93053, Regensburg, Germany.
- Regensburg Center of Biochemistry (RCB), University of Regensburg, 93053, Regensburg, Germany.
| |
Collapse
|
4
|
Kramm K, Endesfelder U, Grohmann D. A Single-Molecule View of Archaeal Transcription. J Mol Biol 2019; 431:4116-4131. [PMID: 31207238 DOI: 10.1016/j.jmb.2019.06.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 04/11/2019] [Revised: 05/27/2019] [Accepted: 06/06/2019] [Indexed: 01/03/2023]
Abstract
The discovery of the archaeal domain of life is tightly connected to an in-depth analysis of the prokaryotic RNA world. In addition to Carl Woese's approach to use the sequence of the 16S rRNA gene as phylogenetic marker, the finding of Karl Stetter and Wolfram Zillig that archaeal RNA polymerases (RNAPs) were nothing like the bacterial RNAP but are more complex enzymes that resemble the eukaryotic RNAPII was one of the key findings supporting the idea that archaea constitute the third major branch on the tree of life. This breakthrough in transcriptional research 40years ago paved the way for in-depth studies of the transcription machinery in archaea. However, although the archaeal RNAP and the basal transcription factors that fine-tune the activity of the RNAP during the transcription cycle are long known, we still lack information concerning the architecture and dynamics of archaeal transcription complexes. In this context, single-molecule measurements were instrumental as they provided crucial insights into the process of transcription initiation, the architecture of the initiation complex and the dynamics of mobile elements of the RNAP. In this review, we discuss single-molecule approaches suitable to examine molecular mechanisms of transcription and highlight findings that shaped our understanding of the archaeal transcription apparatus. We furthermore explore the possibilities and challenges of next-generation single-molecule techniques, for example, super-resolution microscopy and single-molecule tracking, and ask whether these approaches will ultimately allow us to investigate archaeal transcription in vivo.
Collapse
Affiliation(s)
- Kevin Kramm
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Ulrike Endesfelder
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 16, 35043 Marburg, Germany
| | - Dina Grohmann
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.
| |
Collapse
|
5
|
Gust A, Jakob L, Zeitler DM, Bruckmann A, Kramm K, Willkomm S, Tinnefeld P, Meister G, Grohmann D. Site-Specific Labelling of Native Mammalian Proteins for Single-Molecule FRET Measurements. Chembiochem 2018; 19:780-783. [PMID: 29394002 DOI: 10.1002/cbic.201700696] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Indexed: 12/31/2022]
Abstract
Human cells are complex entities in which molecular recognition and selection are critical for cellular processes often driven by structural changes and dynamic interactions. Biomolecules appear in different chemical states, and modifications, such as phosphorylation, affect their function. Hence, using proteins in their chemically native state in biochemical and biophysical assays is essential. Single-molecule FRET measurements allow exploration of the structure, function and dynamics of biomolecules but cannot be fully exploited for the human proteome, as a method for the site-specific coupling of organic dyes into native, non-recombinant mammalian proteins is lacking. We address this issue showing the site-specific engineering of fluorescent dyes into human proteins on the basis of bioorthogonal reactions. We show the applicability of the method to study functional and post-translationally modified proteins on the single-molecule level, among them the hitherto inaccessible human Argonaute 2.
Collapse
Affiliation(s)
- Alexander Gust
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, Single-Molecule Biochemistry Lab, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Leonhard Jakob
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, Single-Molecule Biochemistry Lab, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Daniela M Zeitler
- Department for Biochemistry I, Biochemistry Centre University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Astrid Bruckmann
- Department for Biochemistry I, Biochemistry Centre University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Kevin Kramm
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, Single-Molecule Biochemistry Lab, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Sarah Willkomm
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, Single-Molecule Biochemistry Lab, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377, München, Germany
| | - Gunter Meister
- Department for Biochemistry I, Biochemistry Centre University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Dina Grohmann
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, Single-Molecule Biochemistry Lab, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| |
Collapse
|
6
|
Gouge J, Guthertz N, Kramm K, Dergai O, Abascal-Palacios G, Satia K, Cousin P, Hernandez N, Grohmann D, Vannini A. Molecular mechanisms of Bdp1 in TFIIIB assembly and RNA polymerase III transcription initiation. Nat Commun 2017; 8:130. [PMID: 28743884 PMCID: PMC5526994 DOI: 10.1038/s41467-017-00126-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [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: 02/09/2017] [Accepted: 06/02/2017] [Indexed: 12/14/2022] Open
Abstract
Initiation of gene transcription by RNA polymerase (Pol) III requires the activity of TFIIIB, a complex formed by Brf1 (or Brf2), TBP (TATA-binding protein), and Bdp1. TFIIIB is required for recruitment of Pol III and to promote the transition from a closed to an open Pol III pre-initiation complex, a process dependent on the activity of the Bdp1 subunit. Here, we present a crystal structure of a Brf2-TBP-Bdp1 complex bound to DNA at 2.7 Å resolution, integrated with single-molecule FRET analysis and in vitro biochemical assays. Our study provides a structural insight on how Bdp1 is assembled into TFIIIB complexes, reveals structural and functional similarities between Bdp1 and Pol II factors TFIIA and TFIIF, and unravels essential interactions with DNA and with the upstream factor SNAPc. Furthermore, our data support the idea of a concerted mechanism involving TFIIIB and RNA polymerase III subunits for the closed to open pre-initiation complex transition.Transcription initiation by RNA polymerase III requires TFIIIB, a complex formed by Brf1/Brf2, TBP and Bdp1. Here, the authors describe the crystal structure of a Brf2-TBP-Bdp1 complex bound to a DNA promoter and characterize the role of Bdp1 in TFIIIB assembly and pre-initiation complex formation.
Collapse
Affiliation(s)
- Jerome Gouge
- The Institute of Cancer Research, London, SW7 3RP, UK
| | | | - Kevin Kramm
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, University of Regensburg, 93053, Regensburg, Germany
| | - Oleksandr Dergai
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
| | | | | | - Pascal Cousin
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
| | - Nouria Hernandez
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
| | - Dina Grohmann
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, University of Regensburg, 93053, Regensburg, Germany
| | | |
Collapse
|
7
|
Jakob L, Treiber T, Treiber N, Gust A, Kramm K, Hansen K, Stotz M, Wankerl L, Herzog F, Hannus S, Grohmann D, Meister G. Structural and functional insights into the fly microRNA biogenesis factor Loquacious. RNA 2016; 22:383-396. [PMID: 26769856 PMCID: PMC4748816 DOI: 10.1261/rna.055426.115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 12/02/2015] [Indexed: 06/05/2023]
Abstract
In the microRNA (miRNA) pathway, Dicer processes precursors to mature miRNAs. For efficient processing, double-stranded RNA-binding proteins support Dicer proteins. In flies, Loquacious (Loqs) interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. Here, we have solved the structure of the third double-stranded RNA-binding domain (dsRBD) of Loqs and define specific structural elements that interact with dmDcr1. In addition, we show that the linker preceding dsRBD3 contributes significantly to dmDcr1 binding. Furthermore, our structural work demonstrates that the third dsRBD of Loqs forms homodimers. Mutations in the dimerization interface abrogate dmDcr1 interaction. Loqs, however, binds to dmDcr1 as a monomer using the identified dimerization surface, which suggests that Loqs might form dimers under conditions where dmDcr1 is absent or not accessible. Since critical sequence elements are conserved, we suggest that dimerization might be a general feature of dsRBD proteins in gene silencing.
Collapse
Affiliation(s)
- Leonhard Jakob
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Thomas Treiber
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Nora Treiber
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Alexander Gust
- Department of Microbiology and Archaea Centre, Laboratory of Single-Molecule Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Kevin Kramm
- Department of Microbiology and Archaea Centre, Laboratory of Single-Molecule Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Kerrin Hansen
- Intana Bioscience GmbH, 82152 Planegg, Martinsried, Germany
| | - Mathias Stotz
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Ludwig Wankerl
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Franz Herzog
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University, 81377 München, Germany
| | - Stefan Hannus
- Intana Bioscience GmbH, 82152 Planegg, Martinsried, Germany
| | - Dina Grohmann
- Department of Microbiology and Archaea Centre, Laboratory of Single-Molecule Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| |
Collapse
|
8
|
Schulz S, Kramm K, Werner F, Grohmann D. Fluorescently labeled recombinant RNAP system to probe archaeal transcription initiation. Methods 2015; 86:10-8. [PMID: 25912642 DOI: 10.1016/j.ymeth.2015.04.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 04/14/2015] [Accepted: 04/16/2015] [Indexed: 10/24/2022] Open
Abstract
The transcriptional apparatus is one of the most complex cellular machineries and in order to fully appreciate the behavior of these protein-nucleic acid assemblies one has to understand the molecular details of the system. In addition to classical biochemical and structural studies, fluorescence-based techniques turned out as an important--and sometimes the critical--tool to obtain information about the molecular mechanisms of transcription. Fluorescence is not only a multi-modal parameter that can report on molecular interactions, environment and oligomerization status. Measured on the single-molecule level it also informs about the heterogeneity of the system and gives access to distances and distance changes in the molecular relevant nanometer regime. A pre-requisite for fluorescence-based measurements is the site-specific incorporation of one or multiple fluorescent dyes. In this respect, the archaeal transcription system is ideally suited as it is available in a fully recombinant form and thus allows for site-specific modification via sophisticated labeling schemes. The application of fluorescence based approaches to the archaeal transcription apparatus changed our understanding of the molecular mechanisms and dynamics that drive archaeal transcription and unraveled the architecture of transcriptional complexes not amenable to structural interrogation.
Collapse
Affiliation(s)
- Sarah Schulz
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Straße 10, 38106 Braunschweig, Germany
| | - Kevin Kramm
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Straße 10, 38106 Braunschweig, Germany
| | - Finn Werner
- RNAP Laboratory, University College London, Institute of Structural and Molecular Biology, Division of Biosciences, Gower St, London WC1E 6BT, UK
| | - Dina Grohmann
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Straße 10, 38106 Braunschweig, Germany.
| |
Collapse
|
9
|
Kaminsky R, Kallweit S, Weber H, Simons A, Kramm K, Jazwik K, Moll J, Verdonck P. 3D high speed piv assessment of a new aortic heart valve prototype. J Biomech 2006. [DOI: 10.1016/s0021-9290(06)84187-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
10
|
Kaminsky RK, Weber HJ, Simons AP, Kallweit S, Kramm K, Verdonck PR. Comparison of the flow downstream two prototypes of a new monoleaflet artificial aortic heart valve by means of PIV visualization. Comput Methods Biomech Biomed Engin 2005. [DOI: 10.1080/10255840512331388740] [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]
|