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Gerstenmaier L, Colasanti O, Behrens H, Kolonko M, Hammann C, Hagedorn M. Recruitment of both the ESCRT and autophagic machineries to ejecting Mycobacterium marinum. Mol Microbiol 2024; 121:385-393. [PMID: 37230756 DOI: 10.1111/mmi.15075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/24/2023] [Accepted: 05/01/2023] [Indexed: 05/27/2023]
Abstract
Cytosolic Mycobacterium marinum are ejected from host cells such as macrophages or the amoeba Dictyostelium discoideum in a non-lytic fashion. As described previously, the autophagic machinery is recruited to ejecting bacteria and supports host cell integrity during egress. Here, we show that the ESCRT machinery is also recruited to ejecting bacteria, partially dependent on an intact autophagic pathway. As such, the AAA-ATPase Vps4 shows a distinct localization at the ejectosome structure in comparison to fluorescently tagged Vps32, Tsg101 and Alix. Along the bacterium engaged in ejection, ESCRT and the autophagic component Atg8 show partial colocalization. We hypothesize that both, the ESCRT and autophagic machinery localize to the bacterium as part of a membrane damage response, as well as part of a "frustrated autophagosome" that is unable to engulf the ejecting bacterium.
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Affiliation(s)
| | | | - Hannah Behrens
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Margot Kolonko
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Christian Hammann
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Bremen, Germany
- Health and Medical University, Potsdam, Germany
| | - Monica Hagedorn
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Bremen, Germany
- Health and Medical University, Potsdam, Germany
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2
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Helm M, Bohnsack MT, Carell T, Dalpke A, Entian KD, Ehrenhofer-Murray A, Ficner R, Hammann C, Höbartner C, Jäschke A, Jeltsch A, Kaiser S, Klassen R, Leidel SA, Marx A, Mörl M, Meier JC, Meister G, Rentmeister A, Rodnina M, Roignant JY, Schaffrath R, Stadler P, Stafforst T. Experience with German Research Consortia in the Field of Chemical Biology of Native Nucleic Acid Modifications. ACS Chem Biol 2023; 18:2441-2449. [PMID: 37962075 DOI: 10.1021/acschembio.3c00586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The chemical biology of native nucleic acid modifications has seen an intense upswing, first concerning DNA modifications in the field of epigenetics and then concerning RNA modifications in a field that was correspondingly rebaptized epitranscriptomics by analogy. The German Research Foundation (DFG) has funded several consortia with a scientific focus in these fields, strengthening the traditionally well-developed nucleic acid chemistry community and inciting it to team up with colleagues from the life sciences and data science to tackle interdisciplinary challenges. This Perspective focuses on the genesis, scientific outcome, and downstream impact of the DFG priority program SPP1784 and offers insight into how it fecundated further consortia in the field. Pertinent research was funded from mid-2015 to 2022, including an extension related to the coronavirus pandemic. Despite being a detriment to research activity in general, the pandemic has resulted in tremendously boosted interest in the field of RNA and RNA modifications as a consequence of their widespread and successful use in vaccination campaigns against SARS-CoV-2. Funded principal investigators published over 250 pertinent papers with a very substantial impact on the field. The program also helped to redirect numerous laboratories toward this dynamic field. Finally, SPP1784 spawned initiatives for several funded consortia that continue to drive the fields of nucleic acid modification.
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Affiliation(s)
- Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Alexander Dalpke
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Karl-Dieter Entian
- Institute for Molecular Biosciences, Goethe-University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | | | - Ralf Ficner
- Institute for Microbiology and Genetics, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Christian Hammann
- Department of Medicine, HMU Health and Medical University, 14471 Potsdam, Germany
| | - Claudia Höbartner
- Institute for Organic Chemistry, Julius-Maximilians-University of Würzburg, 97074 Würzburg, Germany
| | - Andres Jäschke
- Institute for Pharmacy and Molecular Biotechnology, Ruprecht-Karls-University Heidelberg, 69120 Heidelberg, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Stefanie Kaiser
- Institute for Pharmaceutical Chemistry, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Roland Klassen
- Institute for Biology - Microbiology, University of Kassel, 34132 Kassel, Germany
| | - Sebastian A Leidel
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Andreas Marx
- Department of Chemistry - Organic/Cellular Chemistry, University of Constance, 78457 Constance, Germany
| | - Mario Mörl
- Institute of Biochemistry, University of Leipzig, 04103 Leipzig, Germany
| | - Jochen C Meier
- Department of Cell Physiology, Technical University of Braunschweig, 38106 Brunswick, Germany
| | - Gunter Meister
- Institute of Biochemistry, Genetics and Microbiology - Biochemistry I, University of Regensburg, 93053 Regensburg, Germany
| | - Andrea Rentmeister
- Institute for Biochemistry, Westphalian Wilhelms University Münster, 48149 Münster, Germany
| | - Marina Rodnina
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Jean-Yves Roignant
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
- Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Raffael Schaffrath
- Institute for Biology - Microbiology, University of Kassel, 34132 Kassel, Germany
| | - Peter Stadler
- Institute for Computer Science - Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Thorsten Stafforst
- Interfaculty Institute for Biochemistry, Eberhard Karls University Tübingen, 72074 Tübingen, Germany
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3
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Jermann N, Krusche B, Metag V, Afzal F, Badea M, Beck R, Bielefeldt P, Bieling J, Biroth M, Blanke E, Borisov N, Bornstein M, Brinkmann KT, Ciupka S, Crede V, Dolzhikov A, Drexler P, Dutz H, Elsner D, Fedorov A, Frommberger F, Gardner S, Ghosal D, Goertz S, Gorodnov I, Grüner M, Hammann C, Hartmann J, Hillert W, Hoffmeister P, Honisch C, Jude TC, Kalischewski F, Ketzer B, Klassen P, Klein F, Klempt E, Knaust J, Kolanus N, Kreit J, Krönert P, Lang M, Lazarev AB, Livingston K, Lutterer S, Mahlberg P, Meier C, Meyer W, Mitlasoczki B, Müllers J, Nanova M, Neganov A, Nikonov K, Noël JF, Ostrick M, Ottnad J, Otto B, Penman G, Poller T, Proft D, Reicherz G, Reinartz N, Richter L, Runkel S, Salisbury B, Sarantsev AV, Schaab D, Schmidt C, Schmieden H, Schultes J, Seifen T, Spieker K, Stausberg N, Steinacher M, Taubert F, Thiel A, Thoma U, Thomas A, Urban M, Urff G, Usov Y, van Pee H, Wang YC, Wendel C, Wiedner U, Wunderlich Y. Measurement of polarization observables T, P, and H in π0 and η photoproduction off quasi-free nucleons. Eur Phys J A Hadron Nucl 2023; 59:232. [PMID: 37860634 PMCID: PMC10582157 DOI: 10.1140/epja/s10050-023-01134-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023]
Abstract
The target asymmetry T, recoil asymmetry P, and beam-target double polarization observable H were determined in exclusive π 0 and η photoproduction off quasi-free protons and, for the first time, off quasi-free neutrons. The experiment was performed at the electron stretcher accelerator ELSA in Bonn, Germany, with the Crystal Barrel/TAPS detector setup, using a linearly polarized photon beam and a transversely polarized deuterated butanol target. Effects from the Fermi motion of the nucleons within deuterium were removed by a full kinematic reconstruction of the final state invariant mass. A comparison of the data obtained on the proton and on the neutron provides new insight into the isospin structure of the electromagnetic excitation of the nucleon. Earlier measurements of polarization observables in the γ p → π 0 p and γ p → η p reactions are confirmed. The data obtained on the neutron are of particular relevance for clarifying the origin of the narrow structure in the η n system at W = 1.68 GeV . A comparison with recent partial wave analyses favors the interpretation of this structure as arising from interference of the S 11 ( 1535 ) and S 11 ( 1650 ) resonances within the S 11 -partial wave.
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Affiliation(s)
- N. Jermann
- Department of Physics, University of Basel, Basel, Switzerland
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - B. Krusche
- Department of Physics, University of Basel, Basel, Switzerland
| | - V. Metag
- II. Physikalisches Institut, University of Giessen, Giessen, Germany
| | - F. Afzal
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - M. Badea
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - R. Beck
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - P. Bielefeldt
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - J. Bieling
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - M. Biroth
- Institut für Kernphysik, University of Mainz, Mainz, Germany
| | - E. Blanke
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - N. Borisov
- Joint Institute for Nuclear Research, Dubna, Russia
| | - M. Bornstein
- Physikalisches Institut, University of Bonn, Bonn, Germany
| | - K.-T. Brinkmann
- II. Physikalisches Institut, University of Giessen, Giessen, Germany
| | - S. Ciupka
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - V. Crede
- Department of Physics, Florida State University, Tallahassee, USA
| | - A. Dolzhikov
- Joint Institute for Nuclear Research, Dubna, Russia
| | - P. Drexler
- Institut für Kernphysik, University of Mainz, Mainz, Germany
| | - H. Dutz
- Physikalisches Institut, University of Bonn, Bonn, Germany
| | - D. Elsner
- Physikalisches Institut, University of Bonn, Bonn, Germany
| | - A. Fedorov
- Joint Institute for Nuclear Research, Dubna, Russia
| | - F. Frommberger
- Physikalisches Institut, University of Bonn, Bonn, Germany
| | - S. Gardner
- SUPA School of Physics and Astronomy, University of Glasgow, Glasgow, UK
| | - D. Ghosal
- Department of Physics, University of Basel, Basel, Switzerland
- Present Address: resent address: University of Liverpool, Liverpool, UK
| | - S. Goertz
- Physikalisches Institut, University of Bonn, Bonn, Germany
| | - I. Gorodnov
- Joint Institute for Nuclear Research, Dubna, Russia
| | - M. Grüner
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - C. Hammann
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - J. Hartmann
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - W. Hillert
- Physikalisches Institut, University of Bonn, Bonn, Germany
- Present Address: resent address: University of Hamburg, Hamburg, Germany
| | - P. Hoffmeister
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - C. Honisch
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - T. C. Jude
- Physikalisches Institut, University of Bonn, Bonn, Germany
| | - F. Kalischewski
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - B. Ketzer
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - P. Klassen
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - F. Klein
- Physikalisches Institut, University of Bonn, Bonn, Germany
| | - E. Klempt
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - J. Knaust
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - N. Kolanus
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - J. Kreit
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - P. Krönert
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - M. Lang
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | | | - K. Livingston
- SUPA School of Physics and Astronomy, University of Glasgow, Glasgow, UK
| | - S. Lutterer
- Department of Physics, University of Basel, Basel, Switzerland
- Present Address: resent address: Ruhr University Bochum, Bochum, Germany
| | - P. Mahlberg
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - C. Meier
- Department of Physics, University of Basel, Basel, Switzerland
| | - W. Meyer
- Institut für Experimentalphysik I, Ruhr University Bochum, Bochum, Germany
| | - B. Mitlasoczki
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - J. Müllers
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - M. Nanova
- II. Physikalisches Institut, University of Giessen, Giessen, Germany
| | - A. Neganov
- Joint Institute for Nuclear Research, Dubna, Russia
| | - K. Nikonov
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - J. F. Noël
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - M. Ostrick
- Institut für Kernphysik, University of Mainz, Mainz, Germany
| | - J. Ottnad
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - B. Otto
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - G. Penman
- SUPA School of Physics and Astronomy, University of Glasgow, Glasgow, UK
| | - T. Poller
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - D. Proft
- Physikalisches Institut, University of Bonn, Bonn, Germany
| | - G. Reicherz
- Institut für Experimentalphysik I, Ruhr University Bochum, Bochum, Germany
| | - N. Reinartz
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - L. Richter
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - S. Runkel
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
- Physikalisches Institut, University of Bonn, Bonn, Germany
| | - B. Salisbury
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - A. V. Sarantsev
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - D. Schaab
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - C. Schmidt
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - H. Schmieden
- Physikalisches Institut, University of Bonn, Bonn, Germany
| | - J. Schultes
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - T. Seifen
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - K. Spieker
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - N. Stausberg
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - M. Steinacher
- Department of Physics, University of Basel, Basel, Switzerland
| | - F. Taubert
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - A. Thiel
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - U. Thoma
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - A. Thomas
- Institut für Kernphysik, University of Mainz, Mainz, Germany
| | - M. Urban
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - G. Urff
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - Y. Usov
- Joint Institute for Nuclear Research, Dubna, Russia
| | - H. van Pee
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - Y. C. Wang
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - C. Wendel
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - U. Wiedner
- Institut für Experimentalphysik I, Ruhr University Bochum, Bochum, Germany
| | - Y. Wunderlich
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
| | - CBELSA/TAPS Collaboration
- Department of Physics, University of Basel, Basel, Switzerland
- Helmholtz-Institut für Strahlen-und Kernphysik, University of Bonn, Bonn, Germany
- II. Physikalisches Institut, University of Giessen, Giessen, Germany
- Institut für Kernphysik, University of Mainz, Mainz, Germany
- Joint Institute for Nuclear Research, Dubna, Russia
- Department of Physics, Florida State University, Tallahassee, USA
- Physikalisches Institut, University of Bonn, Bonn, Germany
- SUPA School of Physics and Astronomy, University of Glasgow, Glasgow, UK
- Institut für Experimentalphysik I, Ruhr University Bochum, Bochum, Germany
- Present Address: resent address: University of Liverpool, Liverpool, UK
- Present Address: resent address: University of Hamburg, Hamburg, Germany
- Present Address: resent address: Ruhr University Bochum, Bochum, Germany
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4
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Afzal F, Wunderlich Y, Anisovich AV, Bayadilov D, Beck R, Becker M, Blanke E, Brinkmann KT, Ciupka S, Crede V, Dieterle M, Dutz H, Elsner D, Friedrich S, Frommberger F, Gridnev A, Gottschall M, Grüner M, Gutz E, Hammann C, Hannappel J, Hartmann J, Hillert W, Hoff J, Hoffmeister P, Honisch C, Jude T, Kalinowsky H, Kalischewski F, Keshelashvili I, Klassen P, Klein F, Klempt E, Koop K, Kroenert P, Krusche B, Lang M, Lopatin I, Mahlberg P, Meißner UG, Messi F, Metag V, Meyer W, Mitlasóczki B, Müller J, Müllers J, Nanova M, Nikonov K, Nikonov V, Novinskiy V, Novotny R, Piontek D, Reicherz G, Richter L, Rönchen D, Rostomyan T, Salisbury B, Sarantsev A, Schaab D, Schmidt C, Schmieden H, Schultes J, Seifen T, Sokhoyan V, Sowa C, Spieker K, Stausberg N, Thiel A, Thoma U, Triffterer T, Urban M, Urff G, van Pee H, Walther D, Wendel C, Wiedner U, Wilson A, Winnebeck A, Witthauer L. Observation of the pη^{'} Cusp in the New Precise Beam Asymmetry Σ Data for γp→pη. Phys Rev Lett 2020; 125:152002. [PMID: 33095637 DOI: 10.1103/physrevlett.125.152002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/24/2020] [Accepted: 08/28/2020] [Indexed: 06/11/2023]
Abstract
Data on the beam asymmetry Σ in the photoproduction of η mesons off protons are reported for tagged photon energies from 1130 to 1790 MeV (mass range from W=1748 MeV to W=2045 MeV). The data cover the full solid angle that allows for a precise moment analysis. For the first time, a strong cusp effect in a polarization observable has been observed that is an effect of a branch-point singularity at the pη^{'} threshold [E_{γ}=1447 MeV (W=1896 MeV)]. The latest BnGa partial wave analysis includes the new beam asymmetry data and yields a strong indication for the N(1895)1/2^{-} nucleon resonance, demonstrating the importance of including all singularities for a correct determination of partial waves and resonance parameters.
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Affiliation(s)
- F Afzal
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - Y Wunderlich
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - A V Anisovich
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
- National Research Centre "Kurchatov Institute", Petersburg Nuclear Physics Institute, Gatchina, Russia
| | - D Bayadilov
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
- National Research Centre "Kurchatov Institute", Petersburg Nuclear Physics Institute, Gatchina, Russia
| | - R Beck
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - M Becker
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - E Blanke
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - K-Th Brinkmann
- II. Physikalisches Institut, Universität Giessen, Germany
| | - S Ciupka
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - V Crede
- Department of Physics, Florida State University, Tallahassee, Florida 32306, USA
| | - M Dieterle
- Physikalisches Institut, Universität Basel, Switzerland
| | - H Dutz
- Physikalisches Institut, Universität Bonn, Germany
| | - D Elsner
- Physikalisches Institut, Universität Bonn, Germany
| | - S Friedrich
- II. Physikalisches Institut, Universität Giessen, Germany
| | | | - A Gridnev
- National Research Centre "Kurchatov Institute", Petersburg Nuclear Physics Institute, Gatchina, Russia
| | - M Gottschall
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - M Grüner
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - E Gutz
- II. Physikalisches Institut, Universität Giessen, Germany
| | - C Hammann
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - J Hannappel
- Physikalisches Institut, Universität Bonn, Germany
| | - J Hartmann
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - W Hillert
- Physikalisches Institut, Universität Bonn, Germany
| | - J Hoff
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - P Hoffmeister
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - C Honisch
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - T Jude
- Physikalisches Institut, Universität Bonn, Germany
| | - H Kalinowsky
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - F Kalischewski
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | | | - P Klassen
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - F Klein
- Physikalisches Institut, Universität Bonn, Germany
| | - E Klempt
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - K Koop
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - P Kroenert
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - B Krusche
- Physikalisches Institut, Universität Basel, Switzerland
| | - M Lang
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - I Lopatin
- National Research Centre "Kurchatov Institute", Petersburg Nuclear Physics Institute, Gatchina, Russia
| | - P Mahlberg
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - U-G Meißner
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
- Institute for Advanced Simulation, Institut für Kernphysik and Jülich Center for Hadron Physics, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - F Messi
- Physikalisches Institut, Universität Bonn, Germany
| | - V Metag
- II. Physikalisches Institut, Universität Giessen, Germany
| | - W Meyer
- Institut für Experimentalphysik I, Ruhr Universität Bochum, Germany
| | - B Mitlasóczki
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - J Müller
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - J Müllers
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - M Nanova
- II. Physikalisches Institut, Universität Giessen, Germany
| | - K Nikonov
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
- National Research Centre "Kurchatov Institute", Petersburg Nuclear Physics Institute, Gatchina, Russia
| | - V Nikonov
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
- National Research Centre "Kurchatov Institute", Petersburg Nuclear Physics Institute, Gatchina, Russia
| | - V Novinskiy
- National Research Centre "Kurchatov Institute", Petersburg Nuclear Physics Institute, Gatchina, Russia
| | - R Novotny
- II. Physikalisches Institut, Universität Giessen, Germany
| | - D Piontek
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - G Reicherz
- Institut für Experimentalphysik I, Ruhr Universität Bochum, Germany
| | - L Richter
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - D Rönchen
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - T Rostomyan
- Physikalisches Institut, Universität Basel, Switzerland
| | - B Salisbury
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - A Sarantsev
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
- National Research Centre "Kurchatov Institute", Petersburg Nuclear Physics Institute, Gatchina, Russia
| | - D Schaab
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - C Schmidt
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - H Schmieden
- Physikalisches Institut, Universität Bonn, Germany
| | - J Schultes
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - T Seifen
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - V Sokhoyan
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - C Sowa
- Institut für Experimentalphysik I, Ruhr Universität Bochum, Germany
| | - K Spieker
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - N Stausberg
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - A Thiel
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - U Thoma
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - T Triffterer
- Institut für Experimentalphysik I, Ruhr Universität Bochum, Germany
| | - M Urban
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - G Urff
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - H van Pee
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - D Walther
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - Ch Wendel
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - U Wiedner
- Institut für Experimentalphysik I, Ruhr Universität Bochum, Germany
| | - A Wilson
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
- Department of Physics, Florida State University, Tallahassee, Florida 32306, USA
| | - A Winnebeck
- Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn, Germany
| | - L Witthauer
- Physikalisches Institut, Universität Basel, Switzerland
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5
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Schäck MA, Jablonski KP, Gräf S, Klassen R, Schaffrath R, Kellner S, Hammann C. Eukaryotic life without tQCUG: the role of Elongator-dependent tRNA modifications in Dictyostelium discoideum. Nucleic Acids Res 2020; 48:7899-7913. [PMID: 32609816 PMCID: PMC7430636 DOI: 10.1093/nar/gkaa560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/16/2020] [Accepted: 06/18/2020] [Indexed: 12/23/2022] Open
Abstract
In the Elongator-dependent modification pathway, chemical modifications are introduced at the wobble uridines at position 34 in transfer RNAs (tRNAs), which serve to optimize codon translation rates. Here, we show that this three-step modification pathway exists in Dictyostelium discoideum, model of the evolutionary superfamily Amoebozoa. Not only are previously established modifications observable by mass spectrometry in strains with the most conserved genes of each step deleted, but also additional modifications are detected, indicating a certain plasticity of the pathway in the amoeba. Unlike described for yeast, D. discoideum allows for an unconditional deletion of the single tQCUG gene, as long as the Elongator-dependent modification pathway is intact. In gene deletion strains of the modification pathway, protein amounts are significantly reduced as shown by flow cytometry and Western blotting, using strains expressing different glutamine leader constructs fused to GFP. Most dramatic are these effects, when the tQCUG gene is deleted, or Elp3, the catalytic component of the Elongator complex is missing. In addition, Elp3 is the most strongly conserved protein of the modification pathway, as our phylogenetic analysis reveals. The implications of this observation are discussed with respect to the evolutionary age of the components acting in the Elongator-dependent modification pathway.
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Affiliation(s)
- Manfred A Schäck
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, DE 28759 Bremen, Germany
| | - Kim Philipp Jablonski
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, DE 28759 Bremen, Germany
| | - Stefan Gräf
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Roland Klassen
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Stefanie Kellner
- Department of Chemistry and Pharmacy, Ludwig-Maximilians University Munich, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Christian Hammann
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, DE 28759 Bremen, Germany
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6
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Erber L, Hoffmann A, Fallmann J, Hagedorn M, Hammann C, Stadler PF, Betat H, Prohaska S, Mörl M. Unusual Occurrence of Two Bona-Fide CCA-Adding Enzymes in Dictyostelium discoideum. Int J Mol Sci 2020; 21:ijms21155210. [PMID: 32717856 PMCID: PMC7432833 DOI: 10.3390/ijms21155210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 04/14/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 01/12/2023] Open
Abstract
Dictyostelium discoideum, the model organism for the evolutionary supergroup of Amoebozoa, is a social amoeba that, upon starvation, undergoes transition from a unicellular to a multicellular organism. In its genome, we identified two genes encoding for tRNA nucleotidyltransferases. Such pairs of tRNA nucleotidyltransferases usually represent collaborating partial activities catalyzing CC- and A-addition to the tRNA 3'-end, respectively. In D. discoideum, however, both enzymes exhibit identical activities, representing bona-fide CCA-adding enzymes. Detailed characterization of the corresponding activities revealed that both enzymes seem to be essential and are regulated inversely during different developmental stages of D. discoideum. Intriguingly, this is the first description of two functionally equivalent CCA-adding enzymes using the same set of tRNAs and showing a similar distribution within the cell. This situation seems to be a common feature in Dictyostelia, as other members of this phylum carry similar pairs of tRNA nucleotidyltransferase genes in their genome.
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Affiliation(s)
- Lieselotte Erber
- Institute for Biochemistry, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany; (L.E.); (H.B.)
| | - Anne Hoffmann
- Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany; (A.H.); (J.F.); (P.F.S.); (S.P.)
| | - Jörg Fallmann
- Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany; (A.H.); (J.F.); (P.F.S.); (S.P.)
| | - Monica Hagedorn
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany; (M.H.); (C.H.)
| | - Christian Hammann
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany; (M.H.); (C.H.)
| | - Peter F. Stadler
- Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany; (A.H.); (J.F.); (P.F.S.); (S.P.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases, Leipzig University, 04103 Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, 04103 Leipzig, Germany
- Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Carrera 45 No. 26-85, Colombia
- Santa Fe Institute for Complex Systems, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
- Department of Theoretical Chemistry of the University of Vienna, A-1090 Vienna, Austria
| | - Heike Betat
- Institute for Biochemistry, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany; (L.E.); (H.B.)
| | - Sonja Prohaska
- Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany; (A.H.); (J.F.); (P.F.S.); (S.P.)
- Computational EvoDevo Group, Department of Computer Science, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Mario Mörl
- Institute for Biochemistry, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany; (L.E.); (H.B.)
- Correspondence: ; Tel.: +49-341-9736-911; Fax: +49-341-9736-919
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7
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Malicki M, Spaller T, Winckler T, Hammann C. DIRS retrotransposons amplify via linear, single-stranded cDNA intermediates. Nucleic Acids Res 2020; 48:4230-4243. [PMID: 32170321 PMCID: PMC7192593 DOI: 10.1093/nar/gkaa160] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 10/02/2019] [Revised: 02/14/2020] [Accepted: 03/04/2020] [Indexed: 12/11/2022] Open
Abstract
The Dictyostelium Intermediate Repeat Sequence 1 (DIRS-1) is the name-giving member of the DIRS order of tyrosine recombinase retrotransposons. In Dictyostelium discoideum, DIRS-1 is highly amplified and enriched in heterochromatic centromers of the D. discoideum genome. We show here that DIRS-1 it tightly controlled by the D. discoideum RNA interference machinery and is only mobilized in mutants lacking either the RNA dependent RNA polymerase RrpC or the Argonaute protein AgnA. DIRS retrotransposons contain an internal complementary region (ICR) that is thought to be required to reconstitute a full-length element from incomplete RNA transcripts. Using different versions of D. discoideum DIRS-1 equipped with retrotransposition marker genes, we show experimentally that the ICR is in fact essential to complete retrotransposition. We further show that DIRS-1 produces a mixture of single-stranded, mostly linear extrachromosomal cDNA intermediates. If this cDNA is isolated and transformed into D. discoideum cells, it can be used by DIRS-1 proteins to complete productive retrotransposition. This work provides the first experimental evidence to propose a general retrotransposition mechanism of the class of DIRS like tyrosine recombinase retrotransposons.
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Affiliation(s)
- Marek Malicki
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, DE 28759 Bremen, Germany
| | - Thomas Spaller
- Institute of Pharmacy, Pharmaceutical Biology, Friedrich Schiller University Jena, Semmelweisstraße 10, DE 07743 Jena, Germany
| | - Thomas Winckler
- Institute of Pharmacy, Pharmaceutical Biology, Friedrich Schiller University Jena, Semmelweisstraße 10, DE 07743 Jena, Germany
| | - Christian Hammann
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, DE 28759 Bremen, Germany
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8
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Weinberg CE, Weinberg Z, Hammann C. Novel ribozymes: discovery, catalytic mechanisms, and the quest to understand biological function. Nucleic Acids Res 2019; 47:9480-9494. [PMID: 31504786 PMCID: PMC6765202 DOI: 10.1093/nar/gkz737] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [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: 02/23/2019] [Revised: 08/08/2019] [Accepted: 08/21/2019] [Indexed: 12/21/2022] Open
Abstract
Small endonucleolytic ribozymes promote the self-cleavage of their own phosphodiester backbone at a specific linkage. The structures of and the reactions catalysed by members of individual families have been studied in great detail in the past decades. In recent years, bioinformatics studies have uncovered a considerable number of new examples of known catalytic RNA motifs. Importantly, entirely novel ribozyme classes were also discovered, for most of which both structural and biochemical information became rapidly available. However, for the majority of the new ribozymes, which are found in the genomes of a variety of species, a biological function remains elusive. Here, we concentrate on the different approaches to find catalytic RNA motifs in sequence databases. We summarize the emerging principles of RNA catalysis as observed for small endonucleolytic ribozymes. Finally, we address the biological functions of those ribozymes, where relevant information is available and common themes on their cellular activities are emerging. We conclude by speculating on the possibility that the identification and characterization of proteins that we hypothesize to be endogenously associated with catalytic RNA might help in answering the ever-present question of the biological function of the growing number of genomically encoded, small endonucleolytic ribozymes.
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Affiliation(s)
- Christina E Weinberg
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany
| | - Zasha Weinberg
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16–18, 04107 Leipzig, Germany
| | - Christian Hammann
- Ribogenetics & Biochemistry, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
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9
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Borland K, Diesend J, Ito-Kureha T, Heissmeyer V, Hammann C, Buck AH, Michalakis S, Kellner S. Production and Application of Stable Isotope-Labeled Internal Standards for RNA Modification Analysis. Genes (Basel) 2019; 10:E26. [PMID: 30621251 PMCID: PMC6356711 DOI: 10.3390/genes10010026] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [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: 11/13/2018] [Revised: 12/17/2018] [Accepted: 12/26/2018] [Indexed: 12/04/2022] Open
Abstract
Post-transcriptional RNA modifications have been found to be present in a wide variety of organisms and in different types of RNA. Nucleoside modifications are interesting due to their already known roles in translation fidelity, enzyme recognition, disease progression, and RNA stability. In addition, the abundance of modified nucleosides fluctuates based on growth phase, external stress, or possibly other factors not yet explored. With modifications ever changing, a method to determine absolute quantities for multiple nucleoside modifications is required. Here, we report metabolic isotope labeling to produce isotopically labeled internal standards in bacteria and yeast. These can be used for the quantification of 26 different modified nucleosides. We explain in detail how these internal standards are produced and show their mass spectrometric characterization. We apply our internal standards and quantify the modification content of transfer RNA (tRNA) from bacteria and various eukaryotes. We can show that the origin of the internal standard has no impact on the quantification result. Furthermore, we use our internal standard for the quantification of modified nucleosides in mouse tissue messenger RNA (mRNA), where we find different modification profiles in liver and brain tissue.
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Affiliation(s)
- Kayla Borland
- Department of Chemistry, Ludwig Maximilians University Munich, Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Jan Diesend
- Department of Life Sciences and Chemistry, Jacobs University Bremen GmbH, Campus Ring 1, 28759 Bremen, Germany.
| | - Taku Ito-Kureha
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.
| | - Vigo Heissmeyer
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.
- Helmholtz Zentrum München, Research Unit Molecular Immune Regulation, Marchioninistr. 25, 81377 Munich, Germany.
| | - Christian Hammann
- Department of Life Sciences and Chemistry, Jacobs University Bremen GmbH, Campus Ring 1, 28759 Bremen, Germany.
| | - Amy H Buck
- Institute of Immunology & Infection and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.
| | - Stylianos Michalakis
- Center for Integrated Protein Science Munich CiPSM at the Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Stefanie Kellner
- Department of Chemistry, Ludwig Maximilians University Munich, Butenandtstr. 5-13, 81377 Munich, Germany.
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10
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Diesend J, Kruse J, Hagedorn M, Hammann C. Amoebae, Giant Viruses, and Virophages Make Up a Complex, Multilayered Threesome. Front Cell Infect Microbiol 2018; 7:527. [PMID: 29376032 PMCID: PMC5768912 DOI: 10.3389/fcimb.2017.00527] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 12/13/2017] [Indexed: 01/28/2023] Open
Abstract
Viral infection had not been observed for amoebae, until the Acanthamoeba polyphaga mimivirus (APMV) was discovered in 2003. APMV belongs to the nucleocytoplasmatic large DNA virus (NCLDV) family and infects not only A. polyphaga, but also other professional phagocytes. Here, we review the Megavirales to give an overview of the current members of the Mimi- and Marseilleviridae families and their structural features during amoebal infection. We summarize the different steps of their infection cycle in A. polyphaga and Acanthamoeba castellani. Furthermore, we dive into the emerging field of virophages, which parasitize upon viral factories of the Megavirales family. The discovery of virophages in 2008 and research in recent years revealed an increasingly complex network of interactions between cell, giant virus, and virophage. Virophages seem to be highly abundant in the environment and occupy the same niches as the Mimiviridae and their hosts. Establishment of metagenomic and co-culture approaches rapidly increased the number of detected virophages over the recent years. Genetic interaction of cell and virophage might constitute a potent defense machinery against giant viruses and seems to be important for survival of the infected cell during mimivirus infections. Nonetheless, the molecular events during co-infection and the interactions of cell, giant virus, and virophage have not been elucidated, yet. However, the genetic interactions of these three, suggest an intricate, multilayered network during amoebal (co-)infections. Understanding these interactions could elucidate molecular events essential for proper viral factory activity and could implicate new ways of treating viruses that form viral factories.
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Affiliation(s)
- Jan Diesend
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Janis Kruse
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Monica Hagedorn
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Christian Hammann
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
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11
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Abstract
Transposable elements, identified in all eukaryotes, are mobile genetic units that can change their genomic position. Transposons usually employ an excision and reintegration mechanism, by which they change position, but not copy number. In contrast, retrotransposons amplify via RNA intermediates, increasing their genomic copy number. Hence, they represent a particular threat to the structural and informational integrity of the invaded genome. The social amoeba Dictyostelium discoideum, model organism of the evolutionary Amoebozoa supergroup, features a haploid, gene-dense genome that offers limited space for damage-free transposition. Several of its contemporary retrotransposons display intrinsic integration preferences, for example by inserting next to transfer RNA genes or other retroelements. Likely, any retrotransposons that invaded the genome of the amoeba in a non-directed manner were lost during evolution, as this would result in decreased fitness of the organism. Thus, the positional preference of the Dictyostelium retroelements might represent a domestication of the selfish elements. Likewise, the reduced danger of such domesticated transposable elements led to their accumulation, and they represent about 10% of the current genome of D. discoideum. To prevent the uncontrolled spreading of retrotransposons, the amoeba employs control mechanisms including RNA interference and heterochromatization. Here, we review TRE5-A, DIRS-1 and Skipper-1, as representatives of the three retrotransposon classes in D. discoideum, which make up 5.7% of the Dictyostelium genome. We compile open questions with respect to their mobility and cellular regulation, and suggest strategies, how these questions might be addressed experimentally.
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Affiliation(s)
- Marek Malicki
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Maro Iliopoulou
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Christian Hammann
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
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12
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Kruse J, Meier D, Zenk F, Rehders M, Nellen W, Hammann C. The protein domains of the Dictyostelium microprocessor that are required for correct subcellular localization and for microRNA maturation. RNA Biol 2016; 13:1000-1010. [PMID: 27416267 PMCID: PMC5056781 DOI: 10.1080/15476286.2016.1212153] [Citation(s) in RCA: 7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The maturation pathways of microRNAs (miRNAs) have been delineated for plants and several animals, belonging to the evolutionary supergroups of Archaeplastida and Opisthokonta, respectively. Recently, we reported the discovery of the microprocessor complex in Dictyostelium discoideum of the Amoebozoa supergroup. The complex is composed of the Dicer DrnB and the dsRBD (double-stranded RNA binding domain) containing protein RbdB. Both proteins localize at nucleoli, where they physically interact, and both are required for miRNA maturation. Here we show that the miRNA phenotype of a ΔdrnB gene deletion strain can be rescued by ectopic expression of a series of DrnB GFP fusion proteins, which consistently showed punctate perinucleolar localization in fluorescence microscopy. These punctate foci appear surprisingly stable, as they persist both disintegration of nucleoli and degradation of cellular nucleic acids. We observed that DrnB expression levels influence the number of microprocessor foci and alter RbdB accumulation. An investigation of DrnB variants revealed that its newly identified nuclear localization signal is necessary, but not sufficient for the perinucleolar localization. Biogenesis of miRNAs, which are RNA Pol II transcripts, is correlated with that localization. Besides its bidentate RNase III domains, DrnB contains only a dsRBD, which surprisingly is dispensable for miRNA maturation. This dsRBD can, however, functionally replace the homologous domain in RbdB. Based on the unique setup of the Dictyostelium microprocessor with a subcellular localization similar to plants, but a protein domain composition similar to animals, we propose a model for the evolutionary origin of RNase III proteins acting in miRNA maturation.
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Affiliation(s)
- Janis Kruse
- a Department of Life Sciences and Chemistry, Molecular Life Sciences Research Center, Ribogenetics Biochemistry Lab , Jacobs University Bremen , Bremen , Germany
| | - Doreen Meier
- b Abteilung Genetik, Universität Kassel , Kassel , Germany
| | - Fides Zenk
- b Abteilung Genetik, Universität Kassel , Kassel , Germany
| | - Maren Rehders
- a Department of Life Sciences and Chemistry, Molecular Life Sciences Research Center, Ribogenetics Biochemistry Lab , Jacobs University Bremen , Bremen , Germany
| | | | - Christian Hammann
- a Department of Life Sciences and Chemistry, Molecular Life Sciences Research Center, Ribogenetics Biochemistry Lab , Jacobs University Bremen , Bremen , Germany
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13
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Abstract
An association between hammerhead ribozymes and non-autonomous, long terminal repeat retrotransposons is uncovered in plants, shedding light on the biological function of genomically encoded ribozymes.
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Affiliation(s)
- Christian Hammann
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Molecular Life Sciences Research Center, Jacobs University Bremen, Campus Ring 1, DE 28759, Bremen, Germany.
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14
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Meier D, Kruse J, Buttlar J, Friedrich M, Zenk F, Boesler B, Förstner KU, Hammann C, Nellen W. Analysis of the Microprocessor in Dictyostelium: The Role of RbdB, a dsRNA Binding Protein. PLoS Genet 2016; 12:e1006057. [PMID: 27272207 PMCID: PMC4894637 DOI: 10.1371/journal.pgen.1006057] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 04/26/2016] [Indexed: 11/28/2022] Open
Abstract
We identified the dsRNA binding protein RbdB as an essential component in miRNA processing in Dictyostelium discoideum. RbdB is a nuclear protein that accumulates, together with Dicer B, in nucleolar foci reminiscent of plant dicing bodies. Disruption of rbdB results in loss of miRNAs and accumulation of primary miRNAs. The phenotype can be rescued by ectopic expression of RbdB thus allowing for a detailed analysis of domain function. The lack of cytoplasmic dsRBD proteins involved in miRNA processing, suggests that both processing steps take place in the nucleus thus resembling the plant pathway. However, we also find features e.g. in the domain structure of Dicer which suggest similarities to animals. Reduction of miRNAs in the rbdB- strain and their increase in the Argonaute A knock out allowed the definition of new miRNAs one of which appears to belong to a new non-canonical class. miRNAs are essential regulators in eukaryotic cells and serve to control translation and stability of mRNAs. Processing of primary miRNA transcripts is carried out in two steps by evolutionary conserved machineries consisting mainly of double-strand specific RNases of the Dicer family and accessory double-strand RNA binding proteins (dsRBPs). Regulation occurs by effector proteins of the Argonaute family. While processing in plants is confined to the nucleus, the mechanisms is split into a nuclear and a cytoplasmic step in animals. By knock-out and complementation experiments, we identify RbdB in the amoebozoa Dictyostelium as the accessory dsRBP processing component for both steps. Fluorescence microscopy shows that RbdB co-localizes with the RNaseIII Dicer B in nucleolar foci suggesting mechanistic similarities to plants. Functional domain analysis of RbdB and the structure of Dicers, however, indicate similarities to animals. This places Dictyostelium at an evolutionary branch point between plants and animals. Deep sequencing reveals that the rbdB knock-out strain shows reduced accumulation of microRNAs. Comparison with the wild type and the miRNA overexpressing agnA knock-out strain, allowed for the identification of new miRNAs in Dictyostelium which may have escaped detection by other methods.
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Affiliation(s)
- Doreen Meier
- Department of Genetics, FB10, Kassel University, Kassel, Germany
| | - Janis Kruse
- Ribogenetics Biochemistry Laboratory, Department of Life Science and Chemistry, Molecular Life Sciences Research Center, Jacobs University, Bremen, Germany
| | - Jann Buttlar
- Department of Genetics, FB10, Kassel University, Kassel, Germany
| | | | - Fides Zenk
- Department of Genetics, FB10, Kassel University, Kassel, Germany
| | - Benjamin Boesler
- Department of Genetics, FB10, Kassel University, Kassel, Germany
| | | | - Christian Hammann
- Ribogenetics Biochemistry Laboratory, Department of Life Science and Chemistry, Molecular Life Sciences Research Center, Jacobs University, Bremen, Germany
| | - Wolfgang Nellen
- Department of Genetics, FB10, Kassel University, Kassel, Germany
- * E-mail:
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15
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Duchardt-Ferner E, Gottstein-Schmidtke SR, Weigand JE, Ohlenschläger O, Wurm JP, Hammann C, Suess B, Wöhnert J. Eine OH-Gruppe ändert alles: konformative Dynamik als Grundlage für die Ligandenspezifität des Neomycin-bindenden RNA-Schalters. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201507365] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Elke Duchardt-Ferner
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ); Goethe-Universität Frankfurt; Max-von-Laue-Straße 9 60438 Frankfurt/M Deutschland
| | - Sina R. Gottstein-Schmidtke
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ); Goethe-Universität Frankfurt; Max-von-Laue-Straße 9 60438 Frankfurt/M Deutschland
| | - Julia E. Weigand
- Fachbereich Biologie; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Deutschland
| | - Oliver Ohlenschläger
- Biomolekulare NMR-Spektroskopie; Leibniz-Institut für Altersforschung (Fritz-Lipmann-Institut); Beutenbergstraße 11 07745 Jena Deutschland
| | - Jan-Philip Wurm
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ); Goethe-Universität Frankfurt; Max-von-Laue-Straße 9 60438 Frankfurt/M Deutschland
| | - Christian Hammann
- Ribogenetics Biochemistry Lab; Jacobs Universität Bremen; 28759 Bremen Deutschland
| | - Beatrix Suess
- Fachbereich Biologie; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Deutschland
| | - Jens Wöhnert
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ); Goethe-Universität Frankfurt; Max-von-Laue-Straße 9 60438 Frankfurt/M Deutschland
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16
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Duchardt-Ferner E, Gottstein-Schmidtke SR, Weigand JE, Ohlenschläger O, Wurm JP, Hammann C, Suess B, Wöhnert J. What a Difference an OH Makes: Conformational Dynamics as the Basis for the Ligand Specificity of the Neomycin-Sensing Riboswitch. Angew Chem Int Ed Engl 2015; 55:1527-30. [PMID: 26661511 DOI: 10.1002/anie.201507365] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [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: 08/07/2015] [Indexed: 01/13/2023]
Abstract
To ensure appropriate metabolic regulation, riboswitches must discriminate efficiently between their target ligands and chemically similar molecules that are also present in the cell. A remarkable example of efficient ligand discrimination is a synthetic neomycin-sensing riboswitch. Paromomycin, which differs from neomycin only by the substitution of a single amino group with a hydroxy group, also binds but does not flip the riboswitch. Interestingly, the solution structures of the two riboswitch-ligand complexes are virtually identical. In this work, we demonstrate that the local loss of key intermolecular interactions at the substitution site is translated through a defined network of intramolecular interactions into global changes in RNA conformational dynamics. The remarkable specificity of this riboswitch is thus based on structural dynamics rather than static structural differences. In this respect, the neomycin riboswitch is a model for many of its natural counterparts.
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Affiliation(s)
- Elke Duchardt-Ferner
- Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/M, Deutschland
| | - Sina R Gottstein-Schmidtke
- Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/M, Deutschland
| | - Julia E Weigand
- Fachbereich Biologie, Technische Universität Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Deutschland
| | - Oliver Ohlenschläger
- Biomolekulare NMR-Spektroskopie, Leibniz Institut für Altersforschung (Fritz-Lipmann-Institut), Beutenbergstrasse 11, 07745, Jena, Deutschland
| | - Jan-Philip Wurm
- Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/M, Deutschland
| | - Christian Hammann
- Ribogenetics Biochemistry Lab, Jacobs Universität Bremen, 28759, Bremen, Deutschland
| | - Beatrix Suess
- Fachbereich Biologie, Technische Universität Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Deutschland
| | - Jens Wöhnert
- Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/M, Deutschland.
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17
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Schmith A, Spaller T, Gaube F, Fransson Å, Boesler B, Ojha S, Nellen W, Hammann C, Söderbom F, Winckler T. A host factor supports retrotransposition of the TRE5-A population in Dictyostelium cells by suppressing an Argonaute protein. Mob DNA 2015; 6:14. [PMID: 26339297 PMCID: PMC4559204 DOI: 10.1186/s13100-015-0045-5] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 08/26/2015] [Indexed: 11/30/2022] Open
Abstract
Background In the compact and haploid genome of Dictyostelium discoideum control of transposon activity is of particular importance to maintain viability. The non-long terminal repeat retrotransposon TRE5-A amplifies continuously in D. discoideum cells even though it produces considerable amounts of minus-strand (antisense) RNA in the presence of an active RNA interference machinery. Removal of the host-encoded C-module-binding factor (CbfA) from D. discoideum cells resulted in a more than 90 % reduction of both plus- and minus-strand RNA of TRE5-A and a strong decrease of the retrotransposition activity of the cellular TRE5-A population. Transcriptome analysis revealed an approximately 230-fold overexpression of the gene coding for the Argonaute-like protein AgnC in a CbfA-depleted mutant. Results The D. discoideum genome contains orthologs of RNA-dependent RNA polymerases, Dicer-like proteins, and Argonaute proteins that are supposed to represent RNA interference pathways. We analyzed available mutants in these genes for altered expression of TRE5-A. We found that the retrotransposon was overexpressed in mutants lacking the Argonaute proteins AgnC and AgnE. Because the agnC gene is barely expressed in wild-type cells, probably due to repression by CbfA, we employed a new method of promoter-swapping to overexpress agnC in a CbfA-independent manner. In these strains we established an in vivo retrotransposition assay that determines the retrotransposition frequency of the cellular TRE5-A population. We observed that both the TRE5-A steady-state RNA level and retrotransposition rate dropped to less than 10 % of wild-type in the agnC overexpressor strains. Conclusions The data suggest that TRE5-A amplification is controlled by a distinct pathway of the Dictyostelium RNA interference machinery that does not require RNA-dependent RNA polymerases but involves AgnC. This control is at least partially overcome by the activity of CbfA, a factor derived from the retrotransposon’s host. This unusual regulation of mobile element activity most likely had a profound effect on genome evolution in D. discoideum. Electronic supplementary material The online version of this article (doi:10.1186/s13100-015-0045-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anika Schmith
- Department of Pharmaceutical Biology, Institute of Pharmacy, University of Jena, Semmelweisstrasse 10, 07743 Jena, Germany
| | - Thomas Spaller
- Department of Pharmaceutical Biology, Institute of Pharmacy, University of Jena, Semmelweisstrasse 10, 07743 Jena, Germany
| | - Friedemann Gaube
- Department of Pharmaceutical Biology, Institute of Pharmacy, University of Jena, Semmelweisstrasse 10, 07743 Jena, Germany
| | - Åsa Fransson
- Department of Molecular Biology, Biomedical Center, Swedish University of Agricultural Sciences, Uppsala, Sweden ; Present address: Aprea AB, Karolinska Institutet Science Park, Nobels väg 3, 17175 Solna, Sweden
| | - Benjamin Boesler
- Institute of Biology - Genetics, University of Kassel, Kassel, Germany
| | - Sandeep Ojha
- Ribogenetics@Biochemistry Lab, Department of Life Sciences and Chemistry, Molecular Life Sciences Research Center, Jacobs University Bremen, Bremen, Germany
| | - Wolfgang Nellen
- Institute of Biology - Genetics, University of Kassel, Kassel, Germany ; Present address: Department of Biology, Brawijaya University, Jl. Veteran, Malang, East Java Indonesia
| | - Christian Hammann
- Ribogenetics@Biochemistry Lab, Department of Life Sciences and Chemistry, Molecular Life Sciences Research Center, Jacobs University Bremen, Bremen, Germany
| | - Fredrik Söderbom
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Thomas Winckler
- Department of Pharmaceutical Biology, Institute of Pharmacy, University of Jena, Semmelweisstrasse 10, 07743 Jena, Germany
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18
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Boesler B, Meier D, Förstner KU, Friedrich M, Hammann C, Sharma CM, Nellen W. Argonaute proteins affect siRNA levels and accumulation of a novel extrachromosomal DNA from the Dictyostelium retrotransposon DIRS-1. J Biol Chem 2014; 289:35124-38. [PMID: 25352599 DOI: 10.1074/jbc.m114.612663] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The retrotransposon DIRS-1 is the most abundant retroelement in Dictyostelium discoideum and constitutes the pericentromeric heterochromatin of the six chromosomes in D. discoideum. The vast majority of cellular siRNAs is derived from DIRS-1, suggesting that the element is controlled by RNAi-related mechanisms. We investigated the role of two of the five Argonaute proteins of D. discoideum, AgnA and AgnB, in DIRS-1 silencing. Deletion of agnA resulted in the accumulation of DIRS-1 transcripts, the expression of DIRS-1-encoded proteins, and the loss of most DIRS-1-derived secondary siRNAs. Simultaneously, extrachromosomal single-stranded DIRS-1 DNA accumulated in the cytoplasm of agnA- strains. These DNA molecules appear to be products of reverse transcription and thus could represent intermediate structures before transposition. We further show that transitivity of endogenous siRNAs is impaired in agnA- strains. The deletion of agnB alone had no strong effect on DIRS-1 transposon regulation. However, in agnA-/agnB- double mutant strains strongly reduced accumulation of extrachromosomal DNA compared with the single agnA- strains was observed.
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Affiliation(s)
- Benjamin Boesler
- From the Department of Genetics, FB10, Kassel University, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Doreen Meier
- From the Department of Genetics, FB10, Kassel University, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Konrad U Förstner
- Research Center for Infectious Diseases (ZINF), University of Würzburg, Josef-Schneider-Strasse 2/Bau D15, 97080 Würzburg, Germany, and
| | - Michael Friedrich
- From the Department of Genetics, FB10, Kassel University, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Christian Hammann
- Ribogenetics Biochemistry Laboratory, School of Engineering and Science, Molecular Life Sciences Research Center, Jacobs University, Campus Ring 1, DE-28759 Bremen, Germany
| | - Cynthia M Sharma
- Research Center for Infectious Diseases (ZINF), University of Würzburg, Josef-Schneider-Strasse 2/Bau D15, 97080 Würzburg, Germany, and
| | - Wolfgang Nellen
- From the Department of Genetics, FB10, Kassel University, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany,
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19
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Abstract
Hairpin ribozymes are small RNA catalytic motifs naturally found in the satellite RNAs of tobacco ringspot virus (TRsV), chicory yellow mottle virus (CYMoV), and arabis mosaic virus (ArMV). The catalytic activity of the hairpin ribozyme extends to both cleavage and ligation reactions. Here we describe methods for the kinetic analysis of the self-cleavage reaction under transcription reaction conditions. We also describe methods for the generation of DNA templates for subsequent in vitro transcription reaction of hairpin ribozymes. This is followed by a description of the preparation of the suitable RNA molecules for ligation reaction and their kinetic analysis.
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Affiliation(s)
- Preeti Bajaj
- Department of Insect Resistance, International Center for Genetic Engineering and Biotechnology, New Delhi, India
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20
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Wiegand S, Meier D, Seehafer C, Malicki M, Hofmann P, Schmith A, Winckler T, Földesi B, Boesler B, Nellen W, Reimegård J, Käller M, Hällman J, Emanuelsson O, Avesson L, Söderbom F, Hammann C. The Dictyostelium discoideum RNA-dependent RNA polymerase RrpC silences the centromeric retrotransposon DIRS-1 post-transcriptionally and is required for the spreading of RNA silencing signals. Nucleic Acids Res 2013; 42:3330-45. [PMID: 24369430 PMCID: PMC3950715 DOI: 10.1093/nar/gkt1337] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [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: 12/16/2022] Open
Abstract
Dictyostelium intermediate repeat sequence 1 (DIRS-1) is the founding member of a poorly characterized class of retrotransposable elements that contain inverse long terminal repeats and tyrosine recombinase instead of DDE-type integrase enzymes. In Dictyostelium discoideum, DIRS-1 forms clusters that adopt the function of centromeres, rendering tight retrotransposition control critical to maintaining chromosome integrity. We report that in deletion strains of the RNA-dependent RNA polymerase RrpC, full-length and shorter DIRS-1 messenger RNAs are strongly enriched. Shorter versions of a hitherto unknown long non-coding RNA in DIRS-1 antisense orientation are also enriched in rrpC– strains. Concurrent with the accumulation of long transcripts, the vast majority of small (21 mer) DIRS-1 RNAs vanish in rrpC– strains. RNASeq reveals an asymmetric distribution of the DIRS-1 small RNAs, both along DIRS-1 and with respect to sense and antisense orientation. We show that RrpC is required for post-transcriptional DIRS-1 silencing and also for spreading of RNA silencing signals. Finally, DIRS-1 mis-regulation in the absence of RrpC leads to retrotransposon mobilization. In summary, our data reveal RrpC as a key player in the silencing of centromeric retrotransposon DIRS-1. RrpC acts at the post-transcriptional level and is involved in spreading of RNA silencing signals, both in the 5′ and 3′ directions.
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Affiliation(s)
- Stephan Wiegand
- Ribogenetics@Biochemistry Lab, School of Engineering and Science, Molecular Life Sciences Research Center, Jacobs University Bremen, Campus Ring 1, DE-28759 Bremen, Germany, Abteilung Genetik, Universität Kassel, Heinrich-Plett-Strasse 40, DE-34132 Kassel, Germany, Friedrich-Schiller-Universität Jena, Institut für Pharmazie, Lehrstuhl für Pharmazeutische Biologie, Semmelweisstraße 10, DE-07743 Jena, Germany, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory (SciLifeLab Stockholm), School of Biotechnology, SE-171 65 Solna, Sweden, Garvan Institute of Medical Research, 384 Victoria St Darlinghurst, NSW 2010, Australia, Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, PO Box 596, S-75124 Uppsala, Sweden and Science for Life Laboratory, SE-75124 Uppsala, Sweden
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21
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Kalweit A, Hammann C. G17-modified hammerhead ribozymes are active in vitro and in vivo. RNA 2013; 19:1595-1604. [PMID: 24145822 PMCID: PMC3884650 DOI: 10.1261/rna.040543.113] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 09/06/2013] [Indexed: 06/02/2023]
Abstract
Natural hammerhead ribozymes (HHRz) feature tertiary interactions between hairpin loops or bulges in two of three helices that surround the catalytic core of conserved nucleotides. Their conservation was originally established on minimal versions lacking the tertiary interactions. While those sequence requirements in general also apply to natural versions, we show here differences for the HHRz cleavage site N17. A guanosine at this position strongly impairs cleavage activity in minimal versions, whereas we observe for the G17 variants of four tertiary stabilized HHRz significant cleavage and ligation activity in vitro. Kinetic analyses of these variants revealed a reduced rate and extent of cleavage, compared with wild-type sequences, while variants with distorted tertiary interactions cleaved at a reduced rate, but to the same extent. Contrary to this, G17 variants exhibit similar in vitro ligation activity as compared with the respective wild-type motif. To also address the catalytic performance of these motifs in vivo, we have inserted HHRz cassettes in the lacZ gene and tested this β-galactosidase reporter in Dictyostelium discoideum. In colorimetric assays, we observe differences in the enzymatic activity of β-galactosidase, which correlate well with the activity of the different HHRz variants in vitro and which can be unambiguously attributed to ribozyme cleavage by primer extension analysis.
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22
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Wiegand S, Hammann C. The 5' spreading of small RNAs in Dictyostelium discoideum depends on the RNA-dependent RNA polymerase RrpC and on the dicer-related nuclease DrnB. PLoS One 2013; 8:e64804. [PMID: 23724097 PMCID: PMC3661229 DOI: 10.1371/journal.pone.0064804] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 04/16/2013] [Indexed: 11/19/2022] Open
Abstract
RNA interference (RNAi) is a gene-regulatory mechanism in eukarya that is based on the presence of double stranded RNA and that can act on both, the transcription or post-transcriptional level. In many species, RNA-dependent RNA polymerases (RdRPs) are required for RNAi. To study the function of the three RdRPs in the amoeba Dictyostelium discoideum, we have deleted the encoding genes rrpA, rrpB and rrpC in all possible combinations. In these strains, expression of either antisense or hairpin RNA constructs against the transgene lacZ resulted in a 50% reduced β-Galactosidase activity. Northern blots surprisingly revealed unchanged lacZ mRNA levels, indicative of post-transcriptional regulation. Only in rrpC knock out strains, low levels of β-gal small interfering RNAs (siRNAs) could be detected in antisense RNA expressing strains. In contrast to this, and at considerably higher levels, all hairpin RNA expressing strains featured β-gal siRNAs. Spreading of the silencing signal to mRNA sequences 5′ of the original hairpin trigger was observed in all strains, except when the rrpC gene or that of the dicer-related nuclease DrnB was deleted. Thus, our data indicate that transitivity of an RNA silencing signal exists in D. discoideum and that it requires the two enzymes RrpC and DrnB.
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Affiliation(s)
- Stephan Wiegand
- Ribogenetics@Biochemistry Lab, School of Engineering and Science, MOLIFE Research Center, Jacobs University Bremen, Bremen, Germany
| | - Christian Hammann
- Ribogenetics@Biochemistry Lab, School of Engineering and Science, MOLIFE Research Center, Jacobs University Bremen, Bremen, Germany
- * E-mail:
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23
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Hofmann P, Kruse J, Hammann C. Transcript localization in Dictyostelium discoideum cells by RNA FISH. Methods Mol Biol 2013; 983:311-23. [PMID: 23494315 DOI: 10.1007/978-1-62703-302-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Biogenesis of ribosomal RNA (rRNA) takes place preliminary in the nucleolus of eukaryotic cells, the site of rDNA transcription. Several processing steps of rRNA molecules have been implied to take place in the cytoplasm. To follow these processing events we have adapted protocols for fluorescence in situ hybridization (FISH) for use in Dictyostelium discoideum. We describe methods for the generation of suitable fluorescently labeled probes and the fixation of cells, by which we have localized different precursor and mature rRNA molecules to the nucleolus or the cytoplasm, respectively.
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Affiliation(s)
- Patrick Hofmann
- Heisenberg Research Group Ribogenetics, Technical University of Darmstadt, Darmstadt, Germany
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24
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Abstract
Viroids are the smallest autonomous infectious nucleic acids known today. They are non-coding, unencapsidated, circular RNAs with sizes ranging from 250 to 400 nucleotides and infect certain plants. These RNAs are transcribed by rolling-circle mechanisms in the plant host's nuclei (Pospiviroidae) or chloroplasts (Avsunviroidae). Since viroids lack any open reading frame, their pathogenicity has for a long time been a conundrum. Recent findings, however, show that viroid infection is associated with the appearance of viroid-specific small RNA (vsRNA). These have sizes similar to endogenous small interfering RNA and microRNA and thus might alter the normal gene expression in the host plant. In this review we will summarize the current knowledge on vsRNA and discuss the current hypotheses how they connect to the induced symptoms, which vary dramatically, depending on both the plant cultivar and the viroid strain.
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Affiliation(s)
- Christian Hammann
- Heisenberg Research Group Ribogenetics, Technical University of Darmstadt, Darmstadt, Germany.
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25
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Abstract
The hammerhead ribozyme is a small catalytic RNA motif capable of endonucleolytic (self-) cleavage. It is composed of a catalytic core of conserved nucleotides flanked by three helices, two of which form essential tertiary interactions for fast self-scission under physiological conditions. Originally discovered in subviral plant pathogens, its presence in several eukaryotic genomes has been reported since. More recently, this catalytic RNA motif has been shown to reside in a large number of genomes. We review the different approaches in discovering these new hammerhead ribozyme sequences and discuss possible biological functions of the genomic motifs.
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Affiliation(s)
- Christian Hammann
- Heisenberg Research Group Ribogenetics, Technical University of Darmstadt, 64287 Darmstadt, Germany
- Corresponding authors.E-mail .E-mail .E-mail .E-mail .
| | - Andrej Luptak
- Department of Pharmaceutical Sciences, University of California–Irvine, Irvine, California 92697, USA
- Corresponding authors.E-mail .E-mail .E-mail .E-mail .
| | - Jonathan Perreault
- Centre INRS – Institut Armand-Frappier, Laval, Québec, H7V 1B7, Canada
- Corresponding authors.E-mail .E-mail .E-mail .E-mail .
| | - Marcos de la Peña
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), 46022 Valencia, Spain
- Corresponding authors.E-mail .E-mail .E-mail .E-mail .
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26
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Abstract
Abstract Hairpin ribozymes occur naturally only in the satellite RNAs of tobacco ringspot virus (TRsV), chicory yellow mottle virus (CYMoV) and arabis mosaic virus (ArMV). The catalytic centre of the predominantly studied sTRsV hairpin ribozyme, and of sArMV is organised around a four-way helical junction. We show here that sCYMoV features a five-way helical junction instead. Mutational analysis indicates that the fifth stem does not influence kinetic parameters of the sCYMoV hairpin ribozyme in vitro reactions, and therefore seems an appendix to that junction in the other ribozymes. We report further that all three ribozymes feature a three-way helical junction outside the catalytic core in stem A, with Watson-Crick complementarity to loop nucleotides in stem B. Kinetic analyses of cleavage and ligation reactions of several variants of the sTRsV and sCYMoV hairpin ribozymes in vitro show that the presence of this junction interferes with their reactions, particularly the ligation. We provide evidence that this is not due to a presumed interaction of the afore-mentioned elements in stems A and B. The evolutionary survival of this cis-inhibiting element seems rather to be caused by the coincidence of its position with that of the hammerhead ribozyme in the other RNA polarity.
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Affiliation(s)
- Preeti Bajaj
- Heisenberg Research Group Ribogenetics, Technical University of Darmstadt, Germany
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27
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Abstract
Higher order RNA structures can mask splicing signals, loop out exons, or constitute riboswitches all of which contributes to the complexity of splicing regulation. We identified a G to A substitution between branch point (BP) and 3′ splice site (3′ss) of Saccharomyces cerevisiae COF1 intron, which dramatically impaired its splicing. RNA structure prediction and in-line probing showed that this mutation disrupted a stem in the BP-3′ss region. Analyses of various COF1 intron modifications revealed that the secondary structure brought about the reduction of BP to 3′ss distance and masked potential 3′ss. We demonstrated the same structural requisite for the splicing of UBC13 intron. Moreover, RNAfold predicted stable structures for almost all distant BP introns in S. cerevisiae and for selected examples in several other Saccharomycotina species. The employment of intramolecular structure to localize 3′ss for the second splicing step suggests the existence of pre-mRNA structure-based mechanism of 3′ss recognition.
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Affiliation(s)
- Ondřej Gahura
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
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Boesler C, Kruse J, Söderbom F, Hammann C. Sequence and generation of mature ribosomal RNA transcripts in Dictyostelium discoideum. J Biol Chem 2011; 286:17693-703. [PMID: 21454536 DOI: 10.1074/jbc.m110.208306] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The amoeba Dictyostelium discoideum is a well established model organism for studying numerous aspects of cellular and developmental functions. Its ribosomal RNA (rRNA) is encoded in an extrachromosomal palindrome that exists in ∼100 copies in the cell. In this study, we have set out to investigate the sequence of the expressed rRNA. For this, we have ligated the rRNA ends and performed RT-PCR on these circular RNAs. Sequencing revealed that the mature 26 S, 17 S, 5.8 S, and 5 S rRNAs have sizes of 3741, 1871, 162, and 112 nucleotides, respectively. Unlike the published data, all mature rRNAs of the same type uniformly display the same start and end nucleotides in the analyzed AX2 strain. We show the existence of a short lived primary transcript covering the rRNA transcription unit of 17 S, 5.8 S, and 26 S rRNA. Northern blots and RT-PCR reveal that from this primary transcript two precursor molecules of the 17 S and two precursors of the 26 S rRNA are generated. We have also determined the sequences of these precursor molecules, and based on these data, we propose a model for the maturation of the rRNAs in Dictyostelium discoideum that we compare with the processing of the rRNA transcription unit of Saccharomyces cerevisiae.
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Affiliation(s)
- Carsten Boesler
- Heisenberg Research Group Ribogenetics, Technical University of Darmstadt, 64287 Darmstadt, Germany
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29
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Wiegand S, Kruse J, Gronemann S, Hammann C. Efficient generation of gene knockout plasmids for Dictyostelium discoideum using one-step cloning. Genomics 2011; 97:321-5. [PMID: 21316445 DOI: 10.1016/j.ygeno.2011.02.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 02/03/2011] [Indexed: 11/18/2022]
Abstract
The amoeba Dictyostelium discoideum is a well-established model organism for studying numerous aspects of cellular and developmental functions. Its rather small (~34Mb) chromosomal genome and the high efficiency of gene disruption by homologous recombination have enabled researchers to dissect various specific gene functions. We describe here the use of one-step cloning for the fast and efficient generation of deletion vectors that are produced in a one-step reaction by inserting two PCR products into an organism-specific, generic acceptor system. This worked efficiently for all 16 tested constructs directed against genes in the amoeba Dictyostelium discoideum. Saving cost and time, the used protocol represents a significant advancement in the generation of such plasmids compared to the conventionally applied restriction enzyme/ligation approach. Using appropriate selection markers, similar systems could also be useful in other organisms, where genes can be knocked out by homologous recombination.
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Affiliation(s)
- Stephan Wiegand
- Department for Microbiology and Genetics, Technische Universität Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
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30
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Giulieri S, Morisod B, Edney T, Odman M, Genne D, Malinverni R, Hammann C, Musumeci E, Voide C, Greub G, Masserey E, Bille J, Cavassini M, Jaton K. Outbreak of Mycobacterium haemophilum Infections after Permanent Makeup of the Eyebrows. Clin Infect Dis 2011; 52:488-91. [DOI: 10.1093/cid/ciq191] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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31
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Abstract
The hammerhead ribozyme was originally discovered in subviral plant pathogens and was subsequently also found in a few other genomic locations. Using a secondary structure-based descriptor, we have searched publicly accessible sequence databases for new examples of type III hammerhead ribozymes. The more than 60,000 entries fulfilling the descriptor were filtered with respect to folding and stability parameters that were experimentally validated. This resulted in a set of 284 unique motifs, of which 124 represent database entries of known hammerhead ribozymes from subviral plant pathogens and A. thaliana. The remainder are 160 novel ribozyme candidates in 50 different eukaryotic genomes. With a few exceptions, the ribozymes were found either in repetitive DNA sequences or in introns of protein coding genes. Our data, which is complementary to a study by De la Peña and García-Robles in 2010, indicate that the hammerhead is the most abundant small endonucleolytic ribozyme, which, in view of no sequence conservation beyond the essential nucleotides, likely has evolved independently in different organisms.
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32
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Weigand JE, Schmidtke SR, Will TJ, Duchardt-Ferner E, Hammann C, Wöhnert J, Suess B. Mechanistic insights into an engineered riboswitch: a switching element which confers riboswitch activity. Nucleic Acids Res 2010; 39:3363-72. [PMID: 21149263 PMCID: PMC3082870 DOI: 10.1093/nar/gkq946] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [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: 01/09/2023] Open
Abstract
While many different RNA aptamers have been identified that bind to a plethora of small molecules only very few are capable of acting as engineered riboswitches. Even for aptamers binding the same ligand large differences in their regulatory potential were observed. We address here the molecular basis for these differences by using a set of unrelated neomycin-binding aptamers. UV melting analyses showed that regulating aptamers are thermally stabilized to a significantly higher degree upon ligand binding than inactive ones. Regulating aptamers show high ligand-binding affinity in the low nanomolar range which is necessary but not sufficient for regulation. NMR data showed that a destabilized, open ground state accompanied by extensive structural changes upon ligand binding is important for regulation. In contrast, inactive aptamers are already pre-formed in the absence of the ligand. By a combination of genetic, biochemical and structural analyses, we identified a switching element responsible for destabilizing the ligand free state without compromising the bound form. Our results explain for the first time the molecular mechanism of an engineered riboswitch.
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Affiliation(s)
- Julia E Weigand
- RNA Biochemistry, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt/M, Germany
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33
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Abstract
Despite its small size, the complex behavior of the hammerhead ribozyme keeps surprising us, even more than 20 years after its discovery. Here, we summarize recent developments in the field, in particular the discovery of the first split hammerhead ribozyme.
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Affiliation(s)
- Christian Hammann
- Research Group Molecular Interactions, Department of Genetics, FB 18 Naturwissenschaften, Heinrich-Plett-Str. 40, Universität Kassel, D-34132 Kassel, Germany.
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Abstract
A discussion of experimental approaches and theoretical difficulties in the identification of ribozymes with novel catalytic functions. New regulatory RNAs with complex structures have recently been discovered, among them the first catalytic riboswitch, a gene-regulatory RNA sequence with catalytic activity. Here we discuss some of the experimental approaches and theoretical difficulties attached to the identification of new ribozymes in genomes.
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Affiliation(s)
- Christian Hammann
- Research Group Molecular Interactions, Department of Genetics, FB 18 Naturwissenschaften, Universität Kassel, D-34132 Kassel, Germany
| | - Eric Westhof
- Architecture et Réactivité de l'ARN, Université Louis Pasteur de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, CNRS, rue René Descartes, F-67084 Strasbourg Cedex, France
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35
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Przybilski R, Hammann C. The tolerance to exchanges of the Watson Crick base pair in the hammerhead ribozyme core is determined by surrounding elements. RNA 2007; 13:1625-30. [PMID: 17666711 PMCID: PMC1986816 DOI: 10.1261/rna.631207] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Tertiary interacting elements are important features of functional RNA molecules, for example, in all small nucleolytic ribozymes. The recent crystal structure of a tertiary stabilized type I hammerhead ribozyme revealed a conventional Watson-Crick base pair in the catalytic core, formed between nucleotides C3 and G8. We show that any Watson-Crick base pair between these positions retains cleavage competence in two type III ribozymes. In the Arabidopsis thaliana sequence, only moderate differences in cleavage rates are observed for the different base pairs, while the peach latent mosaic viroid (PLMVd) ribozyme exhibits a preference for a pyrimidine at position 3 and a purine at position 8. To understand these differences, we created a series of chimeric ribozymes in which we swapped sequence elements that surround the catalytic core. The kinetic characterization of the resulting ribozymes revealed that the tertiary interacting loop sequences of the PLMVd ribozyme are sufficient to induce the preference for Y3-R8 base pairs in the A. thaliana hammerhead ribozyme. In contrast to this, only when the entire stem-loops I and II of the A. thaliana sequences are grafted on the PLMVd ribozyme is any Watson-Crick base pair similarly tolerated. The data provide evidence for a complex interplay of secondary and tertiary structure elements that lead, mediated by long-range effects, to an individual modulation of the local structure in the catalytic core of different hammerhead ribozymes.
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Abstract
The hammerhead ribozyme is a small RNA endonuclease found in sub-viral plant pathogens, in transcripts from certain animal satellite DNAs and encoded at distinct loci of Arabidopsis thaliana. Kinetic analyses of tertiary stabilised ribozymes from peach latent mosaic viroid (PLMVd), Schistosoma mansoni and A. thaliana revealed a ten-fold difference in cleavage rates. Core nucleotide variations affected cleavage reactions least in the A. thaliana ribozyme, and most in the S. mansoni ribozyme. The reverse ligation reaction was catalysed efficiently by the PLMVd and A. thaliana ribozymes. The different behaviour of the individual hammerhead ribozymes is discussed in terms of structure and function.
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Affiliation(s)
- Rita Przybilski
- AG Molecular Interactions, Department of Genetics, University of Kassel, Heinrich-Plett-Str 40, Kassel, Germany
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Abstract
We have investigated the thermodynamic parameters and binding of a regulatory subunit of cAMP-dependent protein kinase (PKA) to its natural low-molecular-weight ligand, cAMP, and analogues thereof. For analysis of this model system, we compared side-by-side isothermal titration calorimetry (ITC) with surface plasmon resonance (SPR). Both ITC and SPR analyses revealed that binding of the protein to cAMP or its analogues was enthalpically driven and characterised by similar free energy values (DeltaG=-9.4 to -10.7 kcal mol-1) for all interactions. Despite the similar affinities, binding of the cyclic nucleotides used here was characterised by significant differences in the contribution of entropy (-TDeltaS) and enthalpy (DeltaH) to DeltaG. The comparison of ITC and SPR data for one cAMP analogue further revealed deviations caused by the method. These equilibrium parameters could be complemented by thermodynamic data of the transition state (DeltaHnot equal, DeltaGnot equal, DeltaSnot equal) for both association and dissociation measured by SPR. This direct comparison of ITC and SPR highlights method-specific advantages and drawbacks for thermodynamic analyses of protein/ligand interactions.
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Affiliation(s)
- Daniela Moll
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, D-34132 Kassel, Germany
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39
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Affiliation(s)
- Rita Przybilski
- AG Molecular Interactions, Department of Genetics, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
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40
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Manzano S, Guggisberg D, Hammann C, Laubscher B. Pustulose exanthématique aiguë généralisée : premier cas décrit en relation avec une infection à Chlamydia pneumoniae. Arch Pediatr 2006; 13:1230-2. [PMID: 16919427 DOI: 10.1016/j.arcped.2006.06.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2005] [Accepted: 05/22/2006] [Indexed: 11/20/2022]
Abstract
UNLABELLED Skin reactions to drugs or infections can be very important. CASE REPORT A 14-year-old boy developed fever, a diffuse pustular rash and a respiratory distress. Chest X-rays and serology were consistent with an acute Chlamydia pneumoniae infection. A skin biopsy revealed an acute generalized exanthematous pustulosis. CONCLUSION Acute generalized exanthematous pustulosis (AGEP) is a disease manifested by a diffuse eruption of follicular sterile pustules. Most of the cases are drug induced, but they may be secondary to viral or bacterial infections. We report the first case of AGEP in a child with an acute C. pneumoniae infection.
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Affiliation(s)
- S Manzano
- Département de pédiatrie, hôpital Pourtalès, Maladière 45, 2000 Neuchâtel, Suisse.
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41
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Kuhlmann M, Borisova BE, Kaller M, Larsson P, Stach D, Na J, Eichinger L, Lyko F, Ambros V, Söderbom F, Hammann C, Nellen W. Silencing of retrotransposons in Dictyostelium by DNA methylation and RNAi. Nucleic Acids Res 2005; 33:6405-17. [PMID: 16282589 PMCID: PMC1283529 DOI: 10.1093/nar/gki952] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We have identified a DNA methyltransferase of the Dnmt2 family in Dictyostelium that was denominated DnmA. Expression of the dnmA gene is downregulated during the developmental cycle. Overall DNA methylation in Dictyostelium is ∼0.2% of the cytosine residues, which indicates its restriction to a limited set of genomic loci. Bisulfite sequencing of specific sites revealed that DnmA is responsible for methylation of mostly asymmetric C-residues in the retrotransposons DIRS-1 and Skipper. Disruption of the gene resulted in a loss of methylation and in increased transcription and mobilization of Skipper. Skipper transcription was also upregulated in strains that had genes encoding components of the RNA interference pathway disrupted. In contrast, DIRS-1 expression was not affected by a loss of DnmA but was strongly increased in strains that had the RNA-directed RNA polymerase gene rrpC disrupted. A large number of siRNAs were found that corresponded to the DIRS-1 sequence, suggesting concerted regulation of DIRS-1 expression by RNAi and DNA modification. No siRNAs corresponding to the standard Skipper element were found. The data show that DNA methylation plays a crucial role in epigenetic gene silencing in Dictyostelium but that different, partially overlapping mechanisms control transposon silencing.
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Affiliation(s)
| | | | | | - Pontus Larsson
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala UniversityBox 596, S-751 24 Uppsala, Sweden
| | - Dirk Stach
- Arbeitsgruppe Epigenetik, Deutsches KrebsforschungszentrumIm Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Jianbo Na
- Institut fuer Biochemie I, Medizinische Einrichtungen der Universitaet zu KoelnJoseph-Stelzmann-Str. 52, 50931 Koeln, Germany
| | - Ludwig Eichinger
- Institut fuer Biochemie I, Medizinische Einrichtungen der Universitaet zu KoelnJoseph-Stelzmann-Str. 52, 50931 Koeln, Germany
| | - Frank Lyko
- Arbeitsgruppe Epigenetik, Deutsches KrebsforschungszentrumIm Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Victor Ambros
- Department of Genetics, Dartmouth Medical SchoolHanover, NH 03755, USA
| | - Fredrik Söderbom
- Department of Molecular Biology, Biomedical Center, Swedish University of Agricultural SciencesBox 590, S-75124 Uppsala, Sweden
| | | | - Wolfgang Nellen
- To whom correspondence should be addressed. Tel: +49 561 8044805; Fax: +49 561 8044800;
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Abstract
The hammerhead ribozyme is the smallest naturally occurring RNA endonuclease. It is found in subviral plant pathogens and transcripts of satellite DNA from a limited number of organisms. We have performed a database search for novel examples of this catalytic RNA, taking into consideration the recently defined structural requirements for an efficient cleavage under physiological magnesium ion concentrations. In this search, we find, apart from the known examples, several hundreds of motifs in organisms of all kingdoms of life. In a first set of experiments, we analysed hammerhead ribozymes from Arabidopsis thaliana. We found that these sequences are tissue-specifically expressed and that they undergo self-cleavage in planta. Furthermore, their activity under physiological magnesium ion concentrations depends on functional loop-loop interactions, as shown by the lack of activity of appropriate mutants.
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Affiliation(s)
- S Gräf
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
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Przybilski R, Gräf S, Lescoute A, Nellen W, Westhof E, Steger G, Hammann C. Functional hammerhead ribozymes naturally encoded in the genome of Arabidopsis thaliana. Plant Cell 2005; 17:1877-85. [PMID: 15937227 PMCID: PMC1167538 DOI: 10.1105/tpc.105.032730] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The hammerhead ribozyme (HHRz) is an autocatalytic RNA motif found in subviral plant pathogens and transcripts of repetitive DNA sequences in animals. Here, we report the discovery and characterization of unique HHRzs encoded in a plant genome. Two novel sequences were identified on chromosome IV of Arabidopsis thaliana in a database search, which took into account recently defined structural requirements. The HHRzs are expressed in several tissues and coexist in vivo as both cleaved and noncleaved species. In vitro, both sequences cleave efficiently at physiological Mg(2+) concentrations, indicative of functional loop-loop interactions. Kinetic analysis of loop nucleotide variants was used to determine a three-dimensional model of these tertiary interactions. Based on these results, on the lack of infectivity of hammerhead-carrying viroids in Arabidopsis, and on extensive sequence comparisons, we propose that the ribozyme sequences did not invade this plant by horizontal transfer but have evolved independently to perform a specific, yet unidentified, biological function.
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Affiliation(s)
- Rita Przybilski
- Arbeitsgruppe Molecular Interactions, Department of Genetics, Universität Kassel, D-34132 Kassel, Germany
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44
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Abstract
In eukaryotic cells, double-stranded RNA is degraded to 21mers and triggers RNA interference. Using a pattern description language, we have searched the EMBL database for sequences with the potential to form double strands in cis in Dictyostelium discoideum. No extended inverted repeats were found in mRNAs. However, the antisense direction of some mRNAs encoding regulatory or developmentally regulated proteins showed the ability to form double-stranded regions. In EST archives, we found potential double strands derived from a few genes, but these transcripts are not continuously encoded in the genome. Most likely, they represent hybrid molecules of sense and antisense RNAs.
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Affiliation(s)
- Stefan Gräf
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, D-40225 Düsseldorf, Germany
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46
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Hammann C, Nellen W. Web Site: RNA: Zwei auf einen Streich. Angew Chem Int Ed Engl 2003. [DOI: 10.1002/ange.200390165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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47
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Abstract
The hammerhead is the smallest of the nucleolytic ribozymes, that undergo backbone cleavage by a transesterification reaction in the presence of magnesium ions. The RNA is induced to fold into its active conformation by the binding of metal ions in two stages. These generate domain 2, the scaffold on which the ribozyme is built, and domain 1, the active centre of the ribozyme. Further local structural rearrangement during the activation of the ribozyme is suggested by a number of crystal structures. The 10(5)-fold rate enhancement is probably brought about by a combination of metal-ion participation and stereochemical factors in the environment of the folded RNA structure.
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Affiliation(s)
- Christian Hammann
- Department of Biochemistry, MSI/WTB Complex, Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee DD1 5EH, Scotland (UK)
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48
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49
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Abstract
The hammerhead is the smallest of the nucleolytic ribozymes, that undergo backbone cleavage by a transesterification reaction in the presence of magnesium ions. The RNA is induced to fold into its active conformation by the binding of metal ions in two stages. These generate domain 2, the scaffold on which the ribozyme is built, and domain 1, the active centre of the ribozyme. Further local structural rearrangement during the activation of the ribozyme is suggested by a number of crystal structures. The 10(5)-fold rate enhancement is probably brought about by a combination of metal-ion participation and stereochemical factors in the environment of the folded RNA structure.
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Affiliation(s)
- Christian Hammann
- Department of Biochemistry, MSI/WTB Complex, Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee DD1 5EH, Scotland (UK)
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50
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Abstract
We have used (19)F NMR to analyze the metal ion-induced folding of the hammerhead ribozyme by selective incorporation of 5fluorouridine. We have studied the chemical shift and linewidths of (19)F resonances of 5-fluorouridine at the 4 and 7 positions in the ribozyme core as a function of added Mg(2+). The data fit well to a simple two-state model whereby the formation of domain 1 is induced by the noncooperative binding of Mg(2+) with an association constant in the range of 100 to 500 M(-1), depending on the concentration of monovalent ions present. The results are in excellent agreement with data reporting on changes in the global shape of the ribozyme. However, the NMR experiments exploit reporters located in the center of the RNA sections undergoing the folding transitions, thereby allowing the assignment of specific nucleotides to the separate stages. The results define the folding pathway at high resolution and provide a time scale for the first transition in the millisecond range.
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Affiliation(s)
- C Hammann
- Cancer Research Campaign Nucleic Acid Structure Research Group, Department of Biochemistry, University of Dundee, Dundee DD1 4HN, United Kingdom
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