1
|
Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Müller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD. Visualizing the DNA repair process by a photolyase at atomic resolution. Science 2023; 382:eadd7795. [PMID: 38033054 DOI: 10.1126/science.add7795] [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] [Received: 07/12/2022] [Accepted: 10/05/2023] [Indexed: 12/02/2023]
Abstract
Photolyases, a ubiquitous class of flavoproteins, use blue light to repair DNA photolesions. In this work, we determined the structural mechanism of the photolyase-catalyzed repair of a cyclobutane pyrimidine dimer (CPD) lesion using time-resolved serial femtosecond crystallography (TR-SFX). We obtained 18 snapshots that show time-dependent changes in four reaction loci. We used these results to create a movie that depicts the repair of CPD lesions in the picosecond-to-nanosecond range, followed by the recovery of the enzymatic moieties involved in catalysis, completing the formation of the fully reduced enzyme-product complex at 500 nanoseconds. Finally, back-flip intermediates of the thymine bases to reanneal the DNA were captured at 25 to 200 microseconds. Our data cover the complete molecular mechanism of a photolyase and, importantly, its chemistry and enzymatic catalysis at work across a wide timescale and at atomic resolution.
Collapse
Affiliation(s)
- Manuel Maestre-Reyna
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Po-Hsun Wang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Yuhei Hosokawa
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Martin Saft
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Antonia Furrer
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Cheng-Han Yang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | | | - Wen-Jin Wu
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Hans-Joachim Emmerich
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Nicolas Caramello
- European Synchrotron Radiation Facility, 38043 Grenoble, France
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
| | - Sophie Franz-Badur
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Chao Yang
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Sylvain Engilberge
- European Synchrotron Radiation Facility, 38043 Grenoble, France
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38044 Grenoble, France
| | - Maximilian Wranik
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | | | - Tobias Weinert
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Hsiang-Yi Wu
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Cheng-Chung Lee
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Wei-Cheng Huang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Yao-Kai Chang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Jiahn-Haur Liao
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Jui-Hung Weng
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Wael Gad
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Chiung-Wen Chang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Allan H Pang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Kai-Chun Yang
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Wei-Ting Lin
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Yu-Chen Chang
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Dardan Gashi
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Emma Beale
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Dmitry Ozerov
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Karol Nass
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Gregor Knopp
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Philip J M Johnson
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Claudio Cirelli
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Chris Milne
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Camila Bacellar
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | | | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Yasumasa Joti
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Ayumi Yamashita
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Fangjia Luo
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Wiktoria Zarzycka
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Pavel Müller
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Maisa Alkheder Alahmad
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Filipp Bezold
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Valerie Fuchs
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Petra Gnau
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Stephan Kiontke
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Lukas Korf
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Viktoria Reithofer
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Christian Joshua Rosner
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Elisa Marie Seiler
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Mohamed Watad
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Laura Werel
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Roberta Spadaccini
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
- Dipartimento di Scienze e tecnologie, Universita degli studi del Sannio, Benevento, Italy
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Dongping Zhong
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for Ultrafast Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jörg Standfuss
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Antoine Royant
- European Synchrotron Radiation Facility, 38043 Grenoble, France
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38044 Grenoble, France
| | - Yoshitaka Bessho
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| |
Collapse
|
2
|
Shvarev D, Schoppe J, König C, Perz A, Füllbrunn N, Kiontke S, Langemeyer L, Januliene D, Schnelle K, Kümmel D, Fröhlich F, Moeller A, Ungermann C. Structure of the HOPS tethering complex, a lysosomal membrane fusion machinery. eLife 2022; 11:80901. [PMID: 36098503 PMCID: PMC9592082 DOI: 10.7554/elife.80901] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [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: 06/08/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022] Open
Abstract
Lysosomes are essential for cellular recycling, nutrient signaling, autophagy, and pathogenic bacteria and viruses invasion. Lysosomal fusion is fundamental to cell survival and requires HOPS, a conserved heterohexameric tethering complex. On the membranes to be fused, HOPS binds small membrane-associated GTPases and assembles SNAREs for fusion, but how the complex fulfills its function remained speculative. Here, we used cryo-electron microscopy to reveal the structure of HOPS. Unlike previously reported, significant flexibility of HOPS is confined to its extremities, where GTPase binding occurs. The SNARE-binding module is firmly attached to the core, therefore, ideally positioned between the membranes to catalyze fusion. Our data suggest a model for how HOPS fulfills its dual functionality of tethering and fusion and indicate why it is an essential part of the membrane fusion machinery. Our cells break down the nutrients that they receive from the body to create the building blocks needed to keep us alive. This is done by compartments called lysosomes that are filled with a cocktail of proteins called enzymes, which speed up the breakdown process. Lysosomes are surrounded by a membrane, a barrier of fatty molecules that protects the rest of the cell from being digested. When new nutrients reach the cell, they travel to the lysosome packaged in vesicles, which have their own fatty membrane. To allow the nutrients to enter the lysosome without creating a leak, the membranes of the vesicles and the lysosome must fuse. The mechanism through which these membranes fuse is not fully clear. It is known that both fusing membranes must contain proteins called SNAREs, which wind around each other when they interact. However, this alone is not enough. Other proteins are also required to tether the membranes together before they fuse. To understand how these tethers play a role, Shvarev, Schoppe, König et al. studied the structure of the HOPS complex from yeast. This assembly of six proteins is vital for lysosomal fusion and, has a composition similar to the equivalent complex in humans. Using cryo-electron microscopy, a technique that relies on freezing purified proteins to image them with an electron microscope and reveal their structure, allowed Shvarev, Schoppe, König et al. to provide a model for how HOPS interacts with SNAREs and membranes. In addition to HOPS acting as a tether to bring the membranes together, it can also bind directly to SNAREs. This creates a bridge that allows the proteins to wrap around each other, driving the membranes to fuse. HOPS is a crucial component in the cellular machinery, and mutations in the complex can cause devastating neurological defects. The complex is also targeted by viruses – such as SARS-CoV-2 – that manipulate HOPS to reduce its activity. Shvarev, Schoppe, König et al.’s findings could help researchers to develop drugs to maintain or recover the activity of HOPS. However, this will require additional information about its structure and how the complex acts in the biological environment of the cell.
Collapse
Affiliation(s)
- Dmitry Shvarev
- Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Jannis Schoppe
- Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Caroline König
- Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Angela Perz
- Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Nadia Füllbrunn
- Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Stephan Kiontke
- Department of Plant Physiology and Photo Biology, Philipp University of Marburg, Marburg, Germany
| | - Lars Langemeyer
- Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Dovile Januliene
- Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Kilian Schnelle
- Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Daniel Kümmel
- Department of Chemistry and Pharmacy, University of Münster, Münster, Germany
| | - Florian Fröhlich
- Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Arne Moeller
- Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | | |
Collapse
|
3
|
Kiontke S, Göbel T, Brych A, Batschauer A. DASH-type cryptochromes - solved and open questions. Biol Chem 2021; 401:1487-1493. [PMID: 32663167 DOI: 10.1515/hsz-2020-0182] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/09/2020] [Indexed: 01/04/2023]
Abstract
Drosophila, Arabidopsis, Synechocystis, human (DASH)-type cryptochromes (cry-DASHs) form one subclade of the cryptochrome/photolyase family (CPF). CPF members are flavoproteins that act as DNA-repair enzymes (DNA-photolyases), or as ultraviolet(UV)-A/blue light photoreceptors (cryptochromes). In mammals, cryptochromes are essential components of the circadian clock feed-back loop. Cry-DASHs are present in almost all major taxa and were initially considered as photoreceptors. Later studies demonstrated DNA-repair activity that was, however, restricted to UV-lesions in single-stranded DNA. Very recent studies, particularly on microbial organisms, substantiated photoreceptor functions of cry-DASHs suggesting that they could be transitions between photolyases and cryptochromes.
Collapse
Affiliation(s)
- Stephan Kiontke
- University of Marburg, Department of Biology, Molecular Plant Physiology and Photobiology, D-35032 Marburg, Germany
| | - Tanja Göbel
- University of Marburg, Department of Biology, Molecular Plant Physiology and Photobiology, D-35032 Marburg, Germany
| | - Annika Brych
- University of Marburg, Department of Biology, Molecular Plant Physiology and Photobiology, D-35032 Marburg, Germany
| | - Alfred Batschauer
- University of Marburg, Department of Biology, Molecular Plant Physiology and Photobiology, D-35032 Marburg, Germany
| |
Collapse
|
4
|
Brych A, Haas FB, Parzefall K, Panzer S, Schermuly J, Altmüller J, Engelsdorf T, Terpitz U, Rensing SA, Kiontke S, Batschauer A. Coregulation of gene expression by White collar 1 and phytochrome in Ustilago maydis. Fungal Genet Biol 2021; 152:103570. [PMID: 34004340 DOI: 10.1016/j.fgb.2021.103570] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 12/12/2022]
Abstract
Ustilago maydis encodes ten predicted light-sensing proteins. The biological functions of only a few of them are elucidated. Among the characterized ones are two DNA-photolyases and two rhodopsins that act as DNA-repair enzymes or green light-driven proton pumps, respectively. Here we report on the role of two other photoreceptors in U. maydis, namely White collar 1 (Wco1) and Phytochrome 1 (Phy1). We show that they bind flavins or biliverdin as chromophores, respectively. Both photoreceptors undergo a photocycle in vitro. Wco1 is the dominant blue light receptor in the saprophytic phase, controlling all of the 324 differentially expressed genes in blue light. U. maydis also responds to red and far-red light. However, the number of red or far-red light-controlled genes is less compared to blue light-regulated ones. Moreover, most of the red and far-red light-controlled genes not only depend on Phy1 but also on Wco1, indicating partial coregulation of gene expression by both photoreceptors. GFP-fused Wco1 is preferentially located in the nucleus, Phy1 in the cytosol, thus providing no hint that these photoreceptors directly interact or operate within the same complex. This is the first report on a functional characterization and coaction of White collar 1 and phytochrome orthologs in basidiomycetes.
Collapse
Affiliation(s)
- Annika Brych
- University of Marburg, Department of Biology, Plant Physiology and Photobiology, Marburg, Germany
| | - Fabian B Haas
- University of Marburg, Department of Biology, Plant Cell Biology, Marburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany; LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University of Marburg, Germany
| | - Katharina Parzefall
- University of Marburg, Department of Biology, Plant Physiology and Photobiology, Marburg, Germany
| | - Sabine Panzer
- Theodor-Boveri-Institute, Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilian-University, Würzburg, Germany
| | - Jeanette Schermuly
- University of Marburg, Department of Biology, Plant Physiology and Photobiology, Marburg, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Timo Engelsdorf
- University of Marburg, Department of Biology, Plant Physiology and Photobiology, Marburg, Germany
| | - Ulrich Terpitz
- Theodor-Boveri-Institute, Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilian-University, Würzburg, Germany
| | - Stefan A Rensing
- University of Marburg, Department of Biology, Plant Cell Biology, Marburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany; LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University of Marburg, Germany
| | - Stephan Kiontke
- University of Marburg, Department of Biology, Plant Physiology and Photobiology, Marburg, Germany
| | - Alfred Batschauer
- University of Marburg, Department of Biology, Plant Physiology and Photobiology, Marburg, Germany.
| |
Collapse
|
5
|
Lynagh T, Kiontke S, Meyhoff-Madsen M, Gless BH, Johannesen J, Kattelmann S, Christiansen A, Dufva M, Laustsen AH, Devkota K, Olsen CA, Kümmel D, Pless SA, Lohse B. Peptide Inhibitors of the α-Cobratoxin-Nicotinic Acetylcholine Receptor Interaction. J Med Chem 2020; 63:13709-13718. [PMID: 33143415 PMCID: PMC7705965 DOI: 10.1021/acs.jmedchem.0c01202] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
Venomous snakebites cause >100
000 deaths every year, in many cases
via potent depression of human neuromuscular signaling by snake α-neurotoxins.
Emergency therapy still relies on antibody-based antivenom, hampered
by poor access, frequent adverse reactions, and cumbersome production/purification.
Combining high-throughput discovery and subsequent structure–function
characterization, we present simple peptides that bind α-cobratoxin
(α-Cbtx) and prevent its inhibition of nicotinic acetylcholine
receptors (nAChRs) as a lead for the development of alternative antivenoms.
Candidate peptides were identified by phage display and deep sequencing,
and hits were characterized by electrophysiological recordings, leading
to an 8-mer peptide that prevented α-Cbtx inhibition of nAChRs.
We also solved the peptide:α-Cbtx cocrystal structure, revealing
that the peptide, although of unique primary sequence, binds to α-Cbtx
by mimicking structural features of the nAChR binding pocket. This
demonstrates the potential of small peptides to neutralize lethal
snake toxins in vitro, establishing a potential route to simple, synthetic,
low-cost antivenoms.
Collapse
Affiliation(s)
- Timothy Lynagh
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway.,Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Stephan Kiontke
- Division of Structural Biology, Department of Biology/Chemistry, University of Osnabrück, Barbarastraße 13, Osnabrück 49076, Germany.,Faculty of Biology, Department of Plant Physiology and Photobiology, Philipps-Universität Marburg, Karl-von-Frisch-Straße 8, 35032 Marburg, Germany
| | - Maria Meyhoff-Madsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Bengt H Gless
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Jónas Johannesen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Sabrina Kattelmann
- Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Anders Christiansen
- Fluid Array Systems and Technology, Nano and Bio-physical Systems, Department of Health Technology, Technical University of Denmark, Building 423 Produktionstorvet, DK-2800 Kongens Lyngby, Denmark
| | - Martin Dufva
- Fluid Array Systems and Technology, Nano and Bio-physical Systems, Department of Health Technology, Technical University of Denmark, Building 423 Produktionstorvet, DK-2800 Kongens Lyngby, Denmark
| | - Andreas H Laustsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Kanchan Devkota
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Daniel Kümmel
- Division of Structural Biology, Department of Biology/Chemistry, University of Osnabrück, Barbarastraße 13, Osnabrück 49076, Germany.,Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Stephan Alexander Pless
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Brian Lohse
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| |
Collapse
|
6
|
Navarro E, Niemann N, Kock D, Dadaeva T, Gutiérrez G, Engelsdorf T, Kiontke S, Corrochano LM, Batschauer A, Garre V. The DASH-type Cryptochrome from the Fungus Mucor circinelloides Is a Canonical CPD-Photolyase. Curr Biol 2020; 30:4483-4490.e4. [DOI: 10.1016/j.cub.2020.08.051] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/31/2020] [Accepted: 08/13/2020] [Indexed: 12/12/2022]
|
7
|
Hansmann P, Brückner A, Kiontke S, Berkenfeld B, Seebohm G, Brouillard P, Vikkula M, Jansen FE, Nellist M, Oeckinghaus A, Kümmel D. Structure of the TSC2 GAP Domain: Mechanistic Insight into Catalysis and Pathogenic Mutations. Structure 2020; 28:933-942.e4. [PMID: 32502382 DOI: 10.1016/j.str.2020.05.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 02/06/2020] [Accepted: 05/15/2020] [Indexed: 12/17/2022]
Abstract
The TSC complex is the cognate GTPase-activating protein (GAP) for the small GTPase Rheb and a crucial regulator of the mechanistic target of rapamycin complex 1 (mTORC1). Mutations in the TSC1 and TSC2 subunits of the complex cause tuberous sclerosis complex (TSC). We present the crystal structure of the catalytic asparagine-thumb GAP domain of TSC2. A model of the TSC2-Rheb complex and molecular dynamics simulations suggest that TSC2 Asn1643 and Rheb Tyr35 are key active site residues, while Rheb Arg15 and Asp65, previously proposed as catalytic residues, contribute to the TSC2-Rheb interface and indirectly aid catalysis. The TSC2 GAP domain is further stabilized by interactions with other TSC2 domains. We characterize TSC2 variants that partially affect TSC2 functionality and are associated with atypical symptoms in patients, suggesting that mutations in TSC1 and TSC2 might predispose to neurological and vascular disorders without fulfilling the clinical criteria for TSC.
Collapse
Affiliation(s)
- Patrick Hansmann
- Westfälische Wilhelms-Universität, Institute of Biochemistry, Wilhelm Klemm-Str. 2, 48149 Münster, Germany
| | - Anne Brückner
- Westfälische Wilhelms-Universität, Institute of Biochemistry, Wilhelm Klemm-Str. 2, 48149 Münster, Germany; Westfälische Wilhelms-Universität, Institute of Molecular Tumor Biology, Robert-Koch-Str. 43, 48149 Münster, Germany
| | - Stephan Kiontke
- Philipps-Universität Marburg, Faculty of Biology, Department of Plant Physiology and Photobiology, Karl-von-Frisch-Str. 8, 35032 Marburg, Germany
| | - Bianca Berkenfeld
- Westfälische Wilhelms-Universität, Institute of Biochemistry, Wilhelm Klemm-Str. 2, 48149 Münster, Germany
| | - Guiscard Seebohm
- University Hospital Münster, Institute for Genetics of Heart Diseases, Department of Cardiovascular Medicine, Robert-Koch-Str. 45, 48149 Münster, Germany
| | - Pascal Brouillard
- Université Catholique de Louvain, de Duve Institute, Human Molecular Genetics, Brussels, Belgium
| | - Miikka Vikkula
- Université Catholique de Louvain, de Duve Institute, Human Molecular Genetics, Brussels, Belgium; WELBIO (Walloon Excellence in Lifesciences and Biotechnology), de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Floor E Jansen
- Department of Child Neurology, Brain Center UMC Utrecht, Utrecht, the Netherlands
| | - Mark Nellist
- Department of Clinical Genetics, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands
| | - Andrea Oeckinghaus
- Westfälische Wilhelms-Universität, Institute of Molecular Tumor Biology, Robert-Koch-Str. 43, 48149 Münster, Germany
| | - Daniel Kümmel
- Westfälische Wilhelms-Universität, Institute of Biochemistry, Wilhelm Klemm-Str. 2, 48149 Münster, Germany.
| |
Collapse
|
8
|
Marter P, Schmidt S, Kiontke S, Moog D. Optimized mRuby3 is a Suitable Fluorescent Protein for in vivo Co-localization Studies with GFP in the Diatom Phaeodactylum tricornutum. Protist 2020; 171:125715. [PMID: 32062589 DOI: 10.1016/j.protis.2020.125715] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 12/19/2019] [Accepted: 12/27/2019] [Indexed: 11/19/2022]
Abstract
Phaeodactylum tricornutum is an ecologically and evolutionarily relevant microalga that has developed into an important model for molecular biological studies on organisms with complex plastids. The diatom is particularly suitable for in vivo protein localization analyses via fluorescence microscopy in which the green fluorescent protein (GFP) and its derivatives are dominantly used. Whereas GFP fluorescence emission is usually measured between 500 and 520nm in confocal microscopy, the autofluorescence of the P. tricornutum plastid is detected above 625nm. Here we established the fluorescent protein mRuby3 as tag for efficient in vivo protein localization studies by expressing a codon-optimized gene in P. tricornutum. mRuby3 was directed to seven different subcellular localizations by means of full-length marker protein or N-/C-terminal targeting signal fusions; its emission was detected efficiently between 580 and 605nm, being unequivocally distinguishable from the plastid autofluorescence in vivo. Moreover, mRuby3 proved to be highly suitable for co-localization experiments using confocal laser scanning microscopy in which mRuby3 fusion proteins were expressed in parallel with GFP-tagged proteins. Our results show the potential of mRuby3 for its application in studying protein targeting and localization in P. tricornutum, particularly underlining its compatibility with GFP and the plastid autofluorescence in signal detection.
Collapse
Affiliation(s)
- Pia Marter
- Laboratory for Cell Biology, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35032 Marburg, Germany
| | - Sebastian Schmidt
- Laboratory for Cell Biology, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35032 Marburg, Germany
| | - Stephan Kiontke
- Molecular Plant Physiology and Photobiology, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35032 Marburg, Germany
| | - Daniel Moog
- Laboratory for Cell Biology, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35032 Marburg, Germany; SYNMIKRO Research Center, Hans-Meerwein-Str. 6, 35032 Marburg, Germany.
| |
Collapse
|
9
|
Araguirang GE, Niemann N, Kiontke S, Eckel M, Dionisio-Sese ML, Batschauer A. The Arabidopsis cryptochrome 2 I404F mutant is hypersensitive and shows flavin reduction even in the absence of light. Planta 2019; 251:33. [PMID: 31832774 DOI: 10.1007/s00425-019-03323-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/03/2019] [Indexed: 06/10/2023]
Abstract
The cryptochrome photoreceptor mutant cry2I404F exhibits hyperactivity in the dark, hypersensitivity in different light conditions, and in contrast to the wild-type protein, its flavin chromophore is reducible even in the absence of light. Plant cryptochromes (cry) are blue-light photoreceptors involved in multiple signaling pathways and various photomorphogenic responses. One biologically hyperactive mutant of a plant cryptochrome that was previously characterized is Arabidopsis cry1L407F (Exner et al. in Plant Physiol 154:1633-1645, 2010). Protein sequence alignments of different cryptochromes revealed that L407 in cry1 corresponds to I404 in cry2. Point mutation of Ile to Phe in cry2 in this position created a novel mutant. The present study provided a baseline data on the elucidation of the properties of cry2I404F. This mutant was still able to bind ATP-triggering conformational changes, as confirmed by partial tryptic digestion and thermo-FAD assays. Surprisingly, the FAD cofactor of cry2I404F was reduced by the addition of reductant even in the absence of light. In vivo, cry2I404F exhibited a cop phenotype in the dark and hypersensitivity to various light conditions compared to cry2 wild type. Overall, these data suggest that the hypersensitivity to red and blue light and hyperactivity of this novel mutant in the dark can be mostly accounted to structural alterations brought forth by the Ile to Phe mutation at position 404 that allows reduction of the flavin chromophore even in the absence of light.
Collapse
Affiliation(s)
- Galileo Estopare Araguirang
- Graduate School, University of the Philippines Los Baños, College, 4031, Laguna, Philippines
- Department of Plant Adaptation, Leibniz-Institut für Gemüse- und Zierpflanzenbau (IGZ), Großbeeren, 14979, Germany
| | - Nils Niemann
- Department of Plant Physiology and Photobiology, Faculty of Biology, Philipps-University Marburg, 35032, Marburg, Germany
| | - Stephan Kiontke
- Department of Plant Physiology and Photobiology, Faculty of Biology, Philipps-University Marburg, 35032, Marburg, Germany
| | - Maike Eckel
- Department of Plant Physiology and Photobiology, Faculty of Biology, Philipps-University Marburg, 35032, Marburg, Germany
| | - Maribel L Dionisio-Sese
- Graduate School, University of the Philippines Los Baños, College, 4031, Laguna, Philippines
- Plant Biology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, College, 4031, Laguna, Philippines
| | - Alfred Batschauer
- Department of Plant Physiology and Photobiology, Faculty of Biology, Philipps-University Marburg, 35032, Marburg, Germany.
| |
Collapse
|
10
|
Lacombat F, Espagne A, Dozova N, Plaza P, Ignatz E, Kiontke S, Essen LO. Delocalized hole transport coupled to sub-ns tryptophanyl deprotonation promotes photoreduction of class II photolyases. Phys Chem Chem Phys 2018; 20:25446-25457. [PMID: 30272080 DOI: 10.1039/c8cp04548h] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Class II photolyases utilize for the photoreduction of their flavin cofactor (FAD) a completely different tryptophan triad than most other photolyases and cryptochromes. To counter sped-up back electron transfer, they evolved an unusually fast deprotonation of the distal tryptophanyl radical cation (WH˙+) that is produced after excitation of the flavin. We studied the primary aspects of oxidized FAD photoreduction by ultrafast transient absorption spectroscopy, using the class II photolyase from Methanosarcina mazei. With a time constant of 9.2 ps, the initial reduction step of the excited flavin by the proximal W381 tryptophan proceeds almost twentyfold slower than in other photolyases carrying oxidized FAD, most likely because of the larger distance between the flavin and the proximal tryptophan. The thus formed W381H˙+ radical is tracked by transient anisotropy measurements to migrate in 29 ps with delocalization over several members of the tryptophan triad. This 29 ps phase also includes the decay of a small fraction of excited flavin, reacting on a slower timescale, and partial recombination of the FAD˙-/WH˙+ radical pair. A final kinetic phase in 230 ps is assigned to the deprotonation of W388H˙+ that occurs in competition with partial charge recombination. Interestingly, we show by comparison with the Y345F mutant that this last phase additionally involves oxidation of the Y345 phenolic group by W388H˙+, producing a small amount of neutral tyrosyl radical (YO˙). The rate of this electron transfer step is about six orders of magnitude faster than the corresponding oxidation of Y345 by the deprotonated W388˙ radical. Unlike conventional photolyases, where the electron hole accumulates on the distal tryptophan before the much slower tryptophanyl deprotonation, our data show that delocalized hole transport is concomitantly concluded by ultrafast deprotonation of W388H˙+.
Collapse
Affiliation(s)
- Fabien Lacombat
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | | | | | | | | | | | | |
Collapse
|
11
|
Müller P, Ignatz E, Kiontke S, Brettel K, Essen LO. Sub-nanosecond tryptophan radical deprotonation mediated by a protein-bound water cluster in class II DNA photolyases. Chem Sci 2017; 9:1200-1212. [PMID: 29675165 PMCID: PMC5885780 DOI: 10.1039/c7sc03969g] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 12/10/2017] [Indexed: 01/01/2023] Open
Abstract
Light activation of class II DNA photolyases is enhanced by a unique cluster of protein-bound water molecules.
Class II DNA photolyases are flavoenzymes occurring in both prokaryotes and eukaryotes including higher plants and animals. Despite considerable structural deviations from the well-studied class I DNA photolyases, they share the main biological function, namely light-driven repair of the most common UV-induced lesions in DNA, the cyclobutane pyrimidine dimers (CPDs). For DNA repair activity, photolyases require the fully reduced flavin adenine dinucleotide cofactor, FADH–, which can be obtained from oxidized or semi-reduced FAD by a process called photoactivation. Using transient absorption spectroscopy, we have examined the initial electron and proton transfer reactions leading to photoactivation of the class II DNA photolyase from Methanosarcina mazei. Upon photoexcitation, FAD is reduced via a distinct (class II-specific) chain of three tryptophans, giving rise to an FAD˙– TrpH˙+ radical pair. The distal Trp388H˙+ deprotonates to Trp388˙ in 350 ps, i.e., by three orders of magnitude faster than TrpH˙+ in aqueous solution or in any previously studied photolyase. We identified a class II-specific cluster of protein-bound water molecules ideally positioned to serve as the primary proton acceptor. The high rate of Trp388H˙+ deprotonation counters futile radical pair recombination and ensures efficient photoactivation.
Collapse
Affiliation(s)
- Pavel Müller
- Institute for Integrative Biology of the Cell (I2BC) , CEA , CNRS , Univ. Paris-Sud , Université Paris-Saclay , 91198 , Gif-sur-Yvette cedex , France .
| | - Elisabeth Ignatz
- Department of Chemistry , LOEWE Center for Synthetic Microbiology , Philipps University , 35032 Marburg , Germany .
| | - Stephan Kiontke
- Department of Chemistry , LOEWE Center for Synthetic Microbiology , Philipps University , 35032 Marburg , Germany .
| | - Klaus Brettel
- Institute for Integrative Biology of the Cell (I2BC) , CEA , CNRS , Univ. Paris-Sud , Université Paris-Saclay , 91198 , Gif-sur-Yvette cedex , France .
| | - Lars-Oliver Essen
- Department of Chemistry , LOEWE Center for Synthetic Microbiology , Philipps University , 35032 Marburg , Germany .
| |
Collapse
|
12
|
Ignatz E, Geisselbrecht Y, Kiontke S, Essen LO. Nicotinamide Adenine Dinucleotides Arrest Photoreduction of Class II DNA Photolyases in FADH ˙ State. Photochem Photobiol 2017; 94:81-87. [PMID: 28858395 DOI: 10.1111/php.12834] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/17/2017] [Indexed: 12/24/2022]
Abstract
All light-sensitive members of the photolyase/cryptochrome family rely on FAD as catalytic cofactor. Its activity is regulated by photoreduction, a light-triggered electron transfer process from a conserved tryptophan triad to the flavin. The stability of the reduced flavin depends on available external electron donors and oxygen. In this study, we show for the class II photolyase of Methanosarcina mazei, MmCPDII, that it utilizes physiologically relevant redox cofactors NADH and NADPH for the formation of the semiquinoid FAD in a light-dependent reaction. Using redox-inert variants MmCPDII/W388F and MmCPDII/W360F, we demonstrate that photoreduction by NADH and NADPH requires the class II-specific tryptophan cascade of MmCPDII. Finally, we confirmed that mutations in the tryptophan cascade can be introduced without any substantial structural disturbances by analyzing crystal structures of MmCPDII/W388F, MmCPDII/W360F and MmCPDII/Y345F.
Collapse
Affiliation(s)
- Elisabeth Ignatz
- Department of Chemistry, LOEWE Center for Synthetic Microbiology, Philipps University, Marburg, Germany
| | - Yann Geisselbrecht
- Department of Chemistry, LOEWE Center for Synthetic Microbiology, Philipps University, Marburg, Germany
| | - Stephan Kiontke
- Department of Chemistry, LOEWE Center for Synthetic Microbiology, Philipps University, Marburg, Germany.,Department of Biology/Chemistry, Division of Structural Biology, University of Osnabrück, Osnabrück, Germany
| | - Lars-Oliver Essen
- Department of Chemistry, LOEWE Center for Synthetic Microbiology, Philipps University, Marburg, Germany
| |
Collapse
|
13
|
Zech R, Kiontke S, Mueller U, Oeckinghaus A, Kümmel D. Structure of the Tuberous Sclerosis Complex 2 (TSC2) N Terminus Provides Insight into Complex Assembly and Tuberous Sclerosis Pathogenesis. J Biol Chem 2016; 291:20008-20. [PMID: 27493206 DOI: 10.1074/jbc.m116.732446] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Indexed: 12/12/2022] Open
Abstract
Tuberous sclerosis complex (TSC) is caused by mutations in the TSC1 and TSC2 tumor suppressor genes. The gene products hamartin and tuberin form the TSC complex that acts as GTPase-activating protein for Rheb and negatively regulates the mammalian target of rapamycin complex 1 (mTORC1). Tuberin contains a RapGAP homology domain responsible for inactivation of Rheb, but functions of other protein domains remain elusive. Here we show that the TSC2 N terminus interacts with the TSC1 C terminus to mediate complex formation. The structure of the TSC2 N-terminal domain from Chaetomium thermophilum and a homology model of the human tuberin N terminus are presented. We characterize the molecular requirements for TSC1-TSC2 interactions and analyze pathological point mutations in tuberin. Many mutations are structural and produce improperly folded protein, explaining their effect in pathology, but we identify one point mutant that abrogates complex formation without affecting protein structure. We provide the first structural information on TSC2/tuberin with novel insight into the molecular function.
Collapse
Affiliation(s)
- Reinhard Zech
- From the Structural Biology Section, FB5 Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - Stephan Kiontke
- From the Structural Biology Section, FB5 Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - Uwe Mueller
- Macromolecular Crystallography (BESSY-MX), Helmholtz-Zentrum Berlin für Materialien und Energie, 12489 Berlin, Germany, and
| | - Andrea Oeckinghaus
- Institute of Molecular Tumor Biology, Medical Faculty of the WWU Münster, 48149 Münster Germany
| | - Daniel Kümmel
- From the Structural Biology Section, FB5 Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany,
| |
Collapse
|
14
|
Kiontke S, Gnau P, Haselsberger R, Batschauer A, Essen LO. Structural and evolutionary aspects of antenna chromophore usage by class II photolyases. J Biol Chem 2014; 289:19659-69. [PMID: 24849603 DOI: 10.1074/jbc.m113.542431] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Light-harvesting and resonance energy transfer to the catalytic FAD cofactor are key roles for the antenna chromophores of light-driven DNA photolyases, which remove UV-induced DNA lesions. So far, five chemically diverse chromophores have been described for several photolyases and related cryptochromes, but no correlation between phylogeny and used antenna has been found. Despite a common protein topology, structural analysis of the distantly related class II photolyase from the archaeon Methanosarcina mazei (MmCPDII) as well as plantal orthologues indicated several differences in terms of DNA and FAD binding and electron transfer pathways. For MmCPDII we identify 8-hydroxydeazaflavin (8-HDF) as cognate antenna by in vitro and in vivo reconstitution, whereas the higher plant class II photolyase from Arabidopsis thaliana fails to bind any of the known chromophores. According to the 1.9 Å structure of the MmCPDII·8-HDF complex, its antenna binding site differs from other members of the photolyase-cryptochrome superfamily by an antenna loop that changes its conformation by 12 Å upon 8-HDF binding. Additionally, so-called N- and C-motifs contribute as conserved elements to the binding of deprotonated 8-HDF and allow predicting 8-HDF binding for most of the class II photolyases in the whole phylome. The 8-HDF antenna is used throughout the viridiplantae ranging from green microalgae to bryophyta and pteridophyta, i.e. mosses and ferns, but interestingly not in higher plants. Overall, we suggest that 8-hydroxydeazaflavin is a crucial factor for the survival of most higher eukaryotes which depend on class II photolyases to struggle with the genotoxic effects of solar UV exposure.
Collapse
Affiliation(s)
- Stephan Kiontke
- From the Biomedical Research Centre/FB15, Unit for Structural Biochemistry, Philipps-University, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
| | - Petra Gnau
- From the Biomedical Research Centre/FB15, Unit for Structural Biochemistry, Philipps-University, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
| | - Reinhard Haselsberger
- the School of Physical and Mathematical Sciences, Division of Physics and Applied Physics, Nanyang Technological University, SPMS-PAP-03-11, 21 Nanyang Link, Singapore 637371, and
| | - Alfred Batschauer
- the Faculty of Biology, Department of Plant Physiology and Photobiology, Philipps-University, Karl-von-Frisch-Strasse 8, D-35032 Marburg, Germany
| | - Lars-Oliver Essen
- From the Biomedical Research Centre/FB15, Unit for Structural Biochemistry, Philipps-University, Hans-Meerwein-Strasse, D-35032 Marburg, Germany,
| |
Collapse
|
15
|
Kiontke S, Geisselbrecht Y, Pokorny R, Carell T, Batschauer A, Essen LO. Crystal structures of an archaeal class II DNA photolyase and its complex with UV-damaged duplex DNA. EMBO J 2011; 30:4437-49. [PMID: 21892138 DOI: 10.1038/emboj.2011.313] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 08/02/2011] [Indexed: 01/29/2023] Open
Abstract
Class II photolyases ubiquitously occur in plants, animals, prokaryotes and some viruses. Like the distantly related microbial class I photolyases, these enzymes repair UV-induced cyclobutane pyrimidine dimer (CPD) lesions within duplex DNA using blue/near-UV light. Methanosarcina mazei Mm0852 is a class II photolyase of the archaeal order of Methanosarcinales, and is closely related to plant and metazoan counterparts. Mm0852 catalyses light-driven DNA repair and photoreduction, but in contrast to class I enzymes lacks a high degree of binding discrimination between UV-damaged and intact duplex DNA. We solved crystal structures of Mm0852, the first one for a class II photolyase, alone and in complex with CPD lesion-containing duplex DNA. The lesion-binding mode differs from other photolyases by a larger DNA-binding site, and an unrepaired CPD lesion is found flipped into the active site and recognized by a cluster of five water molecules next to the bound 3'-thymine base. Different from other members of the photolyase-cryptochrome family, class II photolyases appear to utilize an unusual, conserved tryptophane dyad as electron transfer pathway to the catalytic FAD cofactor.
Collapse
Affiliation(s)
- Stephan Kiontke
- Faculty of Chemistry, Department of Biochemistry, Philipps University, Marburg, Germany
| | | | | | | | | | | |
Collapse
|
16
|
Anders K, von Stetten D, Mailliet J, Kiontke S, Sineshchekov VA, Hildebrandt P, Hughes J, Essen L. Spectroscopic and Photochemical Characterization of the Red‐Light Sensitive Photosensory Module of Cph2 from Synechocystis PCC 6803. Photochem Photobiol 2011; 87:160-173. [DOI: https:/doi.org/10.1111/j.1751-1097.2010.00845.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
AbstractCyanobacterial phytochromes are a diverse family of light receptors controlling various biological functions including phototaxis. In addition to canonical bona fide phytochromes of the well characterized Cph1/plant‐like clade, cyanobacteria also harbor phytochromes that absorb green, violet or blue light. The Synechocystis PCC 6803 Cph2 photoreceptor, a phototaxis inhibitor, is unconventional in bearing two distinct chromophore‐binding GAF domains. Whereas the C‐terminal GAF domain is most likely involved in blue‐light perception, the first two domains correspond to a Cph1‐like photosensory module lacking the PAS domain. Biochemical and spectroscopic studies show that this region switches between red (Pr) and far‐red (Pfr) absorbing states. Unlike Cph1, the Pfr state of Cph2 decays rapidly in darkness. Mutations close to the PCB chromophore further destabilize the Pfr state without drastically affecting the spectroscopic features such as the quantum efficiency of Pr→Pfr conversion, fluorescence, or the Resonance‐Raman signature of the chromophore. Overall, the PAS‐less photosensory module of Cph2 resembles Cph1 including its mode of isomerisation, but the Pfr state is unstable.
Collapse
|
17
|
Anders K, von Stetten D, Mailliet J, Kiontke S, Sineshchekov VA, Hildebrandt P, Hughes J, Essen LO. Spectroscopic and photochemical characterization of the red-light sensitive photosensory module of Cph2 from Synechocystis PCC 6803. Photochem Photobiol 2010; 87:160-73. [PMID: 21091956 DOI: 10.1111/j.1751-1097.2010.00845.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyanobacterial phytochromes are a diverse family of light receptors controlling various biological functions including phototaxis. In addition to canonical bona fide phytochromes of the well characterized Cph1/plant-like clade, cyanobacteria also harbor phytochromes that absorb green, violet or blue light. The Synechocystis PCC 6803 Cph2 photoreceptor, a phototaxis inhibitor, is unconventional in bearing two distinct chromophore-binding GAF domains. Whereas the C-terminal GAF domain is most likely involved in blue-light perception, the first two domains correspond to a Cph1-like photosensory module lacking the PAS domain. Biochemical and spectroscopic studies show that this region switches between red (P(r) ) and far-red (P(fr) ) absorbing states. Unlike Cph1, the P(fr) state of Cph2 decays rapidly in darkness. Mutations close to the PCB chromophore further destabilize the P(fr) state without drastically affecting the spectroscopic features such as the quantum efficiency of P(r) →P(fr) conversion, fluorescence, or the Resonance-Raman signature of the chromophore. Overall, the PAS-less photosensory module of Cph2 resembles Cph1 including its mode of isomerisation, but the P(fr) state is unstable.
Collapse
Affiliation(s)
- Katrin Anders
- Department of Chemistry, Philipps University, Marburg, Germany
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Benabdelhak H, Kiontke S, Horn C, Ernst R, Blight MA, Holland IB, Schmitt L. A specific interaction between the NBD of the ABC-transporter HlyB and a C-terminal fragment of its transport substrate haemolysin A. J Mol Biol 2003; 327:1169-79. [PMID: 12662939 DOI: 10.1016/s0022-2836(03)00204-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A member of the family of RTX toxins, Escherichia coli haemolysin A, is secreted from Gram-negative bacteria. It carries a C-terminal secretion signal of approximately 50 residues, targeting the protein to the secretion or translocation complex, in which the ABC-transporter HlyB is a central element. We have purified the nucleotide-binding domain of HlyB (HlyB-NBD) and a C-terminal 23kDa fragment of HlyA plus the His-tag (HlyA1), which contains the secretion sequence. Employing surface plasmon resonance, we were able to demonstrate that the HlyB-NBD and HlyA1 interact with a K(D) of approximately 4 microM. No interaction was detected between the HlyA fragment and unrelated NBDs, OpuAA, involved in import of osmoprotectants, and human TAP1-NBD, involved in the export of antigenic peptides. Moreover, a truncated version of HlyA1, lacking the secretion signal, failed to interact with the HlyB-NBD. In addition, we showed that ATP accelerated the dissociation of the HlyB-NBD/HlyA1 complex. Taking these results together, we propose a model for an early stage of initiation of secretion in vivo, in which the NBD of HlyB, specifically recognizes the C terminus of the transport substrate, HlyA, and where secretion is initiated by subsequent displacement of HlyA from HlyB by ATP.
Collapse
Affiliation(s)
- Houssain Benabdelhak
- Institut de Génétique et Microbiologie, Bât. 409, Université de Paris XI, 91405, Orsay, France
| | | | | | | | | | | | | |
Collapse
|