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Orekhov P, Bothe A, Steinhoff HJ, Shaitan KV, Raunser S, Fotiadis D, Schlesinger R, Klare JP, Engelhard M. Sensory Rhodopsin I and Sensory Rhodopsin II Form Trimers of Dimers in Complex with their Cognate Transducers. Photochem Photobiol 2018; 93:796-804. [PMID: 28500714 DOI: 10.1111/php.12763] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 03/02/2017] [Indexed: 12/28/2022]
Abstract
Archaeal photoreceptors consist of sensory rhodopsins in complex with their cognate transducers. After light excitation, a two-component signaling chain is activated, which is homologous to the chemotactic signaling cascades in enterobacteria. The latter system has been studied in detail. From structural and functional studies, a picture emerges which includes stable signaling complexes, which assemble to receptor arrays displaying hexagonal structural elements. At this higher order structural level, signal amplification and sensory adaptation occur. Here, we describe electron microscopy data, which show that also the archaeal phototaxis receptors sensory rhodopsin I and II in complex with their cognate transducers can form hexagonal lattices even in the presence of a detergent. This result could be confirmed by molecular dynamics calculations, which revealed similar structural elements. Calculations of the global modes of motion displayed one mode, which resembles the "U"-"V" transition of the NpSRII:NpHtrII complex, which was previously argued to represent a functionally relevant global conformational change accompanying the activation process [Ishchenko et al. (2013) J. Photochem. Photobiol. B 123, 55-58]. A model of cooperativity at the transmembrane level is discussed.
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Affiliation(s)
- Philipp Orekhov
- Department of Physics, University of Osnabrück, Osnabrück, Germany.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Arne Bothe
- Department Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | | | - Stefan Raunser
- Department Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Ramona Schlesinger
- Department of Physics, Institute of Experimental Physics, Genetic Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Johann P Klare
- Department of Physics, University of Osnabrück, Osnabrück, Germany
| | - Martin Engelhard
- Department Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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2
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Abstract
Microbial rhodopsins (MRs) are a large family of photoactive membrane proteins, found in microorganisms belonging to all kingdoms of life, with new members being constantly discovered. Among the MRs are light-driven proton, cation and anion pumps, light-gated cation and anion channels, and various photoreceptors. Due to their abundance and amenability to studies, MRs served as model systems for a great variety of biophysical techniques, and recently found a great application as optogenetic tools. While the basic aspects of microbial rhodopsins functioning have been known for some time, there is still a plenty of unanswered questions. This chapter presents and summarizes the available knowledge, focusing on the functional and structural studies.
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Affiliation(s)
- Ivan Gushchin
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.
| | - Valentin Gordeliy
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.
- University of Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France.
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany.
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3
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Gushchin I, Gordeliy V. Transmembrane Signal Transduction in Two-Component Systems: Piston, Scissoring, or Helical Rotation? Bioessays 2017; 40. [PMID: 29280502 DOI: 10.1002/bies.201700197] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 11/30/2017] [Indexed: 11/10/2022]
Abstract
Allosteric and transmembrane (TM) signaling are among the major questions of structural biology. Here, we review and discuss signal transduction in four-helical TM bundles, focusing on histidine kinases and chemoreceptors found in two-component systems. Previously, piston, scissors, and helical rotation have been proposed as the mechanisms of TM signaling. We discuss theoretically possible conformational changes and examine the available experimental data, including the recent crystallographic structures of nitrate/nitrite sensor histidine kinase NarQ and phototaxis system NpSRII:NpHtrII. We show that TM helices can flex at multiple points and argue that the various conformational changes are not mutually exclusive, and often are observed concomitantly, throughout the TM domain or in its part. The piston and scissoring motions are the most prominent motions in the structures, but more research is needed for definitive conclusions.
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Affiliation(s)
- Ivan Gushchin
- Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
| | - Valentin Gordeliy
- Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia.,Université Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France.,Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425, Jülich, Germany
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4
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Sahoo BR, Fujiwara T. Conformational states of HAMP domains interacting with sensory rhodopsin membrane systems: an integrated all-atom and coarse-grained molecular dynamics simulation approach. MOLECULAR BIOSYSTEMS 2017; 13:193-207. [PMID: 27901172 DOI: 10.1039/c6mb00730a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Understanding the downstream signaling mechanism of sensory rhodopsin and its cognate transducer complex (srII-htrII) has long been a challenge in the field of photoreceptor research. Here, an integration of all-atom and coarse-grained (CG) molecular dynamics (MD) simulations in different srII-htrII complex states is carried out. It is shown that the cytoplasmic four-helix HAMP dimer gives rise to a gear-box model interaction with discrete hydrophobic packing in Natronomonas pharaonis (Np). Structural analysis in all-atom and CG-MD reveals a stable conformational state in the physiological environment (323 K and 1.15 M salt). Comparative analysis in the ground and intermediate state conformations reveals substantial inter-HAMP interactions in the intermediate state with uniform clockwise (+10° to +30°) and counterclockwise (-20° to -40°) rotations in the α1 helix and the α2 helix of the monomer, respectively. Low temperature and low salt environments (283 K and 0.15 M) significantly affect srII-htrII binding affinity in both states with unusual helix bending. The distinguished control cable, knob-into-holes packing and piston-like movements in HAMP helices are found in the intermediate state complex. The N-terminal htrII (159 residues) coupled with srII yields a binding energy (ΔGbind) of -309.22, -436.53 and -331.11 kJ mol-1 in the MM/PBSA calculation for the NphtrII homodimer, the NpsrII-htrII ground state conformation and the NpsrII-htrII intermediate state conformation, respectively. Only the HAMP1 domain shows a very low ΔGbind value (-21.03 kJ mol-1) for the ground state in comparison to that for the intermediate state (-54.68 kJ mol-1). The structural analysis highlights the key residues that include Y199srII, T189srII, E43htrII, T86htrII, M100htrII, E116htrII, E126htrII and S130htrII for complex stabilization and signal transduction.
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Affiliation(s)
- Bikash Ranjan Sahoo
- Laboratory of Molecular Biophysics, Institute for Protein Research, Osaka University, 5650871, Japan.
| | - Toshimichi Fujiwara
- Laboratory of Molecular Biophysics, Institute for Protein Research, Osaka University, 5650871, Japan.
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5
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Gushchin I, Melnikov I, Polovinkin V, Ishchenko A, Yuzhakova A, Buslaev P, Bourenkov G, Grudinin S, Round E, Balandin T, Borshchevskiy V, Willbold D, Leonard G, Büldt G, Popov A, Gordeliy V. Mechanism of transmembrane signaling by sensor histidine kinases. Science 2017; 356:science.aah6345. [PMID: 28522691 DOI: 10.1126/science.aah6345] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 05/08/2017] [Indexed: 11/02/2022]
Abstract
One of the major and essential classes of transmembrane (TM) receptors, present in all domains of life, is sensor histidine kinases, parts of two-component signaling systems (TCSs). The structural mechanisms of TM signaling by these sensors are poorly understood. We present crystal structures of the periplasmic sensor domain, the TM domain, and the cytoplasmic HAMP domain of the Escherichia coli nitrate/nitrite sensor histidine kinase NarQ in the ligand-bound and mutated ligand-free states. The structures reveal that the ligand binding induces rearrangements and pistonlike shifts of TM helices. The HAMP domain protomers undergo leverlike motions and convert these pistonlike motions into helical rotations. Our findings provide the structural framework for complete understanding of TM TCS signaling and for development of antimicrobial treatments targeting TCSs.
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Affiliation(s)
- Ivan Gushchin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany. .,Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - Igor Melnikov
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | - Vitaly Polovinkin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia.,Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Andrii Ishchenko
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Institute of Crystallography, University of Aachen (RWTH), 52056 Aachen, Germany
| | - Anastasia Yuzhakova
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - Pavel Buslaev
- Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - Gleb Bourenkov
- European Molecular Biology Laboratory, Hamburg Outstation, 22607 Hamburg, Germany
| | - Sergei Grudinin
- Université Grenoble Alpes, LJK, F-38000 Grenoble, France.,CNRS, LJK, F-38000 Grenoble, France.,Inria, F-38000 Grenoble, France
| | - Ekaterina Round
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Taras Balandin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany
| | - Valentin Borshchevskiy
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - Dieter Willbold
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Institute of Physical Biology, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Gordon Leonard
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | - Georg Büldt
- Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - Alexander Popov
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | - Valentin Gordeliy
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany. .,Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia.,Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
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6
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Voskoboynikova N, Mosslehy W, Colbasevici A, Ismagulova TT, Bagrov DV, Akovantseva AA, Timashev PS, Mulkidjanian AY, Bagratashvili VN, Shaitan KV, Kirpichnikov MP, Steinhoff HJ. Characterization of an archaeal photoreceptor/transducer complex from Natronomonas pharaonis assembled within styrene–maleic acid lipid particles. RSC Adv 2017. [DOI: 10.1039/c7ra10756k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The archaeal receptor/transducer complex NpSRII/NpHtrII retains its integrity upon reconstitution in styrene–maleic acid lipid particles.
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Affiliation(s)
| | - W. Mosslehy
- Department of Physics
- University of Osnabrück
- Osnabrück
- Germany
| | - A. Colbasevici
- Department of Physics
- University of Osnabrück
- Osnabrück
- Germany
| | - T. T. Ismagulova
- Department of Bioengineering
- Faculty of Biology
- Lomonosov Moscow State University
- Moscow
- Russia
| | - D. V. Bagrov
- Department of Bioengineering
- Faculty of Biology
- Lomonosov Moscow State University
- Moscow
- Russia
| | - A. A. Akovantseva
- Institute of Photonic Technologies of Research Center “Crystallography and Photonics” of RAS
- Moscow
- Russia
| | - P. S. Timashev
- Institute for Regenerative Medicine of I. M. Sechenov First Moscow State Medical University
- Moscow
- Russia
- Institute of Photonic Technologies of Research Center “Crystallography and Photonics” of RAS
- Moscow
| | | | - V. N. Bagratashvili
- Institute of Photonic Technologies of Research Center “Crystallography and Photonics” of RAS
- Moscow
- Russia
| | - K. V. Shaitan
- Department of Bioengineering
- Faculty of Biology
- Lomonosov Moscow State University
- Moscow
- Russia
| | - M. P. Kirpichnikov
- Department of Bioengineering
- Faculty of Biology
- Lomonosov Moscow State University
- Moscow
- Russia
| | - H.-J. Steinhoff
- Department of Physics
- University of Osnabrück
- Osnabrück
- Germany
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7
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Becker EA, Yao AI, Seitzer PM, Kind T, Wang T, Eigenheer R, Shao KSY, Yarov-Yarovoy V, Facciotti MT. A Large and Phylogenetically Diverse Class of Type 1 Opsins Lacking a Canonical Retinal Binding Site. PLoS One 2016; 11:e0156543. [PMID: 27327432 PMCID: PMC4915679 DOI: 10.1371/journal.pone.0156543] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 04/19/2016] [Indexed: 11/24/2022] Open
Abstract
Opsins are photosensitive proteins catalyzing light-dependent processes across the tree of life. For both microbial (type 1) and metazoan (type 2) opsins, photosensing depends upon covalent interaction between a retinal chromophore and a conserved lysine residue. Despite recent discoveries of potential opsin homologs lacking this residue, phylogenetic dispersal and functional significance of these abnormal sequences have not yet been investigated. We report discovery of a large group of putatively non-retinal binding opsins, present in a number of fungal and microbial genomes and comprising nearly 30% of opsins in the Halobacteriacea, a model clade for opsin photobiology. We report phylogenetic analyses, structural modeling, genomic context analysis and biochemistry, to describe the evolutionary relationship of these recently described proteins with other opsins, show that they are expressed and do not bind retinal in a canonical manner. Given these data, we propose a hypothesis that these abnormal opsin homologs may represent a novel family of sensory opsins which may be involved in taxis response to one or more non-light stimuli. If true, this finding would challenge our current understanding of microbial opsins as a light-specific sensory family, and provides a potential analogy with the highly diverse signaling capabilities of the eukaryotic G-protein coupled receptors (GPCRs), of which metazoan type 2 opsins are a light-specific sub-clade.
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Affiliation(s)
- Erin A. Becker
- Genome Center, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
- Microbiology Graduate Group, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
| | - Andrew I. Yao
- Genome Center, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
- Department of Biomedical Engineering, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
| | - Phillip M. Seitzer
- Genome Center, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
- Department of Biomedical Engineering, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
- Proteome Software, 1340 SW Bertha Blvd., Portland, Oregon, United States of America
| | - Tobias Kind
- Genome Center, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
| | - Ting Wang
- Genome Center, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
| | - Rich Eigenheer
- California Department of Food and Agriculture, 1220 N St., Sacramento, CA, 95814, United States of America
| | - Katie S. Y. Shao
- William’s College, 880 Main St., Williamstown, MA, 01267, United States of America
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
| | - Marc T. Facciotti
- Genome Center, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
- Microbiology Graduate Group, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
- Department of Biomedical Engineering, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
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8
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Orekhov PS, Klose D, Mulkidjanian AY, Shaitan KV, Engelhard M, Klare JP, Steinhoff HJ. Signaling and Adaptation Modulate the Dynamics of the Photosensoric Complex of Natronomonas pharaonis. PLoS Comput Biol 2015; 11:e1004561. [PMID: 26496122 PMCID: PMC4651059 DOI: 10.1371/journal.pcbi.1004561] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 09/18/2015] [Indexed: 11/19/2022] Open
Abstract
Motile bacteria and archaea respond to chemical and physical stimuli seeking optimal conditions for survival. To this end transmembrane chemo- and photoreceptors organized in large arrays initiate signaling cascades and ultimately regulate the rotation of flagellar motors. To unravel the molecular mechanism of signaling in an archaeal phototaxis complex we performed coarse-grained molecular dynamics simulations of a trimer of receptor/transducer dimers, namely NpSRII/NpHtrII from Natronomonas pharaonis. Signaling is regulated by a reversible methylation mechanism called adaptation, which also influences the level of basal receptor activation. Mimicking two extreme methylation states in our simulations we found conformational changes for the transmembrane region of NpSRII/NpHtrII which resemble experimentally observed light-induced changes. Further downstream in the cytoplasmic domain of the transducer the signal propagates via distinct changes in the dynamics of HAMP1, HAMP2, the adaptation domain and the binding region for the kinase CheA, where conformational rearrangements were found to be subtle. Overall these observations suggest a signaling mechanism based on dynamic allostery resembling models previously proposed for E. coli chemoreceptors, indicating similar properties of signal transduction for archaeal photoreceptors and bacterial chemoreceptors. Achaea and bacteria can “see” and “sniffle”, they have photo- and chemosensors that measure the environment. On the cell poles, these sensor proteins form large arrays built of several thousands of different receptors. The receptors comprise extracellular or transmembrane sensory domains and elongated homodimeric coiled-coil bundles, which transduce the signals from the membrane across ~20 nm to a conserved cytoplasmic signaling subdomain in an unknown manner. In our study we performed coarse-grained molecular dynamics simulations of the phototactic receptor/transducer complex from Natronomonas pharaonis. Comparing fully methylated and demethylated complexes reveals an interconversion between states of different dynamics along the coiled-coil bundle, which might represent the essential characteristics of the signal transfer from the membrane to the binding sites of the downstream kinase CheA.
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Affiliation(s)
- Philipp S. Orekhov
- Department of Physics, University of Osnabrueck, Osnabrueck, Germany
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Daniel Klose
- Department of Physics, University of Osnabrueck, Osnabrueck, Germany
| | - Armen Y. Mulkidjanian
- Department of Physics, University of Osnabrueck, Osnabrueck, Germany
- Department of Bioengineering and Bioinformatics and A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Martin Engelhard
- Max-Planck-Institute for Molecular Physiology, Dortmund, Germany
| | - Johann P. Klare
- Department of Physics, University of Osnabrueck, Osnabrueck, Germany
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9
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Light-induced switching of HAMP domain conformation and dynamics revealed by time-resolved EPR spectroscopy. FEBS Lett 2014; 588:3970-6. [PMID: 25240192 DOI: 10.1016/j.febslet.2014.09.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/30/2014] [Accepted: 09/03/2014] [Indexed: 12/31/2022]
Abstract
HAMP domains are widely abundant signaling modules. The putative mechanism of their function comprises switching between two distinct states. To unravel these conformational transitions, we apply site-directed spin labeling and time-resolved EPR spectroscopy to the phototactic receptor/transducer complex NpSRII/NpHtrII. We characterize the kinetic coupling of NpHtrII to NpSRII along with the activation period of the transducer and follow the transient conformational signal. The observed transient shift towards a more compact state of the HAMP domain upon light-activation agrees with structure-based calculations. It thereby validates the two modeled signaling states and integrates the domain's dynamics into the current model.
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