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Methner A, Kuzyk SB, Petersen J, Bauer S, Brinkmann H, Sichau K, Wanner G, Wolf J, Neumann-Schaal M, Henke P, Tank M, Spröer C, Bunk B, Overmann J. Thiorhodovibrio frisius and Trv. litoralis spp. nov., Two Novel Members from a Clade of Fastidious Purple Sulfur Bacteria That Exhibit Unique Red-Shifted Light-Harvesting Capabilities. Microorganisms 2023; 11:2394. [PMID: 37894052 PMCID: PMC10609205 DOI: 10.3390/microorganisms11102394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/21/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
In the pursuit of cultivating anaerobic anoxygenic phototrophs with unusual absorbance spectra, a purple sulfur bacterium was isolated from the shoreline of Baltrum, a North Sea island of Germany. It was designated strain 970, due to a predominant light harvesting complex (LH) absorption maximum at 963-966 nm, which represents the furthest infrared-shift documented for such complexes containing bacteriochlorophyll a. A polyphasic approach to bacterial systematics was performed, comparing genomic, biochemical, and physiological properties. Strain 970 is related to Thiorhodovibrio winogradskyi DSM 6702T by 26.5, 81.9, and 98.0% similarity via dDDH, ANI, and 16S rRNA gene comparisons, respectively. The photosynthetic properties of strain 970 were unlike other Thiorhodovibrio spp., which contained typical LH absorbing characteristics of 800-870 nm, as well as a newly discovered absorption band at 908 nm. Strain 970 also had a different photosynthetic operon composition. Upon genomic comparisons with the original Thiorhodovibrio strains DSM 6702T and strain 06511, the latter was found to be divergent, with 25.3, 79.1, and 97.5% similarity via dDDH, ANI, and 16S rRNA gene homology to Trv. winogradskyi, respectively. Strain 06511 (=DSM 116345T) is thereby described as Thiorhodovibrio litoralis sp. nov., and the unique strain 970 (=DSM 111777T) as Thiorhodovibrio frisius sp. nov.
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Affiliation(s)
- Anika Methner
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Steven B Kuzyk
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Jörn Petersen
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Sabine Bauer
- Former Institution: Paläomikrobiologie, Institut für Chemie und Biologie des Meeres, Universität Oldenburg, Postfach 2503, 26111 Oldenburg, Germany
| | - Henner Brinkmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Katja Sichau
- Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Gerhard Wanner
- Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Jacqueline Wolf
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Petra Henke
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Marcus Tank
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Boyke Bunk
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Jörg Overmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
- Former Institution: Paläomikrobiologie, Institut für Chemie und Biologie des Meeres, Universität Oldenburg, Postfach 2503, 26111 Oldenburg, Germany
- Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
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2
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Kimura Y, Tani K, Madigan MT, Wang-Otomo ZY. Advances in the Spectroscopic and Structural Characterization of Core Light-Harvesting Complexes from Purple Phototrophic Bacteria. J Phys Chem B 2023; 127:6-17. [PMID: 36594654 DOI: 10.1021/acs.jpcb.2c06638] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Purple phototrophic bacteria are ancient anoxygenic phototrophs and attractive research tools because they capture light energy in the near-infrared (NIR) region of the spectrum and transform it into chemical energy by way of uphill energy transfers. The heart of this reaction occurs in light-harvesting 1-reaction center (LH1-RC) complexes, which are the simplest model systems for understanding basic photosynthetic reactions within type-II (quinone-utilizing) reaction centers. In this Perspective, we highlight structure-function relationships concerning unresolved fundamental processes in purple bacterial photosynthesis, including the diversified light-harvesting capacity of LH1-associated BChl molecules, energies necessary for photoelectric conversion in the RC special pairs, and quinone transport mechanisms. Based on recent progress in the spectroscopic and structural analysis of LH1-RC complexes from a variety of purple phototrophs, we discuss several key factors for understanding how purple bacteria resource light energy in the inherently energy-poor NIR region of the electromagnetic spectrum.
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Affiliation(s)
- Yukihiro Kimura
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe 657-8501, Japan
| | - Kazutoshi Tani
- Graduate School of Medicine, Mie University, Tsu 514-8507, Japan
| | - Michael T Madigan
- Department of Microbiology, School of Biological Sciences, Southern Illinois University, Carbondale, Illinois 62901, United States
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3
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Tani K, Kobayashi K, Hosogi N, Ji XC, Nagashima S, Nagashima KVP, Izumida A, Inoue K, Tsukatani Y, Kanno R, Hall M, Yu LJ, Ishikawa I, Okura Y, Madigan MT, Mizoguchi A, Humbel BM, Kimura Y, Wang-Otomo ZY. A Ca 2+-binding motif underlies the unusual properties of certain photosynthetic bacterial core light-harvesting complexes. J Biol Chem 2022; 298:101967. [PMID: 35460693 PMCID: PMC9133646 DOI: 10.1016/j.jbc.2022.101967] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 01/24/2023] Open
Abstract
The mildly thermophilic purple phototrophic bacterium Allochromatium tepidum provides a unique model for investigating various intermediate phenotypes observed between those of thermophilic and mesophilic counterparts. The core light-harvesting (LH1) complex from A. tepidum exhibits an absorption maximum at 890 nm and mildly enhanced thermostability, both of which are Ca2+-dependent. However, it is unknown what structural determinants might contribute to these properties. Here, we present a cryo-EM structure of the reaction center–associated LH1 complex at 2.81 Å resolution, in which we identify multiple pigment-binding α- and β-polypeptides within an LH1 ring. Of the 16 α-polypeptides, we show that six (α1) bind Ca2+ along with β1- or β3-polypeptides to form the Ca2+-binding sites. This structure differs from that of fully Ca2+-bound LH1 from Thermochromatium tepidum, enabling determination of the minimum structural requirements for Ca2+-binding. We also identified three amino acids (Trp44, Asp47, and Ile49) in the C-terminal region of the A. tepidum α1-polypeptide that ligate each Ca ion, forming a Ca2+-binding WxxDxI motif that is conserved in all Ca2+-bound LH1 α-polypeptides from other species with reported structures. The partial Ca2+-bound structure further explains the unusual phenotypic properties observed for this bacterium in terms of its Ca2+-requirements for thermostability, spectroscopy, and phototrophic growth, and supports the hypothesis that A. tepidum may represent a “transitional” species between mesophilic and thermophilic purple sulfur bacteria. The characteristic arrangement of multiple αβ-polypeptides also suggests a mechanism of molecular recognition in the expression and/or assembly of the LH1 complex that could be regulated through interactions with reaction center subunits.
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Affiliation(s)
- Kazutoshi Tani
- Graduate School of Medicine, Mie University, Tsu, Japan.
| | - Kazumi Kobayashi
- EM Business Unit, JEOL Ltd 3-1-2 Musashino, Akishima, Tokyo, Japan
| | - Naoki Hosogi
- EM Business Unit, JEOL Ltd 3-1-2 Musashino, Akishima, Tokyo, Japan
| | | | - Sakiko Nagashima
- Research Institute for Integrated Science, Kanagawa University, Hiratsuka, Kanagawa, Japan
| | - Kenji V P Nagashima
- Research Institute for Integrated Science, Kanagawa University, Hiratsuka, Kanagawa, Japan
| | - Airi Izumida
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Hiratsuka, Kanagawa, Japan
| | - Kazuhito Inoue
- Research Institute for Integrated Science, Kanagawa University, Hiratsuka, Kanagawa, Japan; Department of Biological Sciences, Faculty of Science, Kanagawa University, Hiratsuka, Kanagawa, Japan
| | - Yusuke Tsukatani
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa, Japan
| | - Ryo Kanno
- Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), Kunigami-gun, Okinawa, Japan
| | - Malgorzata Hall
- Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), Kunigami-gun, Okinawa, Japan
| | - Long-Jiang Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Isamu Ishikawa
- EM Business Unit, JEOL Ltd 3-1-2 Musashino, Akishima, Tokyo, Japan
| | - Yoshihiro Okura
- EM Business Unit, JEOL Ltd 3-1-2 Musashino, Akishima, Tokyo, Japan
| | - Michael T Madigan
- School of Biological Sciences, Department of Microbiology, Southern Illinois University, Carbondale, Illinois, USA
| | | | - Bruno M Humbel
- Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), Kunigami-gun, Okinawa, Japan
| | - Yukihiro Kimura
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, Japan.
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Kimura Y, Imanishi M, Li Y, Yura Y, Ohno T, Saga Y, Madigan MT, Wang-Otomo ZY. Identification of metal-sensitive structural changes in the Ca 2+-binding photocomplex from Thermochromatium tepidum by isotope-edited vibrational spectroscopy. J Chem Phys 2022; 156:105101. [DOI: 10.1063/5.0075600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Calcium ions play a dual role in expanding the spectral diversity and structural stability of photocomplexes from several Ca2+-requiring purple sulfur phototrophic bacteria. Here, metal-sensitive structural changes in the isotopically labeled light-harvesting 1 reaction center (LH1-RC) complexes from the thermophilic purple sulfur bacterium Thermochromatium ( Tch.) tepidum were investigated by perfusion-induced attenuated total reflection (ATR) Fourier transform infrared (FTIR) spectroscopy. The ATR-FTIR difference spectra induced by exchanges between native Ca2+ and exogenous Ba2+ exhibited interconvertible structural and/or conformational changes in the metal binding sites at the LH1 C-terminal region. Most of the characteristic Ba2+/Ca2+ difference bands were detected even when only Ca ions were removed from the LH1-RC complexes, strongly indicating the pivotal roles of Ca2+ in maintaining the LH1-RC structure of Tch. tepidum. Upon 15N-, 13C- or 2H-labeling, the LH1-RC complexes exhibited characteristic 15N/14N-, 13C/12C-, or 2H/1H-isotopic shifts for the Ba2+/Ca2+ difference bands. Some of the 15N/14N or 13C/12C bands were also sensitive to further 2H-labelings. Given the band frequencies and their isotopic shifts along with the structural information of the Tch. tepidum LH1-RC complexes, metal-sensitive FTIR bands were tentatively identified to the vibrational modes of the polypeptide main chains and side chains comprising the metal binding sites. Furthermore, important new IR marker bands highly sensitive to the LH1 BChl a conformation in the Ca2+-bound states were revealed based on both ATR-FTIR and near-infrared Raman analyses. The present approach provides valuable insights concerning the dynamic equilibrium between the Ca2+- and Ba2+-bound states statically resolved by x-ray crystallography.
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Affiliation(s)
- Yukihiro Kimura
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Michie Imanishi
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Yong Li
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Yuki Yura
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Takashi Ohno
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Yoshitaka Saga
- Department of Chemistry, Faculty of Science and Engineering, Kindai University, Higashi-Osaka 577-8502, Japan
| | - Michael T. Madigan
- School of Biological Sciences, Department of Microbiology, Southern Illinois University, Carbondale, Illinois 62901, USA
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5
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Yang Z, Qi C, Liu W, Yin D, Yu L, Li L, Guo X. Revealing Conformational Transition Dynamics of Photosynthetic Proteins in Single-Molecule Electrical Circuits. J Phys Chem Lett 2021; 12:3853-3859. [PMID: 33856226 DOI: 10.1021/acs.jpclett.1c00884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The function of proteins depends on their structural flexibility and conformational change. By utilizing silicon-nanowire-based single-molecule electrical circuits, here we present a label-free real-time measurement method that can directly monitor conformational changes of a photosynthetic LH1-RC complex, reaching the ultimate goal of analytic chemistry. These results manifest that the conformation of the LH1-RC complex vibrates among four conformations with strong temperature dependence. At the optimal temperature, States 2 and 3 occupy the main conformations of the LH1-RC complex, and its conformational variation mostly emerges as anharmonic vibration modes, which contributes to photon acquisition and heat transmission. The influence of light activation on occurrence percentage is observed, resulting from light-driven quivering of pigments. Therefore, this avenue proves to be an efficient platform for revealing the fundamental mechanisms of various biological processes in vitro.
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Affiliation(s)
- Zhiheng Yang
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - Chenhui Qi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, P. R. China
| | - Wenzhe Liu
- Beijing National Laboratory for Molecular Sciences State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Dongbao Yin
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - Longjiang Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, P. R. China
| | - Lidong Li
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Sciences State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
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6
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Tani K, Kanno R, Makino Y, Hall M, Takenouchi M, Imanishi M, Yu LJ, Overmann J, Madigan MT, Kimura Y, Mizoguchi A, Humbel BM, Wang-Otomo ZY. Cryo-EM structure of a Ca 2+-bound photosynthetic LH1-RC complex containing multiple αβ-polypeptides. Nat Commun 2020; 11:4955. [PMID: 33009385 PMCID: PMC7532537 DOI: 10.1038/s41467-020-18748-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 09/09/2020] [Indexed: 11/13/2022] Open
Abstract
The light-harvesting-reaction center complex (LH1-RC) from the purple phototrophic bacterium Thiorhodovibrio strain 970 exhibits an LH1 absorption maximum at 960 nm, the most red-shifted absorption for any bacteriochlorophyll (BChl) a-containing species. Here we present a cryo-EM structure of the strain 970 LH1-RC complex at 2.82 Å resolution. The LH1 forms a closed ring structure composed of sixteen pairs of the αβ-polypeptides. Sixteen Ca ions are present in the LH1 C-terminal domain and are coordinated by residues from the αβ-polypeptides that are hydrogen-bonded to BChl a. The Ca2+-facilitated hydrogen-bonding network forms the structural basis of the unusual LH1 redshift. The structure also revealed the arrangement of multiple forms of α- and β-polypeptides in an individual LH1 ring. Such organization indicates a mechanism of interplay between the expression and assembly of the LH1 complex that is regulated through interactions with the RC subunits inside. Here the authors report a cryo-EM structure of the light-harvesting-reaction center complex (LH1- RC) from the purple phototrophic bacterium Thiorhodovibrio strain 970, providing insights into the mechanisms that underlie the absorbance properties of both the LH1 and the RC of this spectrally unusual purple bacterium.
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Affiliation(s)
- Kazutoshi Tani
- Graduate School of Medicine, Mie University, Tsu, 514-8507, Japan.
| | - Ryo Kanno
- Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Yuki Makino
- Faculty of Science, Ibaraki University, Mito, 310-8512, Japan
| | - Malgorzata Hall
- Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | | | - Michie Imanishi
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, 657-8501, Japan
| | - Long-Jiang Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jörg Overmann
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany.,Faculty of Life Science, Institute of Microbiology, Braunschweig University of Technology, Braunschweig, Germany
| | - Michael T Madigan
- Department of Microbiology, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Yukihiro Kimura
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, 657-8501, Japan
| | - Akira Mizoguchi
- Graduate School of Medicine, Mie University, Tsu, 514-8507, Japan
| | - Bruno M Humbel
- Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
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Imanishi M, Takenouchi M, Takaichi S, Nakagawa S, Saga Y, Takenaka S, Madigan MT, Overmann J, Wang-Otomo ZY, Kimura Y. A Dual Role for Ca 2+ in Expanding the Spectral Diversity and Stability of Light-Harvesting 1 Reaction Center Photocomplexes of Purple Phototrophic Bacteria. Biochemistry 2019; 58:2844-2852. [PMID: 31145583 DOI: 10.1021/acs.biochem.9b00351] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The light-harvesting 1 reaction center (LH1-RC) complex in the purple sulfur bacterium Thiorhodovibrio ( Trv.) strain 970 cells exhibits its LH1 Q y transition at 973 nm, the lowest-energy Q y absorption among purple bacteria containing bacteriochlorophyll a (BChl a). Here we characterize the origin of this extremely red-shifted Q y transition. Growth of Trv. strain 970 did not occur in cultures free of Ca2+, and elemental analysis of Ca2+-grown cells confirmed that purified Trv. strain 970 LH1-RC complexes contained Ca2+. The LH1 Q y band of Trv. strain 970 was blue-shifted from 959 to 875 nm upon Ca2+ depletion, but the original spectral properties were restored upon Ca2+ reconstitution, which also occurs with the thermophilic purple bacterium Thermochromatium ( Tch.) tepidum. The amino acid sequences of the LH1 α- and β-polypeptides from Trv. strain 970 closely resemble those of Tch. tepidum; however, Ca2+ binding in the Trv. strain 970 LH1-RC occurred more selectively than in Tch. tepidum LH1-RC and with a reduced affinity. Ultraviolet resonance Raman analysis indicated that the number of hydrogen-bonding interactions between BChl a and LH1 proteins of Trv. strain 970 was significantly greater than for Tch. tepidum and that Ca2+ was indispensable for maintaining these bonds. Furthermore, perfusion-induced Fourier transform infrared analyses detected Ca2+-induced conformational changes in the binding site closely related to the unique spectral properties of Trv. strain 970. Collectively, our results reveal an ecological strategy employed by Trv. strain 970 of integrating Ca2+ into its LH1-RC complex to extend its light-harvesting capacity to regions of the near-infrared spectrum unused by other purple bacteria.
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Affiliation(s)
- Michie Imanishi
- Graduate School of Agricultural Science , Kobe University , Nada, Kobe 657-8501 , Japan
| | - Mizuki Takenouchi
- Faculty of Science , Ibaraki University , Bunkyo, Mito 310-8512 , Japan
| | - Shinichi Takaichi
- Faculty of Life Sciences , Tokyo University of Agriculture , Setagaya, Tokyo 156-8502 , Japan
| | - Shiori Nakagawa
- Department of Chemistry , Kindai University , Higashi-Osaka, Osaka 577-8502 , Japan
| | - Yoshitaka Saga
- Department of Chemistry , Kindai University , Higashi-Osaka, Osaka 577-8502 , Japan
| | - Shinji Takenaka
- Graduate School of Agricultural Science , Kobe University , Nada, Kobe 657-8501 , Japan
| | - Michael T Madigan
- Department of Microbiology , Southern Illinois University , Carbondale , Illinois 62901 , United States
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures , 38124 Braunschweig , Germany.,Microbiology , Braunschweig University of Technology , 38106 Braunschweig , Germany
| | | | - Yukihiro Kimura
- Graduate School of Agricultural Science , Kobe University , Nada, Kobe 657-8501 , Japan
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8
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Yu LJ, Suga M, Wang-Otomo ZY, Shen JR. Novel features of LH1-RC from Thermochromatium tepidum revealed from its atomic resolution structure. FEBS J 2018; 285:4359-4366. [PMID: 30328658 DOI: 10.1111/febs.14679] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 10/09/2018] [Indexed: 11/28/2022]
Abstract
Light-harvesting-1 (LH1)-reaction center (RC) super-complex is a membrane protein-pigment complex existing in purple photosynthetic bacteria, where LH1 absorbs light energy and transfers them rapidly and efficiently to RC to initiate the charge separation and electron transfer reactions. The structure of LH1-RC has been reported at relatively low resolutions from several different species of bacteria previously, but was solved at an atomic resolution recently from a thermophilic photosynthetic bacterium Thermochromatium tepidum. This high-resolution structure revealed the detailed organization of the super-complex including a number of unique features that are important for its functioning, such as a more intact RC structure, transporting routes for quinones to replace the bound QB as well as for the in-and-out of the closed LH1 ring, detailed coordinating environment of the Ca2+ ions in LH1 important for the remarkable red shift of the absorption spectrum, as well as for the enhanced thermostability. These results thus greatly advance our understanding on the mechanisms of energy transfer, quinone exchange, the red shift in the LH1-Qy transition and the enhanced thermal stability, in this super-complex.
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Affiliation(s)
- Long-Jiang Yu
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Japan
| | - Michihiro Suga
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Japan
| | | | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Japan
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9
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Yu LJ, Suga M, Wang-Otomo ZY, Shen JR. Structure of photosynthetic LH1-RC supercomplex at 1.9 Å resolution. Nature 2018; 556:209-213. [PMID: 29618814 DOI: 10.1038/s41586-018-0002-9] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 02/23/2018] [Indexed: 11/09/2022]
Abstract
Light-harvesting complex 1 (LH1) and the reaction centre (RC) form a membrane-protein supercomplex that performs the primary reactions of photosynthesis in purple photosynthetic bacteria. The structure of the LH1-RC complex can provide information on the arrangement of protein subunits and cofactors; however, so far it has been resolved only at a relatively low resolution. Here we report the crystal structure of the calcium-ion-bound LH1-RC supercomplex of Thermochromatium tepidum at a resolution of 1.9 Å. This atomic-resolution structure revealed several new features about the organization of protein subunits and cofactors. We describe the loop regions of RC in their intact states, the interaction of these loop regions with the LH1 subunits, the exchange route for the bound quinone QB with free quinone molecules, the transport of free quinones between the inside and outside of the LH1 ring structure, and the detailed calcium-ion-binding environment. This structure provides a solid basis for the detailed examination of the light reactions that occur during bacterial photosynthesis.
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Affiliation(s)
- Long-Jiang Yu
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Michihiro Suga
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | | | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan.
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10
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11
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Li Y, Kimura Y, Arikawa T, Wang-Otomo ZY, Ohno T. ATR–FTIR Detection of Metal-Sensitive Structural Changes in the Light-Harvesting 1 Reaction Center Complex from the Thermophilic Purple Sulfur Bacterium Thermochromatium tepidum. Biochemistry 2013; 52:9001-8. [DOI: 10.1021/bi401033y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yong Li
- Department
of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe 657-8501, Japan
| | - Yukihiro Kimura
- Department
of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe 657-8501, Japan
| | - Teruhisa Arikawa
- Department
of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe 657-8501, Japan
| | | | - Takashi Ohno
- Department
of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe 657-8501, Japan
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Kimura Y, Inada Y, Numata T, Arikawa T, Li Y, Zhang JP, Wang ZY, Ohno T. Metal cations modulate the bacteriochlorophyll–protein interaction in the light-harvesting 1 core complex from Thermochromatium tepidum. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1022-9. [DOI: 10.1016/j.bbabio.2012.03.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 03/07/2012] [Accepted: 03/11/2012] [Indexed: 11/16/2022]
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