1
|
Yan YH, Wang GL, Yue XY, Ma F, Madigan MT, Wang-Otomo ZY, Zou MJ, Yu LJ. Molecular structure and characterization of the Thermochromatium tepidum light-harvesting 1 photocomplex produced in a foreign host. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149050. [PMID: 38806091 DOI: 10.1016/j.bbabio.2024.149050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 05/30/2024]
Abstract
Purple phototrophic bacteria possess light-harvesting 1 and reaction center (LH1-RC) core complexes that play a key role in converting solar energy to chemical energy. High-resolution structures of LH1-RC and RC complexes have been intensively studied and have yielded critical insight into the architecture and interactions of their proteins, pigments, and cofactors. Nevertheless, a detailed picture of the structure and assembly of LH1-only complexes is lacking due to the intimate association between LH1 and the RC. To study the intrinsic properties and structure of an LH1-only complex, a genetic system was constructed to express the Thermochromatium (Tch.) tepidum LH1 complex heterologously in a modified Rhodospirillum rubrum mutant strain. The heterologously expressed Tch. tepidum LH1 complex was isolated in a pure form free of the RC and exhibited the characteristic absorption properties of Tch. tepidum. Cryo-EM structures of the LH1-only complexes revealed a closed circular ring consisting of either 14 or 15 αβ-subunits, making it the smallest completely closed LH1 complex discovered thus far. Surprisingly, the Tch. tepidum LH1-only complex displayed even higher thermostability than that of the native LH1-RC complex. These results reveal previously unsuspected plasticity of the LH1 complex, provide new insights into the structure and assembly of the LH1-RC complex, and show how molecular genetics can be exploited to study membrane proteins from phototrophic organisms whose genetic manipulation is not yet possible.
Collapse
Affiliation(s)
- Yi-Hao Yan
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guang-Lei Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xing-Yu Yue
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Ma
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Michael T Madigan
- School of Biological Sciences, Department of Microbiology, Southern Illinois University, Carbondale, IL 62901, USA
| | | | - Mei-Juan Zou
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Long-Jiang Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
2
|
Tani K, Kanno R, Harada A, Kobayashi Y, Minamino A, Takenaka S, Nakamura N, Ji XC, Purba ER, Hall M, Yu LJ, Madigan MT, Mizoguchi A, Iwasaki K, Humbel BM, Kimura Y, Wang-Otomo ZY. High-resolution structure and biochemical properties of the LH1-RC photocomplex from the model purple sulfur bacterium, Allochromatium vinosum. Commun Biol 2024; 7:176. [PMID: 38347078 PMCID: PMC10861460 DOI: 10.1038/s42003-024-05863-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/26/2024] [Indexed: 02/15/2024] Open
Abstract
The mesophilic purple sulfur phototrophic bacterium Allochromatium (Alc.) vinosum (bacterial family Chromatiaceae) has been a favored model for studies of bacterial photosynthesis and sulfur metabolism, and its core light-harvesting (LH1) complex has been a focus of numerous studies of photosynthetic light reactions. However, despite intense efforts, no high-resolution structure and thorough biochemical analysis of the Alc. vinosum LH1 complex have been reported. Here we present cryo-EM structures of the Alc. vinosum LH1 complex associated with reaction center (RC) at 2.24 Å resolution. The overall structure of the Alc. vinosum LH1 resembles that of its moderately thermophilic relative Alc. tepidum in that it contains multiple pigment-binding α- and β-polypeptides. Unexpectedly, however, six Ca ions were identified in the Alc. vinosum LH1 bound to certain α1/β1- or α1/β3-polypeptides through a different Ca2+-binding motif from that seen in Alc. tepidum and other Chromatiaceae that contain Ca2+-bound LH1 complexes. Two water molecules were identified as additional Ca2+-coordinating ligands. Based on these results, we reexamined biochemical and spectroscopic properties of the Alc. vinosum LH1-RC. While modest but distinct effects of Ca2+ were detected in the absorption spectrum of the Alc. vinosum LH1 complex, a marked decrease in thermostability of its LH1-RC complex was observed upon removal of Ca2+. The presence of Ca2+ in the photocomplex of Alc. vinosum suggests that Ca2+-binding to LH1 complexes may be a common adaptation in species of Chromatiaceae for conferring spectral and thermal flexibility on this key component of their photosynthetic machinery.
Collapse
Affiliation(s)
- Kazutoshi Tani
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.
- Graduate School of Medicine, Mie University, 1577 Kurimamachiyacho, Tsu, 514-8507, Japan.
| | - Ryo Kanno
- Quantum Wave Microscopy Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Ayaka Harada
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Yuki Kobayashi
- Faculty of Science, Ibaraki University, Mito, 310-8512, Japan
| | - Akane Minamino
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, 657-8501, Japan
| | - Shinji Takenaka
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, 657-8501, Japan
| | | | - Xuan-Cheng Ji
- Faculty of Science, Ibaraki University, Mito, 310-8512, Japan
| | - Endang R Purba
- Scientific 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
| | - Malgorzata Hall
- Scientific 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
| | - Long-Jiang Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Michael T Madigan
- School of Biological Sciences, Program in Microbiology, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Akira Mizoguchi
- Graduate School of Medicine, Mie University, 1577 Kurimamachiyacho, Tsu, 514-8507, Japan
| | - Kenji Iwasaki
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Bruno M Humbel
- Provost Office, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
- Department of Cell Biology and Neuroscience, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Yukihiro Kimura
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, 657-8501, Japan.
| | | |
Collapse
|
3
|
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: 8] [Impact Index Per Article: 8.0] [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.
Collapse
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
| | | |
Collapse
|
4
|
Salt- and pH-Dependent Thermal Stability of Photocomplexes from Extremophilic Bacteriochlorophyll b-Containing Halo-rhodospira Species. Microorganisms 2022; 10:microorganisms10050959. [PMID: 35630403 PMCID: PMC9146400 DOI: 10.3390/microorganisms10050959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 11/22/2022] Open
Abstract
Halorhodospira (Hlr.) species are the most halophilic and alkaliphilic of all purple bacteria. Hlr. halochloris exhibits the lowest LH1 Qy transition energy among phototrophic organisms and is the only known triply extremophilic anoxygenic phototroph, displaying a thermophilic, halophilic, and alkaliphilic phenotype. Recently, we reported that electrostatic charges are responsible for the unusual spectroscopic properties of the Hlr. halochloris LH1 complex. In the present work, we examined the effects of salt and pH on the spectroscopic properties and thermal stability of LH1-RCs from Hlr. halochloris compared with its mesophilic counterpart, Hlr. abdelmalekii. Experiments in which the photocomplexes were subjected to different levels of salt or variable pH revealed that the thermal stability of LH1-RCs from both species was largely retained in the presence of high salt concentrations and/or at alkaline pH but was markedly reduced by lowering the salt concentration and/or pH. Based on the amino acid sequences of LH1 polypeptides and their composition of acidic/basic residues and the Hofmeister series for cation/anion species, we discuss the importance of electrostatic charge in stabilizing the Hlr. halochloris LH1-RC complex to allow it to perform photosynthesis in its warm, hypersaline, and alkaline habitat.
Collapse
|
5
|
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.
Collapse
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.
| | | |
Collapse
|
6
|
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.
Collapse
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
| | | |
Collapse
|
7
|
Allochromatium tepidum, sp. nov., a hot spring species of purple sulfur bacteria. Arch Microbiol 2022; 204:115. [PMID: 34984587 DOI: 10.1007/s00203-021-02715-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/30/2022]
Abstract
We describe a new species of purple sulfur bacteria (Chromatiaceae, anoxygenic phototrophic bacteria) isolated from a microbial mat in the sulfidic geothermal outflow of a hot spring in Rotorua, New Zealand. This phototroph, designated as strain NZ, grew optimally near 45 °C but did not show an absorption maximum at 915 nm for the light-harvesting-reaction center core complex (LH1-RC) characteristic of other thermophilic purple sulfur bacteria. Strain NZ had a similar carotenoid composition as Thermochromatium tepidum, but unlike Tch. tepidum, grew photoheterotrophically on acetate in the absence of sulfide and metabolized thiosulfate. The genome of strain NZ was significantly larger than that of Tch. tepidum but slightly smaller than that of Allochromatium vinosum. Strain NZ was phylogenetically more closely related to mesophilic purple sulfur bacteria of the genus Allochromatium than to Tch. tepidum. This conclusion was reached from phylogenetic analyses of strain NZ genes encoding 16S rRNA and the photosynthetic functional gene pufM, from phylogenetic analyses of entire genomes, and from a phylogenetic tree constructed from the concatenated sequence of 1090 orthologous proteins. Moreover, average nucleotide identities and digital DNA:DNA hybridizations of the strain NZ genome against those of related species of Chromatiaceae supported the phylogenetic analyses. From this collection of properties, we describe strain NZ here as the first thermophilic species of the genus Allochromatium, Allochromatium tepidum NZT, sp. nov.
Collapse
|
8
|
Sattley WM, Swingley WD, Burchell BM, Dewey ED, Hayward MK, Renbarger TL, Shaffer KN, Stokes LM, Gurbani SA, Kujawa CM, Nuccio DA, Schladweiler J, Touchman JW, Wang-Otomo ZY, Blankenship RE, Madigan MT. Complete genome of the thermophilic purple sulfur Bacterium Thermochromatium tepidum compared to Allochromatium vinosum and other Chromatiaceae. PHOTOSYNTHESIS RESEARCH 2022; 151:125-142. [PMID: 34669148 DOI: 10.1007/s11120-021-00870-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/07/2021] [Indexed: 06/13/2023]
Abstract
The complete genome sequence of the thermophilic purple sulfur bacterium Thermochromatium tepidum strain MCT (DSM 3771T) is described and contrasted with that of its mesophilic relative Allochromatium vinosum strain D (DSM 180T) and other Chromatiaceae. The Tch. tepidum genome is a single circular chromosome of 2,958,290 base pairs with no plasmids and is substantially smaller than the genome of Alc. vinosum. The Tch. tepidum genome encodes two forms of RuBisCO and contains nifHDK and several other genes encoding a molybdenum nitrogenase but lacks a gene encoding a protein that assembles the Fe-S cluster required to form a functional nitrogenase molybdenum-iron cofactor, leaving the phototroph phenotypically Nif-. Tch. tepidum contains genes necessary for oxidizing sulfide to sulfate as photosynthetic electron donor but is genetically unequipped to either oxidize thiosulfate as an electron donor or carry out assimilative sulfate reduction, both of which are physiological hallmarks of Alc. vinosum. Also unlike Alc. vinosum, Tch. tepidum is obligately phototrophic and unable to grow chemotrophically in darkness by respiration. Several genes present in the Alc. vinosum genome that are absent from the genome of Tch. tepidum likely contribute to the major physiological differences observed between these related purple sulfur bacteria that inhabit distinct ecological niches.
Collapse
Affiliation(s)
- W Matthew Sattley
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN, 46953, USA.
| | - Wesley D Swingley
- Department of Biological Sciences, Northern Illinois University, Dekalb, IL, 60115, USA
| | - Brad M Burchell
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN, 46953, USA
| | - Emma D Dewey
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN, 46953, USA
| | - Mackenzie K Hayward
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN, 46953, USA
| | - Tara L Renbarger
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN, 46953, USA
| | - Kathryn N Shaffer
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN, 46953, USA
| | - Lynn M Stokes
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN, 46953, USA
| | - Sonja A Gurbani
- Department of Biological Sciences, Northern Illinois University, Dekalb, IL, 60115, USA
| | - Catrina M Kujawa
- Department of Biological Sciences, Northern Illinois University, Dekalb, IL, 60115, USA
| | - D Adam Nuccio
- Department of Biological Sciences, Northern Illinois University, Dekalb, IL, 60115, USA
| | - Jacob Schladweiler
- Department of Biological Sciences, Northern Illinois University, Dekalb, IL, 60115, USA
| | - Jeffrey W Touchman
- School of Life Sciences, Arizona State University, Tempe, AR, 85287, USA
| | | | - Robert E Blankenship
- Departments of Chemistry and Biology, Washington University, St. Louis, MO, 63130, USA
| | - Michael T Madigan
- Department of Microbiology, School of Biological Sciences, Southern Illinois University, Carbondale, IL, 62901, USA
| |
Collapse
|
9
|
Kimura Y, Nojima S, Nakata K, Yamashita T, Wang XP, Takenaka S, Akimoto S, Kobayashi M, Madigan MT, Wang-Otomo ZY, Yu LJ. Electrostatic charge controls the lowest LH1 Q y transition energy in the triply extremophilic purple phototrophic bacterium, Halorhodospira halochloris. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148473. [PMID: 34310933 DOI: 10.1016/j.bbabio.2021.148473] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/18/2021] [Accepted: 07/19/2021] [Indexed: 10/20/2022]
Abstract
Halorhodospira (Hlr.) halochloris is a unique phototrophic purple bacterium because it is a triple extremophile-the organism is thermophilic, alkalophilic, and halophilic. The most striking photosynthetic feature of Hlr. halochloris is that the bacteriochlorophyll (BChl) b-containing core light-harvesting (LH1) complex surrounding its reaction center (RC) exhibits its LH1 Qy absorption maximum at 1016 nm, which is the lowest transition energy among phototrophic organisms. Here we report that this extraordinarily red-shifted LH1 Qy band of Hlr. halochloris exhibits interconvertible spectral shifts depending on the electrostatic charge distribution around the BChl b molecules. The 1016 nm band of the Hlr. halochloris LH1-RC complex was blue-shifted to 958 nm upon desalting or pH decrease but returned to its original position when supplemented with salts or pH increase. Resonance Raman analysis demonstrated that these interconvertible spectral shifts are not associated with the strength of hydrogen-bonding interactions between BChl b and LH1 polypeptides. Furthermore, circular dichroism signals for the LH1 Qy transition of Hlr. halochloris appeared with a positive sign (as in BChl b-containing Blastochloris species) and opposite those of BChl a-containing purple bacteria, possibly due to a combined effect of slight differences in the transition dipole moments between BChl a and BChl b and in the interactions between adjacent BChls in their assembled state. Based on these findings and LH1 amino acid sequences, it is proposed that Hlr. halochloris evolved its unique and tunable light-harvesting system with electrostatic charges in order to carry out photosynthesis and thrive in its punishing hypersaline and alkaline habitat.
Collapse
Affiliation(s)
- Yukihiro Kimura
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe 657-8501, Japan.
| | - Shingo Nojima
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe 657-8501, Japan
| | - Kazuna Nakata
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe 657-8501, Japan
| | | | - Xiang-Ping Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shinji Takenaka
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe 657-8501, Japan
| | - Seiji Akimoto
- Department of Science, Graduate School of Science, Kobe University, Nada, Kobe 657-8501, Japan
| | | | - Michael T Madigan
- Department of Microbiology, Southern Illinois University, Carbondale, IL 62901, USA
| | | | - Long-Jiang Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| |
Collapse
|
10
|
Saga Y, Tanaka A, Yamashita M, Shinoda T, Tomo T, Kimura Y. Spectral Properties of Chlorophyll f in the B800 Cavity of Light-harvesting Complex 2 from the Purple Photosynthetic Bacterium Rhodoblastus acidophilus. Photochem Photobiol 2021; 98:169-174. [PMID: 34293183 DOI: 10.1111/php.13491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 11/29/2022]
Abstract
The interactions of chlorophyll (Chl) and bacteriochlorophyll (BChl) pigments with the polypeptides in photosynthetic light-harvesting proteins are responsible for controlling the absorption energy of (B)Chls in protein matrixes. The binding pocket of B800 BChl a in LH2 proteins, which are peripheral light-harvesting proteins in purple photosynthetic bacteria, is useful for studying such structure-property relationships. We report the reconstitution of Chl f, which has the formyl group at the 2-position, in the B800 cavity of LH2 from the purple bacterium Rhodoblastus acidophilus. The Qy absorption band of Chl f in the B800 cavity was shifted by 14 nm to longer wavelength compared to that of the corresponding five-coordinated monomer in acetone. This redshift was larger than that of Chl a and Chl b. Resonance Raman spectroscopy indicated hydrogen bonding between the 2-formyl group of Chl f and the LH2 polypeptide. These results suggest that this hydrogen bonding contributes to the Qy redshift of Chl f. Furthermore, the Qy redshift of Chl f in the B800 cavity was smaller than that of Chl d. This may have arisen from the different patterns of hydrogen bonding between Chl f and Chl d and/or from the steric hindrance of the 3-vinyl group in Chl f.
Collapse
Affiliation(s)
- Yoshitaka Saga
- Department of Chemistry, Faculty of Science and Engineering, Kindai University, Osaka, Japan
| | - Aiko Tanaka
- Department of Chemistry, Faculty of Science and Engineering, Kindai University, Osaka, Japan
| | - Madoka Yamashita
- Department of Chemistry, Faculty of Science and Engineering, Kindai University, Osaka, Japan
| | - Toshiyuki Shinoda
- Graduate School of Science, Tokyo University of Science, Tokyo, Japan
| | - Tatsuya Tomo
- Graduate School of Science, Tokyo University of Science, Tokyo, Japan
| | - Yukihiro Kimura
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| |
Collapse
|
11
|
Kimura Y, Yamashita T, Seto R, Imanishi M, Honda M, Nakagawa S, Saga Y, Takenaka S, Yu LJ, Madigan MT, Wang-Otomo ZY. Circular dichroism and resonance Raman spectroscopies of bacteriochlorophyll b-containing LH1-RC complexes. PHOTOSYNTHESIS RESEARCH 2021; 148:77-86. [PMID: 33834357 DOI: 10.1007/s11120-021-00831-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
The core light-harvesting complexes (LH1) in bacteriochlorophyll (BChl) b-containing purple phototrophic bacteria are characterized by a near-infrared absorption maximum around 1010 nm. The determinative cause for this ultra-redshift remains unclear. Here, we present results of circular dichroism (CD) and resonance Raman measurements on the purified LH1 complexes in a reaction center-associated form from a mesophilic and a thermophilic Blastochloris species. Both the LH1 complexes displayed purely positive CD signals for their Qy transitions, in contrast to those of BChl a-containing LH1 complexes. This may reflect differences in the conjugation system of the bacteriochlorin between BChl b and BChl a and/or the differences in the pigment organization between the BChl b- and BChl a-containing LH1 complexes. Resonance Raman spectroscopy revealed remarkably large redshifts of the Raman bands for the BChl b C3-acetyl group, indicating unusually strong hydrogen bonds formed with LH1 polypeptides, results that were verified by a published structure. A linear correlation was found between the redshift of the Raman band for the BChl C3-acetyl group and the change in LH1-Qy transition for all native BChl a- and BChl b-containing LH1 complexes examined. The strong hydrogen bonding and π-π interactions between BChl b and nearby aromatic residues in the LH1 polypeptides, along with the CD results, provide crucial insights into the spectral and structural origins for the ultra-redshift of the long-wavelength absorption maximum of BChl b-containing phototrophs.
Collapse
Affiliation(s)
- Y Kimura
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, 657-8501, Japan.
| | - T Yamashita
- Faculty of Science, Ibaraki University, Mito, 310-8512, Japan
| | - R Seto
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, 657-8501, Japan
| | - M Imanishi
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, 657-8501, Japan
| | - M Honda
- Faculty of Science, Ibaraki University, Mito, 310-8512, Japan
| | - S Nakagawa
- Department of Chemistry, Kindai University, Higashi-Osaka, 577-8502, Japan
| | - Y Saga
- Department of Chemistry, Kindai University, Higashi-Osaka, 577-8502, Japan
| | - S Takenaka
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, 657-8501, Japan
| | - L-J Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - M T Madigan
- Department of Microbiology, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Z-Y Wang-Otomo
- Faculty of Science, Ibaraki University, Mito, 310-8512, Japan.
| |
Collapse
|
12
|
Kawakami T, Yu LJ, Liang T, Okazaki K, Madigan MT, Kimura Y, Wang-Otomo ZY. Crystal structure of a photosynthetic LH1-RC in complex with its electron donor HiPIP. Nat Commun 2021; 12:1104. [PMID: 33597527 PMCID: PMC7889895 DOI: 10.1038/s41467-021-21397-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 01/26/2021] [Indexed: 11/12/2022] Open
Abstract
Photosynthetic electron transfers occur through multiple components ranging from small soluble proteins to large integral membrane protein complexes. Co-crystallization of a bacterial photosynthetic electron transfer complex that employs weak hydrophobic interactions was achieved by using high-molar-ratio mixtures of a soluble donor protein (high-potential iron-sulfur protein, HiPIP) with a membrane-embedded acceptor protein (reaction center, RC) at acidic pH. The structure of the co-complex offers a snapshot of a transient bioenergetic event and revealed a molecular basis for thermodynamically unfavorable interprotein electron tunneling. HiPIP binds to the surface of the tetraheme cytochrome subunit in the light-harvesting (LH1) complex-associated RC in close proximity to the low-potential heme-1 group. The binding interface between the two proteins is primarily formed by uncharged residues and is characterized by hydrophobic features. This co-crystal structure provides a model for the detailed study of long-range trans-protein electron tunneling pathways in biological systems. The high potential iron-sulfur (HiPIP) proteins are direct electron donors to the light-harvesting-reaction center complexes (LH1-RC) in photosynthetic β- and γ-Proteobacteria. Here, the authors present the 2.9 Å crystal structure of the HiPIP-bound LH1-RC complex from the thermophilic purple sulfur bacterium Thermochromatium tepidum and discuss mechanistic implications for the electron transfer pathway.
Collapse
Affiliation(s)
| | - Long-Jiang Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
| | - Tai Liang
- Faculty of Science, Ibaraki University, Mito, Japan
| | | | - Michael T Madigan
- Department of Microbiology, Southern Illinois University, Carbondale, IL, USA
| | - Yukihiro Kimura
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, Japan.
| | | |
Collapse
|
13
|
Saini MK, ChihChe W, Soulier N, Sebastian A, Albert I, Thiel V, Bryant DA, Hanada S, Tank M. Caldichromatium japonicum gen. nov., sp. nov., a novel thermophilic phototrophic purple sulphur bacterium of the Chromatiaceae isolated from Nakabusa hot springs, Japan. Int J Syst Evol Microbiol 2020; 70:5701-5710. [PMID: 32931408 DOI: 10.1099/ijsem.0.004465] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A novel thermophilic phototrophic purple sulphur bacterium was isolated from microbial mats (56 °C) at Nakabusa hot springs, Nagano prefecture, Japan. Cells were motile, rod-shaped, stain Gram-negative and stored sulphur globules intracellularly. Bacteriochlorophyll a and carotenoids of the normal spirilloxanthin series were the major pigments. Dense liquid cultures were red in colour. Strain No.7T was able to grow photoautotrophically using sulfide, thiosulfate, sulfite and hydrogen (in the presence of sulfide) as electron donors and bicarbonate as the sole carbon source. Optimum growth occurred under anaerobic conditions in the light at 50 °C (range, 40-56 °C) and pH 7.2 (range, pH 7-8). Major fatty acids were C16 : 0 (46.8 %), C16 : 1 ω7c (19.9 %), C18 : 1 ω7c (21.1 %), C14 : 0 (4.6 %) and C18 : 0 (2.4 %). The polar lipid profile showed phosphatidylglycerol and unidentified aminophospholipids to be the major lipids. The only quinone detected was ubiquinone-8. 16S rRNA gene sequence comparisons indicated that the novel bacterium is only distantly related to Thermochromatium tepidum with a nucleotide identity of 90.4 %. The phylogenetic analysis supported the high novelty of strain No.7T with a long-branching phylogenetic position within the Chromatiaceae next to Thermochromatium tepidum. The genome comprised a circular chromosome of 2.99 Mbp (2 989 870 bp), included no plasmids and had a DNA G+C content of 61.2 mol%. Polyphasic taxonomic analyses of the isolate suggested strain No.7T is a novel genus within the Chromatiaceae. The proposed genus name of the second truly thermophilic purple sulphur bacterium is Caldichromatium gen. nov. with the type species Caldichromatium japonicum sp. nov. (DSM 110881=JCM 39101).
Collapse
Affiliation(s)
- Mohit Kumar Saini
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 1920397, Japan
| | - Weng ChihChe
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 1920397, Japan
| | - Nathan Soulier
- Department of Biochemistry and Molecular Biology, Eberly College of Science, The Pennsylvania State University, PA 16802, USA
| | - Aswathy Sebastian
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Istvan Albert
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.,Department of Biochemistry and Molecular Biology, Eberly College of Science, The Pennsylvania State University, PA 16802, USA
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 1920397, Japan
| | - Donald A Bryant
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.,Department of Biochemistry and Molecular Biology, Eberly College of Science, The Pennsylvania State University, PA 16802, USA
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 1920397, Japan
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 1920397, Japan.,DSMZ - German Culture Collection of Microorganisms and Cell Cultures, GmbH Inhoffenstraße 7B 38124 Braunschweig, Germany
| |
Collapse
|
14
|
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.
Collapse
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
| | | |
Collapse
|
15
|
Quinone transport in the closed light-harvesting 1 reaction center complex from the thermophilic purple bacterium Thermochromatium tepidum. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148307. [PMID: 32926863 DOI: 10.1016/j.bbabio.2020.148307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/03/2020] [Accepted: 09/09/2020] [Indexed: 11/22/2022]
Abstract
Redox-active quinones play essential roles in efficient light energy conversion in type-II reaction centers of purple phototrophic bacteria. In the light-harvesting 1 reaction center (LH1-RC) complex of purple bacteria, QB is converted to QBH2 upon light-induced reduction and QBH2 is transported to the quinone pool in the membrane through the LH1 ring. In the purple bacterium Rhodobacter sphaeroides, the C-shaped LH1 ring contains a gap for quinone transport. In contrast, the thermophilic purple bacterium Thermochromatium (Tch.) tepidum has a closed O-shaped LH1 ring that lacks a gap, and hence the mechanism of photosynthetic quinone transport is unclear. Here we detected light-induced Fourier transform infrared (FTIR) signals responsible for changes of QB and its binding site that accompany photosynthetic quinone reduction in Tch. tepidum and characterized QB and QBH2 marker bands based on their 15N- and 13C-isotopic shifts. Quinone exchanges were monitored using reconstituted photosynthetic membranes comprised of solubilized photosynthetic proteins, membrane lipids, and exogenous ubiquinone (UQ) molecules. In combination with 13C-labeling of the LH1-RC and replacement of native UQ8 by ubiquinones of different tail lengths, we demonstrated that quinone exchanges occur efficiently within the hydrophobic environment of the lipid membrane and depend on the side chain length of UQ. These results strongly indicate that unlike the process in Rba. sphaeroides, quinone transport in Tch. tepidum occurs through the size-restricted hydrophobic channels in the closed LH1 ring and are consistent with structural studies that have revealed narrow hydrophobic channels in the Tch. tepidum LH1 transmembrane region.
Collapse
|
16
|
Seto R, Takaichi S, Kurihara T, Kishi R, Honda M, Takenaka S, Tsukatani Y, Madigan MT, Wang-Otomo ZY, Kimura Y. Lycopene-Family Carotenoids Confer Thermostability on Photocomplexes from a New Thermophilic Purple Bacterium. Biochemistry 2020; 59:2351-2358. [DOI: 10.1021/acs.biochem.0c00192] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ryuta Seto
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe 657-8501, Japan
| | - Shinichi Takaichi
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | | | - Rikako Kishi
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe 657-8501, Japan
| | - Mai Honda
- Faculty of Science, Ibaraki University, Mito 310-8512, Japan
| | - Shinji Takenaka
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe 657-8501, 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 237-0061, Japan
| | - Michael T. Madigan
- Department of Microbiology, Southern Illinois University, Carbondale, Illinois 62901, United States
| | | | - Yukihiro Kimura
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe 657-8501, Japan
| |
Collapse
|
17
|
Takaichi S, Okoshi A, Otomo S, Misumi M, Sonoike K, Harada J. Direct injection of pigment-protein complexes and membrane fragments suspended in water from phototrophs to C 18 HPLC. PHOTOSYNTHESIS RESEARCH 2020; 144:101-107. [PMID: 32198677 DOI: 10.1007/s11120-020-00735-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/12/2020] [Indexed: 06/10/2023]
Abstract
We discovered that pigments including carotenoids and (bacterio)chlorophylls in pigment-protein complexes, membrane fragments, and chlorosomes suspended in water could be injected directly into C18 HPLC and analyzed without any other treatments. We applied this method to LH1-RC and chromatophores of purple bacteria, chlorosomes of green sulfur bacteria, thylakoid membranes of cyanobacteria, and PSII and thylakoid membranes of spinach. HPLC elution profiles and pigment composition were the same as those of the conventional extraction method. The principle of this method might be that samples are first trapped on top of column, followed by the immediate extraction of the pigments with the HPLC eluent and their separation using the C18 column, as usual. In the conventional extraction method, pigments are first extracted with organic solvents, followed by evaporation of the solvents. The dried pigments are then dissolved in organic solvents and injected into C18 HPLC after filtration. The advantages of this method include the preventions of pigment isomerization and oxidation and the possibility of injecting all samples. Its drawbacks include the accumulation of denatured proteins at the top of column, causing increased HPLC pressure. The use of a guard column might solve this problem. Many factors, such as samples, column, and HPLC systems, may affect this method. Nevertheless, we think that some samples can be analyzed using this method.
Collapse
Affiliation(s)
- Shinichi Takaichi
- Department of Molecular Microbiology, Faculty of Science, Tokyo University of Agriculture, Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan.
| | - Akira Okoshi
- Faculty of Science, Ibaraki University, Mito, 310-8512, Japan
| | - Seiu Otomo
- Faculty of Science, Ibaraki University, Mito, 310-8512, Japan
| | - Masahiro Misumi
- Faculty of Education and Integrated Arts and Sciences, Waseda University, Wakamatsu, Shinjuku, Tokyo, 162-8480, Japan
| | - Kintake Sonoike
- Faculty of Education and Integrated Arts and Sciences, Waseda University, Wakamatsu, Shinjuku, Tokyo, 162-8480, Japan
| | - Jiro Harada
- Department of Biochemistry, Kurume University School of Medicine, Kurume, Fukuoka, 830-0011, Japan
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Nagatsuma S, Gotou K, Yamashita T, Yu LJ, Shen JR, Madigan M, Kimura Y, Wang-Otomo ZY. Phospholipid distributions in purple phototrophic bacteria and LH1-RC core complexes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:461-468. [DOI: 10.1016/j.bbabio.2019.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/06/2019] [Accepted: 04/07/2019] [Indexed: 02/06/2023]
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Kimura Y, Hashimoto K, Akimoto S, Takenouchi M, Suzuki K, Kishi R, Imanishi M, Takenaka S, Madigan MT, Nagashima KVP, Wang-Otomo ZY. Biochemical and Spectroscopic Characterizations of a Hybrid Light-Harvesting Reaction Center Core Complex. Biochemistry 2018; 57:4496-4503. [PMID: 29965735 DOI: 10.1021/acs.biochem.8b00644] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The light-harvesting 1 reaction center (LH1-RC) complex from Thermochromatium tepidum exhibits a largely red-shifted LH1 Q y absorption at 915 nm due to binding of Ca2+, resulting in an "uphill" energy transfer from LH1 to the reaction center (RC). In a recent study, we developed a heterologous expression system (strain TS2) to construct a functional hybrid LH1-RC with LH1 from Tch. tepidum and the RC from Rhodobacter sphaeroides [Nagashima, K. V. P., et al. (2017) Proc. Natl. Acad. Sci. U. S. A. 114, 10906]. Here, we present detailed characterizations of the hybrid LH1-RC from strain TS2. Effects of metal cations on the phototrophic growth of strain TS2 revealed that Ca2+ is an indispensable element for its growth, which is also true for Tch. tepidum but not for Rba. sphaeroides. The thermal stability of the TS2 LH1-RC was strongly dependent on Ca2+ in a manner similar to that of the native Tch. tepidum, but interactions between the heterologous LH1 and RC became relatively weaker in strain TS2. A Fourier transform infrared analysis demonstrated that the Ca2+-binding site of TS2 LH1 was similar but not identical to that of Tch. tepidum. Steady-state and time-resolved fluorescence measurements revealed that the uphill energy transfer rate from LH1 to the RC was related to the energy gap in an order of Rba. sphaeroides, Tch. tepidum, and strain TS2; however, the quantum yields of LH1 fluorescence did not exhibit such a correlation. On the basis of these findings, we discuss the roles of Ca2+, interactions between LH1 and the RC from different species, and the uphill energy transfer mechanisms.
Collapse
Affiliation(s)
- Yukihiro Kimura
- Department of Agrobioscience, Graduate School of Agriculture , Kobe University , Nada, Kobe 657-8501 , Japan
| | - Kanako Hashimoto
- Department of Agrobioscience, Graduate School of Agriculture , Kobe University , Nada, Kobe 657-8501 , Japan
| | - Seiji Akimoto
- Department of Science, Graduate School of Science , Kobe University , Nada, Kobe 657-8501 , Japan
| | - Mizuki Takenouchi
- Faculty of Science , Ibaraki University , Bunkyo, Mito 310-8512 , Japan
| | - Kengo Suzuki
- Hamamatsu Photonics K. K. , Joko-cho, Hamamatsu 431-3196 , Japan
| | - Rikako Kishi
- Department of Agrobioscience, Graduate School of Agriculture , Kobe University , Nada, Kobe 657-8501 , Japan
| | - Michie Imanishi
- Department of Agrobioscience, Graduate School of Agriculture , Kobe University , Nada, Kobe 657-8501 , Japan
| | - Shinji Takenaka
- Department of Agrobioscience, Graduate School of Agriculture , Kobe University , Nada, Kobe 657-8501 , Japan
| | - Michael T Madigan
- Department of Microbiology , Southern Illinois University , Carbondale , Illinois 62901 , United States
| | - Kenji V P Nagashima
- Research Institute for Photobiological Hydrogen Production , Kanagawa University , Tsuchiya, Hiratsuka 259-1293 , Japan
| | | |
Collapse
|
22
|
Probing structure-function relationships in early events in photosynthesis using a chimeric photocomplex. Proc Natl Acad Sci U S A 2017; 114:10906-10911. [PMID: 28935692 DOI: 10.1073/pnas.1703584114] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The native core light-harvesting complex (LH1) from the thermophilic purple phototrophic bacterium Thermochromatium tepidum requires Ca2+ for its thermal stability and characteristic absorption maximum at 915 nm. To explore the role of specific amino acid residues of the LH1 polypeptides in Ca-binding behavior, we constructed a genetic system for heterologously expressing the Tch. tepidum LH1 complex in an engineered Rhodobacter sphaeroides mutant strain. This system contained a chimeric pufBALM gene cluster (pufBA from Tch. tepidum and pufLM from Rba. sphaeroides) and was subsequently deployed for introducing site-directed mutations on the LH1 polypeptides. All mutant strains were capable of phototrophic (anoxic/light) growth. The heterologously expressed Tch. tepidum wild-type LH1 complex was isolated in a reaction center (RC)-associated form and displayed the characteristic absorption properties of this thermophilic phototroph. Spheroidene (the major carotenoid in Rba. sphaeroides) was incorporated into the Tch. tepidum LH1 complex in place of its native spirilloxanthins with one carotenoid molecule present per αβ-subunit. The hybrid LH1-RC complexes expressed in Rba. sphaeroides were characterized using absorption, fluorescence excitation, and resonance Raman spectroscopy. Site-specific mutagenesis combined with spectroscopic measurements revealed that α-D49, β-L46, and a deletion at position 43 of the α-polypeptide play critical roles in Ca binding in the Tch. tepidum LH1 complex; in contrast, α-N50 does not participate in Ca2+ coordination. These findings build on recent structural data obtained from a high-resolution crystallographic structure of the membrane integrated Tch. tepidum LH1-RC complex and have unambiguously identified the location of Ca2+ within this key antenna complex.
Collapse
|