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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.
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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.
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2
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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.
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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.
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3
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Bedard DL, Van Slyke G, Nübel U, Bateson MM, Brumfield S, An YJ, Becraft ED, Wood JM, Thiel V, Ward DM. Geographic and Ecological Diversity of Green Sulfur Bacteria in Hot Spring Mat Communities. Microorganisms 2023; 11:2921. [PMID: 38138064 PMCID: PMC10746008 DOI: 10.3390/microorganisms11122921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Three strains of thermophilic green sulfur bacteria (GSB) are known; all are from microbial mats in hot springs in Rotorua, New Zealand (NZ) and belong to the species Chlorobaculum tepidum. Here, we describe diverse populations of GSB inhabiting Travel Lodge Spring (TLS) (NZ) and hot springs ranging from 36.1 °C to 51.1 °C in the Republic of the Philippines (PHL) and Yellowstone National Park (YNP), Wyoming, USA. Using targeted amplification and restriction fragment length polymorphism analysis, GSB 16S rRNA sequences were detected in mats in TLS, one PHL site, and three regions of YNP. GSB enrichments from YNP and PHL mats contained small, green, nonmotile rods possessing chlorosomes, chlorobactene, and bacteriochlorophyll c. Partial 16S rRNA gene sequences from YNP, NZ, and PHL mats and enrichments from YNP and PHL samples formed distinct phylogenetic clades, suggesting geographic isolation, and were associated with samples differing in temperature and pH, suggesting adaptations to these parameters. Sequences from enrichments and corresponding mats formed clades that were sometimes distinct, increasing the diversity detected. Sequence differences, monophyly, distribution patterns, and evolutionary simulation modeling support our discovery of at least four new putative moderately thermophilic Chlorobaculum species that grew rapidly at 40 °C to 44 °C.
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Affiliation(s)
- Donna L. Bedard
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; (D.L.B.); (G.V.S.)
| | - Greta Van Slyke
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; (D.L.B.); (G.V.S.)
| | - Ulrich Nübel
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA; (U.N.); (M.M.B.); (E.D.B.); (J.M.W.)
- Leibniz-Institute DSMZ German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany;
| | - Mary M. Bateson
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA; (U.N.); (M.M.B.); (E.D.B.); (J.M.W.)
| | - Sue Brumfield
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA;
| | - Yong Jun An
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; (D.L.B.); (G.V.S.)
| | - Eric D. Becraft
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA; (U.N.); (M.M.B.); (E.D.B.); (J.M.W.)
- Department of Biology, University of North Alabama, Florence, AL 35632, USA
| | - Jason M. Wood
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA; (U.N.); (M.M.B.); (E.D.B.); (J.M.W.)
- Research Informatics Core, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Vera Thiel
- Leibniz-Institute DSMZ German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany;
| | - David M. Ward
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA; (U.N.); (M.M.B.); (E.D.B.); (J.M.W.)
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Morimoto M, Hirao H, Kondo M, Dewa T, Kimura Y, Wang-Otomo ZY, Asakawa H, Saga Y. Atomic force microscopic analysis of the light-harvesting complex 2 from purple photosynthetic bacterium Thermochromatium tepidum. PHOTOSYNTHESIS RESEARCH 2023:10.1007/s11120-023-01010-4. [PMID: 36930432 DOI: 10.1007/s11120-023-01010-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Structural information on the circular arrangements of repeating pigment-polypeptide subunits in antenna proteins of purple photosynthetic bacteria is a clue to a better understanding of molecular mechanisms for the ring-structure formation and efficient light harvesting of such antennas. Here, we have analyzed the ring structure of light-harvesting complex 2 (LH2) from the thermophilic purple bacterium Thermochromatium tepidum (tepidum-LH2) by atomic force microscopy. The circular arrangement of the tepidum-LH2 subunits was successfully visualized in a lipid bilayer. The average top-to-top distance of the ring structure, which is correlated with the ring size, was 4.8 ± 0.3 nm. This value was close to the top-to-top distance of the octameric LH2 from Phaeospirillum molischianum (molischianum-LH2) by the previous analysis. Gaussian distribution of the angles of the segments consisting of neighboring subunits in the ring structures of tepidum-LH2 yielded a median of 44°, which corresponds to the angle for the octameric circular arrangement (45°). These results indicate that tepidum-LH2 has a ring structure consisting of eight repeating subunits. The coincidence of an octameric ring structure of tepidum-LH2 with that of molischianum-LH2 is consistent with the homology of amino acid sequences of the polypeptides between tepidum-LH2 and molischianum-LH2.
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Affiliation(s)
- Masayuki Morimoto
- Nanomaterials Research Institute (NanoMaRi), Kanazawa University, Kanazawa, 920-1192, Japan
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Haruna Hirao
- Faculty of Science and Engineering, Kindai University, Higashi-Osaka, Osaka, 577-8502, Japan
| | - Masaharu Kondo
- Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, 466-8555, Japan
| | - Takehisa Dewa
- Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, 466-8555, Japan
| | - Yukihiro Kimura
- Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
| | | | - Hitoshi Asakawa
- Nanomaterials Research Institute (NanoMaRi), Kanazawa University, Kanazawa, 920-1192, Japan.
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, 920-1192, Japan.
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, 920-1192, Japan.
| | - Yoshitaka Saga
- Faculty of Science and Engineering, Kindai University, Higashi-Osaka, Osaka, 577-8502, Japan.
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5
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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: 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.
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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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6
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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.
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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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8
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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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9
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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.
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10
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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.
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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
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11
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Bolshakov MA, Ashikhmin AA, Makhneva ZK, Moskalenko AA. Inhibition of Carotenoid Biosynthesis in LH2 and LH1-RC Pigment-Protein Complexes of a Purple Sulfur Bacterium Thermochromatium tepidum. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721060047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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12
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Nagashima KVP, Nagashima S, Kitashima M, Inoue K, Madigan MT, Kimura Y, Wang-Otomo ZY. Photosynthetic Growth and Energy Conversion in an Engineered Phototroph Containing Thermochromatium tepidum Light-Harvesting Complex 1 and the Rhodobacter sphaeroides Reaction Center Complex. Biochemistry 2021; 60:2685-2690. [PMID: 34448581 DOI: 10.1021/acs.biochem.1c00462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Light-harvesting complex 1 (LH1) of the thermophilic purple sulfur bacterium Thermochromatium tepidum can be expressed in the purple non-sulfur bacterium Rhodobacter sphaeroides and forms a functional RC-LH1 complex with the native Rba. sphaeroides reaction center (Nagashima, K. V. P., et al. Proc. Natl. Acad. Sci. U. S. A. 2017, 114, 10906-10911). Although there is a large uphill energy gap between Tch. tepidum LH1 and the Rba. sphaeroides RC in this chimeric complex, it has been shown that light energy can be transferred, consistent with that seen in the native Rba. sphaeroides RC-LH1 complex. In this study, the contribution of this chimeric complex to growth and photosynthetic energy conversion in the hybrid organism was quantified. The mutant synthesizing this chimeric complex was grown phototrophically under 940 nm light-emitting diode (LED) light preferentially absorbed by Tch. tepidum LH1 and showed faster growth at low intensities of this wavelength than both a mutant strain of Rba. sphaeroides lacking LH2 and a mutant lacking all light-harvesting complexes. When grown with 850 nm LED light, the strain containing the native Rba. sphaeroides LH1-RC grew faster than the chimeric strain. Electron transfer from the RC to the membrane-integrated cytochrome bc1 complex was also estimated by flash-induced absorption changes in heme b. The rate of ubiquinone transport through the LH1 ring structure in the chimeric strain was virtually the same as that in native Rba. sphaeroides. We conclude that Tch. tepidum LH1 can perform the physiological functions of native LH1 in Rba. sphaeroides.
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Affiliation(s)
- Kenji V P Nagashima
- Research Institute for Integrated Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan
| | - Sakiko Nagashima
- Research Institute for Integrated Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan
| | - Masaharu Kitashima
- Department of Biological Sciences, Faculty of Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan
| | - Kazuhito Inoue
- Research Institute for Integrated Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan.,Department of Biological Sciences, Faculty of Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293, 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
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13
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Fujii S, Kobayashi S, Yoshimi T, Kobayashi Y, Wakai S, Yamanaka M, Sambongi Y. Thermal stability tuning without affecting gas-binding function of Thermochromatium tepidum cytochrome c'. Biosci Biotechnol Biochem 2021; 85:1846-1852. [PMID: 34124760 DOI: 10.1093/bbb/zbab108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/07/2021] [Indexed: 12/17/2022]
Abstract
Hydrogenophilus thermoluteolus, Thermochromatium tepidum, and Allochromatium vinosum, which grow optimally at 52, 49, and 25 °C, respectively, have homologous cytochromes c' (PHCP, TTCP, and AVCP, respectively) exhibiting at least 50% amino acid sequence identity. Here, the thermal stability of the recombinant TTCP protein was first confirmed to be between those of PHCP and AVCP. Structure comparison of the 3 proteins and a mutagenesis study on TTCP revealed that hydrogen bonds and hydrophobic interactions between the heme and amino acid residues were responsible for their stability differences. In addition, PHCP, TTCP, and AVCP and their variants with altered stability similarly bound nitric oxide and carbon oxide, but not oxygen. Therefore, the thermal stability of TTCP together with PHCP and AVCP can be tuned through specific interactions around the heme without affecting their gas-binding function. These cytochromes c' will be useful as specific gas sensor proteins exhibiting a wide thermal stability range.
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Affiliation(s)
- Sotaro Fujii
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Satoru Kobayashi
- Graduate School of Biosphere Science, Hiroshima University, Hiroshima, Japan
| | - Taisuke Yoshimi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Yuji Kobayashi
- Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Satoshi Wakai
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research, Japan Agency for Marine-Earth Science and Technology, Kanagawa, Japan
| | - Masaru Yamanaka
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Yoshihiro Sambongi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
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14
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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.
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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.
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15
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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).
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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
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16
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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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17
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Kangur L, Rätsep M, Timpmann K, Wang-Otomo ZY, Freiberg A. The two light-harvesting membrane chromoproteins of Thermochromatium tepidum expose distinct robustness against temperature and pressure. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148205. [PMID: 32305413 DOI: 10.1016/j.bbabio.2020.148205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/17/2020] [Accepted: 04/14/2020] [Indexed: 01/26/2023]
Abstract
An increased robustness against high temperature and the much red-shifted near-infrared absorption spectrum of excitons in the LH1-RC core pigment-protein complex from the thermophilic photosynthetic purple sulfur bacterium Thermochromatium tepidum has recently attracted much interest. In the present work, thermal and hydrostatic pressure stability of the peripheral LH2 and core LH1-RC complexes from this bacterium were in parallel investigated by various optical spectroscopy techniques applied over a wide spectral range from far-ultraviolet to near-infrared. In contrast to expectations, very distinct robustness of the complexes was established, while the sturdiness of LH2 surpassed that of LH1-RC both with respect to temperatures between 288 and 360 K, and pressures between 1 bar and 14 kbar. Subtle structural variances related to the hydrogen bond network are likely responsible for the extra stability of LH2.
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Affiliation(s)
- Liina Kangur
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411 Tartu, Estonia
| | - Margus Rätsep
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411 Tartu, Estonia
| | - Kõu Timpmann
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411 Tartu, Estonia
| | | | - Arvi Freiberg
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411 Tartu, Estonia; Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia; Estonian Academy of Sciences, Kohtu 6, 10130 Tallinn, Estonia.
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18
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Blastochloris tepida, sp. nov., a thermophilic species of the bacteriochlorophyll b-containing genus Blastochloris. Arch Microbiol 2019; 201:1351-1359. [PMID: 31317227 DOI: 10.1007/s00203-019-01701-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/01/2019] [Accepted: 07/03/2019] [Indexed: 10/26/2022]
Abstract
A new taxon is created for the thermophilic purple nonsulfur bacterium previously designated as Rhodopseudomonas strain GI. Strain GI was isolated from a New Mexico (USA) hot spring microbial mat and grows optimally above 40 °C and to a maximum of 47 °C. Strain GI is a bacteriochlorophyll b-containing species of purple nonsulfur bacteria and displays a budding morphology, typical of species of the genus Blastochloris. Although resembling the species Blc. viridis in many respects, the absorption spectrum, carotenoid content, and lipid fatty acid profile of strain GI is distinct from that of Blc. viridis strain DSM133T and other recognized Blastochloris species. Strain GI forms its own subclade within the Blastochloris clade of purple nonsulfur bacteria based on comparative 16S rRNA gene sequences, and its genome is significantly larger than that of strain DSM133T; average nucleotide identity between the genomes of Blc. viridis and strain GI was below 85%. Moreover, concatenated sequence analyses of PufLM and DnaK clearly showed strain GI to be distinct from both Blc. viridis and Blc. sulfoviridis. Because of its unique assortment of properties, it is proposed to classify strain GI as a new species of the genus Blastochloris, as Blc. tepida, sp.n., with strain GIT designated as the type strain (= ATCC TSD-138 = DSM 106918).
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19
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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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20
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Niedzwiedzki DM, Gardiner AT, Blankenship RE, Cogdell RJ. Energy transfer in purple bacterial photosynthetic units from cells grown in various light intensities. PHOTOSYNTHESIS RESEARCH 2018; 137:389-402. [PMID: 29725994 DOI: 10.1007/s11120-018-0512-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/23/2018] [Indexed: 06/08/2023]
Abstract
Three photosynthetic membranes, called intra-cytoplasmic membranes (ICMs), from wild-type and the ∆pucBAabce mutant of the purple phototrophic bacterium Rps. palustris were investigated using optical spectroscopy. The ICMs contain identical light-harvesting complex 1-reaction centers (LH1-RC) but have various spectral forms of light-harvesting complex 2 (LH2). Spectroscopic studies involving steady-state absorption, fluorescence, and femtosecond time-resolved absorption at room temperature and at 77 K focused on inter-protein excitation energy transfer. The studies investigated how energy transfer is affected by altered spectral features of the LH2 complexes as those develop under growth at different light conditions. The study shows that LH1 → LH2 excitation energy transfer is strongly affected if the LH2 complex alters its spectroscopic signature. The LH1 → LH2 excitation energy transfer rate modeled with the Förster mechanism and kinetic simulations of transient absorption of the ICMs demonstrated that the transfer rate will be 2-3 times larger for ICMs accumulating LH2 complexes with the classical B800-850 spectral signature (grown in high light) compared to the ICMs from the same strain grown in low light. For the ICMs from the ∆pucBAabce mutant, in which the B850 band of the LH2 complex is blue-shifted and almost degenerate with the B800 band, the LH1 → LH2 excitation energy transfer was not observed nor predicted by calculations.
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Affiliation(s)
- Dariusz M Niedzwiedzki
- Photosynthetic Antenna Research Center, University in St Louis, Campus Box 1138, St. Louis, MO, 63130, USA.
| | - Alastair T Gardiner
- Davidson Building, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Robert E Blankenship
- Photosynthetic Antenna Research Center, University in St Louis, Campus Box 1138, St. Louis, MO, 63130, USA
- Department of Biology, Washington University in St Louis, St. Louis, MO, 63130, USA
- Department of Chemistry, Washington University in St Louis, St. Louis, MO, 63130, USA
| | - Richard J Cogdell
- Davidson Building, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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21
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Dai L, Tan LM, Jiang YL, Shi Y, Wang P, Zhang JP, Otomo ZY. Orientation assignment of LH2 and LH1-RC complexes from Thermochromatium tepidum reconstituted in PC liposome and their ultrafast excitation dynamics comparison between in artificial and in natural chromatophores. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.05.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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22
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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.
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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
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23
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Bol’shakov MA, Ashikhmin AA, Makhneva ZK, Moskalenko AA. Effect of Light with Different Spectral Composition on Cell Growth and Pigment Composition of the Membranes of Purple Sulfur Bacteria Allochromatium minutissimum and Allochromatium vinosum. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718020042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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24
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Kimura Y, Kawakami T, Arikawa T, Li Y, Yu LJ, Ohno T, Madigan MT, Wang-Otomo ZY. C-terminal cleavage of the LH1 α-polypeptide in the Sr 2+-cultured Thermochromatium tepidum. PHOTOSYNTHESIS RESEARCH 2018; 135:23-31. [PMID: 28493058 DOI: 10.1007/s11120-017-0393-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/02/2017] [Indexed: 06/07/2023]
Abstract
The light-harvesting 1 reaction center (LH1-RC) complex in the thermophilic purple sulfur bacterium Thermochromatium (Tch.) tepidum binds Ca ions as cofactors, and Ca-binding is largely involved in its characteristic Q y absorption at 915 nm and enhanced thermostability. Ca2+ can be biosynthetically replaced by Sr2+ in growing cultures of Tch. tepidum. However, the resulting Sr2+-substituted LH1-RC complexes in such cells do not display the absorption maximum and thermostability of those from Ca2+-grown cells, signaling that inherent structural differences exist in the LH1 complexes between the Ca2+- and Sr2+-cultured cells. In this study, we examined the effects of the biosynthetic Sr2+-substitution and limited proteolysis on the spectral properties and thermostability of the Tch. tepidum LH1-RC complex. Preferential truncation of two consecutive, positively charged Lys residues at the C-terminus of the LH1 α-polypeptide was observed for the Sr2+-cultured cells. A proportion of the truncated LH1 α-polypeptide increased during repeated subculturing in the Sr2+-substituted medium. This result suggests that the truncation is a biochemical adaptation to reduce the electrostatic interactions and/or steric repulsion at the C-terminus when Sr2+ substitutes for Ca2+ in the LH1 complex. Limited proteolysis of the native Ca2+-LH1 complex with lysyl protease revealed selective truncations at the Lys residues in both C- and N-terminal extensions of the α- and β-polypeptides. The spectral properties and thermostability of the partially digested native LH1-RC complexes were similar to those of the biosynthetically Sr2+-substituted LH1-RC complexes in their Ca2+-bound forms. Based on these findings, we propose that the C-terminal domain of the LH1 α-polypeptide plays important roles in retaining proper structure and function of the LH1-RC complex in Tch. tepidum.
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Affiliation(s)
- 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
| | - Yong Li
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, 657-8501, Japan
| | - Long-Jiang Yu
- Faculty of Science, Ibaraki University, Mito, 310-8512, Japan
| | - Takashi Ohno
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, 657-8501, Japan
| | - Michael T Madigan
- Department of Microbiology, Southern Illinois University, Carbondale, IL, 62901, USA
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25
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Rätsep M, Timpmann K, Kawakami T, Wang-Otomo ZY, Freiberg A. Spectrally Selective Spectroscopy of Native Ca-Containing and Ba-Substituted LH1-RC Core Complexes from Thermochromatium tepidum. J Phys Chem B 2017; 121:10318-10326. [PMID: 29058423 DOI: 10.1021/acs.jpcb.7b07841] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The LH1-RC core complex from the thermophilic photosynthetic purple sulfur bacterium Thermochromatium tepidum has recently attracted interest of many researchers because of its several unique properties, such as increased robustness against environmental hardships and the much red-shifted near-infrared absorption spectrum of the LH1 antenna exciton polarons. The known near-atomic-resolution crystal structure of the complex well supported this attention. Yet several mechanistic aspects of the complex prominence remained to be understood. In this work, samples of the native, Ca2+-containing core complexes were investigated along with those destabilized by Ba2+ substitution, using various spectrally selective steady-state and picosecond time-resolved spectroscopic techniques at physiological and cryogenic temperatures. As a result, the current interpretation of exciton spectra of the complex was significantly clarified. Specifically, by evaluating the homogeneous and inhomogeneous compositions of the spectra, we showed that there is little to no effect of cation substitution on the dynamic or kinetic properties of antenna excitons. Reasons of the extra red shift of absorption/fluorescence spectra observed in the Ca-LH1-RC and not in the Ba-LH1-RC complex should thus be searched in subtle structural differences following the inclusion of different cations into the core complex scaffold.
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Affiliation(s)
- Margus Rätsep
- Institute of Physics, University of Tartu , W. Ostwald Str. 1, 50411 Tartu, Estonia
| | - Kõu Timpmann
- Institute of Physics, University of Tartu , W. Ostwald Str. 1, 50411 Tartu, Estonia
| | | | | | - Arvi Freiberg
- Institute of Physics, University of Tartu , W. Ostwald Str. 1, 50411 Tartu, Estonia.,Institute of Molecular and Cell Biology, University of Tartu , Riia 23, 51010 Tartu, Estonia
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26
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Heterologous Production of the Photosynthetic Reaction Center and Light Harvesting 1 Complexes of the Thermophile Thermochromatium tepidum in the Mesophile Rhodobacter sphaeroides and Thermal Stability of a Hybrid Core Complex. Appl Environ Microbiol 2017; 83:AEM.01481-17. [PMID: 28821545 DOI: 10.1128/aem.01481-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/11/2017] [Indexed: 11/20/2022] Open
Abstract
The photosynthetic complexes of the thermophile Thermochromatium tepidum are of considerable interest in biohybrid solar cell applications because of the ability of thermophilic proteins to tolerate elevated temperatures. Synthetic operons encoding reaction center (RC) and light harvesting 1 (LH1) pigment-protein complexes of T. tepidum were expressed in the mesophile Rhodobacter sphaeroides The T. tepidum RC (TRC) was assembled and was found to be functional with the addition of menadione to populate the QA pocket. The production of T. tepidum LH1 (TLH1) was increased by selection of a phototrophy-capable mutant after UV irradiation mutagenesis, which yielded a hybrid RC-TLH1 core complex consisting of the R. sphaeroides RC and T. tepidum TLH1, confirmed by the absorbance peak of TLH1 at 915 nm. Affinity chromatography partial purification and subsequent sucrose gradient analysis of the hybrid RC-TLH1 core complex indicated that this core complex assembled as a monomer. Furthermore, the RC-TLH1 hybrid core complex was more tolerant of a temperature of 70°C than the R. sphaeroides RC-LH1 core complexes in both the dimeric and monomeric forms; after 1 h, the hybrid complex retained 58% of the initial starting value, compared to values of 11% and 53% for the R. sphaeroides RC-LH1 dimer and monomer forms, respectively.IMPORTANCE This work is important because it is a new approach to bioengineering of photosynthesis proteins for potential use in biophotovoltaic solar energy capture. The work establishes a proof of principle for future biohybrid solar cell applications.
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27
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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.
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28
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Swainsbury DJK, Martin EC, Vasilev C, Parkes-Loach PS, Loach PA, Neil Hunter C. Engineering of a calcium-ion binding site into the RC-LH1-PufX complex of Rhodobacter sphaeroides to enable ion-dependent spectral red-shifting. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:927-938. [PMID: 28826909 PMCID: PMC5604489 DOI: 10.1016/j.bbabio.2017.08.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/02/2017] [Accepted: 08/17/2017] [Indexed: 01/01/2023]
Abstract
The reaction centre-light harvesting 1 (RC-LH1) complex of Thermochromatium (Tch.) tepidum has a unique calcium-ion binding site that enhances thermal stability and red-shifts the absorption of LH1 from 880nm to 915nm in the presence of calcium-ions. The LH1 antenna of mesophilic species of phototrophic bacteria such as Rhodobacter (Rba.) sphaeroides does not possess such properties. We have engineered calcium-ion binding into the LH1 antenna of Rba. sphaeroides by progressively modifying the native LH1 polypeptides with sequences from Tch. tepidum. We show that acquisition of the C-terminal domains from LH1 α and β of Tch. tepidum is sufficient to activate calcium-ion binding and the extent of red-shifting increases with the proportion of Tch. tepidum sequence incorporated. However, full exchange of the LH1 polypeptides with those of Tch. tepidum results in misassembled core complexes. Isolated α and β polypeptides from our most successful mutant were reconstituted in vitro with BChl a to form an LH1-type complex, which was stabilised 3-fold by calcium-ions. Additionally, carotenoid specificity was changed from spheroidene found in Rba. sphaeroides to spirilloxanthin found in Tch. tepidum, with the latter enhancing in vitro formation of LH1. These data show that the C-terminal LH1 α/β domains of Tch. tepidum behave autonomously, and are able to transmit calcium-ion induced conformational changes to BChls bound to the rest of a foreign antenna complex. Thus, elements of foreign antenna complexes, such as calcium-ion binding and blue/red switching of absorption, can be ported into Rhodobacter sphaeroides using careful design processes.
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Affiliation(s)
- David J K Swainsbury
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, United Kingdom.
| | - Elizabeth C Martin
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, United Kingdom
| | - Cvetelin Vasilev
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, United Kingdom
| | - Pamela S Parkes-Loach
- Department of Molecular Biosciences, Northwestern University, Hogan 2100, 2205 Tech Drive, Evanston, IL 60208, United States
| | - Paul A Loach
- Department of Molecular Biosciences, Northwestern University, Hogan 2100, 2205 Tech Drive, Evanston, IL 60208, United States
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, United Kingdom
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29
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Kimura Y, Lyu S, Okoshi A, Okazaki K, Nakamura N, Ohashi A, Ohno T, Kobayashi M, Imanishi M, Takaichi S, Madigan MT, Wang-Otomo ZY. Effects of Calcium Ions on the Thermostability and Spectroscopic Properties of the LH1-RC Complex from a New Thermophilic Purple Bacterium Allochromatium tepidum. J Phys Chem B 2017; 121:5025-5032. [DOI: 10.1021/acs.jpcb.7b03341] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yukihiro Kimura
- Department
of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe 657-8501, Japan
| | - Shuwen Lyu
- Department
of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe 657-8501, Japan
| | - Akira Okoshi
- Faculty
of Science, Ibaraki University, Mito 310-8512, Japan
| | - Koudai Okazaki
- Faculty
of Science, Ibaraki University, Mito 310-8512, Japan
| | | | - Akira Ohashi
- Faculty
of Science, Ibaraki University, Mito 310-8512, Japan
| | - Takashi Ohno
- Department
of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe 657-8501, Japan
| | - Manami Kobayashi
- 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
| | - Shinichi Takaichi
- Department
of Biology, Nippon Medical School, Kyonan-cho, Musashino, Tokyo 180-0023, Japan
| | - Michael T. Madigan
- Department
of Microbiology, Southern Illinois University, Carbondale, Illinois 62901, United States
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30
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Shi Y, Yu J, Yu LJ, Wang P, Fu LM, Zhang JP, Wang-Otomo ZY. Dependence of the hydration status of bacterial light-harvesting complex 2 on polyol cosolvents. Photochem Photobiol Sci 2017; 16:795-807. [DOI: 10.1039/c6pp00270f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tch. tepidumLH2 hydration correlates with water activity in water–polyol binary solvents as sensitively probed by near infrared electronic spectra and characteristic triplet carotenoid–bacteriochlorophyll interaction bands.
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Affiliation(s)
- Ying Shi
- Department of Chemistry
- Renmin University of China
- Beijing 1000872
- P. R. China
| | - Jie Yu
- Department of Chemistry
- Renmin University of China
- Beijing 1000872
- P. R. China
| | - Long-Jiang Yu
- Faculty of Science
- Ibaraki University
- Mito 310-8512
- Japan
| | - Peng Wang
- Department of Chemistry
- Renmin University of China
- Beijing 1000872
- P. R. China
| | - Li-Min Fu
- Department of Chemistry
- Renmin University of China
- Beijing 1000872
- P. R. China
| | - Jian-Ping Zhang
- Department of Chemistry
- Renmin University of China
- Beijing 1000872
- P. R. China
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31
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Kimura Y, Yura Y, Hayashi Y, Li Y, Onoda M, Yu LJ, Wang-Otomo ZY, Ohno T. Spectroscopic and Thermodynamic Characterization of the Metal-Binding Sites in the LH1–RC Complex from Thermophilic Photosynthetic Bacterium Thermochromatium tepidum. J Phys Chem B 2016; 120:12466-12473. [DOI: 10.1021/acs.jpcb.6b10068] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Yukihiro Kimura
- Graduate
School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Yuki Yura
- Graduate
School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Yusuke Hayashi
- Graduate
School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Yong Li
- Graduate
School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Moe Onoda
- Graduate
School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Long-Jiang Yu
- Graduate
School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | | | - Takashi Ohno
- Graduate
School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
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32
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Yu LJ, Kawakami T, Kimura Y, Wang-Otomo ZY. Structural Basis for the Unusual Q y Red-Shift and Enhanced Thermostability of the LH1 Complex from Thermochromatium tepidum. Biochemistry 2016; 55:6495-6504. [PMID: 27933779 DOI: 10.1021/acs.biochem.6b00742] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While the majority of the core light-harvesting complexes (LH1) in purple photosynthetic bacteria exhibit a Qy absorption band in the range of 870-890 nm, LH1 from the thermophilic bacterium Thermochromatium tepidum displays the Qy band at 915 nm with an enhanced thermostability. These properties are regulated by Ca2+ ions. Substitution of the Ca2+ with other divalent metal ions results in a complex with the Qy band blue-shifted to 880-890 nm and a reduced thermostability. Following the recent publication of the structure of the Ca-bound LH1-reaction center (RC) complex [Niwa, S., et al. (2014) Nature 508, 228], we have determined the crystal structures of the Sr- and Ba-substituted LH1-RC complexes with the LH1 Qy band at 888 nm. Sixteen Sr2+ and Ba2+ ions are identified in the LH1 complexes. Both Sr2+ and Ba2+ are located at the same positions, and these are clearly different from, though close to, the Ca2+-binding sites. Conformational rearrangement induced by the substitution is limited to the metal-binding sites. Unlike the Ca-LH1-RC complex, only the α-polypeptides are involved in the Sr and Ba coordinations in LH1. The difference in the thermostability between these complexes can be attributed to the different patterns of the network formed by metal binding. The Sr- and Ba-LH1-RC complexes form a single-ring network by the LH1 α-polypeptides only, in contrast to the double-ring network composed of both α- and β-polypeptides in the Ca-LH1-RC complex. On the basis of the structural information, a combined effect of hydrogen bonding, structural integrity, and charge distribution is considered to influence the spectral properties of the core antenna complex.
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Affiliation(s)
- Long-Jiang Yu
- Faculty of Science, Ibaraki University , Mito 310-8512, Japan
| | | | - Yukihiro Kimura
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University , Nada, Kobe 657-8501, Japan
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33
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Zheng F, Jin M, Mančal T, Zhao Y. Study of Electronic Structures and Pigment–Protein Interactions in the Reaction Center of Thermochromatium tepidum with a Dynamic Environment. J Phys Chem B 2016; 120:10046-10058. [DOI: 10.1021/acs.jpcb.6b06628] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fulu Zheng
- Division
of Materials Science, Nanyang Technological University, Singapore 639798, Singapore
| | - Mengting Jin
- Division
of Materials Science, Nanyang Technological University, Singapore 639798, Singapore
| | - Tomáš Mančal
- Faculty
of Mathematics and Physics, Charles University in Prague, Ke Karlovu
5, 121 16 Prague
2, Czech Republic
| | - Yang Zhao
- Division
of Materials Science, Nanyang Technological University, Singapore 639798, Singapore
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34
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Challenges facing an understanding of the nature of low-energy excited states in photosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1627-1640. [PMID: 27372198 DOI: 10.1016/j.bbabio.2016.06.010] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/27/2016] [Accepted: 06/28/2016] [Indexed: 01/09/2023]
Abstract
While the majority of the photochemical states and pathways related to the biological capture of solar energy are now well understood and provide paradigms for artificial device design, additional low-energy states have been discovered in many systems with obscure origins and significance. However, as low-energy states are naively expected to be critical to function, these observations pose important challenges. A review of known properties of low energy states covering eight photochemical systems, and options for their interpretation, are presented. A concerted experimental and theoretical research strategy is suggested and outlined, this being aimed at providing a fully comprehensive understanding.
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35
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Ma F, Yu LJ, Wang-Otomo ZY, van Grondelle R. Temperature dependent LH1 → RC energy transfer in purple bacteria Tch. tepidum with shiftable LH1-Q y band: A natural system to investigate thermally activated energy transfer in photosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:408-14. [DOI: 10.1016/j.bbabio.2015.12.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/16/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
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36
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Shi Y, Zhao NJ, Wang P, Fu LM, Yu LJ, Zhang JP, Wang-Otomo ZY. Thermal Adaptability of the Light-Harvesting Complex 2 from Thermochromatium tepidum: Temperature-Dependent Excitation Transfer Dynamics. J Phys Chem B 2015; 119:14871-9. [DOI: 10.1021/acs.jpcb.5b09023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ying Shi
- Department
of Chemistry, Renmin University of China, Beijing 1000872, P. R. China
| | - Ning-Jiu Zhao
- Department
of Chemistry, Renmin University of China, Beijing 1000872, P. R. China
| | - Peng Wang
- Department
of Chemistry, Renmin University of China, Beijing 1000872, P. R. China
| | - Li-Min Fu
- Department
of Chemistry, Renmin University of China, Beijing 1000872, P. R. China
| | - Long-Jiang Yu
- Faculty
of Science, Ibaraki University, Mito 310-8512, Japan
| | - Jian-Ping Zhang
- Department
of Chemistry, Renmin University of China, Beijing 1000872, P. R. China
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37
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Ma F, Yu LJ, Wang-Otomo ZY, van Grondelle R. The origin of the unusual Qy red shift in LH1-RC complexes from purple bacteria Thermochromatium tepidum as revealed by Stark absorption spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1479-86. [PMID: 26341015 DOI: 10.1016/j.bbabio.2015.08.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 08/24/2015] [Accepted: 08/27/2015] [Indexed: 10/23/2022]
Abstract
Native LH1-RC of photosynthetic purple bacteria Thermochromatium (Tch.) tepidum, B915, has an ultra-red BChl a Qy absorption. Two blue-shifted complexes obtained by chemical modification, B893 and B882, have increasing full widths at half maximum (FWHM) and decreasing transition dipole oscillator strength. 77K Stark absorption spectroscopy studies were employed for the three complexes, trying to understand the origin of the 915 nm absorption. We found that Tr(∆α) and |∆μ| of both Qy and carotenoid (Car) bands are larger than for other purple bacterial LH complexes reported previously. Moreover, the red shifts of the Qy bands are associated with (1) increasing Tr(∆α) and |∆μ| of the Qy band, (2) the red shift of the Car Stark signal and (3) the increasing |∆μ| of the Car band. Based on the results and the crystal structure, a combined effect of exciton-charge transfer (CT) states mixing, and inhomogeneous narrowing of the BChl a site energy is proposed to be the origin of the 915 nm absorption. CT-exciton state mixing has long been found to be the origin of strong Stark signal in LH1 and special pair, and the more extent of the mixing in Tch. tepidum LH1 is mainly the consequence of the shorter BChl-BChl distances. The less flexible protein structure results in a smaller site energy disorder (inhomogeneous narrowing), which was demonstrated to be able to influence |∆μ| and absorption.
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Affiliation(s)
- Fei Ma
- Department of Biophysics, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.
| | - Long-Jiang Yu
- Faculty of Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | | | - Rienk van Grondelle
- Department of Biophysics, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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38
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Kimura Y, Kasuga S, Unno M, Furusawa T, Osoegawa S, Sasaki Y, Ohno T, Wang-Otomo ZY. The roles of C-terminal residues on the thermal stability and local heme environment of cytochrome c' from the thermophilic purple sulfur bacterium Thermochromatium tepidum. PHOTOSYNTHESIS RESEARCH 2015; 124:19-29. [PMID: 25519852 DOI: 10.1007/s11120-014-0069-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 12/11/2014] [Indexed: 06/04/2023]
Abstract
A soluble cytochrome (Cyt) c' from thermophilic purple sulfur photosynthetic bacterium Thermochromatium (Tch.) tepidum exhibits marked thermal tolerance compared with that from the closely related mesophilic counterpart Allochromatium vinosum. Here, we focused on the difference in the C-terminal region of the two Cyts c' and examined the effects of D131 and R129 mutations on the thermal stability and local heme environment of Cyt c' by differential scanning calorimetry (DSC) and resonance Raman (RR) spectroscopy. In the oxidized forms, D131K and D131G mutants exhibited denaturing temperatures significantly lower than that of the recombinant control Cyt c'. In contrast, R129K and R129A mutants denatured at nearly identical temperatures with the control Cyt c', indicating that the C-terminal D131 is an important residue maintaining the enhanced thermal stability of Tch. tepidum Cyt c'. The control Cyt c' and all of the mutants increased their thermal stability upon the reduction. Interestingly, D131K exhibited narrow DSC curves and unusual thermodynamic parameters in both redox states. The RR spectra of the control Cyt c' exhibited characteristic bands at 1,635 and 1,625 cm(-1), ascribed to intermediate spin (IS) and high spin (HS) states, respectively. The IS/HS distribution was differently affected by the D131 and R129 mutations and pH changes. Furthermore, R129 mutants suggested the lowering of their redox potentials. These results strongly indicate that the D131 and R129 residues play significant roles in maintaining the thermal stability and modulating the local heme environment of Tch. tepidum Cyt c'.
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Affiliation(s)
- Yukihiro Kimura
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Nada, Kobe, 657-8501, Japan,
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39
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Nemukhin AV, Khrenova MG, Polyakov IV, Grigorenko BL, Moscovsky AA. Computer modeling of components of photoreceptor systems. Russ Chem Bull 2014. [DOI: 10.1007/s11172-014-0656-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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40
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Structure of the LH1–RC complex from Thermochromatium tepidum at 3.0 Å. Nature 2014; 508:228-32. [DOI: 10.1038/nature13197] [Citation(s) in RCA: 174] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 03/04/2014] [Indexed: 11/08/2022]
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41
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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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42
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Klatt CG, Inskeep WP, Herrgard MJ, Jay ZJ, Rusch DB, Tringe SG, Niki Parenteau M, Ward DM, Boomer SM, Bryant DA, Miller SR. Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments. Front Microbiol 2013; 4:106. [PMID: 23761787 PMCID: PMC3669762 DOI: 10.3389/fmicb.2013.00106] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Accepted: 04/13/2013] [Indexed: 11/13/2022] Open
Abstract
Six phototrophic microbial mat communities from different geothermal springs (YNP) were studied using metagenome sequencing and geochemical analyses. The primary goals of this work were to determine differences in community composition of high-temperature phototrophic mats distributed across the Yellowstone geothermal ecosystem, and to identify metabolic attributes of predominant organisms present in these communities that may correlate with environmental attributes important in niche differentiation. Random shotgun metagenome sequences from six phototrophic communities (average ∼53 Mbp/site) were subjected to multiple taxonomic, phylogenetic, and functional analyses. All methods, including G + C content distribution, MEGAN analyses, and oligonucleotide frequency-based clustering, provided strong support for the dominant community members present in each site. Cyanobacteria were only observed in non-sulfidic sites; de novo assemblies were obtained for Synechococcus-like populations at Chocolate Pots (CP_7) and Fischerella-like populations at White Creek (WC_6). Chloroflexi-like sequences (esp. Roseiflexus and/or Chloroflexus spp.) were observed in all six samples and contained genes involved in bacteriochlorophyll biosynthesis and the 3-hydroxypropionate carbon fixation pathway. Other major sequence assemblies were obtained for a Chlorobiales population from CP_7 (proposed family Thermochlorobacteriaceae), and an anoxygenic, sulfur-oxidizing Thermochromatium-like (Gamma-proteobacteria) population from Bath Lake Vista Annex (BLVA_20). Additional sequence coverage is necessary to establish more complete assemblies of other novel bacteria in these sites (e.g., Bacteroidetes and Firmicutes); however, current assemblies suggested that several of these organisms play important roles in heterotrophic and fermentative metabolisms. Definitive linkages were established between several of the dominant phylotypes present in these habitats and important functional processes such as photosynthesis, carbon fixation, sulfur oxidation, and fermentation.
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Affiliation(s)
- Christian G Klatt
- Department of Land Resources and Environmental Sciences, Montana State University , Bozeman, MT , USA ; Thermal Biology Institute, Montana State University , Bozeman, MT , USA
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43
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Hirano Y, Kimura Y, Suzuki H, Miki K, Wang ZY. Structure Analysis and Comparative Characterization of the Cytochrome c′ and Flavocytochrome c from Thermophilic Purple Photosynthetic Bacterium Thermochromatium tepidum. Biochemistry 2012; 51:6556-67. [DOI: 10.1021/bi3005522] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yu Hirano
- Faculty of Science, Ibaraki University, Mito 310-8512, Japan
- Department of Chemistry, Graduate
School of Science, Kyoto University, Sakyo-ku,
Kyoto 606-8502, Japan
| | - Yukihiro Kimura
- Organization
of Advanced Science
and Technology, Kobe University, Nada,
Kobe 657-8501, Japan
| | - Hideaki Suzuki
- Faculty of Science, Ibaraki University, Mito 310-8512, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate
School of Science, Kyoto University, Sakyo-ku,
Kyoto 606-8502, Japan
| | - Zheng-Yu Wang
- Faculty of Science, Ibaraki University, Mito 310-8512, Japan
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44
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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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Jakob-Grun S, Radeck J, Braun P. Ca(2+)-binding reduces conformational flexibility of RC-LH1 core complex from thermophile Thermochromatium tepidum. PHOTOSYNTHESIS RESEARCH 2012; 111:139-147. [PMID: 22367594 DOI: 10.1007/s11120-012-9727-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 02/09/2012] [Indexed: 05/31/2023]
Abstract
The light-harvesting complex, LH1, of thermophile purple bacteria Thermochromatium tepidum consists of an array of α- and β-polypeptides which assemble the photoactive bacteriochlorophyll and closely interact with the membrane-lipids. In this study, we investigated the effect of calcium and manganese ions on the protein structure and thermostability of the reaction centre (RC)-LH1/lipid complex. The binding of Ca(2+), but not Mn(2+) is shown to shift the LH1 Q ( y ) absorption maximum from ~889 to 915 nm and to significantly raise the thermostability of the RC-LH1 complex. The ATR-FTIR spectra indicate that interaction of Ca(2+) as monitored by the carboxylates' vibration of aspartate residues, but not Mn(2+) induces changes in the α-helix packing arrangement. The reduced rate of (1)H/(2)H exchange of proteins' amide protons shows that the accessibility to (2)H(2)O is significantly lowered in Ca(2+)-substituted RC-LH1/lipid complexes. In particular, exchange with the associated lipid molecules, is significantly retarded. These results suggest that the thermostability of the RC-LH1 complex is raised by the distinct interaction with calcium cations which reduces the RC-LH1/lipid dynamics, particularly, at the membrane-water interface.
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Affiliation(s)
- Selma Jakob-Grun
- Department Biology I, Botany, Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
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46
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Niedzwiedzki DM, Fuciman M, Kobayashi M, Frank HA, Blankenship RE. Ultrafast time-resolved spectroscopy of the light-harvesting complex 2 (LH2) from the photosynthetic bacterium Thermochromatium tepidum. PHOTOSYNTHESIS RESEARCH 2011; 110:49-60. [PMID: 21984346 DOI: 10.1007/s11120-011-9692-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 09/21/2011] [Indexed: 05/31/2023]
Abstract
The light-harvesting complex 2 from the thermophilic purple bacterium Thermochromatium tepidum was purified and studied by steady-state absorption and fluorescence, sub-nanosecond-time-resolved fluorescence and femtosecond time-resolved transient absorption spectroscopy. The measurements were performed at room temperature and at 10 K. The combination of both ultrafast and steady-state optical spectroscopy methods at ambient and cryogenic temperatures allowed the detailed study of carotenoid (Car)-to-bacteriochlorophyll (BChl) as well BChl-to-BChl excitation energy transfer in the complex. The studies show that the dominant Cars rhodopin (N=11) and spirilloxanthin (N=13) do not play a significant role as supportive energy donors for BChl a. This is related with their photophysical properties regulated by long π-electron conjugation. On the other hand, such properties favor some of the Cars, particularly spirilloxanthin (N=13) to play the role of the direct quencher of the excited singlet state of BChl.
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Affiliation(s)
- Dariusz M Niedzwiedzki
- Photosynthetic Antenna Research Center, Washington University in St. Louis, Campus Box 1138, St. Louis, MO 63130, USA.
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47
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Rücker O, Köhler A, Behammer B, Sichau K, Overmann J. Puf operon sequences and inferred structures of light-harvesting complexes of three closely related Chromatiaceae exhibiting different absorption characteristics. Arch Microbiol 2011; 194:123-34. [DOI: 10.1007/s00203-011-0735-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 07/05/2011] [Accepted: 07/08/2011] [Indexed: 11/30/2022]
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48
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Yang F, Yu LJ, Wang P, Ai XC, Wang ZY, Zhang JP. Effects of Aggregation on the Excitation Dynamics of LH2 from Thermochromatium tepidum in Aqueous Phase and in Chromatophores. J Phys Chem B 2011; 115:7906-13. [DOI: 10.1021/jp1097537] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fan Yang
- Department of Chemistry, Renmin University of China, Beijing 100872, People's Repulic of China
- College of Electronic Science and Engineering, Jilin University, Changchun 130012, People's Republic of China
| | - Long-Jiang Yu
- Faculty of Science, Ibaraki University, Mito 310-8512, Japan
| | - Peng Wang
- Department of Chemistry, Renmin University of China, Beijing 100872, People's Repulic of China
| | - Xi-Cheng Ai
- Department of Chemistry, Renmin University of China, Beijing 100872, People's Repulic of China
| | - Zheng-Yu Wang
- Faculty of Science, Ibaraki University, Mito 310-8512, Japan
| | - Jian-Ping Zhang
- Department of Chemistry, Renmin University of China, Beijing 100872, People's Repulic of China
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49
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Kimura Y, Inada Y, Yu LJ, Wang ZY, Ohno T. A Spectroscopic Variant of the Light-Harvesting 1 Core Complex from the Thermophilic Purple Sulfur Bacterium Thermochromatium tepidum. Biochemistry 2011; 50:3638-48. [DOI: 10.1021/bi200278u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yukihiro Kimura
- Organization of Advanced Science and Technology, Kobe University, Nada, Kobe 657-8501, Japan
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe 657-8501, Japan
| | - Yuta Inada
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe 657-8501, Japan
| | - Long-Jiang Yu
- Faculty of Science, Ibaraki University, Bunkyo, Mito 310-8512, Japan
| | - Zheng-Yu Wang
- Faculty of Science, Ibaraki University, Bunkyo, Mito 310-8512, Japan
| | - Takashi Ohno
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe 657-8501, Japan
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50
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Niedzwiedzki DM, Kobayashi M, Blankenship RE. Triplet excited state spectra and dynamics of carotenoids from the thermophilic purple photosynthetic bacterium Thermochromatium tepidum. PHOTOSYNTHESIS RESEARCH 2011; 107:177-186. [PMID: 21229315 DOI: 10.1007/s11120-011-9620-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 12/31/2010] [Indexed: 05/30/2023]
Abstract
Light-harvesting complex 2 from the anoxygenic phototrophic purple bacterium Thermochromatium tepidum was purified and studied by steady-state absorption, fluorescence and flash photolysis spectroscopy. Steady-state absorption and fluorescence measurements show that carotenoids play a negligible role as supportive energy donors and transfer excitation to bacteriochlorophyll-a with low energy transfer efficiency of ~30%. HPLC analysis determined that the dominant carotenoids in the complex are rhodopin and spirilloxanthin. Carotenoid excited triplet state formation upon direct (carotenoid) or indirect (bacteriochlorophyll-a Q(x) band) excitation shows that carotenoid triplets are mostly localized on spirilloxanthin. In addition, no triplet excitation transfer between carotenoids was observed. Such specific carotenoid composition and spectroscopic results strongly suggest that this organism optimized carotenoid composition in the light-harvesting complex 2 in order to maximize photoprotective capabilities of carotenoids but subsequently drastically suppressed their supporting role in light-harvesting process.
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