1
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Kushkevych I, Procházka V, Vítězová M, Dordević D, Abd El-Salam M, Rittmann SKMR. Anoxygenic photosynthesis with emphasis on green sulfur bacteria and a perspective for hydrogen sulfide detoxification of anoxic environments. Front Microbiol 2024; 15:1417714. [PMID: 39056005 PMCID: PMC11269200 DOI: 10.3389/fmicb.2024.1417714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/12/2024] [Indexed: 07/28/2024] Open
Abstract
The bacterial light-dependent energy metabolism can be divided into two types: oxygenic and anoxygenic photosynthesis. Bacterial oxygenic photosynthesis is similar to plants and is characteristic for cyanobacteria. Bacterial anoxygenic photosynthesis is performed by anoxygenic phototrophs, especially green sulfur bacteria (GSB; family Chlorobiaceae) and purple sulfur bacteria (PSB; family Chromatiaceae). In anoxygenic photosynthesis, hydrogen sulfide (H2S) is used as the main electron donor, which differs from plants or cyanobacteria where water is the main source of electrons. This review mainly focuses on the microbiology of GSB, which may be found in water or soil ecosystems where H2S is abundant. GSB oxidize H2S to elemental sulfur. GSB possess special structures-chlorosomes-wherein photosynthetic pigments are located. Chlorosomes are vesicles that are surrounded by a lipid monolayer that serve as light-collecting antennas. The carbon source of GSB is carbon dioxide, which is assimilated through the reverse tricarboxylic acid cycle. Our review provides a thorough introduction to the comparative eco-physiology of GSB and discusses selected application possibilities of anoxygenic phototrophs in the fields of environmental management, bioremediation, and biotechnology.
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Affiliation(s)
- Ivan Kushkevych
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Vít Procházka
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Monika Vítězová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Dani Dordević
- Department of Plant Origin Foodstuffs Hygiene and Technology, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences, Brno, Czechia
| | - Mohamed Abd El-Salam
- Department of Pharmacognosy, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa, Egypt
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Simon K.-M. R. Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Wien, Austria
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2
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Lyratzakis A, Daskalakis V, Xie H, Tsiotis G. The synergy between the PscC subunits for electron transfer to the P 840 special pair in Chlorobaculum tepidum. PHOTOSYNTHESIS RESEARCH 2024; 160:87-96. [PMID: 38625595 PMCID: PMC11108878 DOI: 10.1007/s11120-024-01093-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/08/2024] [Indexed: 04/17/2024]
Abstract
The primary photochemical reaction of photosynthesis in green sulfur bacteria occurs in the homodimer PscA core proteins by a special chlorophyll pair. The light induced excited state of the special pair producing P840+ is rapidly reduced by electron transfer from one of the two PscC subunits. Molecular dynamics (MD) simulations are combined with bioinformatic tools herein to provide structural and dynamic insight into the complex between the two PscA core proteins and the two PscC subunits. The microscopic dynamic model involves extensive sampling at atomic resolution and at a cumulative time-scale of 22µs and reveals well defined protein-protein interactions. The membrane complex is composed of the two PscA and the two PscC subunits and macroscopic connections are revealed within a putative electron transfer pathway from the PscC subunit to the special pair P840 located within the PscA subunits. Our results provide a structural basis for understanding the electron transport to the homodimer RC of the green sulfur bacteria. The MD based approach can provide the basis to further probe the PscA-PscC complex dynamics and observe electron transfer therein at the quantum level. Furthermore, the transmembrane helices of the different PscC subunits exert distinct dynamics in the complex.
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Affiliation(s)
- Alexandros Lyratzakis
- Department of Chemistry, School of Science and Engineering, University of Crete, Heraklion, 70013, Greece
| | - Vangelis Daskalakis
- Department of Chemical Engineering, School of Engineering, University of Patras, Rion, Patras, 26504, Greece
| | - Hao Xie
- Max Planck Institute of Biophysics, 60438, Frankfurt am Main, Germany
| | - Georgios Tsiotis
- Department of Chemistry, School of Science and Engineering, University of Crete, Heraklion, 70013, Greece.
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3
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Rodríguez Del Río Á, Giner-Lamia J, Cantalapiedra CP, Botas J, Deng Z, Hernández-Plaza A, Munar-Palmer M, Santamaría-Hernando S, Rodríguez-Herva JJ, Ruscheweyh HJ, Paoli L, Schmidt TSB, Sunagawa S, Bork P, López-Solanilla E, Coelho LP, Huerta-Cepas J. Functional and evolutionary significance of unknown genes from uncultivated taxa. Nature 2024; 626:377-384. [PMID: 38109938 PMCID: PMC10849945 DOI: 10.1038/s41586-023-06955-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 12/08/2023] [Indexed: 12/20/2023]
Abstract
Many of the Earth's microbes remain uncultured and understudied, limiting our understanding of the functional and evolutionary aspects of their genetic material, which remain largely overlooked in most metagenomic studies1. Here we analysed 149,842 environmental genomes from multiple habitats2-6 and compiled a curated catalogue of 404,085 functionally and evolutionarily significant novel (FESNov) gene families exclusive to uncultivated prokaryotic taxa. All FESNov families span multiple species, exhibit strong signals of purifying selection and qualify as new orthologous groups, thus nearly tripling the number of bacterial and archaeal gene families described to date. The FESNov catalogue is enriched in clade-specific traits, including 1,034 novel families that can distinguish entire uncultivated phyla, classes and orders, probably representing synapomorphies that facilitated their evolutionary divergence. Using genomic context analysis and structural alignments we predicted functional associations for 32.4% of FESNov families, including 4,349 high-confidence associations with important biological processes. These predictions provide a valuable hypothesis-driven framework that we used for experimental validatation of a new gene family involved in cell motility and a novel set of antimicrobial peptides. We also demonstrate that the relative abundance profiles of novel families can discriminate between environments and clinical conditions, leading to the discovery of potentially new biomarkers associated with colorectal cancer. We expect this work to enhance future metagenomics studies and expand our knowledge of the genetic repertory of uncultivated organisms.
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Affiliation(s)
- Álvaro Rodríguez Del Río
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Joaquín Giner-Lamia
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Instituto de Bioquímica Vegetal y Fotosíntesis (IBVF), Universidad de Sevilla-CSIC, Seville, Spain
| | - Carlos P Cantalapiedra
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Jorge Botas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Ziqi Deng
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Ana Hernández-Plaza
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Martí Munar-Palmer
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Saray Santamaría-Hernando
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - José J Rodríguez-Herva
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Thomas S B Schmidt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Emilia López-Solanilla
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Shanghai, China
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain.
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4
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Nelson N. Coupling and Slips in Photosynthetic Reactions-From Femtoseconds to Eons. PLANTS (BASEL, SWITZERLAND) 2023; 12:3878. [PMID: 38005774 PMCID: PMC10674687 DOI: 10.3390/plants12223878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023]
Abstract
Photosynthesis stands as a unique biological phenomenon that can be comprehensively explored across a wide spectrum, from femtoseconds to eons. Across each timespan, a delicate interplay exists between coupling and inherent deviations that are essential for sustaining the overall efficiency of the system. Both quantum mechanics and thermodynamics act as guiding principles for the diverse processes occurring from femtoseconds to eons. Processes such as excitation energy transfer and the accumulation of oxygen in the atmosphere, along with the proliferation of organic matter on the Earth's surface, are all governed by the coupling-slip principle. This article will delve into select time points along this expansive scale. It will highlight the interconnections between photosynthesis, the global population, disorder, and the issue of global warming.
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Affiliation(s)
- Nathan Nelson
- Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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5
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Delgado F, Enríquez M. Quantum Entanglement and State-Transference in Fenna-Matthews-Olson Complexes: A Post-Experimental Simulation Analysis in the Computational Biology Domain. Int J Mol Sci 2023; 24:10862. [PMID: 37446061 DOI: 10.3390/ijms241310862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/13/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Fenna-Mathews-Olson complexes participate in the photosynthetic process of Sulfur Green Bacteria. These biological subsystems exhibit quantum features which possibly are responsible for their high efficiency; the latter may comprise multipartite entanglement and the apparent tunnelling of the initial quantum state. At first, to study these aspects, a multidisciplinary approach including experimental biology, spectroscopy, physics, and math modelling is required. Then, a global computer modelling analysis is achieved in the computational biology domain. The current work implements the Hierarchical Equations of Motion to numerically solve the open quantum system problem regarding this complex. The time-evolved states obtained with this method are then analysed under several measures of entanglement, some of them already proposed in the literature. However, for the first time, the maximum overlap with respect to the closest separable state is employed. This authentic multipartite entanglement measure provides information on the correlations, not only based on the system bipartitions as in the usual analysis. Our study has led us to note a different view of FMO multipartite entanglement as tiny contributions to the global entanglement suggested by other more basic measurements. Additionally, in another related trend, the initial state, considered as a Förster Resonance Energy Transfer, is tracked using a novel approach, considering how it could be followed under the fidelity measure on all possible permutations of the FMO subsystems through its dynamical evolution by observing the tunnelling in the most probable locations. Both analyses demanded significant computational work, making for a clear example of the complexity required in computational biology.
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Affiliation(s)
- Francisco Delgado
- School of Engineering and Sciences, Tecnologico de Monterrey, Atizapan 52926, Mexico
| | - Marco Enríquez
- School of Engineering and Sciences, Tecnologico de Monterrey, Santa Fe 01389, Mexico
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6
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Kishimoto H, Azai C, Yamamoto T, Mutoh R, Nakaniwa T, Tanaka H, Miyanoiri Y, Kurisu G, Oh-oka H. Soluble domains of cytochrome c-556 and Rieske iron-sulfur protein from Chlorobaculum tepidum: Crystal structures and interaction analysis. Curr Res Struct Biol 2023; 5:100101. [PMID: 37180033 PMCID: PMC10172866 DOI: 10.1016/j.crstbi.2023.100101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 05/15/2023] Open
Abstract
In photosynthetic green sulfur bacteria, the electron transfer reaction from menaquinol:cytochrome c oxidoreductase to the P840 reaction center (RC) complex occurs directly without any involvement of soluble electron carrier protein(s). X-ray crystallography has determined the three-dimensional structures of the soluble domains of the CT0073 gene product and Rieske iron-sulfur protein (ISP). The former is a mono-heme cytochrome c with an α-absorption peak at 556 nm. The overall fold of the soluble domain of cytochrome c-556 (designated as cyt c-556sol) consists of four α-helices and is very similar to that of water-soluble cyt c-554 that independently functions as an electron donor to the P840 RC complex. However, the latter's remarkably long and flexible loop between the α3 and α4 helices seems to make it impossible to be a substitute for the former. The structure of the soluble domain of the Rieske ISP (Rieskesol protein) shows a typical β-sheets-dominated fold with a small cluster-binding and a large subdomain. The architecture of the Rieskesol protein is bilobal and belongs to those of b6f-type Rieske ISPs. Nuclear magnetic resonance (NMR) measurements revealed weak non-polar but specific interaction sites on Rieskesol protein when mixed with cyt c-556sol. Therefore, menaquinol:cytochrome c oxidoreductase in green sulfur bacteria features a Rieske/cytb complex tightly associated with membrane-anchored cyt c-556.
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Affiliation(s)
- Hiraku Kishimoto
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Chihiro Azai
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Tomoya Yamamoto
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Risa Mutoh
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Tetsuko Nakaniwa
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Hideaki Tanaka
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yohei Miyanoiri
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
- Corresponding author.
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
- Corresponding author.
| | - Hirozo Oh-oka
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
- Center for Education in Liberal Arts and Sciences, Osaka University, Toyonaka, Osaka, 560-0043, Japan
- Corresponding author. Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan.
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7
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Chen JH, Wang W, Wang C, Kuang T, Shen JR, Zhang X. Cryo-electron microscopy structure of the intact photosynthetic light-harvesting antenna-reaction center complex from a green sulfur bacterium. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:223-234. [PMID: 36125941 DOI: 10.1111/jipb.13367] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 09/19/2022] [Indexed: 06/15/2023]
Abstract
The photosynthetic reaction center complex (RCC) of green sulfur bacteria (GSB) consists of the membrane-imbedded RC core and the peripheric energy transmitting proteins called Fenna-Matthews-Olson (FMO). Functionally, FMO transfers the absorbed energy from a huge peripheral light-harvesting antenna named chlorosome to the RC core where charge separation occurs. In vivo, one RC was found to bind two FMOs, however, the intact structure of RCC as well as the energy transfer mechanism within RCC remain to be clarified. Here we report a structure of intact RCC which contains a RC core and two FMO trimers from a thermophilic green sulfur bacterium Chlorobaculum tepidum at 2.9 Å resolution by cryo-electron microscopy. The second FMO trimer is attached at the cytoplasmic side asymmetrically relative to the first FMO trimer reported previously. We also observed two new subunits (PscE and PscF) and the N-terminal transmembrane domain of a cytochrome-containing subunit (PscC) in the structure. These two novel subunits possibly function to facilitate the binding of FMOs to RC core and to stabilize the whole complex. A new bacteriochlorophyll (numbered as 816) was identified at the interspace between PscF and PscA-1, causing an asymmetrical energy transfer from the two FMO trimers to RC core. Based on the structure, we propose an energy transfer network within this photosynthetic apparatus.
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Affiliation(s)
- Jing-Hua Chen
- College of Life Science, Zhejiang University, Hangzhou, 310058, China
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Weiwei Wang
- College of Life Science, Zhejiang University, Hangzhou, 310058, China
| | - Chen Wang
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Tingyun Kuang
- Key Laboratory of Photobiology, Institute of Botany, Photosynthesis Research Center, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Jian-Ren Shen
- Key Laboratory of Photobiology, Institute of Botany, Photosynthesis Research Center, the Chinese Academy of Sciences, Beijing, 100093, China
- Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Xing Zhang
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Center of Cryo Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, 310058, China
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8
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Kanda T, Ishikita H. Energetics of the Electron Transfer Pathways in the Homodimeric Photosynthetic Reaction Center. Biochemistry 2022; 61:2621-2627. [PMID: 36322126 PMCID: PMC9671125 DOI: 10.1021/acs.biochem.2c00524] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/09/2022] [Indexed: 11/06/2022]
Abstract
Photosynthetic reaction centers from a green sulfur bacterium (GsbRC), the PscA/PscA proteins, and photosystem I (PSI), PsaA/PsaB proteins, share structural similarities. Here, we report the redox potential (Em) values of GsbRC by solving the linear Poisson-Boltzmann equation and considering the protonation states of all titratable sites in the entire GsbRC protein and identify the factors that shift the Em values with respect to PSI. The Em values for one-electron reduction of the accessory (A-1) and adjacent (A0) chlorophylls in GsbRC are 100-250 mV higher than those in PSI, whereas the Em values for the Fe4S4 cluster (FX) are at the same level. The PsaA-Trp697/PsaB-Trp677 pair in PSI, which forms the A1-quinone binding site, is replaced with PscA-Arg638 in GsbRC. PsaB-Asp575 in PSI, which is responsible for the Em difference between A1A and A1B quinones in PSI, is absent in GsbRC. These discrepancies also contribute to the upshift in Em(A-1) and Em(A0) in GsbRC with respect to PSI. It seems likely that the upshifted Em for chlorophylls in GsbRC ultimately originates from the characteristics of the electrostatic environment that corresponds to the A1 site of PSI.
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Affiliation(s)
- Tomoki Kanda
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroshi Ishikita
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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9
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Puskar R, Du Truong C, Swain K, Chowdhury S, Chan KY, Li S, Cheng KW, Wang TY, Poh YP, Mazor Y, Liu H, Chou TF, Nannenga BL, Chiu PL. Molecular asymmetry of a photosynthetic supercomplex from green sulfur bacteria. Nat Commun 2022; 13:5824. [PMID: 36192412 PMCID: PMC9529944 DOI: 10.1038/s41467-022-33505-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/20/2022] [Indexed: 11/21/2022] Open
Abstract
The photochemical reaction center (RC) features a dimeric architecture for charge separation across the membrane. In green sulfur bacteria (GSB), the trimeric Fenna-Matthews-Olson (FMO) complex mediates the transfer of light energy from the chlorosome antenna complex to the RC. Here we determine the structure of the photosynthetic supercomplex from the GSB Chlorobaculum tepidum using single-particle cryogenic electron microscopy (cryo-EM) and identify the cytochrome c subunit (PscC), two accessory protein subunits (PscE and PscF), a second FMO trimeric complex, and a linker pigment between FMO and the RC core. The protein subunits that are assembled with the symmetric RC core generate an asymmetric photosynthetic supercomplex. One linker bacteriochlorophyll (BChl) is located in one of the two FMO-PscA interfaces, leading to differential efficiencies of the two energy transfer branches. The two FMO trimeric complexes establish two different binding interfaces with the RC cytoplasmic surface, driven by the associated accessory subunits. This structure of the GSB photosynthetic supercomplex provides mechanistic insight into the light excitation energy transfer routes and a possible evolutionary transition intermediate of the bacterial photosynthetic supercomplex from the primitive homodimeric RC.
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Affiliation(s)
- Ryan Puskar
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Chloe Du Truong
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
- Rampart Bioscience, Monrovia, CA, 91016, USA
| | - Kyle Swain
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, 85287, USA
| | - Saborni Chowdhury
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Ka-Yi Chan
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Shan Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Kai-Wen Cheng
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Ting Yu Wang
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Yu-Ping Poh
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Yuval Mazor
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Haijun Liu
- Department of Biology, Washington University, St. Louis, MO, 63130, USA
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Brent L Nannenga
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, 85287, USA
| | - Po-Lin Chiu
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA.
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10
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Proteomic Time-Course Analysis of the Filamentous Anoxygenic Phototrophic Bacterium, Chloroflexus aurantiacus, during the Transition from Respiration to Phototrophy. Microorganisms 2022; 10:microorganisms10071288. [PMID: 35889008 PMCID: PMC9316378 DOI: 10.3390/microorganisms10071288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 02/05/2023] Open
Abstract
Chloroflexus aurantiacus is a filamentous anoxygenic phototrophic bacterium that grows chemotrophically under oxic conditions and phototrophically under anoxic conditions. Because photosynthesis-related genes are scattered without any gene clusters in the genome, it is still unclear how this bacterium regulates protein expression in response to environmental changes. In this study, we performed a proteomic time-course analysis of how C. aurantiacus expresses proteins to acclimate to environmental changes, namely the transition from chemoheterotrophic respiratory to photoheterotrophic growth mode. Proteomic analysis detected a total of 2520 proteins out of 3934 coding sequences in the C. aurantiacus genome from samples collected at 13 time points. Almost all proteins for reaction centers, light-harvesting chlorosomes, and carbon fixation pathways were successfully detected during the growing phases in which optical densities and relative bacteriochlorophyll c contents increased simultaneously. Combination of proteomics and pigment analysis suggests that the self-aggregation of bacteriochlorophyllide c could precede the esterification of the hydrophobic farnesyl tail in cells. Cytoplasmic subunits of alternative complex III were interchanged between oxic and anoxic conditions, although membrane-bound subunits were used for both conditions. These data highlight the protein expression dynamics of phototrophy-related genes during the transition from respiration to phototrophy.
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11
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Gorka M, Baldansuren A, Malnati A, Gruszecki E, Golbeck JH, Lakshmi KV. Shedding Light on Primary Donors in Photosynthetic Reaction Centers. Front Microbiol 2021; 12:735666. [PMID: 34659164 PMCID: PMC8517396 DOI: 10.3389/fmicb.2021.735666] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 08/30/2021] [Indexed: 11/17/2022] Open
Abstract
Chlorophylls (Chl)s exist in a variety of flavors and are ubiquitous in both the energy and electron transfer processes of photosynthesis. The functions they perform often occur on the ultrafast (fs-ns) time scale and until recently, these have been difficult to measure in real time. Further, the complexity of the binding pockets and the resulting protein-matrix effects that alter the respective electronic properties have rendered theoretical modeling of these states difficult. Recent advances in experimental methodology, computational modeling, and emergence of new reaction center (RC) structures have renewed interest in these processes and allowed researchers to elucidate previously ambiguous functions of Chls and related pheophytins. This is complemented by a wealth of experimental data obtained from decades of prior research. Studying the electronic properties of Chl molecules has advanced our understanding of both the nature of the primary charge separation and subsequent electron transfer processes of RCs. In this review, we examine the structures of primary electron donors in Type I and Type II RCs in relation to the vast body of spectroscopic research that has been performed on them to date. Further, we present density functional theory calculations on each oxidized primary donor to study both their electronic properties and our ability to model experimental spectroscopic data. This allows us to directly compare the electronic properties of hetero- and homodimeric RCs.
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Affiliation(s)
- Michael Gorka
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Amgalanbaatar Baldansuren
- Department of Chemistry and Chemical Biology and The Baruch ’60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Amanda Malnati
- Department of Chemistry and Chemical Biology and The Baruch ’60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Elijah Gruszecki
- Department of Chemistry and Chemical Biology and The Baruch ’60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - John H. Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - K. V. Lakshmi
- Department of Chemistry and Chemical Biology and The Baruch ’60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY, United States
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12
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Gisriel CJ, Azai C, Cardona T. Recent advances in the structural diversity of reaction centers. PHOTOSYNTHESIS RESEARCH 2021; 149:329-343. [PMID: 34173168 PMCID: PMC8452559 DOI: 10.1007/s11120-021-00857-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
Photosynthetic reaction centers (RC) catalyze the conversion of light to chemical energy that supports life on Earth, but they exhibit substantial diversity among different phyla. This is exemplified in a recent structure of the RC from an anoxygenic green sulfur bacterium (GsbRC) which has characteristics that may challenge the canonical view of RC classification. The GsbRC structure is analyzed and compared with other RCs, and the observations reveal important but unstudied research directions that are vital for disentangling RC evolution and diversity. Namely, (1) common themes of electron donation implicate a Ca2+ site whose role is unknown; (2) a previously unidentified lipid molecule with unclear functional significance is involved in the axial ligation of a cofactor in the electron transfer chain; (3) the GsbRC features surprising structural similarities with the distantly-related photosystem II; and (4) a structural basis for energy quenching in the GsbRC can be gleaned that exemplifies the importance of how exposure to oxygen has shaped the evolution of RCs. The analysis highlights these novel avenues of research that are critical for revealing evolutionary relationships that underpin the great diversity observed in extant RCs.
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Affiliation(s)
| | - Chihiro Azai
- College of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Tanai Cardona
- Department of Life Sciences, Imperial College London, London, UK
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13
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Molecular Physiology of Anaerobic Phototrophic Purple and Green Sulfur Bacteria. Int J Mol Sci 2021; 22:ijms22126398. [PMID: 34203823 PMCID: PMC8232776 DOI: 10.3390/ijms22126398] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/24/2021] [Accepted: 06/11/2021] [Indexed: 12/04/2022] Open
Abstract
There are two main types of bacterial photosynthesis: oxygenic (cyanobacteria) and anoxygenic (sulfur and non-sulfur phototrophs). Molecular mechanisms of photosynthesis in the phototrophic microorganisms can differ and depend on their location and pigments in the cells. This paper describes bacteria capable of molecular oxidizing hydrogen sulfide, specifically the families Chromatiaceae and Chlorobiaceae, also known as purple and green sulfur bacteria in the process of anoxygenic photosynthesis. Further, it analyzes certain important physiological processes, especially those which are characteristic for these bacterial families. Primarily, the molecular metabolism of sulfur, which oxidizes hydrogen sulfide to elementary molecular sulfur, as well as photosynthetic processes taking place inside of cells are presented. Particular attention is paid to the description of the molecular structure of the photosynthetic apparatus in these two families of phototrophs. Moreover, some of their molecular biotechnological perspectives are discussed.
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14
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Kushkevych I, Bosáková V, Vítězová M, Rittmann SKMR. Anoxygenic Photosynthesis in Photolithotrophic Sulfur Bacteria and Their Role in Detoxication of Hydrogen Sulfide. Antioxidants (Basel) 2021; 10:antiox10060829. [PMID: 34067364 PMCID: PMC8224592 DOI: 10.3390/antiox10060829] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/12/2021] [Accepted: 05/20/2021] [Indexed: 11/26/2022] Open
Abstract
Hydrogen sulfide is a toxic compound that can affect various groups of water microorganisms. Photolithotrophic sulfur bacteria including Chromatiaceae and Chlorobiaceae are able to convert inorganic substrate (hydrogen sulfide and carbon dioxide) into organic matter deriving energy from photosynthesis. This process takes place in the absence of molecular oxygen and is referred to as anoxygenic photosynthesis, in which exogenous electron donors are needed. These donors may be reduced sulfur compounds such as hydrogen sulfide. This paper deals with the description of this metabolic process, representatives of the above-mentioned families, and discusses the possibility using anoxygenic phototrophic microorganisms for the detoxification of toxic hydrogen sulfide. Moreover, their general characteristics, morphology, metabolism, and taxonomy are described as well as the conditions for isolation and cultivation of these microorganisms will be presented.
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Affiliation(s)
- Ivan Kushkevych
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; (V.B.); (M.V.)
- Correspondence: (I.K.); (S.K.-M.R.R.); Tel.: +420-549-495-315 (I.K.); +431-427-776-513 (S.K.-M.R.R.)
| | - Veronika Bosáková
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; (V.B.); (M.V.)
- Department of Biology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic
| | - Monika Vítězová
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; (V.B.); (M.V.)
| | - Simon K.-M. R. Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, 1090 Vienna, Austria
- Correspondence: (I.K.); (S.K.-M.R.R.); Tel.: +420-549-495-315 (I.K.); +431-427-776-513 (S.K.-M.R.R.)
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15
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Kimura A, Kitoh-Nishioka H, Shigeta Y, Itoh S. Comparison between the Light-Harvesting Mechanisms of Type-I Photosynthetic Reaction Centers of Heliobacteria and Photosystem I: Pigment Site Energy Distribution and Exciton State. J Phys Chem B 2021; 125:3727-3738. [DOI: 10.1021/acs.jpcb.0c09400] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Akihiro Kimura
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Hirotaka Kitoh-Nishioka
- JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
- Graduate School of System Informatics, Kobe University, Kobe 657-8501, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
| | - Shigeru Itoh
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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16
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Chen JH, Wu H, Xu C, Liu XC, Huang Z, Chang S, Wang W, Han G, Kuang T, Shen JR, Zhang X. Architecture of the photosynthetic complex from a green sulfur bacterium. Science 2021; 370:370/6519/eabb6350. [PMID: 33214250 DOI: 10.1126/science.abb6350] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 09/09/2020] [Indexed: 01/09/2023]
Abstract
The photosynthetic apparatus of green sulfur bacteria (GSB) contains a peripheral antenna chlorosome, light-harvesting Fenna-Matthews-Olson proteins (FMO), and a reaction center (GsbRC). We used cryo-electron microscopy to determine a 2.7-angstrom structure of the FMO-GsbRC supercomplex from Chlorobaculum tepidum The GsbRC binds considerably fewer (bacterio)chlorophylls [(B)Chls] than other known type I RCs do, and the organization of (B)Chls is similar to that in photosystem II. Two BChl layers in GsbRC are not connected by Chls, as seen in other RCs, but associate with two carotenoid derivatives. Relatively long distances of 22 to 33 angstroms were observed between BChls of FMO and GsbRC, consistent with the inefficient energy transfer between these entities. The structure contains common features of both type I and type II RCs and provides insight into the evolution of photosynthetic RCs.
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Affiliation(s)
- Jing-Hua Chen
- Department of Pathology of Sir Run Run Shaw Hospital and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China.,Center of Cryo-Electron Microscopy, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Hangjun Wu
- Department of Pathology of Sir Run Run Shaw Hospital and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China.,Center of Cryo-Electron Microscopy, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Caihuang Xu
- Department of Pathology of Sir Run Run Shaw Hospital and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China
| | - Xiao-Chi Liu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China
| | - Zihui Huang
- Department of Pathology of Sir Run Run Shaw Hospital and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China
| | - Shenghai Chang
- Department of Pathology of Sir Run Run Shaw Hospital and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China.,Center of Cryo-Electron Microscopy, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Wenda Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China
| | - Guangye Han
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China
| | - Tingyun Kuang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China.
| | - Jian-Ren Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China. .,Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 700-8530 Okayama, Japan
| | - Xing Zhang
- Department of Pathology of Sir Run Run Shaw Hospital and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China. .,Center of Cryo-Electron Microscopy, Zhejiang University, Hangzhou, 310058 Zhejiang, China.,Zhejiang Laboratory for System and Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121 Zhejiang, China
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17
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Azai C, Harada J, Fujimoto S, Masuda S, Kosumi D. Anaerobic energy dissipation by glycosylated carotenoids in the green sulfur bacterium Chlorobaculum tepidum. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2020.112828] [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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18
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Supramolecular chlorophyll aggregates inspired from specific light-harvesting antenna “chlorosome”: Static nanostructure, dynamic construction process, and versatile application. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C: PHOTOCHEMISTRY REVIEWS 2020. [DOI: 10.1016/j.jphotochemrev.2020.100385] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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19
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Orf GS, Redding KE. Perturbation of the primary acceptor chlorophyll site in the heliobacterial reaction center by coordinating amino acid substitution. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148324. [PMID: 33039349 DOI: 10.1016/j.bbabio.2020.148324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 11/19/2022]
Abstract
All known Type I photochemical reaction center protein complexes contain a form of the pigment chlorophyll a in their primary electron acceptor site (termed ec3). In the reaction center from the primitive heliobacteria (HbRC), all of the pigment cofactors are bacteriochlorophyll g except in the ec3 sites, which contain 81-hydroxychlorophyll a. To explore the energetic flexibility of this site, we performed site-directed mutagenesis on two of the amino acids of the PshA core polypeptide responsible for coordinating the 81-hydroxychlorophyll a. These two amino acids are serine-545, which coordinates the central Mg(II) through an intermediary water molecule, and serine-553, which participates in a hydrogen bond with the 131-keto O atom. Mutagenesis of serine-545 to histidine (S545H) changes how the chlorophyll's central Mg(II) is coordinated, with the result of decreasing the chlorophyll's site energy. Mutagenesis of serine-545 to methionine (S545M), which was made to mimic the ec3 site of Photosystem I, abolishes chlorophyll binding and charge separation altogether. Mutagenesis of serine-553 to alanine (S553A) removes the aforementioned hydrogen bond, increasing the site energy of the chlorophyll. In the S545H and S553A mutants, the forward and reverse electron transfer rates from ec3 are both faster. This coincides with a decrease in both the quantum yield of initial charge separation and the overall photochemical quantum yield. Taken together, these data indicate that wild-type HbRC is optimized for overall photochemical efficiency, rather than just for maximizing the forward electron transfer rate. The necessity for a chlorophyll a derivative at the ec3 site is also discussed.
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Affiliation(s)
- Gregory S Orf
- Center for Bioenergy and Photosynthesis, School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Kevin E Redding
- Center for Bioenergy and Photosynthesis, School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
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20
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Doloman A, Seefeldt LC. An Experimentally Evaluated Thermodynamic Approach to Estimate Growth of Photoheterotrophic Purple Non-sulfur Bacteria. Front Microbiol 2020; 11:540378. [PMID: 33013778 PMCID: PMC7494753 DOI: 10.3389/fmicb.2020.540378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 08/17/2020] [Indexed: 11/21/2022] Open
Abstract
Distribution of energy during the growth and formation of useful chemicals by microorganisms can define the overall performance of a biotechnological system. However, to date, this distribution has not been used to reliably predict growth characteristics of phototrophic microorganisms. The presented research addresses this application by estimating the photon-associated Gibbs energy delivered for the photoheterotrophic growth of purple non-sulfur bacteria and production of dihydrogen. The approach is successfully evaluated with the data from a fed-batch growth of Rhodopseudomonas palustris nifA∗ fixing N2 gas in phototrophic conditions and a reliable prediction of growth characteristics is demonstrated. Additionally, literature-available experimental data is collected and used for evaluation of the presented thermodynamic approach to predict photoheterotrophic growth yields. A proposed thermodynamic framework with modification to account for the phototrophic growth can be used to predict growth rates in broader environmental niches and to assess the possibility for the development of novel biotechnological applications in light-induced biological systems.
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Affiliation(s)
- Anna Doloman
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, United States
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21
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Kondo T, Mutoh R, Tabe H, Kurisu G, Oh-Oka H, Fujiyoshi S, Matsushita M. Cryogenic Single-Molecule Spectroscopy of the Primary Electron Acceptor in the Photosynthetic Reaction Center. J Phys Chem Lett 2020; 11:3980-3986. [PMID: 32352789 DOI: 10.1021/acs.jpclett.0c00891] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The photosynthetic reaction center (RC) converts light energy into electrochemical energy. The RC of heliobacteria (hRC) is a primitive homodimeric RC containing 58 bacteriochlorophylls and 2 chlorophyll as. The chlorophyll serves as the primary electron acceptor (Chl a-A0) responsible for light harvesting and charge separation. The single-molecule spectroscopy of Chl a-A0 can be used to investigate heterogeneities of the RC photochemical function, though the low fluorescence quantum yield (0.1%) makes it difficult. Here, we show the fluorescence excitation spectroscopy of individual Chl a-A0s in single hRCs at 6 K. The fluorescence quantum yield and absorption cross section of Chl a-A0 increase 2- and 4-fold, respectively, compared to those at room temperature. The two Chl a-A0s in single hRCs are identified as two distinct peaks in the fluorescence excitation spectrum, exhibiting different excitation polarization dependences. The spectral changes caused by photobleaching indicate the energy transfer across subunits in the hRC.
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Affiliation(s)
- Toru Kondo
- Department of Physics, Graduate School of Science and Engineering, Tokyo Institute of Technology, Meguro, Tokyo 152-8551, Japan
| | - Risa Mutoh
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hiroaki Tabe
- Department of Physics, Graduate School of Science and Engineering, Tokyo Institute of Technology, Meguro, Tokyo 152-8551, Japan
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hirozo Oh-Oka
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Satoru Fujiyoshi
- Department of Physics, Graduate School of Science and Engineering, Tokyo Institute of Technology, Meguro, Tokyo 152-8551, Japan
| | - Michio Matsushita
- Department of Physics, Graduate School of Science and Engineering, Tokyo Institute of Technology, Meguro, Tokyo 152-8551, Japan
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22
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Liu J, Friebe VM, Frese RN, Jones MR. Polychromatic solar energy conversion in pigment-protein chimeras that unite the two kingdoms of (bacterio)chlorophyll-based photosynthesis. Nat Commun 2020; 11:1542. [PMID: 32210238 PMCID: PMC7093453 DOI: 10.1038/s41467-020-15321-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/03/2020] [Indexed: 12/01/2022] Open
Abstract
Natural photosynthesis can be divided between the chlorophyll-containing plants, algae and cyanobacteria that make up the oxygenic phototrophs and a diversity of bacteriochlorophyll-containing bacteria that make up the anoxygenic phototrophs. Photosynthetic light harvesting and reaction centre proteins from both kingdoms have been exploited for solar energy conversion, solar fuel synthesis and sensing technologies, but the energy harvesting abilities of these devices are limited by each protein's individual palette of pigments. In this work we demonstrate a range of genetically-encoded, self-assembling photosystems in which recombinant plant light harvesting complexes are covalently locked with reaction centres from a purple photosynthetic bacterium, producing macromolecular chimeras that display mechanisms of polychromatic solar energy harvesting and conversion. Our findings illustrate the power of a synthetic biology approach in which bottom-up construction of photosystems using naturally diverse but mechanistically complementary components can be achieved in a predictable fashion through the encoding of adaptable, plug-and-play covalent interfaces.
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Affiliation(s)
- Juntai Liu
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Vincent M Friebe
- Department of Physics and Astronomy, LaserLaB Amsterdam, VU University Amsterdam, De Boelelaan 1081, Amsterdam, 1081 HV, The Netherlands
| | - Raoul N Frese
- Department of Physics and Astronomy, LaserLaB Amsterdam, VU University Amsterdam, De Boelelaan 1081, Amsterdam, 1081 HV, The Netherlands
| | - Michael R Jones
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, BS8 1TD, UK.
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23
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Liu Z, Wang K, Chen Y, Tan T, Nielsen J. Third-generation biorefineries as the means to produce fuels and chemicals from CO2. Nat Catal 2020. [DOI: 10.1038/s41929-019-0421-5] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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24
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Bertsova YV, Mamedov MD, Bogachev AV. Na+-Translocating Ferredoxin:NAD+ Oxidoreductase Is a Component of Photosynthetic Electron Transport Chain in Green Sulfur Bacteria. BIOCHEMISTRY (MOSCOW) 2019; 84:1403-1410. [PMID: 31760926 DOI: 10.1134/s0006297919110142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Genomes of photoautotrophic organisms containing type I photosynthetic reaction center were searched for the rnf genes encoding Na+-translocating ferredoxin:NAD+ oxidoreductase (RNF). These genes were absent in heliobacteria, cyanobacteria, algae, and plants; however, genomes of many green sulfur bacteria (especially marine ones) were found to contain the full rnf operon. Analysis of RNA isolated from the marine green sulfur bacterium Chlorobium phaeovibrioides revealed a high level of rnf expression. It was found that the activity of Na+-dependent flavodoxin:NAD+ oxidoreductase detected in the membrane fraction of Chl. phaeovibrioides was absent in the membrane fraction of the freshwater green sulfur bacterium Chlorobaculum limnaeum, which is closely related to Chl. phaeovibrioides but whose genome lacks the rnf genes. Illumination of the membrane fraction of Chl. phaeovibrioides but not of Cba. limnaeum resulted in the light-induced NAD+ reduction. Based on the obtained data, we concluded that in some green sulfur bacteria, RNF may be involved in the NADH formation that should increase the efficiency of light energy conservation in these microorganisms and can serve as the first example of the use of Na+ energetics in photosynthetic electron transport chains.
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Affiliation(s)
- Y V Bertsova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - M D Mamedov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - A V Bogachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
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25
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Bertsova YV, Kulik LV, Mamedov MD, Baykov AA, Bogachev AV. Flavodoxin with an air-stable flavin semiquinone in a green sulfur bacterium. PHOTOSYNTHESIS RESEARCH 2019; 142:127-136. [PMID: 31302833 DOI: 10.1007/s11120-019-00658-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/04/2019] [Indexed: 06/10/2023]
Abstract
Flavodoxins are small proteins with a non-covalently bound FMN that can accept two electrons and accordingly adopt three redox states: oxidized (quinone), one-electron reduced (semiquinone), and two-electron reduced (quinol). In iron-deficient cyanobacteria and algae, flavodoxin can substitute for ferredoxin as the electron carrier in the photosynthetic electron transport chain. Here, we demonstrate a similar function for flavodoxin from the green sulfur bacterium Chlorobium phaeovibrioides (cp-Fld). The expression of the cp-Fld gene, found in a close proximity with the genes for other proteins associated with iron transport and storage, increased in a low-iron medium. cp-Fld produced in Escherichia coli exhibited the optical, ERP, and electron-nuclear double resonance spectra that were similar to those of known flavodoxins. However, unlike all other flavodoxins, cp-Fld exhibited unprecedented stability of FMN semiquinone to oxidation by air and difference in midpoint redox potentials for the quinone-semiquinone and semiquinone-quinol couples (- 110 and - 530 mV, respectively). cp-Fld could be reduced by pyruvate:ferredoxin oxidoreductase found in the membrane-free extract of Chl. phaeovibrioides cells and photo-reduced by the photosynthetic reaction center found in membrane vesicles from these cells. The green sulfur bacterium Chl. phaeovibrioides appears thus to be a new type of the photosynthetic organisms that can use flavodoxin as an alternative electron carrier to cope with iron deficiency.
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Affiliation(s)
- Yulia V Bertsova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119234
| | - Leonid V Kulik
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk, Russia, 630090
- Novosibirsk State University, Novosibirsk, Russia, 630090
| | - Mahir D Mamedov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119234
| | - Alexander A Baykov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119234
| | - Alexander V Bogachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119234.
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Hamilton TL. The trouble with oxygen: The ecophysiology of extant phototrophs and implications for the evolution of oxygenic photosynthesis. Free Radic Biol Med 2019; 140:233-249. [PMID: 31078729 DOI: 10.1016/j.freeradbiomed.2019.05.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 04/03/2019] [Accepted: 05/02/2019] [Indexed: 12/11/2022]
Abstract
The ability to harvest light to drive chemical reactions and gain energy provided microbes access to high energy electron donors which fueled primary productivity, biogeochemical cycles, and microbial evolution. Oxygenic photosynthesis is often cited as the most important microbial innovation-the emergence of oxygen-evolving photosynthesis, aided by geologic events, is credited with tipping the scale from a reducing early Earth to an oxygenated world that eventually lead to complex life. Anoxygenic photosynthesis predates oxygen-evolving photosynthesis and played a key role in developing and fine-tuning the photosystem architecture of modern oxygenic phototrophs. The release of oxygen as a by-product of metabolic activity would have caused oxidative damage to anaerobic microbiota that evolved under the anoxic, reducing conditions of early Earth. Photosynthetic machinery is particularly susceptible to the adverse effects of oxygen and reactive oxygen species and these effects are compounded by light. As a result, phototrophs employ additional detoxification mechanisms to mitigate oxidative stress and have evolved alternative oxygen-dependent enzymes for chlorophyll biosynthesis. Phylogenetic reconstruction studies and biochemical characterization suggest photosynthetic reactions centers, particularly in Cyanobacteria, evolved to both increase efficiency of electron transfer and avoid photodamage caused by chlorophyll radicals that is acute in the presence of oxygen. Here we review the oxygen and reactive oxygen species detoxification mechanisms observed in extant anoxygenic and oxygenic photosynthetic bacteria as well as the emergence of these mechanisms over evolutionary time. We examine the distribution of phototrophs in modern systems and phylogenetic reconstructions to evaluate the emergence of mechanisms to mediate oxidative damage and highlight changes in photosystems and reaction centers, chlorophyll biosynthesis, and niche space in response to oxygen production. This synthesis supports an emergence of H2S-driven anoxygenic photosynthesis in Cyanobacteria prior to the evolution of oxygenic photosynthesis and underscores a role for the former metabolism in fueling fine-tuning of the oxygen evolving complex and mechanisms to repair oxidative damage. In contrast, we note the lack of elaborate mechanisms to deal with oxygen in non-cyanobacterial anoxygenic phototrophs suggesting these microbes have occupied similar niche space throughout Earth's history.
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Affiliation(s)
- Trinity L Hamilton
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA; Biotechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA.
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27
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Fufina TY, Leonova MM, Khatypov RA, Khristin AM, Shuvalov VA, Vasilieva LG. Features of Bacteriochlorophylls Axial Ligation in the Photosynthetic Reaction Center of Purple Bacteria. BIOCHEMISTRY (MOSCOW) 2019; 84:370-379. [DOI: 10.1134/s0006297919040047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Singh D, Dasgupta S. Role of Coherence in Excitation Transfer Efficiency to the Reaction Center in Photosynthetic Bacteria
Chlorobium tepidum. ChemistrySelect 2019. [DOI: 10.1002/slct.201803554] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Davinder Singh
- Department of PhysicsIndian Institute of Technology Ropar, Rupnagar Punjab - 140001 India
| | - Shubhrangshu Dasgupta
- Department of PhysicsIndian Institute of Technology Ropar, Rupnagar Punjab - 140001 India
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29
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Magdaong NCM, Niedzwiedzki DM, Saer RG, Goodson C, Blankenship RE. Excitation energy transfer kinetics and efficiency in phototrophic green sulfur bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:1180-1190. [DOI: 10.1016/j.bbabio.2018.07.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/25/2018] [Accepted: 07/30/2018] [Indexed: 01/16/2023]
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30
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Blankenship RE, Brune DC, Olson JC. Remembering John M. Olson (1929-2017). PHOTOSYNTHESIS RESEARCH 2018; 137:161-169. [PMID: 29460034 DOI: 10.1007/s11120-018-0489-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 02/15/2018] [Indexed: 06/08/2023]
Abstract
Here we provide reflections of and a tribute to John M. Olson, a pioneering researcher in photosynthesis. We trace his career, which began at Wesleyan University and the University of Pennsylvania, and continued at Utrech in The Netherlands, Brookhaven National Laboratory, and Odense University in Denmark. He was the world expert on pigment organization in the green photosynthetic bacteria, and discovered and characterized the first chlorophyll-containing protein, which has come to be known as the Fenna-Matthews-Olson (FMO) protein. He also thought and wrote extensively on the origin and early evolution of photosynthesis. We include personal comments from Brian Matthews, Raymond Cox, Paolo Gerola, Beverly Pierson and Jon Olson.
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Affiliation(s)
- Robert E Blankenship
- Departments of Biology and Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA.
| | - Daniel C Brune
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Jon C Olson
- Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, Amherst, MA, 01002, USA
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Fulton JM, Arthur MA, Thomas B, Freeman KH. Pigment carbon and nitrogen isotopic signatures in euxinic basins. GEOBIOLOGY 2018; 16:429-445. [PMID: 29577577 DOI: 10.1111/gbi.12285] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 02/12/2018] [Indexed: 06/08/2023]
Abstract
The carbon and nitrogen isotopic signatures of chloropigments and porphyrins from the sediments of redox-stratified lakes and marine basins reveal details of past biogeochemical nutrient cycling. Such interpretations are strengthened by modern calibration studies, and here, we report on the C and N isotopic composition of pigments and nutrients in the water column and surface sediment of redox-stratified Fayetteville Green Lake (FGL; New York). We also report δ13 C and δ15 N values for pyropheophytin a (Pphe a) and bacteriochlorophyll e (Bchl e) deposited in the Black Sea during its transition to a redox-stratified basin ca. 7.8 ka. We propose a model for evolving nutrient cycling in the Black Sea from 7.8 to 6.4 ka, informed by the new pigment data from FGL. The seasonal study of water column nutrients and pigments at FGL revealed population dynamics in surface and deep waters that were also captured in the sediments. Biomass was greatest near the chemocline, where cyanobacteria, purple sulfur bacteria (PSB), and green sulfur bacteria (GSB) had seasonally variable populations. Bulk organic matter in the surface sediment, however, was derived mainly from the oxygenated surface waters. Surface sediment pigment δ13 C and δ15 N values indicate intact chlorophyll a (Chl a) was derived from near the chemocline, but its degradation product pheophytin a (Phe a) was derived primarily from surface waters. Bacteriopheophytin a (Bphe a) and Bchl e in the sediments came from chemocline populations of PSB and GSB, respectively. The distinctive δ13 C and δ15 N values for Chl a, Phe a, and Bphe a in the surface sediment are inputs to an isotopic mixing model that shows their decomposition to a common porphyrin derivative can produce non-specific sedimentary isotope signatures. This model serves as a caveat for paleobiogeochemical interpretations in basins that had diverse populations near a shallow chemocline.
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Affiliation(s)
- J M Fulton
- Department of Geosciences, Baylor University, Waco, TX, USA
| | - M A Arthur
- Department of Geosciences, The Pennsylvania State University, University Park, PA, USA
| | - B Thomas
- Department of Environmental and Earth Sciences, Willamette University, Salem, OR, USA
| | - K H Freeman
- Department of Geosciences, The Pennsylvania State University, University Park, PA, USA
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Identification and characterization of diverse coherences in the Fenna-Matthews-Olson complex. Nat Chem 2018; 10:780-786. [PMID: 29785033 DOI: 10.1038/s41557-018-0060-5] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 04/04/2018] [Indexed: 11/08/2022]
Abstract
The idea that excitonic (electronic) coherences are of fundamental importance to natural photosynthesis gained popularity when slowly dephasing quantum beats (QBs) were observed in the two-dimensional electronic spectra of the Fenna-Matthews-Olson (FMO) complex at 77 K. These were assigned to superpositions of excitonic states, a controversial interpretation, as the strong chromophore-environment interactions in the complex suggest fast dephasing. Although it has been pointed out that vibrational motion produces similar spectral signatures, a concrete assignment of these oscillatory signals to distinct physical processes is still lacking. Here we revisit the coherence dynamics of the FMO complex using polarization-controlled two-dimensional electronic spectroscopy, supported by theoretical modelling. We show that the long-lived QBs are exclusively vibrational in origin, whereas the dephasing of the electronic coherences is completed within 240 fs even at 77 K. We further find that specific vibrational coherences are produced via vibronically coupled excited states. The presence of such states suggests that vibronic coupling is relevant for photosynthetic energy transfer.
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33
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Haas S, de Beer D, Klatt JM, Fink A, Rench RM, Hamilton TL, Meyer V, Kakuk B, Macalady JL. Low-Light Anoxygenic Photosynthesis and Fe-S-Biogeochemistry in a Microbial Mat. Front Microbiol 2018; 9:858. [PMID: 29755448 PMCID: PMC5934491 DOI: 10.3389/fmicb.2018.00858] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 04/13/2018] [Indexed: 11/24/2022] Open
Abstract
We report extremely low-light-adapted anoxygenic photosynthesis in a thick microbial mat in Magical Blue Hole, Abaco Island, The Bahamas. Sulfur cycling was reduced by iron oxides and organic carbon limitation. The mat grows below the halocline/oxycline at 30 m depth on the walls of the flooded sinkhole. In situ irradiance at the mat surface on a sunny December day was between 0.021 and 0.084 μmol photons m-2 s-1, and UV light (<400 nm) was the most abundant part of the spectrum followed by green wavelengths (475–530 nm). We measured a light-dependent carbon uptake rate of 14.5 nmol C cm-2 d-1. A 16S rRNA clone library of the green surface mat layer was dominated (74%) by a cluster (>97% sequence identity) of clones affiliated with Prosthecochloris, a genus within the green sulfur bacteria (GSB), which are obligate anoxygenic phototrophs. Typical photopigments of brown-colored GSB, bacteriochlorophyll e and (β-)isorenieratene, were abundant in mat samples and their absorption properties are well-adapted to harvest light in the available green and possibly even UV-A spectra. Sulfide from the water column (3–6 μmol L-1) was the main source of sulfide to the mat as sulfate reduction rates in the mats were very low (undetectable-99.2 nmol cm-3 d-1). The anoxic water column was oligotrophic and low in dissolved organic carbon (175–228 μmol L-1). High concentrations of pyrite (FeS2; 1–47 μmol cm-3) together with low microbial process rates (sulfate reduction, CO2 fixation) indicate that the mats function as net sulfide sinks mainly by abiotic processes. We suggest that abundant Fe(III) (4.3–22.2 μmol cm-3) is the major source of oxidizing power in the mat, and that abiotic Fe-S-reactions play the main role in pyrite formation. Limitation of sulfate reduction by low organic carbon availability along with the presence of abundant sulfide-scavenging iron oxides considerably slowed down sulfur cycling in these mats.
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Affiliation(s)
- Sebastian Haas
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Department of Oceanography, Dalhousie University, Halifax, NS, Canada
| | - Dirk de Beer
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Judith M Klatt
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, United States
| | - Artur Fink
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rebecca McCauley Rench
- Geosciences Department, Pennsylvania State University, University Park, PA, United States
| | - Trinity L Hamilton
- Department of Plant and Microbial Biology, University of Minnesota, Minneapolis, MN, United States
| | - Volker Meyer
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Brian Kakuk
- Bahamas Caves Research Foundation, Marsh Harbour, Bahamas
| | - Jennifer L Macalady
- Geosciences Department, Pennsylvania State University, University Park, PA, United States
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Hamilton TL, Welander PV, Albrecht HL, Fulton JM, Schaperdoth I, Bird LR, Summons RE, Freeman KH, Macalady JL. Microbial communities and organic biomarkers in a Proterozoic-analog sinkhole. GEOBIOLOGY 2017; 15:784-797. [PMID: 29035021 DOI: 10.1111/gbi.12252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 07/07/2017] [Indexed: 06/07/2023]
Abstract
Little Salt Spring (Sarasota County, FL, USA) is a sinkhole with groundwater vents at ~77 m depth. The entire water column experiences sulfidic (~50 μM) conditions seasonally, resulting in a system poised between oxic and sulfidic conditions. Red pinnacle mats occupy the sediment-water interface in the sunlit upper basin of the sinkhole, and yielded 16S rRNA gene clones affiliated with Cyanobacteria, Chlorobi, and sulfate-reducing clades of Deltaproteobacteria. Nine bacteriochlorophyll e homologues and isorenieratene indicate contributions from Chlorobi, and abundant chlorophyll a and pheophytin a are consistent with the presence of Cyanobacteria. The red pinnacle mat contains hopanoids, including 2-methyl structures that have been interpreted as biomarkers for Cyanobacteria. A single sequence of hpnP, the gene required for methylation of hopanoids at the C-2 position, was recovered in both DNA and cDNA libraries from the red pinnacle mat. The hpnP sequence was most closely related to cyanobacterial hpnP sequences, implying that Cyanobacteria are a source of 2-methyl hopanoids present in the mat. The mats are capable of light-dependent primary productivity as evidenced by 13 C-bicarbonate photoassimilation. We also observed 13 C-bicarbonate photoassimilation in the presence of DCMU, an inhibitor of electron transfer to Photosystem II. Our results indicate that the mats carry out light-driven primary production in the absence of oxygen production-a mechanism that may have delayed the oxygenation of the Earth's oceans and atmosphere during the Proterozoic Eon. Furthermore, our observations of the production of 2-methyl hopanoids by Cyanobacteria under conditions of low oxygen and low light are consistent with the recovery of these structures from ancient black shales as well as their paucity in modern marine environments.
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Affiliation(s)
- T L Hamilton
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - P V Welander
- Department of Earth System Science, Stanford University, Stanford, CA, USA
| | - H L Albrecht
- Department of Geosciences and the Penn State Astrobiology Research Center (PSARC), The Pennsylvania State University, University Park, PA, USA
| | - J M Fulton
- Department of Geosciences, Baylor University, Waco, TX, USA
| | - I Schaperdoth
- Department of Geosciences and the Penn State Astrobiology Research Center (PSARC), The Pennsylvania State University, University Park, PA, USA
| | - L R Bird
- Department of Geosciences and the Penn State Astrobiology Research Center (PSARC), The Pennsylvania State University, University Park, PA, USA
| | - R E Summons
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - K H Freeman
- Department of Geosciences and the Penn State Astrobiology Research Center (PSARC), The Pennsylvania State University, University Park, PA, USA
| | - J L Macalady
- Department of Geosciences and the Penn State Astrobiology Research Center (PSARC), The Pennsylvania State University, University Park, PA, USA
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35
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Light harvesting in phototrophic bacteria: structure and function. Biochem J 2017; 474:2107-2131. [DOI: 10.1042/bcj20160753] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/03/2017] [Accepted: 04/06/2017] [Indexed: 12/23/2022]
Abstract
This review serves as an introduction to the variety of light-harvesting (LH) structures present in phototrophic prokaryotes. It provides an overview of the LH complexes of purple bacteria, green sulfur bacteria (GSB), acidobacteria, filamentous anoxygenic phototrophs (FAP), and cyanobacteria. Bacteria have adapted their LH systems for efficient operation under a multitude of different habitats and light qualities, performing both oxygenic (oxygen-evolving) and anoxygenic (non-oxygen-evolving) photosynthesis. For each LH system, emphasis is placed on the overall architecture of the pigment–protein complex, as well as any relevant information on energy transfer rates and pathways. This review addresses also some of the more recent findings in the field, such as the structure of the CsmA chlorosome baseplate and the whole-cell kinetics of energy transfer in GSB, while also pointing out some areas in need of further investigation.
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36
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Two-dimensional electronic spectra of the photosynthetic apparatus of green sulfur bacteria. Sci Rep 2017; 7:45245. [PMID: 28345621 PMCID: PMC5366913 DOI: 10.1038/srep45245] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 02/21/2017] [Indexed: 12/25/2022] Open
Abstract
Advances in time resolved spectroscopy have provided new insight into the energy transmission in natural photosynthetic complexes. Novel theoretical tools and models are being developed in order to explain the experimental results. We provide a model calculation for the two-dimensional electronic spectra of Cholorobaculum tepidum which correctly describes the main features and transfer time scales found in recent experiments. From our calculation one can infer the coupling of the antenna chlorosome with the environment and the coupling between the chlorosome and the Fenna-Matthews-Olson complex. We show that environment assisted transport between the subunits is the required mechanism to reproduce the experimental two-dimensional electronic spectra.
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Ferlez B, Agostini A, Carbonera D, Golbeck JH, van der Est A. Triplet Charge Recombination in Heliobacterial Reaction Centers Does Not Produce a Spin-Polarized EPR Spectrum. Z PHYS CHEM 2016. [DOI: 10.1515/zpch-2016-0825] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
In photosynthetic reaction centers, reduction of the secondary acceptors leads to triplet charge recombination of the primary radical pair (RP). This process is spin selective and in a magnetic field it populates only the T0 state of the donor triplet state. As a result, the triplet state of the donor has a distinctive spin polarization pattern that can be measured by transient electron paramagnetic resonance (TREPR) spectroscopy. In heliobacterial reaction centers (HbRCs), the primary donor, P800, is composed of two bacteriochlorophyll g′ molecules and its triplet state has not been studied as extensively as those of other reaction centers. Here, we present TREPR and optically detected magnetic resonance (ODMR) data of 3P800 and show that although it can be detected by ODMR it is not observed in the TREPR data. We demonstrate that the absence of the TREPR spectrum is a result of the fact that the zero-field splitting (ZFS) tensor of 3P800 is maximally rhombic, which results in complete cancelation of the absorptive and emissive polarization in randomly oriented samples.
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Affiliation(s)
- Bryan Ferlez
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States of America
| | - Alessandro Agostini
- Dipartimento di Scienze Chimiche, Università di Padova, Via Marzolo, 1, 35131 Padova, Italy
| | - Donatella Carbonera
- Dipartimento di Scienze Chimiche, Università di Padova, Via Marzolo, 1, 35131 Padova, Italy
| | - John H. Golbeck
- Department of Biochemistry and Molecular Biology and Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States of America
- Freiburg Institute of Advanced Studies (FRIAS), Albert-Ludwigs-Universität Freiburg, Albertstr.19, 79104 Freiburg, Germany
| | - Art van der Est
- Freiburg Institute of Advanced Studies (FRIAS), Albert-Ludwigs-Universität Freiburg, Albertstr.19, 79104 Freiburg, Germany
- Departments of Chemistry and Physics, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON, Canada L2S 3A1
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Orf GS, Saer RG, Niedzwiedzki DM, Zhang H, McIntosh CL, Schultz JW, Mirica LM, Blankenship RE. Evidence for a cysteine-mediated mechanism of excitation energy regulation in a photosynthetic antenna complex. Proc Natl Acad Sci U S A 2016; 113:E4486-93. [PMID: 27335466 PMCID: PMC4978306 DOI: 10.1073/pnas.1603330113] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Light-harvesting antenna complexes not only aid in the capture of solar energy for photosynthesis, but regulate the quantity of transferred energy as well. Light-harvesting regulation is important for protecting reaction center complexes from overexcitation, generation of reactive oxygen species, and metabolic overload. Usually, this regulation is controlled by the association of light-harvesting antennas with accessory quenchers such as carotenoids. One antenna complex, the Fenna-Matthews-Olson (FMO) antenna protein from green sulfur bacteria, completely lacks carotenoids and other known accessory quenchers. Nonetheless, the FMO protein is able to quench energy transfer in aerobic conditions effectively, indicating a previously unidentified type of regulatory mechanism. Through de novo sequencing MS, chemical modification, and mutagenesis, we have pinpointed the source of the quenching action to cysteine residues (Cys49 and Cys353) situated near two low-energy bacteriochlorophylls in the FMO protein from Chlorobaculum tepidum Removal of these cysteines (particularly removal of the completely conserved Cys353) through N-ethylmaleimide modification or mutagenesis to alanine abolishes the aerobic quenching effect. Electrochemical analysis and electron paramagnetic resonance spectra suggest that in aerobic conditions the cysteine thiols are converted to thiyl radicals which then are capable of quenching bacteriochlorophyll excited states through electron transfer photochemistry. This simple mechanism has implications for the design of bio-inspired light-harvesting antennas and the redesign of natural photosynthetic systems.
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Affiliation(s)
- Gregory S Orf
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130; Department of Biology, Washington University in St. Louis, St. Louis, MO 63130; Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, MO 63130
| | - Rafael G Saer
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130; Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, MO 63130
| | - Dariusz M Niedzwiedzki
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, MO 63130
| | - Hao Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130; Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, MO 63130
| | - Chelsea L McIntosh
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Jason W Schultz
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Liviu M Mirica
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Robert E Blankenship
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130; Department of Biology, Washington University in St. Louis, St. Louis, MO 63130; Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, MO 63130
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Ho MY, Shen G, Canniffe DP, Zhao C, Bryant DA. Light-dependent chlorophyll f synthase is a highly divergent paralog of PsbA of photosystem II. Science 2016; 353:science.aaf9178. [PMID: 27386923 DOI: 10.1126/science.aaf9178] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 06/22/2016] [Indexed: 12/22/2022]
Abstract
Chlorophyll f (Chl f) permits some cyanobacteria to expand the spectral range for photosynthesis by absorbing far-red light. We used reverse genetics and heterologous expression to identify the enzyme for Chl f synthesis. Null mutants of "super-rogue" psbA4 genes, divergent paralogs of psbA genes encoding the D1 core subunit of photosystem II, abolished Chl f synthesis in two cyanobacteria that grow in far-red light. Heterologous expression of the psbA4 gene, which we rename chlF, enables Chl f biosynthesis in Synechococcus sp. PCC 7002. Because the reaction requires light, Chl f synthase is probably a photo-oxidoreductase that employs catalytically useful Chl a molecules, tyrosine YZ, and plastoquinone (as does photosystem II) but lacks a Mn4Ca1O5 cluster. Introduction of Chl f biosynthesis into crop plants could expand their ability to use solar energy.
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Affiliation(s)
- Ming-Yang Ho
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Gaozhong Shen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Daniel P Canniffe
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Chi Zhao
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802, USA. Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA. Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore.
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40
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In situ mapping of the energy flow through the entire photosynthetic apparatus. Nat Chem 2016; 8:705-10. [PMID: 27325098 DOI: 10.1038/nchem.2525] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 04/05/2016] [Indexed: 12/21/2022]
Abstract
Absorption of sunlight is the first step in photosynthesis, which provides energy for the vast majority of organisms on Earth. The primary processes of photosynthesis have been studied extensively in isolated light-harvesting complexes and reaction centres, however, to understand fully the way in which organisms capture light it is crucial to also reveal the functional relationships between the individual complexes. Here we report the use of two-dimensional electronic spectroscopy to track directly the excitation-energy flow through the entire photosynthetic system of green sulfur bacteria. We unravel the functional organization of individual complexes in the photosynthetic unit and show that, whereas energy is transferred within subunits on a timescale of subpicoseconds to a few picoseconds, across the complexes the energy flows at a timescale of tens of picoseconds. Thus, we demonstrate that the bottleneck of energy transfer is between the constituents.
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41
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Nowicka B, Kruk J. Powered by light: Phototrophy and photosynthesis in prokaryotes and its evolution. Microbiol Res 2016; 186-187:99-118. [PMID: 27242148 DOI: 10.1016/j.micres.2016.04.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/12/2016] [Accepted: 04/01/2016] [Indexed: 11/29/2022]
Abstract
Photosynthesis is a complex metabolic process enabling photosynthetic organisms to use solar energy for the reduction of carbon dioxide into biomass. This ancient pathway has revolutionized life on Earth. The most important event was the development of oxygenic photosynthesis. It had a tremendous impact on the Earth's geochemistry and the evolution of living beings, as the rise of atmospheric molecular oxygen enabled the development of a highly efficient aerobic metabolism, which later led to the evolution of complex multicellular organisms. The mechanism of photosynthesis has been the subject of intensive research and a great body of data has been accumulated. However, the evolution of this process is not fully understood, and the development of photosynthesis in prokaryota in particular remains an unresolved question. This review is devoted to the occurrence and main features of phototrophy and photosynthesis in prokaryotes. Hypotheses concerning the origin and spread of photosynthetic traits in bacteria are also discussed.
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Affiliation(s)
- Beatrycze Nowicka
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
| | - Jerzy Kruk
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
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42
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Bína D, Gardian Z, Vácha F, Litvín R. Native FMO-reaction center supercomplex in green sulfur bacteria: an electron microscopy study. PHOTOSYNTHESIS RESEARCH 2016; 128:93-102. [PMID: 26589322 DOI: 10.1007/s11120-015-0205-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/12/2015] [Indexed: 06/05/2023]
Abstract
Chlorobaculum tepidum is a representative of green sulfur bacteria, a group of anoxygenic photoautotrophs that employ chlorosomes as the main light-harvesting structures. Chlorosomes are coupled to a ferredoxin-reducing reaction center by means of the Fenna-Matthews-Olson (FMO) protein. While the biochemical properties and physical functioning of all the individual components of this photosynthetic machinery are quite well understood, the native architecture of the photosynthetic supercomplexes is not. Here we report observations of membrane-bound FMO and the analysis of the respective FMO-reaction center complex. We propose the existence of a supercomplex formed by two reaction centers and four FMO trimers based on the single-particle analysis of the complexes attached to native membrane. Moreover, the structure of the photosynthetic unit comprising the chlorosome with the associated pool of RC-FMO supercomplexes is proposed.
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Affiliation(s)
- David Bína
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic.
- Institute of Plant Molecular Biology, Biology Centre CAS, Branišovská 31, 370 05, České Budějovice, Czech Republic.
| | - Zdenko Gardian
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
- Institute of Plant Molecular Biology, Biology Centre CAS, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - František Vácha
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
- Institute of Plant Molecular Biology, Biology Centre CAS, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Radek Litvín
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
- Institute of Plant Molecular Biology, Biology Centre CAS, Branišovská 31, 370 05, České Budějovice, Czech Republic
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43
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Azai C, Sano Y, Kato Y, Noguchi T, Oh-oka H. Mutation-induced perturbation of the special pair P840 in the homodimeric reaction center in green sulfur bacteria. Sci Rep 2016; 6:19878. [PMID: 26804137 PMCID: PMC4726426 DOI: 10.1038/srep19878] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/18/2015] [Indexed: 11/11/2022] Open
Abstract
Homodimeric photosynthetic reaction centers (RCs) in green sulfur bacteria and heliobacteria are functional homologs of Photosystem (PS) I in oxygenic phototrophs. They show unique features in their electron transfer reactions; however, detailed structural information has not been available so far. We mutated PscA-Leu688 and PscA-Val689 to cysteine residues in the green sulfur bacterium Chlorobaculum tepidum; these residues were predicted to interact with the special pair P840, based on sequence comparison with PS I. Spectroelectrochemical measurements showed that the L688C and V689C mutations altered a near-infrared difference spectrum upon P840 oxidation, as well as the redox potential of P840. Light-induced Fourier transform infrared difference measurements showed that the L688C mutation induced a differential signal of the S-H stretching vibration in the P840+/P840 spectrum, as reported in P800+/P800 difference spectrum in a heliobacterial RC. Spectral changes in the 131-keto C=O region, caused by both mutations, revealed corresponding changes in the electronic structure of P840 and in the hydrogen-bonding interaction at the 131-keto C=O group. These results suggest that there is a common spatial configuration around the special pair sites among type 1 RCs. The data also provided evidence that P840 has a symmetric electronic structure, as expected from a homodimeric RC.
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Affiliation(s)
- Chihiro Azai
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Yuko Sano
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Yuki Kato
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Takumi Noguchi
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Hirozo Oh-oka
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
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44
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Kondo T, Itoh S, Matsuoka M, Azai C, Oh-oka H. Menaquinone as the Secondary Electron Acceptor in the Type I Homodimeric Photosynthetic Reaction Center of Heliobacterium modesticaldum. J Phys Chem B 2015; 119:8480-9. [PMID: 26075484 DOI: 10.1021/acs.jpcb.5b03723] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The type I photosynthetic reaction center (RC) of heliobacteria (hRC) is a homodimer containing cofactors almost analogous to those in the plant photosystem I (PS I). However, its three-dimensional structure is not yet clear. PS I uses phylloquinone (PhyQ) as a secondary electron acceptor (A1), while the available evidence has suggested that menaquinone (MQ) in hRC has no function as A1. The present study identified a new transient electron spin-polarized electron paramagnetic resonance (ESP-EPR) signal, arising from the radical pair of the oxidized electron donor and the reduced electron acceptor (P800(+)MQ(-)), in the hRC core complex and membranes from Heliobacterium modesticaldum. The ESP signal could be detected at 5-20 K upon flash excitation only after prereduction of the iron-sulfur center, F(X), and was selectively lost by extraction of MQ with diethyl ether. MQ was suggested to be located closer to F(X) than PhyQ in PS I based on the simulation of the unique A/E (A, absorption; E, emission) ESP pattern, the reduction/oxidation rates of MQ, and the power saturation property of the static MQ(-) signal. The result revealed the quinone usage as the secondary electron acceptor in hRC, as in the case of PS I.
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Affiliation(s)
| | | | - Masahiro Matsuoka
- §Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Chihiro Azai
- §Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Hirozo Oh-oka
- §Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
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45
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He G, Niedzwiedzki DM, Orf GS, Zhang H, Blankenship RE. Dynamics of Energy and Electron Transfer in the FMO-Reaction Center Core Complex from the Phototrophic Green Sulfur Bacterium Chlorobaculum tepidum. J Phys Chem B 2015; 119:8321-9. [PMID: 26061391 DOI: 10.1021/acs.jpcb.5b04170] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The reaction center core (RCC) complex and the RCC with associated Fenna-Matthews-Olson protein (FMO-RCC) complex from the green sulfur bacterium Chlorobaculum tepidum were studied comparatively by steady-state and time-resolved fluorescence (TRF) and femtosecond time-resolved transient absorption (TA) spectroscopies. The energy transfer efficiency from the FMO to the RCC complex was calculated to be ∼40% based on the steady-state fluorescence. TRF showed that most of the FMO complexes (66%), regardless of the fact that they were physically attached to the RCC, were not able to transfer excitation energy to the reaction center. The TA spectra of the RCC complex showed a 30-38 ps lifetime component regardless of the excitation wavelengths, which is attributed to charge separation. Excitonic equilibration was shown in TA spectra of the RCC complex when excited into the BChl a Qx band at 590 nm and the Chl a Qy band at 670 nm, while excitation at 840 nm directly populated the low-energy excited state and equilibration within the excitonic BChl a manifold was not observed. The TA spectra for the FMO-RCC complex excited into the BChl a Qx band could be interpreted by a combination of the excited FMO protein and RCC complex. The FMO-RCC complex showed an additional fast kinetic component compared with the FMO protein and the RCC complex, which may be due to FMO-to-RCC energy transfer.
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Affiliation(s)
- Guannan He
- †Departments of Chemistry and Biology and ‡Photosynthetic Antenna Research Center (PARC), Washington University in St. Louis, St Louis, Missouri 63130, United States
| | - Dariusz M Niedzwiedzki
- †Departments of Chemistry and Biology and ‡Photosynthetic Antenna Research Center (PARC), Washington University in St. Louis, St Louis, Missouri 63130, United States
| | - Gregory S Orf
- †Departments of Chemistry and Biology and ‡Photosynthetic Antenna Research Center (PARC), Washington University in St. Louis, St Louis, Missouri 63130, United States
| | - Hao Zhang
- †Departments of Chemistry and Biology and ‡Photosynthetic Antenna Research Center (PARC), Washington University in St. Louis, St Louis, Missouri 63130, United States
| | - Robert E Blankenship
- †Departments of Chemistry and Biology and ‡Photosynthetic Antenna Research Center (PARC), Washington University in St. Louis, St Louis, Missouri 63130, United States
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Abstract
Technical progress in laser-sources and detectors has allowed the temporal and spatial resolution of chemical reactions down to femtoseconds and Å-units. In photon-excitable systems the key to chemical kinetics, trajectories across the vibrational saddle landscape, are experimentally accessible. Simple and thus well-defined chemical compounds are preferred objects for calibrating new methodologies and carving out paradigms of chemical dynamics, as shown in several contributions to this Faraday Discussion. Aerobic life on earth is powered by solar energy, which is captured by microorganisms and plants. Oxygenic photosynthesis relies on a three billion year old molecular machinery which is as well defined as simpler chemical constructs. It has been analysed to a very high precision. The transfer of excitation between pigments in antennae proteins, of electrons between redox-cofactors in reaction centres, and the oxidation of water by a Mn4Ca-cluster are solid state reactions. ATP, the general energy currency of the cell, is synthesized by a most agile, rotary molecular machine. While the efficiency of photosynthesis competes well with photovoltaics at the time scale of nanoseconds, it is lower by an order of magnitude for crops and again lower for bio-fuels. The enormous energy demand of mankind calls for engineered (bio-mimetic or bio-inspired) solar-electric and solar-fuel devices.
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Affiliation(s)
- Wolfgang Junge
- Dept. Biology & Chemistry, University of Osnabrück, R. 35/E42 Barbarastrasse 11, 49076 Osnabrück, Germany.
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47
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Abstract
Oxygenic photosynthesis is the principal converter of sunlight into chemical energy on Earth. Cyanobacteria and plants provide the oxygen, food, fuel, fibers, and platform chemicals for life on Earth. The conversion of solar energy into chemical energy is catalyzed by two multisubunit membrane protein complexes, photosystem I (PSI) and photosystem II (PSII). Light is absorbed by the pigment cofactors, and excitation energy is transferred among the antennae pigments and converted into chemical energy at very high efficiency. Oxygenic photosynthesis has existed for more than three billion years, during which its molecular machinery was perfected to minimize wasteful reactions. Light excitation transfer and singlet trapping won over fluorescence, radiation-less decay, and triplet formation. Photosynthetic reaction centers operate in organisms ranging from bacteria to higher plants. They are all evolutionarily linked. The crystal structure determination of photosynthetic protein complexes sheds light on the various partial reactions and explains how they are protected against wasteful pathways and why their function is robust. This review discusses the efficiency of photosynthetic solar energy conversion.
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Affiliation(s)
- Nathan Nelson
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel;
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48
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Kudryashev M, Aktoudianaki A, Dedoglou D, Stahlberg H, Tsiotis G. The ultrastructure of Chlorobaculum tepidum revealed by cryo-electron tomography. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1635-42. [DOI: 10.1016/j.bbabio.2014.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 06/04/2014] [Accepted: 06/10/2014] [Indexed: 11/28/2022]
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49
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He G, Zhang H, King JD, Blankenship RE. Structural analysis of the homodimeric reaction center complex from the photosynthetic green sulfur bacterium Chlorobaculum tepidum. Biochemistry 2014; 53:4924-30. [PMID: 25014729 PMCID: PMC4372062 DOI: 10.1021/bi5006464] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
The reaction center (RC) complex
of the green sulfur bacterium Chlorobaculum tepidum is composed of the Fenna–Matthews–Olson
antenna protein (FMO) and the reaction center core (RCC) complex.
The RCC complex has four subunits: PscA, PscB, PscC, and PscD. We
studied the FMO/RCC complex by chemically cross-linking the purified
sample followed by biochemical and spectroscopic analysis. Blue-native
gels showed that there were two types of FMO/RCC complexes, which
are consistent with complexes with one copy of FMO per RCC and two
copies of FMO per RCC. Sodium dodecyl sulfate–polyacrylamide
gel electrophoresis analysis of the samples after cross-linking showed
that all five subunits of the RC can be linked by three different
cross-linkers: bissulfosuccinimidyl suberate, disuccinimidyl suberate,
and 3,3-dithiobis-sulfosuccinimidyl propionate. The interaction sites
of the cross-linked complex were also studied using liquid chromatography
coupled to tandem mass spectrometry. The results indicated that FMO,
PscB, PscD, and part of PscA are exposed on the cytoplasmic side of
the membrane. PscD helps stabilize FMO to the reaction center and
may facilitate transfer of the electron from the RC to ferredoxin.
The soluble domain of the heme-containing cytochrome subunit PscC
and part of the core subunit PscA are located on the periplasmic side
of the membrane. There is a close relationship between the periplasmic
portions of PscA and PscC, which is needed for the efficient transfer
of the electron between PscC and P840.
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Affiliation(s)
- Guannan He
- Department of Chemistry, Washington University in St. Louis , St. Louis, Missouri 63130, United States
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50
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Kashey TS, Cowgill JB, McConnell MD, Flores M, Redding KE. Expression and characterization of cytochrome c553 from Heliobacterium modesticaldum. PHOTOSYNTHESIS RESEARCH 2014; 120:291-299. [PMID: 24557489 DOI: 10.1007/s11120-014-9982-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 02/05/2014] [Indexed: 06/03/2023]
Abstract
Cytochrome c553 of Heliobacterium modesticaldum is the donor to P800 (+), the primary electron donor of the heliobacterial reaction center (HbRC). It is a membrane-anchored 14-kDa cytochrome that accomplishes electron transfer from the cytochrome bc complex to the HbRC. The petJ gene encoding cyt c 553 was cloned and expressed in Escherichia coli with a hexahistidine tag replacing the lipid attachment site to create a soluble donor that could be made in a preparative scale. The recombinant cytochrome had spectral characteristics typical of a c-type cytochrome, including an asymmetric α-band, and a slightly red-shifted Soret band when reduced. The EPR spectrum of the oxidized protein was characteristic of a low-spin cytochrome. The midpoint potential of the recombinant cytochrome was +217 ± 10 mV. The interaction between soluble recombinant cytochrome c 553 and the HbRC was also studied. Re-reduction of photooxidized P800 (+) was accelerated by addition of reduced cytochrome c 553. The kinetics were characteristic of a bimolecular reaction with a second order rate of 1.53 × 10(4) M(-1) s(-1) at room temperature. The rate manifested a steep temperature dependence, with a calculated activation energy of 91 kJ mol(-1), similar to that of the native protein in Heliobacillus gestii cells. These data demonstrate that the recombinant soluble cytochrome is comparable to the native protein, and likely lacks a discrete electrostatic binding site on the HbRC.
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Affiliation(s)
- Trevor S Kashey
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, 85287-1604, USA
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