1
|
Hao JF, Yamano N, Qi CH, Zhang Y, Ma F, Wang P, Yu LJ, Zhang JP. Carotenoid-Mediated Long-Range Energy Transfer in the Light Harvesting-Reaction Center Complex from Photosynthetic Bacterium Roseiflexus castenholzii. J Phys Chem B 2023; 127:10360-10369. [PMID: 37983555 DOI: 10.1021/acs.jpcb.3c07087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The light harvesting-reaction center complex (LH-RC) of Roseiflexus castenholzii binds bacteriochlorophylls a (BChls a), B800 and B880, absorbing around 800 and 880 nm, respectively. We comparatively investigated the interband excitation energy transfer (EET) dynamics of the wild-type LH-RC (wt-LH-RC) of Rfl. castenholzii and its carotenoid (Car)-less mutant (m-LH-RC) and found that Car can boost the B800 → B880 EET rate from (2.43 ps)-1 to (1.75 ps)-1, accounting for 38% acceleration of the EET process. Interestingly, photoexcitation of wt-LH-RC at 800 nm induced pronounced excitation dynamics of Car despite the insufficient photon energy for direct Car excitation, a phenomenon which is attributed to the BChl-Car exciplex 1[B800(↑↑)···Car(↓↓)]*. Such an exciplex is suggested to play an essential role in promoting the B800 → B880 EET process, as corroborated by the recently reported cryo-EM structures of wt-LH-RC and m-LH-RC. The mechanism of Car-mediated EET will be helpful to deepen the understanding of the role of Car in bacterial photosynthesis.
Collapse
Affiliation(s)
- Jin-Fang Hao
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, Department of Chemistry, Renmin University of China, Beijing 100872, P. R. China
| | - Nami Yamano
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, Department of Chemistry, Renmin University of China, Beijing 100872, P. R. China
| | - Chen-Hui Qi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, P. R. China
| | - Yan Zhang
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, Department of Chemistry, Renmin University of China, Beijing 100872, P. R. China
| | - Fei Ma
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, P. R. China
| | - Peng Wang
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, Department of Chemistry, Renmin University of China, Beijing 100872, P. R. China
| | - Long-Jiang Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, P. R. China
| | - Jian-Ping Zhang
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, Department of Chemistry, Renmin University of China, Beijing 100872, P. R. China
| |
Collapse
|
2
|
Zabelin AA, Shkuropatov AY. Pigment-modified reaction centers of Chloroflexus aurantiacus: chemical exchange of bacteriopheophytins with plant-type pheophytins. PHOTOSYNTHESIS RESEARCH 2021; 149:313-328. [PMID: 34138452 DOI: 10.1007/s11120-021-00855-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/06/2021] [Indexed: 06/12/2023]
Abstract
The pigment composition of isolated reaction centers (RCs) of the green filamentous bacterium Chloroflexus (Cfl.) aurantiacus was changed by chemical exchange of native bacteriopheophytin a (BPheo) molecules with externally added pheophytin a (Pheo) or [3-acetyl]-Pheo upon incubation of RC/pheophytin mixtures at room temperature and 45 °C. The modified RCs were characterized by Vis/NIR absorption spectroscopy, and the effect of pigment exchange on RC photochemical activity was assessed by measuring the photoaccumulation of the reduced pigment at the binding site HA. It is shown that both pheophytins can be exchanged into the HA site instead of BPheo by incubation at room temperature. While the newly introduced Pheo molecule is not active in electron transfer, the [3-acetyl]-Pheo molecule is able to replace functionally the photoreducible HA BPheo molecule with the formation of the [3-acetyl]-Pheo- radical anion instead of the BPheo-. After incubation at 45 °C, the majority (~ 90%) of HA BPheo molecules is replaced by both Pheo and [3-acetyl]-Pheo. Only a partial replacement of inactive BPheo molecules with pheophytins is observed even when the incubation temperature is raised to 50 °C. The results are discussed in terms of (i) differences in the accessibility of BPheo binding sites for extraneous pigments depending on structural constraints and incubation temperature and (ii) the effect of the reduction potential of pigments introduced into the HA site on the energetics of the charge separation process. The possible implication of Pheo-exchanged preparations for studying early electron-transfer events in Cfl. aurantiacus RCs is considered.
Collapse
Affiliation(s)
- Alexey A Zabelin
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Institute of Basic Biological Problems of the Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russian Federation
| | - Anatoly Ya Shkuropatov
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Institute of Basic Biological Problems of the Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russian Federation.
| |
Collapse
|
3
|
Yang Z, Qi C, Liu W, Yin D, Yu L, Li L, Guo X. Revealing Conformational Transition Dynamics of Photosynthetic Proteins in Single-Molecule Electrical Circuits. J Phys Chem Lett 2021; 12:3853-3859. [PMID: 33856226 DOI: 10.1021/acs.jpclett.1c00884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The function of proteins depends on their structural flexibility and conformational change. By utilizing silicon-nanowire-based single-molecule electrical circuits, here we present a label-free real-time measurement method that can directly monitor conformational changes of a photosynthetic LH1-RC complex, reaching the ultimate goal of analytic chemistry. These results manifest that the conformation of the LH1-RC complex vibrates among four conformations with strong temperature dependence. At the optimal temperature, States 2 and 3 occupy the main conformations of the LH1-RC complex, and its conformational variation mostly emerges as anharmonic vibration modes, which contributes to photon acquisition and heat transmission. The influence of light activation on occurrence percentage is observed, resulting from light-driven quivering of pigments. Therefore, this avenue proves to be an efficient platform for revealing the fundamental mechanisms of various biological processes in vitro.
Collapse
Affiliation(s)
- Zhiheng Yang
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - Chenhui Qi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, P. R. China
| | - Wenzhe Liu
- Beijing National Laboratory for Molecular Sciences State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Dongbao Yin
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - Longjiang Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, P. R. China
| | - Lidong Li
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Sciences State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| |
Collapse
|
4
|
Gardiner AT, Nguyen-Phan TC, Cogdell RJ. A comparative look at structural variation among RC-LH1 'Core' complexes present in anoxygenic phototrophic bacteria. PHOTOSYNTHESIS RESEARCH 2020; 145:83-96. [PMID: 32430765 PMCID: PMC7423801 DOI: 10.1007/s11120-020-00758-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/10/2020] [Indexed: 05/30/2023]
Abstract
All purple photosynthetic bacteria contain RC-LH1 'Core' complexes. The structure of this complex from Rhodobacter sphaeroides, Rhodopseudomonas palustris and Thermochromatium tepidum has been solved using X-ray crystallography. Recently, the application of single particle cryo-EM has revolutionised structural biology and the structure of the RC-LH1 'Core' complex from Blastochloris viridis has been solved using this technique, as well as the complex from the non-purple Chloroflexi species, Roseiflexus castenholzii. It is apparent that these structures are variations on a theme, although with a greater degree of structural diversity within them than previously thought. Furthermore, it has recently been discovered that the only phototrophic representative from the phylum Gemmatimonadetes, Gemmatimonas phototrophica, also contains a RC-LH1 'Core' complex. At present only a low-resolution EM-projection map exists but this shows that the Gemmatimonas phototrophica complex contains a double LH1 ring. This short review compares these different structures and looks at the functional significance of these variations from two main standpoints: energy transfer and quinone exchange.
Collapse
Affiliation(s)
- Alastair T Gardiner
- Institute of Molecular, Cellular and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
- Laboratory of Anoxygenic Phototrophs, Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Novohradska 237, 379 01, Třeboň, Czech Republic.
| | - Tu C Nguyen-Phan
- Institute of Molecular, Cellular and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Richard J Cogdell
- Institute of Molecular, Cellular and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| |
Collapse
|
5
|
Wang C, Xin Y, Min Z, Qi J, Zhang C, Xu X. Structural basis underlying the electron transfer features of a blue copper protein auracyanin from the photosynthetic bacterium Roseiflexus castenholzii. PHOTOSYNTHESIS RESEARCH 2020; 143:301-314. [PMID: 31933173 DOI: 10.1007/s11120-020-00709-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 01/07/2020] [Indexed: 06/10/2023]
Abstract
Auracyanin (Ac) is a blue copper protein that mediates the electron transfer between Alternative Complex III (ACIII) and downstream electron acceptors in both fort chains of filamentous anoxygenic phototrophs. Here, we extracted and purified the air-oxidized RfxAc from the photoheterotrophically grown Roseiflexus castenholzii, and we illustrated the structural basis underlying its electron transferring features. Spectroscopic and enzymatic analyses demonstrated the reduction of air-oxidized RfxAc by the ACIII upon oxidation of menaquinol-4 and menaquinol-7. Crystal structures of the air-oxidized and Na-dithionite-reduced RfxAc at 2.2 and 2.0 Å resolutions, respectively, showed that the copper ions are coordinated by His77, His146, Cys141, and Met151 in minor different geometries. The Cu1-Sδ bond length increase of Met151, and the electron density Fourier differences at Cu1 and His77 demonstrated their essential roles in the dithionite-induced reduction. Structural comparisons further revealed that the RfxAc contains a Chloroflexus aurantiacus Ac-A-like copper binding pocket and a hydrophobic patch surrounding the exposed edge of His146 imidazole, as well as an Ac-B-like Ser- and Thr-rich polar patch located at a different site on the surface. These spectroscopic and structural features allow RfxAc to mediate electron transfers between the ACIII and redox partners different from those of Ac-A and Ac-B. These results provide a structural basis for further investigating the electron transfer and energy transformation mechanism of bacterial photosynthesis, and the diversity and evolution of electron transport chains.
Collapse
Affiliation(s)
- Chao Wang
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Yueyong Xin
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
- Photosynthesis Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Zhenzhen Min
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Junjie Qi
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Chenyun Zhang
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Xiaoling Xu
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China.
- Institute of Cardiovascular Disease Research, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China.
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Hangzhou Normal University School of Medicine, Hangzhou, 311121, Zhejiang, China.
- Photosynthesis Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China.
| |
Collapse
|
6
|
Ward LM, Cardona T, Holland-Moritz H. Evolutionary Implications of Anoxygenic Phototrophy in the Bacterial Phylum Candidatus Eremiobacterota (WPS-2). Front Microbiol 2019; 10:1658. [PMID: 31396180 PMCID: PMC6664022 DOI: 10.3389/fmicb.2019.01658] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/04/2019] [Indexed: 12/15/2022] Open
Abstract
Genome-resolved environmental metagenomic sequencing has uncovered substantial previously unrecognized microbial diversity relevant for understanding the ecology and evolution of the biosphere, providing a more nuanced view of the distribution and ecological significance of traits including phototrophy across diverse niches. Recently, the capacity for bacteriochlorophyll-based anoxygenic photosynthesis has been proposed in the uncultured bacterial WPS-2 phylum (recently proposed as Candidatus Eremiobacterota) that are in close association with boreal moss. Here, we use phylogenomic analysis to investigate the diversity and evolution of phototrophic WPS-2. We demonstrate that phototrophic WPS-2 show significant genetic and metabolic divergence from other phototrophic and non-phototrophic lineages. The genomes of these organisms encode a new family of anoxygenic Type II photochemical reaction centers and other phototrophy-related proteins that are both phylogenetically and structurally distinct from those found in previously described phototrophs. We propose the name Candidatus Baltobacterales for the order-level aerobic WPS-2 clade which contains phototrophic lineages, from the Greek for "bog" or "swamp," in reference to the typical habitat of phototrophic members of this clade.
Collapse
Affiliation(s)
- Lewis M. Ward
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
| | - Tanai Cardona
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Hannah Holland-Moritz
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, United States
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| |
Collapse
|
7
|
Xin Y, Shi Y, Niu T, Wang Q, Niu W, Huang X, Ding W, Yang L, Blankenship RE, Xu X, Sun F. Cryo-EM structure of the RC-LH core complex from an early branching photosynthetic prokaryote. Nat Commun 2018; 9:1568. [PMID: 29674684 PMCID: PMC5908803 DOI: 10.1038/s41467-018-03881-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 03/19/2018] [Indexed: 11/29/2022] Open
Abstract
Photosynthetic prokaryotes evolved diverse light-harvesting (LH) antennas to absorb sunlight and transfer energy to reaction centers (RC). The filamentous anoxygenic phototrophs (FAPs) are important early branching photosynthetic bacteria in understanding the origin and evolution of photosynthesis. How their photosynthetic machinery assembles for efficient energy transfer is yet to be elucidated. Here, we report the 4.1 Å structure of photosynthetic core complex from Roseiflexus castenholzii by cryo-electron microscopy. The RC–LH complex has a tetra-heme cytochrome c bound RC encompassed by an elliptical LH ring that is assembled from 15 LHαβ subunits. An N-terminal transmembrane helix of cytochrome c inserts into the LH ring, not only yielding a tightly bound cytochrome c for rapid electron transfer, but also opening a slit in the LH ring, which is further flanked by a transmembrane helix from a newly discovered subunit X. These structural features suggest an unusual quinone exchange model of prokaryotic photosynthetic machinery. Filamentous anoxygenic phototrophs (FAPs) are phylogenetically distant from other anoxygenic photosynthetic bacteria. Here the authors present the 4.1 Å cryo-EM structure of the photosynthetic core complex from the FAP Roseiflexus castenholzii and propose a model for energy and electron transfer.
Collapse
Affiliation(s)
- Yueyong Xin
- Hangzhou Normal University, 2318 Yuhangtang Road, Cangqian, Yuhang District, Hangzhou, 311121, Zhejiang Province, China
| | - Yang Shi
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, 100101, Beijing, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, 100049, Beijing, China
| | - Tongxin Niu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, 100101, Beijing, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, 100049, Beijing, China
| | - Qingqiang Wang
- Hangzhou Normal University, 2318 Yuhangtang Road, Cangqian, Yuhang District, Hangzhou, 311121, Zhejiang Province, China
| | - Wanqiang Niu
- Hangzhou Normal University, 2318 Yuhangtang Road, Cangqian, Yuhang District, Hangzhou, 311121, Zhejiang Province, China
| | - Xiaojun Huang
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, 100101, Beijing, China
| | - Wei Ding
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, 100101, Beijing, China
| | - Lei Yang
- Hangzhou Normal University, 2318 Yuhangtang Road, Cangqian, Yuhang District, Hangzhou, 311121, Zhejiang Province, China
| | - Robert E Blankenship
- Departments of Biology and Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Xiaoling Xu
- Hangzhou Normal University, 2318 Yuhangtang Road, Cangqian, Yuhang District, Hangzhou, 311121, Zhejiang Province, China.
| | - Fei Sun
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, 100101, Beijing, China. .,University of Chinese Academy of Sciences, 19 Yuquan Road, 100049, Beijing, China. .,Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, 100101, Beijing, China.
| |
Collapse
|
8
|
Genomics of a phototrophic nitrite oxidizer: insights into the evolution of photosynthesis and nitrification. ISME JOURNAL 2016; 10:2669-2678. [PMID: 27093047 DOI: 10.1038/ismej.2016.56] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 02/24/2016] [Accepted: 03/04/2016] [Indexed: 11/09/2022]
Abstract
Oxygenic photosynthesis evolved from anoxygenic ancestors before the rise of oxygen ~2.32 billion years ago; however, little is known about this transition. A high redox potential reaction center is a prerequisite for the evolution of the water-oxidizing complex of photosystem II. Therefore, it is likely that high-potential phototrophy originally evolved to oxidize alternative electron donors that utilized simpler redox chemistry, such as nitrite or Mn. To determine whether nitrite could have had a role in the transition to high-potential phototrophy, we sequenced and analyzed the genome of Thiocapsa KS1, a Gammaproteobacteria capable of anoxygenic phototrophic nitrite oxidation. The genome revealed a high metabolic flexibility, which likely allows Thiocapsa KS1 to colonize a great variety of habitats and to persist under fluctuating environmental conditions. We demonstrate that Thiocapsa KS1 does not utilize a high-potential reaction center for phototrophic nitrite oxidation, which suggests that this type of phototrophic nitrite oxidation did not drive the evolution of high-potential phototrophy. In addition, phylogenetic and biochemical analyses of the nitrite oxidoreductase (NXR) from Thiocapsa KS1 illuminate a complex evolutionary history of nitrite oxidation. Our results indicate that the NXR in Thiocapsa originates from a different nitrate reductase clade than the NXRs in chemolithotrophic nitrite oxidizers, suggesting that multiple evolutionary trajectories led to modern nitrite-oxidizing bacteria.
Collapse
|
9
|
Yu C, Reddy AP, Simmons CW, Simmons BA, Singer SW, VanderGheynst JS. Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:206. [PMID: 26633993 PMCID: PMC4667496 DOI: 10.1186/s13068-015-0392-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/17/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Microbial communities enriched from diverse environments have shown considerable promise for the targeted discovery of microorganisms and enzymes for bioconversion of lignocellulose to liquid fuels. While preservation of microbial communities is important for commercialization and research, few studies have examined storage conditions ideal for preservation. The goal of this study was to evaluate the impact of preservation method on composition of microbial communities enriched on switchgrass before and after storage. The enrichments were completed in a high-solid and aerobic environment at 55 °C. Community composition was examined for each enrichment to determine when a stable community was achieved. Preservation methods included cryopreservation with the cryoprotective agents DMSO and glycerol, and cryopreservation without cryoprotective agents. Revived communities were examined for their ability to decompose switchgrass under high-solid and thermophilic conditions. RESULTS High-throughput 16S rRNA gene sequencing of DNA extracted from enrichment samples showed that the majority of the shift in composition of the switchgrass-degrading community occurred during the initial three 2-week enrichments. Shifts in community structure upon storage occurred in all cryopreserved samples. Storage in liquid nitrogen in the absence of cryoprotectant resulted in variable preservation of dominant microorganisms in enriched samples. Cryopreservation with either DMSO or glycerol provided consistent and equivalent preservation of dominant organisms. CONCLUSIONS A stable switchgrass-degrading microbial community was achieved after three 2-week enrichments. Dominant microorganisms were preserved equally well with DMSO and glycerol. DMSO-preserved communities required more incubation time upon revival to achieve pre-storage activity levels during high-solid thermophilic cultivation on switchgrass. Despite shifts in the community with storage, the samples were active upon revival under thermophilic and high-solid conditions. The results suggest that the presence of microorganisms may be more important than their relative abundance in retaining an active microbial community.
Collapse
Affiliation(s)
- Chaowei Yu
- />Department of Biological and Agricultural Engineering, University of California, One Shields Ave, Davis, CA 95616 USA
| | - Amitha P. Reddy
- />Department of Biological and Agricultural Engineering, University of California, One Shields Ave, Davis, CA 95616 USA
- />Joint BioEnergy Institute, Emeryville, CA 94608 USA
| | - Christopher W. Simmons
- />Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Department of Food Science and Technology, University of California, Davis, CA 95616 USA
| | - Blake A. Simmons
- />Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Biological and Materials Science Center, Sandia National Laboratories, Livermore, CA 94551 USA
| | - Steven W. Singer
- />Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Jean S. VanderGheynst
- />Department of Biological and Agricultural Engineering, University of California, One Shields Ave, Davis, CA 95616 USA
- />Joint BioEnergy Institute, Emeryville, CA 94608 USA
| |
Collapse
|
10
|
Jacob CR, Neugebauer J. Subsystem density-functional theory. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2014. [DOI: 10.1002/wcms.1175] [Citation(s) in RCA: 229] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Christoph R. Jacob
- Center for Functional Nanostructures and Institute of Physical Chemistry; Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut; Westfälische Wilhelms-Universität Münster; Münster Germany
| |
Collapse
|
11
|
Strümpfer J, Schulten K. Excited state dynamics in photosynthetic reaction center and light harvesting complex 1. J Chem Phys 2012; 137:065101. [PMID: 22897312 DOI: 10.1063/1.4738953] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Key to efficient harvesting of sunlight in photosynthesis is the first energy conversion process in which electronic excitation establishes a trans-membrane charge gradient. This conversion is accomplished by the photosynthetic reaction center (RC) that is, in case of the purple photosynthetic bacterium Rhodobacter sphaeroides studied here, surrounded by light harvesting complex 1 (LH1). The RC employs six pigment molecules to initiate the conversion: four bacteriochlorophylls and two bacteriopheophytins. The excited states of these pigments interact very strongly and are simultaneously influenced by the surrounding thermal protein environment. Likewise, LH1 employs 32 bacteriochlorophylls influenced in their excited state dynamics by strong interaction between the pigments and by interaction with the protein environment. Modeling the excited state dynamics in the RC as well as in LH1 requires theoretical methods, which account for both pigment-pigment interaction and pigment-environment interaction. In the present study we describe the excitation dynamics within a RC and excitation transfer between light harvesting complex 1 (LH1) and RC, employing the hierarchical equation of motion method. For this purpose a set of model parameters that reproduce RC as well as LH1 spectra and observed oscillatory excitation dynamics in the RC is suggested. We find that the environment has a significant effect on LH1-RC excitation transfer and that excitation transfers incoherently between LH1 and RC.
Collapse
Affiliation(s)
- Johan Strümpfer
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | | |
Collapse
|
12
|
Solovyeva A, Pavanello M, Neugebauer J. Spin densities from subsystem density-functional theory: Assessment and application to a photosynthetic reaction center complex model. J Chem Phys 2012; 136:194104. [DOI: 10.1063/1.4709771] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
|
13
|
Xin Y, Pan J, Collins AM, Lin S, Blankenship RE. Excitation energy transfer and trapping dynamics in the core complex of the filamentous photosynthetic bacterium Roseiflexus castenholzii. PHOTOSYNTHESIS RESEARCH 2012; 111:149-156. [PMID: 21792612 DOI: 10.1007/s11120-011-9669-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 07/02/2011] [Indexed: 05/31/2023]
Abstract
The light-harvesting core complex of the thermophilic filamentous anoxygenic phototrophic bacterium Roseiflexus castenholzii is intrinsic to the cytoplasmic membrane and intimately bound to the reaction center (RC). Using ultrafast transient absorption and time-resolved fluorescence spectroscopy with selective excitation, energy transfer, and trapping dynamics in the core complex have been investigated at room temperature in both open and closed RCs. Results presented in this report revealed that the excited energy transfer from the BChl 800 to the BChl 880 band of the antenna takes about 2 ps independent of the trapping by the RC. The time constants for excitation quenching in the core antenna BChl 880 by open and closed RCs were found to be 60 and 210 ps, respectively. Assuming that the light harvesting complex is generally similar to LH1 of purple bacteria, the possible structural and functional aspects of this unique antenna complex are discussed. The results show that the core complex of Roseiflexus castenholzii contains characteristics of both purple bacteria and Chloroflexus aurantiacus.
Collapse
Affiliation(s)
- Yueyong Xin
- Departments of Biology and Chemistry, Washington University, St. Louis, MO 63130, USA.
| | | | | | | | | |
Collapse
|
14
|
Zabelin AA, Shkuropatova VA, Shuvalov VA, Shkuropatov AY. FTIR spectroscopy of the reaction center of Chloroflexus aurantiacus: Photoreduction of the bacteriopheophytin electron acceptor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1013-21. [DOI: 10.1016/j.bbabio.2011.05.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 05/18/2011] [Accepted: 05/19/2011] [Indexed: 11/25/2022]
|
15
|
Guo Z, Lin S, Xin Y, Wang H, Blankenship RE, Woodbury NW. Comparing the temperature dependence of photosynthetic electron transfer in Chloroflexus aurantiacus and Rhodobactor sphaeroides reaction centers. J Phys Chem B 2011; 115:11230-8. [PMID: 21827152 DOI: 10.1021/jp204239v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The process of electron transfer from the special pair, P, to the primary electron donor, H(A), in quinone-depleted reaction centers (RCs) of Chloroflexus (Cf.) aurantiacus has been investigated over the temperature range from 10 to 295 K using time-resolved pump-probe spectroscopic techniques. The kinetics of the electron transfer reaction, P* → P(+)H(A)(-), was found to be nonexponential, and the degree of nonexponentiality increased strongly as temperature decreased. The temperature-dependent behavior of electron transfer in Cf. aurantiacus RCs was compared with that of the purple bacterium Rhodobacter (Rb.) sphaeroides . Distinct transitions were found in the temperature-dependent kinetics of both Cf. aurantiacus and Rb. sphaeroides RCs, at around 220 and 160 K, respectively. Structural differences between these two RCs, which may be associated with those differences, are discussed. It is suggested that weaker protein-cofactor hydrogen bonding, stronger electrostatic interactions at the protein surface, and larger solvent interactions likely contribute to the higher transition temperature in Cf. aurantiacus RCs temperature-dependent kinetics compared with that of Rb. sphaeroides RCs. The reaction-diffusion model provides an accurate description for the room-temperature electron transfer kinetics in Cf. aurantiacus RCs with no free parameters, using coupling and reorganization energy values previously determined for Rb. sphaeroides , along with an experimental measure of protein conformational diffusion dynamics and an experimental literature value of the free energy gap between P* and P(+)H(A)(-).
Collapse
Affiliation(s)
- Zhi Guo
- The Biodesign Institute at Arizona State University, Arizona State University, Tempe, Arizona 85287-5201, USA
| | | | | | | | | | | |
Collapse
|