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Zhang YZ, Li K, Qin BY, Guo JP, Zhang QB, Zhao DL, Chen XL, Gao J, Liu LN, Zhao LS. Structure of cryptophyte photosystem II-light-harvesting antennae supercomplex. Nat Commun 2024; 15:4999. [PMID: 38866834 PMCID: PMC11169493 DOI: 10.1038/s41467-024-49453-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024] Open
Abstract
Cryptophytes are ancestral photosynthetic organisms evolved from red algae through secondary endosymbiosis. They have developed alloxanthin-chlorophyll a/c2-binding proteins (ACPs) as light-harvesting complexes (LHCs). The distinctive properties of cryptophytes contribute to efficient oxygenic photosynthesis and underscore the evolutionary relationships of red-lineage plastids. Here we present the cryo-electron microscopy structure of the Photosystem II (PSII)-ACPII supercomplex from the cryptophyte Chroomonas placoidea. The structure includes a PSII dimer and twelve ACPII monomers forming four linear trimers. These trimers structurally resemble red algae LHCs and cryptophyte ACPI trimers that associate with Photosystem I (PSI), suggesting their close evolutionary links. We also determine a Chl a-binding subunit, Psb-γ, essential for stabilizing PSII-ACPII association. Furthermore, computational calculation provides insights into the excitation energy transfer pathways. Our study lays a solid structural foundation for understanding the light-energy capture and transfer in cryptophyte PSII-ACPII, evolutionary variations in PSII-LHCII, and the origin of red-lineage LHCIIs.
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Affiliation(s)
- Yu-Zhong Zhang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
| | - Kang Li
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Bing-Yue Qin
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jian-Ping Guo
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Quan-Bao Zhang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Dian-Li Zhao
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Xiu-Lan Chen
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China.
| | - Lu-Ning Liu
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
| | - Long-Sheng Zhao
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
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Zhao LS, Wang N, Li K, Li CY, Guo JP, He FY, Liu GM, Chen XL, Gao J, Liu LN, Zhang YZ. Architecture of symbiotic dinoflagellate photosystem I-light-harvesting supercomplex in Symbiodinium. Nat Commun 2024; 15:2392. [PMID: 38493166 PMCID: PMC10944487 DOI: 10.1038/s41467-024-46791-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/11/2024] [Indexed: 03/18/2024] Open
Abstract
Symbiodinium are the photosynthetic endosymbionts for corals and play a vital role in supplying their coral hosts with photosynthetic products, forming the nutritional foundation for high-yield coral reef ecosystems. Here, we determine the cryo-electron microscopy structure of Symbiodinium photosystem I (PSI) supercomplex with a PSI core composed of 13 subunits including 2 previously unidentified subunits, PsaT and PsaU, as well as 13 peridinin-Chl a/c-binding light-harvesting antenna proteins (AcpPCIs). The PSI-AcpPCI supercomplex exhibits distinctive structural features compared to their red lineage counterparts, including extended termini of PsaD/E/I/J/L/M/R and AcpPCI-1/3/5/7/8/11 subunits, conformational changes in the surface loops of PsaA and PsaB subunits, facilitating the association between the PSI core and peripheral antennae. Structural analysis and computational calculation of excitation energy transfer rates unravel specific pigment networks in Symbiodinium PSI-AcpPCI for efficient excitation energy transfer. Overall, this study provides a structural basis for deciphering the mechanisms governing light harvesting and energy transfer in Symbiodinium PSI-AcpPCI supercomplexes adapted to their symbiotic ecosystem, as well as insights into the evolutionary diversity of PSI-LHCI among various photosynthetic organisms.
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Affiliation(s)
- Long-Sheng Zhao
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266237, China
| | - Ning Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Kang Li
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266237, China
| | - Chun-Yang Li
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266237, China
| | - Jian-Ping Guo
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fei-Yu He
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Gui-Ming Liu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, 100097, Beijing, China
| | - Xiu-Lan Chen
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266237, China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Lu-Ning Liu
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | - Yu-Zhong Zhang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266237, China.
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Zhang Y, Wen R, Hu J, Guan D, Qiu X, Zhang Y, Kohane DS, Liu Q. Enhancement of single upconversion nanoparticle imaging by topologically segregated core-shell structure with inward energy migration. Nat Commun 2022; 13:5927. [PMID: 36207318 PMCID: PMC9546905 DOI: 10.1038/s41467-022-33660-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 09/27/2022] [Indexed: 11/09/2022] Open
Abstract
Manipulating topological arrangement is a powerful tool for tuning energy migration in natural photosynthetic proteins and artificial polymers. Here, we report an inorganic optical nanosystem composed of NaErF4 and NaYbF4, in which topological arrangement enhanced upconversion luminescence. Three architectures are designed for considerations pertaining to energy migration and energy transfer within nanoparticles: outside-in, inside-out, and local energy transfer. The outside-in architecture produces the maximum upconversion luminescence, around 6-times brighter than that of the inside-out at the single-particle level. Monte Carlo simulation suggests a topology-dependent energy migration favoring the upconversion luminescence of outside-in structure. The optimized outside-in structure shows more than an order of magnitude enhancement of upconversion brightness compared to the conventional core-shell structure at the single-particle level and is used for long-term single-particle tracking in living cells. Our findings enable rational nanoprobe engineering for single-molecule imaging and also reveal counter-intuitive relationships between upconversion nanoparticle structure and optical properties.
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Affiliation(s)
- Yanxin Zhang
- grid.8547.e0000 0001 0125 2443Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438 China
| | - Rongrong Wen
- grid.8547.e0000 0001 0125 2443Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438 China
| | - Jialing Hu
- grid.8547.e0000 0001 0125 2443Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438 China
| | - Daoming Guan
- grid.8547.e0000 0001 0125 2443Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438 China
| | - Xiaochen Qiu
- grid.8547.e0000 0001 0125 2443Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438 China
| | - Yunxiang Zhang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438, China.
| | - Daniel S. Kohane
- grid.38142.3c000000041936754XLaboratory for Biomaterials and Drug Delivery, Division of Critical Care Medicine, Children’s Hospital Boston, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115 USA
| | - Qian Liu
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438, China.
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Kosenkov D. PyFREC 2.0: Software for excitation energy transfer modeling. J Comput Chem 2022; 43:1320-1328. [PMID: 35608241 DOI: 10.1002/jcc.26930] [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: 03/08/2022] [Revised: 04/21/2022] [Accepted: 04/28/2022] [Indexed: 11/11/2022]
Abstract
Excitation energy transfer is a ubiquitous process of fundamental importance for understanding natural phenomena, such as photosynthesis, as well as advancing technologies ranging from photovoltaics to development of photosensitizers and fluorescent probes used to explore molecular interactions inside living cells. The current version of PyFREC 2.0 is an advancement of the previously reported software (D. Kosenkov, J. Comput. Chem. 2016, 37, 1847-1854). The current update is primarily focused on providing a computational tool based on Förster theory for bridging a gap between theoretically calculated molecular properties (e.g., electronic couplings, orientation factors, etc.) and experimentally measured emission and absorption spectra of molecules. The software is aimed to facilitate deeper understanding of photochemical mechanisms of fluorescence resonance energy transfer (FRET) in donor-acceptor pairs. Specific updates of the software include implementations of overlap integrals between donor emission and acceptor absorption spectra of FRET pairs, estimation of Strickler-Berg fluorescence lifetimes, calculation of Förster radii, energy transfer efficiency, and radiation zones that, in particular, determine applicability of the Förster theory.
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Affiliation(s)
- Dmitri Kosenkov
- Department of Chemistry and Physics, Monmouth University, West Long Branch, New Jersey, USA
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Kosenkov YK, Kosenkov D. Quantum dynamics of vibration-assisted excitation energy transfer in phycobiliprotein light-harvesting complex. J Chem Phys 2019; 151:144101. [PMID: 31615220 DOI: 10.1063/1.5116555] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Phycobiliprotein is a light-harvesting complex containing linear tetrapyrrole bilin pigments that are responsible for absorption and funneling the sun's energy in cryptophytes algae. In particular, the protein structure determines relative positions and orientations of the pigments and thus controls energy transfer pathways. The present research reveals the impact of molecular vibrations (in the 850-2700 cm-1 region) on excitation energy transfer in phycobiliprotein. The analysis of the excitation energy transfer pathways indicates a possibility of the coherent mechanism of energy transfer (delocalization) in central dihydrobiliverdin pigments and incoherent vibration-assisted energy transfer to peripheral phycocyanobilin pigments at a sub-picosecond time scale. A computational approach that enables modeling the dynamics of the excitation energy transfer with the quantum master equation formalism employing Huang-Rhys factors to describe electronic-vibrational coupling has been developed. The computational methodology has been implemented in PyFREC software.
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Affiliation(s)
- Yana Kholod Kosenkov
- Department of Chemistry and Physics, Monmouth University, 400 Cedar Avenue, West Long Branch, New Jersey 07764, USA
| | - Dmitri Kosenkov
- Department of Chemistry and Physics, Monmouth University, 400 Cedar Avenue, West Long Branch, New Jersey 07764, USA
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Linden G, Zhang L, Pieck F, Linne U, Kosenkov D, Tonner R, Vázquez O. Gezielte Singulett‐Sauerstofferzeugung durch bioorthogonale DNA‐basierte Tetrazin‐Ligation. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907093] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Greta Linden
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Straße 4 35043 Marburg Deutschland
| | - Lei Zhang
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Straße 4 35043 Marburg Deutschland
| | - Fabian Pieck
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Straße 4 35043 Marburg Deutschland
| | - Uwe Linne
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Straße 4 35043 Marburg Deutschland
| | - Dmitri Kosenkov
- Department of Chemistry and Physics Monmouth University 400 Cedar Avenue West Long Branch NJ 07764 USA
| | - Ralf Tonner
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Straße 4 35043 Marburg Deutschland
| | - Olalla Vázquez
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Straße 4 35043 Marburg Deutschland
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Linden G, Zhang L, Pieck F, Linne U, Kosenkov D, Tonner R, Vázquez O. Conditional Singlet Oxygen Generation through a Bioorthogonal DNA-targeted Tetrazine Reaction. Angew Chem Int Ed Engl 2019; 58:12868-12873. [PMID: 31291504 DOI: 10.1002/anie.201907093] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Indexed: 12/22/2022]
Abstract
We report the use of bioorthogonal reactions as an original strategy in photodynamic therapy to achieve conditional phototoxicity and specific subcellular localization simultaneously. Our novel halogenated BODIPY-tetrazine probes only become efficient photosensitizers (ΦΔ ≈0.50) through an intracellular inverse-electron-demand Diels-Alder reaction with a suitable dienophile. Ab initio computations reveal an activation-dependent change in decay channels that controls 1 O2 generation. Our bioorthogonal approach also enables spatial control. As a proof-of-concept, we demonstrate the feasibility of the selective activation of our dormant photosensitizer in cellular nuclei, causing cancer cell death upon irradiation. Thus, our dual biorthogonal, activatable photosensitizers open new venues to combat current limitations of photodynamic therapy.
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Affiliation(s)
- Greta Linden
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35043, Marburg, Germany
| | - Lei Zhang
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35043, Marburg, Germany
| | - Fabian Pieck
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35043, Marburg, Germany
| | - Uwe Linne
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35043, Marburg, Germany
| | - Dmitri Kosenkov
- Department of Chemistry and Physics, Monmouth University, 400 Cedar Avenue, West Long Branch, NJ, 07764, USA
| | - Ralf Tonner
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35043, Marburg, Germany
| | - Olalla Vázquez
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35043, Marburg, Germany
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