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Alseekh S, Karakas E, Zhu F, Wijesingha Ahchige M, Fernie AR. Plant biochemical genetics in the multiomics era. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4293-4307. [PMID: 37170864 PMCID: PMC10433942 DOI: 10.1093/jxb/erad177] [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: 12/13/2022] [Accepted: 05/09/2023] [Indexed: 05/13/2023]
Abstract
Our understanding of plant biology has been revolutionized by modern genetics and biochemistry. However, biochemical genetics can be traced back to the foundation of Mendelian genetics; indeed, one of Mendel's milestone discoveries of seven characteristics of pea plants later came to be ascribed to a mutation in a starch branching enzyme. Here, we review both current and historical strategies for the elucidation of plant metabolic pathways and the genes that encode their component enzymes and regulators. We use this historical review to discuss a range of classical genetic phenomena including epistasis, canalization, and heterosis as viewed through the lens of contemporary high-throughput data obtained via the array of approaches currently adopted in multiomics studies.
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Affiliation(s)
- Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Esra Karakas
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Feng Zhu
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070 Wuhan, China
| | | | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
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2
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Makita H, Zhang M, Yano J, Kern J. Room temperature crystallography and X-ray spectroscopy of metalloenzymes. Methods Enzymol 2023; 688:307-348. [PMID: 37748830 PMCID: PMC10799221 DOI: 10.1016/bs.mie.2023.07.009] [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] [Indexed: 09/27/2023]
Abstract
The ultrashort (10s of femtoseconds) X-ray pulses generated by X-ray free electron lasers enable the measurement of X-ray diffraction and spectroscopic data from radiation-sensitive metalloenzymes at room temperature while mostly avoiding the effects of radiation damage usually encountered when performing such experiments at synchrotron sources. Here we discuss an approach to measure both X-ray emission and X-ray crystallographic data at the same time from the same sample volume. The droplet-on-tape setup described allows for efficient sample use and the integration of different reaction triggering options in order to conduct time-resolved studies with limited sample amounts. The approach is illustrated by two examples, photosystem II that catalyzes the light-driven oxidation of water to oxygen, and isopenicillin N synthase, an enzyme that catalyzes the double ring cyclization of a tripeptide precursor into the β-lactam isopenicillin and can be activated by oxygen exposure. We describe the necessary steps to obtain microcrystals of both proteins as well as the operation procedure for the drop-on-tape setup and details of the data acquisition and processing involved in this experiment. At the end, we present how the combination of time-resolved X-ray emission spectra and diffraction data can be used to improve the knowledge about the enzyme reaction mechanism.
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Affiliation(s)
- Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Miao Zhang
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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3
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Bečková M, Sobotka R, Komenda J. Photosystem II antenna modules CP43 and CP47 do not form a stable 'no reaction centre complex' in the cyanobacterium Synechocystis sp. PCC 6803. PHOTOSYNTHESIS RESEARCH 2022; 152:363-371. [PMID: 35015206 PMCID: PMC9458580 DOI: 10.1007/s11120-022-00896-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/31/2021] [Indexed: 05/05/2023]
Abstract
The repair of photosystem II is a key mechanism that keeps the light reactions of oxygenic photosynthesis functional. During this process, the PSII central subunit D1 is replaced with a newly synthesized copy while the neighbouring CP43 antenna with adjacent small subunits (CP43 module) is transiently detached. When the D2 protein is also damaged, it is degraded together with D1 leaving both the CP43 module and the second PSII antenna module CP47 unassembled. In the cyanobacterium Synechocystis sp. PCC 6803, the released CP43 and CP47 modules have been recently suggested to form a so-called no reaction centre complex (NRC). However, the data supporting the presence of NRC can also be interpreted as a co-migration of CP43 and CP47 modules during electrophoresis and ultracentrifugation without forming a mutual complex. To address the existence of NRC, we analysed Synechocystis PSII mutants accumulating one or both unassembled antenna modules as well as Synechocystis wild-type cells stressed with high light. The obtained results were not compatible with the existence of a stable NRC since each unassembled module was present as a separate protein complex with a mutually similar electrophoretic mobility regardless of the presence of the second module. The non-existence of NRC was further supported by isolation of the His-tagged CP43 and CP47 modules from strains lacking either D1 or D2 and their migration patterns on native gels.
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Affiliation(s)
- Martina Bečková
- Laboratory of Photosynthesis, Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Opatovický mlýn, 37981, Třeboň, Czech Republic
| | - Roman Sobotka
- Laboratory of Photosynthesis, Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Opatovický mlýn, 37981, Třeboň, Czech Republic
| | - Josef Komenda
- Laboratory of Photosynthesis, Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Opatovický mlýn, 37981, Třeboň, Czech Republic.
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4
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Golub M, Hussein R, Ibrahim M, Hecht M, Wieland DCF, Martel A, Machado B, Zouni A, Pieper J. Solution Structure of the Detergent-Photosystem II Core Complex Investigated by Small-Angle Scattering Techniques. J Phys Chem B 2020; 124:8583-8592. [PMID: 32816484 DOI: 10.1021/acs.jpcb.0c07169] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Albeit achieving the X-ray diffraction structure of dimeric photosystem II core complexes (dPSIIcc) at the atomic resolution, the nature of the detergent belt surrounding dPSIIcc remains ambiguous. Therefore, the solution structure of the whole detergent-protein complex of dPSIIcc of Thermosynechococcus elongatus (T. elongatus) solubilized in n-dodecyl-ß-d-maltoside (ßDM) was investigated by a combination of small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) with contrast variation. First, the structure of dPSIIcc was studied separately in SANS experiments using a contrast of 5% D2O. Guinier analysis reveals that the dPSIIcc solution is virtually free of aggregation in the studied concentration range of 2-10 mg/mL dPSIIcc, and characterized by a radius of gyration of 62 Å. A structure reconstitution shows that dPSIIcc in buffer solution widely retains the crystal structure reported by X-ray free electron laser studies at room temperature with a slight expansion of the entire protein. Additional SANS experiments on dPSIIcc samples in a buffer solution containing 75% D2O provide information about the size and shape of the whole detergent-dPSIIcc. The maximum position of P(r) function increases to 68 Å, i.e., it is about 6 Å larger than that of dPSIIcc only, thus indicating the presence of an additional structure. Thus, it can be concluded that dPSIIcc is surrounded by a monomolecular belt of detergent molecules under appropriate solubilization conditions. The homogeneity of the ßDM-dPSIIcc solutions was also verified using dynamic light scattering. Complementary SAXS experiments indicate the presence of unbound detergent micelles by a separate peak consistent with a spherical shape possessing a radius of about 40 Å. The latter structure also contributes to the SANS data but rather broadens the SANS curve artificially. Without the simultaneous inspection of SANS and SAXS data, this effect may lead to an apparent underestimation of the size of the PS II-detergent complex. The formation of larger unbound detergent aggregates in solution prior to crystallization may have a significant effect on the crystal formation or quality of the ßDM-dPSIIcc.
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Affiliation(s)
- Maksym Golub
- Institute of Physics, University of Tartu, Wilhelm Ostwald str. 1, 50411 Tartu, Estonia
| | - Rana Hussein
- Humboldt Universität zu Berlin, Philipp Str. 13, 10115 Berlin, Germany
| | - Mohamed Ibrahim
- Humboldt Universität zu Berlin, Philipp Str. 13, 10115 Berlin, Germany
| | - Max Hecht
- Institute of Physics, University of Tartu, Wilhelm Ostwald str. 1, 50411 Tartu, Estonia
| | | | - Anne Martel
- Institut Laue-Langevin, 71 avenue des Martyrs, 38043 Grenoble, France
| | - Barbara Machado
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, 38043 Grenoble, France
| | - Athina Zouni
- Humboldt Universität zu Berlin, Philipp Str. 13, 10115 Berlin, Germany
| | - Jörg Pieper
- Institute of Physics, University of Tartu, Wilhelm Ostwald str. 1, 50411 Tartu, Estonia
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Litvín R, Bína D, Herbstová M, Pazderník M, Kotabová E, Gardian Z, Trtílek M, Prášil O, Vácha F. Red-shifted light-harvesting system of freshwater eukaryotic alga Trachydiscus minutus (Eustigmatophyta, Stramenopila). PHOTOSYNTHESIS RESEARCH 2019; 142:137-151. [PMID: 31375979 DOI: 10.1007/s11120-019-00662-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/22/2019] [Indexed: 06/10/2023]
Abstract
Survival of phototrophic organisms depends on their ability to collect and convert enough light energy to support their metabolism. Phototrophs can extend their absorption cross section by using diverse pigments and by tuning the properties of these pigments via pigment-pigment and pigment-protein interaction. It is well known that some cyanobacteria can grow in heavily shaded habitats by utilizing far-red light harvested with far-red-absorbing chlorophylls d and f. We describe a red-shifted light-harvesting system based on chlorophyll a from a freshwater eustigmatophyte alga Trachydiscus minutus (Eustigmatophyceae, Goniochloridales). A comprehensive characterization of the photosynthetic apparatus of T. minutus is presented. We show that thylakoid membranes of T. minutus contain light-harvesting complexes of several sizes differing in the relative amount of far-red chlorophyll a forms absorbing around 700 nm. The pigment arrangement of the major red-shifted light-harvesting complex is similar to that of the red-shifted antenna of a marine alveolate alga Chromera velia. Evolutionary aspects of the algal far-red light-harvesting complexes are discussed. The presence of these antennas in eustigmatophyte algae opens up new ways to modify organisms of this promising group for effective use of far-red light in mass cultures.
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Affiliation(s)
- Radek Litvín
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
- Biology Centre, The Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - David Bína
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic.
- Biology Centre, The Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic.
| | - Miroslava Herbstová
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
- Biology Centre, The Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Marek Pazderník
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 379 81, Třeboň, Czech Republic
| | - Eva Kotabová
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 379 81, Třeboň, Czech Republic
| | - Zdenko Gardian
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
- Biology Centre, The Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Martin Trtílek
- PSI (Photon Systems Instruments), spol. s r.o. Drásov 470, 664 24, Drásov, Czech Republic
| | - Ondřej Prášil
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 379 81, Třeboň, Czech Republic
| | - František Vácha
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
- Biology Centre, The Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic
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A novel chlorophyll protein complex in the repair cycle of photosystem II. Proc Natl Acad Sci U S A 2019; 116:21907-21913. [PMID: 31594847 DOI: 10.1073/pnas.1909644116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In oxygenic photosynthetic organisms, photosystem II (PSII) is a unique membrane protein complex that catalyzes light-driven oxidation of water. PSII undergoes frequent damage due to its demanding photochemistry. It must undergo a repair and reassembly process following photodamage, many facets of which remain unknown. We have discovered a PSII subcomplex that lacks 5 key PSII core reaction center polypeptides: D1, D2, PsbE, PsbF, and PsbI. This pigment-protein complex does contain the PSII core antenna proteins CP47 and CP43, as well as most of their associated low molecular mass subunits, and the assembly factor Psb27. Immunoblotting, mass spectrometry, and ultrafast spectroscopic results support the absence of a functional reaction center in this complex, which we call the "no reaction center" complex (NRC). Analytical ultracentrifugation and clear native PAGE analysis show that NRC is a stable pigment-protein complex and not a mixture of free CP47 and CP43 proteins. NRC appears in higher abundance in cells exposed to high light and impaired protein synthesis, and genetic deletion of PsbO on the PSII luminal side results in an increased NRC population, indicative that NRC forms in response to photodamage as part of the PSII repair process. Our finding challenges the current model of the PSII repair cycle and implies an alternative PSII repair strategy. Formation of this complex may maximize PSII repair economy by preserving intact PSII core antennas in a single complex available for PSII reassembly, minimizing the risk of randomly diluting multiple recycling components in the thylakoid membrane following a photodamage event.
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7
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Distinguishing Between Monomeric scFv and Diabody in Solution Using Light and Small Angle X-ray Scattering. Antibodies (Basel) 2019; 8:antib8040048. [PMID: 31548495 PMCID: PMC6963988 DOI: 10.3390/antib8040048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 09/10/2019] [Accepted: 09/13/2019] [Indexed: 11/17/2022] Open
Abstract
Depending on the linker length between the VH and the VL domain, single-chain Fv (scFv) antibody fragments form monomers, dimers (diabodies) or higher oligomers. We aimed at generating a diabody of the anti-MET antibody 3H3 to use it as crystallization chaperone to promote crystallization of the MET ectodomain through the introduction of a pre-formed twofold axis of symmetry. Size exclusion chromatography, however, suggested the protein to be monomeric. Hence, we used scattering techniques applied to solutions to further investigate its oligomerization state. The small angle X-ray scattering (SAXS) curve measured for our protein nicely fits to the scattering curve calculated from the known crystal structure of a diabody. In addition, concentration-dependent photon correlation spectroscopy (PCS) measurements revealed a hydrodynamic radius of 3.4 nm at infinite dilution and a negative interaction parameter kD, indicating attractive interactions that are beneficial for crystallization. Both SAXS and PCS measurements clearly suggest our antibody fragment to be a diabody in solution. Chemical cross-linking with glutaraldehyde and cell motility assays confirmed this conclusion.
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8
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Energy transfer dynamics in a red-shifted violaxanthin-chlorophyll a light-harvesting complex. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:111-120. [DOI: 10.1016/j.bbabio.2018.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 10/15/2018] [Accepted: 11/07/2018] [Indexed: 11/21/2022]
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9
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Neira JL, Martínez-Rodríguez S, Hernández-Cifre JG, Cámara-Artigas A, Clemente P, Peralta S, Fernández-Moreno MÁ, Garesse R, García de la Torre J, Rizzuti B. Human COA3 Is an Oligomeric Highly Flexible Protein in Solution. Biochemistry 2016; 55:6209-6220. [PMID: 27791355 DOI: 10.1021/acs.biochem.6b00644] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The assembly of the protein complex of cytochrome c oxidase (COX), which participates in the mitochondrial respiratory chain, requires a large number of accessory proteins (the so-called assembly factors). Human COX assembly factor 3 (hCOA3), also known as MITRAC12 or coiled-coil domain-containing protein 56 (CCDC56), interacts with the first subunit protein of COX to form its catalytic core and promotes its assemblage with the other units. Therefore, hCOA3 is involved in COX biogenesis in humans and can be exploited as a drug target in patients with mitochondrial dysfunctions. However, to be considered a molecular target, its structure and conformational stability must first be elucidated. We have embarked on the description of such features by using spectroscopic and hydrodynamic techniques, in aqueous solution and in the presence of detergents, together with computational methods. Our results show that hCOA3 is an oligomeric protein, forming aggregates of different molecular masses in aqueous solution. Moreover, on the basis of fluorescence and circular dichroism results, the protein has (i) its unique tryptophan partially shielded from solvent and (ii) a relatively high percentage of secondary structure. However, this structure is highly flexible and does not involve hydrogen bonding. Experiments in the presence of detergents suggest a slightly higher content of nonrigid helical structure. Theoretical results, based on studies of the primary structure of the protein, further support the idea that hCOA3 is a disordered protein. We suggest that the flexibility of hCOA3 is crucial for its interaction with other proteins to favor mitochondrial protein translocation and assembly of proteins involved in the respiratory chain.
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Affiliation(s)
- José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández , Elche, Alicante, Spain.,Biocomputation and Complex Systems Physics Institute , Zaragoza, Spain
| | | | | | - Ana Cámara-Artigas
- Department of Chemistry and Physics, University of Almería , Agrifood Campus of International Excellence (ceiA3), Almería, Spain
| | - Paula Clemente
- Departamento de Bioquímica-Instituto de Investigaciones Biomédicas "Alberto Sols", Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) , Madrid, Spain.,Instituto de Investigación Sanitaria, Hospital 12 de Octubre (i+12) , Madrid, Spain
| | - Susana Peralta
- Departamento de Bioquímica-Instituto de Investigaciones Biomédicas "Alberto Sols", Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) , Madrid, Spain.,Instituto de Investigación Sanitaria, Hospital 12 de Octubre (i+12) , Madrid, Spain
| | - Miguel Ángel Fernández-Moreno
- Departamento de Bioquímica-Instituto de Investigaciones Biomédicas "Alberto Sols", Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) , Madrid, Spain.,Instituto de Investigación Sanitaria, Hospital 12 de Octubre (i+12) , Madrid, Spain
| | - Rafael Garesse
- Departamento de Bioquímica-Instituto de Investigaciones Biomédicas "Alberto Sols", Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) , Madrid, Spain.,Instituto de Investigación Sanitaria, Hospital 12 de Octubre (i+12) , Madrid, Spain
| | | | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria , 87036 Rende, Italy
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Shibata M, Koeda S, Noji T, Kawakami K, Ido Y, Amano Y, Umezawa N, Higuchi T, Dewa T, Itoh S, Kamiya N, Mizuno T. Design of New Extraction Surfactants for Membrane Proteins from Peptide Gemini Surfactants. Bioconjug Chem 2016; 27:2469-2479. [PMID: 27571354 DOI: 10.1021/acs.bioconjchem.6b00417] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The development of additional extraction surfactants for membrane proteins is necessary for membrane protein research, since optimal combinations for the successful extraction of target membrane proteins from biological membranes that minimize protein denaturation are hard to predict. In particular, those that have a unique basal molecular framework are quite attractive and highly desired in this research field. In this study, we successfully constructed a new extraction surfactant for membrane proteins, NPDGC12KK, from the peptide-gemini-surfactant (PG-surfactant) molecular framework. The PG-surfactant is a U-shaped lipopeptide scaffold, consisting of a short linker peptide (-X-) between two long alkyl-chain-modified Cys residues and a peripheral peptide (Y-) at the N-terminal side of long alkyl-chain-modified Cys residues. Using photosystem I (PSI) and photosystem II (PSII) derived from Thermosynecoccus vulcanus as representative membrane proteins, we evaluated whether NPDGC12KK could solubilize membrane proteins while maintaining structure and functions. Neither the membrane integral domain nor the cytoplasmic domain of PSI and PSII suffered any damage upon the use of NPDGC12KK based on detailed photophysical measurements. Using thylakoid membranes of T. vulcanus as a representative biological membrane sample, we performed experiments to extract membrane proteins, such as PSI and PSII. Based on the extraction efficiency and maintenance of protein supramolecular structure established using clear native-PAGE analyses, we proved that NPDGC12KK functions as a novel class of peptide-containing extraction surfactants for membrane proteins.
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Affiliation(s)
- Masahide Shibata
- Graduate School of Engineering, Nagoya Institute of Technology , Gokiso-cho, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Shuhei Koeda
- Graduate School of Engineering, Nagoya Institute of Technology , Gokiso-cho, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Tomoyasu Noji
- Osaka City University , The OCU Advanced Research Institute for Natural Science & Technology (OCARINA), 3-3-138 Sugimoto-cho, Sumiyoshi, Osaka 558-8585, Japan
| | - Keisuke Kawakami
- Osaka City University , The OCU Advanced Research Institute for Natural Science & Technology (OCARINA), 3-3-138 Sugimoto-cho, Sumiyoshi, Osaka 558-8585, Japan
| | - Yuya Ido
- Graduate School of Engineering, Nagoya Institute of Technology , Gokiso-cho, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Yuichi Amano
- Graduate School of Pharmaceutical Sciences, Nagoya City University , 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Naoki Umezawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University , 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Tsunehiko Higuchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University , 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Takehisa Dewa
- Graduate School of Engineering, Nagoya Institute of Technology , Gokiso-cho, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Shigeru Itoh
- Graduate School of Science, Nagoya University , Furo-cho, Chikusa-ku Nagoya, Aichi 464-8602, Japan
| | - Nobuo Kamiya
- Osaka City University , The OCU Advanced Research Institute for Natural Science & Technology (OCARINA), 3-3-138 Sugimoto-cho, Sumiyoshi, Osaka 558-8585, Japan
| | - Toshihisa Mizuno
- Graduate School of Engineering, Nagoya Institute of Technology , Gokiso-cho, Showa-ku, Nagoya, Aichi 466-8555, Japan
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11
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Noji T, Kawakami K, Shen JR, Dewa T, Nango M, Kamiya N, Itoh S, Jin T. Oxygen-Evolving Porous Glass Plates Containing the Photosynthetic Photosystem II Pigment-Protein Complex. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:7796-7805. [PMID: 27400072 DOI: 10.1021/acs.langmuir.6b02106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The development of artificial photosynthesis has focused on the efficient coupling of reaction at photoanode and cathode, wherein the production of hydrogen (or energy carriers) is coupled to the electrons derived from water-splitting reactions. The natural photosystem II (PSII) complex splits water efficiently using light energy. The PSII complex is a large pigment-protein complex (20 nm in diameter) containing a manganese cluster. A new photoanodic device was constructed incorporating stable PSII purified from a cyanobacterium Thermosynechococcus vulcanus through immobilization within 20 or 50 nm nanopores contained in porous glass plates (PGPs). PSII in the nanopores retained its native structure and high photoinduced water splitting activity. The photocatalytic rate (turnover frequency) of PSII in PGP was enhanced 11-fold compared to that in solution, yielding a rate of 50-300 mol e(-)/(mol PSII·s) with 2,6-dichloroindophenol (DCIP) as an electron acceptor. The PGP system realized high local concentrations of PSII and DCIP to enhance the collisional reactions in nanotubes with low disturbance of light penetration. The system allows direct visualization/determination of the reaction inside the nanotubes, which contributes to optimize the local reaction condition. The PSII/PGP device will substantively contribute to the construction of artificial photosynthesis using water as the ultimate electron source.
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Affiliation(s)
- Tomoyasu Noji
- The OCU Advanced Research Institute for Natural Science & Technology (OCARINA), Osaka City University , 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Keisuke Kawakami
- The OCU Advanced Research Institute for Natural Science & Technology (OCARINA), Osaka City University , 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Jian-Ren Shen
- Photosynthesis Research Center, Graduate School of Natural Science and Technology/Faculty of Science, Okayama University , Okayama 700-8530, Japan
| | - Takehisa Dewa
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology , Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Mamoru Nango
- The OCU Advanced Research Institute for Natural Science & Technology (OCARINA), Osaka City University , 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Nobuo Kamiya
- The OCU Advanced Research Institute for Natural Science & Technology (OCARINA), Osaka City University , 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Shigeru Itoh
- Graduate School of Science, Nagoya University , Furo-cho, Chikusa-ku Nagoya, Aichi 464-8602, Japan
| | - Tetsuro Jin
- Inorganic Functional Materials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , 1-8-31, Midorigaoka, Ikeda, Osaka 563-8577, Japan
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12
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Ibrahim M, Chatterjee R, Hellmich J, Tran R, Bommer M, Yachandra VK, Yano J, Kern J, Zouni A. Improvements in serial femtosecond crystallography of photosystem II by optimizing crystal uniformity using microseeding procedures. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2016; 2:041705. [PMID: 26726311 PMCID: PMC4697744 DOI: 10.1063/1.4919741] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 04/23/2015] [Indexed: 05/05/2023]
Abstract
In photosynthesis, photosystem II (PSII) is the multi-subunit membrane protein complex that catalyzes photo-oxidation of water into dioxygen through the oxygen evolving complex (OEC). To understand the water oxidation reaction, it is important to get structural information about the transient and intermediate states of the OEC in the dimeric PSII core complex (dPSIIcc). In recent times, femtosecond X-ray pulses from the free electron laser (XFEL) are being used to obtain X-ray diffraction (XRD) data of dPSIIcc microcrystals at room temperature that are free of radiation damage. In our experiments at the XFEL, we used an electrospun liquid microjet setup that requires microcrystals less than 40 μm in size. In this study, we explored various microseeding techniques to get a high yield of monodisperse uniform-sized microcrystals. Monodisperse microcrystals of dPSIIcc of uniform size were a key to improve the stability of the jet and the quality of XRD data obtained at the XFEL. This was evident by an improvement of the quality of the datasets obtained, from 6.5Å, using crystals grown without the micro seeding approach, to 4.5Å using crystals generated with the new method.
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Affiliation(s)
- Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany ; Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universitüt, D-10623 Berlin, Germany
| | - Ruchira Chatterjee
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Julia Hellmich
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany ; Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universitüt, D-10623 Berlin, Germany
| | - Rosalie Tran
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Martin Bommer
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Vittal K Yachandra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jan Kern
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA ; LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany ; Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universitüt, D-10623 Berlin, Germany
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13
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Skandary S, Hussels M, Konrad A, Renger T, Müh F, Bommer M, Zouni A, Meixner A, Brecht M. Variation of exciton-vibrational coupling in photosystem II core complexes from Thermosynechococcus elongatus as revealed by single-molecule spectroscopy. J Phys Chem B 2015; 119:4203-10. [PMID: 25708355 PMCID: PMC4368080 DOI: 10.1021/jp510631x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 02/20/2015] [Indexed: 01/01/2023]
Abstract
The spectral properties and dynamics of the fluorescence emission of photosystem II core complexes are investigated by single-molecule spectroscopy at 1.6 K. The emission spectra are dominated by sharp zero-phonon lines (ZPLs). The sharp ZPLs are the result of weak to intermediate exciton-vibrational coupling and slow spectral diffusion. For several data sets, it is possible to surpass the effect of spectral diffusion by applying a shifting algorithm. The increased signal-to-noise ratio enables us to determine the exciton-vibrational coupling strength (Huang-Rhys factor) with high precision. The Huang-Rhys factors vary between 0.03 and 0.8. The values of the Huang-Rhys factors show no obvious correlation between coupling strength and wavelength position. From this result, we conclude that electrostatic rather than exchange or dispersive interactions are the main contributors to the exciton-vibrational coupling in this system.
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Affiliation(s)
| | - Martin Hussels
- IPTC
and Lisa+ Center, Universität Tübingen, Tübingen, Germany
| | | | - Thomas Renger
- Institut
für Theoretische Physik, Johannes
Kepler Universität, Linz, Austria
| | - Frank Müh
- Institut
für Theoretische Physik, Johannes
Kepler Universität, Linz, Austria
| | - Martin Bommer
- Institut
für Biologie, Humboldt Universität
zu Berlin, Berlin, Germany
| | - Athina Zouni
- Institut
für Biologie, Humboldt Universität
zu Berlin, Berlin, Germany
| | | | - Marc Brecht
- IPTC
and Lisa+ Center, Universität Tübingen, Tübingen, Germany
- Zurich University
of Applied Science Winterthur (ZHAW), Winterthur, Switzerland
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14
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Hellmich J, Bommer M, Burkhardt A, Ibrahim M, Kern J, Meents A, Müh F, Dobbek H, Zouni A. Native-like Photosystem II Superstructure at 2.44 Å Resolution through Detergent Extraction from the Protein Crystal. Structure 2014; 22:1607-15. [DOI: 10.1016/j.str.2014.09.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/26/2014] [Accepted: 09/10/2014] [Indexed: 10/24/2022]
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15
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Ikeda Y, Yamagishi A, Komura M, Suzuki T, Dohmae N, Shibata Y, Itoh S, Koike H, Satoh K. Two types of fucoxanthin-chlorophyll-binding proteins I tightly bound to the photosystem I core complex in marine centric diatoms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:529-39. [PMID: 23416844 DOI: 10.1016/j.bbabio.2013.02.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 01/31/2013] [Accepted: 02/06/2013] [Indexed: 12/30/2022]
Abstract
Intact fucoxanthin (Fucox)-chlorophyll (Chl)-binding protein I-photosystem I supercomplexes (FCPI-PSIs) were prepared by a newly developed simple fast procedure from centric diatoms Chaetoceros gracilis and Thalassiosira pseudonana to study the mechanism of their efficient solar energy accumulation. FCPI-PSI purified from C. gracilis contained 252 Chl a, 23 Chl c, 56 Fucox, 34 diadinoxanthin+diatoxanthin, 1 violaxanthin, 21 ß-carotene, and 2 menaquinone-4 per P700. The complex showed a high electron transfer activity at 185,000μmolmg Chl a(-1)·h(-1) to reduce methyl viologen from added cytochrome c6. We identified 14 and 21 FCP proteins in FCPI-PSI of C. gracilis and T. pseudonana, respectively, determined by N-terminal and internal amino acid sequences and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses. PsaO and a red lineage Chla/b-binding-like protein (RedCAP), Thaps3:270215, were also identified. Severe detergent treatment of FCPI-PSI released FCPI-1 first, leaving the FCPI-2-PSI-core complex. FCPI-1 contained more Chl c and showed Chl a fluorescence at a shorter wavelength than FCPI-2, suggesting an excitation-energy transfer from FCPI-1 to FCPI-2 and then to the PSI core. Fluorescence emission spectra at 17K in FCPI-2 varied depending on the excitation wavelength, suggesting two independent energy transfer routes. We formulated a model of FCPI-PSI based on the biochemical assay results.
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Affiliation(s)
- Yohei Ikeda
- Graduate School of Life Science, University of Hyogo, Harima Science Garden City, Hyogo 678-1297, Japan.
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16
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Sobotka R, Tichy M, Wilde A, Hunter CN. Functional assignments for the carboxyl-terminal domains of the ferrochelatase from Synechocystis PCC 6803: the CAB domain plays a regulatory role, and region II is essential for catalysis. PLANT PHYSIOLOGY 2011; 155:1735-47. [PMID: 21081693 PMCID: PMC3091120 DOI: 10.1104/pp.110.167528] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Accepted: 11/09/2010] [Indexed: 05/20/2023]
Abstract
Ferrochelatase (FeCH) catalyzes the insertion of Fe(2+) into protoporphyrin, forming protoheme. In photosynthetic organisms, FeCH and magnesium chelatase lie at a biosynthetic branch point where partitioning down the heme and chlorophyll (Chl) pathways occurs. Unlike their mammalian, yeast, and other bacterial counterparts, cyanobacterial and algal FeCHs as well as FeCH2 isoform from plants possess a carboxyl-terminal Chl a/b-binding (CAB) domain with a conserved Chl-binding motif. The CAB domain is connected to the FeCH catalytic core by a proline-rich linker sequence (region II). In order to dissect the regulatory, catalytic, and structural roles of the region II and CAB domains, we analyzed a FeCH ΔH347 mutant that retains region II but lacks the CAB domain and compared it with the ΔH324-FeCH mutant that lacks both these domains. We found that the CAB domain is not required for catalytic activity but is essential for dimerization of FeCH; its absence causes aberrant accumulation of Chl-protein complexes under high light accompanied by high levels of the Chl precursor chlorophyllide. Thus, the CAB domain appears to serve mainly a regulatory function, possibly in balancing Chl biosynthesis with the synthesis of cognate apoproteins. Region II is essential for the catalytic function of the plastid-type FeCH enzyme, although the low residual activity of the ΔH324-FeCH is more than sufficient to furnish the cellular demand for heme. We propose that the apparent surplus of FeCH activity in the wild type is critical for cell viability under high light due to a regulatory role of FeCH in the distribution of Chl into apoproteins.
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Affiliation(s)
- Roman Sobotka
- Institute of Microbiology, Department of Autotrophic Microorganisms, 379 81 Trebon, Czech Republic.
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17
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The DFPase from Loligo vulgaris in sugar surfactant-based bicontinuous microemulsions: structure, dynamics, and enzyme activity. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:761-74. [DOI: 10.1007/s00249-011-0689-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 02/11/2011] [Accepted: 02/17/2011] [Indexed: 11/25/2022]
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18
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Noji T, Kamidaki C, Kawakami K, Shen JR, Kajino T, Fukushima Y, Sekitoh T, Itoh S. Photosynthetic oxygen evolution in mesoporous silica material: adsorption of photosystem II reaction center complex into 23 nm nanopores in SBA. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:705-13. [PMID: 21171572 DOI: 10.1021/la1032916] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
An oxygen-evolving photosynthetic reaction center complex (PSII) was adsorbed into nanopores in SBA, a mesoporous silica compound. We purified the dimer of PSII complex from a thermophilic cyanobacterium, Thermosynechococcus vulcanus, which grows optimally at 57 °C. The thermally stable PSII dimeric complex has a diameter of 20 nm and a molecular mass of 756 kDa and binds more than 60 chlorophylls. The SBA particles, with average internal pore diameters of 15 nm (SBA(15)) and 23 nm (SBA(23)), adsorbed 4.7 and 15 mg of PSII/g SBA, respectively. Measurement with a confocal laser-scanning microscope indicated the adsorption of PSII to the surface and the inner space of the SBA(23) particles, indicating the adsorption of PSII into the 23 nm silica nanopores. PSII did not bind to the inner pores of SBA(15). PSII bound to SBA(23) showed the high and stable activity of a photosynthetic oxygen-evolving reaction, indicating the light-driven electron transport from water to the quinone molecules added in the outer medium. The PSII-SBA conjugate can be a new material for photosensors and artificial photosynthetic systems.
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Affiliation(s)
- Tomoyasu Noji
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya, Aichi 464-8602, Japan
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19
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Broser M, Gabdulkhakov A, Kern J, Guskov A, Müh F, Saenger W, Zouni A. Crystal structure of monomeric photosystem II from Thermosynechococcus elongatus at 3.6-a resolution. J Biol Chem 2010; 285:26255-62. [PMID: 20558739 DOI: 10.1074/jbc.m110.127589] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The membrane-embedded photosystem II core complex (PSIIcc) uses light energy to oxidize water in photosynthesis. Information about the spatial structure of PSIIcc obtained from x-ray crystallography was so far derived from homodimeric PSIIcc of thermophilic cyanobacteria. Here, we report the first crystallization and structural analysis of the monomeric form of PSIIcc with high oxygen evolution capacity, isolated from Thermosynechococcus elongatus. The crystals belong to the space group C222(1), contain one monomer per asymmetric unit, and diffract to a resolution of 3.6 A. The x-ray diffraction pattern of the PSIIcc-monomer crystals exhibit less anisotropy (dependence of resolution on crystal orientation) compared with crystals of dimeric PSIIcc, and the packing of the molecules within the unit cell is different. In the monomer, 19 protein subunits, 35 chlorophylls, two pheophytins, the non-heme iron, the primary plastoquinone Q(A), two heme groups, 11 beta-carotenes, 22 lipids, seven detergent molecules, and the Mn(4)Ca cluster of the water oxidizing complex could be assigned analogous to the dimer. Based on the new structural information, the roles of lipids and protein subunits in dimer formation of PSIIcc are discussed. Due to the lack of non-crystallographic symmetry and the orientation of the membrane normal of PSIIcc perpendicular ( approximately 87 degrees ) to the crystallographic b-axis, further information about the structure of the Mn(4)Ca cluster is expected to become available from orientation-dependent spectroscopy on this new crystal form.
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Affiliation(s)
- Matthias Broser
- Institute of Chemistry, Max Volmer Laboratory of Biophysical Chemistry, Technische Universität Berlin, Berlin, Germany
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20
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Guskov A, Gabdulkhakov A, Broser M, Glöckner C, Hellmich J, Kern J, Frank J, Müh F, Saenger W, Zouni A. Recent Progress in the Crystallographic Studies of Photosystem II. Chemphyschem 2010; 11:1160-71. [DOI: 10.1002/cphc.200900901] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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21
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Gabdulkhakov A, Guskov A, Broser M, Kern J, Müh F, Saenger W, Zouni A. Probing the Accessibility of the Mn4Ca Cluster in Photosystem II: Channels Calculation, Noble Gas Derivatization, and Cocrystallization with DMSO. Structure 2009; 17:1223-34. [DOI: 10.1016/j.str.2009.07.010] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Revised: 07/16/2009] [Accepted: 07/21/2009] [Indexed: 01/05/2023]
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22
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Müh F, Zouni A. Micelle formation in the presence of photosystem I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:2298-307. [DOI: 10.1016/j.bbamem.2008.05.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2008] [Revised: 05/26/2008] [Accepted: 05/29/2008] [Indexed: 11/16/2022]
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23
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Müh F, Renger T, Zouni A. Crystal structure of cyanobacterial photosystem II at 3.0 A resolution: a closer look at the antenna system and the small membrane-intrinsic subunits. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2008; 46:238-64. [PMID: 18313317 DOI: 10.1016/j.plaphy.2008.01.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Indexed: 05/04/2023]
Abstract
Photosystem II (PSII) is a homodimeric protein-cofactor complex embedded in the thylakoid membrane that catalyses light-driven charge separation accompanied by the water splitting reaction during oxygenic photosynthesis. In the first part of this review, we describe the current state of the crystal structure at 3.0 A resolution of cyanobacterial PSII from Thermosynechococcus elongatus [B. Loll et al., Towards complete cofactor arrangement in the 3.0 A resolution structure of photosystem II, Nature 438 (2005) 1040-1044] with emphasis on the core antenna subunits CP43 and CP47 and the small membrane-intrinsic subunits. The second part describes first the general theory of optical spectra and excitation energy transfer and how the parameters of the theory can be obtained from the structural data. Next, structure-function relationships are discussed that were identified from stationary and time-resolved experiments and simulations of optical spectra and energy transfer processes.
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Affiliation(s)
- Frank Müh
- Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, D-14195 Berlin, Germany
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24
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The C-terminal extension of ferrochelatase is critical for enzyme activity and for functioning of the tetrapyrrole pathway in Synechocystis strain PCC 6803. J Bacteriol 2008; 190:2086-95. [PMID: 18192382 DOI: 10.1128/jb.01678-07] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Heme and chlorophyll (Chl) share a common biosynthetic pathway up to the branch point where magnesium chelatase and ferrochelatase (FeCH) insert either magnesium for Chl biosynthesis or ferrous iron for heme biosynthesis. A distinctive feature of FeCHs in cyanobacteria is their C-terminal extension, which forms a putative transmembrane segment containing a Chl-binding motif. We analyzed the deltaH324 strain of Synechocystis sp. strain PCC 6803, which contains a truncated FeCH enzyme lacking this C-terminal domain. Truncated FeCH was localized to the membrane fraction, suggesting that the C-terminal domain is not necessary for membrane association of the enzyme. Measurements of enzyme activity and complementation experiments revealed that the deltaH324 mutation dramatically reduced activity of the FeCH, which resulted in highly upregulated 5-aminolevulinic acid synthesis in the deltaH324 mutant, implying a direct role for heme in the regulation of flux through the pathway. Moreover, the deltaH324 mutant accumulated a large amount of protoporphyrin IX, and levels of Chl precursors were also significantly increased, suggesting that some, but not all, of the "extra" flux can be diverted down the Chl branch. Analysis of the recombinant full-length and truncated FeCHs demonstrated that the C-terminal extension is critical for activity of the FeCH and that it is strictly required for oligomerization of this enzyme. The observed changes in tetrapyrrole trafficking and the role of the C terminus in the functioning of FeCH are discussed.
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25
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Kantzilakis K, Aivaliotis M, Kotakis C, Krasanakis F, Rizos AK, Kotzabasis K, Tsiotis G. A comparative approach towards thylakoid membrane proteome analysis of unicellular green alga Scenedesmus obliquus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:2271-9. [PMID: 17574204 DOI: 10.1016/j.bbamem.2007.04.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Revised: 04/21/2007] [Accepted: 04/24/2007] [Indexed: 12/29/2022]
Abstract
The chlorophyll (Chl)-containing membrane protein complexes from the green alga Scenedesmus obliquus have been isolated from the thylakoid membranes by solubilization with dodecyl-beta-maltoside and fractionation using a sucrose density gradient. The Chl-containing protein fractions were characterized by absorption spectroscopy, tricine SDS PAGE, BN-PAGE, and dynamic light scattering (DLS). BN-PAGE showed the presence of seven protein complexes with molecular weights in the range of 68, 118, 157, 320, 494, 828 and 955 kDa, respectively. Furthermore, light scattering reveals the simultaneous presence of particles of different sizes in the 3-4 nm and 6.0-7.5 nm range, respectively. The smaller size is related to the hydrodynamic radius of the trimer Light Harvesting Complex (LHCII), whereas the larger size is associated with the presence of photosystem I and photosystem II reaction centers. Additionally, functional information regarding protein-protein interactions was deconvoluted using coupling 2-D BN-PAGE, MALDI-TOF MS and a detailed mapping of S. obliquus photosynthetic proteome of the solubilized thylakoid membranes is therefore presented.
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Affiliation(s)
- Konstantinos Kantzilakis
- Division of Biochemistry, Department of Chemistry, University of Crete, P.O. Box 2208, 71003 Voutes Heraklion, Greece
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26
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Kern J, Biesiadka J, Loll B, Saenger W, Zouni A. Structure of the Mn4-Ca cluster as derived from X-ray diffraction. PHOTOSYNTHESIS RESEARCH 2007; 92:389-405. [PMID: 17492491 DOI: 10.1007/s11120-007-9173-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2006] [Accepted: 04/10/2007] [Indexed: 05/15/2023]
Abstract
The catalytic centre for light-induced water oxidation in photosystem II (PSII) is a multinuclear metal cluster containing four manganese and one calcium cations. Knowing the structure of this biological catalyst is of utmost importance for unravelling the mechanism of water oxidation in photosynthesis. In this review we describe the current state of the X-ray structure determination at 3.0 A resolution of the water oxidation complex (WOC) of PSII. The arrangement of metal cations in the cluster, their coordination and protein surroundings are discussed with regard to spectroscopic and mutagenesis studies. Limitations of the presently available structural data are pointed out and possible perspectives for the future are outlined, including the combination of X-ray diffraction and X-ray spectroscopy on single crystals.
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Affiliation(s)
- Jan Kern
- Institut für Chemie, Max Volmer Laboratorium für Biophysikalische Chemie, Sekr. PC 14, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany.
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27
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Oligomeric behavior of the RND transporters CusA and AcrB in micellar solution of detergent. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:1567-73. [PMID: 17467658 DOI: 10.1016/j.bbamem.2007.03.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Revised: 02/12/2007] [Accepted: 03/08/2007] [Indexed: 10/23/2022]
Abstract
We have used analytical ultracentrifugation to explore the oligomeric states of AcrB and CusA in micellar solution of detergent. These two proteins belong to the resistance, nodulation and cell division (RND) family of efflux proteins that are involved in multiple drug and heavy metal resistance. Only the structure of AcrB has been determined so far. Although functional RND proteins should assemble as trimers as AcrB does, both AcrB and CusA form a mixture of quaternary structures (from monomer to heavy oligomer) in detergent solution. The distribution of the oligomeric states was studied as a function of different parameters: nature and concentration of the detergent, ionic strength, pH, protein concentration. This pseudo-heterogeneity does not hamper the crystallization of AcrB as a homotrimer.
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28
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Zimmermann K, Heck M, Frank J, Kern J, Vass I, Zouni A. Herbicide binding and thermal stability of photosystem II isolated from Thermosynechococcus elongatus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:106-14. [PMID: 16472760 DOI: 10.1016/j.bbabio.2005.12.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Revised: 11/30/2005] [Accepted: 12/05/2005] [Indexed: 10/25/2022]
Abstract
Binding of herbicides to photosystem II inhibits the electron transfer from Q(A) to Q(B) due to competition of herbicides with plastoquinone bound at the Q(B) site. We investigated herbicide binding to monomeric and dimeric photosystem II core complexes (PSIIcc) isolated from Thermosynechococcus elongatus by a combination of different methods (isothermal titration and differential scanning calorimetry, CD spectroscopy and measurements of the oxygen evolution) yielding binding constants, enthalpies and stoichiometries for various herbicides as well as information regarding stabilization/destabilization of the complex. Herbicide binding to detergent-solubilized PSIIcc can be described by a model of single independent binding sites present on this important membrane protein. Interestingly, binding stoichiometries herbicide:PSIIcc are lower than 1:1 and vary depending on the herbicide under study. Strong binding herbicides such as terbutryn stabilize PSIIcc in thermal unfolding experiments and endothermically binding herbicides like ioxynil probably cause large structural changes accompanied with the binding process as shown by differential scanning calorimetry experiments of the unfolding reaction of PSIIcc monomer in the presence of ioxynil. In addition we studied the occupancy of the Q(B) sites with plastoquinone (PQ9) by measuring flash induced fluorescence relaxation yielding a possible explanation for the deviations of herbicide binding from a 1:1 herbicide/binding site model.
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Affiliation(s)
- K Zimmermann
- Institute for Medical Physics and Biophysics, Charité-Universitätsmedizin, D-10098 Berlin, Schumann Str. 21/22, Germany
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29
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Kern J, Loll B, Zouni A, Saenger W, Irrgang KD, Biesiadka J. Cyanobacterial photosystem II at 3.2 A resolution - the plastoquinone binding pockets. PHOTOSYNTHESIS RESEARCH 2005; 84:153-9. [PMID: 16049768 DOI: 10.1007/s11120-004-7077-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2004] [Accepted: 12/02/2004] [Indexed: 05/03/2023]
Abstract
Photosystem II from thylakoid membranes of the thermophilic cyanobacterium Thermosynechococcus elongatus was solubilized with n-beta-dodecylmaltoside and purified using anion exchange chromatography. Molecular weight, pigment stoichiometry and subunit composition were assayed using various techniques. The holocomplex is dimeric with a molecular mass of 756 +/- 18 kDa and functionally fully active. Crystals obtained from these samples showed significantly improved quality leading to a 3D structure at 3.2 A resolution. Several loop regions of the principal protein subunits are now defined that were not interpretable at lower (3.8 A) resolution, thus resulting in a more complete model. The head groups of the cofactors of the electron transfer chain and of the antennae have been modeled, coordinating and hydrogen bonding amino acids identified and the nature of the binding pockets derived. The orientations of these cofactors resemble those of the reaction centre from anoxygenic purple bacteria. For the two plastoquinones, electron density was only found for the head group of QA and none for QB indicating low or even no occupancy of this site in the crystal structure. Both binding pockets and problems related to the QB site are discussed here and compared to the situation in the purple bacterial reaction centre.
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Affiliation(s)
- Jan Kern
- Max-Volmer-Laboratories for Biophysical Chemistry, Technical University Berlin, Strasse des 17 Juni 135, 10623 Berlin, Germany
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Müh F, Zouni A. Extinction coefficients and critical solubilisation concentrations of photosystems I and II from Thermosynechococcus elongatus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2005; 1708:219-28. [PMID: 15953478 DOI: 10.1016/j.bbabio.2005.03.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2004] [Revised: 03/10/2005] [Accepted: 03/13/2005] [Indexed: 10/25/2022]
Abstract
The absorption properties of chlorophyll a (Chla) in active core complexes of photosystems I (PSI) and II (PSII) isolated in high purity from the thermophilic cyanobacterium Thermosynechococcus elongatus were correlated with those of extracts in 80% acetone to determine effective extinction coefficients of protein-bound Chla and molar extinction coefficients of core complexes and reaction centers (RC). These coefficients allow a quick determination of Chla and protein concentrations from steady-state absorption spectra of intact samples without the need for pigment extraction and protein destruction. In the visible range, epsilon(680)(p) = 57 mM(-1) cm(-1) for trimeric PSI (PSIt) and epsilon(674)(p) = 70 mM(-1) cm(-1) for dimeric (PSIId) and monomeric (PSIIm) PSII (error +/-6%; superscript "p" refers to Chla bound to intact protein, subscripts are the peak maxima in nm). The integral extinction coefficient phi(p) = 2.8 nm microM(-1) cm(-1) for the wavelength interval between 550 and 800 nm and the extinction coefficient epsilon(B)(p) = 14 mM(-1) cm(-1) for the smaller absorption maximum (B = 632 nm for PSI and 627 nm for PSII) were found to be essentially the same for both types of PS. The coefficients of PSIt are shown to remain unaltered when 65% (v/v) of the buffer is replaced with glycerol. Molar extinction coefficients of core complexes were determined using Chla/RC ratios of 96+/-1 for PSI and 35+/-2 for PSII based on X-ray data. In addition, the critical solubilisation concentration of n-dodecyl-beta-d-maltoside (betaDM), necessary to keep the core complexes in solution, was determined by turbidimetric titrations. It was found that at least approximately 500 betaDM molecules per PSIt ( approximately 2 betaDM per Chla) and 190 betaDM molecules per PSIIm ( approximately 5 betaDM per Chla, also for PSIId) in excess of the critical micelle concentration of 0.16 +/- 0.03 mM are necessary for a complete solubilisation of the core complexes.
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Affiliation(s)
- Frank Müh
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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