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Ishii N, Odahara T. Investigation of the Efficacy of Lanthanoid Heavy Metal Acetates as Electron Staining Reagents for Biomembrane Vesicles. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:2080-2089. [PMID: 37832148 DOI: 10.1093/micmic/ozad107] [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: 05/30/2023] [Revised: 07/25/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023]
Abstract
Transmission electron microscopy (TEM) has revolutionized our understanding of protein structures by enabling atomic-resolution visualization without the need for crystallography, thanks to advancements in cryo-TEM and single particle analysis methods. However, conventional electron microscopy remains relevant for studying stained samples, as it allows the practical determination of optimal conditions through extensive experimentation. TEM also facilitates the examination of supramolecular complexes encompassing proteins, lipids, and nucleic acids. In this study, we investigated the applicability of lanthanoid reagents as electron-staining alternatives to uranyl acetate, which is globally regulated as a nuclear fuel material. We focus on a model biomembrane vesicle system, the chromatophores from the purple photosynthetic eubacterium Rhodospirillum rubrum, which integrate proteins and lipids. Through density distribution analysis of electron micrographs, we evaluated the efficacy of various lanthanoid acetates and found that triacetates of neodymium, samarium, and gadolinium exhibited similar staining effectiveness to uranyl acetate. Additionally, triacetates of praseodymium, erbium, and lutetium, followed by europium show promising results as secondary candidates. Our findings suggest that lanthanoid transition heavy metal acetates could serve as viable alternatives for electron staining in TEM, offering potential advantages over uranyl acetate.
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Affiliation(s)
- Noriyuki Ishii
- Cellular and Molecular Biotechnology Research Institute, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central-6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
- Electron Microscopy Facility, Open Research Facilities Station, Open Research Platform Unit, Tsukuba Innovation Arena (TIA) Central Office, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central-6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
- The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Takayuki Odahara
- Biomedical Research Institute, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central-6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
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Mickoleit F, Rosenfeldt S, Toro-Nahuelpan M, Schaffer M, Schenk AS, Plitzko JM, Schüler D. High-Yield Production, Characterization, and Functionalization of Recombinant Magnetosomes in the Synthetic Bacterium Rhodospirillum rubrum "magneticum". Adv Biol (Weinh) 2021; 5:e2101017. [PMID: 34296829 DOI: 10.1002/adbi.202101017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/10/2021] [Indexed: 01/02/2023]
Abstract
Recently, the photosynthetic Rhodospirillum rubrum has been endowed with the ability of magnetosome biosynthesis by transfer and expression of biosynthetic gene clusters from the magnetotactic bacterium Magnetospirillum gryphiswaldense. However, the growth conditions for efficient magnetite biomineralization in the synthetic R. rubrum "magneticum", as well as the particles themselves (i.e., structure and composition), have so far not been fully characterized. In this study, different cultivation strategies, particularly the influence of temperature and light intensity, are systematically investigated to achieve optimal magnetosome biosynthesis. Reduced temperatures ≤16 °C and gradual increase in light intensities favor magnetite biomineralization at high rates, suggesting that magnetosome formation might utilize cellular processes, cofactors, and/or pathways that are linked to photosynthetic growth. Magnetosome yields of up to 13.6 mg magnetite per liter cell culture are obtained upon photoheterotrophic large-scale cultivation. Furthermore, it is shown that even more complex, i.e., oligomeric, catalytically active functional moieties like enzyme proteins can be efficiently expressed on the magnetosome surface, thereby enabling the in vivo functionalization by genetic engineering. In summary, it is demonstrated that the synthetic R. rubrum "magneticum" is a suitable host for high-yield magnetosome biosynthesis and the sustainable production of genetically engineered, bioconjugated magnetosomes.
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Affiliation(s)
- Frank Mickoleit
- Dept. Microbiology, University of Bayreuth, D-95447, Bayreuth, Germany
| | - Sabine Rosenfeldt
- Bavarian Polymer Institute (BPI)/Physical Chemistry 1, University of Bayreuth, D-95447, Bayreuth, Germany
| | - Mauricio Toro-Nahuelpan
- Dept. Microbiology, University of Bayreuth, D-95447, Bayreuth, Germany.,Dept. Molecular Structural Biology, Max Planck Institute of Biochemistry, D-82152, Martinsried, Germany
| | - Miroslava Schaffer
- Dept. Molecular Structural Biology, Max Planck Institute of Biochemistry, D-82152, Martinsried, Germany
| | - Anna S Schenk
- Bavarian Polymer Institute (BPI)/Physical Chemistry - Colloidal Systems, University of Bayreuth, D-95447, Bayreuth, Germany
| | - Jürgen M Plitzko
- Dept. Molecular Structural Biology, Max Planck Institute of Biochemistry, D-82152, Martinsried, Germany
| | - Dirk Schüler
- Dept. Microbiology, University of Bayreuth, D-95447, Bayreuth, Germany
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Kaftan D, Bína D, Koblížek M. Temperature dependence of photosynthetic reaction centre activity in Rhodospirillum rubrum. PHOTOSYNTHESIS RESEARCH 2019; 142:181-193. [PMID: 31267356 PMCID: PMC6848049 DOI: 10.1007/s11120-019-00652-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 06/03/2019] [Indexed: 06/09/2023]
Abstract
The influence of temperature on photosynthetic reactions was investigated by a combination of time-resolved bacteriochlorophyll fluorescence, steady-state and differential absorption spectroscopy, and polarographic respiration measurements in intact cells of purple non-sulphur bacterium Rhodospirillum rubrum. Using variable bacteriochlorophyll fluorescence, it was found that the electron-transport activity increased with the increasing temperature up to 41 °C. The fast and medium components of the fluorescence decay kinetics followed the ideal Arrhenius equation. The calculated activation energy for the fast component was Ea1 = 16 kJ mol-1, while that of the medium component was more than double, with Ea2 = 38 kJ mol-1. At temperatures between 41 and 59 °C, the electron transport was gradually, irreversibly inhibited. Interestingly, the primary charge separation remained fully competent from 20 to 59 °C as documented by both BChl fluorescence and differential absorption spectroscopy of the P870+ signal. At temperatures above 60 °C, the primary photochemistry became reversibly inhibited, which was manifested by an increase in minimal fluorescence, F0, whereas maximal fluorescence, FM, slowly declined. Finally, above 71 °C, the photosynthetic complexes began to disassemble as seen in the decline of all fluorometric parameters and the disappearance of the LH1 absorption band at 880 nm. The extended optimal temperature of photosynthetic reaction centre in a model species of Rhodospirillales adds on the evidence that the good thermostability of the photosynthetic reaction centres is present across all Alphaproteobacteria.
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Affiliation(s)
- David Kaftan
- Center Algatech, Institute of Microbiology CAS, 37981, Třeboň, Czech Republic.
- Faculty of Science, University of South Bohemia, 37005, Ceske Budejovice, Czech Republic.
| | - David Bína
- Faculty of Science, University of South Bohemia, 37005, Ceske Budejovice, Czech Republic
- Biology Centre, Czech Academy of Sciences, Branišovská 31, Ceske Budejovice, Czech Republic
| | - Michal Koblížek
- Center Algatech, Institute of Microbiology CAS, 37981, Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia, 37005, Ceske Budejovice, Czech Republic
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Odahara T, Odahara K. Various salts employed as precipitant in combination with polyethylene glycol in protein/detergent particle association. Heliyon 2019; 4:e01073. [PMID: 30603706 PMCID: PMC6307348 DOI: 10.1016/j.heliyon.2018.e01073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 11/27/2018] [Accepted: 12/17/2018] [Indexed: 11/29/2022] Open
Abstract
Salt/polyethylene glycol (PEG) mixtures are employed as precipitants for biological macromolecules. The dependence of precipitation curves (PCs) on salt species was investigated for integral membrane protein/detergent particles. By relating this dependence to properties of ions dissociated from added salts, the following roles and effects of various ions were clarified. In the presence of ions whose interaction with water is stronger than water-water interaction, the coordination of solvent molecules is rearranged so as to strengthen short-range steric repulsion and hydrophobic attraction. Ions whose interaction with water is weaker than water-water interaction can be a hindrance to hydrophobic-hydrophobic contact. Moreover, strong electric fields of divalent cations can cause an attractive effect between electronegative or polar groups of neighboring particles. The variations of particle-particle and particle-PEG interactions depending on the state of particles and surrounding solvents were correlative. Due to this, the relationship between the horizontal positions of PC and the species of salts added could be formulated as a binary linear function of cationic and anionic species composing the salts.
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Affiliation(s)
- Takayuki Odahara
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central-6, 1-1 Higashi, Tsukuba, Ibaraki, 305-8566 Japan
| | - Koji Odahara
- Fukuoka Prefectural Association of Agricultural Production and Materials, Fukuoka Prefectural Office, Hakata, Fukuoka, 812-8577 Japan
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Yang Z, Zhou Q, Mok L, Singh A, Swartz DJ, Urbatsch IL, Brouillette CG. Interactions and cooperativity between P-glycoprotein structural domains determined by thermal unfolding provides insights into its solution structure and function. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:48-60. [PMID: 27783926 DOI: 10.1016/j.bbamem.2016.10.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 09/19/2016] [Accepted: 10/21/2016] [Indexed: 12/16/2022]
Abstract
Structural changes in mouse P-glycoprotein (Pgp) induced by thermal unfolding were studied by differential scanning calorimetry (DSC), circular dichroism and fluorescence spectroscopy to gain insight into the solution conformation(s) of this ABC transporter that may not be apparent from current crystal structures. DSC of reconstituted Pgp showed two thermal unfolding transitions in the absence of MgATP, suggesting that each transition involved the cooperative unfolding of two or more interacting structural domains. A low calorimetric unfolding enthalpy and minimal structural changes were observed, which are hallmarks of the thermal unfolding of α-helical membrane proteins, because generally only the extramembranous regions undergo significant unfolding. Nucleotide binding increased the unfolding temperature of both transitions to the same extent, suggesting that one nucleotide binding domain (NBD) unfolds with each transition. Combined with the results from the two isolated NBDs, we propose that each DSC transition represents the cooperative unfolding of one NBD and the two contacting intracellular loops. Further, the presence of two transitions in both apo and MgATP bound wild-type Pgp suggests the NBD-dimeric conformation is transient, and that Pgp resides predominantly in the crystallographically observed inward-facing conformation with NBDs separated, even under conditions supporting continuous MgATP hydrolysis. In contrast, DSC of the vanadate-trapped MgADP·Pgp complex and the MgATP-bound catalytically inactive mutant, E552A/E1197A, show an additional transition at much higher temperature, corresponding to the unfolding of the nucleotide-trapped NBD-dimeric outward-facing conformation. The collective results indicate a strong preference for an NBD dissociated, inward-facing conformation of Pgp.
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Affiliation(s)
- Zhengrong Yang
- Center for Structural Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Qingxian Zhou
- Center for Structural Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Leo Mok
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Anukriti Singh
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Douglas J Swartz
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Ina L Urbatsch
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
| | - Christie G Brouillette
- Center for Structural Biology, University of Alabama at Birmingham, Birmingham, AL, USA; Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA.
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Odahara T, Odahara K. Data in support of intermolecular interactions at early stage of protein/detergent particle association induced by salt/polyethylene glycol mixtures. Data Brief 2016; 7:1283-7. [PMID: 27135050 PMCID: PMC4835637 DOI: 10.1016/j.dib.2016.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 03/28/2016] [Accepted: 04/01/2016] [Indexed: 11/06/2022] Open
Abstract
The data provide information in support of the research article, “Intermolecular interactions at early stage of protein/detergent particle association induced by salt/polyethylene glycol mixtures” [1]. The data regarding variation of absorption spectra is used as an indicator of the duration of Rp. viridis PRU and RC, Rb. sphaeroides RC and LH2, and Rb. capsulatus LH2 in the native state in the presence of NaCl/polyethylene glycol (PEG) mixture. The data about minimum concentrations of salt and PEG whose aqueous phases are mutually separated presents information on additional influence of Tris buffer and N-octyl-β-d-glucoside on the salt–PEG phase separation.
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Affiliation(s)
- Takayuki Odahara
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central-6, 1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Koji Odahara
- Fukuoka Agriculture and Forestry Research Center, Chikusion, Fukuoka 818-8549, Japan
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Odahara T, Odahara K. Intermolecular interactions at early stage of protein/detergent particle association induced by salt/polyethylene glycol mixtures. Protein Expr Purif 2015; 120:72-86. [PMID: 26705098 DOI: 10.1016/j.pep.2015.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 12/07/2015] [Accepted: 12/11/2015] [Indexed: 11/26/2022]
Abstract
Mixtures of neutral salts and polyethylene glycol are used for various purposes in biological studies. Although the effects of each component of the mixtures are theoretically well investigated, comprehension of their integrated effects remains insufficient. In this work, their roles and effects as a precipitant were clarified by studying dependence of precipitation curves on salt concentration for integral membrane protein/detergent particles of different physicochemical properties. The dependence of precipitation curves was reasonably related to intermolecular interactions among relevant molecules such as protein, detergent and polyethylene glycol by considering their physicochemical properties. The obtained relationships are useful as basic information to learn the early stage of biological macromolecular associations.
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Affiliation(s)
- Takayuki Odahara
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central-6, 1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan.
| | - Koji Odahara
- Fukuoka Agriculture and Forestry Research Center, Chikusino, Fukuoka, 818-8549, Japan
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Yue H, Zhao C, Li K, Yang S. Absorption spectral change of peripheral-light harvesting complexes 2 induced by magnesium protoporphyrin IX monomethyl ester association. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 137:1153-1157. [PMID: 25305606 DOI: 10.1016/j.saa.2014.08.132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 08/15/2014] [Accepted: 08/31/2014] [Indexed: 06/04/2023]
Abstract
Several spectrally different types of peripheral light harvesting complexes (LH) have been reported in anoxygenic phototrophic bacteria in response to environmental changes. In this study, two spectral forms of LH2 (T-LH2 and U-LH2) were isolated from Rhodobacter azotoformans. The absorption of T-LH2 was extremely similar to the LH2 isolated from Rhodobacter sphaeroides. U-LH2 showed an extra peak at ∼423 nm in the carotenoid region. To explore the spectral origin of this absorption peak, the difference in pigment compositions of two LH2 was analyzed. Spheroidene and bacteriochlorophyll aP were both contained in the two LH2. And magnesium protoporphyrin IX monomethyl ester (MPE) was only contained in U-LH2. It is known that spheroidene and bacteriochlorophyll aP do not produce ∼423 nm absorption peak either in vivo or in vitro. Whether MPE accumulation was mainly responsible for the formation of the ∼423 nm peak? The interactions between MPE and different proteins were further studied. The results showed that the maximum absorption of MPE was red-shifted from ∼415 nm to ∼423 nm when it was mixed with T-LH2 and its apoproteins, nevertheless, the Qy transitions of the bound bacteriochlorophylls in LH2 were almost unaffected, which indicated that the formation of the ∼423 nm peak was related to MPE-LH2 protein interaction. MPE did not bind to sites involved in the spectral tuning of BChls, but the conformation of integral LH2 was affected by MPE association, the alkaline stability of U-LH2 was lower than T-LH2, and the fluorescence intensity at 860 nm was decreased after MPE combination.
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Affiliation(s)
- Huiying Yue
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, China.
| | - Chungui Zhao
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, China.
| | - Kai Li
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, China.
| | - Suping Yang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, China.
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