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Grützner J, Remes B, Eisenhardt KMH, Scheller D, Kretz J, Madhugiri R, McIntosh M, Klug G. sRNA-mediated RNA processing regulates bacterial cell division. Nucleic Acids Res 2021; 49:7035-7052. [PMID: 34125915 PMCID: PMC8266604 DOI: 10.1093/nar/gkab491] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/17/2021] [Accepted: 05/28/2021] [Indexed: 01/16/2023] Open
Abstract
Tight control of cell division is essential for survival of most organisms. For prokaryotes, the regulatory mechanisms involved in the control of cell division are mostly unknown. We show that the small non-coding sRNA StsR has an important role in controlling cell division and growth in the alpha-proteobacterium Rhodobacter sphaeroides. StsR is strongly induced by stress conditions and in stationary phase by the alternative sigma factors RpoHI/HII, thereby providing a regulatory link between cell division and environmental cues. Compared to the wild type, a mutant lacking StsR enters stationary phase later and more rapidly resumes growth after stationary phase. A target of StsR is UpsM, the most abundant sRNA in the exponential phase. It is derived from partial transcriptional termination within the 5' untranslated region of the mRNA of the division and cell wall (dcw) gene cluster. StsR binds to UpsM as well as to the 5' UTR of the dcw mRNA and the sRNA-sRNA and sRNA-mRNA interactions lead to a conformational change that triggers cleavage by the ribonuclease RNase E, affecting the level of dcw mRNAs and limiting growth. These findings provide interesting new insights into the role of sRNA-mediated regulation of cell division during the adaptation to environmental changes.
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Affiliation(s)
- Julian Grützner
- Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Bernhard Remes
- Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Katrin M H Eisenhardt
- Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Daniel Scheller
- Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Jonas Kretz
- Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Ramakanth Madhugiri
- Institute of Medical Virology, University of Giessen, Schubertstr. 81, D-35392 Giessen, Germany
| | - Matthew McIntosh
- Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
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Dahlberg PD, Ting PC, Massey SC, Martin EC, Hunter CN, Engel GS. Electronic Structure and Dynamics of Higher-Lying Excited States in Light Harvesting Complex 1 from Rhodobacter sphaeroides. J Phys Chem A 2016; 120:4124-30. [PMID: 27232937 PMCID: PMC5668141 DOI: 10.1021/acs.jpca.6b04146] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Light harvesting in photosynthetic organisms involves efficient transfer of energy from peripheral antenna complexes to core antenna complexes, and ultimately to the reaction center where charge separation drives downstream photosynthetic processes. Antenna complexes contain many strongly coupled chromophores, which complicates analysis of their electronic structure. Two-dimensional electronic spectroscopy (2DES) provides information on energetic coupling and ultrafast energy transfer dynamics, making the technique well suited for the study of photosynthetic antennae. Here, we present 2DES results on excited state properties and dynamics of a core antenna complex, light harvesting complex 1 (LH1), embedded in the photosynthetic membrane of Rhodobacter sphaeroides. The experiment reveals weakly allowed higher-lying excited states in LH1 at 770 nm, which transfer energy to the strongly allowed states at 875 nm with a lifetime of 40 fs. The presence of higher-lying excited states is in agreement with effective Hamiltonians constructed using parameters from crystal structures and atomic force microscopy (AFM) studies. The energy transfer dynamics between the higher- and lower-lying excited states agree with Redfield theory calculations.
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Affiliation(s)
- Peter D. Dahlberg
- Graduate Program in the Biophysical Sciences, Institute for Biophysical Dynamics, and the James Franck Institute, The University of Chicago, Chicago, IL 60637
| | - Po-Chieh Ting
- Department of Chemistry, Institute for Biophysical Dynamics, and the James Franck Institute, The University of Chicago, Chicago, IL 60637
| | - Sara C. Massey
- Department of Chemistry, Institute for Biophysical Dynamics, and the James Franck Institute, The University of Chicago, Chicago, IL 60637
| | - Elizabeth C. Martin
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - C. Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Gregory S. Engel
- Department of Chemistry, Institute for Biophysical Dynamics, and the James Franck Institute, The University of Chicago, Chicago, IL 60637
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Verméglio A, Lavergne J, Rappaport F. Connectivity of the intracytoplasmic membrane of Rhodobacter sphaeroides: a functional approach. Photosynth Res 2016; 127:13-24. [PMID: 25512104 DOI: 10.1007/s11120-014-0068-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 12/09/2014] [Indexed: 06/04/2023]
Abstract
The photosynthetic apparatus in the bacterium Rhodobacter sphaeroides is mostly present in intracytoplasmic membrane invaginations. It has long been debated whether these invaginations remain in topological continuity with the cytoplasmic membrane, or form isolated chromatophore vesicles. This issue is revisited here by functional approaches. The ionophore gramicidin was used as a probe of the relative size of the electro-osmotic units in isolated chromatophores, spheroplasts, or intact cells. The decay of the membrane potential was monitored from the electrochromic shift of carotenoids. The half-time of the decay induced by a single channel in intact cells was about 6 ms, thus three orders of magnitude slower than in isolated chromatophores. In spheroplasts obtained by lysis of the cell wall, the single channel decay was still slower (~23 ms) and the sensitivity toward the gramicidin concentration was enhanced 1,000-fold with respect to isolated chromatophores. These results indicate that the area of the functional membrane in cells or spheroplasts is about three orders of magnitude larger than that of isolated chromatophores. Intracytoplasmic vesicles, if present, could contribute to at most 10% of the photosynthetic apparatus in intact cells of Rba. sphaeroides. Similar conclusions were obtained from the effect of a ∆pH-induced diffusion potential in intact cells. This caused a large electrochromic response of carotenoids, of similar amplitude as the light-induced change, indicating that most of the system is sensitive to a pH change of the external medium. A single internal membrane and periplasmic space may offer significant advantages concerning renewal of the photosynthetic apparatus and reallocation of the components shared with other bioenergetic pathways.
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Affiliation(s)
- André Verméglio
- CEA, IBEB, Laboratoire de Bioénergétique Cellulaire, 13108, Saint-Paul-Lez-Durance, France.
- CNRS, UMR 7265 Biol Veget & Microbiol Environ, 13108, Saint-Paul-Lez-Durance, France.
- Aix Marseille Université, BVME UMR7265, 13284, Marseille, France.
| | - Jérôme Lavergne
- CEA, IBEB, Laboratoire de Bioénergétique Cellulaire, 13108, Saint-Paul-Lez-Durance, France
- CNRS, UMR 7265 Biol Veget & Microbiol Environ, 13108, Saint-Paul-Lez-Durance, France
- Aix Marseille Université, BVME UMR7265, 13284, Marseille, France
| | - Fabrice Rappaport
- Institut de Biologie Physico-Chimique, UMR 7141 CNRS-UPMC, 13, rue Pierre et Marie Curie, 75005, Paris, France
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Asztalos E, Sipka G, Maróti P. Fluorescence relaxation in intact cells of photosynthetic bacteria: donor and acceptor side limitations of reopening of the reaction center. Photosynth Res 2015; 124:31-44. [PMID: 25527461 DOI: 10.1007/s11120-014-0070-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 12/12/2014] [Indexed: 06/04/2023]
Abstract
The dark relaxation of the yield of variable BChl fluorescence in the 10(-5)-10 s time range is measured after laser diode (808 nm) excitation of variable duration in intact cells of photosynthetic bacteria Rba. sphaeroides, Rsp. rubrum, and Rvx. gelatinosus under various treatments of redox agents, inhibitors, and temperature. The kinetics of the relaxation is complex and much wider extended than a monoexponential function. The longer is the excitation, the slower is the relaxation which is determined by the redox states, sizes, and accessibility of the pools of cytochrome [Formula: see text] and quinone for donor and acceptor side-limited bacterial strains, respectively. The kinetics of fluorescence decay reflects the opening kinetics of the closed RC. The relaxation is controlled preferentially by the rate of re-reduction of the oxidized dimer by mobile cytochrome [Formula: see text] in Rba. sphaeroides and Rsp. rubrum and by the rate constant of the [Formula: see text] interquinone electron transfer, (350 μs)(-1) and/or the quinol/quinone exchange at the acceptor side in Rvx. gelatinosus. The commonly used acceptor side inhibitors (e.g., terbutryn) demonstrate kinetically limited block of re-oxidation of the primary quinone. The observations are interpreted in frame of a minimum kinetic and energetic model of electron transfer reactions in bacterial RC of intact cells.
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Affiliation(s)
- Emese Asztalos
- Department of Medical Physics, University of Szeged, Szeged, Rerrich Béla tér 1, 6720, Hungary
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Shum H, Gaffney EA. Hydrodynamic analysis of flagellated bacteria swimming near one and between two no-slip plane boundaries. Phys Rev E Stat Nonlin Soft Matter Phys 2015; 91:033012. [PMID: 25871207 DOI: 10.1103/physreve.91.033012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Indexed: 05/27/2023]
Abstract
The motility of swimming bacteria near solid surfaces has implications in a wide range of scenarios, including water treatment facilities, microfluidics, and biomedical implants. Using the boundary element method to numerically solve the equations of low Reynolds number fluid flow, we investigate the dynamics of a model swimmer propelled by rotating a single helical flagellum. Building on previous simulation results for swimmers near a single plane boundary, we introduce a second, parallel boundary and show that the bacterial trajectories change as the two plates are brought closer together. Analysis of this dynamical system shows that the configuration in the center of the channel and parallel to the walls is an unstable equilibrium state for large plate separations, but it becomes the only stable position for swimmers when the plate separation is reduced to three to four times the cell width. Our model also predicts that transient trajectories, i.e., those not at steady states, can exhibit curvature in the opposite sense to that expected from the well-known explanation for circular bacterial paths near a single wall.
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Affiliation(s)
- Henry Shum
- Department of Chemical & Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Eamonn A Gaffney
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford OX2 6GG, United Kingdom
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Bigdeli S, Dettloff RO, Frank CW, Davis RW, Crosby LD. A simple method for encapsulating single cells in alginate microspheres allows for direct PCR and whole genome amplification. PLoS One 2015; 10:e0117738. [PMID: 25689864 PMCID: PMC4331554 DOI: 10.1371/journal.pone.0117738] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 01/02/2015] [Indexed: 12/19/2022] Open
Abstract
Microdroplets are an effective platform for segregating individual cells and amplifying DNA. However, a key challenge is to recover the contents of individual droplets for downstream analysis. This paper offers a method for embedding cells in alginate microspheres and performing multiple serial operations on the isolated cells. Rhodobacter sphaeroides cells were diluted in alginate polymer and sprayed into microdroplets using a fingertip aerosol sprayer. The encapsulated cells were lysed and subjected either to conventional PCR, or whole genome amplification using either multiple displacement amplification (MDA) or a two-step PCR protocol. Microscopic examination after PCR showed that the lumen of the occupied microspheres contained fluorescently stained DNA product, but multiple displacement amplification with phi29 produced only a small number of polymerase colonies. The 2-step WGA protocol was successful in generating fluorescent material, and quantitative PCR from DNA extracted from aliquots of microspheres suggested that the copy number inside the microspheres was amplified up to 3 orders of magnitude. Microspheres containing fluorescent material were sorted by a dilution series and screened with a fluorescent plate reader to identify single microspheres. The DNA was extracted from individual isolates, re-amplified with full-length sequencing adapters, and then a single isolate was sequenced using the Illumina MiSeq platform. After filtering the reads, the only sequences that collectively matched a genome in the NCBI nucleotide database belonged to R. sphaeroides. This demonstrated that sequencing-ready DNA could be generated from the contents of a single microsphere without culturing. However, the 2-step WGA strategy showed limitations in terms of low genome coverage and an uneven frequency distribution of reads across the genome. This paper offers a simple method for embedding cells in alginate microspheres and performing PCR on isolated cells in common bulk reactions, although further work must be done to improve the amplification coverage of single genomes.
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Affiliation(s)
- Saharnaz Bigdeli
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, 3165 Porter Drive, Palo Alto, CA 94304, United States of America
- Department of Chemical Engineering, Stanford University, Stanford, CA, United States of America
| | - Roger O. Dettloff
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, 3165 Porter Drive, Palo Alto, CA 94304, United States of America
- Caerus Molecular Diagnostics, Mountain View, CA, United States of America
| | - Curtis W. Frank
- Department of Chemical Engineering, Stanford University, Stanford, CA, United States of America
| | - Ronald W. Davis
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, 3165 Porter Drive, Palo Alto, CA 94304, United States of America
| | - Laurel D. Crosby
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, 3165 Porter Drive, Palo Alto, CA 94304, United States of America
- * E-mail:
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7
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Kis M, Asztalos E, Sipka G, Maróti P. Assembly of photosynthetic apparatus in Rhodobacter sphaeroides as revealed by functional assessments at different growth phases and in synchronized and greening cells. Photosynth Res 2014; 122:261-273. [PMID: 25022916 DOI: 10.1007/s11120-014-0026-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Accepted: 06/30/2014] [Indexed: 06/03/2023]
Abstract
The development of photosynthetic membranes of intact cells of Rhodobacter sphaeroides was tracked by light-induced absorption spectroscopy and induction and relaxation of the bacteriochlorophyll fluorescence. Changes in membrane structure were induced by three methods: synchronization of cell growth, adjustment of different growth phases and transfer from aerobic to anaerobic conditions (greening) of the bacteria. While the production of the bacteriochlorophyll and carotenoid pigments and the activation of light harvesting and reaction center complexes showed cell-cycle independent and continuous increase with characteristic lag phases, the accumulation of phospholipids and membrane potential (electrochromism) exhibited stepwise increase controlled by cell division. Cells in the stationary phase of growth demonstrated closer packing and tighter energetic coupling of the photosynthetic units (PSU) than in their early logarithmic stage. The greening resulted in rapid (within 0-4 h) induction of BChl synthesis accompanied with a dominating role for the peripheral light harvesting system (up to LH2/LH1 ~2.5), significantly increased rate (~7·10(4) s(-1)) and yield (F v/F max ~0.7) of photochemistry and modest (~2.5-fold) decrease of the rate of electron transfer (~1.5·10(4) s(-1)). The results are discussed in frame of a model of sequential assembly of the PSU with emphasis on crowding the LH2 complexes resulting in an increase of the connectivity and yield of light capture on the one hand and increase of hindrance to diffusion of mobile redox agents on the other hand.
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Affiliation(s)
- M Kis
- Department of Medical Physics, University of Szeged, Rerrich Béla tér 1, Szeged, 6720, Hungary
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Nuss AM, Adnan F, Weber L, Berghoff BA, Glaeser J, Klug G. DegS and RseP homologous proteases are involved in singlet oxygen dependent activation of RpoE in Rhodobacter sphaeroides. PLoS One 2013; 8:e79520. [PMID: 24223961 PMCID: PMC3818230 DOI: 10.1371/journal.pone.0079520] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 10/01/2013] [Indexed: 01/01/2023] Open
Abstract
Singlet oxygen ((1)O2) is the main agent of photooxidative stress and is generated by photosensitizers as (bacterio)chlorophylls. It leads to the damage of cellular macromolecules and therefore photosynthetic organisms have to mount an adaptive response to (1)O2 formation. A major player of the photooxidative stress response in Rhodobacter sphaeroides is the alternative sigma factor RpoE, which is inactivated under non-stress conditions by its cognate anti-sigma factor ChrR. By using random mutagenesis we identified RSP_1090 to be required for full activation of the RpoE response under (1)O2 stress, but not under organic peroxide stress. In this study we show that both RSP_1090 and RSP_1091 are required for full resistance towards (1)O2. Moreover, we revealed that the DegS and RseP homologs RSP_3242 and RSP_2710 contribute to (1)O2 resistance and promote ChrR proteolysis. The RpoE signaling pathway in R. sphaeroides is therefore highly similar to that of Escherichia coli, although very different anti-sigma factors control RpoE activity. Based on the acquired results, the current model for RpoE activation in response to (1)O2 exposure in R. sphaeroides was extended.
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Affiliation(s)
- Aaron M. Nuss
- Institute of Microbiology and Molecular Biology, Giessen University, Giessen, Germany
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Fazal Adnan
- Institute of Microbiology and Molecular Biology, Giessen University, Giessen, Germany
| | - Lennart Weber
- Institute of Microbiology and Molecular Biology, Giessen University, Giessen, Germany
| | - Bork A. Berghoff
- Institute of Microbiology and Molecular Biology, Giessen University, Giessen, Germany
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Jens Glaeser
- Institute of Microbiology and Molecular Biology, Giessen University, Giessen, Germany
- * E-mail: ;
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, Giessen University, Giessen, Germany
- * E-mail: ;
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Obara B, Roberts MAJ, Armitage JP, Grau V. Bacterial cell identification in differential interference contrast microscopy images. BMC Bioinformatics 2013; 14:134. [PMID: 23617824 PMCID: PMC3734120 DOI: 10.1186/1471-2105-14-134] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 02/11/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microscopy image segmentation lays the foundation for shape analysis, motion tracking, and classification of biological objects. Despite its importance, automated segmentation remains challenging for several widely used non-fluorescence, interference-based microscopy imaging modalities. For example in differential interference contrast microscopy which plays an important role in modern bacterial cell biology. Therefore, new revolutions in the field require the development of tools, technologies and work-flows to extract and exploit information from interference-based imaging data so as to achieve new fundamental biological insights and understanding. RESULTS We have developed and evaluated a high-throughput image analysis and processing approach to detect and characterize bacterial cells and chemotaxis proteins. Its performance was evaluated using differential interference contrast and fluorescence microscopy images of Rhodobacter sphaeroides. CONCLUSIONS Results demonstrate that the proposed approach provides a fast and robust method for detection and analysis of spatial relationship between bacterial cells and their chemotaxis proteins.
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Affiliation(s)
- Boguslaw Obara
- School of Engineering and Computing Sciences, University of Durham, Durham, UK
| | - Mark AJ Roberts
- Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Judith P Armitage
- Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Vicente Grau
- Oxford e-Research Centre, University of Oxford, Oxford, UK
- Institute of Biomedical Engineering, University of Oxford, Oxford, UK
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Kim DH, Kim MS. Semi-continuous photo-fermentative H2 production by Rhodobacter sphaeroides: effect of decanting volume ratio. Bioresour Technol 2012; 103:481-483. [PMID: 22036913 DOI: 10.1016/j.biortech.2011.09.082] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 09/19/2011] [Accepted: 09/20/2011] [Indexed: 05/31/2023]
Abstract
In this study, a semi-continuous operation of photo-fermentative H2-producing reactor was attempted at various decanting volume ratios (DVR, decanting volume per day/total working volume, %), ranging 30-70%, using Rhodobacter sphaeroides KD131. H2 production was not efficient with showing low H2 yields of 0.2 and 0.5 mol H2/mol succinate(added) at 30% and 40% DVR, respectively. The low performance ascribed to the fact that over 70% of substrate electrons were diverted towards cell growth under these conditions. Meanwhile, cell growth was limited at DVR≥50%; therefore, higher H2 yields (>2.0 mol H2/mol succinateadded) were observed. Both the highest H2 yield of 3.7 mol H2/mol succinateadded and production rate of 1494 mL H2/L-reactor/d were achieved at 60% DVR. The content of soluble microbial products (SMPs) was measured, which accounted for 3-15% of substrate electrons. It was found that the largest (65-75%) portion of SMPs comprised low molecular-weight (<3 kDa).
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Affiliation(s)
- Dong-Hoon Kim
- Wastes Energy Center, Korea Institute of Energy Research, 102 Gajeong-ro, Yuseong-gu, Daejeon 305-343, Republic of Korea
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Bína D, Litvín R, Vácha F. Absorbance changes accompanying the fast fluorescence induction in the purple bacterium Rhodobacter sphaeroides. Photosynth Res 2010; 105:115-121. [PMID: 20574750 DOI: 10.1007/s11120-010-9569-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Accepted: 05/30/2010] [Indexed: 05/29/2023]
Abstract
The authors present a study of the fluorescence and absorbance transients occurring in whole cells of purple nonsulfur bacterium Rhodobacter sphaeroides on the millisecond timescale under pulsed actinic illumination. The fluorescence induction curve is interpreted in terms of combination of effects of redox changes in the reaction center and the membrane potential. The results of this study support the view that the membrane potential act predominantly to increase the fluorescence yield. Advantages of the pulsed actinic illumination for study of the operation of the electron transport chain in vivo are discussed.
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Affiliation(s)
- David Bína
- Biology Centre ASCR, v.v.i, Institute of Plant Molecular Biology and Faculty of Science, University of South Bohemia, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic
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12
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Şener M, Strümpfer J, Timney JA, Freiberg A, Hunter CN, Schulten K. Photosynthetic vesicle architecture and constraints on efficient energy harvesting. Biophys J 2010; 99:67-75. [PMID: 20655834 PMCID: PMC2895385 DOI: 10.1016/j.bpj.2010.04.013] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 03/16/2010] [Accepted: 04/05/2010] [Indexed: 11/24/2022] Open
Abstract
Photosynthetic chromatophore vesicles found in some purple bacteria constitute one of the simplest light-harvesting systems in nature. The overall architecture of chromatophore vesicles and the structural integration of vesicle function remain poorly understood despite structural information being available on individual constituent proteins. An all-atom structural model for an entire chromatophore vesicle is presented, which improves upon earlier models by taking into account the stoichiometry of core and antenna complexes determined by the absorption spectrum of intact vesicles in Rhodobacter sphaeroides, as well as the well-established curvature-inducing properties of the dimeric core complex. The absorption spectrum of low-light-adapted vesicles is shown to correspond to a light-harvesting-complex 2 to reaction center ratio of 3:1. A structural model for a vesicle consistent with this stoichiometry is developed and used in the computation of excitonic properties. Considered also is the packing density of antenna and core complexes that is high enough for efficient energy transfer and low enough for quinone diffusion from reaction centers to cytochrome bc(1) complexes.
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Affiliation(s)
- Melih Şener
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Johan Strümpfer
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - John A. Timney
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Arvi Freiberg
- Institute of Physics, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - C. Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Klaus Schulten
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
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Jaschke PR, Drake I, Beatty JT. Modification of a French pressure cell to improve microbial cell disruption. Photosynth Res 2009; 102:95-97. [PMID: 19731071 DOI: 10.1007/s11120-009-9493-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Accepted: 08/24/2009] [Indexed: 05/28/2023]
Abstract
A procedure for modification of the valve stem of a 40 K French pressure cell is described. The modification should be done by a machinist and requires a metalworking lathe. After modification of the valve stem, a torlon 4203 plastic ball is used between the valve stem and valve seat to control the pressure within the cell. The torlon plastic ball is a key component needed to obtain the high pressures required for efficient disruption of microbial cells.
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Affiliation(s)
- Paul R Jaschke
- Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada
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Abstract
Photo fermentation is a biological process that can be applied for hydrogen production. The process is environmental friendly which is operated under mild conditions using renewable resources. In order to increase yield of H2 produced by Rhodobacter sphaeroides, some experimental factors that may enhance H2 production were studied. The effect of operating parameters including agitation, aeration and light on hydrogen production using R. sphaeroides NCIMB 8253 was investigated. Rhodobacter sphaeroides NCIMB 8253 was grown in 100 mL serum bottle containing growth medium with maliec acid as the sole organic carbon source. The cultures were incubated anaerobically at 30 degrees C with tungsten lamp (100 W) as the light source (3.8 klux) and argon gas was purged for maintaining anaerobic condition. The results show that maximum hydrogen produced was higher (54.37 mL) in static culture with 69.98% of H2 in the total gas compared with shake culture (11.57 mL) with 57.86% of H2. By using static culture, H2 produced was five times higher compared with non-static in both aerobic and anaerobic condition. It was found that growth and H2 production with fluorescent lamp showed better results than growth and H2 production with tungsten light.
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Affiliation(s)
- S Za'imah Syed Jaapar
- Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
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15
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Sangkharak K, Prasertsan P. Optimization of polyhydroxybutyrate production from a wild type and two mutant strains of Rhodobacter sphaeroides using statistical method. J Biotechnol 2007; 132:331-40. [PMID: 17765994 DOI: 10.1016/j.jbiotec.2007.07.721] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2006] [Revised: 04/20/2007] [Accepted: 07/10/2007] [Indexed: 10/23/2022]
Abstract
Interaction studies using central composite design (CCD) gave the optimum concentrations of acetate at 4 g l(-1) and (NH4)2SO4 at 0.01 g l(-1) with an optimum temperature of 35 degrees C. Rhodobacter sphaeroides N20 gave the highest PHB (7.8 g l(-1)) and biomass (DCW) (8.2 g l(-1)) values compared to the wild type strain and the mutant strain U7. The CCD results predicted that the optimum medium for the mutant strain N20 consisted of 3.90 g l(-1) acetate, 0.01 g l(-1) (NH4)2SO4 at 33.5 degrees C (R2=0.985). Validation of this model by culturing the mutant strain in this optimum medium exhibited similar values of PHB (7.76 g l(-1)), biomass (8.32 g l(-1)) and the PHB content in the cell 93.2% of DCW. Similar amounts of PHB were also obtained in batch fermentations using a 5-l bioreactor. The effect of pH and aeration rate was also studied and the optimum values were found to be pH 7.0 with an aeration rate of 1.0 vvm. Under these optimal conditions, strain N20 produced the highest amount of PHB production (8.76 g l(-1)), PHB content (95.4% of DCW) as well as the product yield (Yp/x) (0.72). These results are the highest values ever obtained from photosynthetic bacteria reported so far.
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Affiliation(s)
- Kanokphorn Sangkharak
- Department of Industrial Biotechnology, Faculty of Agro-Industry, Prince of Songkla University, Hatyai 90112, Thailand
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16
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Abstract
Anoxygenic photosynthetic bacteria have provided us with crucial insights into the process of solar energy capture, pathways of metabolic and societal importance, specialized differentiation of membrane domains, function or assembly of bioenergetic enzymes, and into the genetic control of these and other activities. Recent insights into the organization of this bioenergetic membrane system, the genetic control of this specialized domain of the inner membrane and the process by which potentially photosynthetic and non-photosynthetic cells protect themselves from an important class of reactive oxygen species will provide an unparalleled understanding of solar energy capture and facilitate the design of solar-powered microbial biorefineries.
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Affiliation(s)
- Christine L Tavano
- Bacteriology Department, University of Wisconsin-Madison, Madison, WI 53706, USA
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17
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Callister SJ, Dominguez MA, Nicora CD, Zeng X, Tavano CL, Kaplan S, Donohue TJ, Smith RD, Lipton MS. Application of the accurate mass and time tag approach to the proteome analysis of sub-cellular fractions obtained from Rhodobacter sphaeroides 2.4.1. Aerobic and photosynthetic cell cultures. J Proteome Res 2006; 5:1940-7. [PMID: 16889416 PMCID: PMC2794423 DOI: 10.1021/pr060050o] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The high-throughput accurate mass and time (AMT) tag proteomic approach was utilized to characterize the proteomes for cytoplasm, cytoplasmic membrane, periplasm, and outer membrane fractions from aerobic and photosynthetic cultures of the gram-nagtive bacterium Rhodobacter sphaeroides 2.4.1. In addition, we analyzed the proteins within purified chromatophore fractions that house the photosynthetic apparatus from photosynthetically grown cells. In total, 8,300 peptides were identified with high confidence from at least one subcellular fraction from either cell culture. These peptides were derived from 1,514 genes or 35% percent of proteins predicted to be encoded by the genome. A significant number of these proteins were detected within a single subcellular fraction and their localization was compared to in silico predictions. However, the majority of proteins were observed in multiple subcellular fractions, and the most likely subcellular localization for these proteins was investigated using a Z-score analysis of estimated protein abundance along with clustering techniques. Good (81%) agreement was observed between the experimental results and in silico predictions. The AMT tag approach provides localization evidence for those proteins that have no predicted localization information, those annotated as putative proteins, and/or for those proteins annotated as hypothetical and conserved hypothetical.
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Affiliation(s)
- Stephen J. Callister
- Biological Separations and Mass Spectrometry, Pacific Northwest National Laboratory, Richland Washington, 99352
| | - Miguel A. Dominguez
- Department of Genetics, University of Wisconsin—Madison, Madison Wisconsin, 53706
| | - Carrie D. Nicora
- Biological Separations and Mass Spectrometry, Pacific Northwest National Laboratory, Richland Washington, 99352
| | - Xiaohua Zeng
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston Texas, 77030
| | - Christine L. Tavano
- Department of Bacteriology, University of Wisconsin—Madison, Madison Wisconsin, 53706
| | - Samuel Kaplan
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston Texas, 77030
| | - Timothy J. Donohue
- Department of Bacteriology, University of Wisconsin—Madison, Madison Wisconsin, 53706
| | - Richard D. Smith
- Biological Separations and Mass Spectrometry, Pacific Northwest National Laboratory, Richland Washington, 99352
| | - Mary S. Lipton
- Biological Separations and Mass Spectrometry, Pacific Northwest National Laboratory, Richland Washington, 99352
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18
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Abstract
In Rhodobacter sphaeroides, MreB, MreC, MreD, PBP2, and RodA are encoded at the same locus. The localizations of PBP2, MreB, and MreC, which have all been implicated in the synthesis of the peptidoglycan layer, were investigated under different growth conditions to gain insight into the relationships between these proteins. Immunofluorescence microscopy showed that PBP2 localized to specific sites at the midcell of elongating cells under both aerobic and photoheterotrophic conditions. Visualizing PBP2 at different stages of the cell cycle showed that in elongating cells, PBP2 was found predominately at the midcell, with asymmetric foci and bands across the cell. PBP2 remained at midcell until the start of septation, after which it moved to midcell of the daughter cells. Deconvolution and three-dimensional reconstructions suggested that PBP2 forms a partial ring at the midcell of newly divided cells and elongated cells, while in septating cells, partial PBP2 rings were present at one-quarter and three-quarter positions. Due to the diffraction limits of light microscopy, these partial rings could represent unresolved helices. Colocalization studies showed that MreC always colocalized with PBP2, while MreB colocalized with PBP2 only during elongation; during septation, MreB remained at the septation site, whereas PBP2 relocalized to the one-quarter and three-quarter positions. These results suggest that PBP2 and MreC are involved in peptidoglycan synthesis during elongation and that this occurs at specific sites close to midcell in R. sphaeroides.
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Affiliation(s)
- Peter M Slovak
- Microbiology Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
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19
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Abstract
Many proteins have recently been shown to localize to different regions of the bacterial cell. This is most striking in the case of the Escherichia coli chemotaxis pathway in which the components localize at the cell poles. Rhodobacter sphaeroides has a more complex chemotaxis system with two complete pathways, each localizing to different positions, one pathway at the pole and one at a discrete cluster within the cytoplasm of the bacterium. Using genomic replacement of the wild-type chemotaxis genes in R. sphaeroides with their corresponding fluorescent protein fusions in conjunction with in frame deletions of other chemotaxis genes, we have investigated which proteins are required for the formation of the polar and cytoplasmic chemotaxis protein clusters. As in E. coli, the polarly targeted CheA and CheW homologues are required for the formation of the polar cluster. However, the formation of the cytoplasmic cluster requires the cytoplasmic chemoreceptors and CheW but not the CheAs. Interestingly, even when deletion of a component resulted in the chemotaxis proteins of one pathway becoming delocalized and diffuse in the cytoplasm, in no case were any chemotaxis proteins seen to localize to the other signalling cluster.
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Affiliation(s)
- George H Wadhams
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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20
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Slovak PM, Wadhams GH, Armitage JP. Localization of MreB in Rhodobacter sphaeroides under conditions causing changes in cell shape and membrane structure. J Bacteriol 2005; 187:54-64. [PMID: 15601688 PMCID: PMC538805 DOI: 10.1128/jb.187.1.54-64.2005] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
MreB is thought to be a bacterial actin homolog that defines the morphology of rod-shaped bacteria. Rhodobacter sphaeroides changes shape, from a rod to coccobacillus, and undergoes extensive cytoplasmic membrane invagination when it switches from aerobic to photoheterotrophic growth. The role of MreB in defining R. sphaeroides shape was therefore investigated. Attempts at deleting or insertionally inactivating mreB were unsuccessful under all growth conditions. Immunofluorescence microscopy showed MreB localized to mid-cell in elongating cells under both aerobic and photoheterotrophic conditions. Three-dimensional reconstruction showed that MreB formed a ring at mid-cell. MreB remained at mid-cell as septation began but localized to new sites in the daughter cells before the completion of septation. MreB localized to putative septation sites in cephalexin-treated filamentous cells. Genomic single-copy mreB was replaced with gfp-mreB, and green fluorescent protein (GFP)-MreB localized in the same pattern, as seen with immunofluorescence microscopy. Some of the cells expressing GFP-MreB were abnormal, principally displaying an increase in cell width, suggesting that the fusion was not fully functional in all cells. GFP-MreB localized to swellings at mid-cell in cells treated with the penicillin-binding protein 2 inhibitor amdinocillin. These data suggest that MreB is essential in R. sphaeroides, performing a role at mid-cell in elongating cells, and in early septation, putatively in the cytoplasmic control of the peptidoglycan synthetic complexes.
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Affiliation(s)
- Peter M Slovak
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford, OX1 3QU United Kingdom
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21
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Abstract
Recent AFM data demonstrate that mature photosynthetic membranes of R. sphaeroides are composed of rows of dimeric RC-LH1-PufX complexes with some LH2 complexes 'sandwiched' between these rows of core complexes, and others in discrete LH2-only domains which might form the light-responsive complement of the LH2 antenna. The present work applies membrane fractionation, radiolabelling and LDS-PAGE techniques to investigate the response of R. sphaeroides to lowered light intensity. The kinetics underlying this adaptation to low light conditions were revealed by radiolabelling with the bacteriochlorophyll (bchl) biosynthetic precursor, delta-aminolevulinate, which allowed us to measure only the bchls synthesised after the light intensity shift. We show that (1) the increase in LH2 antenna size is mainly restricted to the mature ICM membrane fraction, and the antenna composition of the precursor upper pigmented band (UPB) membrane remains constant, (2) the precursor UPB membrane is enriched in bchl synthase, the terminal enzyme of the bchl biosynthetic pathway, and (3) the LH2 and the complexes of intermediate migration in LDS-PAGE exhibit completely different labelling kinetics. Thus, new photosynthetic complexes, mainly LH2, are synthesised and assembled at the membrane initiation UPB sites, where the LH2 rings pack between the rows of dimeric cores fostering new LH2-LH1 interactions. Mature membranes also assemble new LH2 rings, but in this case the 'sandwich' regions between the rows of core dimers are already fully occupied and the bulk antenna pool is the favoured location for these new LH2 complexes.
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Affiliation(s)
- C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK S10 2TN
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22
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Bahatyrova S, Frese RN, Siebert CA, Olsen JD, Van Der Werf KO, Van Grondelle R, Niederman RA, Bullough PA, Otto C, Hunter CN. The native architecture of a photosynthetic membrane. Nature 2004; 430:1058-62. [PMID: 15329728 DOI: 10.1038/nature02823] [Citation(s) in RCA: 329] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2004] [Accepted: 07/08/2004] [Indexed: 11/09/2022]
Abstract
In photosynthesis, the harvesting of solar energy and its subsequent conversion into a stable charge separation are dependent upon an interconnected macromolecular network of membrane-associated chlorophyll-protein complexes. Although the detailed structure of each complex has been determined, the size and organization of this network are unknown. Here we show the use of atomic force microscopy to directly reveal a native bacterial photosynthetic membrane. This first view of any multi-component membrane shows the relative positions and associations of the photosynthetic complexes and reveals crucial new features of the organization of the network: we found that the membrane is divided into specialized domains each with a different network organization and in which one type of complex predominates. Two types of organization were found for the peripheral light-harvesting LH2 complex. In the first, groups of 10-20 molecules of LH2 form light-capture domains that interconnect linear arrays of dimers of core reaction centre (RC)-light-harvesting 1 (RC-LH1-PufX) complexes; in the second they were found outside these arrays in larger clusters. The LH1 complex is ideally positioned to function as an energy collection hub, temporarily storing it before transfer to the RC where photochemistry occurs: the elegant economy of the photosynthetic membrane is demonstrated by the close packing of these linear arrays, which are often only separated by narrow 'energy conduits' of LH2 just two or three complexes wide.
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Affiliation(s)
- Svetlana Bahatyrova
- Biophysical Techniques Group, Department of Science & Technology, BMTI, MESA, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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23
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Celis H, Franco B, Escobedo S, Romero I. Rhodobacter sphaeroides has a family II pyrophosphatase: comparison with other species of photosynthetic bacteria. Arch Microbiol 2003; 179:368-76. [PMID: 12669192 DOI: 10.1007/s00203-003-0539-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2002] [Revised: 12/16/2002] [Accepted: 01/13/2003] [Indexed: 10/20/2022]
Abstract
The cytoplasmic pyrophosphatase from Rhodobacter sphaeroides was purified and characterized. The enzyme is a homodimer of 64 kDa. The N-terminus was sequenced and used to obtain the complete pyrophosphatase sequence from the preliminary genome sequence of Rba. sphaeroides, showing extensive sequence similarity to family II or class C pyrophosphatases. The enzyme hydrolyzes only Mg-PP(i) and Mn-PP(i) with a K(m) of 0.35 mM for both substrates. It is not activated by free Mg (2+), in contrast to the cytoplasmic pyrophosphatase from Rhodospirillum rubrum, and it is not inhibited by NaF, methylendiphosphate, or imidodiphosphate. This work shows that Rba. sphaeroides and Rhodobacter capsulatus cytoplasmic pyrophosphatases belong to family II, in contrast to Rsp. rubrum, Rhodopseudomonas palustris, Rhodopseudomonas gelatinosa, and Rhodomicrobium vannielii cytoplasmic pyrophosphatases which should be classified as members of family I. This is the first report of family II cytoplasmic pyrophosphatases in photosynthetic bacteria and in a gram-negative organism.
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Affiliation(s)
- Heliodoro Celis
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-243, 04510, D.F. México, México.
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24
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Abstract
The purple photosynthetic bacterium Rhodobacter sphaeroides has three loci encoding multiple homologues of the bacterial chemosensory proteins: 13 putative chemoreceptors, four CheW, four CheA, six CheY, two CheB and three CheR. Previously, studies have shown that, although deletion of cheOp1 led to only minor changes in behaviour, deletion of cheOp2 led to a loss of taxis. The third locus encodes two CheA, one CheR, one CheB, one CheW, one CheY, a putative cytoplasmic chemoreceptor (TlpT) and a protein showing homology to the chromosomal partitioning factor Soj (designated Slp). Here, we show that every protein encoded by this locus is essential for normal chemotaxis. Phototaxis is also dependent upon all the components of this locus, except CheB2 and Slp. The two putative CheA proteins encoded in this locus are unusual. CheA3 has only the P1 domain and the P5 regulatory domain linked by a large internal domain, whereas CheA4 lacks the P1 and P2 domains required for phosphorylation and response regulator binding. These data indicate that the minimal set of proteins required for normal chemotaxis in R. sphaeroides is all the proteins encoded by cheOp2 and the third chemotaxis locus, and that the multiple chemosensory protein homologues found in R. sphaeroides are not redundant.
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25
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Buchanan G, Kuper J, Mendel RR, Schwarz G, Palmer T. Characterisation of the mob locus of Rhodobacter sphaeroides WS8: mobA is the only gene required for molybdopterin guanine dinucleotide synthesis. Arch Microbiol 2001; 176:62-8. [PMID: 11479704 DOI: 10.1007/s002030100291] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2001] [Accepted: 04/24/2001] [Indexed: 10/27/2022]
Abstract
The mob genes of several bacteria have been implicated in the conversion of molybdopterin to molybdopterin guanine dinucleotide. The mob locus of Rhodobacter sphaeroides WS8 comprises three genes, mobABC. Chromosomal in-frame deletions in each of the mob genes have been constructed. The mobA mutant strain has inactive DMSO reductase and periplasmic nitrate reductase activities (both molybdopterin guanine dinucleotide-requiring enzymes), but the activity of xanthine dehydrogenase, a molybdopterin enzyme, is unaffected. The inability of a mobA mutant to synthesise molybdopterin guanine dinucleotide is confirmed by analysis of cell extracts of the mobA strain for molybdenum cofactor forms following iodine oxidation. Mutations in mobB and mobC are not impaired for molybdoenzyme activities and accumulate wild-type levels of molybdopterin and molybdopterin guanine dinucleotide, indicating they are not compromised in molybdenum cofactor synthesis. In the mobA mutant strain, the inactive DMSO reductase is found in the periplasm, suggesting that molybdenum cofactor insertion is not necessarily a pre-requisite for export.
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Affiliation(s)
- G Buchanan
- Centre for Metalloprotein Spectroscopy and Biology, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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26
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Poggio S, Aguilar C, Osorio A, González-Pedrajo B, Dreyfus G, Camarena L. sigma(54) Promoters control expression of genes encoding the hook and basal body complex in Rhodobacter sphaeroides. J Bacteriol 2000; 182:5787-92. [PMID: 11004178 PMCID: PMC94701 DOI: 10.1128/jb.182.20.5787-5792.2000] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gene expression of the flagellar system is tightly controlled by external stimuli or intracellular signals. A general picture of this regulation has been obtained from studies of Salmonella enterica serovar Typhimurium. However, these regulatory mechanisms do not apply to all bacterial groups. In this study, we have investigated regulation of the flagellar genetic system in Rhodobacter sphaeroides. Deletion analysis, site-directed mutagenesis, and 5'-end mapping were conducted in order to identify the fliO promoter. Our results indicate that this promoter is recognized by the factor sigma(54). Additionally, 5'-end mapping of the flgB and fliK transcripts suggests that these mRNAs are also transcribed from sigma(54) promoters. Finally, we showed evidence that suggests that fliC transcription is not entirely dependent on the presence of a complete basal body-hook structure. Our results are discussed in the context of a possible regulatory hierarchy controlling flagellar gene expression in R. sphaeroides.
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Affiliation(s)
- S Poggio
- Departamento de Biología Molecular, Instituto de Investigaciones Biomédicas, 04510 Mexico City, Mexico
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27
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Abstract
Both aerobically and photosynthetically grown wild-type Rhodobacter sphaeroides swarmed through soft nutrient agar. However, individual aerobically and photosynthetically grown tethered cells showed different responses to steps in concentrations of some attractants. Photosynthetically grown cells showed little response to a step-up in attractant, but large response to a step-down. Aerobically grown cells showed a large but opposite response to a step-up of chemoeffectors such as succinate and aspartate. The responses in che operon deletion mutants were also investigated and indicated that the aerobic response may depend on the protein products of che operon 1.
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Affiliation(s)
- H L Packer
- Microbiology Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU,
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28
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Abstract
The regulation of the Rhodobacter sphaeroides lexA gene has been analyzed using both gel-mobility experiments and lacZ gene fusions. PCR-mediated mutagenesis demonstrated that the second GAAC motif in the sequence GAACN7GAACN7GAAC located upstream of the R. sphaeroides lexA gene is absolutely necessary for its DNA damage-mediated induction. Moreover, mutagenesis of either the first or the third GAAC motif in this sequence reduced, but did not abolish, the inducibility of the R. sphaeroides lexA gene. A R. sphaeroides lexA-defective (Def) mutant has also been constructed by replacing the active lexA gene with an inactivated gene copy constructed in vitro. Crude extracts of the R. sphaeroides lexA(Def) strain are unable to form any protein-DNA complex when added to the wild-type lexA promoter of R. sphaeroides. Likewise, the R. sphaeroides lexA(Def) cells constitutively express the recA and lexA genes. All these data clearly indicate that the lexA gene product is the negative regulator of the R. sphaeroides SOS response. Furthermore, the morphology, growth and viability of R. sphaeroides lexA(Def) cultures do not show any significant change relative to those of the wild-type strain. Hence, R. sphaeroides is so far the only bacterial species whose viability is known not to be affected by the presence of a lexA(Def) mutation.
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Affiliation(s)
- A Tapias
- Department of Genetics and Microbiology, Autonomous University of Barcelona, Bellaterra, Spain
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29
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Francia F, Wang J, Venturoli G, Melandri BA, Barz WP, Oesterhelt D. The reaction center-LH1 antenna complex of Rhodobacter sphaeroides contains one PufX molecule which is involved in dimerization of this complex. Biochemistry 1999; 38:6834-45. [PMID: 10346905 DOI: 10.1021/bi982891h] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The PufX membrane protein is essential for photosynthetic growth of Rhodobacter sphaeroides wild-type cells. PufX is associated with the reaction center-light harvesting 1 (RC-LH1) core complex and plays a key role in lateral ubiquinone/ubiquinol transfer. We have determined the PufX/RC stoichiometry by quantitative Western blot analysis and RC photobleaching. Independent of copy number effects and growth conditions, one PufX molecule per RC was observed in native membranes as well as in detergent-solubilized RC-LH1 complexes which had been purified over sucrose gradients. Surprisingly, two gradient bands with significantly different sedimentation coefficients were found to have a similar subunit composition, as judged by absorption spectroscopy and protein gel electrophoresis. Gel filtration chromatography and electron microscopy revealed that these membrane complexes represent a monomeric and a dimeric form of the RC-LH1 complex. Since PufX is strictly required for the isolation of dimeric core complexes, we suggest that PufX has a central structural role in forming dimeric RC-LH1 complexes, thus allowing efficient ubiquinone/ubiquinol exchange through the LH1 ring surrounding the RC.
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Affiliation(s)
- F Francia
- Department of Membrane Biochemistry, Max-Planck-Institute for Biochemistry, 82152 Martinsried, Germany
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30
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Abstract
A large chemotaxis operon was identified in Rhodobacter sphaeroides WS8-N using a probe based on the 3' terminal portion of the Rhizobium meliloti cheA gene. Two genes homologous to the enteric cheY were identified in an operon also containing cheA, cheW, and cheR homologues. The deduced protein sequences of che gene products were aligned with those from Escherichia coli and shown to be highly conserved. A mutant with an interrupted copy of cheA showed normal patterns of swimming, unlike the equivalent mutants in E. coli which are smooth swimming. Tethered cheA mutant cells showed normal responses to changes in organic acids, but increased, inverted responses to sugars. The unusual behaviour of the cheA mutant and the identification of two homologues of cheY suggests that R. sphaeroides has at least two pathways controlling motor activity. To identify functional similarity between the newly identified R. sphaeroides Che pathway and the methyl-accepting chemotaxis protein (MCP)-dependent pathway in enteric bacteria, the R. sphaeroides cheW gene was expressed in a cheW mutant strain of E. coli and found to complement, causing a partial return to a swarming phenotype. In addition, expression of the R. sphaeroides gene in wild-type E. coli resulted in the same increased tumbling and reduced swarming as seen when the native gene is overexpressed in E. coli. The identification of che homologues in R. sphaeroides and complementation by cheW suggests the presence of MCPs in an organism previously considered to use only MCP-independent sensing. The MCP-dependent pathway, appears conserved.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- M J Ward
- Department of Biochemistry, University of Oxford, UK
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31
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Abstract
Sliding-window averaging of amino acid properties is a standard method for predicting protein secondary structure. For example, transmembrane segments are predicted to occur near the peaks in a hydropathy plot of a membrane protein. Such a scheme (linear convolutional recognizer, LCR) assigns a number (weight) to each type of monomer, and then convolutes some window function with the sequence of weights. The window has commonly been rectangular, and the weights derived from singlet amino acid frequencies in proteins of known secondary structure or from physical properties of amino acids. The accuracy of the windows and weights have remained unknown. We use linear optimization theory to develop a general method for approximating the optimal window and weights for a LCR. The method assumes that one knows the sequences of one or more chains and the locations of their "features", regions having the secondary structure of interest. We present formulae for quantifying the accuracy of predictors. We show why the optimal LCR is more accurate than methods based on the differences between singlet monomer frequencies inside and outside features. The advantage of an optimal LCR is that its weights inherently include correlations between nearby monomer positions. The optimal predictor is not perfect though. We argue that its inaccuracy is an intrinsic limitation of linear predictors based on monomer weights. As a practical example, we study predictors for transbilayer segments of membrane proteins. We estimate the optimal weights and windows for the two bacterial photosynthetic reaction centers whose three-dimensional structures are known. The resultant LCR, which is more accurate than previous ones, is still inexact. We apply it to bacteriorhodopsin and halorhodopsin. Several non-linear generalizations are examined as possible improvements to the LCR method: non-linear combinations of linear predictors and windowed Fourier transforms of the weight sequences. The former do not significantly increase the accuracy, while the latter reveal a weak negative correlation between the segments and periodic variations of the weights.
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Affiliation(s)
- J Edelman
- Department of Physiology and Biophysics, University of California, Irvine 92717
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Lueking DR, Campbell TB, Burghardt RC. Light-induced division and genomic synchrony in phototrophically growing cultures of Rhodopseudomonas sphaeroides. J Bacteriol 1981; 146:790-7. [PMID: 7012139 PMCID: PMC217026 DOI: 10.1128/jb.146.2.790-797.1981] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
An experimental procedure for rapidly obtaining cell populations of phototrophically growing Rhodopseudomonas sphaeroides which display division and genomic synchrony has been developed. The basis of the procedure resides with the normal physiological response displayed by cells of R. sphaeroides that have been subjected to an immediate decrease in incident light intensity. After an abrupt high- to low-light transition of an asynchronously dividing cell population, an immediate cessation of increases in culture turbidity, total cell number, and net accumulations of culture deoxyribonucleic acid and phospholipid occurs. Total cell number remains constant for 2.5 h after the transition to low light, after which time, it undergoes a sharp increase. Reinitiation of high-light conditions of growth 1 h subsequent to this increase in total cell number results in a cell population possessing a high degree of division and genomic synchrony. A characterization of this procedure, together with a demonstration of its utility for studies on intracytoplasmic membrane assembly, is presented.
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Cain BD, Deal CD, Fraley RT, Kaplan S. In vivo intermembrane transfer of phospholipids in the photosynthetic bacterium Rhodopseudomonas sphaeroides. J Bacteriol 1981; 145:1154-66. [PMID: 6970743 PMCID: PMC217116 DOI: 10.1128/jb.145.3.1154-1166.1981] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The kinetics of accumulation of phospholipids into the intracytoplasmic membrane of Rhodopseudomonas sphaeroides have been examined. We have previously demonstrated that accumulation of phospholipids in the intracytoplasmic membrane is discontinuous with respect to the cell cycle. In this study we demonstrated a sevenfold increase in the rate of phospholipid incorporation into the intracytoplasmic membrane concurrent with the onset of cell division. Pulse-chase labeling studies revealed that the increase in the rate of phospholipid accumulation into the intracytoplasmic membrane results from the transfer of phospholipid from a site other than the intracytoplasmic membrane, and that the transfer of phospholipid, rather than synthesis of phospholipid, is most likely subject to cell cycle-specific regulation. The rates of synthesis of the individual phospholipid species (phosphatidylethanolamine, phosphatidyglycerol, and an unknown phospholipid) remained constant with respect to one another throughout the cell cycle. Similarly, each of these phospholipid species appeared to be transferred simultaneously to the intracytoplasmic membrane. We also present preliminary kinetic evidence which suggested that phosphatidylethanolamine may be converted to phosphatidycholine within the intracytoplasmic membrane.
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Fraley RT, Lueking DR, Kaplan S. The relationship of intracytoplasmic membrane assembly to the cell division cycle in Rhodopseudomonas sphaeroides. J Biol Chem 1979; 254:1980-6. [PMID: 311360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Abstract
A membrane potential jump was induced by the addition of valinomycin in the presence of a KCl concentration gradient across the membrane of Rhodopseudomonas sphaeroides chromatophores. As well as a carotenoid band shift, which is known to be an indicator of membrane potential, absorbance changes due to the oxidation-reduction reactions of cytochromes accompanied the jump. Under aerobic conditions with no reductant added, a part of cytochrome c2 was reduced by an inside-positive potential jump of about 100 mV in the time range of tens of seconds. This can be explained by the location of the cytochrome on the inner side of the chromatophore membrane and electrophoretic flow of electrons across the membrane. On the other hand, in the presence of 1 mM ascorbate, a similar jump of membrane potential induced a rapid oxidation of cytochrome c2 and a subsequent reduction. A rapid reduction of b-type cytochrome was also observed. Antimycin A inhibited the c2 oxidation, but did not inhibit the b reduction. The oxidation of cytochrome c2 may be explained by a diffusion-potential-induced electron flow to cytochrome b and a simultaneous electron donation by cytochrome b and cytochrome c2 to a common electron acceptor, possibly a quinone.
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Rafferty CN, Clayton RK. Properties of reaction centers of Rhodopseudomonas sphaeroides in dried gelatin films. Linear dichroism and low temperature spectra. Biochim Biophys Acta 1978; 502:51-60. [PMID: 305788 DOI: 10.1016/0005-2728(78)90131-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Abstract
A cell envelope fraction had been prepared after mechanical disruption of lysozyme-EDTA spheroplasts from depigmented Rhodopseudomonas sphaeroides (aerobically grown in the light). On linear sucrose gradients this fraction can be separated in a cytoplasmic membrane fraction and an outer membrane fraction. The cytoplasmic fraction (buoyant density: 1.18 g/cm3) has been characterized by its succinic dehydrogenase activity and by its composition. The outer membrane fraction (buoyant density: 1.21 g/cm3) does not contain any respiratory activity nor hemoproteins. The same fractionation has been done on cells repigmented in the dark by lowering the O2 pressure. In that case the same two fractions have been detected in addition to the chromatophore fraction (buoyant density: 1.14 g/cm3). However both, and specially the outer membrane fraction, were contaminated by chromatophore material.
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Cogdell RJ, Brune DC, Clayton RK. Effects of extraction and replacement of ubiquinone upon the photochemical activity of reaction centers and chromatophores from Rhodopseudomonas spheriodes. FEBS Lett 1974; 45:344-7. [PMID: 4547199 DOI: 10.1016/0014-5793(74)80877-x] [Citation(s) in RCA: 84] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Jones OT, Plewis KM. Reconstitution of light-dependent electron transport in membranes from a bacteriochlorophyll-less mutant of Rhodopseudomonas spheroides. Biochim Biophys Acta 1974; 357:204-14. [PMID: 4153913 DOI: 10.1016/0005-2728(74)90061-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Breton J. The state of chlorophyll and carotenoid in vivo. II. A linear dichroism study of pigment orientation in photosynthetic bacteria. Biochem Biophys Res Commun 1974; 59:1011-7. [PMID: 4547333 DOI: 10.1016/s0006-291x(74)80080-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Takemoto J, Lascelles J. Function of membrane proteins coupled to bacteriochlorophyll synthesis. Studies with wild type and mutant strains of Rhodopseudomonas spheroides. Arch Biochem Biophys 1974; 163:507-14. [PMID: 4547213 DOI: 10.1016/0003-9861(74)90508-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Leigh JS, Dutton PL. Reaction center bacteriochlorophyll triplet states: redox potential dependence and kinetics. Biochim Biophys Acta 1974; 357:67-77. [PMID: 4370313 DOI: 10.1016/0005-2728(74)90113-3] [Citation(s) in RCA: 97] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Prince RC, Crofts AR, Steinrauf LK. A comparison of beauvericin, enniatin and valinomycin as calcium transporting agents in liposomes and chromatophores. Biochem Biophys Res Commun 1974; 59:697-703. [PMID: 4546705 DOI: 10.1016/s0006-291x(74)80036-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Cogdell RJ, Crofts AR. H+ uptake by chromatophores from Rhodopseudomonas spheroides. The relation between rapid H+ uptake and the H+ pump. Biochim Biophys Acta 1974; 347:264-72. [PMID: 4546206 DOI: 10.1016/0005-2728(74)90050-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Pape EH, Menke W, Weick D, Hosemann R. Small angle x-ray scattering of the thylakoid membranes of Rhodopseudomonas speroides in aqueous suspensions. Biophys J 1974; 14:221-32. [PMID: 4545071 PMCID: PMC1334497 DOI: 10.1016/s0006-3495(74)85909-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The diffraction patterns of particles which have the shape of hollow spheres, i.e. vesicles, can be satisfactorily analyzed by means of a new formula of Weick (1974). This formula is used for the small angle X-ray scattering analysis of aqueous suspensions of thylakoids of Rhodopseudomonas spheroides. Some essential results are: (a) The membrane has a rather asymmetric structure with one layer of low electron density at its inner side and two layers of high electron density near the outer surface of the thylakoids. (b) The distance of the electron density maxima of the latter two layers is 45 +/- 5 A. (c) Between the two maxima is a region of an electron density nearly equal to that of water. (d) The sequence of the peaks is - + 0 + with increasing radius. The peaks extend over an interval of 120 +/- 10 A. (e) The thylakoids are strikingly of the same size. Their diameters, if defined by the outmost layer, vary statistically by about 4% and have an average value of approximately 640 A.
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Fanica-Gaignier M, Clément-Métral J. Cellular compartmentation of two species of delta-aminolevulinic acid synthetase in a facultative photohetero-trophic bacterium (Rps. spheroides Y.). Biochem Biophys Res Commun 1973; 55:610-5. [PMID: 4543401 DOI: 10.1016/0006-291x(73)91187-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Hall RL, Kung MC, Fu M, Hales BJ, Loach PA. Comparison of phototrap complexes from chromatophores of Rhodospirillum rubrum, Rhodopseudomonas spheroides, and the R-26 mutant of Rhodopseudomonas spheroides. Photochem Photobiol 1973; 18:505-20. [PMID: 4204253 DOI: 10.1111/j.1751-1097.1973.tb06456.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Berger TJ, Orlando JA. Purification and some properties of a protein factor required for light-dependent transhydrogenase in Rhodopseudomonas spheroides. Arch Biochem Biophys 1973; 159:25-31. [PMID: 4150340 DOI: 10.1016/0003-9861(73)90425-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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