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effects of the measuring light on the photochemistry of the bacterial photosynthetic reaction center from rhodobacter sphaeroides.the bacterial reaction center (rc) has become a reference model in the study of the diverse interactions of quinones with electron transfer complexes. in these studies, the rc functionality was probed through flash-induced absorption changes where the state of the primary donor is probed by means of a continuous measuring beam and the electron transfer is triggered by a short intense light pulse. the single-beam set-up implies the use as reference of the transmittance measured before the light p ...201121785991
electron transport in acetate-grown methanosarcina acetivorans.abstract: background: acetate is the major source of methane in nature. the majority of investigations have focused on acetotrophic methanogens for which energy-conserving electron transport is dependent on the production and consumption of h2 as an intermediate, although the great majority of acetotrophs are unable to metabolize h2. the presence of cytochrome c and a complex (ma-rnf) homologous to the rnf (rhodobacter nitrogen fixation) complexes distributed in the domain bacteria distinguishes ...201121781343
irsp1095: a genome-scale reconstruction of the rhodobacter sphaeroides metabolic network.abstract: background: rhodobacter sphaeroides is one of the best studied purple non-sulfur photosynthetic bacteria and serves as an excellent model for the study of photosynthesis and the metabolic capabilities of this and related facultative organisms. the ability of r. sphaeroides to produce hydrogen (h2), polyhydroxybutyrate (phb) or other hydrocarbons, as well as its ability to utilize atmospheric carbon dioxide (co2) as a carbon source under defined conditions, make it an excellent candidat ...201121777427
immobilized purple bacteria for light-driven h(2) production from starch and potato fermentation effluents.the goal of the study was to show that immobilized purple bacteria could photoproduce h(2) using dark fermentation effluent (fe) as substrate. simple pretreatment of an inexpensive glass-fiber matrix accelerated the immobilization process. photobioreactors (phbr) containing immobilized rhodobacter sphaeroides gl produced 0.128 l h(2) h(-1) l(-1) of phbr volume (0.570 l h(-1) l(-1) of matrix) for up to 3 months when continuously fed artificial media with volatile fatty acids (vfas) or fe from pot ...201121751433
zinc inhibition of bacterial cytochrome bc(1) reveals the role of cytochrome b e295 in proton release at the q(o) site.the cytochrome (cyt) bc(1) complex (cyt bc(1)) plays a major role in the electrogenic extrusion of protons across the membrane responsible for the proton motive force to produce atp. proton-coupled electron transfer underlying the catalysis of cyt bc(1) is generally accepted, but the molecular basis of coupling and associated proton efflux pathway(s) remains unclear. herein we studied zn(2+)-induced inhibition of rhodobacter capsulatus cyt bc(1) using enzyme kinetics, isothermal titration calori ...201121500804
a bchd (magnesium chelatase) mutant of rhodobacter sphaeroides synthesizes zinc bacteriochlorophyll through novel zinc-containing intermediates.heme and bacteriochlorophyll a (bchl) biosyntheses share the same pathway to protoporphyrin ix, which then branches as follows. fe(2+) chelation into the macrocycle by ferrochelatase results in heme formation, and mg(2+) addition by mg-chelatase commits the porphyrin to bchl synthesis. it was recently discovered that a bchd (mg-chelatase) mutant of rhodobacter sphaeroides produces an alternative bchl in which mg(2+) is substituted by zn(2+). zn-bchl has been found in only one other organism befo ...201121502322
acetyl group orientation modulates the electronic ground-state asymmetry of the special pair in purple bacterial reaction centers.recent experimental data point to an asymmetric ground-state electronic distribution in the special pair (p) of purple bacterial reaction centers, which acts as the primary electron donor in photosynthesis. we have performed a density functional theory investigation on an extended model including the bacteriochlorophyll dimer and a few relevant surrounding residues to explore the origin of this asymmetry. we find strong evidence that the ground-state electron density in p is intrinsically asymme ...201121512686
the photosynthetic membrane proteome of rhodobacter sphaeroides r-26.1 exposed to cobalt.cells of the carotenoidless strain r-26.1 of rhodobacter sphaeroides were grown in the presence of a high concentration (5 mm) of cobalt ions. the photosynthetic intracytoplasmic membranes were isolated and investigated by proteomic analysis using non-denaturating blue native electrophoresis in combination with lc-esi-ms/ms. comparison with intracytoplasmic membranes of cells grown under control conditions showed a change in the relative amount of proteins belonging to the photosynthetic apparat ...201121515364
major phylogenetic groups of marine bacteria differ in growth response to natural phytoplankton blooms in the western north pacific.growth and productivity of phytoplankton substantially change organic matter characteristics, which affect bacterial abundance, productivity, and community structure in aquatic ecosystems. we analyzed bacterial community structures and measured activities inside and outside of phytoplankton blooms in the northwest pacific ocean by using bromodeoxyuridine immunocytochemistry fluorescence in situ hybridization (bic-fish). roseobacter/rhodobacter, sar11, betaproteobacteria, alteromonas, sar86, and ...201121515719
use of a new motion analysis system to characterise the chemosensory response kinetics of rhodobacter sphaeroides under different growth conditions.we developed a new set of software tools which enable the speed and response kinetics of large numbers of tethered bacterial cells to be rapidly measured and analysed. the software provides precision, accuracy and good signal to noise ratio combined with ease of data handling and processing. the software was tested on the single-cell chemosensory response kinetics of large numbers of rhodobacter sphaeroides cells grown under either aerobic or photoheterotrophic conditions and either in chemostat ...201121515726
[characteristics of biodegradation of triphenyltin by rhodopseudomonos spheroids].the biodegradation of triphenyltin (tpt) by rhodopseudomonos spheroids was investigated in this study. the results illuminated that r. spheroids was an effective strain for the biodegradation of tpt. the maximum removal ratio was attained when the growth temperature of r. spheroids was 30 degrees c. after treating for 3 hours, the removal ratios of 3 mg x l(-1) tpt were 13.82% to 47.29% using 0.49 g x l(-1) (based on dry weight) biomass of r. spheroids. the experiments on biodegradation of tpt w ...201121528580
contribution of hfq to photooxidative stress resistance and global regulation in rhodobacter sphaeroides.the photosynthetic alphaproteobacterium rhodobacter sphaeroides has to cope with photooxidative stress that is caused by the bacteriochlorophyll a-mediated formation of singlet oxygen ((1) o(2) ). exposure to (1) o(2) induces the alternative sigma factors rpoe and rpoh(ii) which then promote transcription of photooxidative stress-related genes, including small rnas (srnas). the ubiquitous rna chaperone hfq is well established to interact with and facilitate the base-pairing of srnas and target m ...201121535243
direct visualization of exciton reequilibration in the lh1 and lh2 complexes of rhodobacter sphaeroides by multipulse spectroscopy.the dynamics of the excited states of the light-harvesting complexes lh1 and lh2 of rhodobacter sphaeroides are governed, mainly, by the excitonic nature of these ring-systems. in a pump-dump-probe experiment, the first pulse promotes lh1 or lh2 to its excited state and the second pulse dumps a portion of the excited state. by selective dumping, we can disentangle the dynamics normally hidden in the excited-state manifold. we find that by using this multiple-excitation technique we can visualize ...201121539791
single-shot ultrabroadband two-dimensional electronic spectroscopy of the light-harvesting complex lh2.here we present two-dimensional (2d) electronic spectra of the light-harvesting complex lh2 from purple bacteria using coherent pulses with bandwidth of over 100 nm fwhm. this broadband excitation and detection has allowed the simultaneous capture of both the b800 and b850 bands using a single light source. we demonstrate that one laser pulse is sufficient to capture the entire 2d electronic spectrum with a high signal-to-noise ratio. at a waiting time of 800 fs, we observe population transfer f ...201121540962
2d-seira spectroscopy to highlight conformational changes of the cytochrome c oxidase induced by direct electron transfer.potentiometric titrations of the cytochrome c oxidase (cco) immobilized in a biomimetic membrane system were followed by two-dimensional surface-enhanced ir absorption spectroscopy (2d seiras) in the atr-mode. direct electron transfer was employed to vary the redox state of the enzyme. the cco was shown to undergo a conformational transition from a non-activated to an activated state after it was allowed to turnover in the presence of oxygen. differences between the non-activated and activated s ...201121541411
[on the influence of local molecular environment on the redox potential of electron transfer cofactors in bacterial photosynthetic reaction centers].the addition of cryosolvents (glycerol, dimethylsulfoxide) to a water solution containing bacterial photosynthetic reaction centers changes the redox potential of the bacteriochlorophyll dimer, but does not affect the redox potential of the quinone primary acceptor. it has been shown that the change in redox potential can be produced by changes of the electrostatic interactions between cofactors and the local molecular environment modified by additives entered into the solution. the degree of in ...201121542354
ubiquinol formation in isolated photosynthetic reaction centres monitored by time-resolved differential ftir in combination with 2d correlation spectroscopy and multivariate curve resolution.two-dimensional correlation analysis was carried out in combination with multivariate curve resolution-alternating least squares (mcr-als) to analyse time-resolved infrared (ir) difference spectra probing photoinduced ubiquinol formation in detergent-isolated reaction centres from rhodobacter sphaeroides. the dynamic 2d ir correlation spectra have not only allowed the determination of the concomitance or non-concomitance of different chemical events through known marker bands but also have helpe ...201121061002
light-induced conformational changes in photosynthetic reaction centers: impact of detergents and lipids on the electronic structure of the primary electron donor.light-induced hypsochromic shifts of the q(y) absorption band of the bacteriochlorophyll dimer (p) from 865 to 850 nm were identified using continuous illumination of dark-adapted reaction centers (rcs) from rhodobacter capsulatus when dispersed in the most commonly used detergent, the zwitterionic lauryl n-dimethylamine-n-oxide. such a shift is known to be the consequence of the decreased degree of delocalization of p. a 2-fold acceleration of the recovery kinetics of p(+) was found in rcs that ...201121561160
native architecture of the photosynthetic membrane from rhodobacter veldkampii.the photosynthetic membrane in purple bacteria contains several pigment-protein complexes that assure light capture and establishment of the chemiosmotic gradient. the bioenergetic tasks of the photosynthetic membrane require the strong interaction between these various complexes. in the present work, we acquired the first images of the native outer membrane architecture and the supramolecular organization of the photosynthetic apparatus in vesicular chromatophores of rhodobacter (rb.) veldkampi ...201120797440
glu-286 rotation and water wire reorientation are unlikely the gating elements for proton pumping in cytochrome c oxidase.one of the key unresolved issues regarding proton pumping in cytochrome c oxidase (cco) is the identity of the gating element that prevents the backflow of protons. in this study, we analyze two popular proposals for this element: isomerization of the key branching residue (glu-286) and (re)orientation of water molecules in the hydrophobic cavity. using a multifaceted set of computational analyses that involve cco embedded in either an implicit or explicit treatment of lipid membrane, we show th ...201121723815
fructose increases the resistance of rhodobacter capsulatus to the toxic oxyanion tellurite through repression of acetate permease (actp).the highly toxic oxyanion tellurite (teo(3) (2-)) enters the cells of the facultative photosynthetic bacterium rhodobacter capsulatus through an acetate permease. here we show that actp gene expression is down-regulated by fructose and this in turn determines a strong decrease of tellurite uptake and a parallel increase in the cells resistance to the toxic metalloid (from a minimal inhibitory concentration of 8-á++m up to 400-á++m tellurite under aerobic growth conditions). this demonstrates tha ...201121735076
the effects of protein crowding in bacterial photosynthetic membranes on the flow of quinone redox species between the photochemical reaction center and the ubiquinol-cytochrome c(2) oxidoreductase.atomic force microscopy (afm) of the native architecture of the intracytoplasmic membrane (icm) of a variety of species of purple photosynthetic bacteria, obtained at submolecular resolution, shows a tightly packed arrangement of light harvesting (lh) and reaction center (rc) complexes. since there are no unattributed structures or gaps with space sufficient for the cytochrome bc(1) or atpase complexes, they are localized in membrane domains distinct from the flat regions imaged by afm. this has ...201121691621
stepwise increase of resveratrol biosynthesis in yeast saccharomyces cerevisiae by metabolic engineering.resveratrol is a unique, natural polyphenolic compound with diverse health benefits. in the present study, we attempted to improve resveratrol biosynthesis in yeast by different methods of metabolic engineering. we first mutated and then re-synthesized tyrosine ammonia lyase (tal) by replacing the bacteria codons with yeast-preferred codons, which increased translation and improved p-coumaric acid and resveratrol biosynthesis drastically. we then demonstrated that low-affinity, high-capacity bac ...201121570474
coordinated, long-range, solid substrate movement of the purple photosynthetic bacterium rhodobacter capsulatus.the long-range movement of rhodobacter capsulatus cells in the glass-agar interstitial region of borosilicate petri plates was found to be due to a subset of the cells inoculated into plates. the macroscopic appearance of plates indicated that a small group of cells moved in a coordinated manner to form a visible satellite cluster of cells. satellite clusters were initially separated from the point of inoculation by the absence of visible cell density, but after 20 to 24 hours this space was col ...201121573194
feedback control architecture and the bacterial chemotaxis network.bacteria move towards favourable and away from toxic environments by changing their swimming pattern. this response is regulated by the chemotaxis signalling pathway, which has an important feature: it uses feedback to 'reset' (adapt) the bacterial sensing ability, which allows the bacteria to sense a range of background environmental changes. the role of this feedback has been studied extensively in the simple chemotaxis pathway of escherichia coli. however it has been recently found that the m ...201121573199
modeling the light- and redox-dependent interaction of ppsr/appa in rhodobacter sphaeroides.facultative photosynthetic bacteria switch their energy generation mechanism from respiration to photosynthesis depending on oxygen tension and light. part of this transition is mediated by the aerobic transcriptional repressor ppsr. in rhodobacter sphaeroides, the repressive action of ppsr is antagonized by the redox- and blue-light-sensitive flavoprotein appa which results in a unique phenotype: the repression of photosynthesis genes at intermediate oxygen levels and high light intensity, whic ...201121575568
properties of rhodobacter sphaeroides photosynthetic reaction center with double amino acid substitution i(l177)h+h(m182)l.histidine m182 in the reaction center (rc) of rhodobacter sphaeroides serves as the fifth ligand of the bacteriochlorophyll (bchl) b(b) mg atom. when this his is substituted by an amino acid that is not able to coordinate mg, bacteriopheophytin appears in the b(b) binding site instead of bchl (katilius, e., et al. (1999) j. phys. chem. b, 103, 7386-7389). we have shown that in the presence of the additional mutation i(l177)h the coordination of the bchl b(b) mg atom in the double mutant i(l177)h ...201121585320
insights into structure and function of the active site of soxax cytochromes.soxax cytochromes catalyze the formation of heterodisulfide bonds between inorganic sulfur compounds and a carrier protein, soxyz. they contain unusual his/cys ligated heme groups with complex spectroscopic signatures. the heme ligating cysteine has been implicated in soxax-catalysis, but neither the soxax spectroscopic properties nor its catalysis are fully understood at present. we have solved the first crystal structure for a group2 soxax protein (snsoxax), where an n-terminal extension of so ...201121592966
reconstitution of bacterial photosynthetic unit in a lipid bilayer studied by single-molecule spectroscopy at 5 k.as a model of photosynthetic unit (psu), self-assembled aggregates of pigment-protein complexes from photosynthetic bacteria were prepared in a lipid bilayer by reconstitution of the light-harvesting 2 (lh2) complex and light-harvesting 1-reaction center (lh1-rc) complex through detergent removal of their micelles in the presence of lipids. by performing polarization-controlled fluorescence and fluorescence-excitation spectroscopy on single aggregates at a temperature of 5 k, the composition of ...201121597611
mapping lipid and detergent molecules at the surface of membrane proteins.electron-density maps for the crystal structures of membrane proteins often show features suggesting binding of lipids and/or detergent molecules on the hydrophobic surface, but usually it is difficult to identify the bound molecules. in our studies, heavy-atom-labelled phospholipids and detergents have been used to unequivocally identify these binding sites at the surfaces of test membrane proteins, the reaction centres from rhodobacter sphaeroides and blastochloris viridis. the generality of t ...201121599648
modification of the genome of rhodobacter sphaeroides and construction of synthetic operons.the α-proteobacterium rhodobacter sphaeroides is an exemplary model organism for the creation and study of novel protein expression systems, especially membrane protein complexes that harvest light energy to yield electrical energy. advantages of this organism include a sequenced genome, tools for genetic engineering, a well-characterized metabolism, and a large membrane surface area when grown under hypoxic or anoxic conditions. this chapter provides a framework for the utilization of r. sphaer ...201121601102
configuration of spheroidene in the photosynthetic reaction center of rhodobacter sphaeroides : a comparison of wild-type and reconstituted r26.we compare the resonance raman spectra acquired at two excitation wavelengths, 496.5 and 514.5 nm, of spheroidene in the wild-type reaction center of rhodobacter sphaeroides and reconstituted into the reaction center of the rhodobacter sphaeroides mutant r26. our earlier work showed that the reconstituted r26 reaction center holds spheroidene in two configurations: 15,15'-cis and another configuration. here we show that in the wild-type reaction center only 15,15'-cis spheroidene is present. in ...201121604722
molecular basis of proton uptake in single and double mutants of cytochrome c oxidase.cytochrome c oxidase, the terminal enzyme of the respiratory chain, utilizes the reduction of dioxygen into water to pump protons across the mitochondrial inner membrane. the principal pathway of proton uptake into the enzyme, the d channel, is a 2.5 nm long channel-like cavity named after a conserved, negatively charged aspartic acid (d) residue thought to help recruiting protons to its entrance (d132 in the first subunit of the s. sphaeroides enzyme). the single-point mutation of d132 to aspar ...201121613706
genome sequence of rhodobacter sphaeroides strain ws8n.r. sphaeroides is a metabolically diverse photosynthetic alpha-proteobacterium found ubiquitously in soil and in fresh water habitats. here we present the annotated genome sequence of rhodobacter sphaeroides ws8n.201121622735
the hydrogen-bond switch reaction of the blrb bluf domain of rhodobacter sphaeroides.the blrb protein from rhodobacter sphaeroides is a small 136 amino acid photoreceptor belonging to the bluf family of blue light receptors. it contains merely the conserved bluf fold responsible for binding the flavin pigment and a short c-terminal extension of unknown function. we investigated the primary photoreactions of blrb by picosecond fluorescence and transient absorption spectroscopy. after excitation of the flavin the fluorescence decays in an h/d isotope independent manner with time c ...201121627064
comparing the temperature dependence of photosynthetic electron transfer in chloroflexus aurantiacus and rhodobactor sphaeroides reaction centers.the process of electron transfer from the special pair, p, to the primary electron donor, h(a), in quinone-depleted reaction centers (rcs) of chloroflexus (cf.) aurantiacu s has been investigated over the temperature range from 10 to 295 k using time-resolved pump-probe spectroscopic techniques. the kinetics of the electron transfer reaction, p* ôåæ p(+)h(a)(-), was found to be nonexponential, and the degree of nonexponentiality increased strongly as temperature decreased. the temperature-depend ...201121827152
singlet oxygen stress in microorganisms.singlet oxygen is the primary agent of photooxidative stress in microorganisms. in photosynthetic microorganisms, sensitized generation by pigments of the photosystems is the main source of singlet oxygen and, in nonphotosynthetic microorganisms, cellular cofactors such as flavins, rhodopsins, quinones, and porphyrins serve as photosensitizer. singlet oxygen rapidly reacts with a wide range of cellular macromolecules including proteins, lipids, dna, and rna, and thereby further reactive substanc ...201121722793
nitrate-dependent degradation of acetone by alicycliphilus and paracoccus strains and comparison of acetone carboxylase enzymes.a novel acetone-degrading, nitrate-reducing bacterium, strain kn bun08, was isolated from an enrichment culture with butanone and nitrate as the sole sources of carbon and energy. the cells were motile short rods, 0.5 to 1 by 1 to 2 μm in size, which gave gram-positive staining results in the exponential growth phase and gram-negative staining results in the stationary-growth phase. based on 16s rrna gene sequence analysis, the isolate was assigned to the genus alicycliphilus. besides butanone a ...201121841031
adaptation of aerobic respiration to low o2 environments.aerobic respiration in bacteria, archaea, and mitochondria is performed by oxygen reductase members of the heme-copper oxidoreductase superfamily. these enzymes are redox-driven proton pumps which conserve part of the free energy released from oxygen reduction to generate a proton motive force. the oxygen reductases can be divided into three main families based on evolutionary and structural analyses (a-, b- and c-families), with the b- and c-families evolving after the a-family. the a-family ut ...201121844375
Role of PufX in Photochemical Charge Separation in the RC-LH1 Complex from Rhodobacter sphaeroides : An Ultrafast Mid-IR Pump-Probe Investigation.Photochemical charge separation in isolated reaction center-light harvesting 1 (RC-LH1) complexes from Rhodobacter sphaeroides was examined using time-resolved mid-infrared pump-probe spectroscopy. Absorption difference spectra were recorded between 1760 and 1610 cm(-1) with subpicosecond time resolution to characterize excited-state and radical pair dynamics in these complexes, via the induced absorption changes in the keto carbonyl modes of the bacteriochlorophylls and bacteriopheophytins. E ...201122146012
kinetic design of the respiratory oxidases.energy conservation in all kingdoms of life involves electron transfer, through a number of membrane-bound proteins, associated with proton transfer across the membrane. in aerobic organisms, the last component of this electron-transfer chain is a respiratory heme-copper oxidase that catalyzes reduction of o(2) to h(2)o, linking this process to transmembrane proton pumping. so far, the molecular mechanism of proton pumping is not known for any system that is driven by electron transfer. here, we ...201121690359
differential effects of glutamate-286 mutations in the aa(3)-type cytochrome c oxidase from rhodobacter sphaeroides and the cytochrome bo(3) ubiquinol oxidase from escherichia coli.both the aa(3)-type cytochrome c oxidase from rhodobacter sphaeroides (rscco(aa3)) and the closely related bo(3)-type ubiquinol oxidase from escherichia coli (ecqo(bo3)) possess a proton-conducting d-channel that terminates at a glutamic acid, e286, which is critical for controlling proton transfer to the active site for oxygen chemistry and to a proton loading site for proton pumping. e286 mutations in each enzyme block proton flux and, therefore, inhibit oxidase function. in the current work, ...201121684251
atp-dependent fructose uptake system in deinococcus radiodurans.the bacterial phosphoenolpyruvate (pep)-dependent group translocation system (pts) requires the presence of both membrane-bound and cytoplasmic components to phosphorylate and translocate sugar. deinococcus radiodurans has a functional frua gene coding for the membrane-bound components of the fructose-specific pts. however, frub gene coding for the fructose-specific cytosolic components of pts is a pseudogene. yet, this bacterium metabolized fructose readily. in vitro studies showed that both ce ...201121822900
testosterone-mineralizing culture enriched from swine manure: characterization of degradation pathways and microbial community composition.environmental releases and fate of steroid sex hormones from livestock and wastewater treatment plants are of increasing regulatory concern. despite the detection of these hormones in manures, biosolids, and the environment, little attention has been paid to characterization of fecal bacteria capable of hormone degradation. the enrichments of (swine) manure-borne bacteria capable of aerobic testosterone degradation were prepared and the testosterone mineralization pathway was elucidated. six dna ...201121740029
deep-uv resonance raman analysis of the rhodobacter capsulatus cytochrome bc1 complex reveals a potential marker for the transmembrane peptide backbone.classical strategies for structure analysis of proteins interacting with a lipid phase typically correlate ensemble secondary structure content measurements with changes in the spectroscopic responses of localized aromatic residues or reporter molecules to map regional solvent environments. deep-uv resonance raman (duvrr) spectroscopy probes the vibrational modes of the peptide backbone itself, is very sensitive to the ensemble secondary structures of a protein, and has been shown to be sensitiv ...201121718040
Bacterial nitrate assimilation: gene distribution and regulation.In the context of the global nitrogen cycle, the importance of inorganic nitrate for the nutrition and growth of marine and freshwater autotrophic phytoplankton has long been recognized. In contrast, the utilization of nitrate by heterotrophic bacteria has historically received less attention because the primary role of these organisms has classically been considered to be the decomposition and mineralization of dissolved and particulate organic nitrogen. In the pre-genome sequence era, it was k ...201122103536
Use of specific gene analysis to assess the effectiveness of surfactant-enhanced trichloroethylene cometabolism.The objective of this study was to evaluate the effectiveness of in situ bioremediation of trichloroethylene (TCE)-contaminated groundwater using specific gene analyses under the following conditions: (1) pretreatment with biodegradable surfactants [Simple Green™ (SG) and soya lecithin (SL)] to enhance TCE desorption and dissolution, and (2) supplementation with SG, SL, and cane molasses as primary substrates to enhance the aerobic cometabolism of TCE. Polymerase chain reaction (PCR), denaturing ...201122071259
Lipid binding to the carotenoid binding site in photosynthetic reaction centers.Lipid binding to the carotenoid binding site near the inactive bacteriochlorophyll monomer was probed in the reaction centers of carotenoid-less mutant, R-26 from Rhodobacter sphaeroides. Recently, a marked light-induced change of the local dielectric constant in the vicinity of the inactive bacteriochlorophyll monomer was reported in wild type that was attributed to structural changes that ultimately lengthened the lifetime of the charge-separated state by 3 orders of magnitude (Deshmukh, S. S. ...201121894992
role of a short lov protein in blue light- and singlet oxygen-dependent gene regulation in rhodobacter sphaeroides.the facultatively photosynthetic bacterium rhodobacter sphaeroides harbors an unusual lov (light, oxygen, voltage) domain protein, rslov. while showing a characteristic photocycle, the protein misses a c-terminal output domain, similar to ppsb2 in pseudomonas putida. oxygen tension and light quantity are the two main responsible factors controlling the expression of photosynthesis genes in rhodobacter sphaeroides. two photoreceptor proteins are known to be involved in this regulation: the intens ...201122053008
Efficient hydrogen production from acetate through isolated Rhodobacter sphaeroides.Photosynthetic bacteria produce hydrogen from lactate and acetate that are products of hydrogen producing bacteria in the dark. Thus, their coculture is a promising method for hydrogen production. However, the hydrogen production yield from acetate of Rhodobacter sphaeroides RV, which has been shown to possess the highest yield and hydrogen production rate, is low as compared to that from lactate. Photosynthetic bacteria that produce hydrogen from acetate as well as lactate were screened from la ...201121903465
proton transfer in ba(3) cytochrome c oxidase from thermus thermophilus.the respiratory heme-copper oxidases catalyze reduction of o(2) to h(2)o, linking this process to transmembrane proton pumping. these oxidases have been classified according to the architecture, location and number of proton pathways. most structural and functional studies to date have been performed on the a-class oxidases, which includes those that are found in the inner mitochondrial membrane and bacteria such as rhodobacter sphaeroides and paracoccus denitrificans (aa(3)-type oxidases in the ...201122172736
high-mobility group box-1 impairs memory in mice through both toll-like receptor 4 and receptor for advanced glycation end products.high-mobility group box-1 (hmgb1) is a nuclear protein with cytokine-type functions upon its extracellular release. hmgb1 activates inflammatory pathways by stimulating multiple receptors, chiefly toll-like receptor 4 (tlr4) and receptor for advanced glycation end products (rage). tlr4 and rage activation has been implicated in memory impairments, although the endogenous ligand subserving these effects is unknown. we examined whether hmgb1 induced memory deficits using novel object recognition t ...201121884699
cold adaptation of the mononuclear molybdoenzyme periplasmic nitrate reductase from the antarctic bacterium shewanella gelidimarina.the reduction of nitrate to nitrite is catalysed in bacteria by periplasmic nitrate reductase (nap) which describes a system of variable protein subunits encoded by the nap operon. nitrate reduction occurs in the napa subunit, which contains a bis-molybdopterin guanine dinucleotide (mo-mgd) cofactor and one [4fe-4s] iron-sulfur cluster. the activity of periplasmic nitrate reductase (nap) isolated as native protein from the cold-adapted (psychrophilic) antarctic bacterium shewanella gelidimarina ...201122005463
Defluviimonas denitrificans gen. nov., sp. nov., and Pararhodobacter aggregans gen. nov., sp. nov., non-phototrophic Rhodobacteraceae from the biofilter of a marine aquaculture.Three Gram-negative bacterial strains were isolated from the biofilter of a recirculating marine aquaculture. They were non-pigmented rods, mesophiles, moderately halophilic, and showed chemo-organoheterotrophic growth on various sugars, fatty acids, and amino acids, with oxygen as electron acceptor; strains D9-3(T) and D11-58 were in addition able to denitrify. Phototrophic or fermentative growth could not be demonstrated. Phylogenetic analysis of the 16S rRNA gene sequences placed D9-3(T) and ...201121959289
CcmI subunit of CcmFHI heme ligation complex functions as an apocytochrome c chaperone during c-type cytochrome maturation.Cytochrome c maturation (Ccm) is a sophisticated post-translational process. It occurs after translocation of apocytochromes c to the p side of energy transducing membranes and forms stereo-specific thioether bonds between the vinyl groups of heme b (protoporphyrin IX-Fe) and the thiol groups of cysteines at their conserved heme binding sites. In many organisms this process involves up to 10 (CcmABCDEFGHI and CcdA) membrane proteins. One of these proteins is CcmI, which has an N-terminal membran ...201121956106
X-ray structure of the dimeric cytochrome bc(1) complex from the soil bacterium Paracoccus denitrificans at 2.7-Å resolution.The respiratory cytochrome bc(1) complex is a fundamental enzyme in biological energy conversion. It couples electron transfer from ubiquinol to cytochrome c with generation of proton motive force which fuels ATP synthesis. The complex from the a-proteobacterium Paracoccus denitrificans, a model for the medically relevant mitochondrial complexes, lacked structural characterization. We show by LILBID mass spectrometry that truncation of the organism-specific, acidic N-terminus of cytochrome c(1) ...201121996020
Physiological roles for two periplasmic nitrate reductases in Rhodobacter sphaeroides 2.4.3 (ATCC 17025).The metabolically versatile purple bacterium Rhodobacter sphaeroides 2.4.3 is a denitrifier whose genome contains two periplasmic nitrate reductase-encoding gene clusters. This work demonstrates nonredundant physiological roles for these two enzymes. One cluster is expressed aerobically and repressed under low oxygen while the second is maximally expressed under low oxygen. Insertional inactivation of the aerobically expressed nitrate reductase eliminated aerobic nitrate reduction, but cells of ...201121949073
theoretical study of electron transfer in rhodobacter sphaeroides reaction center.we investigate the substitution effects on electron transfer in rhodobacter (rb.) sphaeroides reaction center using ab initio calculations. the overlap of molecular orbitals in the x-ray structure of 1pcr of the protein data bank using gaussian09 can qualitatively explain the tendency of the experimental transition time. the charge effects of proteins on electron transfer in rb. sphaeroides reaction center are also investigated, by employing a simple point charge approximation for proteins. we h ...201121895666
effects of mo(vi) on phototrophic hydrogen production by rhodobacter sphaeroides.effects of mo(6+) concentration on phototrophic hydrogen production of rhodobacter sphaeroides were investigated using lactate as the sole carbon source. results showed that an increase of mo(6+) from nil to 1000 microg l(-1) led to increases in hydrogen yield, maximum production rate, conversion efficiency, biomass yield and lactate removal. at 100 microg-mo l(-1), the maximum rate was 12.0 ml h(-1) with a conversion efficiency of 36.1%, the cell yields were 1.11 g-cell g(-1) -lactate and 2.4 g ...201121970170
role of protein dynamics in guiding electron-transfer pathways in reaction centers from rhodobacter sphaeroides.the role of protein dynamics in guiding multistep electron transfer is explored in the photosynthetic reaction center of rhodobacter sphaeroides . the energetics of the charge-separated intermediates, p(+)b(a)(-) and p(+)h(a)(-) (p is the initial electron donor bacteriochlorophyll pair and b(a) and h(a) are early bacteriochlorophyll and bacteriopheophytin acceptors, respectively), were systematically varied in a series of mutants. a fast phase of p(+)h(a)(-) recombination was resolved that is v ...201122148392
differential assembly of polypeptides of the light-harvesting 2 complex encoded by distinct operons during acclimation of rhodobacter sphaeroides to low light intensity.in order to obtain an improved understanding of the assembly of the bacterial photosynthetic apparatus, we have conducted a proteomic analysis of pigment-protein complexes isolated from the purple bacterium rhodobacter sphaeroides undergoing acclimation to reduced incident light intensity. photoheterotrophically growing cells were shifted from 1,100 to 100 w/m(2) and intracytoplasmic membrane (icm) vesicles isolated over 24-h were subjected to clear native polyacrylamide gel electrophoresis. ban ...201121863386
investigation of the redox interaction between mn-bicarbonate complexes and reaction centers from rhodobacter sphaeroides r-26, chromatium minutissimum, and chloroflexus aurantiacus.the change in the dark reduction rate of photooxidized reaction centers (rc) of type ii from three anoxygenic bacteria (rhodobacter sphaeroides r-26, chromatium minutissimum, and chloroflexus aurantiacus) having different redox potentials of the p(+)/p pair and availability of rc for exogenous electron donors was investigated upon the addition of mn(2+) and hco(3)(-). it was found that the dark reduction of p(870)(+) from rb. sphaeroides r-26 is considerably accelerated upon the combined additio ...201122150281
spinal tlr4 mediates the transition to a persistent mechanical hypersensitivity after the resolution of inflammation in serum-transferred arthritis.persistent pain after resolution of clinically appreciable signs of arthritis poses a therapeutic challenge, and immunosuppressive therapies do not meet this medical need. to investigate this conversion to persistent pain, we utilized the k/bxn serum transfer arthritis model, which has persistent mechanical hypersensitivity despite the resolution of visible inflammation. toll-like receptor (tlr) 4 has been implicated as a potential therapeutic target in neuropathic and other pain models. we comp ...201122019135
salt stress-induced changes in the transcriptome, compatible solutes, and membrane lipids in the facultatively phototrophic bacterium rhodobacter sphaeroides.responses to nacl stress were investigated in phototrophically grown alphaproteobacterium rhodobacter sphaeroides by transcriptome profiling, mutational analysis, and measurements of compatible solutes and membrane phospholipids. after exposure to salt stress, genes encoding two putative glycine betaine uptake systems, provwx and bets, were highly upregulated. mutational analysis revealed that bets, not provwx, was the primary transporter of this compatible solute. upon the addition of salt, exo ...201121908636
coherent phenomena of charge separation in reaction centers of ll131h and ll131h/lm160h/fm197h mutants of rhodobacter sphaeroides.primary stage of charge separation and transfer of charges was studied in reaction centers (rcs) of point mutants ll131h and ll131h/lm160h/fm197h of the purple bacterium rhodobacter sphaeroides by differential absorption spectroscopy with temporal resolution of 18 fsec at 90 k. difference absorption spectra measured at 0-4 psec delays after excitation of dimer p at 870 nm with 30 fsec step were obtained in the spectral range of 935-1060 nm. it was found that a decay of p* due to charge separatio ...201122098236
structure and function of the aaa+ protein cbbx, a red-type rubisco activase.ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco) catalyses the fixation of atmospheric co(2) in photosynthesis, but tends to form inactive complexes with its substrate ribulose 1,5-bisphosphate (rubp). in plants, rubisco is reactivated by the aaa(+) (atpases associated with various cellular activities) protein rubisco activase (rca), but no such protein is known for the rubisco of red algae. here we identify the protein cbbx as an activase of red-type rubisco. the 3.0-å crystal structur ...201122048315
[in process citation]. 201122168003
effects of stimulation of copper bioleaching on microbial community in vineyard soil and copper mining waste.long-term copper application in vineyards and copper mining activities cause heavy metal pollution sites. such sites need remediation to protect soil and water quality. bioremediation of contaminated areas through bioleaching can help to remove copper ions from the contaminated soils. thus, the aim of this work was to evaluate the effects of different treatments for copper bioleaching in two diverse copper-contaminated soils (a 40-year-old vineyard and a copper mining waste) and to evaluate the ...201121947860
in rhodobacter sphaeroides, chemotactic operon 1 regulates rotation of the flagellar system 2.rhodobacter sphaeroides is able to assemble two different flagella, the subpolar flagellum (fla1) and the polar flagella (fla2). in this work, we report the swimming behavior of r. sphaeroides fla2(+) cells lacking each of the proteins encoded by chemotactic operon 1. a model proposing how these proteins control fla2 rotation is presented.201121949068
two-dimensional spectroscopy can distinguish between decoherence and dephasing of zero-quantum coherences.recent experiments on a variety of photosynthetic antenna systems have revealed that coherences among electronic states persist longer than previously anticipated. in an ensemble measurement, the observed dephasing of a coherent state can occur because of either disorder across the ensemble or decoherence from interactions with the bath. distinguishing how much such disorder affects the experimentally observed dephasing rate is paramount for understanding the role that quantum coherence may play ...201122191993
slow dissociation of a charged ligand: analysis of the primary quinone q(a) site of photosynthetic bacterial reaction centers.reaction centers (rcs) are integral membrane proteins that undergo a series of electron transfer reactions during the process of photosynthesis. in the q(a) site of rcs from rhodobacter sphaeroides, ubiquinone-10 is reduced, by a single electron transfer, to its semiquinone. the neutral quinone and anionic semiquinone have similar affinities, which is required for correct in situ reaction thermodynamics. a previous study showed that despite similar affinities, anionic quinones associate and diss ...201121863833
mechanism of recombination of the p+h(a)- radical pair in mutant rhodobacter sphaeroides reaction centers with modified free energy gaps between p+b(a)- and p+h(a)-.the kinetics of recombination of the p(+)h(a)(-) radical pair were compared in wild-type reaction centers from rhodobacter sphaeroides and in seven mutants in which the free energy gap, δg, between the charge separated states p(+)b(a)(-) and p(+)h(a)(-) was either increased or decreased. five of the mutant rcs had been described previously, and x-ray crystal structures of two newly constructed complexes were determined by x-ray crystallography. the charge recombination reaction was accelerated i ...201121970763
effect of dietary rhodobacter capsulatus on lipid fractions and egg-yolk fatty acid composition in laying hens.the present study was conducted to investigate the effect of dietary rhodobacter capsulatus on lipid fractions and egg-yolk fatty acid composition in laying hens. thirty-six laying hens (30 weeks old) were randomly assigned into two dietary groups fed diets with (0.04%) or without (control) r. capsulatus for a 60-day feeding trial. dietary r. capsulatus decreased (p < 0.05) serum and hepatic cholesterol and increased (p < 0.05) the excreta cholesterol, and resultant lower (p < 0.05) cholesterol ...201121929698
the phytoplankton nannochloropsis oculata enhances the ability of roseobacter clade bacteria to inhibit the growth of fish pathogen vibrio anguillarum.phytoplankton cultures are widely used in aquaculture for a variety of applications, especially as feed for fish larvae. phytoplankton cultures are usually grown in outdoor tanks using natural seawater and contain probiotic or potentially pathogenic bacteria. some roseobacter clade isolates suppress growth of the fish pathogen vibrio anguillarum. however, most published information concerns interactions between probiotic and pathogenic bacteria, and little information is available regarding the ...201122053210
a new nitrilase-producing strain named rhodobacter sphaeroides lhs-305: biocatalytic characterization and substrate specificity.the characteristics of the new nitrilase-producing strain rhodobacter sphaeroides lhs-305 were investigated. by investigating several parameters influencing nitrilase production, the specific cell activity was ultimately increased from 24.5 to 75.0 μmol g(-1) min(-1), and hereinto, the choice of inducer proved the most important factor. the aromatic nitriles (such as 3-cyanopyridine and benzonitrile) were found to be the most favorable substrates of the nitrilase by analyzing the substrate spect ...201121938420
pathways involved in reductant distribution during photobiological h(2) production by rhodobacter sphaeroides.we used global transcript analyses and mutant studies to investigate the pathways that impact h(2) production in the photosynthetic bacterium rhodobacter sphaeroides. we found that h(2) production capacity is related to the levels of expression of the nitrogenase and hydrogenase enzymes and the enzymes of the calvin-benson-bassham pathway.201121856820
entrance of the proton pathway in cbb3-type heme-copper oxidases.heme-copper oxidases (hcuos) are the last components of the respiratory chain in mitochondria and many bacteria. they catalyze o(2) reduction and couple it to the maintenance of a proton-motive force across the membrane in which they are embedded. in the mitochondrial-like, a family of hcuos, there are two well established proton transfer pathways leading from the cytosol to the active site, the d and the k pathways. in the c family (cbb(3)) hcuos, recent work indicated the use of only one pathw ...201121997215
monoolein lipid phases as incorporation and enrichment materials for membrane protein crystallization.the crystallization of membrane proteins in amphiphile-rich materials such as lipidic cubic phases is an established methodology in many structural biology laboratories. the standard procedure employed with this methodology requires the generation of a highly viscous lipidic material by mixing lipid, for instance monoolein, with a solution of the detergent solubilized membrane protein. this preparation is often carried out with specialized mixing tools that allow handling of the highly viscous m ...201121909395
methods for the preparation of chlorophyllide a: an intermediate of the chlorophyll biosynthetic pathway.chlorophyllide a is a metabolite late in the biosynthesis of chlorophylls and bacteriochlorophylls. isolation procedures for chlorophyllide a from rhodobacter capsulatus cb1200 and barley (hordeum vulgare l.) are described and compared. r. capsulatus cb1200 is a double mutant in the bacteriochlorophyllide a biosynthetic pathway, and chlorophyllide a is excreted by the cells when grown in tween 80-containing liquid medium. it was purified by liquid or solid phase extraction, yielding 7 mg of chlo ...201121925479
Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria.Purple nonsulfur bacteria (PNSB) are facultative photosynthetic bacteria and exhibit an extremely versatile metabolism. A central focus of research on PNSB dealt with the elucidation of mechanisms by which they manage to balance cellular redox under diverse conditions, in particular under photoheterotrophic growth.201121943387
the rsp_2889 gene product of rhodobacter sphaeroides is a cuer homologue controlling copper-responsive genes.metal homeostasis is important in all living cells in order to provide sufficient amounts of metal ions for biological processes but to prevent toxic effects by excess amounts. here we show that the gene product of rsp_2889 of the facultatively photosynthetic bacterium rhodobacter sphaeroides is homologous to cuer, a regulator of copper metabolism in escherichia coli and other bacteria. cuer binds to the promoter regions of genes for a copper-translocating atpase and for a copper chaperone and i ...201121903751
rhodoferax-related pufm gene cluster dominates the aerobic anoxygenic phototrophic communities in german freshwater lakes.the presence of aerobic anoxygenic phototrophs (aaps) has been repeatedly reported from various marine environments, but their distribution in freshwater lakes was neglected until recently. we investigated the phylogenetic composition of aap communities in 10 lakes in northeastern germany with different trophic status including oligotrophic lake stechlin and humic matter rich lake grosse fuchskuhle. the aap community was composed by members of alpha- and betaproteobacteria, but their contributio ...201121895915
the resonance raman spectra of spheroidene revisited with a first-principles approach.the resonance raman (rr) spectra of different configurations of spheroidene are calculated by means of quantum chemical methods to investigate the nature of the cis configuration of this carotenoid molecule in the photosynthetic reaction center (rc) of the purple bacterium rhodobacter sphaeroides. for validation of our methodology, we also calculate the spectrum of the all-trans structure present in the light-harvesting complexes of this bacterium. while former theoretical resonance raman studie ...201121954132
Cytochrome c oxidase: Charge translocation coupled to single-electron partial steps of the catalytic cycle.The paper presents a survey of time-resolved studies of charge translocation by cytochrome c oxidase coupled to transfer of the 1st, 2nd 3rd and 4th electrons in the catalytic cycle. Single-electron photoreduction experiments carried out with the A-class cytochrome c oxidases of aa(3) type from mitochondria, Rhodobacter sphaeroides and Paracoccus denitrificans as well as with the ba(3)-type oxidase from Thermus thermophilus indicate that the protonmotive mechanisms, although similar, may not be ...201121871433
Coupling between Electron Transfer and Protein-Solvent Dynamics: FTIR and Laser-Flash Spectroscopy Studies in Photosynthetic Reaction Center Films at Different Hydration Levels.We report on the relationship between electron transfer, conformational dynamics, and hydration in photosynthetic reaction centers (RCs) from Rhodobacter sphaeroides. The kinetics of electron transfer from the photoreduced quinone acceptor (Q(A)(-)) to the photo-oxidized primary donor (P(+)), a charge recombination process sensitive to the conformational dynamics of the RC, has been analyzed at room temperature in dehydrated RC-detergent films as a function of the residual water content under co ...201122017517
Theoretical Study of the Electronic-Vibrational Coupling in the Q_Y States of the Photosynthetic Reaction Center in Purple Bacteria.Inspired by the recent observation of correlated excitation energy fluctuations of neighboring chromophores (Lee et al. Science 316, 1462 (2007)), quantum chemistry calculations and molecular dynamics simulations were employed to calculate the electronic-vibrational coupling in the excited states of photosynthetic reaction center of purple bacteria Rhodobacter (Rb.) sphaeroides. The ground states and lowest excited (Qy) states of isolated bacteriochlorophyll a (BChla) and bacteriopheophytin (BPh ...201122188530
primary charge separation within p870* in wild type and heterodimer mutants in femtosecond time domain.primary charge separation dynamics in the reaction center (rc) of purple bacterium rhodobacter sphaeroides and its p870 heterodimer mutants have been studied using femtosecond time-resolved spectroscopy with 20 and 40fs excitation at 870nm at 293k. absorbance increase in the 1060-1130nm region that is presumably attributed to p(a)(δ+) cation radical molecule as a part of mixed state with a charge transfer character p*(p(a)(δ+)p(b)(δ-)) was found. this state appears at 120-180fs time delay in the ...201122209778
Characterization of a newly discovered Mu-like bacteriophage, RcapMu, in Rhodobacter capsulatus strain SB1003.The a-proteobacterium Rhodobacter capsulatus is a model organism for the study of bacterial photosynthesis and the bacteriophage-like gene transfer agent. Characterization of phages that infect Rhodobacter is extremely rare, and scarce for the a-proteobacteria in general. Here, we describe the discovery of the only functional Mu-like transposing phage to have been identified in the a-proteobacteria, RcapMu, resident in the genome-sequenced R. capsulatus SB1003 strain. RcapMu packages ~42kb of to ...201122018635
a comparative spectroscopic and kinetic study of photoexcitations in detergent-isolated and membrane-embedded lh2 light-harvesting complexes.integral membrane proteins constitute more than third of the total number of proteins present in organisms. solubilization with mild detergents is a common technique to study the structure, dynamics, and catalytic activity of these proteins in purified form. however beneficial the use of detergents may be for protein extraction, the membrane proteins are often denatured by detergent solubilization as a result of native lipid membrane interactions having been modified. versatile investigations of ...201122172735
evolutionary origin of the rhodobacter sphaeroides specialized rpon sigma factors.gene duplication and horizontal gene transfer (hgt) are two events that enable the generation of new genes. rhodobacter sphaeroides (ws8 and 2.4.1 strains) has four copies of the rpon gene that are not functionally interchangeable. until now, this is the only example of specialization of this sigma factor. in this work, we aimed to determine whether the multiple copies of this gene originated from hgt or through gene duplication. our results suggest a multiplication origin of the different rpon ...201122093079
Biogenesis of cbb(3)-type cytochrome c oxidase in Rhodobacter capsulatus.The cbb(3)-type cytochrome c oxidases (cbb(3)-Cox) constitute the second most abundant cytochrome c oxidase (Cox) group after the mitochondrial-like aa(3)-type Cox. They are present in bacteria only, and are considered to represent a primordial innovation in the domain of Eubacteria due to their phylogenetic distribution and their similarity to nitric oxide (NO) reductases. They are crucial for the onset of many anaerobic biological processes, such as anoxygenic photosynthesis or nitrogen fixati ...201122079199
effects of ethanol, formaldehyde, and gentle heat fixation in confocal resonance raman microscopy of purple nonsulfur bacteria.resonance raman microscopy is well suited to examine living bacterial samples without further preparation. therefore, comparatively little thought has been given to its compatibility with common fixation methods. however, fixation of cell samples is a very important tool in the microbiological sciences, allowing the preservation of samples in a specific condition for further examination, future measurements, transport, or later reference. we examined the effects of three common fixatives-ethanol ...201120544803
light-generated paramagnetic intermediates in bluf domains.blue-light sensitive photoreceptory bluf domains are flavoproteins, which regulate various, mostly stress-related processes in bacteria and eukaryotes. the photoreactivity of the flavin adenine dinucleotide (fad) cofactor in three bluf domains from rhodobacter sphaeroides, synechocystis sp. pcc 6803 and escherichia coli have been studied at low temperature using time-resolved electron paramagnetic resonance. photoinduced flavin triplet states and radical-pair species have been detected on a micr ...201121198648
crystallographic and online spectral evidence for role of conformational change and conserved water in cytochrome oxidase proton pump.crystal structures in both oxidized and reduced forms are reported for two bacterial cytochrome c oxidase mutants that define the d and k proton paths, showing conformational change in response to reduction and the loss of strategic waters that can account for inhibition of proton transfer. in the oxidized state both mutants of the rhodobacter sphaeroides enzyme, d132a and k362m, show overall structures similar to wild type, indicating no long-range effects of mutation. in the reduced state, the ...201121205904
evaluation of a semipolar solvent system as a step toward heteronuclear multidimensional nmr-based metabolomics for 13c-labeled bacteria, plants, and animals.nuclear magnetic resonance (nmr) has become a key technology in metabolomics, with the use of stable isotope labeling and advanced heteronuclear multidimensional nmr techniques. in this paper, we focus on the evaluation of extraction solvents to improve nmr-based methodologies for metabolomics. line broadening is a serious barrier to detecting signals and the annotation of metabolites using multidimensional nmr. we evaluated a series of nmr solvents for easy and versatile single-step extraction ...201121208007
bacterial genome chimaerism and the origin of mitochondria.many studies have sought to determine the origin and evolution of mitochondria. although the alphaproteobacteria are thought to be the closest relatives of the mitochondrial progenitor, there is dispute as to what its particular sister group is. some have argued that mitochondria originated from ancestors of the order rickettsiales, or more specifically of the rickettsiaceae family, while others believe that ancestors of the family rhodospirillaceae are also equally likely the progenitors. to re ...201121217797
ultrafast infrared spectroscopy of an isotope-labeled photoactivatable flavoprotein.the blue light using flavin (bluf) domain photosensors, such as the transcriptional antirepressor appa, utilize a noncovalently bound flavin as the chromophore for photoreception. since the isoalloxazine ring of the chromophore is unable to undergo large-scale structural change upon light absorption, there is intense interest in understanding how the bluf protein matrix senses and responds to flavin photoexcitation. light absorption is proposed to result in alterations in the hydrogen-bonding ne ...201121218799
a novel rhodobacter sphaeroides expression system for real-time evaluation of heterologous protein expression levels.heterologous protein expression levels can not be evaluated in real-time by experimental procedures commonly used for most expression systems during host cell culture. rb. sphaeroides has provided an ideal system for studying both photosynthesis and membrane development and exhibited potential as a novel expression system. we constructed the puc1ba and puc2ba mutant strain rb. sphaeroides cqu68 and used it as a novel expression system to heterologously express proteins fused to β-subunit of ligh ...201121235482
unusual regulation of a leaderless operon involved in the catabolism of dimethylsulfoniopropionate in rhodobacter sphaeroides.rhodobacter sphaeroides strain 2.4.1 is a widely studied bacterium that has recently been shown to cleave the abundant marine anti-stress molecule dimethylsulfoniopropionate (dmsp) into acrylate plus gaseous dimethyl sulfide. it does so by using a lyase encoded by dddl, the promoter-distal gene of a three-gene operon, acur-acui-dddl. transcription of the operon was enhanced when cells were pre-grown with the substrate dmsp, but this induction is indirect, and requires the conversion of dmsp to t ...201121249136
the temperature dependence of radiationless transition rates from ab initio computations.the calculation of radiationless transition rates and of their temperature dependence from first principles is addressed by combining reliable electronic computations of the normal modes of the two electronic states with kubo's generating function approach for the evaluation of the franck-condon weighted density of states. the whole sets of normal modes of the involved cofactors have been employed, taking into account the effects of nuclear equilibrium position displacements, of vibrational freq ...201121258672
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