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application of rdna-pcr amplification and dgge fingerprinting for detection of microbial diversity in a malaysian crude oil.two culture-independent methods, namely ribosomal dna libraries and denaturing gradient gel electrophoresis (dgge), were adopted to examine the microbial community of a malaysian light crude oil. in this study, both 16s and 18s rdnas were pcr-amplified from bulk dna of crude oil samples, cloned, and sequenced. analyses of restriction fragment length polymorphism (rflp) and phylogenetics clustered the 16s and 18s rdna sequences into seven and six groups, respectively. the ribosomal dna sequences ...200818633276
ultrafast time-resolved carotenoid to-bacteriochlorophyll energy transfer in lh2 complexes from photosynthetic bacteria.steady-state and ultrafast time-resolved optical spectroscopic investigations have been carried out at 293 and 10 k on lh2 pigment-protein complexes isolated from three different strains of photosynthetic bacteria: rhodobacter (rb.) sphaeroides g1c, rb. sphaeroides 2.4.1 (anaerobically and aerobically grown), and rps. acidophila 10050. the lh2 complexes obtained from these strains contain the carotenoids, neurosporene, spheroidene, spheroidenone, and rhodopin glucoside, respectively. these molec ...200818671366
effects of ph on the peripheral light-harvesting antenna complex for rhodopseudomonas palustris.in this work steady-state absorption spectroscopy, circular dichroism spectroscopy and sub-microsecond time-resolved absorption spectroscopy were used to investigate the effect of ph on the structures and functions of lh2 complex for rhodopseudomonas palustris. the results revealed that: (1) b800 bchla was gradually transformed to free pigments absorbing around 760 nm on the minutes timescale upon the induction of strong acidic ph, and subsequently there disappeared the cd signal for q(y) band o ...200818677604
[assembly of lh2 light-harvesting complexes in rhodopseudomonas palustris cells illuminated by blue and red light].we investigated the formation of the b800-850 complex in cells of the bacterium rhodopseudomonas palustris ab illuminated by red and blue light under anaerobic growth conditions. under red illumination, the b800-850 complex was assembled with a reduced absorption band at 850 nm. the results of re-electrophoresis of the b800-850 complex and oxidation in the presence of potassium iridate suggest its heterogeneity. it may be a mixture of two complexes (b800 and b800-850). the b800-850 complex lacks ...200818683657
photophysical properties of natural light-harvesting complexes studied by subsystem density functional theory.in this study, we investigate the excited states and absorption spectra of a natural light-harvesting system by means of subsystem density functional theory. in systems of this type, both specific interactions of the pigments with surrounding protein side chains as well as excitation energy transfer (eet) couplings resulting from the aggregation behavior of the chromophores modify the photophysical properties of the individual pigment molecules. it is shown that the recently proposed approximate ...200818232685
ultrafast energy transfer dynamics of a bioinspired dyad molecule.a caroteno-purpurin dyad molecule was studied by steady-state and pump-probe spectroscopies to resolve the excited-state deactivation dynamics of the different energy levels as well as the connecting energy flow pathways and corresponding rate constants. the data were analyzed with a two-step multi-parameter global fitting procedure that makes use of an evolutionary algorithm. we found that following ultrafast excitation of the donor (carotenoid) chromophore to its s2 state, the energy flows via ...200818260660
protein dynamics control of electron transfer in photosynthetic reaction centers from rps. sulfoviridis.in the cycle of photosynthetic reaction centers, the initially oxidized special pair of bacteriochlorophyll molecules is subsequently reduced by an electron transferred over a chain of four hemes of the complex. here, we examine the kinetics of electron transfer between the proximal heme c-559 of the chain and the oxidized special pair in the reaction center from rps. sulfoviridis in the range of temperatures from 294 to 40 k. the experimental data were obtained for three redox states of the rea ...200818284231
biological synthesis of gold nanowires using extract of rhodopseudomonas capsulata.an environmentally friendly method using a cell-free extract (cfe) of rhodopseudomonas capsulata is proposed to synthesize gold nanowires with a network structure. this procedure offers control over the shapes of gold nanoparticles with the change of haucl4 concentration. the cfe solutions were added with different concentrations of haucl4, resulting in the bioreduction of gold ions and biosynthesis of morphologies of gold nanostructures. it is probable that proteins acted as the major biomolecu ...200818293997
6-oxocyclohex-1-ene-1-carbonyl-coenzyme a hydrolases from obligately anaerobic bacteria: characterization and identification of its gene as a functional marker for aromatic compounds degrading anaerobes.in anaerobic bacteria, most aromatic growth substrates are channelled into the benzoyl-coenzyme a (coa) degradation pathway where the aromatic ring is dearomatized and cleaved into an aliphatic thiol ester. the initial step of this pathway is catalysed by dearomatizing benzoyl-coa reductases yielding the two electron-reduction product, cyclohexa-1,5-diene-1-carbonyl-coa, to which water is subsequently added by a hydratase. the next two steps have so far only been studied in facultative anaerobes ...200818312395
survey of bacterial diversity in chronic wounds using pyrosequencing, dgge, and full ribosome shotgun sequencing.chronic wound pathogenic biofilms are host-pathogen environments that colonize and exist as a cohabitation of many bacterial species. these bacterial populations cooperate to promote their own survival and the chronic nature of the infection. few studies have performed extensive surveys of the bacterial populations that occur within different types of chronic wound biofilms. the use of 3 separate16s-based molecular amplifications followed by pyrosequencing, shotgun sanger sequencing, and denatur ...200818325110
complete genome sequence of nitrobacter hamburgensis x14 and comparative genomic analysis of species within the genus nitrobacter.the alphaproteobacterium nitrobacter hamburgensis x14 is a gram-negative facultative chemolithoautotroph that conserves energy from the oxidation of nitrite to nitrate. sequencing and analysis of the nitrobacter hamburgensis x14 genome revealed four replicons comprised of one chromosome (4.4 mbp) and three plasmids (294, 188, and 121 kbp). over 20% of the genome is composed of pseudogenes and paralogs. whole-genome comparisons were conducted between n. hamburgensis and the finished and draft gen ...200818326675
effect of linear alkylbenzene sulfonate (las) and atrazine on marine microalgae.five marine microalgae (tetraselmis chuii, rhodomonas salina, chaetoceros sp., isochrysis galbana (t-iso) and nannochloropsis gaditana), in the same biovolume quantity, were exposed to 72h growth-inhibition tests with atrazine and las. in all cases, the inhibition effect of atrazine was higher than that of las up to two orders of magnitude higher in the case of t. chuii. in a second part of the study, initial cellular densities for each microalga strain and fixed organic compound concentration w ...200818331743
how deep is the potential well confining a protein in a specific conformation? a single-molecule study on temperature dependence of conformational change between 5 and 18 k.the fluorescence excitation spectrum of a single chromophore molecule in a photosynthetic pigment-protein complex is known to change in time at liquid helium temperature. the spectral change reflects a conformational change of the protein to which the chromophore binds. this work follows the temporal behavior of the spectrum of a single chromophore in the temperature range between 5 adn 18 k. the temperature dependence reveals two types of conformational change of the protein, i.e., thermally ac ...200818345671
identification of 3,4-didehydrorhodopin as major carotenoid in rhodopseudomonas species.recently we isolated the purple photosynthetic bacterium, rhodopseudomonas sp. rits, which was phylogenetically related to rhodopseudomonas (rps.) palustris. in this study, the light-dependent and time-dependent changes in the carotenoid composition were investigated by hplc analysis of extracts from the cultures. all seven carotenoids in the biosynthetic pathway from lycopene to spirilloxanthin were detected. especially, 3,4-didehydrorhodopin, having twelve conjugated double bonds as well as on ...200818385894
transfer of the high-gc cyclohexane carboxylate degradation pathway from rhodopseudomonas palustris to escherichia coli for production of biotin.this work demonstrates the transfer of the five-gene cyclohexane carboxylate (chc) degradation pathway from the high-gc alphaproteobacterium rhodopseudomonas palustris to escherichia coli, a gammaproteobacterium. the degradation product of this pathway is pimeloyl-coa, a key metabolite in e. coli's biotin biosynthetic pathway. this pathway is useful for biotin overproduction in e. coli; however, the expression of gc-rich genes is troublesome in this host. when the native r. palustris chc degrada ...200818396082
lateral transfer of introns in the cryptophyte plastid genome.cryptophytes are unicellular eukaryotic algae that acquired photosynthesis secondarily through the uptake and retention of a red-algal endosymbiont. the plastid genome of the cryptophyte rhodomonas salina ccmp1319 was recently sequenced and found to contain a genetic element similar to a group ii intron. here, we explore the distribution, structure and function of group ii introns in the plastid genomes of distantly and closely related cryptophytes. the predicted secondary structures of six intr ...200818397952
fitting light saturation curves measured using modulated fluorometry.a blue diode pam (pulse amplitude modulation) fluorometer was used to measure rapid photosynthesis (p) versus irradiance (e) curves (p vs. e curves) in synechococcus (classical cyanobacteria), prochlorothrix (prochlorophyta), chlorella (chlorophyta), rhodomonas (cryptophyta), phaeodactylum (bacillariophyta) acaryochloris (chl d/a cyanobacteria) and subterranean clover (trifolium subterraneum, papilionaceae, angiospermae). effective quantum yield (phi(psii)) versus irradiance curves could be desc ...200818415696
purification, crystallization and preliminary crystallographic analysis of cyp 195a2, a p450 enzyme from rhodopseudomonas palustris.cytochrome p450 monooxygenases are a superfamily of heme-thiolate proteins involved in the metabolism of a wide variety of endogenous and xenobiotic compounds. the p450 enzyme cyp195a2 from rhodopseudomonas palustris cga009, a metabolically versatile bacterium, was overproduced in e. coli and purified. two distinct crystal forms were obtained under separately optimized conditions by the hanging-drop vapor-diffusion method. native data sets extending to resolutions of 2.3 a and 2.8 a have been co ...200818473959
complete sequence and analysis of the mitochondrial genome of hemiselmis andersenii ccmp644 (cryptophyceae).cryptophytes are an enigmatic group of unicellular eukaryotes with plastids derived by secondary (i.e., eukaryote-eukaryote) endosymbiosis. cryptophytes are unusual in that they possess four genomes-a host cell-derived nuclear and mitochondrial genome and an endosymbiont-derived plastid and 'nucleomorph' genome. the evolutionary origins of the host and endosymbiont components of cryptophyte algae are at present poorly understood. thus far, a single complete mitochondrial genome sequence has been ...200818474103
association of chlorophyll a/c(2) complexes to photosystem i and photosystem ii in the cryptophyte rhodomonas cs24.photosynthetic supercomplexes from the cryptophyte rhodomonas cs24 were isolated by a short detergent treatment of membranes from the cryptophyte rhodomonas cs24 and studied by electron microscopy and low-temperature absorption and fluorescence spectroscopy. at least three different types of supercomplexes of photosystem i (psi) monomers and peripheral chl a/c(2) proteins were found. the most common complexes have chl a/c(2) complexes at both sides of the psi core monomer and have dimensions of ...200818513489
discrepancy between experimental and theoretical excitation transfer rates in lh2 bacteriochlorophyll-protein complexes of purple bacteria.discrepancy is revealed between the values of excitation transfer times measured experimentally, and those calculated, for the atomic structures of b800 --> b850 bacteriochlorophylls within the lh2 light-harvesting pigment-protein complex of the purple bacterium rhodopseudomonas acidophila. the value 2.9-3.2 ps for the b800 --> b850 excitation transfer, calculated on the basis of atomic structure of lh2, is about 4-times longer than that measured for this bacterium (0.7 ps). this discrepancy app ...200817628796
phototrophic growth of rubrivivax gelatinosus in poultry slaughterhouse wastewater.rubrivivax gelatinosus was grown in pfennig's synthetic medium (pm) and in treated wastewater from poultry slaughterhouse (tw) to assess growth profiles for biomass production. cultures inoculated at 1% (v/v) were grown under anaerobiosis at 30+/-2 degrees c and 1400+/-200 lux for 12 days. regular absorbance curves for r. gelatinosus were found both on pm and tw. on pm, the highest dry weight of biomass, 0.39 gl(-1), was achieved in the 216-h culture and the highest specific growth rate of 0.296 ...200817905581
composition and localization of bacteriochlorophyll a intermediates in the purple photosynthetic bacterium rhodopseudomonas sp. rits.rhodopseudomonas sp. rits is a recently isolated new species of photosynthetic bacteria and found to accumulate a significantly high amount of bacteriochlorophyll (bchl) a intermediates possessing non-, di- and tetra-hydrogenated geranylgeranyl groups at the 17-propionate as well as normal phytylated bchl a (mizoguchi t et al. (2006) febs lett 580:137-143). a phylogenetic analysis showed that this bacterium was closely related to rhodopseudomonas palustris. the strain rits synthesizes light-harv ...200817912605
comparison of the fluorescence kinetics of detergent-solubilized and membrane-reconstituted lh2 complexes from rps. acidophila and rb. sphaeroides.picosecond time-resolved fluorescence spectroscopy has been used in order to compare the fluorescence kinetics of detergent-solubilized and membrane-reconstituted light-harvesting 2 (lh2) complexes from the purple bacteria rhodopseudomonas (rps.) acidophila and rhodobacter (rb.) sphaeroides. lh2 complexes were reconstituted in phospholipid model membranes at different lipid:protein-ratios and all samples were studied exciting with a wide range of excitation densities. while the detergent-solubil ...200817912609
spectral dynamics of individual bacterial light-harvesting complexes: alternative disorder model.the bacterial (rhodopseudomonas acidophila) photosynthetic peripheral light-harvesting complex of type 2 (lh2) exhibits rich fluorescence spectral dynamics at room temperature. the fluorescence spectrum of individual lh2 shifts either to the blue or to the red during the experimental observation time of a few minutes. these spectral changes are often reversible and occur between levels of a distinctly different peak wavelength. furthermore, they are accompanied by a change of the spectral line s ...200817921215
construction of hybrid photosynthetic units using peripheral and core antennae from two different species of photosynthetic bacteria: detection of the energy transfer from bacteriochlorophyll a in lh2 to bacteriochlorophyll b in lh1.typical purple bacterial photosynthetic units consist of supra-molecular arrays of peripheral (lh2) and core (lh1-rc) antenna complexes. recent atomic force microscopy pictures of photosynthetic units in intact membranes have revealed that the architecture of these units is variable (scheuring et al. (2005) biochim bhiophys acta 1712:109-127). in this study, we describe methods for the construction of heterologous photosynthetic units in lipid-bilayers from mixtures of purified lh2 (from rhodops ...200817926141
spectral diffusion of the lowest exciton component in the core complex from rhodopseudomonas palustris studied by single-molecule spectroscopy.we have recorded fluorescence-excitation spectra from individual rc-lh1 complexes from rhodopseudomonas palustris. the spectra feature a few broad bands accompanied by a sharp line at the low-energy side of the spectrum which is ascribed to the lowest exciton state of the bchl a assembly. recording several fluorescence-excitation spectra from the same individual complex in rapid succession reveals that the linewidth of the lowest exciton transition is determined by spectral diffusion which incre ...200817940849
improved phototrophic h2 production with rhodopseudomonas palustris wp3-5 using acetate and butyrate as dual carbon substrates.an indigenous purple nonsulfur bacterium rhodopseudomonas palustris wp3-5 was used to produce hydrogen phototrophically from acetate (hac) and butyrate (hbu), which are the major soluble products from acidogenic dark fermentation. statistical experimental design methodology was applied to identify optimal composition of the two carbon substrates in the medium, leading to better h2 production performance of r. palustris wp3-5. three performance indexes were used to assess the effectiveness of the ...200817826982
food quality effects on copepod growth and development: implications for bioassays in ecotoxicological testing.we evaluated effects of six algal species in 25 combinations on growth and reproduction of the harpacticoid copepod nitocra spinipes. in the first lifecycle test, rhodomonas salina, phaeodactylum tricornutum, and dunaliella tertiolecta were used. the results showed that r. salina was the best food, whereas p. tricornutum (0% development success) and d. tertiolecta (41.7% malformations) were poor food items. in the second lifecycle test, a mixture of r. salina, tetraselmis suecica, and thalassios ...200918514311
phenotype fingerprinting suggests the involvement of single-genotype consortia in degradation of aromatic compounds by rhodopseudomonas palustris.anaerobic degradation of complex organic compounds by microorganisms is crucial for development of innovative biotechnologies for bioethanol production and for efficient degradation of environmental pollutants. in natural environments, the degradation is usually accomplished by syntrophic consortia comprised of different bacterial species. this strategy allows consortium organisms to reduce efforts required for maintenance of the redox homeostasis at each syntrophic level. cellular mechanisms th ...200919242537
atomic force microscopy studies of native photosynthetic membranes.in addition to providing the earliest surface images of a native photosynthetic membrane at submolecular resolution, examination of the intracytoplasmic membrane (icm) of purple bacteria by atomic force microscopy (afm) has revealed a wide diversity of species-dependent arrangements of closely packed light-harvesting (lh) antennae, capable of fulfilling the basic requirements for efficient collection, transmission, and trapping of radiant energy. a highly organized architecture was observed with ...200919265434
structural and functional similarities between a ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco)-like protein from bacillus subtilis and photosynthetic rubisco.the sequences classified as genes for various ribulose-1,5-bisphosphate (rubp) carboxylase/oxygenase (rubisco)-like proteins (rlps) are widely distributed among bacteria, archaea, and eukaryota. in the phylogenic tree constructed with these sequences, rubiscos and rlps are grouped into four separate clades, forms i-iv. in rubisco enzymes encoded by form i, ii, and iii sequences, 19 conserved amino acid residues are essential for co(2) fixation; however, 1-11 of these 19 residues are substituted ...200919279009
in vitro kinetic studies on the mechanism of oxygen-dependent cellular uptake of copper radiopharmaceuticals.the development of hypoxia-selective radiopharmaceuticals for use as therapeutic and/or imaging agents is of vital importance for both early identification and treatment of cancer and in the design of new drugs. radiotracers based on copper for use in positron emission tomography have received great attention due to the successful application of copper(ii) bis(thiosemicarbazonato) complexes, such as [(60/62/64)cu(ii)atsm] and [(60/62/64)cu(ii)ptsm], as markers for tumour hypoxia and blood perfus ...200919287086
high yield conversion of a crude glycerol fraction from biodiesel production to hydrogen by photofermentation.present biodiesel manufacturing processes inevitably produce a crude glycerol side fraction. projected future volumes of biodiesel will generate enormous quantities of glycerol of a magnitude suggesting that conversion to a fuel is the only viable route. here we have shown that the photosynthetic bacterium rhodopseudomonas palustris is capable of the photofermentative conversion of glycerol, both pure and a crude glycerol fraction, to hydrogen, a proposed future fuel. relatively high yields, up ...200919339176
a family of bacterial cysteine protease type iii effectors utilizes acylation-dependent and -independent strategies to localize to plasma membranes.bacterial phytopathogens employ a type iii secretion system to deliver effector proteins into the plant cell to suppress defense pathways; however, the molecular mechanisms and subcellular localization strategies that drive effector function largely remain a mystery. here, we demonstrate that the plant plasma membrane is the primary site for subcellular localization of the pseudomonas syringae effector avrpphb and five additional cysteine protease family members. avrpphb and two avrpphb-like eff ...200919346252
gut-associated denitrification and in vivo emission of nitrous oxide by the earthworm families megascolecidae and lumbricidae in new zealand.previous studies have documented the capacity of european earthworms belonging to the family lumbricidae to emit the greenhouse gas nitrous oxide (n(2)o), an activity attributed primarily to the activation of ingested soil denitrifiers. to extend the information base to earthworms in the southern hemisphere, four species of earthworms in new zealand were examined for gut-associated denitrification. lumbricus rubellus and aporrectodea rosea (introduced species of lumbricidae) emitted n(2)o, where ...200919346358
photosynthetic system in blastochloris viridis revisited.the bacterium blastochloris viridis carries one of the simplest photosynthetic systems, which includes a single light-harvesting complex that surrounds the reaction center, membrane soluble quinones, and a soluble periplasmic protein cytochrome c(2) that shuttle between the reaction center and the bc(1) complex and act as electron carriers, as well as the atp synthase. the close arrangement of the photosynthetic membranes in bl. viridis, along with the extremely tight arrangement of the photosys ...200919397367
differential accumulation of form i rubisco in rhodopseudomonas palustris cga010 under photoheterotrophic growth conditions with reduced carbon sources.rhodopseudomonas palustris is unique among characterized nonsulfur purple bacteria because of its capacity for anaerobic photoheterotrophic growth using aromatic acids. like growth with other reduced electron donors, this growth typically requires the presence of bicarbonate/co(2) or some other added electron acceptor in the growth medium. proteomic studies indicated that there was specific accumulation of form i ribulose 1, 5-bisphosphate carboxylase/oxygenase (rubisco) subunit proteins (cbbl a ...200919376869
development of bacteria-based bioassays for arsenic detection in natural waters.arsenic contamination of natural waters is a worldwide concern, as the drinking water supplies for large populations can have high concentrations of arsenic. traditional techniques to detect arsenic in natural water samples can be costly and time-consuming; therefore, robust and inexpensive methods to detect arsenic in water are highly desirable. additionally, methods for detecting arsenic in the field have been greatly sought after. this article focuses on the use of bacteria-based assays as an ...200919377836
accumulation and cycling of polycyclic aromatic hydrocarbons in zooplankton.planktonic food webs play an important role driving the environmental fate of persistent organic pollutants, and pop accumulation in phytoplankton has been previously studied for its importance as a first step in the aquatic food webs. however, little is known about the accumulation and cycling of organic pollutants between zooplankton and water. the present study shows the results of laboratory experiments on the bioconcentration (by passive uptake) of polycyclic aromatic hydrocarbons in phytop ...200919452877
plasmon-waveguide resonance studies of ligand binding to integral proteins in membrane fragments derived from bacterial and mammalian cells.a procedure has been developed for directly depositing membrane fragments derived from bacterial cells (chromatophores from rhodopseudomonas sphaeroides) and mammalian cells (mu-opioid receptor- and mc4 receptor-transfected human embryonic kidney (hek) cells and rat trigeminal ganglion cells) on the silica surface of a plasmon-waveguide resonance (pwr) spectrometer. binding of ligands (cytochrome c(2) for the chromatophores, the peptide agonists damgo and melanotan-ii that are specific for the m ...200919454250
evaluation of affinity-tagged protein expression strategies using local and global isotope ratio measurements.elucidation of protein-protein interactions can provide new knowledge on protein function. enrichments of affinity-tagged (or "bait") proteins with interaction partners generally include background, nonspecific protein artifacts. furthermore, in vivo bait expression may introduce additional artifacts arising from altered physiology or metabolism. in this study, we compared these effects for chromosome and plasmid encoding strategies for bait proteins in two microbes: escherichia coli and rhodops ...200919459691
extraction of extracellular polymeric substances from the acidophilic bacterium acidiphilium 3.2sup(5).extraction of extracellular polymeric substances (eps) from acidiphilium 3.2sup(5) was investigated using five methods: edta, naoh, ion exchange resin, heating and centrifugation. the bacterium studied presents promising application in microbial fuel cells (mfcs). the degree of cellular lysis provoked by each method was determined by uv-visible spectroscopy of cultures before and after eps extraction. in addition, two electron microscopy techniques (tem and sem) were employed to determine the de ...200919474490
change in microbial communities in acetate- and glucose-fed microbial fuel cells in the presence of light.power densities produced by microbial fuel cells (mfcs) in natural systems are changed by exposure to light through the enrichment of photosynthetic microorganisms. when mfcs with brush anodes were exposed to light (4000 lx), power densities increased by 8-10% for glucose-fed reactors, and 34% for acetate-fed reactors. denaturing gradient gel electrophoresis (dgge) profiles based on the 16s rrna gene showed that exposure to high light levels changed the microbial communities on the anodes. based ...200919574034
hopanoids play a role in membrane integrity and ph homeostasis in rhodopseudomonas palustris tie-1.sedimentary hopanes are pentacyclic triterpenoids that serve as biomarker proxies for bacteria and certain bacterial metabolisms, such as oxygenic photosynthesis and aerobic methanotrophy. their parent molecules, the bacteriohopanepolyols (bhps), have been hypothesized to be the bacterial equivalent of sterols. however, the actual function of bhps in bacterial cells is poorly understood. here, we report the physiological study of a mutant in rhodopseudomonas palustris tie-1 that is unable to pro ...200919592593
crystal structure of a ferredoxin reductase for the cyp199a2 system from rhodopseudomonas palustris.cytochrome p450-199a2 from rhodopseudomonas palustris oxidizes para-substituted benzoic acids and may play a role in lignin and aromatic acid degradation pathways in the bacterium. cyp199a2 has an associated [2fe-2s] ferredoxin, palustrisredoxin (pux) but not a ferredoxin reductase. a genome search identified the palustrisredoxin reductase (pur) gene. pur was produced in escherichia coli and shown to be a flavin-dependent protein that supports efficient electron transfer from nadh to pux, thus r ...200919626710
structural information from orientationally selective deer spectroscopy.double electron-electron resonance (deer) spectroscopy can determine, from measurement of the dipolar interaction, the distance and orientation between two paramagnetic centres in systems lacking long-range order such as powders or frozen solution samples. in spin systems with considerable anisotropy, the microwave pulses excite only a fraction of the electron paramagnetic resonance (epr) spectrum and the resulting orientation selection needs to be explicitly taken into account if a meaningful d ...200919639159
thermodynamics of loop formation in the denatured state of rhodopseudomonas palustris cytochrome c': scaling exponents and the reconciliation problem.the observation that denatured proteins yield scaling exponents, nu, consistent with random-coil behavior and yet can also have pockets of residual or nonrandom structure has been termed the "reconciliation problem". to provide greater insight into the denatured state of a foldable sequence, we have measured histidine-heme loop formation equilibria in the denatured state of a class ii c-type cytochrome, cytochrome c' from rhodopseudomonas palustris. we have prepared a series of variants that pro ...200919647747
magic angle spinning (mas) nmr: a new tool to study the spatial and electronic structure of photosynthetic complexes.in the last two decades, magic angle spinning (mas) nmr has created its own niche in studies involving photosynthetic membrane protein complexes, owing to its ability to provide structural and functional information at atomic resolution of membrane proteins when in the membrane, in the natural environment. the light-harvesting two (lh2) transmembrane complex from rhodopseudomonas acidophila is used to illustrate the procedure of the technique applicable in photosynthesis research. one- and two-d ...200919669927
an in vivo imaging-based assay for detecting protein interactions over a wide range of binding affinities.identifying and characterizing protein interactions are fundamental steps toward understanding and modeling biological networks. methods that detect protein interactions in intact cells rather than buffered solutions are likely more relevant to natural systems since molecular crowding events in the cytosol can influence the diffusion and reactivity of individual proteins. one in vivo, imaging-based method relies on the colocalization of two proteins of interest fused to diviva, a cell division p ...200919698693
single-molecule spectroscopy reveals that individual low-light lh2 complexes from rhodopseudomonas palustris 2.1.6. have a heterogeneous polypeptide composition.rhodopseudomonas palustris belongs to the group of purple bacteria that have the ability to produce lh2 complexes with unusual absorption spectra when they are grown at low-light intensity. this ability is often related to the presence of multiple genes encoding the antenna apoproteins. here we report, for the first time to our knowledge, direct evidence that individual low-light lh2 complexes have a heterogeneous alphabeta-apoprotein composition that modulates the site energies of bchl a molecu ...200919720038
bioaugmentation for electricity generation from corn stover biomass using microbial fuel cells.corn stover is usually treated by an energy-intensive or expensive process to extract sugars for bioenergy production. however, it is possible to directly generate electricity from corn stover in microbial fuel cells (mfcs) through the addition of microbial consortia specifically acclimated for biomass breakdown. a mixed culture that was developed to have a high saccharification rate with corn stover was added to single-chamber, air-cathode mfcs acclimated for power production using glucose. the ...200919731723
hydrogen production by immobilized r. faecalis rld-53 using soluble metabolites from ethanol fermentation bacteria e. harbinense b49.in order to increase the hydrogen yield from glucose, hydrogen production by immobilized rhodopseudomonas faecalis rld-53 using soluble metabolites from ethanol fermentation bacteria ethanoligenens harbinense b49 was investigated. the soluble metabolites from dark-fermentation mainly were ethanol and acetate, which could be further utilized for photo-hydrogen production. hydrogen production by b49 was noticeably affected by the glucose and phosphate buffer concentration. the maximum hydrogen yie ...200919200719
growth and survival of early juveniles of the marine sponge hymeniacidon perlevis (demospongiae) under controlled conditions.to resolve "the supply problem" in sponge-derived drug development and other biotechnological applications, current research is exploring the possibility of obtaining an alternative sustainable supply of sponge biomass through intensive aquaculture of sponges utilizing artificial seed rearing. this study aimed to investigate the technology of early juvenile sponge cultivation under controlled conditions. the effects of food, temperature, water flow, and light on the growth and survival of early ...200919221840
phycobiliprotein diffusion in chloroplasts of cryptophyte rhodomonas cs24.unicellular cryptophyte algae employ antenna proteins with phycobilin chromophores in their photosynthetic machinery. the mechanism of light harvesting in these organisms is significantly different than the energy funneling processes in phycobilisomes utilized by cyanobacteria and red algae. one of the most striking features of cryptophytes is the location of the water-soluble phycobiliproteins, which are contained within the intrathylakoid spaces and are not on the stromal side of the lamellae ...200919224391
studies of interaction of homo-dimeric ferredoxin-nad(p)+ oxidoreductases of bacillus subtilis and rhodopseudomonas palustris, that are closely related to thioredoxin reductases in amino acid sequence, with ferredoxins and pyridine nucleotide coenzymes.ferredoxin-nadp(+) oxidoreductases (fnrs) of bacillus subtilis (yumc) and rhodopseudomonas palustris cga009 (rpa3954) belong to a novel homo-dimeric type of fnr with high amino acid sequence homology to nadph-thioredoxin reductases. these fnrs were purified from expression constructs in escherichia coli cells, and their steady-state reactions with [2fe-2s] type ferredoxins (fds) from spinach and r. palustris, [4fe-4s] type fd from b. subtilis, nad(p)(+)/nad(p)h and ferricyanide were studied. fro ...200919162251
immobility of phycobilins in the thylakoid lumen of a cryptophyte suggests that protein diffusion in the lumen is very restricted.the thylakoid lumen is an important photosynthetic compartment which is the site of key steps in photosynthetic electron transport. the fluidity of the lumen could be a major constraint on photosynthetic electron transport rates. we used fluorescence recovery after photobleaching in cells of the cryptophyte alga rhodomonas salina to probe the diffusion of phycoerythrin in the lumen and chlorophyll complexes in the thylakoid membrane. in neither case was there any detectable diffusion over a time ...200919166839
biosynthesis of cadmium sulfide nanoparticles by photosynthetic bacteria rhodopseudomonas palustris.a simple route for the synthesis of cadmium sulfide nanoparticles by photosynthetic bacteria rhodopseudomonas palustris has been demonstrated in this work. the cadmium sulfate solution incubated with r. palustris biomass changed to a yellow color from 48 h onward, indicating the formation of cadmium sulfide nanoparticles. the purified solution yielded the maximum absorbance peak at 425 nm due to cds particles in the quantum size regime. also, x-ray analysis of the purified nanoparticles confirme ...200919167198
light-activated cytotoxic compounds from malaysian microorganisms for photodynamic therapy of cancer.photodynamic therapy (pdt) is a promising cancer treatment which involves activation of a photosensitizing drug with light to produce reactive oxygen species that kill tumors without causing damage to unirradiated normal tissues. to date, only photofrin, foscan and levulan have been approved for clinical treatment of cancer. tropical habitats such as those found in malaysia are attractive sources of new therapeutic compounds as tremendous chemical diversity is found in a large number of plants, ...200919125347
viral lysis of phaeocystis pouchetii: implications for algal population dynamics and heterotrophic c, n and p cycling.a model ecosystem with two autotrophic flagellates, phaeocystis pouchetii and rhodomonas salina, a virus specific to p. pouchetii (ppv) and bacteria and heterotrophic nanoflagellates was used to investigate effects of viral lysis on algal population dynamics and heterotrophic nitrogen and phosphorus mineralization. lysis of p. pouchetii by ppv had strong positive effects on bacterial and hnf abundance, and the mass balance of c, n and p suggested an efficient transfer of organic material from p. ...200919129863
enhanced photo-h2 production of r. faecalis rld-53 by separation of co2 from reaction system.the effect of different gases, co(2) concentration, and separation of co(2) from reaction system on photo-fermentation h(2) production was investigated by batch culture in this study. experimental results showed that different gases (ar,n(2),co(2), and air) as gas phase have obviously affected on photo-h(2) production and a high concentration of co(2) can inhibit the growth and h(2) evolution of rhodopseudomonas faecalis rld-53. when co(2) concentration at 5%, cell increased most rapidly the spe ...200918930393
hydrogen production with r. faecalis rld-53 isolated from freshwater pond sludge.the rhodopseudomonas faecalis strain rld-53 was isolated from freshwater pond sludge and was demonstrated it could produce hydrogen. this study to investigate their ability of hydrogen production under some conditions in batch culture experiments. at ph 7.0, temperature 35 degrees c and light intensity of 4000 lux, the h(2) yield was 2.64 mol-h(2)/mol-acetate, 2.34 mol-h(2)/mol-propionate, 1.75 mol-h(2)/mol-lactate and 3.55 mol-h(2)/mol-malate, respectively. the maximal h(2) production rate of 3 ...200918573657
anaerobic baffled reactor (abr) for treating heavy oil produced water with high concentrations of salt and poor nutrient.the start-up and operational performance (total 212 days, including the start-up of 164 days) of an anaerobic baffled reactor (abr), which is used to treat heavy oil produced water, was studied without the temperature control. inoculums were mixtures of acclimated sediment taken from a heavy oil produced water treatment plant and digested sludge from a sewage wastewater treatment plant. the rod-shaped and spherical granules with colors of henna and black, in which clostridia, methanosarcina and ...200918793845
preliminary characterization of extracellular allelochemicals of the toxic marine dinoflagellate alexandrium tamarense using a rhodomonas salina bioassay.members of the marine dinoflagellate genus alexandrium are known to exude allelochemicals, unrelated to well-known neurotoxins (psp-toxins, spirolides), with negative effects on other phytoplankton and marine grazers. physico/chemical characterization of extracellular lytic compounds of a. tamarense, quantified by rhodomonas salina bioassay, showed that the lytic activity, and hence presumably the compounds were stable over wide ranges of temperatures and ph and were refractory to bacterial degr ...200920098594
[isolation, identification and degrading gene cloning of a pyrethroids-degrading bacterium].this study aimed to isolate, identify and clone degrading gene of a synthetic pyrethroids degrading bacterium.200920112682
intrageneric relationships of members of the genus rhodopseudomonas.the intrageneric structure of the genus rhodopseudomonas was evaluated by studying sequence information on 16s rrna genes, 16s-23s rrna gene internal transcribed spacer (its) regions, and puf genes using 33 test strains. the topology of phylogenetic trees based on these sequences was similar to those of every other independent method for tree construction. these phylogenetic data indicated that the test strains were grouped into at least 7 clusters possibly at the species level. this was support ...200920118611
pigment organization and energy level structure in light-harvesting complex 4: insights from two-dimensional electronic spectroscopy.photosynthetic light-harvesting antennae direct energy collected from sunlight to reaction centers with remarkable efficiency and rapidity. despite their common function, the pigment-protein complexes that make up antenna systems in different types of photosynthetic organisms exhibit a wide variety of structural forms. some individual organisms express different types of complexes depending on growth conditions. for example, purple photosynthetic bacteria rp. palustris preferentially synthesize ...200919402730
influence of precursors and inhibitor on the production of extracellular 5-aminolevulinic acid and biomass by rhodopseudomonas palustris kg31.5-aminolevulinic acid (ala) and the biomass of photosynthetic bacteria, rhodopseudomonas palustris kg31, have very high potential for development and exploitation as bioherbicide and biofertilizer respectively. in this work, the effects of two precursors and an inhibitor of aminolevulinic dehydratase (alad) added to the vfa culture medium on the production of ala and biomass were investigated. the experimental runs were carried out according to a box-behnken design. the precursors were added to ...200919420716
toxicity and bioaccumulation of copper and lead in five marine microalgae.on five marine microalgae with the same biovolume quantity (tetraselmis chuii, rhodomonas salina, chaetoceros sp., isochrysis galbana (t-iso) and nannochloropsis gaditana) 72-h exposure toxicity tests with copper and lead were performed. for both metals, 72-h ec50s showed t. chuii as the most tolerant and r. salina as one of the most sensitive. besides copper and lead ec(50) concentrations, metal concentrations in solution and accumulated on/in the cell where also analysed. t. chuii, the most to ...200919427695
spectral diffusion and electron-phonon coupling of the b800 bchl a molecules in lh2 complexes from three different species of purple bacteria.we have investigated the spectral diffusion and the electron-phonon coupling of b800 bacteriochlorophyll a molecules in the peripheral light-harvesting complex lh2 for three different species of purple bacteria, rhodobacter sphaeroides, rhodospirillum molischianum, and rhodopseudomonas acidophila. we come to the conclusion that b800 binding pockets for rhodobacter sphaeroides and rhodopseudomonas acidophila are rather similar with respect to the polarity of the protein environment but that the p ...200919883604
membrane curvature induced by aggregates of lh2s and monomeric lh1s.the photosynthetic apparatus of purple bacteria is contained within organelles called chromatophores, which form as extensions of the cytoplasmic membrane. the shape of these chromatophores can be spherical (as in rhodobacter sphaeroides), lamellar (as in rhodopseudomonas acidophila and phaeospirillum molischianum), or tubular (as in certain rb. sphaeroides mutants). chromatophore shape is thought to be influenced by the integral membrane proteins light harvesting complexes i and ii (lh1 and lh2 ...200919948127
low light adaptation: energy transfer processes in different types of light harvesting complexes from rhodopseudomonas palustris.energy transfer processes in photosynthetic light harvesting 2 (lh2) complexes isolated from purple bacterium rhodopseudomonas palustris grown at different light intensities were studied by ground state and transient absorption spectroscopy. the decomposition of ground state absorption spectra shows contributions from b800 and b850 bacteriochlorophyll (bchl) a rings, the latter component splitting into a low energy and a high energy band in samples grown under low light (ll) conditions. a spectr ...200919948132
biocatalytic synthesis of dihydroxynaphthoic acids by cytochrome p450 cyp199a2.cyp199a2, a bacterial p450 monooxygenase from rhodopseudomonas palustris, was found to exhibit oxidation activity towards three hydroxynaphthoic acids. whole cells of the recombinant escherichia coli strain expressing cyp199a2 efficiently catalyzed the regioselective oxidation of 1-, 3-, and 6-hydroxy-2-naphthoic acids to produce 1,7-, 3,7-, and 6,7-dihydroxynaphthoic acid respectively. these results suggest that cyp199a2 might be a useful oxidation biocatalyst for the synthesis of dihydroxynaph ...200919966465
the complete plastid genome sequence of the secondarily nonphotosynthetic alga cryptomonas paramecium: reduction, compaction, and accelerated evolutionary rate.the cryptomonads are a group of unicellular algae that acquired photosynthesis through the engulfment of a red algal cell, a process called secondary endosymbiosis. here, we present the complete plastid genome sequence of the secondarily nonphotosynthetic species cryptomonas paramecium ccap977/2a. the approximately 78 kilobase pair (kbp) c. paramecium genome contains 82 predicted protein genes, 29 transfer rna genes, and a single pseudogene (atpf). the c. paramecium plastid genome is approximate ...200920333213
reversible n epsilon-lysine acetylation regulates the activity of acyl-coa synthetases involved in anaerobic benzoate catabolism in rhodopseudomonas palustris.rhodopseudomonas palustris grows photoheterotrophically on aromatic compounds available in aquatic environments rich in plant-derived lignin. benzoate degradation is regulated at the transcriptional level in r. palustris in response to anoxia and the presence of benzoate and/or benzoyl-coa (bz-coa). here, we report evidence that anaerobic benzoate catabolism in this bacterium is also regulated at the post-translational level. in this pathway, benzoate is activated to bz-coa by the amp-forming bz ...201020345662
inelastic neutron scattering study of light-induced dynamics of a photosynthetic membrane system.inelastic neutron scattering was employed to study photoeffects on the molecular dynamics of membranes of the photosynthetic bacterium rhodopseudomonas viridis. the main photoactive parts of this biomolecular system are the chlorophyll molecules whose dynamics were found to be affected under illumination by visible light in a twofold manner. first, vibrational modes are excited at energies of 12(2) and 88(21) cm(-1). second, a partial "freezing" of rotational modes is observed at energies of 1.2 ...201020365393
bacteriophytochrome-dependent regulation of light-harvesting complexes in rhodopseudomonas palustris anaerobic cultures.bacteriophytochromes (bphs) are photoreceptors that help bacteria sense changes in light wavelength and intensity. bphs contain a linear tetrapyrrole chromophore that, upon absorption of red or far-red light, undergoes a cis-trans isomerization that leads to a conformational change in the holoprotein. the conformation and type of bph affects the expression of genes. the linear tetrapyrrole bound by bphs is thought to come from o(2)-dependent cleavage of heme by a heme oxygenase. we have discover ...201020369239
driving factors of the phytoplankton functional groups in a deep mediterranean reservoir.the control of phytoplankton growth is mainly related to the availability of light and nutrients. both may select phytoplankton species, but only if they occur in limiting amounts. during the last decade, the functional groups approach, based on the physiological, morphological and ecological attributes of the species, has proved to be a more efficient way to analyze seasonal changes in phytoplankton biomass. we analysed the dynamics of the phytoplankton functional groups sensu reynolds, recogni ...201020398914
selective chemical shift assignment of bacteriochlorophyll a in uniformly [13c-15n]-labeled light-harvesting 1 complexes by solid-state nmr in ultrahigh magnetic field.magic-angle spinning (mas) (13)c-(13)c correlation nmr spectroscopy was used to resolve the electronic ground state characteristics of the bacteriochlorophyll a (bchl a) cofactors in light-harvesting 1 (lh1) complexes of rhodopseudomonas acidophila (strain 10050). the bchl a (13)c isotropic chemical shifts of the lh1 complexes are compared to the (13)c chemical shifts for bchl a dissolved in acetone-d(6) and to (13)c nmr data that has been obtained for the b800 and b850 bchl molecules in rps. ac ...201020408539
identification of a methylase required for 2-methylhopanoid production and implications for the interpretation of sedimentary hopanes.the rise of atmospheric oxygen has driven environmental change and biological evolution throughout much of earth's history and was enabled by the evolution of oxygenic photosynthesis in the cyanobacteria. dating this metabolic innovation using inorganic proxies from sedimentary rocks has been difficult and one important approach has been to study the distributions of fossil lipids, such as steranes and 2-methylhopanes, as biomarkers for this process. 2-methylhopanes arise from degradation of 2-m ...201020421508
structural characterization of the predominant family of histidine kinase sensor domains.histidine kinase (hk) receptors are used ubiquitously by bacteria to monitor environmental changes, and they are also prevalent in plants, fungi, and other protists. typical hk receptors have an extracellular sensor portion that detects a signal, usually a chemical ligand, and an intracellular transmitter portion that includes both the kinase domain itself and the site for histidine phosphorylation. while kinase domains are highly conserved, sensor domains are diverse. hk receptors function as d ...201020435045
proton-transfer and hydrogen-bond interactions determine fluorescence quantum yield and photochemical efficiency of bacteriophytochrome.phytochromes are red-light photoreceptor proteins that regulate a variety of responses and cellular processes in plants, bacteria, and fungi. the phytochrome light activation mechanism involves isomerization around the c15 horizontal linec16 double bond of an open-chain tetrapyrrole chromophore, resulting in a flip of its d-ring. in an important new development, bacteriophytochrome (bph) has been engineered for use as a fluorescent marker in mammalian tissues. here we report that an unusual bph, ...201020435909
molecular factors controlling photosynthetic light harvesting by carotenoids.carotenoids are naturally occurring pigments that absorb light in the spectral region in which the sun irradiates maximally. these molecules transfer this energy to chlorophylls, initiating the primary photochemical events of photosynthesis. carotenoids also regulate the flow of energy within the photosynthetic apparatus and protect it from photoinduced damage caused by excess light absorption. to carry out these functions in nature, carotenoids are bound in discrete pigment-protein complexes in ...201020446691
anaerobic phototrophic nitrite oxidation by thiocapsa sp. strain ks1 and rhodopseudomonas sp. strain lq17.in anaerobic enrichment cultures for phototrophic nitrite-oxidizing bacteria from different freshwater sites, two different cell types, i.e. non-motile cocci and motile, rod-shaped bacteria, always outnumbered all other bacteria. most-probable-number (mpn) dilution series with samples from two freshwater sites yielded only low numbers (<or=3x10(3) cm(-3)) of phototrophic nitrite oxidizers. slightly higher numbers (about 10(4) cm(-3)) were found in activated sewage sludge. anaerobic phototrophic ...201020447994
feeding by the newly described mixotrophic dinoflagellate paragymnodinium shiwhaense: feeding mechanism, prey species, and effect of prey concentration.to investigate the feeding by the newly described mixotrophic dinoflagellate paragymnodinium shiwhaense (genbank accession number=am408889), we explored the feeding process and the kinds of prey species that p. shiwhaense is able to feed on using several different types of microscopes, including a transmission electron microscope and high-resolution video-microscopy. in addition, we measured the growth and ingestion rates of p. shiwhaense on its optimal algal prey amphidinium carterae as a funct ...201020487129
fixk, a global regulator of microaerobic growth, controls photosynthesis in rhodopseudomonas palustris.purple non-sulphur phototrophic bacteria (pnsb) are excellent models for analysing the co-ordination of major metabolisms, including oxidative phosphorylation, photophosphorylation, carbon dioxide fixation and nitrogen fixation. in species studied to date, a two-component system called regba controls these functions and it has been thought that this redox sensing regulatory system is essential for co-ordinating electron flow and cannot be easily replaced. here we show that this is not the case f ...201020487293
growth, lipid content, productivity, and fatty acid composition of tropical microalgae for scale-up production.biomass and lipid productivity, lipid content, and quantitative and qualitative lipid composition are critical parameters in selecting microalgal species for commercial scale-up production. this study compares lipid content and composition, and lipid and biomass productivity during logarithmic, late logarithmic, and stationary phase of nannochloropsis sp., isochrysis sp., tetraselmis sp., and rhodomonas sp. grown in l1-, f/2-, and k-medium. of the tested species, tetraselmis sp. exhibited a lipi ...201020506156
integrative control of carbon, nitrogen, hydrogen, and sulfur metabolism: the central role of the calvin-benson-bassham cycle.nonsulfur purple (nsp) photosynthetic bacteria use the calvin-benson-bassham (cbb) reductive pentose phosphate pathway for the reduction of co(2) via ribulose 1,5-bisphosphate (rubp) carboxylase-oxygenase (rubisco), as a means to build cell mass during chemoautotrophic or photoautotrophic conditions. in addition, the cbb pathway plays an important role in maintaining redox balance during photoheterotrophic growth conditions. in this communication we describe protein-protein interactions between ...201020532746
denatured states of low-complexity polypeptide sequences differ dramatically from those of foldable sequences.how the primary sequence of a protein encodes conformational preferences that operate early in folding to promote efficient formation of the correct native topology is still poorly understood. to address this issue, we have prepared a set of yeast iso-1-cytochrome c variants that contain polyalanine inserts ranging from 6 to 30 residues in length near the n terminus of the protein. we study the thermodynamics and kinetics of his-heme loop formation in the denatured state at 3 and 6 m guanidine-h ...201020534569
green energy from rhodopseudomonas palustris grown at low to high irradiance values, under fed-batch operational conditions.rhodopseudomonas palustris was grown under continuous irradiances of 36, 56, 75, 151, 320, 500, and 803 w m(-2), for a co-production of both bio-h(2) and biodiesel (lipids) using fed-batch conditions. the highest overall bio-h(2) produced [4.2 l(h(2)) l(culture) (-1)] was achieved at 320 w m(-2), while the highest dry biomass (3.18 g l(-1)) was attained at 500 w m(-2). dry biomass contained between 22 and 39% lipid. the total energy conversion efficiency was at its highest (6.9%) at 36 w m(-2).201020013301
selective oxidative demethylation of veratric acid to vanillic acid by cyp199a4 from rhodopseudomonas palustris haa2.cyp199a4 (rpb3613) from rhodopseudomonas palustris haa2 is a heme monooxygenase that catalyzes the hydroxylation of para-substituted benzoic acids. monooxygenase activity of cyp199a4 can be reconstituted in a class i electron transfer chain with an associated [2fe-2s] ferredoxin, hapux, (rpb3614) and the flavin-dependent reductase, hapur, (rpb3656) that is not associated with a cyp gene. cyp199a4 and the ferredoxin hapux are produced in greater quantities using recombinant escherichia coli expre ...201020024082
expanding the family of collagen proteins: recombinant bacterial collagens of varying composition form triple-helices of similar stability.the presence of the (gly-xaa-yaa)(n) open reading frames in different bacteria predicts the existence of an expanded family of collagen-like proteins. to further explore the triple-helix motif and stabilization mechanisms in the absence of hydroxyproline (hyp), predicted novel collagen-like proteins from gram-positive and -negative bacteria were expressed in escherichia coli and characterized. soluble proteins capable of successful folding and in vitro refolding were observed for collagen protei ...201020025291
development of a common oligonucleotide reference standard for microarray data normalization and comparison across different microbial communities.high-density functional gene arrays have become a powerful tool for environmental microbial detection and characterization. however, microarray data normalization and comparison for this type of microarray remain a challenge in environmental microbiology studies because some commonly used normalization methods (e.g., genomic dna) for the study of pure cultures are not applicable. in this study, we developed a common oligonucleotide reference standard (cors) method to address this problem. a uniq ...201020038701
isolation and properties of malic enzyme and its gene in rhodopseudomonas palustris no. 7.malic enzyme (me) was purified as an electrophoretically homogenous protein from rhodopseudomonas palustris no. 7. the molecular weight of me was estimated to be 650 kda and that of its subunit, 86 kda. me activity was remarkably enhanced by di- and mono-valent cations, and the k(a) values for mg(2+) and nh(4)(+) were 0.26 and 0.56 mm respectively. purified me used both nad(+) and nadp(+) as electron acceptors, with k(m) values of 0.11 and 1.8 mm. the k(m) value for l-malate was 1.7 mm using nad ...201020057150
fixk, a global regulator of microaerobic growth, controls photosynthesis in rhodopseudomonas palustris.purple nonsulfur phototrophic bacteria (pnsb) are excellent models for analyzing the coordination of major metabolisms including oxidative phosphorylation, photophosphorylation, carbon dioxide fixation and nitrogen fixation. in species studied to date, a two-component system called regba controls these functions and it has been thought that this redox sensing regulatory system is essential for coordinating electron flow and cannot be easily replaced. here we show that this is not the case for al ...201020059684
production of bio-fuels (hydrogen and lipids) through a photofermentation process.the purple non-sulfur photosynthetic bacteria rhodopseudomonas palustris (strain 42ol) was investigated for a co-production of both bio-h(2) and biodiesel (lipids). the investigation was carried out using malic and glutamic acids in a fed-batch cultivation system under continuous irradiances of 36, 56, 75, 151, 320, 500, and 803 w m(-2). boltzmann's sigmoidal regression model was used to determine growth kinetic parameters during hydrogen photoevolution. the upper limit of volumetric hydrogen ph ...201020060291
polyphasic bacterial community analysis of an aerobic activated sludge removing phenols and thiocyanate from coke plant effluent.biological purification processes are effective tools in the treatment of hazardous wastes such as toxic compounds produced in coal coking. in this study, the microbial community of a lab-scale activated sludge system treating coking effluent was assessed by cultivation-based (strain isolation and identification, biodegradation tests) and culture-independent techniques (sequence-aided t-rflp, taxon-specific pcr). the results of the applied polyphasic approach showed a simple microbial community ...201020093025
nuclear magnetic resonance secondary shifts of a light-harvesting 2 complex reveal local backbone perturbations induced by its higher-order interactions.protein nuclear magnetic resonance (nmr) secondary chemical shifts are widely used to predict the secondary structure, and in solid-state nmr, they are often the only unambiguous structural parameters available. however, the employed prediction methods are empirical in nature, relying on the assumption that secondary shifts are only affected by shielding effects of neighboring atoms. we analyzed the secondary shifts of a photosynthetic membrane protein with a high density of chromophores and ver ...201019954238
protein recognition in ferredoxin-p450 electron transfer in the class i cyp199a2 system from rhodopseudomonas palustris.cyp199a2 from rhodopseudomonas palustris cga009 is a heme monooxygenase that catalyzes the oxidation of para-substituted benzoic acids. cyp199a2 activity is reconstituted by a class i electron transfer chain consisting of the associated [2fe-2s] ferredoxin palustrisredoxin (pux) and a flavoprotein palustrisredoxin reductase (pur). another [2fe-2s] ferredoxin, palustrisredoxin b (puxb; rpa3956) has been identified in the genome. puxb shares sequence identity and motifs with vertebrate-type ferred ...201019904564
purple nonsulfur bacteria diversity in activated sludge and its potential phosphorus-accumulating ability under different cultivation conditions.this study investigates the diversity and the potential phosphorus-accumulating ability among the purple nonsulfur (pns) bacteria. traditional methods and molecular biotechniques were applied. microscopic visualization using 4',6-diamidino-2-phenylindole staining as well as chemical analysis demonstrated that most of the isolated pns bacteria presented different levels of phosphorus accumulation. four of the pure cultures, denoted as rhodopseudomonas palustris cc1, cc7, g11, and ge1, based on th ...201019943045
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