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bacteriophytochromes in anoxygenic photosynthetic bacteria.since the first discovery of a bacteriophytochrome in rhodospirillum centenum, numerous bacteriophytochromes have been identified and characterized in other anoxygenic photosynthetic bacteria. this review is focused on the biochemical and biophysical properties of bacteriophytochromes with a special emphasis on their roles in the synthesis of the photosynthetic apparatus.200818612842
identification and functional characterization of nifa variants that are independent of glnb activation in the photosynthetic bacterium rhodospirillum rubrum.the activity of nifa, the transcriptional activator of the nitrogen fixation (nif) gene, is tightly regulated in response to ammonium and oxygen. however, the mechanisms for the regulation of nifa activity are quite different among various nitrogen-fixing bacteria. unlike the well-studied nifl-nifa regulatory systems in klebsiella pneumoniae and azotobacter vinelandii, in rhodospirillum rubrum nifa is activated by a direct protein-protein interaction with the uridylylated form of glnb, which in ...200818757802
biosilicification of dual-fusion enzyme immobilized on magnetic nanoparticle.rapid recovery, immobilization, and silica encapsulation of a dual-fusion enzyme was achieved by using iminodiacetic acid (ida) modified magnetic nanoparticle as a carrier. d-amino acid oxidase (daao) of rhodosporidium toruloides was used as a model enzyme in which a silica-precipitating peptide r5 and a metal ion complexing peptide (his)(6) were fused to its n- and c-terminal, respectively. after charging the magnetic particle with cu(2+), the dual-fusion daao of 0.43 g could be directly recove ...200818078291
mechanistic diversity in the rubisco superfamily: a novel isomerization reaction catalyzed by the rubisco-like protein from rhodospirillum rubrum.some homologues of d-ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco) do not catalyze carboxylation and are designated rubisco-like proteins (rlps). the rlp from rhodospirillum rubrum (gi:83593333) catalyzes a novel isomerization reaction (overall 1,3-proton transfer reaction; likely, two 1,2-proton transfer reactions) that converts 5-methylthio-d-ribulose 1-phosphate to a 3:1 mixture of 1-methylthioxylulose 5-phosphate and 1-methylthioribulose 5-phosphate. disruption of the gene encodi ...200818826254
cloning and characterization of monofunctional catalase from photosynthetic bacterium rhodospirillum rubrum s1.in this study, an approx. 2.5-kb gene fragment including the catalase gene from rhodospirillum rubrum s1 was cloned and characterized. the determination of the complete nucleotide sequence revealed that the cloned dna fragment was organized into three open reading frames, designated as orf1, catalase, and orf3 in that order. the catalase gene consisted of 1,455 nucleotides and 484 amino acids, including the initiation and stop codons, and was located 326 bp upstream in the opposite direction of ...200718062223
directed evolution of rubisco in escherichia coli reveals a specificity-determining hydrogen bond in the form ii enzyme.ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco) occupies a critical position in photosynthetic co2-fixation and consequently has been the focus of intense study. crystal-structure-guided site-directed mutagenesis studies have met with limited success in engineering kinetic improvements to rubisco, highlighting our inadequate understanding of structural constraints at the atomic level that dictate the enzyme's catalytic chemistry. bioselection provides an alternative random mutagenic ap ...200718004873
differences in carbon isotope discrimination of three variants of d-ribulose-1,5-bisphosphate carboxylase/oxygenase reflect differences in their catalytic mechanisms.the carboxylation kinetic (stable carbon) isotope effect was measured for purified d-ribulose-1,5-bisphosphate carboxylases/oxygenases (rubiscos) with aqueous co(2) as substrate by monitoring rayleigh fractionation using membrane inlet mass spectrometry. this resulted in discriminations (delta) of 27.4 +/- 0.9 per thousand for wild-type tobacco rubisco, 22.2 +/- 2.1 per thousand for rhodospirillum rubrum rubisco, and 11.2 +/- 1.6 per thousand for a large subunit mutant of tobacco rubisco in whic ...200717925403
purification and reconstitution of pyp-phytochrome with biliverdin and 4-hydroxycinnamic acid.pyp-phytochrome (ppr) is a unique photoreceptor that contains a blue light-absorbing photoactive yellow protein (pyp) domain, a red light-absorbing phytochrome domain, and a histidine kinase domain. this chapter describes overexpression of ppr in a strain of escherichia coli that allows covalent attachment of substoichiometric amounts of biliverdin in vivo. ppr is then fully reconstituted with biliverdin, followed by attachment of 4-hydroxycinnamic acid (p-coumaric acid), in vitro. holo-ppr with ...200717628140
on the effects of pufx on the absorption properties of the light-harvesting complexes of rhodobacter sphaeroides.some species of purple bacteria as, e.g., rhodobacter sphaeroides contain the protein pufx. concurrently, the light harvesting complexes 1 (lh1) form dimers of open rings. in mutants without pufx, the lh1s are closed rings and photosynthesis breaks down, because the ubiquinone exchange at the reaction center is blocked. however, the main purpose of the lh1 is light harvesting. we therefore investigate the effects that the pufx-induced dimerization has on the absorption properties of the core com ...200717766331
physiological versatility of the genus rhodocista.a new purple bacterium (strain t4), capable of heterotrophic aerobic and phototrophic anaerobic growth, was isolated from waste water of a noodle factory near hanoi, vietnam. a comparison of 16s rdna sequences revealed its association with the genus rhodocista. the isolate, tentatively named "rhodocista hanoiensis", forms cysts after growth on butyrate-containing plates at 42 degrees c. the vegetative cells form short (under aerobic conditions) or long curve-shaped rods. in contrast to other spe ...200717913074
the photoactivated pyp domain of rhodospirillum centenum ppr accelerates the recovery of the bacteriophytochrome domain after white light illumination.ppr from the purple phototrophic bacterium, rhodospirillum centenum (also known as rhodocista centenaria), is a hybrid of photoactive yellow protein (pyp), bacteriophytochrome (bph), and histidine kinase (hk) domains. the holo-ppr (containing both chromophores) exhibits characteristic absorption maxima at 435 nm due to the pyp domain and at 400, 642, and 701 nm due to the bph domain. illumination of the ppr with white light causes a bleach of both pyp and bph absorbance; weak blue light primaril ...200717590020
specificity and regulation of interaction between the pii and amtb1 proteins in rhodospirillum rubrum.the nitrogen regulatory protein p(ii) and the ammonia gas channel amtb are both found in most prokaryotes. interaction between these two proteins has been observed in several organisms and may regulate the activities of both proteins. the regulation of their interaction is only partially understood, and we show that in rhodospirillum rubrum one p(ii) homolog, glnj, has higher affinity for an amtb(1)-containing membrane than the other two p(ii) homologs, glnb and glnk. this interaction strongly f ...200717644595
engineering of a type iii rubisco from a hyperthermophilic archaeon in order to enhance catalytic performance in mesophilic host cells.the hyperthermophilic archaeon thermococcus kodakaraensis harbors a type iii ribulose 1,5-bisphosphate carboxylase/oxygenase (rbc(tk)). it has previously been shown that rbc(tk) is capable of supporting photoautotrophic and photoheterotrophic growth in a mesophilic host cell, rhodopseudomonas palustris delta3, whose three native rubisco genes had been disrupted. here, we have examined the enzymatic properties of rbc(tk) at 25 degrees c and have constructed mutant proteins in order to enhance its ...200717675435
green and orange cdte quantum dots as effective ph-sensitive fluorescent probes for dual simultaneous and independent detection of viruses.one of the most highlighted and fastest moving interfaces of nanotechnology is the application of quantum dots (qds) in biology. the unparalleled advantages of the size-tunable fluorescent emission and the simultaneous excitation at a single wavelength make qds the great possibility for use in optical encoding detection. in this paper, we report that green and orange cdte qds as convenient, cheap, reversible, and effective ph-sensitive fluorescent probes could monitor the proton (h+) flux driven ...200717887667
substitution of tyrosine 146 in the di component of proton-translocating transhydrogenase leads to reversible dissociation of the active dimer into inactive monomers.transhydrogenase couples the redox reaction between nadh and nadp+ to proton translocation across a membrane. the protein has three components: di binds nadh, diii binds nadp+, and dii spans the membrane. transhydrogenase is a "dimer" of two di-dii-diii "monomers"; x-ray structures suggested that the two catalytic sites alternate during turnover. invariant tyr146 in recombinant di of rhodospirillum rubrum transhydrogenase was substituted with phe and ala (proteins designated di.y146f and di.y146 ...200717911104
growth of rhodospirillum rubrum on synthesis gas: conversion of co to h2 and poly-beta-hydroxyalkanoate.to examine the potential use of synthesis gas as a carbon and energy source in fermentation processes, rhodospirillum rubrum was cultured on synthesis gas generated from discarded seed corn. the growth rates, growth and poly-beta-hydroxyalkanoates (pha) yields, and co oxidation/h(2) evolution rates were evaluated in comparison to the rates observed with an artificial synthesis gas mixture. depending on the gas conditioning system used, synthesis gas either stimulated or inhibited co-oxidation ra ...200717054121
dna binding by an imidazole-sensing cooa variant is dependent on the heme redox state.cooa is a transcription factor from rhodospirillum rubrum that is regulated by the binding of the small molecule effector, co, to a heme moiety in the protein. the heme in cooa is axially ligated by two endogenous donors in the fe(iii) and fe(ii) states of the protein, and co binding to the fe(ii) state results in replacement of the distal ligand. reduction of the heme in the absence of co results in a ligand switch on the proximal side, in which a cysteine thiolate in the fe(iii) state is repla ...200717082920
factors affecting hydrogen production from cassava wastewater by a co-culture of anaerobic sludge and rhodospirillum rubrum.series of batch experiments were used to investigate the effects of environmental factors, i.e., total nitrogen and total phosphorus concentrations, initial ph, illumination pattern and stirring conditions on hydrogen production from cassava wastewater by a co-culture of anaerobic sludge and rhodospirillum rubrum. the maximum of the hydrogen yield of 150.46 and 340.19 ml g-cod(-1) was obtained at the total nitrogen and total phosphorus concentrations of 0.2 and 0.04 m, respectively. an effect of ...200719093464
structures of various cytochromes c evaluated from the redox behaviors using the optically active co(iii) complex-modified au electrode.electrochemical studies of three c-type cytochromes (cyt c from horse heart, cyt c(2) from rhodospirillum rubrum, and cyt c(553) from alcaligenes xylosoxidans gifu 1051) were performed by using the optically active co(iii) complex-modified au electrode. three cytochromes gave different redox behaviors reflected from the respective structural information. from relationship between their redox behaviors and their structural characteristics, we evaluated the solution structure around heme center of ...200719356022
single-enzyme conversion of fmnh2 to 5,6-dimethylbenzimidazole, the lower ligand of b12.the synthesis of 5,6-dimethylbenzimidazole (dmb), the lower ligand of coenzyme b(12), has remained elusive. we report in vitro and in vivo evidence that the blub protein of the photosynthetic bacterium rhodospirillum rubrum is necessary and sufficient for catalysis of the o(2)-dependent conversion of fmnh(2) to dmb. the product of the reaction (dmb) was isolated by using reverse-phase high-pressure liquid chromatography, and its identity was established by uv-visible spectroscopy and ms. no meta ...200717301238
overexpression and characterization of the rhodobacter sphaeroides pufx membrane protein in escherichia coli.heterologous expression of the pufx membrane protein from purple photosynthetic bacterium rhodobacter sphaeroides was attempted by using escherichia (e.) coli cells. the pufx was overexpressed as a recombinant protein with a histidine tag added to the carboxyl terminus, and can be extracted from the cell membrane by various detergents. circular dichroism measurements showed that the expressed pufx protein had alpha-helix contents of 29% in organic solvents and 22-26% in 0.8-2.0% (w/v) n-octyl be ...200716752956
possible pathway for ubiquinone shuttling in rhodospirillum rubrum revealed by molecular dynamics simulation.in the last decade, the structures of many components of the photosynthetic apparatus of purple bacteria, as well as the mutual organization of these components within the purple membrane, were resolved. one key question that emerged concerned the assembly of the core complex consisting of the reaction center (rc) and the light-harvesting 1 (lh1) complex. in some species, like rhodobacter sphaeroides, the ring-shaped lh1 complex was found to be open, whereas other species, like rhodospirillum ru ...200717028136
molecular assembly of artificial photosynthetic antenna core complex on an amino-terminated ito electrode.bacterial photosynthetic membrane proteins, light-harvesting antenna complex (lh1), reaction center (rc), and their combined 'core' complex (lh1-rc) are functional elements in the primary photosynthetic events, i.e., capturing and transferring light energy and subsequent charge separation. these photosynthetic units (psus) isolated from rhodospirillum rubrum (rs. rubrum) were assembled onto an ito electrode modified with 3-aminopropyltriethoxysilane (aps-ito). the near ir absorption spectra of p ...200717142019
mutations within the c-terminus of the gamma subunit of the photosynthetic f1-atpase activate mgatp hydrolysis and attenuate the stimulatory oxyanion effect.two highly conserved amino acid residues near the c-terminus within the gamma subunit of the mitochondrial atp synthase form a "catch" with an anionic loop on one of the three beta subunits within the catalytic alphabeta hexamer of the f1 segment [abrahams, j. p., leslie, a. g. w., lutter, r., and walker, j. e. (1994) nature 370, 621-628]. forming the catch is considered to be an essential step in cooperative nucleotide binding leading to gamma subunit rotation. the analogous residues, arg304 an ...200717288458
crystal structure of co-sensing transcription activator cooa bound to exogenous ligand imidazole.cooa is a co-dependent transcriptional activator and transmits a co-sensing signal to a dna promoter that controls the expression of the genes responsible for co metabolism. cooa contains a b-type heme as the active site for sensing co. co binding to the heme induces a conformational change that switches cooa from an inactive to an active dna-binding form. here, we report the crystal structure of an imidazole-bound form of cooa from carboxydothermus hydrogenoformans (ch-cooa). in the resting for ...200717292914
structures of the di2diii1 complex of proton-translocating transhydrogenase with bound, inactive analogues of nadh and nadph reveal active site geometries.transhydrogenase couples the redox reaction between nadh and nadp+ to proton translocation across a membrane. the enzyme comprises three components; di binds nad(h), diii binds nadp(h), and dii spans the membrane. the 1,4,5,6-tetrahydro analogue of nadh (designated h2nadh) bound to isolated di from rhodospirillum rubrum transhydrogenase with similar affinity to the physiological nucleotide. binding of either nadh or h2nadh led to closure of the di mobile loop. the 1,4,5,6-tetrahydro analogue of ...200717323922
phylogenomics and signature proteins for the alpha proteobacteria and its main groups.alpha proteobacteria are one of the largest and most extensively studied groups within bacteria. however, for these bacteria as a whole and for all of its major subgroups (viz. rhizobiales, rhodobacterales, rhodospirillales, rickettsiales, sphingomonadales and caulobacterales), very few or no distinctive molecular or biochemical characteristics are known.200718045498
structure-based hypothesis on the activation of the co-sensing transcription factor cooa.the cooa family of proteins are prokaryotic co-sensing transcription factors that regulate the expression of genes involved in the utilization of co as an energy source. they are homodimeric proteins that contain two hemes. each monomer contains an n-terminal heme-binding domain and a c-terminal dna-binding domain. binding of co to the heme leads to activation by a large reorientation of the dna-binding domain such that the dna-binding domain is in position for specific dna recognition. the crys ...200717327664
solution structure of the rhodobacter sphaeroides pufx membrane protein: implications for the quinone exchange and protein-protein interactions.pufx membrane protein is found in rhodobacter species of purple photosynthetic bacteria and has been known to play an essential role in ubiquinone/ubiquinol exchange between the reaction center and cytochrome bc1 complex and also contribute to the dimerization of the reaction center-light-harvesting core complex. we have determined the solution structure of the rhodobacter sphaeroides pufx using multidimensional nmr spectroscopy. the pufx, functionally expressed in escherichia coli, forms a stab ...200717335288
in vitro studies of the uridylylation of the three pii protein paralogs from rhodospirillum rubrum: the transferase activity of r. rubrum glnd is regulated by alpha-ketoglutarate and divalent cations but not by glutamine.p(ii) proteins have been shown to be key players in the regulation of nitrogen fixation and ammonia assimilation in bacteria. the mode by which these proteins act as signals is by being in either a form modified by ump or the unmodified form. the modification, as well as demodification, is catalyzed by a bifunctional enzyme encoded by the glnd gene. the regulation of this enzyme is thus of central importance. in rhodospirillum rubrum, three p(ii) paralogs have been identified. in this study, we ...200717337583
[the structural diversity of lipid a from gram-negative bacteria].the majority of gram-negative bacteria are pathogenic to humans and animals. lipopolysaccharide (lps) is the most biologically active component of these microorganisms. this compound is also called endotoxin to emphasize its negative impact on a macroorganism. lipid a, one of the three structural components of the lps molecule, is responsible for the pathophysiological effects associated with gram-negative bacteria infections. although lipid a is considered the conservative component of endotoxi ...200717369779
the activity of adenylyltransferase in rhodospirillum rubrum is only affected by alpha-ketoglutarate and unmodified pii proteins, but not by glutamine, in vitro.ammonium assimilation is tightly regulated in nitrogen-fixing bacteria; the target of regulation is primarily the activity of the key enzyme glutamine synthetase that is regulated by reversible covalent modification by amp groups in reactions catalysed by the bifunctional adenylyltransferase (atase). the properties and regulation of atase from escherichia coli have been studied in great detail. we have investigated the regulation of atase from rhodospirillum rubrum, a photosynthetic nitrogen-fix ...200717419734
[screening and identification of a photosynthetic bacterium reducing selenite to red elemental selenium].selenium is essential element for humans and animals but is very toxic at higher concentrations. in four inorganic states of selenate [seo4 2- ( vi)], selenite [seo3 2- (iv)], elemental selenium [se (0)] and selenide [se2- (- ii )], selenite is well known to be more soluble and higher toxic than other three forms. many microorganisms have the capacity to reduce selenite to red elemental selenium, which provide the potential to cope with the detoxification of pollution and to use the biological a ...200717436622
h+-ppases: yesterday, today and tomorrow.suggestions by calvin about a role of inorganic pyrophosphate (ppi) in early photosynthesis and by lipmann that ppi may have been the original energy-rich phosphate donor in biological energy conversion, were followed in the mid-1960s by experimental results with isolated chromatophore membranes from the purple photosynthetic bacterium rhodospirillum rubrum. ppi was shown to be hydrolysed in an uncoupler stimulated reaction by a membrane-bound inorganic pyrophosphatase (ppase), to be formed at t ...200717454298
ferripyochelin uptake genes are involved in pyochelin-mediated signalling in pseudomonas aeruginosa.in response to iron starvation, pseudomonas aeruginosa produces the siderophore pyochelin. when secreted to the extracellular environment, pyochelin chelates iron and transports it to the bacterial cytoplasm via its specific outer-membrane receptor fpta and the inner-membrane permease fptx. exogenously added pyochelin also acts as a signal which induces the expression of the pyochelin biosynthesis and uptake genes by activating pchr, a cytoplasmic regulatory protein of the arac/xyls family. the ...200717464065
the emitting state of tryptophan in proteins with highly blue-shifted fluorescence. 200717539030
roles of the heme and heme ligands in the activation of cooa, the co-sensing transcriptional activator.cooa of rhodospirillum rubrum is a co-sensing, heme-containing transcriptional activator that regulates the expression of the genes responsible for co oxidation. we randomized the codons for residues 75-77 of cooa which include two proximal heme ligands, screened for both co-dependent and co-independent variants, and characterized in vivo and in vitro properties of selected cooa variants. the analysis showed that small residues at position 75 are critical and that, as previously suspected, his77 ...200616889751
bacterial lateral flagella: an inducible flagella system.flagella are complex surface organelles that allow bacteria to move towards favourable environments and that contribute to the virulence of pathogenic bacteria through adhesion and biofilm formation on host surfaces. there are a few bacteria that possess functional dual flagella systems, such as vibrio parahaemolyticus, some mesophilic aeromonas spp., rhodospirillum centenum and azospirillum brasilense. these bacteria are able to express both a constitutive polar flagellum required for swimming ...200616978346
mori-zwanzig memory analysis in single-molecule spectroscopy.we study the dynamical behavior of the rhodospirillum molischianum lh2 complex based on intensity time series obtained from single-molecule spectroscopy experiments. this is achieved by reconstructing the memory function describing the time-dependent fluctuations of the excited states. we conclude that the apparent stochastic evolution of the dynamics is controlled by at least two different non-markovian main processes.200616986896
functions of carotenoids in xanthorhodopsin and archaerhodopsin, from action spectra of photoinhibition of cell respiration.the recent discovery of a carotenoid light-harvesting antenna in xanthorhodopsin, a retinal-based proton pump in salinibacter ruber, made use of photoinhibition of respiration in whole cells to obtain action spectra [balashov et al. science 309, (2005) 2061-2064]. here we provide further details of this phenomenon, and compare action spectra in three different systems where carotenoids have different functions or efficiencies of light-harvesting. the kinetics of light-induced inhibition of respi ...200617020745
the poor growth of rhodospirillum rubrum mutants lacking pii proteins is due to an excess of glutamine synthetase activity.the p(ii) family of proteins is found in all three domains of life and serves as a central regulator of the function of proteins involved in nitrogen metabolism, reflecting the nitrogen and carbon balance in the cell. the genetic elimination of the genes encoding these proteins typically leads to severe growth problems, but the basis of this effect has been unknown except with escherichia coli. we have analysed a number of the suppressor mutations that correct such growth problems in rhodospiril ...200616762025
two pathways of electron transport to nitrogenase in rhodospirillum rubrum: the major pathway is dependent on the fix gene products.in the photosynthetic bacterium rhodospirillum rubrum, as in many other diazotrophs, electron transport to nitrogenase has not been characterized in great detail. in this study, we show that there are two pathways operating in r. rubrum. the products of the fix genes constitute the major pathway operating under heterotrophic conditions, whereas a pyruvate:ferredoxin oxidoreductase, encoded by the nifj gene, may play a central role under anaerobic conditions in the dark. in both systems, ferredox ...200616790015
effect of amtb homologues on the post-translational regulation of nitrogenase activity in response to ammonium and energy signals in rhodospirillum rubrum.the amtb protein transports uncharged nh(3) into the cell, but it also interacts with the nitrogen regulatory protein p(ii), which in turn regulates a variety of proteins involved in nitrogen fixation and utilization. three p(ii) homologues, glnb, glnk and glnj, have been identified in the photosynthetic bacterium rhodospirillum rubrum, and they have roles in at least four overlapping and distinct functions, one of which is the post-translational regulation of nitrogenase activity. in r. rubrum, ...200616804182
catalytic by-product formation and ligand binding by ribulose bisphosphate carboxylases from different phylogenies.during catalysis, all rubisco (d-ribulose-1,5-bisphosphate carboxylase/oxygenase) enzymes produce traces of several by-products. some of these by-products are released slowly from the active site of rubisco from higher plants, thus progressively inhibiting turnover. prompted by observations that form i rubisco enzymes from cyanobacteria and red algae, and the form ii rubisco enzyme from bacteria, do not show inhibition over time, the production and binding of catalytic by-products was measured t ...200616822231
mechanically driven proton conduction in single delta-free f0f1-atpase.in order to observe mechanically driven proton flux in f(0)f(1)-atpase coupled with artificial driven rotation on f(1) simultaneously, a double channel observation system was established. an artificial delta-free f(0)f(1)-atpase was constructed with alpha(3), beta(3), epsilon, gamma, and c(n) subunits as rotator and a, b(2) as stator. the chromatophore was immobilized on the glass surface through biotin-streptavidin-biotin system, and the magnetic bead was attached to the beta subunit of delta-f ...200616844089
theoretical prediction of spectral and optical properties of bacteriochlorophylls in thermally disordered lh2 antenna complexes.a general approach for calculating spectral and optical properties of pigment-protein complexes of known atomic structure is presented. the method, that combines molecular dynamics simulations, quantum chemistry calculations, and statistical mechanical modeling, is demonstrated by calculating the absorption and circular dichroism spectra of the b800-b850 bacteriochlorophylls of the lh2 antenna complex from rs. molischianum at room temperature. the calculated spectra are found to be in good agree ...200616863329
effect of mutation on the dissociation and recombination dynamics of co in transcriptional regulator cooa: a picosecond infrared transient absorption study.the co ligation process in a mutant (h77g) of cooa, the co-sensing transcriptional regulator in rhodospirillum rubrum, is studied with femtosecond time-resolved transient absorption spectroscopy in the mid-infrared region. following photolyzing excitation, a transient bleach in the vibrational region of bound co due to the co photodissociation is detected. in contrast to the spectra of the wild-type (wt) cooa, the transient bleach spectra of h77g cooa show a bimodal shape with peaks shifting to ...200616866371
heme displacement mechanism of cooa activation: mutational and raman spectroscopic evidence.the heme-containing protein cooa of rhodospirillum rubrum regulates the expression of genes involved in co oxidation. cooa binds its target dna sequence in response to co binding to its heme. activity measurements and resonance raman (rr) spectra are reported for cooa variants that bind dna even in the absence of co, those in which the wild-type residues at the 121-126 positions, tscmrt, are replaced by the residues ayllrl or ryllrl, and also for variants that bind dna poorly in the presence of ...200616873369
modeling proline ligation in the heme-dependent co sensor, cooa, using small-molecule analogs.cooa, the only protein known to employ proline as a heme ligand, is a co-activated transcription factor found in the bacterium rhodospirillum rubrum. proline is a heme ligand in both the fe(iii) and fe(ii) states; the sixth ligand is cysteinate in fe(iii) cooa and histidine in fe(ii) cooa. when co binds to fe(ii) cooa, it selectively replaces the proline ligand, activating the protein. the proposed roles of proline are to stabilize the heme pocket during the redox-mediated ligand switch and to f ...200616724227
purification and characterization of a catalase from photosynthetic bacterium rhodospirillum rubrum s1 grown under anaerobic conditions.the photosynthetic bacterium, rhodospirillum rubrum s1, when grown under anaerobic conditions, generated three different types of catalases. in this study, we purified and characterized the highest molecular weight catalase from the three catalases. the total specific catalase activity of the crude cell extracts was 88 u/mg. after the completion of the final purification step, the specific activity of the purified catalase was 1,256 u/mg. the purified catalase evidenced an estimated molecular ma ...200616728955
a conserved mechanism controls translation of rubisco large subunit in different photosynthetic organisms.we previously proposed a mechanism for control of rubisco expression and assembly during oxidative stress in chlamydomonas reinhardtii. the n terminus of the large subunit (lsu) comprises an rna recognition motif (rrm) that is normally buried in the protein, but becomes exposed under oxidizing conditions when the glutathione pool shifts toward its oxidized form. thus, de novo translation and assembly of rubisco lsu stop with similar kinetics and the unpaired small subunit (ssu) is rapidly degrad ...200616731581
microbial diversity in maras salterns, a hypersaline environment in the peruvian andes.maras salterns are located 3,380 m above sea level in the peruvian andes. these salterns consist of more than 3,000 little ponds which are not interconnected and act as crystallizers where salt precipitates. these ponds are fed by hypersaline spring water rich in sodium and chloride. the microbiota inhabiting these salterns was examined by fluorescence in situ hybridization (fish), 16s rrna gene clone library analysis, and cultivation techniques. the total counts per milliliter in the ponds were ...200616751493
the role of the dna-binding domains in cooa activation.carbon monoxide oxidation activator protein (cooa) is a dimeric carbon monoxide (co) binding transcription factor that in the presence of co promotes the transcription of genes involved in co oxidation in rhodospirillum rubrum. the off state (inactive) of fe(ii) cooa has his and pro as the two axial heme ligands. in contrast, in the on state, which is active in dna binding, the pro ligand bond has been replaced by co. this occurs by the transient loss of the pro ligand, thus generating a pentaco ...200616752905
micro-scale open-tube capillary separations of functional proteins.this article describes a novel technique whereby fully functional proteins or multiprotein complexes are efficiently extracted from biological samples to chemically derivatized walls of fused-silica open-tube capillary columns. proteins are eluted with very high yields into elution volumes that are smaller in volume than the internal volume of the open-tube capillary column itself, thereby achieving 100-fold increases in target protein concentrations from starting samples of less than 1 ml. the ...200616448620
spectral trends in the fluorescence of single bacterial light-harvesting complexes: experiments and modified redfield simulations.in this work we present and discuss the single-molecule fluorescence spectra of a variety of species of light-harvesting complexes: lh2 of rhodopseudomonas acidophila, rhodobacter sphaeroides, and rhodospirillum molischianum and lh1 of rhodobacter sphaeroides. the emission spectrum of these complexes varies as a function of time as was described in earlier work. for each type of complex, we observe a pronounced and well-reproducible characteristic relationship between the fluorescence spectral p ...200616399834
comparative study of spectral flexibilities of bacterial light-harvesting complexes: structural implications.this work presents a comparative study of the frequencies of spectral jumping of individual light-harvesting complexes of six different types: lh2 of rhodopseudomonas acidophila, rhodobacter sphaeroides, and rhodospirillum molischianum; lh1 of rhodobacter sphaeroides; and two "domain swap mutants" of lh2 of rhodobacter sphaeroides: paclh1 and paclh2mol, in which the alpha-polypeptide c-terminus is exchanged with the corresponding sequence from lh1 of rhodobacter sphaeroides or lh2 of rhodospiril ...200616399835
unexpected no-dependent dna binding by the cooa homolog from carboxydothermus hydrogenoformans.cooa, the co-sensing heme protein from rhodospirillum rubrum, regulates the expression of genes that encode a co-oxidation system, allowing r. rubrum to use co as a sole energy source. to better understand the gas-sensing regulation mechanism used by r. rubrum cooa and its homologs in other organisms, we characterized spectroscopically and functionally the fe(ii), fe(ii)-no, and fe(ii)-co forms of cooa from carboxydothermus hydrogenoformans. surprisingly, and unlike r. rubrum cooa, c. hydrogenof ...200616410360
metabolic regulation of nitrogen fixation in rhodospirillum rubrum.nitrogenase activity in rhodospirillum rubrum is post-translationally regulated by drag (dinitrogenase reductase glycohydrolase) and drat (dinitrogenase reductase adp-ribosylation transferase). when a sudden increase in fixed nitrogen concentration or energy depletion is sensed by the cells, drag is inactivated and drat activated. we propose that the regulation of drag is dependent on its location in the cell and the presence of an ammonium-sensing protein.200616417510
evidence for displacements of the c-helix by co ligation and dna binding to cooa revealed by uv resonance raman spectroscopy.the uv and visible resonance raman spectra are reported for cooa from rhodospirillum rubrum, which is a transcriptional regulator activated by growth in a co atmosphere. co binding to heme in its sensor domain causes rearrangement of its dna-binding domain, allowing binding of dna with a specific sequence. the sensor and dna-binding domains are linked by a hinge region that follows a long c-helix. uv resonance raman bands arising from trp-110 in the c-helix revealed local movement around trp-110 ...200616439368
hexacoordination of bacteriochlorophyll in photosynthetic antenna lh1.the ability of chlorophylls to coordinate ligands is of fundamental structural importance for photosynthetic pigment-protein complexes, where in virtually all cases the pigment is thought to be in a pentacoordinated state. in this study, the correlation of the q(x) transition energy with the coordination state of the central metal in bacteriochlorophyll is applied in investigating the pigment coordination state in bacterial photosynthetic antenna lh1. to facilitate a detailed spectral analysis i ...200616460037
design of a minimal polypeptide unit for bacteriochlorophyll binding and self-assembly based on photosynthetic bacterial light-harvesting proteins.we introduce lh1beta24, a minimal 24 amino acid polypeptide that binds and assembles bacteriochlorophylls (bchls) in micelles of octyl beta-glucoside (og) into complexes with spectral properties that resemble those of b820, a universal intermediate in the assembly of native purple bacterial light-harvesting complexes (lhs). lh1beta24 was designed by a survey of sequences and crystal structures of bacterial lh proteins from different organisms combined with currently available information from in ...200616475799
quantum chemical simulation of excited states of chlorophylls, bacteriochlorophylls and their complexes.the present review describes the use of quantum chemical methods in estimation of structures and electronic transition energies of photosynthetic pigments in vacuum, in solution and imbedded in proteins. monomeric mg-porphyrins, chlorophylls and bacteriochlorophylls and their solvent 1:1 and 1:2 complexes were studied. calculations were performed for mg-porphyrin, mg-chlorin, mg-bacteriochlorin, mesochlorophyll a, chlorophylls a, b, c(1), c(2), c(3), d and bacteriochlorophylls a, b, c, d, e, f, ...200616482307
identification of rhodospirillum rubrum glnb variants that are altered in their ability to interact with different targets in response to nitrogen status signals.in rhodospirillum rubrum, nifa, the transcriptional activator for the nif genes, is posttranslationally activated only by the uridylylated form of glnb, one of three p(ii) homologs in the organism. we have used the yeast two-hybrid system to detect variants of glnb that interact better with nifa than does wild-type glnb. when examined for physiological effects in r. rubrum, these glnb* variants activated nifa in the presence of nh(4)(+), which normally blocks nifa activation completely, and in t ...200616484197
investigation of the effects of different carotenoids on the absorption and cd signals of light harvesting 1 complexes.absorption and circular dichroism (cd) spectra of light-harvesting (lh)1 complexes from the purple bacteria rhodobacter (rba.) sphaeroides and rhodospirillum (rsp.) rubrum are presented. the complexes exhibit very low intensity, highly nonconservative, near-infrared (nir) cd spectra. absorption and cd spectra from several mutant and reconstituted lh1 complexes, with the carotenoid neurosporene and the precursor phytoene replacing the wild-type (wt) carotenoids, are also examined. the experiments ...200616494350
calculation of absorption spectra for light-harvesting systems using non-markovian approaches as well as modified redfield theory.for an ensemble of b850 rings of the light-harvesting system lh2 of purple bacteria the linear absorption spectrum is calculated. using different markovian and non-markovian, time-dependent and time-independent methods based on second-order perturbation theory in the coupling between the excitonic system and its surrounding environment as well as the modified redfield theory, the influence of the shape of the spectral density on the linear absorption spectrum is demonstrated for single samples a ...200616512738
enzymic systems proposed to be involved in the dissimilatory reduction of selenite in the purple non-sulfur bacteria rhodospirillum rubrum and rhodobacter capsulatus.various enzymic systems, such as nitrite reductase, sulfite reductase and glutathione reductase, have been proposed for, or suspected to be involved in, the reduction of selenite in bacteria. as alphaproteobacteria have been shown to be highly tolerant to transition metal oxyanions, it seemed interesting to investigate the hypothetical involvement of these different enzymes in the reduction of selenite in the purple non-sulfur bacteria rhodospirillum rubrum and rhodobacter capsulatus. the hypoth ...200616514153
a hybrid of the transhydrogenases from rhodospirillum rubrum and mycobacterium tuberculosis catalyses rapid hydride transfer but not the complete, proton-translocating reaction.all transhydrogenases appear to have three components: di, which binds nad(h), and diii, which binds nadp(h), protrude from the membrane, and dii spans the membrane. however, the polypeptide composition of the enzymes varies amongst species. the transhydrogenases of mycobacterium tuberculosis and of rhodospirillum rubrum have three polypeptides. sequence analysis indicates that an ancestral three-polypeptide enzyme evolved into transhydrogenases with either two polypeptides (such as the escheric ...200616624251
the role of invariant amino acid residues at the hydride transfer site of proton-translocating transhydrogenase.transhydrogenase couples proton translocation across a membrane to hydride transfer between nadh and nadp+. previous x-ray structures of complexes of the nucleotide-binding components of transhydrogenase ("di2diii1" complexes) indicate that the dihydronicotinamide ring of nadh can move from a distal position relative to the nicotinamide ring of nadp+ to a proximal position. the movement might be responsible for gating hydride transfer during proton translocation. we have mutated three invariant ...200616533815
self-assembled monolayer of light-harvesting core complexes of photosynthetic bacteria on an amino-terminated ito electrode.light-harvesting antenna core (lh1-rc) complexes isolated from rhodospirillum rubrum and rhodopseudomonas palustris were successfully self-assembled on an ito electrode modified with 3-aminopropyltriethoxysilane. near infra-red (nir) absorption, fluorescence, and ir spectra of these lh1-rc complexes indicated that these lh1-rc complexes on the electrode were stable on the electrode. an efficient energy transfer and photocurrent responses of these lh1-rc complexes on the electrode were observed u ...200617111238
co-dependent h2 evolution by rhodospirillum rubrum: role of codh:coof complex.upon exposure to co during anaerobic growth, the purple phototrophic bacterium rhodospirillum rubrum expresses a co-oxidizing h(2) evolving enzymatic system. the co-oxidizing enzyme, carbon monoxide dehydrogenase (codh), has been purified and extensively characterized. however the electron transfer pathway from codh to the co-induced hydrogenase that evolves h(2) is not well understood. coof is an fe-s protein that is the proposed mediator of electron transfer between codh and the co-induced hyd ...200617123462
analysis of ancient sequence motifs in the h-ppase family.the unique family of membrane-bound proton-pumping inorganic pyrophosphatases, involving pyrophosphate as the alternative to atp, was investigated by characterizing 166 members of the uniprotkb/swiss-prot + uniprotkb/trembl databases and available completed genomes, using sequence comparisons and a hidden markov model based upon a conserved 57-residue region in the loop between transmembrane segments 5 and 6. the hidden markov model was also used to search the approximately one million sequences ...200617054711
dynamics and diffusion in photosynthetic membranes from rhodospirillum photometricum.photosynthetic organisms drive their metabolism by converting light energy into an electrochemical gradient with high efficiency. this conversion depends on the diffusion of quinones within the membrane. in purple photosynthetic bacteria, quinones reduced by the reaction center (rc) diffuse to the cytochrome bc(1) complex and then return once reoxidized to the rc. in rhodospirillum photometricum the rc-containing core complexes are found in a disordered molecular environment, with fixed light-ha ...200616950840
isotopic labeling of proteins by utilizing photosynthetic bacteria. 200516259936
new insights into the mechanism of nickel insertion into carbon monoxide dehydrogenase: analysis of rhodospirillum rubrum carbon monoxide dehydrogenase variants with substituted ligands to the [fe3s4] portion of the active-site c-cluster.carbon monoxide dehydrogenase (codh) from rhodospirillum rubrum catalyzes the oxidation of co to co2. a unique [nife4s4] cluster, known as the c-cluster, constitutes the active site of the enzyme. when grown in ni-deficient medium r. rubrum accumulates a ni-deficient apo form of codh that is readily activated by ni. it has been previously shown that activation of apo-codh by ni is a two-step process involving the rapid formation of an inactive apo-codh*ni complex prior to conversion to the activ ...200516283394
the puhb protein of rhodobacter capsulatus functions in photosynthetic reaction center assembly with a secondary effect on light-harvesting complex 1.the core of the photosynthetic apparatus of purple photosynthetic bacteria such as rhodobacter capsulatus consists of a reaction center (rc) intimately associated with light-harvesting complex 1 (lh1) and the pufx polypeptide. the abundance of the rc and lh1 components was previously shown to depend on the product of the puhb gene (formerly known as orf214). we report here that disruption of puhb diminishes rc assembly, with an indirect effect on lh1 assembly, and reduces the amount of pufx. und ...200515687197
dual roles of an e-helix residue, glu167, in the transcriptional activator function of cooa.cooa is a transcriptional activator that mediates co-dependent expression of the genes responsible for co oxidation in rhodospirillum rubrum. in this study, we suggest in vitro and in vivo models explaining an unusual requirement of cooa for millimolar levels of divalent cations for high-affinity dna binding. several lines of evidence indicate that an e-helix residue, glu167, plays a central role in this requirement by inhibiting sequence-specific dna binding via charge repulsion in the absence ...200515805503
the presumptive magnetosome protein mms16 is a poly(3-hydroxybutyrate) granule-bound protein (phasin) in magnetospirillum gryphiswaldense.the mms16 protein has been previously found to be associated with isolated magnetosomes from two magnetospirillum strains. a function of this protein as a magnetosome-specific gtpase involved in the formation of intracellular magnetosome membrane vesicles was suggested. here we present a study of the mms16 protein from magnetospirillum gryphiswaldense to clarify its function. insertion-duplication mutagenesis of the mms16 gene did not affect the formation of magnetosome particles but resulted in ...200515774885
spectroscopic and redox properties of a cooa homologue from carboxydothermus hydrogenoformans.cooa is a co-sensing transcriptional activator that contains a b-type heme as the active site for sensing its physiological effector, co. in this study, the spectroscopic and redox properties of a new cooa homologue from carboxydothermus hydrogenoformans (ch-cooa) were studied. spectroscopic and mutagenesis studies revealed that his-82 and the n-terminal alpha-amino group were the axial ligands of the fe(iii) and fe(ii) hemes in ch-cooa and that the n-terminal alpha-amino group was replaced by c ...200515537640
whole-genome shotgun optical mapping of rhodospirillum rubrum.rhodospirillum rubrum is a phototrophic purple nonsulfur bacterium known for its unique and well-studied nitrogen fixation and carbon monoxide oxidation systems and as a source of hydrogen and biodegradable plastic production. to better understand this organism and to facilitate assembly of its sequence, three whole-genome restriction endonuclease maps (xbai, nhei, and hindiii) of r. rubrum strain atcc 11170 were created by optical mapping. optical mapping is a system for creating whole-genome o ...200516151144
x-ray structure of domain i of the proton-pumping membrane protein transhydrogenase from escherichia coli.the dimeric integral membrane protein nicotinamide nucleotide transhydrogenase is required for cellular regeneration of nadph in mitochondria and prokaryotes, for detoxification and biosynthesis purposes. under physiological conditions, transhydrogenase couples the reversible reduction of nadp+ by nadh to an inward proton translocation across the membrane. here, we present crystal structures of the nad(h)-binding domain i of transhydrogenase from escherichia coli, in the absence as well as in th ...200516083909
multivariate analysis of single-molecule spectra: surpassing spectral diffusion.the full exploitation of single-molecule spectroscopy in disordered systems is often hampered by spectral diffusion processes of the optical transitions due to structural fluctuations in the local environment of the probe molecule which leads to temporal averaging of the signal. multivariate statistical pattern recognition techniques, originally developed for single-molecule cryoelectron microscopy, allow us to retrieve detailed information from optical single-molecule spectra. as an example, we ...200516090183
cooa, a paradigm for gas sensing regulatory proteins.the heme-containing transcriptional factor cooa regulates the expression of genes involved in the oxidation of carbon monoxide (co) in the bacterium rhodospirillum rubrum. cooa is both a redox sensor and a specific co sensor, a combination of properties that is unique among heme proteins. extensive biochemical and genetic analyses, interpreted in the context of a crystal structure of one form of the protein, have allowed the creation of hypotheses concerning the mechanism of cooa activation by c ...200515598507
glnd is essential for nifa activation, ntrb/ntrc-regulated gene expression, and posttranslational regulation of nitrogenase activity in the photosynthetic, nitrogen-fixing bacterium rhodospirillum rubrum.glnd is a bifunctional uridylyltransferase/uridylyl-removing enzyme and is thought to be the primary sensor of nitrogen status in the cell. it plays an important role in nitrogen assimilation and metabolism by reversibly regulating the modification of p(ii) proteins, which in turn regulate a variety of other proteins. we report here the characterization of glnd mutants from the photosynthetic, nitrogen-fixing bacterium rhodospirillum rubrum and the analysis of the roles of glnd in the regulation ...200515687189
l-malyl-coenzyme a/beta-methylmalyl-coenzyme a lyase is involved in acetate assimilation of the isocitrate lyase-negative bacterium rhodobacter capsulatus.cell extracts of rhodobacter capsulatus grown on acetate contained an apparent malate synthase activity but lacked isocitrate lyase activity. therefore, r. capsulatus cannot use the glyoxylate cycle for acetate assimilation, and a different pathway must exist. it is shown that the apparent malate synthase activity is due to the combination of a malyl-coenzyme a (coa) lyase and a malyl-coa-hydrolyzing enzyme. malyl-coa lyase activity was 20-fold up-regulated in acetate-grown cells versus glucose- ...200515687206
no evidence for a forced-unfolding mechanism during atp/groes binding to substrate-bound groel: no observable protection of metastable rubisco intermediate or groel-bound rubisco from tritium exchange.in tritium-hydrogen exchange experiments, the large groel substrate rubisco was unfolded and exchanged in urea/acid/tritiated water, then diluted into either protic buffer or protic buffer containing groel. the respective rubisco metastable folding intermediate or rubisco-groel binary complex was then separated from residual tritium after varying times of exchange by centrifugation through p-10 or g-25 resin. no significant tritium was recovered in either case, in contrast to an earlier report. ...200515710410
a che-like signal transduction cascade involved in controlling flagella biosynthesis in rhodospirillum centenum.rhodospirillum centenum is a photosynthetic bacterium capable of undergoing swim cell to swarm cell differentiation that allows this species to be motile on both liquid and solid media. previous experiments have demonstrated that the che1 operon is required for the control of chemotactic and phototactic behaviour of both swim and swarm cells. in this report, we analyse the function of a second che-like gene cluster in r. centenum, the che2 gene cluster. in-frame deletion mutants of chew2, cheb2, ...200515720548
solution structures of the core light-harvesting alpha and beta polypeptides from rhodospirillum rubrum: implications for the pigment-protein and protein-protein interactions.we have determined the solution structures of the core light-harvesting (lh1) alpha and beta-polypeptides from wild-type purple photosynthetic bacterium rhodospirillum rubrum using multidimensional nmr spectroscopy. the two polypeptides form stable alpha helices in organic solution. the structure of alpha-polypeptide consists of a long helix of 32 amino acid residues over the central transmembrane domain and a short helical segment at the n terminus that is followed by a three-residue loop. pigm ...200515740753
fluorescence microscopical investigation of poly(3-hydroxybutyrate) granule formation in bacteria.the early stages of poly(3-hydroxybutyrate) (phb) accumulation were analyzed in vivo by fluorescence microscopy in rhodospirillum rubrum, ralstonia eutropha, and in recombinant escherichia coli harboring the phb biosynthesis genes phacab of r. eutropha. phb granules were stained with nile red and by expression of a phasin-enhanced yellow fluorescent protein fusion protein. distribution of phb granules at the early stages of phb accumulation frequently occurred near the cell poles and near the ce ...200515762619
near-ir absorption and fluorescence spectra and afm observation of the light-harvesting 1 complex on a mica substrate refolded from the subunit light-harvesting 1 complexes of photosynthetic bacteria rhodospirillum rubrum.the subunit light-harvesting 1 (lh 1) complexes isolated from photosynthetic bacteria rhodospirillum rubrum using n-octyl-beta-glucoside were reassociated and adsorbed on a mica substrate using spin-coat methods with the aim of using this lh complex in a nanodevice. the near-ir absorption and fluorescence spectra of the lh 1 complexes indicated that the lh 1 complex on the mica was stable, and efficient energy transfer from a carotenoid to a bacteriochlorophyll a was observed. atomic force micro ...200515779986
trapping of an assembly intermediate of photosynthetic lh1 antenna beyond b820 subunit. significance for the assembly of photosynthetic lh1 antenna.most photosynthetic lh1 antennae undergo dissociation into b820 subunits, suggesting their universal character as structural modules. however, dissociation into subunits seems to occur reversibly only in the absence of carotenoids and the subunits were never found to bind carotenoids. the interactions of carotenoids with b820 have been studied in a newly developed reconstitution assay of the lh1 antenna from rhodospirillum rubrum (fiedor, l., akahane, j., and koyama, y. (2004) biochemistry 43, 1 ...200515788392
electron transport to nitrogenase in rhodospirillum rubrum: identification of a new fdxn gene encoding the primary electron donor to nitrogenase.in our efforts to determine the components participating in the electron transport to nitrogenase in rhodospirillum rubrum, we have identified a gene encoding a new ferredoxin. we have generated mutants in both the new ferredoxin and ferredoxin i and demonstrate that the new ferredoxin, fdn and not the previously identified fdi is the main donor of electrons to nitrogenase.200515837392
zinc ions selectively inhibit steps associated with binding and release of nadp(h) during turnover of proton-translocating transhydrogenase.transhydrogenase couples the redox reaction between nad(h) and nadp(h) to proton translocation across a membrane. in membrane vesicles from escherichia coli and rhodospirillum rubrum, the transhydrogenase reaction (measured in the direction driving inward proton translocation) was inhibited by zn(2+) and cd(2+). however, depending on ph, the metal ions either had no effect on, or stimulated, "cyclic" transhydrogenation. they must, therefore, interfere specifically with steps involving binding/re ...200515878164
involvement of a che-like signal transduction cascade in regulating cyst cell development in rhodospirillum centenum.homologues of the e. coli chemotaxis (che) signal transduction pathway are present in nearly all motile bacteria. although e. coli contains only one che cascade, many other bacteria are known to possess multiple sets of che genes. the role of multiple che-like gene clusters could potentially code for parallel che-like signal transduction pathways that have distinctly different input and output functions. in this study, we describe a che-like gene cluster in rhodospirillum centenum that controls ...200515916598
watching the components of photosynthetic bacterial membranes and their in situ organisation by atomic force microscopy.the atomic force microscope has developed into a powerful tool in structural biology allowing information to be acquired at submolecular resolution on the protruding structures of membrane proteins. it is now a complementary technique to x-ray crystallography and electron microscopy for structure determination of individual membrane proteins after extraction, purification and reconstitution into lipid bilayers. moving on from the structures of individual components of biological membranes, atomi ...200515919049
tributyl phosphate degradation by rhodopseudomonas palustris and other photosynthetic bacteria.tributyl phosphate (tbp) is widely used in nuclear fuel processing and other waste generating chemical industries. although tbp is bacteriostatic, some microbes are resistant to it and may degrade it. under dark aerobiosis, purple non-sulfur photosynthetic bacteria degraded up to 0.6 mm tbp, initially present at 2 mm, within 3 weeks and under photosynthetic conditions, rhodopseudomonas palustris degraded 1.6 mm tbp within 3 weeks. the curing of the rhodopseudomonas palustris endogenous plasmid d ...200515973490
chromatic adaptation of photosynthetic membranes.many biological membranes adapt in response to environmental conditions. we investigated how the composition and architecture of photosynthetic membranes of a bacterium change in response to light, using atomic force microscopy. despite large modifications in the membrane composition, the local environment of core complexes remained unaltered, whereas specialized paracrystalline light-harvesting antenna domains grew under low-light conditions. thus, the protein mixture in the membrane shows eute ...200516020739
detecting proton flux across chromatophores driven by f0f1-atpase using n-(fluorescein-5-thiocarbamoyl)-1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine, triethylammonium salt.n-(fluorescein-5-thiocarbamoyl)-1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine, triethylammonium salt (f-dhpe) is a lipid fluorescence dye sensitive to ph changes and is used in this study for detecting proton flux through f0f1-atpase within chromatophores driven by atp hydrolysis. f-dhpe is easily labeled to the outer surface of chromatophores. in the range of ph 7.0 to 9.0, fluorescence intensity is sensitive to ph changes. the sensitivity is especially great in the range of ph 8.2 to 9.0 ...200516043113
defluvicoccus vanus gen. nov., sp. nov., a novel gram-negative coccus/coccobacillus in the 'alphaproteobacteria' from activated sludge.a novel gram-negative coccus/coccobacillus, strain ben 114(t), growing in tetrads, clusters or aggregates, was isolated from activated sludge by micromanipulation. 16s rrna gene sequence analysis revealed that it belonged to the 'alphaproteobacteria', with no close relatives among cultured bacterial isolates. on the basis of phylogenetic data, this organism is considered to belong to a new genus, defluvicoccus, represented by the species defluvicoccus vanus sp. nov., a name chosen because of the ...200516166717
heme-thiolate proteins.cytochrome p450 was the first hemoprotein found to have a thiolate anion as the axial ligand of the heme. several other heme-thiolate proteins, including nitric oxide synthase, were later found in animals, plants, and microorganisms. both cytochrome p450 and nitric oxide synthase, two major members of the heme-thiolate protein family, catalyze monooxygenase reactions, but the physiological functions of other heme-thiolate proteins are apparently highly diverse. chloroperoxidase of a mold, caldar ...200516198303
the pufx protein of rhodobacter capsulatus affects the properties of bacteriochlorophyll a and carotenoid pigments of light-harvesting complex 1.a pufx gene deletion in the purple bacterium rhodobacter capsulatus causes a severe photosynthetic defect and increases core light-harvesting complex (lh1) protein and bacteriochlorophyll a (bchl) levels. it was suggested that pufx interrupts the lh1 alpha/beta ring around the reaction centre, allowing quinone/quinol exchange. however, naturally pufx(-) purple bacteria grow photosynthetically with an uninterrupted lh1. we discovered that substitutions of the rhodobacter-specific lh1 alpha seryl- ...200516212932
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