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the activator of the rhodospirillum rubrum phb depolymerase is a polypeptide that is extremely resistant to high temperature (121 degrees c) and other physical or chemical stresses.hydrolysis of native (amorphous) polyhydroxybutyrate (nphb) granules isolated from different sources by soluble phb depolymerase of rhodospirillum rubrum in vitro requires the presence of a heat-stable compound (activator). the activator was purified and was resistant against various physical and chemical stresses such as heat (up to 130 degrees c), ph 1-12, dryness, oxidation by h2o2, reducing and denaturing compounds (2-mercaptoethanol, 5 m guanidinium-hcl) and many solvents including phenol/c ...200414757249
characterization of cyst cell formation in the purple photosynthetic bacterium rhodospirillum centenum.rhodospirillum centenum is an anoxygenic photosynthetic bacterium that is capable of differentiating into several cell types. when grown phototrophically in liquid, cells exhibit a vibrioid shape and have a single polar flagellum. when grown on a solid surface, r. centenum will differentiate into rod-shaped swarm cells that display numerous lateral flagella. upon starvation for nutrients, r. centenum also forms desiccation-resistant cysts. in this study, it was determined that r. centenum has he ...200414766916
carbon monoxide dehydrogenase from rhodospirillum rubrum: effect of redox potential on catalysis.the ni-fe-s-containing c-cluster of carbon monoxide dehydrogenases is the active site for catalyzing the reversible oxidation of co to co(2). this cluster can be stabilized in redox states designated c(ox), c(red1), c(int), and c(red2). what had until recently been the best-supported mechanism of catalysis involves a one-electron reductive activation of c(ox) to c(red1) and a catalytic cycle in which the c(red1) state binds and oxidizes co, forming c(red2) and releasing co(2). recent experiments ...200414769031
[an oligonucleotide primer system for amplification of the ribulose-1,5-bisphosphate carboxylase/oxygenase genes of bacteria of various taxonomic groups].based on the analysis of genbank nucleotide sequences of the cbbl and cbbm genes, coding for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (rubpc), the key enzyme of the calvin cycle, a primer system was designed that allows about 800-bp-long fragments of these genes to be pcr-ampliflied in various photo- and chemotrophic bacteria. the efficiency of the designed primer system in detection of rubpc genes was demonstrated in pcr with dna of taxonomically diverse bacteria pos ...200415315232
the reaction center h subunit is not required for high levels of light-harvesting complex 1 in rhodospirillum rubrum mutants.the gene (puha) encoding the h subunit of the reaction center (rc) was deleted by site-directed interposon mutagenesis by using a kanamycin resistance cassette lacking transcriptional terminators to eliminate polar effects in both the wild-type strain rhodospirillum rubrum s1 and the carotenoid-less strain r. rubrum g9. the puha interposon mutants were incapable of photoheterotrophic growth but grew normally under aerobic chemoheterotrophic conditions. absorption spectroscopy and sodium dodecyl ...200415317762
hypercyst mutants in rhodospirillum centenum identify regulatory loci involved in cyst cell differentiation.rhodospirillum centenum is a purple photosynthetic bacterium that forms resting cyst cells when starved for nutrients. in this study, we demonstrate that chalcone synthase gene (chsa) expression is developmentally regulated, with expression of chsa increasing up to 86-fold upon induction of the cyst developmental cycle. screening for mini-tn5-induced mutants that exhibit elevated chsa::lacz expression has led to the isolation of a set of r. centenum mutants that display increased chsa gene expre ...200415317789
active-site conformational changes associated with hydride transfer in proton-translocating transhydrogenase.transhydrogenase couples the redox (hydride-transfer) reaction between nad(h) and nadp(h) to proton translocation across a membrane. the redox reaction is catalyzed at the interface between two components (di and diii) which protrude from the membrane. a complex formed from recombinant di and diii (the di(2)diii(1) complex) from rhodospirillum rubrum transhydrogenase catalyzes fast single-turnover hydride transfer between bound nucleotides. in this report we describe three new crystal structures ...200415323555
circular dichroism of carotenoids in bacterial light-harvesting complexes: experiments and modeling.in this work we investigate the origin and characteristics of the circular dichroism (cd) spectrum of rhodopin glucoside and lycopene in the light-harvesting 2 complex of rhodopseudomonas acidophila and rhodospirillum molischianum, respectively. we successfully model their absorption and cd spectra based on the high-resolution structures. we assume that these spectra originate from seven interacting transition dipole moments: the first corresponds to the 0-0 transition of the carotenoid, whereas ...200415326029
the c-helix in cooa rolls upon co binding to ferrous heme.cooa is a homodimeric transcriptional activator from rhodospirillum rubrum containing one heme in each subunit. co binding to the heme in its sensor domain activates cooa, facilitating the binding to dna by its dna-binding domain. the c-helix links the two domains and shapes an interface between the subunits. to probe the nature of co activation, residues at positions 112-121 on the c-helix were replaced by asn or gln and their effects were evaluated by resonance raman spectroscopy and by the me ...200415326178
changing the ligand specificity of cooa, a highly specific heme-based co sensor.the co-specific heme-based sensor cooa regulates the ability of rhodospirillum rubrum to grow on co as an energy source. only co triggers the conformational change of cooa essential for the protein to function as a transcriptional activator. a structurally informed mutagenesis, followed by an in vivo screening method, allowed the isolation of a series of novel cooa variants that show very substantial response to imidazole. compared with wild-type cooa, the ligand selectivity between imidazole an ...200415326187
co-sensing mechanisms.carbon monoxide (co) has long been known to have dramatic physiological effects on organisms ranging from bacteria to humans, but recently there have a number of suggestions that organisms might have specific sensors for co. this article reviews the current evidence for a variety of proteins with demonstrated or potential co-sensing ability. particular emphasis is placed on the molecular description of cooa, a heme-containing co sensor from rhodospirillum rubrum, since its biological role as a c ...200415353565
the h(+)-pyrophosphatase of rhodospirillum rubrum is predominantly located in polyphosphate-rich acidocalcisomes.acidocalcisomes are acidic, calcium storage compartments with a h(+) pump located in their membrane that have been described in several unicellular eukaryotes, including trypanosomatid and apicomplexan parasites, algae, and slime molds, and have also been found in the bacterium agrobacterium tumefaciens. in this work, we report that the h(+)-pyrophosphatase (h(+)-ppase) of rhodospirillum rubrum, the first enzyme of this type that was identified and thought to be localized only to chromatophore m ...200415371423
similarities between the abiotic reduction of selenite with glutathione and the dissimilatory reaction mediated by rhodospirillum rubrum and escherichia coli.various mechanisms have been proposed to explain the biological dissimilatory reduction of selenite (seo3(2-)) to elemental selenium (se(o)), although none is without controversy. glutathione, the most abundant thiol in the eukaryotic cells, the cyanobacteria, and the alpha, beta, and gamma groups of the proteobacteria, has long been suspected to be involved in selenium metabolism. experiments with the phototrophic alpha proteobacterium rhodospirillum rubrum showed that the rate of selenite redu ...200415371444
importance of rhodospirillum rubrum h(+)-pyrophosphatase under low-energy conditions.the physiological role of the membrane-bound pyrophosphatase of rhodospirillum rubrum was investigated by the characterization of a mutant strain. comparisons of growth levels between the wild type and the mutant under different low-potential conditions and during transitions between different metabolisms indicate that this enzyme provides r. rubrum with an alternative energy source that is important for growth in low-energy states.200415375148
observation of calcium-dependent unidirectional rotational motion in recombinant photosynthetic f1-atpase molecules.atp hydrolysis and synthesis by the f(0)f(1)-atp synthase are coupled to proton translocation across the membrane in the presence of magnesium. calcium is known, however, to disrupt this coupling in the photosynthetic enzyme in a unique way: it does not support atp synthesis, and caatp hydrolysis is decoupled from any proton translocation, but the membrane does not become leaky to protons. understanding the molecular basis of these calcium-dependent effects can shed light on the as yet unclear m ...200415377671
functional expression and characterization of a bacterial light-harvesting membrane protein in escherichia coli and cell-free synthesis systems.heterologous expression of a bacterial light-harvesting (lh) integral membrane protein was attempted using escherichia coli cells and cell-free synthesis systems prepared from e. coli extracts. the alpha-apoprotein of lh1 complex from purple photosynthetic bacterium rhodospirillum rubrum was overexpressed as a recombinant protein with a histidine (his6) tag added to the carboxyl terminus. both of the expression systems produced alpha-apoprotein in a fully functional form as can judged by its abi ...200415388971
characterization of altered regulation variants of dinitrogenase reductase-activating glycohydrolase from rhodospirillum rubrum.in rhodospirillum rubrum, nitrogenase activity is subject to posttranslational regulation through the adenosine diphosphate (adp)-ribosylation of dinitrogenase reductase by dinitrogenase reductase adp-ribosyltransferase (drat) and dinitrogenase reductase-activating glycohydrolase (drag). to study the posttranslational regulation of drag, its gene was mutagenized and colonies screened for altered drag regulation. three different mutants were found and the drag variants displayed different biochem ...200414960312
identification of critical residues in glnb for its activation of nifa activity in the photosynthetic bacterium rhodospirillum rubrum.the p(ii) regulatory protein family is unusually widely distributed, being found in all three domains of life. three p(ii) homologs called glnb, glnk, and glnj have been identified in the photosynthetic bacterium rhodospirillum rubrum. these have roles in at least four distinct functions, one of which is activation of the nitrogen fixation-specific regulatory protein nifa. the activation of nifa requires only the covalently modified (uridylylated) form of glnb. glnk and glnj are not involved. ho ...200414970346
functionally critical elements of cooa-related co sensors.cooa is a heme-containing transcriptional activator that enables rhodospirillum rubrum to sense and grow on co as a sole energy source. we have identified a number of cooa homologs through database searches, expressed these heterologously in escherichia coli, and monitored their ability to respond to co in vivo. further in vitro analysis of two cooa homologs from azotobacter vinelandii and carboxydothermus hydrogenoformans corroborated the in vivo data by revealing the ability of co to bind to t ...200414973040
dynamics of carbon monoxide binding to cooa.cooa is a dimeric co-sensing heme protein from rhodospirillum rubrum. the heme iron in reduced cooa is six-coordinate; the axial ligands are his-77 and pro-2. co displaces pro-2 and induces a conformation change that allows cooa to bind dna and activate transcription of coo genes. equilibrium co binding is cooperative, with a hill coefficient of n = 1.4, p(50) = 2.2 microm, and estimated adair constants k(1) = 0.16 and k(2) = 1.3 microm(-1). the rates of co binding and release are both strongly ...200414990568
flexibility and size heterogeneity of the lh1 light harvesting complex revealed by atomic force microscopy: functional significance for bacterial photosynthesis.previous electron microscopic studies of bacterial rclh1 complexes demonstrated both circular and elliptical conformations of the lh1 ring, and this implied flexibility has been suggested to allow passage of quinol from the q(b) site of the rc to the quinone pool prior to reduction of the cytochrome bc(1) complex. we have used atomic force microscopy to demonstrate that these are just two of many conformations for the lh1 ring, which displays large molecule-to-molecule variations, in terms of bo ...200414993213
roles of heme axial ligands in the regulation of co binding to cooa.cooa is a co-dependent transcription factor of the bacterium rhodospirillum rubrum that contains a six-coordinate heme. it has as its heme axial ligands pro(2) and cys(75) in the ferric state and pro(2) and his(77) in the ferrous state. to probe the regulation of co binding and the ligand switching mechanism in cooa, we have prepared site-directed mutants in which the residues contributing the axial ligands are substituted. the properties of these mutants were investigated by resonance raman and ...200415026411
the fixabcx genes in rhodospirillum rubrum encode a putative membrane complex participating in electron transfer to nitrogenase.in our efforts to identify the components participating in electron transport to nitrogenase in rhodospirillum rubrum, we used mini-tn5 mutagenesis followed by metronidazole selection. one of the mutants isolated, snt-1, exhibited a decreased growth rate and about 25% of the in vivo nitrogenase activity compared to the wild-type values. the in vitro nitrogenase activity was essentially wild type, indicating that the mutation affects electron transport to nitrogenase. sequencing showed that the t ...200415028689
unraveling the function of the rhodospirillum rubrum activator of polyhydroxybutyrate (phb) degradation: the activator is a phb-granule-bound protein (phasin).efficient hydrolysis of native poly(3-hydroxybutyrate) (nphb) granules in vitro by soluble phb depolymerase of rhodospirillum rubrum requires pretreatment of nphb with an activator compound present in r. rubrum cells (j. m. merrick and m. doudoroff, j. bacteriol. 88:60-71, 1964). edman sequencing of the purified activator (17.4 kda; matrix-assisted laser desorption ionization-time of flight mass spectrometry) revealed identity to a hypothetical protein deduced from a partially sequenced r. rubru ...200415060050
low-lying excited states of light-harvesting system ii in purple bacteria.the low-lying excited states of a b850 ring of rhodospirillum (rs.) molischianum are determined accurately by a semiempirical indo/s method. results obtained are found to fit extremely well with a frenkel exciton model with long-range dipolar interactions, and the spatial size of the electron-hole pair is confirmed to fall predominantly within one bacteriochlorophyll with a small leakage to its nearest neighbors. more importantly, the nearest neighbor exciton coupling constants are found to be c ...200415089341
elucidating the role of conserved glutamates in h+-pyrophosphatase of rhodospirillum rubrum.h(+)-pyrophosphatase (h(+)-ppase) catalyzes pyrophosphate-driven proton transport against the electrochemical potential gradient in various biological membranes. all 50 of the known h(+)-ppase amino acid sequences contain four invariant glutamate residues. in this study, we use site-directed mutagenesis in conjunction with functional studies to determine the roles of the glutamate residues glu(197), glu(202), glu(550), and glu(649) in the h(+)-ppase of rhodospirillum rubrum (r-ppase). all residu ...200415107429
carbon monoxide induced decomposition of the active site [ni-4fe-5s] cluster of co dehydrogenase.during the past two years, crystal structures of cu- and mo-containing carbon monoxide dehydrogenases (codhs) and ni- and fe-containing codhs have been reported. the active site of codhs from anaerobic bacteria (cluster c) is composed of ni, fe, and s for which crystallographic studies of the enzymes from carboxydothermus hydrogenoformans, rhodospirillum rubrum, and moorella thermoaceticarevealed structural similarities in the overall protein fold but showed substantial differences in the essent ...200415113209
initial structure modification of tetrahedral to planar nickel(ii) in a nickel-iron-sulfur cluster related to the c-cluster of carbon monoxide dehydrogenase.a method has been devised that creates a planar ni(ii) site from a tetrahedral site in a nife(3)s(4) cubane-type cluster. reaction of [(ph(3)p)nife(3)s(4)(ls(3))](2)(-) (2) with 1,2-bis(dimethylphosphino)ethane affords [(dmpe)nife(3)s(4)(ls(3))](2)(-) (3), isolated in ca. 45% yield as (et(4)n)(2)[3a].2.5mecn and (et(4)n)(2)[3b].0.25mecn, both of which occur in triclinic space group p. each crystalline form contains two crystallographically inequivalent clusters with the same overall structure bu ...200415149242
a genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes.analyses of 55 individual and 31 concatenated protein data sets encoded in reclinomonas americana and marchantia polymorpha mitochondrial genomes revealed that current methods for constructing phylogenetic trees are insufficiently sensitive (or artifact-insensitive) to ascertain the sister of mitochondria among the current sample of eight alpha-proteobacterial genomes using mitochondrially-encoded proteins. however, rhodospirillum rubrum came as close to mitochondria as any alpha-proteobacterium ...200415155797
interactions stabilizing the structure of the core light-harvesting complex (lh1) of photosynthetic bacteria and its subunit (b820).reconstitution experiments with a chemically synthesized core light-harvesting (lh1) beta-polypeptide analogue having 3-methylhistidine instead of histidine in the position that normally donates the coordinating ligand to bacteriochlorophyll (bchl) have provided the experimental data needed to assign to b820 one of the two possible alphabeta.2bchl pairs that are observed in the crystal structure of lh2 from phaeospirillum (formerly rhodospirillum) molischianum, the one with rings iii and v of bc ...200415170338
dual flagellar systems enable motility under different circumstances.flagella are extremely effective organelles of locomotion used by a variety of bacteria and archaea. some bacteria, including aeromonas, azospirillum, rhodospirillum, and vibrio species, possess dual flagellar systems that are suited for movement under different circumstances. swimming in liquid is promoted by a single polar flagellum. swarming over surfaces or in viscous environments is enabled by the production of numerous peritrichous, or lateral, flagella. the polar flagellum is produced con ...200415170400
inhibition studies on rhodospirillum rubrum h(+)-pyrophosphatase expressed in escherichia coli.the membrane-bound proton-pumping inorganic pyrophosphatase from rhodospirillum rubrum was heterologously expressed in escherichia coli c43(de3) cells and was inhibited by 4-bromophenacyl bromide (bpb), n,n'-dicyclohexylcarbodiimid (dccd), diethyl pyrocarbonate (depc) and fluorescein 5'-isothiocyanate (fitc). in each case, the enzyme activity was rather well protected against inhibitory action by the substrate mg(2)ppi. site-directed mutagenesis was employed in attempts to identify target residu ...200415178477
the structure and function of bacterial light-harvesting complexes.the harvesting of solar radiation by purple photosynthetic bacteria is achieved by circular, integral membrane pigment-protein complexes. there are two main types of light-harvesting complex, termed lh2 and lh1, that function to absorb light energy and to transfer that energy rapidly and efficiently to the photochemical reaction centres where it is trapped. this mini-review describes our present understanding of the structure and function of the purple bacterial light-harvesting complexes.200415204626
the nitrogen-fixing gene (nifh) of rhodopseudomonas palustris: a case of lateral gene transfer?nitrogen fixation is catalysed by some photosynthetic bacteria. this paper presents a phylogenetic comparison of a nitrogen fixation gene (nifh) with the aim of elucidating the processes underlying the evolutionary history of rhodopseudomonas palustris. in the nifh phylogeny, strains of rps. palustris were placed in close association with rhodobacter spp. and other phototrophic purple non-sulfur bacteria belonging to the alpha-proteobacteria, separated from its close relatives bradyrhizobium jap ...200415256566
effect of sodium sulfide on ni-containing carbon monoxide dehydrogenases.the structure of the active-site c-cluster in co dehydrogenase from carboxydothermus hydrogenoformans includes a mu(2)-sulfide ion bridged to the ni and unique fe, whereas the same cluster in enzymes from rhodospirillum rubrum (codh(rr)) and moorella thermoacetica (codh(mt)) lack this ion. this difference was investigated by exploring the effects of sodium sulfide on activity and spectral properties. sulfide partially inhibited the co oxidation activity of codh(rr) and generated a lag prior to s ...200415264843
watching the photosynthetic apparatus in native membranes.over the last 9 years, the structures of the various components of the bacterial photosynthetic apparatus or their homologues have been determined by x-ray crystallography to at least 4.8-a resolution. despite this wealth of structural information on the individual proteins, there remains an urgent need to examine the architecture of the photosynthetic apparatus in intact photosynthetic membranes. information on the arrangement of the different complexes in a native system will help us to unders ...200415273291
oxygen-dependent h2o2 production by rubisco.oxygen and ribulose-1,5-bisphosphate dependent, h(2)o(2) production was observed with several wild type rubisco enzymes using a sensitive assay. h(2)o(2) and d-glycero-2,3-pentodiulose-1,5-bisphosphate, a known and potent inhibitor of rubisco activity, are predicted products arising from elimination of h(2)o(2) from a peroxyketone intermediate, specific to oxygenase activity. parallel assays using varying co(2) and o(2) concentrations revealed that the partitioning to h(2)o(2) during o(2) consum ...200415280029
activation mechanisms of transcriptional regulator cooa revealed by small-angle x-ray scattering.cooa, a heme-containing transcriptional activator, binds co to the heme moiety and then undergoes a structural change that promotes the specific binding to the target dna. to elucidate the activation mechanism coupled to co binding, we investigated the co-dependent structural transition of cooa with small-angle x-ray scattering (saxs). in the absence of co, the radius of gyration rg and the second virial coefficient (a2) were 25.3(+/-0.5)a and -0.39(+/-0.25) x 10(-4)ml mol g(-2), respectively. c ...200415288777
differential regulation of soluble and membrane-bound inorganic pyrophosphatases in the photosynthetic bacterium rhodospirillum rubrum provides insights into pyrophosphate-based stress bioenergetics.soluble and membrane-bound inorganic pyrophosphatases (sppase and h(+)-ppase, respectively) of the purple nonsulfur bacterium rhodospirillum rubrum are differentially regulated by environmental growth conditions. both proteins and their transcripts were found in cells of anaerobic phototrophic batch cultures along all growth phases, although they displayed different time patterns. however, in aerobic cells that grow in the dark, which exhibited the highest growth rates, northern and western blot ...200415292143
carotenoid-induced cooperative formation of bacterial photosynthetic lh1 complex.a simple reconstitution technique has been developed and then applied to prepare a series of light-harvesting antenna 1 (lh1) complexes with a programmed carotenoid composition, not available from native photosynthetic membranes. the complexes were reconstituted with different c(40) carotenoids, having two structural parameters variable: the functional side groups and the number of conjugated c-c double bonds, systematically increasing from 9 to 13. the complexes, differing only in the type of c ...200415610043
titration of e. coli transhydrogenase domain iii with bound nadp+ or nadph studied by nmr reveals no ph-dependent conformational change in the physiological ph range.a ph-titration 2d nmr study of escherichia coli transhydrogenase domain iii with bound nadp(+) or nadph has been carried out, in which the ph was varied between 5.4 and 12. in this analysis, individual amide protons served as reporter groups. the apparent pk(a) values of the amide protons, determined from the ph-dependent chemical shift changes, were attributed to actual pk(a) values for several titrating residues in the protein. the essential asp392 is shown to be protonated at neutral ph in bo ...200415863102
investigation of the role of the n-terminal proline, the distal heme ligand in the co sensor cooa.a unique feature of cooa, a heme-containing transcription factor, is that the n-terminal proline is the distal heme ligand in the ferrous state, and this ligand is displaced upon co binding. to investigate the importance of pro(2) in co-dependent dna binding, several cooa variants that alter n-terminal ligation were characterized. electronic absorption, electron paramagnetic resonance, and magnetic circular dichroism spectra of these variants provide the most definitive evidence that pro(2) is t ...200415518565
variable lh2 stoichiometry and core clustering in native membranes of rhodospirillum photometricum.the individual components of the photosynthetic unit (psu), the light-harvesting complexes (lh2 and lh1) and the reaction center (rc), are structurally and functionally known in great detail. an important current challenge is the study of their assembly within native membranes. here, we present afm topographs at 12 a resolution of native membranes containing all constituents of the psu from rhodospirillum photometricum. besides the major technical advance represented by the acquisition of such h ...200415457213
expansion and compression of a protein folding intermediate by groel.the groel-groes chaperonin system is required for the assisted folding of many essential proteins. the precise nature of this assistance remains unclear, however. here we show that denatured rubisco from rhodospirillum rubrum populates a stable, nonaggregating, and kinetically trapped monomeric state at low temperature. productive folding of this nonnative intermediate is fully dependent on groel, groes, and atp. reactivation of the trapped rubisco monomer proceeds through a series of groel-indu ...200415469819
the "intracellular" poly(3-hydroxybutyrate) (phb) depolymerase of rhodospirillum rubrum is a periplasm-located protein with specificity for native phb and with structural similarity to extracellular phb depolymerases.rhodospirillum rubrum possesses a putative intracellular poly(3-hydroxybutyrate) (phb) depolymerase system consisting of a soluble phb depolymerase, a heat-stable activator, and a 3-hydroxybutyrate dimer hydrolase (j. m. merrick and m. doudoroff, j. bacteriol. 88:60-71, 1964). in this study we reinvestigated the soluble r. rubrum phb depolymerase (phaz1). it turned out that phaz1 is a novel type of phb depolymerase with unique properties. purified phaz1 was specific for amorphous short-chain-len ...200415489436
conformational diversity in nad(h) and interacting transhydrogenase nicotinamide nucleotide binding domains.transhydrogenase (th) couples direct and stereospecific hydride transfer between nad(h) and nadp(h), bound within soluble domains i and iii, respectively, to proton translocation across membrane bound domain ii. the cocrystal structure of rhodospirillum rubrum th domains i and iii has been determined in the presence of limiting nadh, under conditions in which the subunits reach equilibrium during crystallization. the crystals contain three heterotrimeric complexes, di(2)diii, in the asymmetric u ...200415670609
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
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
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
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
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
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
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
fluorescence spectroscopy of conformational changes of single lh2 complexes.we have investigated the energy landscape of the bacterial photosynthetic peripheral light-harvesting complex lh2 of purple bacterium rhodopseudomonas acidophila by monitoring sequences of fluorescence spectra of single lh2 assemblies, at room temperature, with different excitation intensities as well as at elevated temperatures, utilizing a confocal microscope. the fluorescence peak wavelength of individual lh2 complexes was found to abruptly move between long-lived quasi-stable levels differin ...200515501944
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
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
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
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
[the mechanism of acetate assimilation in purple nonsulfur bacteria lacking the glyoxylate pathway: enzymes of the citramalate cycle in rhodobacter sphaeroides].the mechanism of acetate assimilation by the purple nonsulfur bacterium rhodobacter sphaeroides, which lacks the glyoxylate shortcut, has been studied. in a previous work, proceeding from data on acetate assimilation by rba. sphaeroides cell suspensions, a suggestion was made regarding the operation, in this bacterium, of the citramalate cycle. this cycle was earlier found in rhodospirillum rubrum in the form of an anaplerotic reaction sequence that operates during growth on acetate instead of t ...200516119844
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
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
nad-, nmn-, and nadp-dependent modification of dinitrogenase reductases from rhodospirillum rubrum and azotobacter vinelandii.nitrogenase activity in the photosynthetic bacterium rhodospirillum rubrum is reversibly regulated by adp-ribosylation of a specific arginine residue of dinitrogenase reductase based on the cellular nitrogen or energy status. in this paper, we have investigated the ability of nicotinamide adenine dinucleotide, nad (the physiological adp-ribose donor), and its analogs to support covalent modification of dinitrogenase reductase in vitro. r. rubrum dinitrogenase reductase can be modified by drat in ...200516225869
combined afm and confocal fluorescence microscope for applications in bio-nanotechnology.we present a custom-designed atomic force fluorescence microscope (affm), which can perform simultaneous optical and topographic measurements with single molecule sensitivity throughout the whole visible to near-infrared spectral region. integration of atomic force microscopy (afm) and confocal fluorescence microscopy combines the high-resolution topographical imaging of afm with the reliable (bio)-chemical identification capability of optical methods. the affm is equipped with a spectrograph en ...200515655068
reversible membrane association of dinitrogenase reductase activating glycohydrolase in the regulation of nitrogenase activity in rhodospirillum rubrum; dependence on glnj and amtb1.in the photosynthetic bacterium rhodospirillum rubrum nitrogenase activity is regulated by reversible adp-ribosylation of dinitrogenase reductase in response to external so called "switch-off" effectors. activation of the modified, inactive form is catalyzed by dinitrogenase reductase activating glycohydrolase (drag) which removes the adp-ribose moiety. this study addresses the signal transduction between external effectors and drag. r. rubrum, wild-type and p(ii) mutant strains, were studied wi ...200516243452
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
architecture of the native photosynthetic apparatus of phaeospirillum molischianum.the ubiquity and importance of photosynthetic organisms in nature has made the molecular mechanisms of photosynthesis a widely studied subject at both structural and functional levels. a current challenge is to understand the supramolecular assembly of the proteins involved in photosynthesis in native membranes. we have used atomic force microscopy to study the architecture of the photosynthetic apparatus and analyze the structure of single molecules in chromatophores of phaeospirillum molischia ...200516330228
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
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
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
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
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
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
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