Publications

a unified description of the electrochemical, charge distribution, and spectroscopic properties of the special-pair radical cation in bacterial photosynthesis.	we apply our four-state 70-vibration vibronic-coupling model for the properties of the photosynthetic special-pair radical cation to: (1) interpret the observed correlations between the midpoint potential and the distribution of spin density between the two bacteriochlorophylls for 30 mutants of rhodobacter sphaeroides, (2) interpret the observed average intervalence hole-transfer absorption energies as a function of spin density for six mutants, and (3) simulate the recently obtained intervalen ...	2004	15053603
effect of oxygen on temporary stabilization of photoreduced quinone acceptors in rhodobacter sphaeroides reaction centers.	the effect of molecular oxygen on the photochemical activity of the rhodobacter sphaeroides reaction centers frozen to 160 k under actinic illumination was investigated by the esr method. about 90% of initially photochemically active bacteriochlorophyll (p) were fixed at 160 k for a long time in aerobic samples in an inactive form. in anaerobic samples, not more than 65% were fixed in an inactive form under the same conditions. in aerobic preparations, a small portion of photochemically active b ...	2004	15061694
x-ray structure determination of three mutants of the bacterial photosynthetic reaction centers from rb. sphaeroides; altered proton transfer pathways.	in the photosynthetic reaction center (rc) from rhodobacter sphaeroides, the reduction of a bound quinone molecule q(b) is coupled with proton uptake. when asp-l213 is replaced by asn, proton transfer is inhibited. proton transfer was restored by two second-site revertant mutations, arg-m233-->cys and arg-h177-->his. kinetic effects of cd(2+) on proton transfer showed that the entry point in revertant rcs to be the same as in the native rc. the structures of the parental and two revertant rcs we ...	2004	15062092
the critical role of tryptophan-116 in the catalytic cycle of dimethylsulfoxide reductase from rhodobacter capsulatus.	in dimethylsulfoxide reductase of rhodobacter capsulatus tryptophan-116 forms a hydrogen bond with a single oxo ligand bound to the molybdenum ion. mutation of this residue to phenylalanine affected the uv/visible spectrum of the purified mo(vi) form of dimethylsulfoxide reductase resulting in the loss of the characteristic transition at 720 nm. results of steady-state kinetic analysis and electrochemical studies suggest that tryptophan 116 plays a critical role in stabilizing the hexacoordinate ...	2004	15063748
glycine 176 affects catalytic properties and stability of the synechococcus sp. strain pcc6301 ribulose-1,5-bisphosphate carboxylase/oxygenase.	a previously described system for biological selection of randomly mutagenized ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) employing the phototrophic bacterium rhodobacter capsulatus was used to select a catalytically altered form of a cyanobacterial (synechococcus sp. strain pcc6301) enzyme. this mutant rubisco, in which conserved glycine 176 was replaced with an aspartate residue, was not able to support co(2)-dependent growth of the host strain. site-directed mutant proteins wer ...	2004	15067012
enzymes and genes of taurine and isethionate dissimilation in paracoccus denitrificans.	growth of the alpha-proteobacterium paracoccus denitrificans nknis with taurine or isethionate as sole source of carbon involves sulfoacetaldehyde acetyltransferase (xsc), which is presumably encoded by an xsc gene in subgroup 3, none of whose gene products has been characterized. the genome of the alpha-proteobacterium rhodobacter sphaeroides 2.4.1 was interpreted to contain a nine-gene cluster encoding the inducible dissimilation of taurine, and this deduced pathway included a regulator, a tri ...	2004	15073291
characterization of the ph-dependent resonance raman transitions of archaeal and bacterial rieske [2fe-2s] proteins.	the ph-dependent resonance raman (rr) spectral changes of the cytochrome bc1-associated, high-potential rieske proteins have frequently been invoked to explain the redox-linked ionization behavior. we report herein rr spectral data of archaeal and bacterial rieske proteins that directly demonstrate the ph-dependent changes near and above pka,ox2, but not around pka,ox1, of the visible circular dichroism (cd) transitions. the rr spectral changes are attributed to modification of the immediate [2f ...	2004	15080677
formation of a semiquinone at the qb site by a- or b-branch electron transfer in the reaction center from rhodobacter sphaeroides.	in rhodobacter sphaeroides reaction centers containing the mutation ala m260 to trp (am260w), transmembrane electron transfer along the a-branch of cofactors is prevented by the loss of the qa ubiquinone. reaction centers that contain this am260w mutation are proposed to photoaccumulate the p(+)qb- radical pair following transmembrane electron transfer along the b-branch of cofactors (wakeham, m. c., goodwin, m. g., mckibbin, c., and jones, m. r. (2003) photoaccumulation of the p(+)qb- radical p ...	2004	15096044
novel cyanide inhibition at cytochrome c1 of rhodobacter capsulatus cytochrome bc1.	oxidized cytochrome c(1) in photosynthetic bacterium rhodobacter capsulatus cytochrome bc(1) reversibly binds cyanide with surprisingly high, micromolar affinity. the binding dramatically lowers the redox midpoint potential of heme c(1) and inhibits steady-state turnover activity of the enzyme. as cytochrome c(1), an auxiliary redox center of the high-potential chain of cytochrome bc(1), does not interact directly with the catalytic quinone/quinol binding sites q(o) and q(i), cyanide introduces ...	2004	15100019
proton-coupled electron transfer at the qo-site of the bc1 complex controls the rate of ubihydroquinone oxidation.	the rate-limiting reaction of the bc(1) complex from rhodobacter sphaeroides is transfer of the first electron from ubihydroquinone (quinol, qh(2)) to the [2fe-2s] cluster of the rieske iron-sulfur protein (isp) at the q(o)-site. formation of the es-complex requires participation of two substrates (s), qh(2) and isp(ox). from the variation of rate with [s], the binding constants for both substrates involved in formation of the complex can be estimated. the configuration of the es-complex likely ...	2004	15100020
modulation of the free energy of the primary quinone acceptor (qa) in reaction centers from rhodobacter sphaeroides: contributions from the protein and protein-lipid(cardiolipin) interactions.	the redox midpoint potential (e(m)) of q(a), the primary quinone of bacterial reaction centers, is substantially modulated by the protein environment. quite subtle mutations in the q(a) binding site, e.g., at residues m218, m252 and m265, cause significant increases in the equilibrium constant for electron transfer to q(b), which indicate relative lowering of the e(m) of q(a). however, reports of functional linkage between the q(a) and q(b) sites make it difficult to partition such effects betwe ...	2004	15100021
surface-mediated proton-transfer reactions in membrane-bound proteins.	as outlined by peter mitchell in the chemiosmotic theory, an intermediate in energy conversion in biological systems is a proton electrochemical potential difference ("proton gradient") across a membrane, generated by membrane-bound protein complexes. these protein complexes accommodate proton-transfer pathways through which protons are conducted. in this review, we focus specifically on the role of the protein-membrane surface and the surface-bulk water interface in the dynamics of proton deliv ...	2004	15100022
the use of stable isotopes and spectroscopy to investigate the energy transducing function of cytochrome c oxidase.	we have used epr and ftir spectroscopy in combination with (17)o and (15)n stable isotopes to investigate the mechanism of cytochrome c oxidase (cco). a high-spin state of heme a(3) was found in high yield by epr, achieved upon turning over the enzyme until it was anaerobic, and shown to be a mixture of heme with a coordinated oxygen-based ligand and five-coordinate heme. allowing the enzyme to consume (17)o(2) for a few milliseconds before freezing, we also showed that the product h(2)(17)o exi ...	2004	15100039
the influence of subunit iii of cytochrome c oxidase on the d pathway, the proton exit pathway and mechanism-based inactivation in subunit i.	although subunit iii of cytochrome c oxidase is part of the catalytic core of the enzyme, its function has remained enigmatic. comparison of the wild-type oxidase and forms lacking subunit iii shows that the presence of subunit iii maintains rapid proton uptake into the d pathway at the ph of the bacterial cytoplasm or mitochondrial matrix, apparently by contributing to the protein environment of d132, the initial proton acceptor of the d pathway. subunit iii also appears to contribute to the co ...	2004	15100048
mass spectrometric detection of protein, lipid and heme components of cytochrome c oxidase from r. sphaeroides and the stabilization of non-covalent complexes from the enzyme.	the cytochrome c oxidase enzyme from the rhodobacter sphaeroides bacteria exists as a complex of four peptide subunits, two hemes, and a variety of lipids and metal ions held together by non-covalent forces. while the native enzyme functions as an associated unit, this complex usually dissociates during maldi- tof analysis. through the use of matrix additives such as sucrose, the complete complex and partial complexes can be stabilized in the maldi-tof experiment. the dissociation of the complex ...	2004	15103107
electron transfer kinetics in photosynthetic reaction centers embedded in polyvinyl alcohol films.	the coupling between electron transfer and protein dynamics has been studied at room temperature in isolated reaction centers (rcs) from the photosynthetic bacterium rhodobacter sphaeroides by incorporating the protein in polyvinyl alcohol (pva) films of different water/rc ratios. the kinetic analysis of charge recombination shows that dehydration of rc-containing pva films causes reversible, inhomogeneous inhibition of electron transfer from the reduced primary quinone acceptor (q(a)(-)) to the ...	2004	15110251
ph-sensitive fluorescent dye as probe for proton uptake in photosynthetic reaction centers.	isolated and purified reaction centers (rc) from rhodobacter sphaeroides r-26.1 were solubilised in detergent with excess quinone and external electron donors and illuminated in the presence of pyranine. the ph change accompanying the reaction center photocycle was monitored by recording the variation of the pyranine fluorescence intensity. using q(b)-depleted reaction centers or blocking the photocycle with terbutryne strongly reduced the ph change. the usefulness and limits of this technique i ...	2004	15110262
noninvasive auto-photoreduction used as a tool for studying structural changes in heme-copper oxidases by ftir spectroscopy.	we demonstrate an efficient fourier transform infrared (ftir) spectroscopic method, termed "auto-photoreduction," that uses anaerobic photo-induced internal electron transfer to monitor reaction-initiated changes of heme-copper oxidases. it can be applied without the use of either expensive electrochemical equipment, or caged compounds, which cause significant background signals. at high irradiation power, carbon monoxide is released from high-spin heme a of cytochrome c oxidase and heme o from ...	2004	15111436
substitution of isoleucine m206 residue by histidine in the rhodobacter sphaeroides reaction centers causes changes in the structure of the special bacteriochlorophyll pair molecule.		2004	15116562
light-induced structural changes in a putative blue-light receptor with a novel fad binding fold sensor of blue-light using fad (bluf); slr1694 of synechocystis sp. pcc6803.	the sensor of blue-light using fad (bluf) domain is the flavin-binding fold categorized to a new class of blue-light sensing domain found in appa from rhodobacter sphaeroides and pac from euglena gracilis, but little is known concerning the mechanism of blue-light perception. an open reading frame slr1694 in a cyanobacterium synechocystis sp. pcc6803 encodes a protein possessing the bluf domain. here, a full-length slr1694 protein retaining fad was expressed and purified and found to be present ...	2004	15122896
[effect of photosynthetic bacteria and compost on degradation of petroleum products in soil].	addition of diesel fuel and waste engine oil to soil was found to cause biostimulation of hydrocarbon-oxidizing microorganisms. corynebacteria constitute a large group of hydrocarbon-oxidizing microorganisms. addition of a liquid culture of photosynthetic bacteria to soil not only facilitates degradation of petroleum products, but also stimulates growth of hydrocarbon-oxidizing microorganisms. combined addition of photosynthetic bacteria and compost to soil polluted with petroleum products cause ...	2004	15125200
regulation of photosynthesis genes in rubrivivax gelatinosus: transcription factor ppsr is involved in both negative and positive control.	induction of biosynthesis of the photosystem in anoxygenic photosynthetic bacteria occurs when the oxygen concentration drops. control of this induction takes place primarily at the transcriptional level, with photosynthesis genes expressed preferentially under anaerobic conditions. here, we report analysis of the transcriptional control of two photosynthesis promoters, pucba and crti, by the ppsr factor in rubrivivax gelatinosus. this was accomplished by analyzing the photosystem production in ...	2004	15126475
involvement of the c-terminal extension of the alpha polypeptide and of the pucc protein in lh2 complex biosynthesis in rubrivivax gelatinosus.	the facultative phototrophic nonsulfur bacterium rubrivivax gelatinosus exhibits several differences from other species of purple bacteria in the organization of its photosynthetic genes. in particular, the puc operon contains only the pucb and puca genes encoding the beta and alpha polypeptides of the light-harvesting 2 (lh2) complex. downstream of the pucba operon is the pucc gene in the opposite transcriptional orientation. the transcription of pucba and pucc has been studied. no pucc transcr ...	2004	15126476
[mechanism of charge separation and their stabilization in bacterial reaction centers].	the nuclear wavepacket formed by 20-fs excitation on the p* potential energy surface in native and mutant (ym210w and ym210l) reaction centers of rhodobacter (rb.) sphaeroides and chloroflexus (c.) aurantiacus rcs was found to be reversibly transferred to the p+ba- surface at 120, 380, and 640-fs delays (monitored by measurements of ba- absorption at 1020-1028 nm). the reaction centers of ym210w(l) mutant show the most simple pattern of fs oscillations with a period of 230 fs in stimulated emiss ...	2004	15129622
secrets of carotenoid binding.		2004	15130464
protein regulation of carotenoid binding; gatekeeper and locking amino acid residues in reaction centers of rhodobacter sphaeroides.	x-ray diffraction was used to determine high-resolution structures of the reaction center (rc) complex from the carotenoidless mutant, rb. sphaeroides r-26.1, without or reconstituted with carotenoids. the results are compared with the structure of the rc from a semiaerobically grown rb. sphaeroides strain 2.4.1. the investigation reveals the structure of the carotenoid in the different protein preparations, the nature of its binding site, and a plausible mechanism by which the carotenoid is inc ...	2004	15130469
the role of cysteine 160 in thiamine diphosphate binding of the calvin-benson-bassham cycle transketolase of rhodobacter sphaeroides.	the transketolase gene (cbbt) that encodes the calvin-benson-bassham pathway transketolase (cbbt) of rhodobacter sphaeroides was overexpressed in escherichia coli and the recombinant protein purified to homogeneity. like other transketolases, r. sphaeroides cbbt was found to be inactivated in the presence of oxygen. at its optimal ph of 7.8, cbbt displays a specific activity of 37 u/mg, a kr5p of 949 microm, a kxu5p of 11 microm, and a kthdp of 1.8 microm. cysteine 160, equivalent to cys159 of t ...	2004	15130781
systematic 16s rrna gene sequencing of atypical clinical isolates identified 27 new bacterial species associated with humans.	clinical microorganisms isolated during a 5-year study in our hospital that could not be identified by conventional criteria were studied by 16s rrna gene sequence analysis. each isolate yielded a > or =1,400-bp sequence containing <5 ambiguities which was compared with the genbank 16s rrna gene library; 1,404 such isolates were tested, and 120 were considered unique (27 isolates) or rare (< or =10 cases reported in the literature) human pathogens. eleven new species, "actinobaculum massiliae," ...	2004	15131188
role of the conserved arginine pair in proton and electron transfer in cytochrome c oxidase.	a hydrogen-bonded network is observed above the hemes in all of the high-resolution crystal structures of cytochrome oxidases. it includes water and a pair of arginines, r481 and r482 (rhodobacter sphaeroides numbering), that interact directly with heme a and the heme a(3) propionates. the hydrogen-bonded network provides potential pathways for proton release. the arginines, and the backbone peptide bond between them, have also been proposed to form part of a facilitated electron transfer route ...	2004	15134449
characterization of cu- and zn-containing superoxide dismutase of rhodobacter sphaeroides.	rhodobacter sphaeroides has a cuprozinc-containing superoxide dismutase (cuznsod) in its periplasm in addition to the cytoplasmic sod that appears to contain iron (fesod). the fesod is constitutively expressed under the growth conditions examined, whereas the cuznsod is detected only when the light-harvesting complexes are found. the cuznsod expression is regulated post-transcriptionally, and the enzyme appears to protect the photoheterotrophic cells from periplasmic superoxide that may be gener ...	2004	15135531
investigation of the thermal stability of porin from paracoccus denitrificans by site-directed mutagenesis and fourier transform infrared spectroscopy.	the folding of membrane proteins was addressed using outer membrane protein porin from the soil bacterium paracoccus denitrificans (p. den.). ir spectroscopy and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (sds-page) analysis were used to probe the effect of mutagenesis on the thermal stability of the protein. secondary structure analysis by amide i ir spectroscopy showed that the wild-type protein was predominantly composed of beta-sheet, which supports the x-ray crystal structure ...	2004	15137100
delayed fluorescence from the photosynthetic reaction center measured by electronic gating of the photomultiplier.	the decay of the delayed fluorescence (920 nm) of reaction centers from the photosynthetic bacterium rhodobacter sphaeroides r26 in the p(+)q(a)(-) charge-separated state (p and q(a) are the primary donor and quinone, respectively) has been monitored in a wide (100 ns to 100 ms) time range. the photomultiplier (hamamatsu r3310-03) was protected from the intense prompt fluorescence by application of gating potential pulses (-280 v) to the first, third, and fifth dynodes during the laser pulse. th ...	2004	15137102
anomalous acceleration of the photocycle in photosynthetic reaction centers inhibited on the acceptor side.	the rate of the photocycle (quinone reduction cycle) was measured under continuous light excitation in an isolated reaction center protein of the photosynthetic bacterium rhodobacter sphaeroides. the rate is determined by the slowest step of the photocycle, which could be the photochemistry (charge separation), the quinone/quinol and cytochrome c(2+)/c(3+) exchanges, or proton delivery to the secondary quinone. the photocycle was driven by high light intensity of a laser diode (5 w/cm(2) at 808 ...	2004	15137103
orientated binding of photosynthetic reaction centers on gold using ni-nta self-assembled monolayers.	coupling of photosynthetic reaction centers (rcs) with inorganic surfaces is attractive for the identification of the mechanisms of interprotein electron transfer (et) and for possible applications in construction of photo- and chemosensors. here we show that rcs from rhodobacter sphaeroides can be immobilized on gold surfaces with the rc primary donor looking towards the substrate by using a genetically engineered poly-histidine tag (his(7)) at the c-terminal end of the m-subunit and a ni-nta t ...	2004	15142599
catellibacterium nectariphilum gen. nov., sp. nov., which requires a diffusible compound from a strain related to the genus sphingomonas for vigorous growth.	a bacterial strain, designated ast4(t), was isolated from activated sludge. the bacterium did not show significant growth on nutrient broth, but growth was clearly stimulated by addition of supernatant from other bacterial cultures. culture filtrate of a strain related to the genus sphingomonas in particular increased the cell yield and growth rate of strain ast4(t). phylogenetic analysis based on the 16s rrna gene sequences showed that strain ast4(t) is located within the 'rhodobacter group' in ...	2004	15143049
protein splicing and auto-cleavage of bacterial intein-like domains lacking a c'-flanking nucleophilic residue.	bacterial intein-like (bil) domains are newly identified homologs of intein protein-splicing domains. the two known types of bil domains together with inteins and hedgehog (hog) auto-processing domains form the hog/intein (hint) superfamily. bil domains are distinct from inteins and hogs in sequence, phylogenetic distribution, and host protein type, but little is known about their biochemical activity. here we experimentally study the auto-processing activity of four bil domains. an a-type bil d ...	2004	15150275
atpase activity of magnesium chelatase subunit i is required to maintain subunit d in vivo.	during biosynthesis of chlorophyll, mg(2+) is inserted into protoporphyrin ix by magnesium chelatase. this enzyme consists of three different subunits of approximately 40, 70 and 140 kda. seven barley mutants deficient in the 40 kda magnesium chelatase subunit were analysed and it was found that this subunit is essential for the maintenance of the 70 kda subunit, but not the 140 kda subunit. the 40 kda subunit has been shown to belong to the family of proteins called "atpases associated with var ...	2004	15153108
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 ...	2004	15170338
photoactive yellow protein, bacteriophytochrome, and sensory rhodopsin in purple phototrophic bacteria.	the purple photosynthetic bacteria contain a large variety of sensory and regulatory proteins, and those responding to light are among the most interesting. these currently include bacteriophytochrome (bph), sensory rhodopsin (sr), and photoactive yellow protein (pyp), which all appear to function as light sensors. we herein interpret new findings within the context of current knowledge. for greater detail, the reader is referred to comprehensive reviews on these topics. of the three proteins, o ...	2004	15170480
effects of light intensity distribution on growth of rhodobacter capsulatus.	for cultivation of photosynthetic cells under defined light intensity distributions, the repeated batch culture, in which a part of culture broth containing grown cells was repeatedly replaced at predetermined time intervals with a fresh medium to keep the cell concentration constant at an initial value, was employed. by use of this method the effects of the light intensity distribution on the growth characteristics of rhodobacter capsulatus were studied. unexpected decreases in the specific gro ...	2004	15176912
characterization of the bonding interactions of q(b) upon photoreduction via a-branch or b-branch electron transfer in mutant reaction centers from rhodobacter sphaeroides.	in rhodobacter sphaeroides reaction centers (rcs) containing the mutation ala m260 to trp (am260w), transmembrane electron transfer along the full-length of the a-branch of cofactors is prevented by the loss of the q(a) ubiquinone, but it is possible to generate the radical pair p(+)h(a)(-) by a-branch electron transfer or the radical pair p(+)q(b)(-) by b-branch electron transfer. in the present study, ftir spectroscopy was used to provide direct evidence for the complete absence of the q(a) ub ...	2004	15178474
quantum molecular dynamics simulation of proton transfer in cytochrome c oxidase.	proton transfer/translocation is studied in cytochrome c oxidase (cco) by a combination of quantum mechanics (qm) for the transferring protons and classical molecular dynamics (md) for the protein and solvent. the possibility of a glutamate, glu286 in the rhodobacter sphaeroides numbering scheme, acting as a rely point for proton translocation is investigated. the md finds a hydrogen-bonded cycle of two waters and the carboxylate oxygens of glu286. the possibility of protonating glu286 to form n ...	2004	15178480
identification of a novel protonation pattern for carboxylic acids upon q(b) photoreduction in rhodobacter sphaeroides reaction center mutants at asp-l213 and glu-l212 sites.	in the reaction center from the photosynthetic purple bacterium rhodobacter sphaeroides, light energy is rapidly converted to chemical energy through coupled electron-proton transfer to a buried quinone molecule q(b). involved in the proton uptake steps are carboxylic acids, which have characteristic infrared vibrations that are observable using light-induced fourier transform infrared (ftir) difference spectroscopy. upon formation, q(b)(-) induces protonation of glu-l212, located within 5 a of ...	2004	15182169
genome organization and localization of the puflm genes of the photosynthesis reaction center in phylogenetically diverse marine alphaproteobacteria.	genome organization, plasmid content and localization of the puflm genes of the photosynthesis reaction center were studied by pulsed-field gel electrophoresis (pfge) in marine phototrophic alphaproteobacteria. both anaerobic phototrophs (rhodobacter veldkampii and rhodobacter sphaeroides) and strictly aerobic anoxygenic phototrophs from the roseobacter-sulfitobacter-silicibacter clade (roseivivax halodurans, roseobacter litoralis, staleya guttiformis, roseovarius tolerans, and five new strains ...	2004	15184132
use of sinorhizobium meliloti as an indicator for specific detection of long-chain n-acyl homoserine lactones.	population-density-dependent gene expression in gram-negative bacteria involves the production of signal molecules characterized as n-acyl homoserine lactones (ahls). the synthesis of ahls by numerous microorganisms has been identified by using biosensor strains based on the agrobacterium tumefaciens and chromobacterium violaceum quorum-sensing systems. the symbiotic nitrogen-fixing bacterium sinorhizobium meliloti is rapidly becoming a model organism for the study of quorum sensing. this organi ...	2004	15184178
phototrophic utilization of taurine by the purple nonsulfur bacteria rhodopseudomonas palustris and rhodobacter sphaeroides.	taurine metabolism by two phototrophically grown purple nonsulfur bacteria enrichment isolates has been examined. rhodopseudomonas palustris (strain tau1) grows with taurine as a sole electron donor, sulfur and nitrogen source during photoautotrophic growth. rhodobacter sphaeroides (strain tau3) grows on the compound as sole electron donor, sulfur and nitrogen source, and partial carbon source, in the presence of co(2) during photoheterotrophic growth. both organisms utilize an inducible taurine ...	2004	15184574
the role of dor gene products in controlling the p2 promoter of the cytochrome c2 gene, cyca, in rhodobacter sphaeroides.	this study explores the regulatory networks controlling anaerobic energy production by the facultative phototroph rhodobacter sphaeroides. the specific aim was to determine why activity of the p2 promoter for the gene (cyca) encoding the essential photosynthetic electron carrier, cytochrome c(2), is decreased when the alternative electron acceptor dmso is added to photosynthetically grown cells. the presence of dmso is believed to activate the dorr response regulator, which controls expression o ...	2004	15184575
autodisplay of active sorbitol dehydrogenase (sdh) yields a whole cell biocatalyst for the synthesis of rare sugars.	whole cell biocatalysts are attractive technological tools for the regio- and enantioselective synthesis of products, especially from substrates with several identical reactive groups. in the present study, a whole cell biocatalyst for the synthesis of rare sugars from polyalcohols was constructed. for this purpose, sorbitol dehydrogenase (sdh) from rhodobacter sphaeroides, a member of the short-chain dehydrogenase/reductase (sdr) family, was expressed on the surface of escherichia coli using au ...	2004	15185373
exploring recombinant flavonoid biosynthesis in metabolically engineered escherichia coli.	flavonoids are important plant-specific secondary metabolites synthesized from 4-coumaroyl coenzyme a (coa), derived from the general phenylpropanoid pathway, and three malonyl-coas. the synthesis involves a plant type iii polyketide synthase, chalcone synthase. we report the cloning and coexpression in escherichia coli of phenylalanine ammonia lyase, cinnamate-4-hydroxylase, 4-coumarate:coa ligase, and chalcone synthase from the model plant arabidopsis thaliana. simultaneous expression of all f ...	2004	15185374
regb/rega, a highly conserved redox-responding global two-component regulatory system.	the reg regulon from rhodobacter capsulatus and rhodobacter sphaeroides encodes proteins involved in numerous energy-generating and energy-utilizing processes such as photosynthesis, carbon fixation, nitrogen fixation, hydrogen utilization, aerobic and anaerobic respiration, denitrification, electron transport, and aerotaxis. the redox signal that is detected by the membrane-bound sensor kinase, regb, appears to originate from the aerobic respiratory chain, given that mutations in cytochrome c o ...	2004	15187184
the proton-driven rotor of atp synthase: ohmic conductance (10 fs), and absence of voltage gating.	the membrane portion of f(0)f(1)-atp synthase, f(0), translocates protons by a rotary mechanism. proton conduction by f(0) was studied in chromatophores of the photosynthetic bacterium rhodobacter capsulatus. the discharge of a light-induced voltage jump was monitored by electrochromic absorption transients to yield the unitary conductance of f(0). the current-voltage relationship of f(0) was linear from 7 to 70 mv. the current was extremely proton-specific (>10(7)) and varied only slightly ( ap ...	2004	15189903
protein dynamics in the region of the sixth ligand methionine revealed by studies of imidazole binding to rhodobacter capsulatus cytochrome c2 hinge mutants.	all class i c-type cytochromes studied to date undergo a dynamic process in the oxidized state, which results in the transient breaking of the iron-methionine-sulfur bond and sufficient movement to allow the binding of exogenous ligands (imidazole in this work). in the case of rhodobacter capsulatus cytochrome c(2), the sixth heme ligand met96 and up to 14 flanking residues (positions 88-100, termed the hinge region), located between two relatively rigid helical regions, may be involved in struc ...	2004	15196014
reconstitution of the rhodobacter sphaeroides cbb3-prrba signal transduction pathway in vitro.	the prrba two-component system in rhodobacter sphaeroides 2.4.1, which is composed of the prrb histidine kinase and the prra response regulator, controls the expression of all of the photosynthesis genes, either directly or indirectly, in response to changes in oxygen tension. in vivo under aerobic conditions it is the cbb(3) cytochrome c oxidase which generates an inhibitory signal preventing the accumulation of activated prra. using purified cbb(3) cytochrome c oxidase, prrb, and prra, we demo ...	2004	15196036
variation of ser-l223 hydrogen bonding with the qb redox state in reaction centers from rhodobacter sphaeroides.	ser-l223 is close to ubiquinone (q(b)) in the b-branch of the bacterial photosynthetic reaction center (brc) from rhodobacter (rb) sphaeroides. therefore, the presence of a hydrogen bond (h bond) between the two was naturally proposed from the crystal structure. the hydrogen bonding pattern of q(b) from the light-exposed structure was studied by generating hydrogen atom coordinates based on the charmm force field. in the q(b) neutral charge state (q(b)(0)), no h bond was found between the oxygen ...	2004	15212556
expression and characteristics of the gene encoding azoreductase from rhodobacter sphaeroides as1.1737.	a gene that encodes a protein with azoreductase activity was obtained by pcr amplification from rhodobacter sphaeroides as1.1737. the enzyme, with a molecular weight of 18.7 kd, was heterologously expressed in escherichia coli and its azoreductase activity was characterized. furthermore, the reduction mechanism of azo dyes catalyzed by the azoreductase was studied in detail. the presence of a hydrazo-intermediate was identified, which provided a convincing evidence for the assumption that azo dy ...	2004	15212802
a novel arabidopsis thaliana protein is a functional peripheral-type benzodiazepine receptor.	a key element in the regulation of mammalian steroid biosynthesis is the 18 kda peripheral-type benzodiazepine receptor (pbr), which mediates mitochondrial cholesterol import. pbr also possess an affinity to the tetrapyrrole metabolite protoporphyrin. the bacterial homolog to the mammalian pbr, the rhodobacter tspo (crtk) protein, was shown to be involved in the bacterial tetrapyrrole metabolism. looking for a similar mitochondrial import mechanism in plants, protein sequences from arabidopsis a ...	2004	15215507
construction and validation of the rhodobacter sphaeroides 2.4.1 dna microarray: transcriptome flexibility at diverse growth modes.	a high-density oligonucleotide dna microarray, a genechip, representing the 4.6-mb genome of the facultative phototrophic proteobacterium, rhodobacter sphaeroides 2.4.1, was custom-designed and manufactured by affymetrix, santa clara, calif. the genechip contains probe sets for 4,292 open reading frames (orfs), 47 rrna and trna genes, and 394 intergenic regions. the probe set sequences were derived from the genome annotation generated by oak ridge national laboratory after extensive revision, wh ...	2004	15231807
temperature and cryoprotectant influence secondary quinone binding position in bacterial reaction centers.	we have determined the first de novo position of the secondary quinone qb in the rhodobacter sphaeroides reaction center (rc) using phases derived by the single wavelength anomalous dispersion method from crystals with selenomethionine substitution. we found that in frozen rc crystals, qb occupies primarily the proximal binding site. in contrast, our room temperature structure showed that qb is largely in the distal position. both data sets were collected in dark-adapted conditions. we estimate ...	2004	15251460
functional activity of human monocytes exposed to lipopolysaccharides of different structure.		2004	15255137
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 ...	2004	15256566
atr-ftir spectroscopy studies of iron-sulfur protein and cytochrome c1 in the rhodobacter capsulatus cytochrome bc1 complex.	redox transitions in the rhodobacter capsulatus cytochrome bc(1) complex were investigated by perfusion-induced attenuated total reflection-fourier transform infrared (atr-ftir) spectroscopy combined with synchronous visible spectroscopy, in both the wild type and a cytochrome c(1) point mutant, m183k, in which the midpoint potential of heme was lowered from the wild-type value of 320 mv to 60 mv. overall redox difference spectra of the wild type and m183k mutant were essentially identical, indi ...	2004	15260490
metal ion modulated electron transfer in photosynthetic proteins.	photosynthetic purple bacterial reaction center (rc) proteins are ideal native systems for addressing basic questions regarding the nature of biological electron transfer because both the protein structure and the electron-transfer reactions are well-characterized. metal ion binding to the rc can affect primary photochemistry and provides a probe for understanding the involvement of local protein environments in electron transfer. the rc has two distinct transition metal ion binding sites, the w ...	2004	15260506
biochemical study of multiple chey response regulators of the chemotactic pathway of rhodobacter sphaeroides.	the six copies of the response regulator chey from rhodobacter sphaeroides bind to the switch protein flim. phosphorylation by acetyl phosphate (acp) was detected by tryptophan fluorescence quenching in three of the four cheys that contain this residue. autophosphorylation with ac(32)p was observed in five chey proteins. we also show that all of the chey genes are expressed simultaneously; therefore, in vivo all of the chey proteins could bind to flim to control the chemotactic response. consequ ...	2004	15262956
composition and activity of the rhodobacter capsulatus degradosome vary under different oxygen concentrations.	the influence of changes in temperature or oxygen tension during growth of rhodobacter capsulatus on the composition and activity of the degradosome, an rna-processing protein complex, was investigated. only minor differences in the amount of specific proteins of the complex were observed after a decrease or increase of the temperature, but dramatic variations were detectable during growth at different oxygen concentrations. in particular, the amount of the transcription factor rho, which was pr ...	2004	15263819
towards higher-throughput membrane protein production for structural genomics initiatives.	integral membrane proteins present unparalleled challenges for structural genomics programs. samples from this class of proteins are not only difficult to produce in quantities sufficient for analysis by x-ray diffraction or nmr, but their hydrophobic properties add extra dimension to their purification and subsequent crystallization. new systems that seek to tackle the production problems are in development. in our laboratory, one such strategy exploits the unique physiology of the rhodobacter ...	2004	15263855
"cystope tagging" for labeling and detection of recombinant protein expression.	a labeling and detection method, based on the addition of a single cysteine residue at the c terminus of a recombinant protein and the subsequent sulfhydryl-specific michael addition to the double bond of maleimide and its derivatives, was developed. the method was named "cystope tagging." sorbit dehydrogenase (sdh) from rhodobacter sphaeroides, a member of the short-chain dehydrogenase family of proteins that contains three inherent cysteines, was used as a model recombinant protein. by labelin ...	2004	15265732
the role of active site glutamate residues in catalysis of rhodobacter capsulatus xanthine dehydrogenase.	xanthine dehydrogenase (xdh) from the bacterium rhodobacter capsulatus catalyzes the hydroxylation of xanthine to uric acid with nad+ as the electron acceptor. r. capsulatus xdh forms an (alphabeta)2 heterotetramer and is highly homologous to homodimeric eukaryotic xanthine oxidoreductases. here we first describe reductive titration and steady state kinetics on recombinant wild-type r. capsulatus xdh purified from escherichia coli, and we then proceed to evaluate the catalytic importance of the ...	2004	15265866
exciton exciton annihilation dynamics in chromophore complexes. ii. intensity dependent transient absorption of the lh2 antenna system.	using the multiexciton density matrix theory of excitation energy transfer in chromophore complexes developed in a foregoing paper [j. chem. phys. 118, 746 (2003)], the computation of ultrafast transient absorption spectra is presented. beside static disorder and standard mechanisms of excitation energy dissipation the theory incorporates exciton exciton annihilation (eea) processes. to elucidate signatures of eea in intensity dependent transient absorption data the approach is applied to the b8 ...	2004	15268371
interactions between the rhodobacter sphaeroides ecf sigma factor, sigma(e), and its anti-sigma factor, chrr.	rhodobacter sphaeroides sigma(e) is a member of the extra cytoplasmic function sigma factor (ecf) family, whose members have been shown to regulate gene expression in response to a variety of signals. the functions of ecf family members are commonly regulated by a specific, reversible interaction with a cognate anti-sigma factor. in r.sphaeroides, sigma(e) activity is inhibited by chrr, a member of a newly discovered family of zinc containing anti-sigma factors. we used gel filtration chromatogr ...	2004	15276828
loktanella salsilacus gen. nov., sp. nov., loktanella fryxellensis sp. nov. and loktanella vestfoldensis sp. nov., new members of the rhodobacter group, isolated from microbial mats in antarctic lakes.	a taxonomic study was performed on 26 strains isolated from microbial mats in antarctic lakes of the vestfold hills and the mcmurdo dry valleys. phylogenetic analysis based on 16s rrna gene sequences placed these strains within the rhodobacter group of the alpha-subclass of the proteobacteria. sequence similarity values for the strains with their nearest phylogenetic neighbours (jannaschia, octadecabacter and ketogulonicigenium) ranged between 94.0 and 95.8%. dna-dna hybridizations and compariso ...	2004	15280301
probing light-induced conformational transitions in bacterial photosynthetic reaction centers embedded in trehalose-water amorphous matrices.	the coupling between electron transfer and protein dynamics has been studied in photosynthetic reaction centers (rc) from rhodobacter sphaeroides by embedding the protein into room temperature solid trehalose-water matrices. electron transfer kinetics from the primary quinone acceptor (q(a)(-)) to the photoxidized donor (p(+)) were measured as a function of the duration of photoexcitation from 20 ns (laser flash) to more than 1 min. decreasing the water content of the matrix down to approximatel ...	2004	15282174
resonance raman detection of the fe2+-c-n modes in heme-copper oxidases: a probe of the active site.	resonance raman spectroscopy has been employed to investigate the reduced cyano complexes of cytochrome aa(3) from bovine heart and rhodobacter sphaeroides and of cytochrome bo(3) from e. coli. in the aa(3)-type oxidases, the frequency of the fe-cn stretching mode is located at 468 cm(-1), and the bending fe-c-n vibration, at 500 cm(-1). the fully reduced cytochrome bo(3)-cn complex gives rise to a stretching vibration at 468 cm(-1), a bending vibration at 491 cm(-1), and a stretching c-n vibrat ...	2004	15285666
a single-amino-acid lid renders a gas-tight compartment within a membrane-bound transporter.	proteins undergo structural fluctuations between nearly isoenergetic substates. such fluctuations are often intimately linked with the functional properties of proteins. however, in some cases, such as in transmembrane ion transporters, the control of the ion transport requires that the protein is designed to restrict the motions in specific regions. in this study, we have investigated the dynamics of a membrane-bound respiratory oxidase, which acts both as an enzyme catalyzing reduction of o(2) ...	2004	15289603
a eukaryotic bluf domain mediates light-dependent gene expression in the purple bacterium rhodobacter sphaeroides 2.4.1.	the flavin-binding bluf domain functions as a blue-light receptor in eukaryotes and bacteria. in the photoreceptor protein photo-activated adenylyl cyclase (pac) from the flagellate euglena gracilis, the bluf domain is linked to an adenylyl cyclase domain. the pac protein mediates a photophobic response. in the appa protein of rhodobacter sphaeroides, the bluf domain is linked to a downstream domain without similarity to known proteins. appa functions as a transcriptional antirepressor, controll ...	2004	15292515
effects of oxygen and light intensity on transcriptome expression in rhodobacter sphaeroides 2.4.1. redox active gene expression profile.	the roles of oxygen and light on the regulation of photosynthesis gene expression in rhodobacter sphaeroides 2.4.1 have been well studied over the past 50 years. more recently, the effects of oxygen and light on gene regulation have been shown to involve the interacting redox chains present in r. sphaeroides under diverse growth conditions, and many of the redox carriers comprising these chains have been well studied. however, the expression patterns of those genes encoding these redox carriers, ...	2004	14662761
protein-template-driven formation of polynuclear iron species.	ferritins are iron-storage proteins capable of holding up to 4500 fe(3+) ions within a single water-soluble protein shell made from 24 polypeptide chains. the glu128arg/glu135arg mutants of escherichia coli and rhodobacter capsulatus bacterioferritins are unable to associate into 24-meric structures, with dimers of polypeptide chains being their stable forms. the aerobic addition to these of up to 8-10 or 14-20 fe(2+) ions per dimer, respectively, results in the oxidation of the added fe(2+) to ...	2004	14719947
rhodobacter capsulatus nifa1 promoter: high-gc -10 regions in high-gc bacteria and the basis for their transcription.	it was previously shown that the rhodobacter capsulatus ntrc enhancer-binding protein activates the r. capsulatus housekeeping rna polymerase but not the escherichia coli rna polymerase at the nifa1 promoter. we have tested the hypothesis that this activity is due to the high g+c content of the -10 sequence. a comparative analysis of r. capsulatus and other alpha-proteobacterial promoters with known transcription start sites suggests that the g+c content of the -10 region is higher than that for ...	2004	14729700
circe is not involved in heat-dependent transcription of groesl but in stabilization of the mrna 5'-end in rhodobacter capsulatus.	the circe element, an inverted dna repeat, is known to be involved in the temperature-dependent regulation of genes for heat shock proteins in a variety of organisms. the circe element was identified as the target for the hrca protein, which represses transcription of heat shock genes under normal growth temperature. our data reveal that the circe element is not involved in the temperature-dependent transcription of the groesl genes in rhodobacter capsulatus. apparently, r.capsulatus does not ha ...	2004	14729923
hydrogen bonds involved in binding the qi-site semiquinone in the bc1 complex, identified through deuterium exchange using pulsed epr.	exchangeable protons in the immediate neighborhood of the semiquinone (sq) at the qi-site of the bc1 complex (ubihydroquinone:cytochrome c oxidoreductase (ec 1.10.2.2)) from rhodobacter sphaeroides have been characterized using electron spin echo envelope modulation (eseem) and hyperfine sublevel correlation spectroscopy (hyscore) and visualized by substitution of h2o by 2h2o. three exchangeable protons interact with the electron spin of the sq. they possess different isotropic and anisotropic h ...	2004	14736869
determination of the topological shape of integral membrane protein light-harvesting complex lh2 from photosynthetic bacteria in the detergent solution by small-angle x-ray scattering.	the topological shape of the integral membrane protein light-harvesting complex lh2 from photosynthetic bacteria rhodobacter spheroides 2.4.1 in detergent solution has been determined from synchrotron small-angle x-ray scattering data using direct curve-fitting by the ellipsoid, ab initio shape determination methods of simulated annealing algorithm and multipole expansion, respectively. the results indicate that the lh2 protein in aqueous solution is encapsulated by a monolayered detergent shell ...	2004	14747343
on the analysis of membrane protein circular dichroism spectra.	analysis of circular dichroism spectra of proteins provides information about protein secondary structure. analytical methods developed for such an analysis use structures and spectra of a set of reference proteins. the reference protein sets currently in use include soluble proteins with a wide range of secondary structures, and perform quite well in analyzing cd spectra of soluble proteins. the utility of soluble protein reference sets in analyzing membrane protein cd spectra, however, has bee ...	2004	14691226
structural, dynamic, and energetic aspects of long-range electron transfer in photosynthetic reaction centers.	intramolecular electron transfer within proteins plays an essential role in biological energy transduction. electron donor and acceptor cofactors are bound in the protein matrix at specific locations, and protein-cofactor interactions as well as protein conformational changes can markedly influence the electron transfer rates. to assess these effects, we have investigated charge recombination from the primary quinone acceptor to the special pair bacteriochlorophyll dimer in wild-type reaction ce ...	2004	14691247
intracellular autoregulation of the mycobacterium tuberculosis prra response regulator.	two-component systems are major regulatory systems for bacterial adaptation to environmental changes. during the infectious cycle of mycobacterium tuberculosis, adaptation to an intracellular environment is critical for multiplication and survival of the micro-organism within the host. the m. tuberculosis prra gene, encoding the regulator of the two-component system prra-prrb, has been shown to be induced upon macrophage phagocytosis and to be transiently required for the early stages of macroph ...	2004	14702417
light and redox control of photosynthesis gene expression in bradyrhizobium: dual roles of two ppsr.	the two closely related bacteria bradyrhizobium and rhodopseudomonas palustris show an unusual mechanism of regulation of photosystem formation by light thanks to a bacteriophytochrome that antirepresses the regulator ppsr. in these two bacteria, we found out, unexpectedly, that two ppsr genes are present. we show that the two bradyrhizobium ppsr proteins exert antagonistic effects in the regulation of photosystem formation with a classical repressor role for ppsr2 and an unexpected activator ro ...	2004	15304477
hydrogen production from propionate by rhodopseudomonas capsulata.	hydrogen production from propionate at various concentrations by rhodopseudomonas capsulata, a purple nonsulfur bacterium, was studied at a temperature of 31 degrees c, a ph of 7.0, and an illumination intensity of 3000 lux. among the six levels of propionate, 3.84 g/l was found to be the optimum propionate concentration for h2 production in terms of substrate utilization efficiency, h2 percentage, cumulative h2 production, and h2 yield. a modified gompertz equation was able to describe properly ...	2004	15304766
[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 ...	2004	15315232
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 ...	2004	15317762
molecular and functional characterization of the azorhizobium caulinodans ors571 hydrogenase gene cluster.	in this work, we report the cloning and sequencing of the azorhizobium caulinodans ors571 hydrogenase gene cluster. sequence analysis revealed the presence of 20 open reading frames huptuvhypfhupslcdfghjk hypabhuprhypcdehupe. the physical and genetic organization of a. caulinodans ors571 hydrogenase system suggests a close relatedness to that of rhodobacter capsulatus. in contrast to the latter species, a gene homologous to rhizobium leguminosarum hupe was identified downstream of the hyp operon ...	2004	15321689
hydroxylamine assimilation by rhodobacter capsulatus e1f1. requirement of the hcp gene (hybrid cluster protein) located in the nitrate assimilation nas gene region for hydroxylamine reduction.	rhodobacter capsulatus e1f1 grows phototrophically with nitrate as nitrogen source. using primers designed for conserved motifs in bacterial assimilatory nitrate reductases, a 450-bp dna was amplified by pcr and used for the screening of a genomic library. a cosmid carrying an insert with four sali fragments of 2.8, 4.1, 4.5, and 5.8 kb was isolated, and dna sequencing revealed that it contains a nitrate assimilation (nas) gene region, including the hcp gene coding for a hybrid cluster protein ( ...	2004	15322098
physiological ligands adp and pi modulate the degree of intrinsic coupling in the atp synthase of the photosynthetic bacterium rhodobacter capsulatus.	the proton-pumping and the atp hydrolysis activities of the atp synthase of rhodobacter capsulatus have been compared as a function of the adp and p(i) concentrations. the proton pumping was measured either with the transmembrane ph difference probe, 9-amino-6-chloro-2-methoxyacridine, or with the transmembrane electric potential difference probe, bis(3-propyl-5-oxoisoxazol-4-yl)pentamethine oxonol, obtaining consistent results. the comparison indicates that an intrinsic uncoupling of atp syntha ...	2004	15323572
thioredoxin can influence gene expression by affecting gyrase activity.	the expression of many genes of facultatively photosynthetic bacteria of the genus rhodobacter is controlled by the oxygen tension. among these are the genes of the puf and puc operons, which encode proteins of the photosynthetic apparatus. previous results revealed that thioredoxins are involved in the regulated expression of these operons, but it remained unsolved as to the mechanisms by which thioredoxins affect puf and puc expression. here we show that reduced trxa of rhodobacter capsulatus ...	2004	15328368
the native architecture of a photosynthetic membrane.	in photosynthesis, the harvesting of solar energy and its subsequent conversion into a stable charge separation are dependent upon an interconnected macromolecular network of membrane-associated chlorophyll-protein complexes. although the detailed structure of each complex has been determined, the size and organization of this network are unknown. here we show the use of atomic force microscopy to directly reveal a native bacterial photosynthetic membrane. this first view of any multi-component ...	2004	15329728
bacterial acetone carboxylase is a manganese-dependent metalloenzyme.	bacterial acetone carboxylase catalyzes the atp-dependent carboxylation of acetone to acetoacetate with the concomitant production of amp and two inorganic phosphates. the importance of manganese in rhodobacter capsulatus acetone carboxylase has been established through a combination of physiological, biochemical, and spectroscopic studies. depletion of manganese from the r. capsulatus growth medium resulted in inhibition of acetone-dependent but not malate-dependent cell growth. under normal gr ...	2004	15337755
the role of extra fragment at the c-terminal of cytochrome b (residues 421-445) in the cytochrome bc1 complex from rhodobacter sphaeroides.	sequence alignment of cytochrome b of the cytochrome bc1 complex from various sources reveals that bacterial cytochrome b contain an extra fragment at the c terminus. to study the role of this fragment in bacterial cytochrome bc1 complex, rhodobacter sphaeroides mutants expressing his-tagged cytochrome bc1 complexes with progressive deletion from this fragment (residues 421-445) were generated and characterized. the cytbdelta-(433-445) bc1 complex, in which 13 residues from the c-terminal end of ...	2004	15339929
regulation of hem gene expression in rhodobacter capsulatus by redox and photosystem regulators rega, crtj, fnrl, and aerr.	biosynthetic pathways for heme and chlorophyll share common intermediates from 5-aminolevulinic acid through protoporphyrin ix. to obtain a better understanding of how photosynthetic organisms coordinate heme and chlorophyll biosynthesis, we have undertaken detailed analysis of the expression pattern of numerous heme biosynthesis genes in the purple photosynthetic bacterium rhodobacter capsulatus. beta-galactosidase reporter assays demonstrated that expression of hema, hemb, hemc, heme and hemz ...	2004	15351643
studies on the interaction of nadph with rhodobacter sphaeroides biotin sulfoxide reductase.	rhodobacter sphaeroides biotin sulfoxide reductase (bsor) contains the bis(molybdopterin guanine dinucleotide)molybdenum cofactor and catalyzes the reduction of d-biotin-d-sulfoxide to biotin. this protein is the only member of the dimethyl sulfoxide reductase family of molybdopterin enzymes that utilizes nadph as the direct electron donor to the catalytic mo center. kinetic studies using stopped-flow spectrophotometry indicate that bsor reduction by nadph (>1000 s(-1)) is faster than steady-sta ...	2004	15366932
nmr structural model of the interaction of herbicides with the photosynthetic reaction center from rhodobacter sphaeroides.	the interaction of the herbicides acifluorfen and paraquat with the photosynthetic reaction center from rhodobacter sphaeroides has been studied by nmr relaxation measurements. interaction in aqueous solution has been demonstrated by evaluating motional features of the bound form through cross-relaxation terms of protons at fixed distances on the herbicides. contributions to longitudinal nonselective relaxation rates different from the proton-proton dipolar relaxation were inferred, most probabl ...	2004	15368575
napf is a cytoplasmic iron-sulfur protein required for fe-s cluster assembly in the periplasmic nitrate reductase.	the periplasmic nitrate reductase (nap) is wide-spread in proteobacteria. napa, the nitrate reductase catalytic subunit, contains a mo-bismgd cofactor and one [4fe-4s] cluster. the nap gene clusters in many bacteria, including rhodobacter sphaeroides dsm158, contain an napf gene, disruption of which drastically decreases both in vitro and in vivo nitrate reductase activities. in spite its importance in the nap system, napf has never been characterized biochemically, and its role remains unknown. ...	2004	15371424
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 ...	2004	15371444
dehydration of (r)-2-hydroxyacyl-coa to enoyl-coa in the fermentation of alpha-amino acids by anaerobic bacteria.	several clostridia and fusobacteria ferment alpha-amino acids via (r)-2-hydroxyacyl-coa, which is dehydrated to enoyl-coa by syn-elimination. this reaction is of great mechanistic interest, since the beta-hydrogen, to be eliminated as proton, is not activated (pk 40-50). a mechanism has been proposed, in which one high-energy electron acts as cofactor and transiently reduces the electrophilic thiol ester carbonyl to a nucleophilic ketyl radical anion. the 2-hydroxyacyl-coa dehydratases are two-c ...	2004	15374661