Publications

characterization of the 70s ribosome from rhodopseudomonas palustris using an integrated "top-down" and "bottom-up" mass spectrometric approach.	we present a comprehensive mass spectrometric approach that integrates intact protein molecular mass measurement ("top-down") and proteolytic fragment identification ("bottom-up") to characterize the 70s ribosome from rhodopseudomonas palustris. forty-two intact protein identifications were obtained by the top-down approach and 53 out of the 54 orthologs to escherichia coli ribosomal proteins were identified from bottom-up analysis. this integrated approach simplified the assignment of post-tran ...	2004	15473684
"paraffin wax-overlay of pour plate", a method for the isolation and enumeration of purple non-sulfur bacteria.	a modification of pour plate technique with an overlay of wax was used for isolation and enumeration of purple non-sulfur bacteria (pnsb) with equal efficiency as that of agar shake culture. the total count of pnsb ranged from 10(5)-10(8) cfu g dry soil(-1) and belonged to the genera of rhodobacter, rhodopseudomonas, rhodocista and rubrivivax.	2004	15488284
structural specificity of photosynthetic reaction centers provides high efficiency of excitation trapping and conversion.	the atomic structures of photosynthetic reaction centers of two species of purple bacteria and two photosystems 2 of cyanobacteria were resolved in the late last century. in this work i put forward the idea that of the huge body of data available thus far, only three structural factors are responsible for the unique function of conversion of physical energy of electronic excitation into electrochemical energy of separated opposite charges in reaction centers at least in purple bacteria and, perh ...	2004	15310284
observation of the energy-level structure of the low-light adapted b800 lh4 complex by single-molecule spectroscopy.	low-light adapted b800 light-harvesting complex 4 (lh4) from rhodopseudomonas palustris is a complex in which the arrangement of the bacteriochloropyll a pigments is very different from the well-known b800-850 lh2 complex. for bulk samples, the main spectroscopic feature in the near-infrared is the occurrence of a single absorption band at 802 nm. single-molecule spectroscopy can resolve the narrow bands that are associated with the exciton states of the individual complexes. the low temperature ...	2004	15326024
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 ...	2004	15326029
genomic islands in rhodopseudomonas palustris.		2004	15340470
sulfoacetate generated by rhodopseudomonas palustris from taurine.	genes thought to encode (a) the regulator of taurine catabolism under carbon-limiting or nitrogen-limiting conditions and (b) taurine dehydrogenase were found in the genome of rhodopseudomonas palustris. the organism utilized taurine quantitatively as a sole source of nitrogen (but not of carbon) for aerobic and photoheterotrophic growth. no sulfate was released, and the c-sulfonate bond was recovered stoichiometrically as sulfoacetate, which was identified by mass spectrometry. an inducible sul ...	2004	15340795
electrostatic interaction between redox cofactors in photosynthetic reaction centers.	intramolecular electron transfer within proteins is an essential process in bioenergetics. redox cofactors are embedded in proteins, and this matrix strongly influences their redox potential. several cofactors are usually found in these complexes, and they are structurally organized in a chain with distances between the electron donor and acceptor short enough to allow rapid electron tunneling. among the different interactions that contribute to the determination of the redox potential of these ...	2004	15347641
[atomic force microscopy: from cell imaging to molecular manipulation].	the atomic force microscope (afm) allows to explore the surface of biological samples bathed in physiological solutions, with vertical and horizontal resolutions ranging from nanometers to angströms. complex biological structures as well as single molecules can be observed and recent examples of the possibilities offered by the afm in the imaging of intact cells, isolated membranes, membrane model systems and single molecules are discussed in this review. applications where the afm tip is used a ...	2004	15368969
physical chemistry: quantum mechanics for plants.		2004	15372016
developing a structure-function model for the cryptophyte phycoerythrin 545 using ultrahigh resolution crystallography and ultrafast laser spectroscopy.	cryptophyte algae differ from cyanobacteria and red algae in the architecture of their photosynthetic light harvesting systems, even though all three are evolutionarily related. central to cryptophyte light harvesting is the soluble antenna protein phycoerythrin 545 (pe545). the ultrahigh resolution crystal structure of pe545, isolated from a unicellular cryptophyte rhodomonas cs24, is reported at both 1.1a and 0.97a resolution, revealing details of the conformation and environments of the chrom ...	2004	15504407
mixotrophy in the phototrophic harmful alga cochlodinium polykrikoides (dinophycean): prey species, the effects of prey concentration, and grazing impact.	we first reported here that the harmful alga cochlodinium polykrikoides, which had been previously known as an autotrophic dinoflagellate, was a mixotrophic species. we investigated the kinds of prey species and the effects of the prey concentration on the growth and ingestion rates of c. polykrikoides when feeding on an unidentified cryptophyte species (equivalent spherical diameter, esd = 5.6 microm). we also calculated grazing coefficients by combining field data on abundances of c. polykriko ...	2004	15537091
bacterial diversity of a soil sample from schirmacher oasis, antarctica.	the bacterial diversity of a soil sample collected in the vicinity of lake zub, schirmacher oasis, antarctica, was determined both by establishing pure colonies of culturable bacteria and by cloning the total 16s rdna of the soil and establishing the phylogeny of the clones. analysis of the 16s rrna gene clones indicated that the bacteria belonged to the classes alpha-proteobacteria, beta-proteobacteria, gamma-proteobacteria, gemmatimonas, bacteriodetes, actinobacteria, chloroflexi and chlamydia ...	2004	15559969
biosynthetic site-specific (13) c labeling of the light-harvesting 2 protein complex: a model for solid state nmr structure determination of transmembrane proteins.	partly biosynthetic site-directed isotopically (13)c enriched photosynthetic light-harvesting 2(lh2) complexes have been prepared from rhodopseudomonas acidophila strain 10050 by using chemically labeled [1,2,3,4-(13)c], [1,4-(13)c] and [2,3-(13)c] succinic acid as a precursor in the growth medium. two-dimensional proton driven spin diffusion (pdsd) solid state nmr correlation spectroscopy has been used to trace each individual (13)c isotope from the labeled succinic acid precursor to its destin ...	2004	15754054
triplet excitation transfer between carotenoids in the lh2 complex from photosynthetic bacterium rhodopseudomonas palustris.	we have studied, by means of sub-microsecond time-resolved absorption spectroscopy, the triplet-excited state dynamics of carotenoids (cars) in the intermediate-light adapted lh2 complex (ml-lh2) from rhodopseudomonas palustris containing cars with different numbers of conjugated double bonds. following pulsed photo-excitation at 590 nm at room temperature, rapid spectral equilibration was observed either as a red shift of the isosbestic wavelength on a time scale of 0.6-1.0 mus, or as a fast de ...	2004	16228615
the photosynthetic reaction centre from the purple bacterium rhodopseudomonas viridis.	we first describe the history and methods of membrane protein crystallization, and show how the structure of the photosynthetic reaction centre from the purple bacterium rhodopseudomonas viridis was solved. the structure of this membrane protein complex is correlated with its function as a light-driven electron pump across the photosynthetic membrane. finally we draw conclusions on the structure of the photosystem ii reaction centre from plants and discuss the aspects of membrane protein structu ...	2004	16134018
my daily constitutional in martinsried.	the three-dimensional structures of bacterial reaction centers have served as the framework for much of our understanding of anoxygenic photosynthesis. a key step in the determination of the structure of the reaction center from rhodobacter sphaeroides was the use the molecular replacement technique. for this technique, we made use of two sets of data. first, x-ray diffraction data had been measured from crystals of the reaction center from r. sphaeroides by our research group in california, led ...	2004	16328817
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
rain or shine--a phototroph that delivers.		2004	14704702
complete genome sequence of the metabolically versatile photosynthetic bacterium rhodopseudomonas palustris.	rhodopseudomonas palustris is among the most metabolically versatile bacteria known. it uses light, inorganic compounds, or organic compounds, for energy. it acquires carbon from many types of green plant-derived compounds or by carbon dioxide fixation, and it fixes nitrogen. here we describe the genome sequence of r. palustris, which consists of a 5,459,213-base-pair (bp) circular chromosome with 4,836 predicted genes and a plasmid of 8,427 bp. the sequence reveals genes that confer a remarkabl ...	2004	14704707
nmr-validated structural model for oxidized rhodopseudomonas palustris cytochrome c(556).	the structure of oxidized rhodopseudomonas palustris cytochrome c(556) has been modeled after that of high-spin cytochrome c' from the same bacterium, the latter being the protein with the greatest sequence identity (35%) among all sequenced proteins in the genomes. the two proteins differ in the number of ligands to iron and in spin state, the former being six-coordinate low-spin and the latter five-coordinate high-spin. in order to validate this modeled structure, several structural restraints ...	2004	14735333
heteronuclear 2d (1h-13c) mas nmr resolves the electronic structure of coordinated histidines in light-harvesting complex ii: assessment of charge transfer and electronic delocalization effect.	in a recent mas nmr study, two types of histidine residues in the light-harvesting complex ii (lh2) of rhodopseudomonas acidophila were resolved: type 1 (neutral) and type 2 (positively charged) (alia et al. j. am. chem. soc. ). the isotropic (13)c shifts of histidines coordinating to b850 bchl a are similar to fully positively charged histidine, while the (15)n shift anisotropy shows a predominantly neutral character. in addition the possibility that the ring currents are quenched by overlap in ...	2004	14755159
hydrophobic pockets at the membrane interface: an original mechanism for membrane protein interactions.	the effect of partial digestion by trypsin and gluc protease on the association of the membrane polypeptides of lh1 from rhodospirillum (rsp.) rubrum was studied. trypsin and gluc protease treatments of lh1 result in the cleavage of the first three amino acids from the alpha polypeptide and of the first 18 amino acids from the beta polypeptide, respectively, without any noticeable reorganization of their secondary structure, as measured by attenuated total reflectance fourier transform ir spectr ...	2004	14756563
[isolation and identification of a photosynthetic bacteria producing coenzyme q10].	13 isolates producing coenzyme q10 (coq10) of purple non sulfur photosynthetic bacteria were enriched out of pond sludge, one isolate named 2c was selected based on its high coq10 content and identified systematically. the gram-negative and short-rod shaped strain 2c is 0.6microm - 0.9microm x 1.2microm - 2.0 microm, has one long flagellum on one end of the cell and contains lamellar intracytoplasmic membrane(icm) system parallel to cytoplasmic membrane. cultures produce red pigments in the ligh ...	2005	16342774
analysis of kinetics of electron transfer in the reaction centers of photosynthetic bacteria using the rips-jortner model.		2005	16480153
crystallization and preliminary x-ray studies on the reaction center-light-harvesting 1 core complex from rhodopseudomonas viridis.	the reaction center-light-harvesting 1 (rc-lh1) core complex is the photosynthetic apparatus in the membrane of the purple photosynthetic bacterium rhodopseudomonas viridis. the rc is surrounded by an lh1 complex that is constituted of oligomers of three types of apoproteins (alpha, beta and gamma chains) with associated bacteriochlorophyll bs and carotenoid. it has been crystallized by the sitting-drop vapour-diffusion method. a promising crystal diffracted to beyond 8.0 a resolution. it belong ...	2005	16508098
biofilm formation characteristics of bacterial isolates retrieved from a reverse osmosis membrane.	high-quality water purification systems using reverse osmosis (ro) membrane separation have faced a major challenge related to biofilm formation on the membrane surface, or biofouling. to understand this issue, the biofilm formation characteristics of four bacterial isolates previously retrieved from an ro membrane treating potable water were investigated. biofilm formation of all four isolates occurred to different extents in microtiter plates and could be related to one or more cell properties ...	2005	16245826
functional genomic analysis of three nitrogenase isozymes in the photosynthetic bacterium rhodopseudomonas palustris.	the photosynthetic bacterium rhodopseudomonas palustris is one of just a few prokaryotes described so far that has vnf and anf genes for alternative vanadium cofactor (v) and iron cofactor (fe) nitrogenases in addition to nif genes for a molybdenum cofactor (mo) nitrogenase. transcriptome data indicated that the 32 genes in the nif gene cluster, but not the anf or vnf genes, were induced in wild-type and mo nitrogenase-expressing strains grown under nitrogen-fixing conditions in mo-containing me ...	2005	16267302
rhodopseudomonas palustris regulons detected by cross-species analysis of alphaproteobacterial genomes.	rhodopseudomonas palustris, an alpha-proteobacterium, carries out three of the chemical reactions that support life on this planet: the conversion of sunlight to chemical-potential energy; the absorption of carbon dioxide, which it converts to cellular material; and the fixation of atmospheric nitrogen into ammonia. insight into the transcription-regulatory network that coordinates these processes is fundamental to understanding the biology of this versatile bacterium. with this goal in mind, we ...	2005	16269786
formation of bacteriochlorophyll form b820 in light harvesting 2 complexes from purple sulfur bacteria treated with dioxane.	treatment of some sulfur bacteria (allochromatium minutissimum, thiorhodospira sibirica, and ectothiorhodospira halovacuolata wn22) with dioxane results in formation of the bacteriochlorophyll form b820 in the light harvesting complex lh2. this form characterized by absorption maximum at 820 nm has the same absorption spectrum as b820 subcomplex from lh1 complex. appearance of the b820 form was accompanied by a sharp decrease in absorption in the carotenoid region. this phenomenon observed in al ...	2005	16271027
secondary transporters for nickel and cobalt ions: theme and variations.	nickel/cobalt transporters (nicots), a family of secondary metal transporters in prokaryotes and fungi, are characterized by an eight-transmembrane-domain (tmd) architecture and mediate high-affinity uptake of cobalt and/or nickel ions into the cells. one of the strongly conserved regions within the nicots is the signature sequence rha(v/f)dadhi within tmd ii. this stretch of amino acid residues plays an important role in the affinity, velocity and specificity of metal transport. some relatives ...	2005	16158232
preferential incorporation of coloured-carotenoids occurs in the lh2 complexes from non-sulphur purple bacteria under carotenoid-limiting conditions.	the effect of growing rhodopseudomonas (rps.) acidophila and rps. palustris in the presence of different concentrations of the carotenoid (car) biosynthetic inhibitor diphenylamine (dpa) has been investigated. growth with sub-maximal concentrations of dpa induces car limitation. the exact response to dpa is species dependent. however, both rps. acidophila and rps. palustris respond by preferentially incorporating the limiting amount of coloured cars into their lh2 complexes at the expense of the ...	2005	16172923
photoheterotrophic metabolism of acrylamide by a newly isolated strain of rhodopseudomonas palustris.	acrylamide, a neurotoxin and suspected carcinogen, is produced by industrial processes and during the heating of foods. in this study, the microbial diversity of acrylamide metabolism has been expanded through the isolation and characterization of a new strain of rhodopseudomonas palustris capable of growth with acrylamide under photoheterotrophic conditions. the newly isolated strain grew rapidly with acrylamide under photoheterotrophic conditions (doubling time of 10 to 12 h) but poorly under ...	2005	16204496
cryptophyceae and rhodophyceae; chemotaxonomy, phylogeny, and application.	the biochemical compositions of seven strains of marine cryptomonad and a rhodophyte were determined in logarithmic phase batch (1.4 l flask) and semi-continuous (10 l carboy) culture. lipid ranged from 13% to 28%, protein ranged from 53% to 68%, and carbohydrate ranged from 9% to 24% of the organic weight. the major lipid classes in the species examined were polar lipids (78-88% of total lipid). the major sterol in the cryptophyceae and the rhodophyceae was 24-methylcholesta-5,22e-dien-3beta-ol ...	2005	16226285
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 ...	2005	15973490
a new type of bacteriophytochrome acts in tandem with a classical bacteriophytochrome to control the antennae synthesis in rhodopseudomonas palustris.	phytochromes are chromoproteins found in plants and bacteria that switch between two photointerconvertible forms via the photoisomerization of their chromophore. these two forms, pr and pfr, absorb red and far-red light, respectively. we have characterized the biophysical and biochemical properties of two bacteriophytochromes, rpbphp2 and rpbphp3, from the photosynthetic bacterium rhodopseudomonas palustris. their genes are contiguous and localized near the pucbad genes encoding the polypeptides ...	2005	16009707
a bacteriophytochrome regulates the synthesis of lh4 complexes in rhodopseudomonas palustris.	the non-sulphur purple bacterium rhodopseudomonas palustris contains five pucab genes for peripheral light-harvesting complexes. bacteria grown under high-light conditions absorb at 800 and 850 nm but in low-light the 850 nm peak is almost absent and lh2 complexes are replaced by lh4. the genome contains six bacteriophytochromes (bph). bphs sense light in the red/far-red through a reversible pr to pfr transformation that controls gene expression. bph3 (rpa1537) controls the expression of a clust ...	2005	16075318
the rhodomonas salina mitochondrial genome: bacteria-like operons, compact gene arrangement and complex repeat region.	to gain insight into the mitochondrial genome structure and gene content of a putatively ancestral group of eukaryotes, the cryptophytes, we sequenced the complete mitochondrial dna of rhodomonas salina. the 48 063 bp circular-mapping molecule codes for 2 rrnas, 27 trnas and 40 proteins including 23 components of oxidative phosphorylation, 15 ribosomal proteins and two subunits of tat translocase. one potential protein (orf161) is without assigned function. only two introns occur in the genome; ...	2005	16085754
isolation and characterization of a genetically tractable photoautotrophic fe(ii)-oxidizing bacterium, rhodopseudomonas palustris strain tie-1.	we report the isolation and characterization of a phototrophic ferrous iron [fe(ii)]-oxidizing bacterium named tie-1 that differs from other fe(ii)-oxidizing phototrophs in that it is genetically tractable. under anaerobic conditions, tie-1 grows photoautotrophically with fe(ii), h2, or thiosulfate as the electron donor and photoheterotrophically with a variety of organic carbon sources. tie-1 also grows chemoheterotrophically in the dark. this isolate appears to be a new strain of the purple no ...	2005	16085840
[bacterial photosynthetic unit: light-harvesting and reaction center complexes].		2005	16104583
[a study of protein structure changes during hydration by diffuse x-ray scattering. i. the intensity and the shape of "10-angstrom" maximum].	the angle dependencies of diffuse x-ray scattering intensities were studied in a wide range of angles from 3 to 80 degrees for water-soluble and membrane proteins with a different structural organization: alpha-helical protein myoglobin, alpha-helical protein serum albumen, alpha + beta protein lysozyme, and transmembrane proteins of photosynthetic reaction centers (rc) from purple bacteria rhodobacter sphaeroides, and blastochlorii (rhodopseudomonas) viridis containing cytocrome c, situated out ...	2005	16358778
the pimfabcde operon from rhodopseudomonas palustris mediates dicarboxylic acid degradation and participates in anaerobic benzoate degradation.	bacteria in anoxic environments typically convert aromatic compounds derived from pollutants or green plants to benzoyl-coa, and then to the c7 dicarboxylic acid derivative 3-hydroxypimelyl-coa. inspection of the recently completed genome sequence of the purple nonsulfur phototroph rhodopseudomonas palustris revealed one predicted cluster of genes for the beta-oxidation of dicarboxylic acids. these genes, annotated as pimfabcde, are predicted to encode acyl-coa ligase, enoyl-coa hydratase, acyl- ...	2005	15758219
genetic diversity of benzoyl coenzyme a reductase genes detected in denitrifying isolates and estuarine sediment communities.	benzoyl coenzyme a (benzoyl-coa) reductase is a central enzyme in the anaerobic degradation of organic carbon, which utilizes a common intermediate (benzoyl-coa) in the metabolism of many aromatic compounds. the diversity of benzoyl-coa reductase genes in denitrifying bacterial isolates capable of degrading aromatic compounds and in river and estuarine sediment samples from the arthur kill in new jersey and the chesapeake bay in maryland was investigated. degenerate primers were developed from t ...	2005	15812036
sulfoacetaldehyde is excreted quantitatively by acinetobacter calcoaceticus sw1 during growth with taurine as sole source of nitrogen.	eighteen enrichment cultures with taurine (2-aminoethanesulfonate) as the sole source of combined nitrogen under aerobic conditions were all successful, and 24 pure cultures were obtained. only three of the cultures yielded an inorganic product, sulfate, from the sulfonate moiety of taurine, and the others were presumed to yield organosulfonates. sulfoacetate, known from rhodopseudomonas palustris cga009 under these conditions, was not detected in any culture, but sulfoacetaldehyde (as a hydrazo ...	2005	15817795
production of extracellular polymeric substances from rhodopseudomonas acidophila in the presence of toxic substances.	a hydrogen-producing photosynthetic bacteria strain, rhodopseudomonas acidophila, was used to investigate the production of extracellular polymeric substances (eps) in the presence of toxic substances and the effect of toxicants on bacterial surface characteristics. addition of the toxic substances including cu(ii), cr(vi), cd(ii) and 2,4-dichlorophenol (2,4-dcp) stimulated the production of eps but reduced the cell dry weight. at concentrations of 30 mg l(-1) cu(ii), 40 mg l(-1) cr(vi), 5 mg l( ...	2005	15843928
development of a pcr method for the detection and quantification of benzoyl-coa reductase genes and its application to monitored natural attenuation.	benzoyl coenzyme a reductase (bcr) catalyzes dearomatization of benzoyl coenzyme a (benzoyl-coa), which is the central step in the anaerobic degradative pathways for a variety of aromatic compounds. this study developed a pcr method for the detection and quantification of bcr genes in bacterial strains and environmental samples. pcr primers were designed by aligning known bcr genes in thauera, azoarcus and rhodopseudomonas species, and their utility was assessed by amplifying bcr fragments from ...	2005	15865350
optimization of glutamate concentration and ph for h production from volatile fatty acids by rhodopseudomonas capsulata.	this study attempted to employ response surface methodology (rsm) to evaluate the effects of glutamate concentration and ph on h(2) production from volatile fatty acids by rhodopseudomonas capsulata.	2005	15892733
biological formation of 5-aminolevulinic acid by photosynthetic bacteria.	in this study, 7 stains of rhodopseudomonas sp. were selected from 36 photosynthetic bacteria stains storied in our laboratory. rhodopseudomonas sp. strain 99-28 has the highest 5-aminolevulinic acid(ala) production ability in these 7 strains. rhodopseudomonas sp. 99-28 strain was mutated using ultraviolet radiation and a mutant strain l-1, which ala production is higher than wild strain 99-28 about one times, was obtained. the elements affecting ala formation of strain 99-28 and l-1 were studie ...	2005	15900779
residual backbone and side-chain 13c and 15n resonance assignments of the intrinsic transmembrane light-harvesting 2 protein complex by solid-state magic angle spinning nmr spectroscopy.	this study reports the sequence specific chemical shifts assignments for 76 residues of the 94 residues containing monomeric unit of the photosynthetic light-harvesting 2 transmembrane protein complex from rhodopseudomonas acidophila strain 10050, using magic angle spinning (mas) nmr in combination with extensive and selective biosynthetic isotope labeling methods. the sequence specific chemical shifts assignment is an essential step for structure determination by mas nmr. assignments have been ...	2005	15928995
toll-like receptor 6-independent signaling by diacylated lipopeptides.	bacterial lipopeptides are strong immune modulators that activate early host responses after infection as well as initiating adjuvant effects on the adaptive immune system. these lipopeptides induce signaling in cells of the immune system through toll-like receptor 2 (tlr2)-tlr1 or tlr2-tlr6 heteromers. so far it has been thought that triacylated lipopeptides, such as the synthetic n-palmitoyl-s-[2,3-bis(palmitoyloxy)-(2rs)-propyl]-(r)-cysteine (pam3)-csk4, signal through tlr2-tlr1 heteromers, w ...	2005	15580661
ndpasa: a novel pairwise protein sequence alignment algorithm that incorporates neighbor-dependent amino acid propensities.	sequence alignment has become one of the essential bioinformatics tools in biomedical research. existing sequence alignment methods can produce reliable alignments for homologous proteins sharing a high percentage of sequence identity. the performance of these methods deteriorates sharply for the sequence pairs sharing less than 25% sequence identity. we report here a new method, ndpasa, for pairwise sequence alignment. this method employs neighbor-dependent propensities of amino acids as a uniq ...	2005	15616964
membrane insertion of rhodopseudomonas acidophila light harvesting complex 2 investigated by high resolution afm.	light harvesting complexes 2 (lh2) are the peripheral antenna proteins in the bacterial photosynthetic apparatus and are built of alpha/beta-heterodimers containing three bacteriochlorophylls and two carotenoids each. previously, we have found in 2d-crystals that the complexes could be inserted within the membrane with a tilt with respect to the membrane plane (rhodobacter sphaeroides) or without tilt (rubrivivax gelatinosus). to investigate whether the tilted insertion represents the native sta ...	2005	15629659
use of the rhodopseudomonas palustris genome sequence to identify a single amino acid that contributes to the activity of a coenzyme a ligase with chlorinated substrates.	rhodopseudomonas palustris strain rcb100 degrades 3-chlorobenzoate (3-cba) anaerobically. we purified from this strain a coenzyme a ligase that is active with 3-cba and determined its n-terminal amino acid sequence to be identical to that of a cyclohexanecarboxylate-coa ligase encoded by alia from the r. palustris strain (cga009) that has been sequenced. strain cga009 differs from strain rcb100 in that it does not use 3-cba as a sole carbon source. the alia gene from the 3-cba degrading strain d ...	2005	15686561
detection of parallel functional modules by comparative analysis of genome sequences.	parallel functional modules are separate sets of proteins in an organism that catalyze the same or similar biochemical reactions but act on different substrates or use different cofactors. they originate by gene duplication during evolution. parallel functional modules provide versatility and complexity to organisms, and increase cellular flexibility and robustness. we have developed a four-step approach for genome-wide discovery of parallel modules from protein functional linkages. from ten gen ...	2005	15696156
selective chemical shift assignment of b800 and b850 bacteriochlorophylls in uniformly [13c,15n]-labeled light-harvesting complexes by solid-state nmr spectroscopy at ultra-high magnetic field.	the electronic ground states of the bacteriochlorophyll a type b800 and type b850 in the light-harvesting 2 complex of rhodopseudomonas acidophila strain 10050 have been characterized by magic angle spinning (mas) dipolar (13)c-(13)c correlation nmr spectroscopy. uniformly [(13)c,(15)n] enriched light-harvesting 2 (lh2) complexes were prepared biosynthetically, while [(13)c,(15)n]-b800 lh2 complexes were obtained after reconstitution of apoprotein with uniformly [(13)c,(15)n]-enriched bacterioch ...	2005	15740162
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 ...	2005	15501944
extraction of extracellular polymeric substances from the photosynthetic bacterium rhodopseudomonas acidophila.	among the four methods for extracting extracellular polymeric substances (eps) from rhodopseudomonas acidophila (edta, naoh, h(2)so(4), heating/centrifugation), edta extraction was found to be the most effective. the contents of the major components of eps from r. acidophila, i.e., carbohydrate, protein and nucleic acid, were 6.5, 58.4 and 5.4 mg g(-1) dry cells, respectively. the optimum extraction time was 1-3 h and the edta dosage was approximately 2.8 g g(-1) dry cells. under these condition ...	2005	15309338
maspic: intensity-based tandem mass spectrometry scoring scheme that improves peptide identification at high confidence.	algorithmic search engines bridge the gap between large tandem mass spectrometry data sets and the identification of proteins associated with biological samples. improvements in these tools can greatly enhance biological discovery. we present a new scoring scheme for comparing tandem mass spectra with a protein sequence database. the maspic (multinomial algorithm for spectral profile-based intensity comparison) scorer converts an experimental tandem mass spectrum into a m/z profile of probabilit ...	2005	16316165
[larvae and postlarvae production of the green-white sea urchin lytechinus variegatus (echinodermata: echinoidea) in culture conditions].	we evaluated the biological feasibility of massive larvae and postlarvae production of the caribbean green-white urchin lytechinus variegatus. experiments were designed to choose the initial larval density and microalgae diets under culture, to study metamorphosis, postlarval and juvenile growth. massive production of competent larvae 650 microm long at 12-13 days is possible using larval densities of 0.25 to 1 larva/ml. the microalgae rhodomonas sp. was suitable for the optimization of larval g ...	2005	17469262
[juvenile production of the red sea urchin strongylocentrotus franciscanus (echinodermata: echinoidea) in baja california, mexico].	the red sea urchin strongylocentrotusfranciscanus (agassiz 1863) is harvested commercially in baja california, mexico, since 1970; however, in the last ten years the capture per unit effort (cpue) has decreased from 310 kg/fishing unit/day to 120 kg/fishing unit/day. for this reason, actions were taken to develop a culture technology allowing massive production of juveniles for re-stocking natural populations or for growing them commercially. we summarize some of the basic studies and main achie ...	2005	17469265
mediation of ultrafast light-harvesting by a central dimer in phycoerythrin 545 studied by transient absorption and global analysis.	we report ultrafast femtosecond transient absorption measurements of energy-transfer dynamics for the antenna protein phycoerythrin 545, pe545, isolated from a unicellular cryptophyte rhodomonas cs24. the phycoerythrobilins are excited at both 485 and 530 nm, and the spectral response is probed between 400 and 700 nm. room-temperature measurements are contrasted with measurements at 77 k. an evolution-associated difference spectra (eads) analysis is combined with estimations of bilin spectral po ...	2005	16852785
production of lipases by four anoxygenic purple non-sulphur phototrophic bacteria.	production of lipases by rhodopseudomonas palustris, rhodobacter sphaeroides, rhodocyclus gelatinosus and rhodocyclus tenuis in different synthetic media was investigated. rc. gelatinosus followed by rb. sphaeroides were good producers of lipases, while rps. palustris and rc. tenuis were poor in lipase secretion. lipase secretion by rc. gelatinosus was adaptive in nature, while other three bacterial behavior was inconsistent. no positive correlation could be observed between growth and lipase pr ...	2005	18697729
characterization of pii family (glnk1, glnk2, and glnb) protein uridylylation in response to nitrogen availability for rhodopseudomonas palustris.	the glnk and glnb proteins are members of the pii signal transduction protein family, which is essential in nitrogen regulation due to this protein family's ability to sense internal cellular ammonium levels and control cellular response. the role of glnk in nitrogen regulation has been studied in a variety of bacteria but previously has been uncharacterized in the purple nonsulfur anoxygenic phototropic bacterium rhodopseudomonas palustris. r. palustris has tremendous metabolic versatility in i ...	2006	16860774
efl gtpase in cryptomonads and the distribution of efl and ef-1alpha in chromalveolates.	efl (ef-like protein) is a member of the gtpase superfamily that includes several translation factors. because it has only been found in a few eukaryotic lineages and its presence correlates with the absence of the related core translation factor ef-1alpha, its distribution is hypothesized to be the result of lateral gene transfer and replacement of ef-1alpha. in one supergroup of eukaryotes, the chromalveolates, two major lineages were found to contain efl (dinoflagellates and haptophytes), whi ...	2006	16904374
regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in rhodopseudomonas palustris.	rhodopseudomonas palustris is a purple, facultatively phototrophic bacterium that uses hydrogen gas as an electron donor for carbon dioxide fixation during photoautotrophic growth or for ammonia synthesis during nitrogen fixation. it also uses hydrogen as an electron supplement to enable the complete assimilation of oxidized carbon compounds, such as malate, into cell material during photoheterotrophic growth. the r. palustris genome predicts a membrane-bound nickel-iron uptake hydrogenase and s ...	2006	16923881
the cyanobacterial genome core and the origin of photosynthesis.	comparative analysis of 15 complete cyanobacterial genome sequences, including "near minimal" genomes of five strains of prochlorococcus spp., revealed 1,054 protein families [core cyanobacterial clusters of orthologous groups of proteins (core cyogs)] encoded in at least 14 of them. the majority of the core cyogs are involved in central cellular functions that are shared with other bacteria; 50 core cyogs are specific for cyanobacteria, whereas 84 are exclusively shared by cyanobacteria and pla ...	2006	16924101
growth characteristics of rhodopseudomonas palustris cultured outdoors, in an underwater tubular photobioreactor, and investigation on photosynthetic efficiency.	the underwater tubular photobioreactor is a fully controlled outdoor system to study photosynthetic bacteria. before growing bacteria cells outdoors, two modified van niel medium (vn-a, vn-b) were tested under artificial light. during exponential growth, the specific growth rates were 0.0416 and 0.0434 h(-1), respectively; vn-b was chosen for outdoor experiments. the growth behavior of rhodopseudomonas palustris was investigated under a natural light-dark cycle (sunrise-sunset, 15l/9d) and a for ...	2006	16944131
characterization of phototrophic purple nonsulfur bacteria forming colored microbial mats in a swine wastewater ditch.	the community structure of pink-colored microbial mats naturally occurring in a swine wastewater ditch was studied by culture-independent biomarker and molecular methods as well as by conventional cultivation methods. the wastewater in the ditch contained acetate and propionate as the major carbon nutrients. thin-section electron microscopy revealed that the microbial mats were dominated by rod-shaped cells containing intracytoplasmic membranes of the lamellar type. smaller numbers of oval cells ...	2006	16957249
probing the electronic structure and conformational flexibility of individual light-harvesting 3 complexes by optical single-molecule spectroscopy.	we present fluorescence-excitation spectra of individual light-harvesting 3 (lh3 or b800-820) complexes of rhodopseudomonas acidophila at 1.2 k. the optical single-molecule studies were employed to investigate the electronic structure as well as the conformational flexibility of the individual pigment-protein complexes. the optical spectra resemble those of individual light-harvesting 2 (lh2) complexes, in agreement with the structural similarity of both types of complexes. although variations a ...	2006	16970502
structures of two bacterial prolyl-trna synthetases with and without a cis-editing domain.	prolyl-trna synthetases (prorss) are unique among synthetases in that they have diverse architectures, notably the variable presence of a cis-editing domain homologous to the freestanding deacylase proteins ybak and prox. here, we describe crystal structures of two bacterial prorss from the pathogen enterococcus faecalis, which possesses an editing domain, and from rhodopseudomonas palustris, which does not. we compare the overall structure and binding mode of atp and prolyl-adenylate with those ...	2006	17027500
robust estimation of peptide abundance ratios and rigorous scoring of their variability and bias in quantitative shotgun proteomics.	the abundance ratio between the light and heavy isotopologues of an isotopically labeled peptide can be estimated from their selected ion chromatograms. however, quantitative shotgun proteomics measurements yield selected ion chromatograms at highly variable signal-to-noise ratios for tens of thousands of peptides. this challenge calls for algorithms that not only robustly estimate the abundance ratios of different peptides but also rigorously score each abundance ratio for the expected estimati ...	2006	17037910
prorata: a quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation.	a profile likelihood algorithm is proposed for quantitative shotgun proteomics to infer the abundance ratios of proteins from the abundance ratios of isotopically labeled peptides derived from proteolysis. previously, we have shown that the estimation variability and bias of peptide abundance ratios can be predicted from their profile signal-to-noise ratios. given multiple quantified peptides for a protein, the profile likelihood algorithm probabilistically weighs the peptide abundance ratios by ...	2006	17037911
the reach of the genome signature in prokaryotes.	with the increased availability of sequenced genomes there have been several initiatives to infer evolutionary relationships by whole genome characteristics. one of these studies suggested good congruence between genome synteny, shared gene content, 16s ribosomal dna identity, codon usage and the genome signature in prokaryotes. here we rigorously test the phylogenetic signal of the genome signature, which consists of the genome-specific relative frequencies of dinucleotides, on 334 sequenced pr ...	2006	17040564
badm is a transcriptional repressor and one of three regulators that control benzoyl coenzyme a reductase gene expression in rhodopseudomonas palustris.	the rate-limiting enzyme of anaerobic benzoate degradation by rhodopseudomonas palustris, benzoyl coenzyme a (coa) reductase, is highly sensitive to oxygen, and its synthesis is tightly regulated. we determined that a previously unknown gene in the benzoate gene cluster, badm, encodes a transcriptional repressor of benzoyl-coa reductase gene expression. badm controls gene expression from the benzoyl-coa reductase promoter in concert with two previously described transcriptional activators.	2006	17041049
lateral organization of a membrane protein in a supported binary lipid domain: direct observation of the organization of bacterial light-harvesting complex 2 by total internal reflection fluorescence microscopy.	a unique method is described for directly observing the lateral organization of a membrane protein (bacterial light-harvesting complex lh2) in a supported lipid bilayer using total internal reflection fluorescence (tirf) microscopy. the supported lipid bilayer consisted of anionic 1,2-dioleoyl-sn-glycero-3-[phospho-rac-(1'-glycerol)] (dopg) and 1,2-distearoly-sn-3-[phospho-rac-(1'-glycerol)] (dspg) and was formed through the rupture of a giant vesicle on a positively charged coverslip. tirf micr ...	2006	16732671
rhodoblastus sphagnicola sp. nov., a novel acidophilic purple non-sulfur bacterium from sphagnum peat bog.	an isolate of purple non-sulfur bacteria was obtained from an acidic sphagnum peat bog and designated strain rs(t). the colour of cell suspensions of this bacterium growing in the light under anaerobic conditions is purplish red. cells of strain rs(t) are rod-shaped, 0.8-1.0 microm wide and 2.0-6.0 microm long, motile by means of polar flagella, reproduce by budding and have a tendency to form rosette-like clusters in older cultures. the cells contain lamellar intracytoplasmic membranes underlyi ...	2006	16738120
detecting differential and correlated protein expression in label-free shotgun proteomics.	recent studies have revealed a relationship between protein abundance and sampling statistics, such as sequence coverage, peptide count, and spectral count, in label-free liquid chromatography-tandem mass spectrometry (lc-ms/ms) shotgun proteomics. the use of sampling statistics offers a promising method of measuring relative protein abundance and detecting differentially expressed or coexpressed proteins. we performed a systematic analysis of various approaches to quantifying differential prote ...	2006	17081042
expressed peptide tags: an additional layer of data for genome annotation.	while genome sequencing is becoming ever more routine, genome annotation remains a challenging process. identification of the coding sequences within the genomic milieu presents a tremendous challenge, especially for eukaryotes with their complex gene architectures. here, we present a method to assist the annotation process through the use of proteomic data and bioinformatics. mass spectra of digested protein preparations of the organism of interest were acquired and searched against a protein d ...	2006	17081056
proton uptake in the reaction center mutant l210dn from rhodobacter sphaeroides via protonated water molecules.	the reaction center (rc) of rhodobacter sphaeroides uses light energy to reduce and protonate a quinone molecule, qb (the secondary quinone electron acceptor), to form quinol, qbh2. asp210 in the l-subunit has been shown to be a catalytic residue in this process. mutation of asp210 to asn leads to a deceleration of reoxidation of qa- in the qa-qb --> qaqb- transition. here we determined the structure of the asp210 to asn mutant to 2.5 a and show that there are no major structural differences as ...	2006	17105193
self-assembled monolayer of light-harvesting core complexes of photosynthetic bacteria on an amino-terminated ito electrode.	light-harvesting antenna core (lh1-rc) complexes isolated from rhodospirillum rubrum and rhodopseudomonas palustris were successfully self-assembled on an ito electrode modified with 3-aminopropyltriethoxysilane. near infra-red (nir) absorption, fluorescence, and ir spectra of these lh1-rc complexes indicated that these lh1-rc complexes on the electrode were stable on the electrode. an efficient energy transfer and photocurrent responses of these lh1-rc complexes on the electrode were observed u ...	2006	17111238
structural determination of dihydro- and tetrahydrogeranylgeranyl groups at the 17-propionate of bacteriochlorophylls-a.	in the final stage of bacteriochlorophyll (bchl) biosynthesis, the presence of bchl-a molecules possessing dihydrogeranylgeranyl and tetrahydrogeranylgeranyl groups at the 17-propionate has been reported. however, the molecular structures of such bchls-a have not yet been determined in terms of the positions of cc double bonds in the 17(2)-ester. in this study, we isolated significant amounts of such pure bchls-a from rhodopseudomonas palustris and determined their structures by both mass spectr ...	2006	17123518
rhodopseudomonas palustris cga009 has two functional ppsr genes, each of which encodes a repressor of photosynthesis gene expression.	the ppsr protein is a regulator of redox-dependent photosystem development in purple phototrophic bacteria. in contrast to most species, rhodopseudomonas palustris contains two ppsr genes. we show that the inactivation of each of the r. palustris strain cga009 ppsr genes results in an elevated level of formation of the photosystem under dark aerobic conditions. absorption spectra of the two ppsr mutants revealed qualitative and quantitative differences in light-harvesting peak amplitude increase ...	2006	17128983
how energy funnels from the phycoerythrin antenna complex to photosystem i and photosystem ii in cryptophyte rhodomonas cs24 cells.	we report an investigation of energy migration dynamics in intact cells of the photosynthetic cryptophyte rhodomonas cs24 using analyses of steady-state and time-resolved fluorescence anisotropy measurements. by fitting a specific model to the fluorescence data, we obtain three time scales (17, 58, and 113 ps) by which the energy is transferred from phycoerythrin 545 (pe545) to the membrane-associated chlorophylls (chls). we propose that these time scales reflect both an angular distribution of ...	2006	17149931
diverse bacteria associated with root nodules of spontaneous legumes in tunisia and first report for nifh-like gene within the genera microbacterium and starkeya.	we characterized 34 endophytic bacterial isolates associated to root nodules collected from spontaneous legumes in the arid zone of tunisia by 16s rdna polymerase chain reaction (pcr)-restriction fragment length polymorphism, whole cell protein sodium dodecyl sulfate-polyacrylamide gel electrophoresis (sds-page), 16s rdna and 16s-23s rdna internal transcribed spacer sequencing. phylogenetically, these isolates belong to the branches containing the genera inquilinus, bosea, rhodopseudomonas, para ...	2006	16598639
simultaneous reduction and alkylation of protein disulfides in a centrifugal ultrafiltration device prior to two-dimensional gel electrophoresis.	reduction and alkylation of protein disulfides prior to ief, when performed directly in a centrifugal ultrafiltration device, provides an effective means of terminating the alkylation reaction, concentrating the proteins for analysis, and removing ionic impurities that interfere with ief. when cells were lysed in "buffers" that support the activity of enzymes such as lysozyme and benzonase, the conductivity of the resulting lysate was an order of magnitude higher than when lysis was induced by c ...	2006	16602706
optimization of wastewater feeding for single-cell protein production in an anaerobic wastewater treatment process utilizing purple non-sulfur bacteria in mixed culture condition.	impacts of operation timing of feeding and withdrawal on anaerobic wastewater treatment utilizing purple non-sulfur bacteria have been investigated in mixed culture condition with acidogenic bacteria. simulated wastewater containing glucose was treated in a laboratory-scale chemostat reactor, changing the timing of wastewater feeding and withdrawal. rhodopseudomonas palustris, which does not utilize glucose as a substrate, was inoculated in the reactor. rps. palustris was detected by a fluoresce ...	2006	16647776
comparative rates of evolution in endosymbiotic nuclear genomes.	the nucleomorphs associated with secondary plastids of cryptomonads and chlorarachniophytes are the sole examples of organelles with eukaryotic nuclear genomes. although not as widespread as their prokaryotic equivalents in mitochondria and plastids, nucleomorph genomes share similarities in terms of reduction and compaction. they also differ in several aspects, not least in that they encode proteins that target to the plastid, and so function in a different compartment from that in which they a ...	2006	16772046
carotenoid stoichiometry in the lh2 crystal: no spectral evidence for the presence of the second molecule in the alpha/beta-apoprotein dimer.	in this work we have investigated the carotenoid-protein interactions in lh2 complexes of rhodopseudomonas acidophila both in "free in solution" mixed-micelles and in three-dimensional crystals by raman spectroscopy in resonance with the carotenoid (car) molecules. we show that the car molecules when bound to their binding pockets show no significant differences when the complexes are "free in solution" or packed in crystalline arrays. furthermore, there is no significant wavelength dependence i ...	2006	16790242
ghp, a new c-type green heme protein from halochromatium salexigens and other proteobacteria.	we have isolated a minor soluble green-colored heme protein (ghp) from the purple sulfur bacterium, halochromatium salexigens, which contains a c-type heme. a similar protein has also been observed in the purple bacteria allochromatium vinosum and rhodopseudomonas cryptolactis. this protein has wavelength maxima at 355, 420, and 540 nm and remains unchanged upon addition of sodium dithionite or potassium ferricyanide, indicating either an unusually low or high redox potential, respectively. the ...	2006	16817906
pleomorphomonas koreensis sp. nov., a nitrogen-fixing species in the order rhizobiales.	a gram-negative, non-motile, non-spore-forming, rod-shaped bacterium (strain y9(t)) was isolated from a contaminated culture of the phototrophic bacterium rhodopseudomonas palustris, and was investigated using a polyphasic taxonomic approach. a phylogenetic analysis based on 16s rrna gene sequences showed that strain y9(t) belonged to the order rhizobiales in the alphaproteobacteria. comparison of phylogenetic data indicated that it was most closely related to pleomorphomonas oryzae (98.5 % simi ...	2006	16825646
physicochemical properties of malate dehydrogenase from the bacterium rhodopseudomonas palustris strain f8pt.	electrophoretically homogenous isoforms of malate dehydrogenase with different quaternary structure were prepared from rhodopseudomonas palustris strain f8pt cultured photolithoheterotrophically on malate and acetate. by selective inhibition of the tricarboxylic acid cycle or glyoxylate cycle, it was shown that the dimeric isoform of the enzyme is responsible for krebs cycle functioning and the tetrameric isoform is involved in functioning of the glyoxylate cycle.	2006	16827662
efficient and specific trypsin digestion of microgram to nanogram quantities of proteins in organic-aqueous solvent systems.	mass spectrometry-based identification of the components of multiprotein complexes often involves solution-phase proteolytic digestion of the complex. the affinity purification of individual protein complexes often yields nanogram to low-microgram amounts of protein, which poses several challenges for enzymatic digestion and protein identification. we tested different solvent systems to optimize trypsin digestions of samples containing limited amounts of protein for subsequent analysis by lc-ms- ...	2006	16383319
high-affinity vanadate transport system in the cyanobacterium anabaena variabilis atcc 29413.	high-affinity vanadate transport systems have not heretofore been identified in any organism. anabaena variabilis, which can fix nitrogen by using an alternative v-dependent nitrogenase, transported vanadate well. the concentration of vanadate giving half-maximum v-nitrogenase activity when added to v-starved cells was about 3 x 10(-9) m. the genes for an abc-type vanadate transport system, vupabc, were found in a. variabilis about 5 kb from the major cluster of genes encoding the v-nitrogenase, ...	2006	16385036
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 ...	2006	16399834
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 ...	2006	16399835
carotenoid-bacteriochlorophyll energy transfer in lh2 complexes studied with 10-fs time resolution.	in this report, we present a study of carotenoid-bacteriochlorophyll energy transfer processes in two peripheral light-harvesting complexes (known as lh2) from purple bacteria. we use transient absorption spectroscopy with approximately 10 fs temporal resolution, which is necessary to observe the very fast energy relaxation processes. by comparing excited-state dynamics of the carotenoids in organic solvents and inside the lh2 complexes, it has been possible to directly evaluate their energy tra ...	2006	16428274
conformational relaxation of single bacterial light-harvesting complexes.	we have employed the technique of single-molecule fluorescence microspectroscopy to investigate the spontaneous conformational evolution of individual peripheral lh2 complexes from the purple bacterium rhodopseudomonas acidophila. fluorescence microscopy is a sensitive tool, which allows the spectral changes of single complexes to be monitored on a time scale from 0.1 s to many minutes. here we have investigated "natural" (occurring in the absence of excitation) spectral diffusion after a spectr ...	2006	16430204
distinctive organization of genes for light-harvesting proteins in the cryptophyte alga rhodomonas.	cryptophyte algae contain two kinds of light-harvesting protein, phycobiliproteins and chlorophyll a,c-binding proteins. the beta subunit of the phycobiliprotein phycoerythrin (pe) is encoded in the chloroplast. genes for the other pe polypeptides are located in the nucleus but little is known of their organization. we cloned and sequenced six cpea genes encoding the phycoerythrin alpha subunit from a genomic library of the cryptophyte rhodomonas cs24. derived peptide sequences of the cpea genes ...	2006	16431038
dynamics of the emission spectrum of a single lh2 complex: interplay of slow and fast nuclear motions.	we have studied the relationship between the realizations of static disorder and the emission spectra observed for a single lh2 complex. we show that the experimentally observed spectral fluctuations reflect realizations of the disorder in the b850 ring associated with different degrees of exciton delocalization and different effective coupling of the excitons to phonon modes. the main spectral features cannot be explained using models with correlated disorder associated with elliptical deformat ...	2006	16443651
arsenic detoxification and evolution of trimethylarsine gas by a microbial arsenite s-adenosylmethionine methyltransferase.	in this article, a mechanism of arsenite [as(iii)]resistance through methylation and subsequent volatization is described. heterologous expression of arsm from rhodopseudomonas palustris was shown to confer as(iii) resistance to an arsenic-sensitive strain of escherichia coli. arsm catalyzes the formation of a number of methylated intermediates from as(iii), with trimethylarsine as the end product. the net result is loss of arsenic, from both the medium and the cells. because arsm homologues are ...	2006	16452170