Publications

identification of the methylhopanes in sediments and petroleum.	three c31 methylhopanes have been prepared by partial synthesis from appropriate diplopterol precursors. 2 alpha-methyldiplopterol (prepared from 22-hydroxyhopan-3-one), 2 beta-methyldiplopterol (isolated from methylobacterium organophilum), and a mixture of diplopterol and 3 beta-methyldiplopterol (isolated from methylococcus capsulatus) were each converted to the corresponding 17 alpha(h), 21 beta(h)-hopane. comparison of these standards, using gas chromatography--mass spectrometry with mult ...	1990	11537193
the effects of growth temperature on the methyl sterol and phospholipid fatty acid composition of methylococcus capsulatus (bath).	growth of methylococcus capsulatus (bath) at temperatures ranging from 30 to 50 degrees c resulted in changes to the whole cell lipid constituents. as temperature was lowered, the overall proportion of hexadecenoic acid (c16:1) increased, and the relative proportions of the delta 9, delta 10 and delta 11 c16:1 double bond positional isomers changed. methyl sterol content also increased as the growth temperature was lowered. the highest amounts of methyl sterol were found in 30 degrees c cells ...	1992	11537858
presence of methyl sterol and bacteriohopanepolyol in an outer-membrane preparation from methylococcus capsulatus (bath).	cytoplasmic/intracytoplasmic and outer membrane preparations of methylococcus capsulatus (bath) were isolated by sucrose density gradient centrifugation of a total membrane fraction prepared by disruption using a french pressure cell. the cytoplasmic and/or intracytoplasmic membrane fraction consisted of two distinct bands, ia and ib (buoyant densities 1.16 and 1.8 g ml-1, respectively) that together contained 57% of the protein, 68% of the phospholipid, 73% of the ubiquinone and 89% of the cn- ...	1992	11538386
carbon isotopic fractionation in lipids from methanotrophic bacteria: relevance for interpretation of the geochemical record of biomarkers.	experiments with cultured aerobic methane oxidising bacteria confirm that their biomarker lipids will be significantly depleted in 13c compared to the substrate. the methanotrophic bacteria methylococcus capsulatus and methylomonas methanica, grown on methane and using the rump cycle for carbon assimilation, show maximum 13c fractionation of approximately 30% in the resultant biomass. in m. capsulatus, the maximum fractionation is observed in the earliest part of the exponential growth stage an ...	1994	11540111
evidence for the synthesis of the multi-positional isomers of monounsaturated fatty acid in methylococcus capsusatus by the anaerobic pathway.	the biosynthesis of the positional isomers of the monounsaturated fatty acids of methylococcus capsulatus (bath) has been investigated by studying the incorporation of [2-14c]malonyl coa into long-chain fatty acids in vitro. the major unsaturated products were delta 9 16 : 1 and delta 11 18 : 1; however, delta 8, delta 10, and delta 11, 16 : 1, as well as, delta 10, delta 12 and delta 13 18 : 1 were also synthesized. the exclusion of o2 from the reaction vessel did not affect the synthesis of ...	1989	11542184
density functional studies of oxidized and reduced methane monooxygenase. optimized geometries and exchange coupling of active site clusters.	the conflicting protein crystallography data for the oxidized form (mmoh(ox)) of methane monooxygenase present a dilemma regarding the identity of the solvent-derived bridging ligands within the active site: do they comprise a diiron unit bridged by 1h2o and 1oh(-) as postulated for methylococcus capsulatus or 2oh(-) ligands as suggested for methylosinus trichosporium? using models derived explicitly from the m. capsulatus and m. trichosporium protein data, spin-unrestricted density functional m ...	2001	11559090
energetics of oxidized and reduced methane monooxygenase active site clusters in the protein environment.	using the density functional optimized active site geometries obtained in the accompanying paper (lovell, t.; li, j.; noodleman, l. inorg. chem. 2001, 40, 5251), a combined density functional and electrostatics approach has been applied to further address attendant uncertainties in the protonation states of the bridging ligands for mmoh(ox). the acidities (pk(a)s) associated with the bridging h(2)o ligand in methylococcus capsulatus and corresponding energetics of each active site cluster intera ...	2001	11559091
eubacterial diterpene cyclase genes essential for production of the isoprenoid antibiotic terpentecin.	a gene cluster containing the mevalonate pathway genes (open reading frame 2 [orf2] to orf7) for the formation of isopentenyl diphosphate and a geranylgeranyl diphosphate (ggdp) synthase gene (orf1) had previously been cloned from streptomyces griseolosporeus strain mf730-n6, a diterpenoid antibiotic, terpentecin (tp) producer (y. hamano, t. dairi, m. yamamoto, t. kawasaki, k kaneda, t. kuzuyama, n. itoh, and h. seto, biosci. biotech. biochem. 65:1627-1635, 2001). sequence analysis in the upstre ...	2001	11567009
family- and genus-level 16s rrna-targeted oligonucleotide probes for ecological studies of methanotrophic bacteria.	methanotrophic bacteria play a major role in the global carbon cycle, degrade xenobiotic pollutants, and have the potential for a variety of biotechnological applications. to facilitate ecological studies of these important organisms, we developed a suite of oligonucleotide probes for quantitative analysis of methanotroph-specific 16s rrna from environmental samples. two probes target methanotrophs in the family methylocystaceae (type ii methanotrophs) as a group. no oligonucleotide signatures t ...	2001	11571178
detection and enumeration of methanotrophs in acidic sphagnum peat by 16s rrna fluorescence in situ hybridization, including the use of newly developed oligonucleotide probes for methylocella palustris.	two 16s rrna-targeted oligonucleotide probes, mcell-1026 and mcell-181, were developed for specific detection of the acidophilic methanotroph methylocella palustris using fluorescence in situ hybridization (fish). the fluorescence signal of probe mcell-181 was enhanced by its combined application with the oligonucleotide helper probe h158. mcell-1026 and mcell-181, as well as 16s rrna oligonucleotide probes with reported group specificity for either type i methanotrophs (probes m-84 and m-705) o ...	2001	11571193
the esat-6 gene cluster of mycobacterium tuberculosis and other high g+c gram-positive bacteria.	the genome of mycobacterium tuberculosis h37rv has five copies of a cluster of genes known as the esat-6 loci. these clusters contain members of the cfp-10 (lhp) and esat-6 (esat-6) gene families (encoding secreted t-cell antigens that lack detectable secretion signals) as well as genes encoding secreted, cell-wall-associated subtilisin-like serine proteases, putative abc transporters, atp-binding proteins and other membrane-associated proteins. these membrane-associated and energy-providing pro ...	2001	11597336
two distinct monooxygenases for alkane oxidation in nocardioides sp. strain cf8.	alkane monooxygenases in nocardioides sp. strain cf8 were examined at the physiological and genetic levels. strain cf8 can utilize alkanes ranging in chain length from c(2) to c(16). butane degradation by butane-grown cells was strongly inhibited by allylthiourea, a copper-selective chelator, while hexane-, octane-, and decane-grown cells showed detectable butane degradation activity in the presence of allylthiourea. growth on butane and hexane was strongly inhibited by 1-hexyne, while 1-hexyne ...	2001	11679317
signature lipids and stable carbon isotope analyses of octopus spring hyperthermophilic communities compared with those of aquificales representatives.	the molecular and isotopic compositions of lipid biomarkers of cultured aquificales genera have been used to study the community and trophic structure of the hyperthermophilic pink streamers and vent biofilm from octopus spring. thermocrinis ruber, thermocrinis sp. strain hi 11/12, hydrogenobacter thermophilus tk-6, aquifex pyrophilus, and aquifex aeolicus all contained glycerol-ether phospholipids as well as acyl glycerides. the n-c(20:1) and cy-c(21) fatty acids dominated all of the aquificale ...	2001	11679343
membrane-associated quinoprotein formaldehyde dehydrogenase from methylococcus capsulatus bath.	a membrane-associated, dye-linked formaldehyde dehydrogenase (dl-faldh) was isolated from the obligate methylotroph methylococcus capsulatus bath. the enzyme was the major formaldehyde-oxidizing enzyme in cells cultured in high (above 1 micromol of cu per mg of cell protein) copper medium and expressing the membrane-associated methane monooxygenase. soluble nad(p)(+)-linked formaldehyde oxidation was the major activity in cells cultured in low-copper medium and expressing the soluble methane mon ...	2001	11698372
why orfy? characterization of mmod, a long overlooked component of the soluble methane monooxygenase from methylococcus capsulatus (bath).	soluble methane monooxygenase (smmo) has been studied intensively to understand the mechanism by which it catalyzes the remarkable oxidation of methane to methanol. the cluster of genes that encode for the three characterized protein components of smmo (mmoh, mmob, and mmor) contains an additional open reading frame (orfy) of unknown function. in the present study, mmod, the protein encoded by orfy, was overexpressed as a fusion protein in escherichia coli. pure mmod was obtained in high yields ...	2002	11709550
consumption of tropospheric levels of methyl bromide by c(1) compound-utilizing bacteria and comparison to saturation kinetics.	pure cultures of methylotrophs and methanotrophs are known to oxidize methyl bromide (mebr); however, their ability to oxidize tropospheric concentrations (parts per trillion by volume [pptv]) has not been tested. methylotrophs and methanotrophs were able to consume mebr provided at levels that mimicked the tropospheric mixing ratio of mebr (12 pptv) at equilibrium with surface waters ( approximately 2 pm). kinetic investigations using picomolar concentrations of mebr in a continuously stirred t ...	2001	11722890
electron-transfer reactions of the reductase component of soluble methane monooxygenase from methylococcus capsulatus (bath).	soluble methane monooxygenase (smmo) catalyzes the hydroxylation of methane by dioxygen to afford methanol and water, the first step of carbon assimilation in methanotrophic bacteria. this enzyme comprises three protein components: a hydroxylase (mmoh) that contains a dinuclear nonheme iron active site; a reductase (mmor) that facilitates electron transfer from nadh to the diiron site of mmoh; and a coupling protein (mmob). mmor uses a noncovalently bound fad cofactor and a [2fe-2s] cluster to m ...	2001	11732913
molecular characterization of structural genes coding for a membrane bound hydrogenase in methylococcus capsulatus (bath).	the first gene cluster encoding for a membrane bound [nife] hydrogenase from a methanotroph, methylococcus capsulatus (bath), was cloned and sequenced. the cluster consisted of the structural genes hups and hupl and accessory genes hupe, hupc and hupd. a deltahupsl deletion mutant of mc. capsulatus was constructed by marker exchange mutagenesis. membrane associated hydrogenase activity disappeared. the membrane associated hydrogenase appeared to have a hydrogen uptake function in vivo.	2001	11750803
directed evolution of toluene ortho-monooxygenase for enhanced 1-naphthol synthesis and chlorinated ethene degradation.	trichloroethylene (tce) is the most frequently detected groundwater contaminant, and 1-naphthol is an important chemical manufacturing intermediate. directed evolution was used to increase the activity of toluene ortho-monooxygenase (tom) of burkholderia cepacia g4 for both chlorinated ethenes and naphthalene oxidation. when expressed in escherichia coli, the variant tom-green degraded tce (2.5 +/- 0.3 versus 1.39 +/- 0.05 nmol/min/mg of protein), 1,1-dichloroethylene, and trans-dichloroethylene ...	2002	11751810
[search for methanotrophic producers of exopolysaccharides].	bacteria that produce exopolysaccharides (eps) and use methane as the only source of carbon were selected by studying a collection of methanotroph strains: methylococcus capsulatus e 494, 874, and 3009; m. thermophilus 111p, 112p, and 119p; methylobacter ucrainicus 159 and 161; m. luteus 57v and 12b; methylobacter sp. 100; methylomonas rubra 15 sh and sk-32; methylosinus trichosporium ov3b, ov5b and 4e; m. sporium 5, 12, a20d, and 90v; and methylocystis parvus ovvp. mesophilic methanotroph strai ...	2001	11771325
nmr structure of the [2fe-2s] ferredoxin domain from soluble methane monooxygenase reductase and interaction with its hydroxylase.	the soluble methane monooxygenase (smmo) from methylococcus capsulatus (bath) is a multicomponent enzyme system required for the conversion of methane to methanol. it comprises a hydroxylase, a regulatory protein, and a reductase. the reductase contains two domains: an nadh-binding and fad-containing flavin domain and a ferredoxin (fd) domain carrying a [2fe-2s] cofactor. here, we report the solution structure of the reduced form of the 98-amino acid fd domain (blazyk, j. l., and lippard, s. j. ...	2002	11772001
duplicate copies of genes encoding methanesulfonate monooxygenase in marinosulfonomonas methylotropha strain tr3 and detection of methanesulfonate utilizers in the environment.	marinosulfonomonas methylotropha strain tr3 is a marine methylotroph that uses methanesulfonic acid (msa) as a sole carbon and energy source. the genes from m. methylotropha strain tr3 encoding methanesulfonate monooxygenase, the enzyme responsible for the initial oxidation of msa to formaldehyde and sulfite, were cloned and sequenced. they were located on two gene clusters on the chromosome of this bacterium. a 5.0-kbp hindiii fragment contained msma, msmb, and msmc, encoding the large and smal ...	2002	11772638
detection and localization of two hydrogenases in methylococcus capsulatus (bath) and their potential role in methane metabolism.	methylococcus capsulatus (bath) was shown to contain two distinct hydrogenases, a soluble hydrogenase and a membrane-bound hydrogenase. this is the first report of a membrane-bound hydrogenase in methanotrophs. both enzymes were expressed apparently constitutively under normal growth conditions. the soluble hydrogenase was capable of reducing nad(+) with molecular hydrogen. the activities of both soluble and particulate methane monooxygenases could be driven by molecular hydrogen. this confirmed ...	2002	11807566
evidence that a type-2 nadh:quinone oxidoreductase mediates electron transfer to particulate methane monooxygenase in methylococcus capsulatus.	nadh readily provides reducing equivalents to membrane-bound methane monooxygenase (pmmo) from methylococcus capsulatus (bath) in isolated membrane fractions, but detergent solubilization disrupts this electron-transfer process. addition of exogenous quinones (especially decyl-plastoquinone and duroquinone) restores the nadh-dependent pmmo activity. results of inhibitor and substrate dependence of this activity indicate the presence of only a type-2 nadh:quinone oxidoreductase (ndh-2). a 100-fol ...	2002	11811946
nature, nomenclature and taxonomy of obligate methanol utilizing strains.	in a screening program, a number of different bacterial strains with the ability to utilize methanol as a sole carbon and energy source were isolated and described. they are well known methanol utilizing genera pseudomonas, klebsiella, micrococcus, methylomonas or, on the contrary, the new, unknown genera and species of methylotrophic bacteria. in the last category, acinetobacter and alcaligenes are the new reported genera of organisms able to use methanol as a sole carbon and energy source. the ...	1999	11845445
positively charged amino acids are essential for electron transfer and protein-protein interactions in the soluble methane monooxygenase complex from methylococcus capsulatus (bath).	the soluble methane monooxygenase (smmo) complex from methylococcus capsulatus (bath) catalyses oxygen- and nad(p)h-dependent oxygenation of methane, propene, and other substrates. whole-complex smmo oxygenase activity requires all three smmo components: the hydroxylase, the reductase, and protein b. also, in the presence of hydrogen peroxide, the hydroxylase alone catalyzes substrate oxygenation via the peroxide shunt reaction. we investigated the effect of amine cross-linking on hydroxylase ac ...	2002	11851404
the ribulose-1,5-bisphosphate carboxylase/oxygenase gene cluster of methylococcus capsulatus (bath).	the genes encoding the ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) from methylococcus capsulatus (bath) were localised to an 8.3-kb ecori fragment of the genome. genes encoding the large subunit ( cbbl), small subunit ( cbbs) and putative regulatory gene ( cbbq) were shown to be located on one cluster. surprisingly, cbbo, a second putative regulatory gene, was not located in the remaining 1.2-kb downstream (3') of cbbq. however, probing of the m. capsulatus (bath) genome with cbbo ...	2002	11889481
methane oxidation by cell-free extracts of methylococcus capsulatus.		1970	11945445
residues near the n-terminus of protein b control autocatalytic proteolysis and the activity of soluble methane mono-oxygenase.	soluble methane mono-oxygenase (smmo) of methylococcus capsulatus (bath) catalyses the o2-dependent and nad(p)h-dependent oxygenation of methane and numerous other substrates. during purification, the smmo enzyme complex, which comprises three components and has a molecular mass in excess of 300 kda, becomes inactivated because of cleavage of just 12 amino acids from the n-terminus of protein b, which is the smallest component of smmo and the only one without prosthetic groups. here we have show ...	2002	11952785
a continuous-wave electron-nuclear double resonance (x-band) study of the cu2+ sites of particulate methane mono-oxygenase of methylococcus capsulatus (strain m) in membrane and pure dopamine beta-mono-oxygenase of the adrenal medulla.	all methanotrophic bacteria express a membrane-bound (particulate) methane mono-oxygenase (pmmo). in the present study, we have investigated pmmo in membrane fragments from methylococcus capsulatus (strain m). pmmo contains a typical type-2 cu(2+) centre with the following epr parameters: g(z) 2.24, g(x,y) 2.06, a(cu)(z) 19.0 mt and a(cu)(x,y) 1.0 mt. simulation of the cu(2+) spectrum yielded a best match by using four equivalent nitrogens (a(n)=1.5 mt, 42 mhz). incubation with ferricyanide neit ...	2002	11964168
heterotrophic bacteria growing in association with methylococcus capsulatus (bath) in a single cell protein production process.	the methanotrophic bacterium methylococcus capsulatus (bath) grows on pure methane. however, in a single cell protein production process using natural gas as methane source, a bacterial consortium is necessary to support growth over longer periods in continuous cultures. in different bioreactors of norferm danmark a/s, three bacteria consistently invaded m. capsulatus cultures growing under semi-sterile conditions in continuous culture. these bacteria have now been identified as a not yet descri ...	2002	12073128
reactions of methane monooxygenase intermediate q with derivatized methanes.	the reactivity of intermediate q of soluble methane monooxygenase from methylococcus capsulatus (bath) with a series of derivatized methanes of general formula ch3-r, where r = cn, no2, and oh, and their deuterated analogues is described. despite relatively slow reactions, significant kinetic isotope effects, kies, are observed in reactions with acetonitrile and nitromethane; however, none is obtained with methanol. in addition, evidence of a substrate-binding step that occurs prior to substrate ...	2002	12137510
worldwide distribution of nitrosococcus oceani, a marine ammonia-oxidizing gamma-proteobacterium, detected by pcr and sequencing of 16s rrna and amoa genes.	diversity of cultured ammonia-oxidizing bacteria in the gamma-subdivision of the proteobacteria was investigated by using strains isolated from various parts of the world ocean. all the strains were very similar to each other on the basis of the sequences of both the 16s rrna and ammonia monooxygenase genes and could be characterized as a single species. sequences were also cloned directly from environmental dna from coastal pacific and atlantic sites, and these sequences represented the first n ...	2002	12147525
[effect of gas mixture component composition on the process of hard materials colonization by methanotrophic bacteria].	a device has been proposed which allows decreasing a possibility to contaminate the inoculum of methane-using bacteria (methanotrophs) under its growing. the gas mixture composition has been investigated for the intensity of grass and polysterene colonization by two species of methanotrophs: methylococcus capsulatus ucm b-3030, possessing hydrophilic surface and hydrophobic methylocystis parvus ukm b-3490t. it has been shown that immobilized methanotrophic bacteria can colonize the above materia ...	2002	12190038
determination of the carbon kinetic isotope effects on propane hydroxylation mediated by the methane monooxygenases from methylococcus capsulatus (bath) by using stable carbon isotopic analysis.	authentic propane with known position-specific carbon isotope composition at each carbon atom was subjected to hydroxylation by the particulate and soluble methane monooxygenase (pmmo and smmo) from methylococcus capsulatus (bath), and the corresponding position-specific carbon isotope content was redetermined for the product 2-propanol. neither the reaction mediated by pmmo nor that with smmo showed an intermolecular (12)c/(13)c kinetic isotope effect effect on the propane hydroxylation at the ...	2002	12203974
cholesterol in health and disease.		2002	12208856
a novel sterol 14alpha-demethylase/ferredoxin fusion protein (mccyp51fx) from methylococcus capsulatus represents a new class of the cytochrome p450 superfamily.	sterol 14alpha-demethylase encoded by cyp51 is a member of the cytochrome p450 (cyp) superfamily of enzymes and has been shown to have an essential role in sterol biosynthesis in eukaryotes, with orthologues recently being described in some bacteria. examination of the genome sequence data for the proteobacterium methylococcus capsulatus, a bacterial species known to produce sterol, revealed the presence of a single cyp with strong homology to cyp51, particularly to a form in mycobacterium tuber ...	2002	12235134
[study of nucleotide sequences of nifh genes in methanotrophic bacteria].	using a previously developed primer system, nifh gene fragments 450 nucleotides long were amplified, cloned, and sequenced for representatives of nitrogen-fixing methanotrophic bacteria of the genera methylococcus, methylocystis and methylosinus. fragments of nifh genes were also detected and sequenced in representatives of the genera methylomonas and methylobacter, which were not considered diazotrophs until recently. phylogenetic analysis revealed remoteness of nifh genes sequences of methanot ...	2002	12244720
biodegradation, biotransformation, and biocatalysis (b3).		2002	12324310
anaerobic oxidation of arsenite in mono lake water and by a facultative, arsenite-oxidizing chemoautotroph, strain mlhe-1.	arsenite [as(iii)]-enriched anoxic bottom water from mono lake, california, produced arsenate [as(v)] during incubation with either nitrate or nitrite. no such oxidation occurred in killed controls or in live samples incubated without added nitrate or nitrite. a small amount of biological as(iii) oxidation was observed in samples amended with fe(iii) chelated with nitrolotriacetic acid, although some chemical oxidation was also evident in killed controls. a pure culture, strain mlhe-1, that was ...	2002	12324322
the membrane-associated form of methane mono-oxygenase from methylococcus capsulatus (bath) is a copper/iron protein.	a protocol has been developed which permits the purification of a membrane-associated methane-oxidizing complex from methylococcus capsulatus (bath). this complex has approximately 5 fold higher specific activity than any purified particulate methane mono-oxygenase (pmmo) previously reported from m. capsulatus (bath). this efficiently functioning methane-oxidizing complex consists of the pmmo hydroxylase (pmmoh) and an unidentified component we have assigned as a potential pmmo reductase (pmmor) ...	2003	12379148
expression of duplicate msa genes in the salmonid pathogen renibacterium salmoninarum.	renibacterium salmoninarum is a gram-positive bacterium responsible for bacterial kidney disease of salmon and trout. r. salmoninarum has two identical copies of the gene encoding major soluble antigen (msa), an immunodominant, extracellular protein. to determine whether one or both copies of msa are expressed, reporter plasmids encoding a fusion of msa and green fluorescent protein controlled by 0.6 kb of promoter region from msa1 or msa2 were constructed and introduced into r. salmoninarum. si ...	2002	12406741
component b binding to the soluble methane monooxygenase hydroxylase by saturation-recovery epr spectroscopy of spin-labeled mmob.	spin-labeled cys89 of the soluble methane monooxygenase regulatory protein (mmob) from methylococcus capsulatus (bath) binds within 15 +/- 4 a of the hydroxylase (mmoh) diiron center, placing the mmob docking site in the mmoh "canyon" region on iron-coordinating helices e and f of the alpha-subunit.	2002	12418885
biochemistry and comparative genomics of sxxk superfamily acyltransferases offer a clue to the mycobacterial paradox: presence of penicillin-susceptible target proteins versus lack of efficiency of penicillin as therapeutic agent.	the bacterial acyltransferases of the sxxk superfamily vary enormously in sequence and function, with conservation of particular amino acid groups and all-alpha and alpha/beta folds. they occur as independent entities (free-standing polypeptides) and as modules linked to other polypeptides (protein fusions). they can be classified into three groups. the group i sxxk d,d-acyltransferases are ubiquitous in the bacterial world. they invariably bear the motifs sxxk, sxn(d), and kt(s)g. anchored in t ...	2002	12456788
expression and characterization of ferredoxin and flavin adenine dinucleotide binding domains of the reductase component of soluble methane monooxygenase from methylococcus capsulatus (bath).	soluble methane monooxygenase (smmo) from methylococcus capsulatus (bath) catalyzes the selective oxidation of methane to methanol, the first step in the primary catabolic pathway of methanotrophic bacteria. a reductase (mmor) mediates electron transfer from nadh through its fad and [2fe-2s] cofactors to the dinuclear non-heme iron sites housed in a hydroxylase (mmoh). the structurally distinct [2fe-2s], fad, and nadh binding domains of mmor facilitated division of the protein into its functiona ...	2002	12501207
novel methylotrophy genes of methylobacterium extorquens am1 identified by using transposon mutagenesis including a putative dihydromethanopterin reductase.	ten novel methylotrophy genes of the facultative methylotroph methylobacterium extorquens am1 were identified from a transposon mutagenesis screen. one of these genes encodes a product having identity with dihydrofolate reductase (dhfr). this mutant has a c(1)-defective and methanol-sensitive phenotype that has previously only been observed for strains defective in tetrahydromethanopterin (h(4)mpt)-dependent formaldehyde oxidation. these results suggest that this gene, dmra, may encode dihydrome ...	2003	12511515
tmrdb (tmrna database).	maintained at the university of texas health science center at tyler, texas, the tmrna database (tmrdb) is accessible at the url http://psyche.uthct.edu/dbs/tmrdb/tmrdb.html with mirror sites located at auburn university, auburn, alabama (http://www.ag.auburn.edu/mirror/tmrdb/) and the bioinformatics research center, aarhus, denmark (http://www.bioinf.au.dk/tmrdb/). the tmrdb collects and distributes information relevant to the study of tmrna. in trans-translation, this molecule combines propert ...	2003	12520048
multiple polypeptide forms observed in two-dimensional gels of methylococcus capsulatus (bath) polypeptides are generated during the separation procedure.	we have examined two-dimensional electrophoresis (2-de) gel maps of polypeptides from the gram-negative bacterium methylococcus capsulatus (bath) and found the same widespread trains of spots as often reported in 2-de gels of polypeptides of other gram-negative bacteria. some of the trains of polypeptides, both from the outer membrane and soluble protein fraction, were shown to be generated during the separation procedure of 2-de, and not by covalent post-translational modifications. the trains ...	2003	12601748
role of rhodobacter sp. strain ps9, a purple non-sulfur photosynthetic bacterium isolated from an anaerobic swine waste lagoon, in odor remediation.	temporal pigmentation changes resulting from the development of a purple color in anaerobic swine waste lagoons were investigated during a 4-year period. the major purple photosynthetic bacterium responsible for these color changes and the corresponding reductions in odor was isolated from nine photosynthetic lagoons. by using morphological, physiological, and phylogenetic characterization methods we identified the predominant photosynthetic bacterium as a new strain of rhodobacter, designated r ...	2003	12620863
purified particulate methane monooxygenase from methylococcus capsulatus (bath) is a dimer with both mononuclear copper and a copper-containing cluster.	particulate methane monooxygenase (pmmo) is a membrane-bound enzyme that catalyzes the oxidation of methane to methanol in methanotropic bacteria. understanding how this enzyme hydroxylates methane at ambient temperature and pressure is of fundamental chemical and potential commercial importance. difficulties in solubilizing and purifying active pmmo have led to conflicting reports regarding its biochemical and biophysical properties, however. we have purified pmmo from methylococcus capsulatus ...	2003	12634423
biological inorganic chemistry at the beginning of the 21st century.	advances in bioinorganic chemistry since the 1970s have been driven by three factors: rapid determination of high-resolution structures of proteins and other biomolecules, utilization of powerful spectroscopic tools for studies of both structures and dynamics, and the widespread use of macromolecular engineering to create new biologically relevant structures. today, very large molecules can be manipulated at will, with the result that certain proteins and nucleic acids themselves have become ver ...	2003	12657732
atmospheric pressure chemical ionisation reversed-phase liquid chromatography/ion trap mass spectrometry of intact bacteriohopanepolyols.	atmospheric pressure chemical ionisation liquid chromatography/multi-stage ion trap mass spectrometry (apci-lc/ms(n)) has been applied to the study of intact bacteriohopanepolyols. spectral characterisation of bacteriohopanepolyols of known structure present in bacterial extracts (zymomonas mobilis and a fermenter containing methanotrophs including methylococcus capsulatus) has revealed greater structural detail than previous liquid chromatography/mass spectrometry (lc/ms) methods and identified ...	2003	12661028
nitrogen isotopomer site preference of n2o produced by nitrosomonas europaea and methylococcus capsulatus bath.	the relative importance of individual microbial pathways in nitrous oxide (n(2)o) production is not well known. the intramolecular distribution of (15)n in n(2)o provides a basis for distinguishing biological pathways. concentrated cell suspensions of methylococcus capsulatus bath and nitrosomonas europaea were used to investigate the site preference of n(2)o by microbial processes during nitrification. the average site preference of n(2)o formed during hydroxylamine oxidation by m. capsulatus b ...	2003	12661029
[physiological activity of mixed cultures of methylcoccus capsulatus ukm b-3030 with bacillus megaterium ukm b-5723t and bacillus subtilis vkpm b-1489 on solid surface colonization].	physiological activity of monoculture of methylococcus capsulatus ucm b-3030 and its mixed cultures with two bacilli species distinguished by proteolytical properties--bacillus megaterium ucm b-5723t and bacillus subtilis bk[symbol: see text]m b-4189 in terms of long-duration cultivation is investigated. it is shown, that the most active methane consumption by methanotrophic bacteria and their mixed cultures with bacilli under solid surface colonization occurred on the second-eighth day of culti ...	2002	12664554
the surface-associated and secreted mope protein of methylococcus capsulatus (bath) responds to changes in the concentration of copper in the growth medium.	expression of surface-associated and secreted protein mope of the methanotrophic bacterium methylococcus capsulatus (bath) in response to the concentration of copper ions in the growth medium was investigated. the level of protein associated with the cells and secreted to the medium changed when the copper concentration in the medium varied and was highest in cells exposed to copper stress.	2003	12676726
methylotrophy in methylobacterium extorquens am1 from a genomic point of view.		2003	12730156
quantitative detection of methanotrophs in soil by novel pmoa-targeted real-time pcr assays.	methane oxidation in soils is mostly accomplished by methanotrophic bacteria. little is known about the abundance of methanotrophs in soils, since quantification by cultivation and microscopic techniques is cumbersome. comparison of 16s ribosomal dna and pmoa (alpha subunit of the particulate methane monooxygenase) phylogenetic trees showed good correlation and revealed five distinct groups of methanotrophs within the alpha and gamma subclasses of proteobacteria: the methylococcus group, the met ...	2003	12732507
the c-terminal domain of salmonella enterica serovar typhimurium ompa is an immunodominant antigen in mice but appears to be only partially exposed on the bacterial cell surface.	we examined the way the major outer membrane protein ompa of salmonella enterica serovar typhimurium is recognized by the mouse immune system, by raising a panel of 12 monoclonal antibodies (mabs) against this protein. interaction between ompa and these mabs is competitively inhibited with several-hundredfold dilutions of mouse polyclonal sera obtained by immunization with live or heat-killed whole cells, suggesting that ompa is one of the immunodominant antigens of serovar typhimurium. all of t ...	2003	12819080
genes involved in the copper-dependent regulation of soluble methane monooxygenase of methylococcus capsulatus (bath): cloning, sequencing and mutational analysis.	the key enzyme in methane metabolism is methane monooxygenase (mmo), which catalyses the oxidation of methane to methanol. some methanotrophs, including methylococcus capsulatus (bath), possess two distinct mmos. the level of copper in the environment regulates the biosynthesis of the mmo enzymes in these methanotrophs. under low-copper conditions, soluble mmo (smmo) is expressed and regulation takes place at the level of transcription. the structural genes of smmo were previously identified as ...	2003	12855730
possibility of bacterial recruitment of plant genes associated with the biosynthesis of secondary metabolites.		2003	12857798
the stereospecific hydroxylation of [2,2-2h2]butane and chiral dideuteriobutanes by the particulate methane monooxygenase from methylococcus capsulatus (bath).	experiments on cryptically chiral ethanes have indicated that the particulate methane monooxygenase (pmmo) from methylococcus capsulatus (bath) catalyzes the hydroxylation of ethane with total retention of configuration at the carbon center attacked. this result would seem to rule out a radical mechanism for the hydroxylation chemistry, at least as mediated by this enzyme. the interpretation of subsequent experiments on n-propane, n-butane, and n-pentane has been complicated by hydroxylation at ...	2003	12909646
wide distribution of a novel pmoa-like gene copy among type ii methanotrophs, and its expression in methylocystis strain sc2.	experiments were conducted to determine if a novel pmoa-like gene (pmoa2) recently discovered in the methane-oxidizing bacterium methylocystis strain sc2 (p. f. dunfield, m. tchawa yimga, s. d. dedysh, u. berger, w. liesack, and j. heyer, fems microbiol. ecol. 41:17-26, 2002) is present in other methane-oxidizing bacteria (mob), and if it is expressed. a newly developed primer combination (pmoa206f-pmoa703b) allowed a differential detection of pmoa1 and pmoa2. by using this primer combination, w ...	2003	12957949
ancient origin of the tryptophan operon and the dynamics of evolutionary change.	the seven conserved enzymatic domains required for tryptophan (trp) biosynthesis are encoded in seven genetic regions that are organized differently (whole-pathway operons, multiple partial-pathway operons, and dispersed genes) in prokaryotes. a comparative bioinformatics evaluation of the conservation and organization of the genes of trp biosynthesis in prokaryotic operons should serve as an excellent model for assessing the feasibility of predicting the evolutionary histories of genes and oper ...	2003	12966138
the membrane-associated methane monooxygenase (pmmo) and pmmo-nadh:quinone oxidoreductase complex from methylococcus capsulatus bath.	improvements in purification of membrane-associated methane monooxygenase (pmmo) have resulted in preparations of pmmo with activities more representative of physiological rates: i.e., >130 nmol.min(-1).mg of protein(-1). altered culture and assay conditions, optimization of the detergent/protein ratio, and simplification of the purification procedure were responsible for the higher-activity preparations. changes in the culture conditions focused on the rate of copper addition. to document the p ...	2003	13129946
production of high-quality particulate methane monooxygenase in high yields from methylococcus capsulatus (bath) with a hollow-fiber membrane bioreactor.	in order to obtain particulate methane monooxygenase (pmmo)-enriched membranes from methylococcus capsulatus (bath) with high activity and in high yields, we devised a method to process cell growth in a fermentor adapted with a hollow-fiber bioreactor that allows easy control and quantitative adjustment of the copper ion concentration in nms medium over the time course of cell culture. this technical improvement in the method for culturing bacterial cells allowed us to study the effects of coppe ...	2003	14526001
identification and characterization of a unique adenosine kinase from mycobacterium tuberculosis.	adenosine kinase (ak) is a purine salvage enzyme that catalyzes the phosphorylation of adenosine to amp. in mycobacterium tuberculosis, ak can also catalyze the phosphorylation of the adenosine analog 2-methyladenosine (methyl-ado), the first step in the metabolism of this compound to an active form. purification of ak from m. tuberculosis yielded a 35-kda protein that existed as a dimer in its native form. adenosine (ado) was preferred as a substrate at least 30-fold (km = 0.8 +/- 0.08 microm) ...	2003	14594827
diversity and activity of methanotrophic bacteria in different upland soils.	samples from diverse upland soils that oxidize atmospheric methane were characterized with regard to methane oxidation activity and the community composition of methanotrophic bacteria (mb). mb were identified on the basis of the detection and comparative sequence analysis of the pmoa gene, which encodes a subunit of particulate methane monooxygenase. mb commonly detected in soils were closely related to methylocaldum spp., methylosinus spp., methylocystis spp., or the "forest sequence cluster" ...	2003	14602631
domain engineering of the reductase component of soluble methane monooxygenase from methylococcus capsulatus (bath).	soluble methane monooxygenase (smmo) from methylococcus capsulatus (bath) is a three-component enzyme system that catalyzes the conversion of methane to methanol. a reductase (mmor), which contains [2fe-2s] and fad cofactors, facilitates electron transfer from nadh to the hydroxylase diiron active sites where dioxygen activation and substrate hydroxylation take place. by separately expressing the ferredoxin (mmorfd, mmor residues 1-98) and fad/nadh (mmor-fad, mmor residues 99-348) domains of the ...	2004	14613937
coevolution of an aminoacyl-trna synthetase with its trna substrates.	glutamyl-trna synthetases (glurss) occur in two types, the discriminating and the nondiscriminating enzymes. they differ in their choice of substrates and use either trnaglu or both trnaglu and trnagln. although most organisms encode only one glurs, a number of bacteria encode two different glurs proteins; yet, the trna specificity of these enzymes and the reason for such gene duplications are unknown. a database search revealed duplicated glurs genes in >20 bacterial species, suggesting that th ...	2003	14615592
propane monooxygenase and nad+-dependent secondary alcohol dehydrogenase in propane metabolism by gordonia sp. strain ty-5.	a new isolate, gordonia sp. strain ty-5, is capable of growth on propane and n-alkanes with c(13) to c(22) carbon chains as the sole source of carbon. in whole-cell reactions, significant propane oxidation to 2-propanol was detected. a gene cluster designated prmabcd, which encodes the components of a putative dinuclear-iron-containing multicomponent monooxygenase, including the large and small subunits of the hydroxylase, an nadh-dependent acceptor oxidoreductase, and a coupling protein, was cl ...	2003	14645271
nitrification and nitrifying bacteria in the lower seine river and estuary (france).	the achères wastewater treatment plant, located just downstream of paris, discharges its effluents into the lower seine river. the effluents contain large numbers of heterotrophic bacteria, organic matter, and ammonium and are a source of nitrifying bacteria. as a result, degradation of organic matter by heterotrophic bacteria and subsequent oxygen depletion occur immediately downstream of the effluent outlet, whereas nitrifying bacteria apparently need to build up a significant biomass before a ...	2003	14660353
phylogenetic and biochemical evidence for sterol synthesis in the bacterium gemmata obscuriglobus.	sterol biosynthesis is viewed primarily as a eukaryotic process, and the frequency of its occurrence in bacteria has long been a subject of controversy. two enzymes, squalene monooxygenase and oxidosqualene cyclase, are the minimum necessary for initial biosynthesis of sterols from squalene. in this work, 19 protein gene sequences for eukaryotic squalene monooxygenase and 12 protein gene sequences for eukaryotic oxidosqualene cyclase were compared with all available complete and partial prokaryo ...	2003	14660793
multiple formate dehydrogenase enzymes in the facultative methylotroph methylobacterium extorquens am1 are dispensable for growth on methanol.	formate dehydrogenase has traditionally been assumed to play an essential role in energy generation during growth on c(1) compounds. however, this assumption has not yet been experimentally tested in methylotrophic bacteria. in this study, a whole-genome analysis approach was used to identify three different formate dehydrogenase systems in the facultative methylotroph methylobacterium extorquens am1 whose expression is affected by either molybdenum or tungsten. a complete set of single, double, ...	2004	14679220
the nifl-nifa system: a multidomain transcriptional regulatory complex that integrates environmental signals.		2004	14729684
inhibition of membrane-bound methane monooxygenase and ammonia monooxygenase by diphenyliodonium: implications for electron transfer.	diphenyliodonium (dpi) is known to irreversibly inactivate flavoproteins. we have found that dpi inhibits both membrane-bound methane monooxygenase (pmmo) from methylococcus capsulatus and ammonia monooxygenase (amo) of nitrosomonas europaea. the effect of dpi on nadh-dependent pmmo activity in vitro is ascribed to inactivation of ndh-2, a flavoprotein which we proposed catalyzes reduction of the quinone pool by nadh. dpi is a potent inhibitor of type 2 nadh:quinone oxidoreductase (ndh-2), with ...	2004	14761987
modular broad-host-range expression vectors for single-protein and protein complex purification.	a set of modular broad-host-range expression vectors with various affinity tags (six-his-tag, flag-tag, strep-tag ii, t7-tag) was created. the complete nucleotide sequences of the vectors are known, and these small vectors can be mobilized by conjugation. they are useful in the purification of proteins and protein complexes from gram-negative bacterial species. the plasmids were easily customized for thiocapsa roseopersicina, rhodobacter capsulatus, and methylococcus capsulatus by inserting an a ...	2004	14766546
formaldehyde dehydrogenase preparations from methylococcus capsulatus (bath) comprise methanol dehydrogenase and methylene tetrahydromethanopterin dehydrogenase.	in methylotrophic bacteria, formaldehyde is an important but potentially toxic metabolic intermediate that can be assimilated into biomass or oxidized to yield energy. previously reported was the purification of an nad(p)(+)-dependent formaldehyde dehydrogenase (fdh) from the obligate methane-oxidizing methylotroph methylococcus capsulatus (bath), presumably important in formaldehyde oxidation, which required a heat-stable factor (known as the modifin) for fdh activity. here, the major protein c ...	2004	14993320
multiple formaldehyde oxidation/detoxification pathways in burkholderia fungorum lb400.	burkholderia species are free-living bacteria with a versatile metabolic lifestyle. the genome of b. fungorum lb400 is predicted to encode three different pathways for formaldehyde oxidation: an nad-linked, glutathione (gsh)-independent formaldehyde dehydrogenase; an nad-linked, gsh-dependent formaldehyde oxidation system; and a tetrahydromethanopterin-methanofuran-dependent formaldehyde oxidation system. the other burkholderia species for which genome sequences are available, b. mallei, b. pseu ...	2004	15028703
analysis of facultative lithotroph distribution and diversity on volcanic deposits by use of the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase.	a 492- to 495-bp fragment of the gene coding for the large subunit of the form i ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco) (rbcl) was amplified by pcr from facultatively lithotrophic aerobic co-oxidizing bacteria, colorless and purple sulfide-oxidizing microbial mats, and genomic dna extracts from tephra and ash deposits from kilauea volcano, for which atmospheric co and hydrogen have been previously documented as important substrates. pcr products from the mats and volcanic site ...	2004	15066819
synthesis of chlorophyll b: localization of chlorophyllide a oxygenase and discovery of a stable radical in the catalytic subunit.	assembly of stable light-harvesting complexes (lhcs) in the chloroplast of green algae and plants requires synthesis of chlorophyll (chl) b, a reaction that involves oxygenation of the 7-methyl group of chl a to a formyl group. this reaction uses molecular oxygen and is catalyzed by chlorophyllide a oxygenase (cao). the amino acid sequence of cao predicts mononuclear iron and rieske iron-sulfur centers in the protein. the mechanism of synthesis of chl b and localization of this reaction in the c ...	2004	15086960
comparative analysis of the conventional and novel pmo (particulate methane monooxygenase) operons from methylocystis strain sc2.	in addition to the conventional pmoa gene (pmoa1) encoding the active site polypeptide of particulate methane monooxygenase, a novel pmoa gene copy (pmoa2) is widely distributed among type ii methanotrophs (methane-oxidizing bacteria [mob]) (m. tchawa yimga, p. f. dunfield, p. ricke, j. heyer, and w. liesack, appl. environ. microbiol. 69:5593-5602, 2003). here we report that the pmoa1 and pmoa2 gene copies in the type ii mob methylocystis strain sc2 are each part of a complete pmocab gene cluste ...	2004	15128567
nifh and nifd phylogenies: an evolutionary basis for understanding nitrogen fixation capabilities of methanotrophic bacteria.	the ability to utilize dinitrogen as a nitrogen source is an important phenotypic trait in most currently known methanotrophic bacteria (mb). this trait is especially important for acidophilic mb, which inhabit acidic oligotrophic environments, highly depleted in available nitrogen compounds. phylogenetically, acidophilic mb are most closely related to heterotrophic dinitrogen-fixing bacteria of the genus beijerinckia: to further explore the phylogenetic linkage between these metabolically diffe ...	2004	15133093
saturation mutagenesis of toluene ortho-monooxygenase of burkholderia cepacia g4 for enhanced 1-naphthol synthesis and chloroform degradation.	directed evolution of toluene ortho-monooxygenase (tom) of burkholderia cepacia g4 previously created the hydroxylase alpha-subunit (toma3) v106a variant (tom-green) with increased activity for both trichloroethylene degradation (twofold enhancement) and naphthalene oxidation (six-times-higher activity). in the present study, saturation mutagenesis was performed at position a106 with escherichia coli tg1/pbs(kan)tomv106a to improve tom activity for both chloroform degradation and naphthalene oxi ...	2004	15184118
protein engineering of toluene-o-xylene monooxygenase from pseudomonas stutzeri ox1 for synthesizing 4-methylresorcinol, methylhydroquinone, and pyrogallol.	toluene-o-xylene monooxygenase (tomo) from pseudomonas stutzeri ox1 oxidizes toluene to 3- and 4-methylcatechol and oxidizes benzene to form phenol; in this study tomo was found to also form catechol and 1,2,3-trihydroxybenzene (1,2,3-thb) from phenol. to synthesize novel dihydroxy and trihydroxy derivatives of benzene and toluene, dna shuffling of the alpha-hydroxylase fragment of tomo (toua) and saturation mutagenesis of the toua active site residues i100, q141, t201, and f205 were used to gen ...	2004	15184119
distribution of rubisco genotypes along a redox gradient in mono lake, california.	partial sequences of ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) (ec 4.1.1.39) genes were retrieved from samples taken along a redox gradient in alkaline, hypersaline mono lake, calif. the form i gene (cbbl) was found in all samples, whereas form ii (cbbm) was not retrieved from any of the samples. none of the rubisco sequences we obtained were closely related (nucleotide similarity, <90%) to sequences in the database. some could be attributed to organisms isolated from the lake (c ...	2004	15184142
comparative genomics of rice and arabidopsis. analysis of 727 cytochrome p450 genes and pseudogenes from a monocot and a dicot.	data mining methods have been used to identify 356 cyt p450 genes and 99 related pseudogenes in the rice (oryza sativa) genome using sequence information available from both the indica and japonica strains. because neither of these genomes is completely available, some genes have been identified in only one strain, and 28 genes remain incomplete. comparison of these rice genes with the 246 p450 genes and 26 pseudogenes in the arabidopsis genome has indicated that most of the known plant p450 fam ...	2004	15208422
inter-genomic displacement via lateral gene transfer of bacterial trp operons in an overall context of vertical genealogy.	the growing conviction that lateral gene transfer plays a significant role in prokaryote genealogy opens up a need for comprehensive evaluations of gene-enzyme systems on a case-by-case basis. genes of tryptophan biosynthesis are frequently organized as whole-pathway operons, an attribute that is expected to facilitate multi-gene transfer in a single step. we have asked whether events of lateral gene transfer are sufficient to have obscured our ability to track the vertical genealogy that underp ...	2004	15214963
altering toluene 4-monooxygenase by active-site engineering for the synthesis of 3-methoxycatechol, methoxyhydroquinone, and methylhydroquinone.	wild-type toluene 4-monooxygenase (t4mo) of pseudomonas mendocina kr1 oxidizes toluene to p-cresol (96%) and oxidizes benzene sequentially to phenol, to catechol, and to 1,2,3-trihydroxybenzene. in this study t4mo was found to oxidize o-cresol to 3-methylcatechol (91%) and methylhydroquinone (9%), to oxidize m-cresol and p-cresol to 4-methylcatechol (100%), and to oxidize o-methoxyphenol to 4-methoxyresorcinol (87%), 3-methoxycatechol (11%), and methoxyhydroquinone (2%). apparent vmax values of ...	2004	15231803
determination by x-ray absorption spectroscopy of the fe-fe separation in the oxidized form of the hydroxylase of methane monooxygenase alone and in the presence of mmod.	the diiron active site in the hydroxylase of methylococcus capsulatus (bath) methane monooxygenase (mmoh) has been studied in the oxidized form by x-ray absorption spectroscopy (xas). previous investigations by xas and x-ray crystallography have identified two different distances (3.0 and 3.4 angstroms) between the two fe atoms in the dinuclear site. the present study has employed a systematic extended x-ray absorption fine structure (exafs) fitting methodology, utilizing known and simulated act ...	2004	15257585
nmr structure of the flavin domain from soluble methane monooxygenase reductase from methylococcus capsulatus (bath).	soluble methane monooxygenase (smmo) catalyzes the hydroxylation of methane by dioxygen to methanol, the first step in carbon assimilation by methanotrophs. this multicomponent system transfers electrons from nadh through a reductase component to the non-heme diiron center in the hydroxylase where o(2) is activated. the reductase component comprises three distinct domains, a [2fe-2s] ferredoxin domain along with fad- and nadh-binding domains. we report the solution structure of the reduced 27.6 ...	2004	15379538
genomic insights into methanotrophy: the complete genome sequence of methylococcus capsulatus (bath).	methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular, substantially reducing emissions of biologically generated methane to the atmosphere. despite their importance, and in contrast to organisms that play roles in other major parts of the carbon cycle such as photosynthesis, no genome-level studies have been published on the biology of methanotrophs. we repo ...	2004	15383840
quantitative proteomic analysis of metabolic regulation by copper ions in methylococcus capsulatus (bath).	copper ions switch the oxidation of methane by soluble methane monooxygenase to particulate methane monooxygenase in methylococcus capsulatus (bath). toward understanding the change in cellular metabolism related to this transcriptional and metabolic switch, we have undertaken genomic sequencing and quantitative comparative analysis of the proteome in m. capsulatus (bath) grown under different copper-to-biomass ratios by cleavable isotope-coded affinity tag technology. of the 682 proteins identi ...	2004	15385566
a challenge for 21st century molecular biology and biochemistry: what are the causes of obligate autotrophy and methanotrophy?	we assess the use to which bioinformatics in the form of bacterial genome sequences, functional gene probes and the protein sequence databases can be applied to hypotheses about obligate autotrophy in eubacteria. obligate methanotrophy and obligate autotrophy among the chemo- and photo-lithotrophic bacteria lack satisfactory explanation a century or more after their discovery. various causes of these phenomena have been suggested, which we review in the light of the information currently availab ...	2004	15449607
[features of solid materials' colonization by pure and mixed cultures of methanotrophs].	the process of colonization of hydrophilic (glass) and hydrophobic (polysterene) carriers by pure cultures of methanotrophs methylocystis parvus ucm b-3490t, methylococcus capsulatus ucm b-3030, as well as by their cultures mixed with bacillus megaterium ucm b 5723t and pseudomonas putida vkpm b-4188 under the conditions efficient for methanotrophic bacteria. m. parvus demonstrated the highest intensity of this process on the above carriers owing to high hydrophobic cell surface. both methanotro ...	2004	15456220
polarized atr-ftir spectroscopy of the membrane-embedded domains of the particulate methane monooxygenase.	the particulate methane monooxygenase (pmmo) of methylococcus capsulatus (bath) is an integral membrane protein that catalyzes the conversion of methane to methanol. to gain some insight into the structure-reactivity pattern of this protein, we have applied attenuated total reflection fourier transform infrared (atr-ftir) spectroscopy to investigate the secondary structure of the pmmo. the results showed that ca. 60% of the amino acid residues were structured as alpha-helices. about 80% of the p ...	2004	15491135
preparation and characterization of a (cu,zn)-pmmo from methylococcus capsulatus (bath).	we report the preparation of a (cu,zn)-particulate methane monooxygenase (pmmo) in which the bulk of the copper ions of the electron-transfer clusters (e-clusters) has been replaced by divalent zn ions. the cu and zn contents in the (cu,zn)-pmmo were determined by both inductively coupled plasma mass spectroscopy (icp-ms) and x-ray absorption k-edge spectroscopy. further characterization of the (cu,zn)-pmmo was provided by pmmo-activity assays as well as low-temperature electron paramagnetic res ...	2004	15541502
preparation and x-ray structures of metal-free, dicobalt and dimanganese forms of soluble methane monooxygenase hydroxylase from methylococcus capsulatus (bath).	a three-component soluble methane monooxygenase (smmo) enzyme system catalyzes the hydroxylation of methane to methanol at a carboxylate-bridged diiron center housed in the alpha-subunit of the hydroxylase (mmoh). catalysis is facilitated by the presence of a regulatory protein (mmob) and inhibited by mmod, a protein of unknown function encoded in the smmo operon. both mmob and mmod are presumed to bind to the same region of the mmoh alpha-subunit. a colorimetric method for monitoring removal of ...	2004	15610020
characterization of ichthyocidal activity of pfiesteria piscicida: dependence on the dinospore cell density.	the ichthyocidal activity of pfiesteria piscicida dinospores was examined in an aquarium bioassay format by exposing fish to either pfiesteria-containing environmental sediments or clonal p. piscicida. the presence of pfiesteria spp. and the complexity of the microbial assemblage in the bioassay were assessed by molecular approaches. cell-free water from bioassays that yielded significant fish mortality failed to show ichthyocidal activity. histopathological examination of moribund and dead fish ...	2005	15640229
identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal cys-loop ion channels.	acetylcholine receptor type ligand-gated ion channels (art-lgic; also known as cys-loop receptors) are a superfamily of proteins that include the receptors for major neurotransmitters such as acetylcholine, serotonin, glycine, gaba, glutamate and histamine, and for zn2+ ions. they play a central role in fast synaptic signaling in animal nervous systems and so far have not been found outside of the metazoa.	2004	15642096
identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal cys-loop ion channels.	acetylcholine receptor type ligand-gated ion channels (art-lgic; also known as cys-loop receptors) are a superfamily of proteins that include the receptors for major neurotransmitters such as acetylcholine, serotonin, glycine, gaba, glutamate and histamine, and for zn2+ ions. they play a central role in fast synaptic signaling in animal nervous systems and so far have not been found outside of the metazoa.	2004	15642096