Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
|---|
| inactivation of the regulatory protein b of soluble methane monooxygenase from methylococcus capsulatus (bath) by proteolysis can be overcome by a gly to gln modification. | the regulatory protein b of soluble methane monooxygenase (smmo) from methylococcus capsulatus (bath), exists as a mixture of the full-length active form and truncated forms, b' and b". electrospray ionisation mass spectrometry (esi-ms) was used to identify a cleavage site between met12 and gly13, such that 12 amino acids were lost from the n-terminus of protein b. this truncate was designated b' and molecular masses were assigned to proteins b and b' of 15,852.6+/-0.4 da and 14,629.5+/-0.3 da, ... | 1997 | 9310362 |
| cytochrome c peroxidase from methylococcus capsulatus bath. | a bacterial cytochrome c peroxidase was purified from the obligate methanotroph methylococcus capsulatus bath in either the fully oxidized or the half reduced form depending on the purification procedure. the cytochrome was a homo-dimer with a subunit mol mass of 35.8 kda and an isoelectric point of 4.5. at physiological temperatures, the enzyme contained one high-spin, low-potential (em7 = -254 mv) and one low-spin, high-potential (em7 = +432 mm ) heme. the low-potential heme center exhibited a ... | 1997 | 9325424 |
| crystal structures of the methane monooxygenase hydroxylase from methylococcus capsulatus (bath): implications for substrate gating and component interactions. | the crystal structure of the nonheme iron-containing hydroxylase component of methane monooxygenase hydroxylase (mmoh) from methylococcus capsulatus (bath) has been solved in two crystal forms, one of which was refined to 1.7 a resolution. the enzyme is composed of two copies each of three subunits (alpha 2 beta 2 gamma 2), and all three subunits are almost completely alpha-helical, with the exception of two beta hairpin structures in the alpha subunit. the active site of each alpha subunit cont ... | 1997 | 9329079 |
| geometry of the soluble methane monooxygenase catalytic diiron center in two oxidation states. | the hydroxylase component of soluble methane monooxygenase (smmo) contains a dinuclear iron center responsible for the oxidation of methane to methanol. as isolated, the center is in the oxidized, diiron(iii) state. the 2.2 a resolution x-ray structure of the oxidized hydroxylase, hox, from methylococcus capsulatus (bath) was previously determined at 4 degrees c. in this structure the two iron atoms are bridged by a glutamate, a hydroxide ion, and an acetate ion, and additionally coordinated to ... | 1995 | 9383443 |
| analysis of 16s rrna and methane monooxygenase gene sequences reveals a novel group of thermotolerant and thermophilic methanotrophs, methylocaldum gen. nov. | two methanotrophic bacteria with optimum growth temperatures above 40 degrees c were isolated. thermotolerant strain lk6 was isolated from agricultural soil, and the moderately thermophilic strain or2 was isolated from the effluent of an underground hot spring. when compared to the described thermophilic methanotrophs methylococcus capsulatus and methylococcus thermophilus, these strains are phenotypically similar to methylococcus thermophilus. however, their 16s rrna gene sequences are markedly ... | 1997 | 9385141 |
| geometry of the soluble methane monooxygenase catalytic diiron center in two oxidation states. | the hydroxylase component of soluble methane monooxygenase (smmo) contains a dinuclear iron center responsible for the oxidation of methane to methanol. as isolated, the center is in the oxidized, diiron(iii) state. the 2.2 a resolution x-ray structure of the oxidized hydroxylase, hox, from methylococcus capsulatus (bath) was previously determined at 4 degrees c. in this structure the two iron atoms are bridged by a glutamate, a hydroxide ion, and an acetate ion, and additionally coordinated to ... | 1995 | 9432288 |
| effect of selected monoterpenes on methane oxidation, denitrification, and aerobic metabolism by bacteria in pure culture. | selected monoterpenes inhibited methane oxidation by methanotrophs (methylosinus trichosporium ob3b, methylobacter luteus), denitrification by environmental isolates, and aerobic metabolism by several heterotrophic pure cultures. inhibition occurred to various extents and was transient. complete inhibition of methane oxidation by methylosinus trichosporium ob3b with 1.1 mm (-)-alpha-pinene lasted for more than 2 days with a culture of optical density of 0.05 before activity resumed. inhibition w ... | 1998 | 9464387 |
| acidophilic methanotrophic communities from sphagnum peat bogs. | highly enriched methanotrophic communities (> 25 serial transfers) were obtained from acidic ombrotrophic peat bogs from four boreal forest sites. the enrichment strategy involved using media conditions that were associated with the highest rates of methane uptake by the original peat samples, namely, the use of diluted mineral medium of low buffering capacity, moderate incubation temperature (20 degrees c), and ph values of 3 to 6. enriched communities contained a mixture of rod-shaped bacteria ... | 1998 | 9501432 |
| isolation of copper biochelates from methylosinus trichosporium ob3b and soluble methane monooxygenase mutants. | methylosinus trichosporium ob3b produces an extracellular copper-binding ligand (cbl) with high affinity for copper. wild-type cells and mutants that express soluble methane monooxygenase (smmo) in the presence and absence of copper (smmoc) were used to obtain cell exudates that were separated and analyzed by size exclusion high-performance liquid chromatography. a single chromatographic peak, when present, contained most of the aqueous-phase cu(ii) present in the culture medium. in mutant cultu ... | 1998 | 9501450 |
| the particulate methane monooxygenase from methylococcus capsulatus (bath) is a novel copper-containing three-subunit enzyme. isolation and characterization. | the particulate methane monooxygenase (pmmo) is known to be very difficult to study mainly due to its unusual activity instability in vitro. by cultivating methylococcus capsulatus (bath) under methane stress conditions and high copper levels in the growth medium, membranes highly enriched in the pmmo with exceptionally stable activity can be isolated from these cells. purified and active pmmo can be subsequently obtained from these membrane preparations using protocols in which an excess of red ... | 1998 | 9525893 |
| squalene-hopene cyclase from methylococcus capsulatus (bath): a bacterium producing hopanoids and steroids. | we report the cloning and characterisation of the methylococcus capsulatus shc gene, which encodes the squalene-hopene cyclase (shc). this enzyme catalyses the complex cyclization of squalene to the pentacyclic triterpene skeleton of hopanoids and represents the key reaction in this biosynthesis. using a combination of pcr amplification and dna hybridization, two overlapping 2.6 kb psti and 3.3 kb sali dna fragments were cloned bearing a 1962 bp open reading frame encoding a 74 kda protein with ... | 1998 | 9555026 |
| rapid consumption of low concentrations of methyl bromide by soil bacteria | a dynamic dilution system for producing low mixing ratios of methyl bromide (mebr) and a sensitive analytical technique were used to study the uptake of mebr by various soils. mebr was removed within minutes from vials incubated with soils and ~10 parts per billion by volume of mebr. killed controls did not consume mebr, and a mixture of the broad-spectrum antibiotics chloramphenicol and tetracycline inhibited mebr uptake by 98%, indicating that all of the uptake of mebr was biological and by ba ... | 1998 | 9572964 |
| ecophysiological and phylogenetic studies of nevskia ramosa in pure culture. | during the last 100 years, the neuston bacterium nevskia ramosa has been described several times. this bacterium forms conspicuous rosette-like microcolonies at the air-water interface. in this study, pure cultures of nevskia ramosa were obtained for the first time, from a bog lake (strain soe1, dsmz 11499t) and a freshwater ditch (strain ol1, dsmz 11500). the isolates showed special adaptations to life in the epineuston. they formed hydrophobic surface films with a dull appearance. n. ramosa is ... | 1998 | 9572968 |
| chloromethane metabolism by methylobacterium sp. strain cm4 | methylobacterium sp. strain cm4 metabolized chloromethane quantitatively with a molar yield of 2.8 g of whole-cell protein/mol of c. this value was similar to that observed after growth with methanol (2.9 g of protein/mol of c) and about three times larger than the yield with formate (0.94 g of protein/mol of c). chloromethane dehalogenation activity was inducible. minitn5 transposon insertion mutants with altered growth characteristics with chloromethane and other c1 compounds were isolated and ... | 1998 | 9572975 |
| helicobacter pylori glutamine synthetase lacks features associated with transcriptional and posttranslational regulation. | helicobacter pylori urease, produced in abundance, is indispensable for the survival of h. pylori in animal hosts. urea is hydrolyzed by the enzyme, resulting in the liberation of excess ammonia, some of which neutralizes gastric acid. the remaining ammonia is assimilated into protein by glutamine synthetase (ec 6.3.1.2), which catalyzes the reaction: nh3 + glutamate + atp-->glutamine + adp + pi. we hypothesized that glutamine synthetase plays an unusually critical role in nitrogen assimilation ... | 1998 | 9573059 |
| a highly selective pcr protocol for detecting 16s rrna genes of the genus pseudomonas (sensu stricto) in environmental samples. | pseudomonas species are plant, animal, and human pathogens; exhibit plant pathogen-suppressing properties useful in biological control; or express metabolic versatilities valued in biotechnology and bioremediation. specific detection of pseudomonas species in the environment may help us gain a more complete understanding of the ecological significance of these microorganisms. the objective of this study was to develop a pcr protocol for selective detection of pseudomonas (sensu stricto) in envir ... | 1998 | 9647828 |
| microbial community changes in a perturbed agricultural soil investigated by molecular and physiological approaches. | changes in soil microbial activity and diversity after incubation either with nitrogen or with a mixture of methane and air were examined. the perturbation by methane and air were characterized in detail and led to reduced diversity and enrichment of methanotrophs which were identified by denaturing gradient gel electrophoresis and 16s rrna sequencing. | 1998 | 9647861 |
| copper-binding compounds from methylosinus trichosporium ob3b. | two copper-binding compounds/cofactors (cbcs) were isolated from the spent media of both the wild type and a constitutive soluble methane monooxygenase (smmoc) mutant, pp319 (p. a. phelps et al., appl. environ. microbiol. 58:3701-3708, 1992), of methylosinus trichosporium ob3b. both cbcs are small polypeptides with molecular masses of 1,218 and 779 da for cbc-l1 and cbc-l2, respectively. the amino acid sequence of cbc-l1 is s?mypgs?m, and that of cbc-l2 is spmp?s. copper-free cbcs showed absorpt ... | 1998 | 9658004 |
| the hydroxylase component of soluble methane monooxygenase from methylococcus capsulatus (bath) exists in several forms as shown by electrospray-ionisation mass spectrometry. | the hydroxylase of the soluble methane monooxygenase from the bacterium methylococcus capsulatus (bath) has been investigated by means of electrospray-ionisation mass spectrometry (esi-ms) and liquid chromatography esi-ms (lc/esi-ms). the hydroxylase is a non-heme diiron protein consisting of three pairs of non-identical subunits (alpha approximately 60 kda, beta approximately 45 kda and gamma approximately 20 kda). liquid chromatographic separation of the hydroxylase subunits was required befor ... | 1998 | 9688272 |
| effect of nitrogen source on growth and trichloroethylene degradation by methane-oxidizing bacteria. | the effect of nitrogen source on methane-oxidizing bacteria with respect to cellular growth and trichloroethylene (tce) degradation ability were examined. one mixed chemostat culture and two pure type ii methane-oxidizing strains, methylosinus trichosporium ob3b and strain cac-2, which was isolated from the chemostat culture, were used in this study. all cultures were able to grow with each of three different nitrogen sources: ammonia, nitrate, and molecular nitrogen. both m. trichosporium ob3b ... | 1998 | 9726896 |
| pseudomonas sp. strain 273, an aerobic alpha, omega-dichloroalkanedegrading bacterium. | a gram-negative, aerobic bacterium was isolated from soil; this bacterium grew in 50% (vol/vol) suspensions of 1,10-dichlorodecane (1,10-dcd) as the sole source of carbon and energy. phenotypic and small-subunit ribosomal rna characterizations identified the organism, designated strain 273, as a member of the genus pseudomonas. after induction with 1,10-dcd, pseudomonas sp. strain 273 released stoichiometric amounts of chloride from c5 to c12 alpha, omega-dichloroalkanes in the presence of oxyge ... | 1998 | 9726906 |
| molecular analysis of bacterial isolates and total community dna from kraft pulp mill effluent treatment systems. | chloroaliphatics are major components of bleached kraft mill effluents. gene probes and oligonucleotide primers were developed to monitor kraft pulp mill effluent treatment systems for the presence of key genes (dehalogenases) responsible for the dehalogenation of chloroaliphatic organics. the primers were used for polymerase chain reaction (pcr) analysis of genomic dna extracted from dehalogenating bacterial isolates and from total community dna extracted from water and sediments of mill efflue ... | 1998 | 9734304 |
| analysis of the gene cluster encoding toluene/o-xylene monooxygenase from pseudomonas stutzeri ox1. | the toluene/o-xylene monooxygenase cloned from pseudomonas stutzeri ox1 displays a very broad range of substrates and a very peculiar regioselectivity, because it is able to hydroxylate more than one position on the aromatic ring of several hydrocarbons and phenols. the nucleotide sequence of the gene cluster coding for this enzymatic system has been determined. the sequence analysis revealed the presence of six open reading frames (orfs) homologous to other genes clustered in operons coding for ... | 1998 | 9758777 |
| low-concentration kinetics of atmospheric ch4 oxidation in soil and mechanism of nh4+ inhibition | nh4+ inhibition kinetics for ch4 oxidation were examined at near-atmospheric ch4 concentrations in three upland forest soils. whether nh4+-independent salt effects could be neutralized by adding nonammoniacal salts to control samples in lieu of deionized water was also investigated. because the levels of exchangeable endogenous nh4+ were very low in the three soils, desorption of endogenous nh4+ was not a significant factor in this study. the km(app) values for water-treated controls were 9.8, 2 ... | 1998 | 9797279 |
| difluoromethane, a new and improved inhibitor of methanotrophy | difluoromethane (hfc-32; dfm) is compared to acetylene and methyl fluoride as an inhibitor of methanotrophy in cultures and soils. dfm was found to be a reversible inhibitor of ch4 oxidation by methylococcus capsulatus (bath). consumption of ch4 in soil was blocked by additions of low levels of dfm (0.03 kpa), and this inhibition was reversed by dfm removal. although a small quantity of dfm was consumed during these incubations, its remaining concentration was sufficiently elevated to sustain in ... | 1998 | 9797290 |
| methanotrophs and methanogens in masonry | methanotrophs were present in 48 of 225 stone samples which were removed from 19 historical buildings in germany and italy. the average cell number of methanotrophs was 20 cfu per g of stone, and their activities ranged between 11 and 42 pmol of ch4 g of stone-1 day-1. twelve strains of methane-oxidizing bacteria were isolated. they belonged to the type ii methanotrophs of the genera methylocystis, methylosinus, and methylobacterium. in masonry, growth substrates like methane or methanol are ava ... | 1998 | 9797318 |
| short-term regulation of nitrogenase activity by nh4+ in rhodobacter capsulatus: multiple in vivo nitrogenase responses to nh4+ addition. | the photosynthetic bacterium rhodobacter capsulatus has been shown to carry out nitrogenase "switch-off," a rapid, reversible inhibition of in vivo activity. here, we demonstrate that highly nitrogen-limited cultures of both the wild-type strain and a drat drag mutant are capable of nitrogenase switch-off while moderately nitrogen-limited cultures show instead a "magnitude" response, with a decrease in in vivo nitrogenase activity that is proportional to the amount of added nh4+. | 1998 | 9829952 |
| assessment of changes in microbial community structure during operation of an ammonia biofilter with molecular tools. | biofiltration has been used for two decades to remove odors and various volatile organic and inorganic compounds in contaminated off-gas streams. although biofiltration is widely practiced, there have been few studies of the bacteria responsible for the removal of air contaminants in biofilters. in this study, molecular techniques were used to identify bacteria in a laboratory-scale ammonia biofilter. both 16s rrna and ammonia monooxygenase (amoa) genes were used to characterize the heterotrophi ... | 1998 | 9835577 |
| cytochrome p460 genes from the methanotroph methylococcus capsulatus bath. | p460 cytochromes catalyze the oxidation of hydroxylamine to nitrite. they have been isolated from the ammonia-oxidizing bacterium nitrosomonas europaea (r. h. erickson and a. b. hooper, biochim. biophys. acta 275:231-244, 1972) and the methane-oxidizing bacterium methylococcus capsulatus bath (j. a. zahn et al., j. bacteriol. 176:5879-5887, 1994). a degenerate oligonucleotide probe was synthesized based on the n-terminal amino acid sequence of cytochrome p460 and used to identify a dna fragment ... | 1998 | 9851984 |
| high-molecular-mass multi-c-heme cytochromes from methylococcus capsulatus bath. | the polypeptide and structural gene for a high-molecular-mass c-type cytochrome, cytochrome c553o, was isolated from the methanotroph methylococcus capsulatus bath. cytochrome c553o is a homodimer with a subunit molecular mass of 124,350 da and an isoelectric point of 6. 0. the heme c concentration was estimated to be 8.2 +/- 0.4 mol of heme c per subunit. the electron paramagnetic resonance spectrum showed the presence of multiple low spin, s = 1/2, hemes. a degenerate oligonucleotide probe syn ... | 1999 | 9922265 |
| influence of light intensity on methanotrophic bacterial activity in petit saut reservoir, french guiana. | one year after impoundment in january 1994, methanotrophic bacteria in petit saut reservoir (french guiana) were active at the oxic-anoxic interface. this activity was revealed by the sudden extinction of diffusive methane emission (600 metric tons of ch4. day-1 for the whole lake surface area, i.e., 360 km2). lifting of inhibition was suspected. after reviewing the potential inhibitors of this physiological guild (o2, nh4+, sulfides) and considering the similarities with nitrifiers, we suggest ... | 1999 | 9925579 |
| inactivation of toluene 2-monooxygenase in burkholderia cepacia g4 by alkynes. | high concentrations of acetylene (10 to 50% [vol/vol] gas phase) were required to inhibit the growth of burkholderia cepacia g4 on toluene, while 1% (vol/vol) (gas phase) propyne or 1-butyne completely inhibited growth. low concentrations of longer-chain alkynes (c5 to c10) were also effective inhibitors of toluene-dependent growth, and 2- and 3-alkynes were more potent inhibitors than their 1-alkyne counterparts. exposure of toluene-grown b. cepacia g4 to alkynes resulted in the irreversible lo ... | 1999 | 9925593 |
| detection of methanotrophs in groundwater by pcr. | methanotrophic bacteria have significant potential for bioremediation, which would require methods for monitoring the presence and activity of these organisms in environmental samples. in this study, pcr was used to detect methanotrophic bacteria. primers were designed on the basis of a partial sequence of pmoa, which encodes one of the proteins of the particulate methane monooxygenase. specific amplification of a portion of pmoa was obtained with template dna isolated from lab strains of methan ... | 1999 | 9925595 |
| 3-hydroxylaminophenol mutase from ralstonia eutropha jmp134 catalyzes a bamberger rearrangement. | 3-hydroxylaminophenol mutase from ralstonia eutropha jmp134 is involved in the degradative pathway of 3-nitrophenol, in which it catalyzes the conversion of 3-hydroxylaminophenol to aminohydroquinone. to show that the reaction was really catalyzed by a single enzyme without the release of intermediates, the corresponding protein was purified to apparent homogeneity from an extract of cells grown on 3-nitrophenol as the nitrogen source and succinate as the carbon and energy source. 3-hydroxylamin ... | 1999 | 10049374 |
| high-affinity methane oxidation by a soil enrichment culture containing a type ii methanotroph. | methanotrophic bacteria in an organic soil were enriched on gaseous mixing ratios of <275 parts per million of volume (ppmv) of methane (ch4). after 4 years of growth and periodic dilution (>10(20) times the initial soil inoculum), a mixed culture was obtained which displayed an apparent half-saturation constant [km(app)] for ch4 of 56 to 186 nm (40 to 132 ppmv). this value was the same as that measured in the soil itself and about 1 order of magnitude lower than reported values for pure culture ... | 1999 | 10049856 |
| molecular analysis of a novel methanesulfonic acid monooxygenase from the methylotroph methylosulfonomonas methylovora. | methylosulfonomonas methylovora m2 is an unusual gram-negative methylotrophic bacterium that can grow on methanesulfonic acid (msa) as the sole source of carbon and energy. oxidation of msa by this bacterium is carried out by a multicomponent msa monooxygenase (msamo). cloning and sequencing of a 7.5-kbp sphi fragment of chromosomal dna revealed four tightly linked genes encoding this novel monooxygenase. analysis of the deduced msamo polypeptide sequences indicated that the enzyme contains a tw ... | 1999 | 10094704 |
| the alkene monooxygenase from xanthobacter strain py2 is closely related to aromatic monooxygenases and catalyzes aromatic monohydroxylation of benzene, toluene, and phenol. | the genes encoding the six polypeptide components of the alkene monooxygenase from xanthobacter strain py2 (xamo) have been located on a 4.9-kb fragment of chromosomal dna previously cloned in cosmid pny2. sequencing and analysis of the predicted amino acid sequences indicate that the components of xamo are homologous to those of the aromatic monooxygenases, toluene 2-, 3-, and 4-monooxygenase and benzene monooxygenase, and that the gene order is identical. the genes and predicted polypeptides a ... | 1999 | 10103255 |
| an epr study of the dinuclear iron site in the soluble methane monooxygenase from methylococcus capsulatus (bath) reduced by one electron at 77 k: the effects of component interactions and the binding of small molecules to the diiron(iii) center. | reduction of the soluble methane monooxygenase hydroxylase (mmoh) from methylococcus capsulatus (bath) in frozen 4:1 buffer/glycerol solutions at 77 k by mobile electrons generated by gamma-irradiation produces an epr-detectable, mixed-valent fe(ii)fe(iii) center. at this temperature the conformation of the enzyme remains essentially unaltered during reduction, so the mixed-valent epr spectra serve to probe the active site structure of the epr-silent, diiron(iii) state. the epr spectra of the cr ... | 1999 | 10194335 |
| reactions of nitric oxide with the reduced non-heme diiron center of the soluble methane monooxygenase hydroxylase. | the soluble methane monooxygenase system from methylococcus capsulatus (bath) catalyzes the oxidation of methane to methanol and water utilizing dioxygen at a non-heme, carboxylate-bridged diiron center housed in the hydroxylase (h) component. to probe the nature of the reductive activation of dioxygen in this system, reactions of an analogous molecule, nitric oxide, with the diiron(ii) form of the enzyme (hred) were investigated by both continuous and discontinuous kinetics methodologies using ... | 1999 | 10194372 |
| oxidation of ultrafast radical clock substrate probes by the soluble methane monooxygenase from methylococcus capsulatus (bath). | radical clock substrate probes were used to assess the viability of a discrete substrate radical species in the mechanism of hydrocarbon oxidation by the soluble methane monooxygenase (smmo) from methylococcus capsulatus (bath). new substituted cyclopropane probes were used with very fast ring-opening rate constants and other desirable attributes, such as the ability to discriminate between radical and cationic intermediates. oxidation of these substrates by a reconstituted smmo system resulted ... | 1999 | 10196150 |
| a low-molecular-mass protein from methylococcus capsulatus (bath) is responsible for the regulation of formaldehyde dehydrogenase activity in vitro. | an 8.6 kda protein, which the authors call a modifin, has been purified from methylococcus capsulatus (bath) and has been shown to alter the substrate specificity and kinetics of nad+-linked formaldehyde dehydrogenase (fdh) isolated from the same organism. purification methods for both the modifin and fdh are presented which reliably produced pure protein for further analysis. analysis of the molecular mass and n-terminal sequence of both fdh and the modifin indicate that they are unique protein ... | 1999 | 10206695 |
| contribution of methanotrophic and nitrifying bacteria to ch4 and nh4+ oxidation in the rhizosphere of rice plants as determined by new methods of discrimination | methanotrophic and nitrifying bacteria are both able to oxidize ch4 as well as nh4+. to date it is not possible to estimate the relative contribution of methanotrophs to nitrification and that of nitrifiers to ch4 oxidation and thus to assess their roles in n and c cycling in soils and sediments. this study presents new options for discrimination between the activities of methanotrophs and nitrifiers, based on the competitive inhibitor ch3f and on recovery after inhibition with c2h2. by using ri ... | 1999 | 10223965 |
| molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16s rrna, particulate methane monooxygenase, and methanol dehydrogenase | rice field soil with a nonsaturated water content induced ch4 consumption activity when it was supplemented with 5% ch4. after a lag phase of 3 days, ch4 was consumed rapidly until the concentration was less than 1.8 parts per million by volume (ppmv). however, the soil was not able to maintain the oxidation activity at near-atmospheric ch4 mixing ratios (i.e., 5 ppmv). the soil microbial community was monitored by performing denaturing gradient gel electrophoresis (dgge) during the oxidation pr ... | 1999 | 10223989 |
| probing the mechanism of c-h activation: oxidation of methylcubane by soluble methane monooxygenase from methylosinus trichosporium ob3b. | the soluble form of methane monooxygenase (mmo) isolated from methanotrophic bacteria catalyzes the o2-dependent conversion of methane to methanol, as well as the adventitious oxidation of many other hydrocarbons. in past studies, it was reported that the oxidation reaction of methylcubane, a radical clock substrate, catalyzed by mmo from methylococcus capsulatus (bath) gave only cubylmethanol as the product rather than methylcubanol(s) or rearranged products characteristic of a radical formed o ... | 1999 | 10320346 |
| inhibition of nitrifiers and methanotrophs from an agricultural humisol by allylsulfide and its implications for environmental studies. | allylsulfide, an inhibitor of ammonia monooxygenase, was tested to determine its ability to inhibit nitrification and methane oxidation in pure cultures, in agricultural humisol enrichment cultures, and in humisol slurries. we confirmed that allylsulfide is a differential inhibitor of cultures of nitrifiers and methanotrophs at concentrations of 1 and 200 microm, respectively, which result in 50% inhibition. however, although a nitrifying enrichment culture added to sterilized humisol was inhibi ... | 1999 | 10347027 |
| heterologous expression of soluble methane monooxygenase genes in methanotrophs containing only particulate methane monooxygenase. | the methanotrophs methylococcus capsulatus (bath) and methylosinus trichosporium ob3b contain particulate methane monooxygenase (pmmo) and soluble methane monooxygenase (smmo) genes. other methanotrophs such as methylomicrobium album bg8 and methylocystis parvus obbp contain only pmmo genes. although molecular genetic techniques are poorly developed in methanotrophs, smmo genes were expressed in methanotrophs normally containing only pmmo genes. this was achieved by conjugation using broad-host- ... | 1999 | 10369892 |
| role of multiple gene copies in particulate methane monooxygenase activity in the methane-oxidizing bacterium methylococcus capsulatus bath. | genes for the subunits of particulate methane monooxygenase, pmoabc, have been sequenced from the gamma-proteobacterial methanotroph methylococcus capsulatus bath. m. capsulatus bath contains two complete copies of pmocab, as well as a third copy of pmoc. the two pmocab regions were almost identical at the nucleotide sequence level, differing in only 13 positions in 3183 bp. at the amino acid level, each translated gene product contained only one differing residue in each copy. however, the pmoc ... | 1999 | 10376840 |
| mutational and structural analyses of the regulatory protein b of soluble methane monooxygenase from methylococcus capsulatus (bath). | the soluble methane monooxygenase (smmo) system in methanotrophic bacteria uses three protein components to catalyze the selective oxidation of methane to methanol. the coupling protein b (mmob) both activates the carboxylate-bridged diiron center in the hydroxylase (mmoh) for substrate oxidation and couples the reaction to electron transfer from nadh through the smmo reductase. although the x-ray structure of the hydroxylase is known, little structural information is available regarding protein ... | 1999 | 10381404 |
| phylogenetic analysis of particle-attached and free-living bacterial communities in the columbia river, its estuary, and the adjacent coastal ocean. | the columbia river estuary is a dynamic system in which estuarine turbidity maxima trap and extend the residence time of particles and particle-attached bacteria over those of the water and free-living bacteria. particle-attached bacteria dominate bacterial activity in the estuary and are an important part of the estuarine food web. pcr-amplified 16s rrna genes from particle-attached and free-living bacteria in the columbia river, its estuary, and the adjacent coastal ocean were cloned, and 239 ... | 1999 | 10388721 |
| structure of the soluble methane monooxygenase regulatory protein b. | the soluble methane monooxygenase (smmo; ec 1.14.13.25) from the pseudothermophile methylococcus capsulatus (bath) is a three-component enzyme system that catalyzes the selective oxidation of methane to methanol. we have used nmr spectroscopy to produce a highly refined structure of mmob, the 16-kda regulatory protein of this system. this structure has a unique and intricate fold containing seven beta-strands forming two beta-sheets oriented perpendicular to each other and bridged by three alpha ... | 1999 | 10393915 |
| characterization of methanotrophic bacterial populations in soils showing atmospheric methane uptake. | the global methane cycle includes both terrestrial and atmospheric processes and may contribute to feedback regulation of the climate. most oxic soils are a net sink for methane, and these soils consume approximately 20 to 60 tg of methane per year. the soil sink for atmospheric methane is microbially mediated and sensitive to disturbance. a decrease in the capacity of this sink may have contributed to the approximately 1%. year(-1) increase in the atmospheric methane level in this century. the ... | 1999 | 10427012 |
| purification and characterization of the soluble methane monooxygenase of the type ii methanotrophic bacterium methylocystis sp. strain wi 14. | methane monooxygenase (mmo) catalyzes the oxidation of methane to methanol as the first step of methane degradation. a soluble nad(p)h-dependent methane monooxygenase (smmo) from the type ii methanotrophic bacterium wi 14 was purified to homogeneity. sequencing of the 16s rdna and comparison with that of other known methanotrophic bacteria confirmed that strain wi 14 is very close to the genus methylocystis. the smmo is expressed only during growth under copper limitation (<0.1 microm) and with ... | 1999 | 10473397 |
| radioactive fingerprinting of microorganisms that oxidize atmospheric methane in different soils. | microorganisms that oxidize atmospheric methane in soils were characterized by radioactive labelling with (14)ch(4) followed by analysis of radiolabelled phospholipid ester-linked fatty acids ((14)c-plfas). the radioactive fingerprinting technique was used to compare active methanotrophs in soil samples from greenland, denmark, the united states, and brazil. the (14)c-plfa fingerprints indicated that closely related methanotrophic bacteria were responsible for the oxidation of atmospheric methan ... | 1999 | 10473417 |
| distribution of tetrahydromethanopterin-dependent enzymes in methylotrophic bacteria and phylogeny of methenyl tetrahydromethanopterin cyclohydrolases. | the methylotrophic proteobacterium methylobacterium extorquens am1 possesses tetrahydromethanopterin (h(4)mpt)-dependent enzymes, which are otherwise specific to methanogenic and sulfate-reducing archaea and which have been suggested to be involved in formaldehyde oxidation to co(2) in m. extorquens am1. the distribution of h(4)mpt-dependent enzyme activities in cell extracts of methylotrophic bacteria from 13 different genera are reported. h(4)mpt-dependent activities were detected in all of th ... | 1999 | 10482517 |
| component interactions in the soluble methane monooxygenase system from methylococcus capsulatus (bath). | the soluble methane monooxygenase system of methylococcus capsulatus (bath) includes three protein components: a 251-kda non-heme dinuclear iron hydroxylase (mmoh), a 39-kda iron-sulfur- and fad-containing reductase (mmor), and a 16-kda regulatory protein (mmob). the thermodynamic stability and kinetics of formation of complexes between oxidized mmoh and mmob or mmor were measured by isothermal titration calorimetry and stopped-flow fluorescence spectroscopy at temperatures ranging from 3.3 to 4 ... | 1999 | 10504247 |
| halomethane:bisulfide/halide ion methyltransferase, an unusual corrinoid enzyme of environmental significance isolated from an aerobic methylotroph using chloromethane as the sole carbon source. | a novel dehalogenating/transhalogenating enzyme, halomethane:bisulfide/halide ion methyltransferase, has been isolated from the facultatively methylotrophic bacterium strain cc495, which uses chloromethane (ch(3)cl) as the sole carbon source. purification of the enzyme to homogeneity was achieved in high yield by anion-exchange chromatography and gel filtration. the methyltransferase was composed of a 67-kda protein with a corrinoid-bound cobalt atom. the purified enzyme was inactive but was act ... | 1999 | 10508052 |
| diversity in butane monooxygenases among butane-grown bacteria. | butane monooxygenases of butane-grown pseudomonas butanovora, mycobacterium vaccae job5, and an environmental isolate, cf8, were compared at the physiological level. the presence of butane monooxygenases in these bacteria was indicated by the following results. (i) o(2) was required for butane degradation. (ii) 1-butanol was produced during butane degradation. (iii) acetylene inhibited both butane oxidation and 1-butanol production. the responses to the known monooxygenase inactivator, ethylene, ... | 1999 | 10508093 |
| methanotroph diversity in landfill soil: isolation of novel type i and type ii methanotrophs whose presence was suggested by culture-independent 16s ribosomal dna analysis. | the diversity of the methanotrophic community in mildly acidic landfill cover soil was assessed by three methods: two culture-independent molecular approaches and a traditional culture-based approach. for the first of the molecular studies, two primer pairs specific for the 16s rrna gene of validly published type i (including the former type x) and type ii methanotrophs were identified and tested. these primers were used to amplify directly extracted soil dna, and the products were used to const ... | 1999 | 10543800 |
| oxidation of methyl halides by the facultative methylotroph strain imb-1. | washed cell suspensions of the facultative methylotroph strain imb-1 grown on methyl bromide (mebr) were able to consume methyl chloride (mecl) and methyl iodide (mei) as well as mebr. consumption of >100 microm mebr by cells grown on glucose, acetate, or monomethylamine required induction. induction was inhibited by chloramphenicol. however, cells had a constitutive ability to consume low concentrations (<20 nm) of mebr. glucose-grown cells were able to readily oxidize [(14)c]formaldehyde to (1 ... | 1999 | 10543820 |
| molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments. | the 16s rrna and pmoa genes from natural populations of methane-oxidizing bacteria (methanotrophs) were pcr amplified from total community dna extracted from lake washington sediments obtained from the area where peak methane oxidation occurred. clone libraries were constructed for each of the genes, and approximately 200 clones from each library were analyzed by using restriction fragment length polymorphism (rflp) and the tetrameric restriction enzymes mspi, haeiii, and hhai. the pcr products ... | 1999 | 10543824 |
| the amo operon in marine, ammonia-oxidizing gamma-proteobacteria. | while there is an extensive database of genes encoding ammonia monooxygenase (amo) found in the ammonia-oxidizing beta-proteobacteria, few amo sequences are available representing the gamma-proteobacteria. we sequenced the complete amo operon (amocab) for nitrosococcus oceani (atcc 19707), a marine, autotrophic, ammonia-oxidizing bacterium belonging to the gamma-subdivision of the proteobacteria. an additional autotrophic, ammonia-oxidizing bacterium isolated from a marine environment (strain c- ... | 1999 | 10547440 |
| bacillus subtilis yckg and yckf encode two key enzymes of the ribulose monophosphate pathway used by methylotrophs, and yckh is required for their expression. | the ribulose monophosphate (rump) pathway is one of the metabolic pathways for the synthesis of compounds containing carbon-carbon bonds from one-carbon units and is found in many methane- and methanol-utilizing bacteria, which are known as methylotrophs. the characteristic enzymes of this pathway are 3-hexulose-6-phosphate synthase (hps) and 6-phospho-3-hexuloisomerase (phi), neither of which was thought to exist outside methylotrophs. however, the presumed yckg gene product (yckg) of bacillus ... | 1999 | 10572115 |
| soluble methane monooxygenase gene clusters from trichloroethylene-degrading methylomonas sp. strains and detection of methanotrophs during in situ bioremediation. | the soluble mmo (smmo) gene clusters from group i methanotrophs were characterized. an 8.1-kb kpni fragment from methylomonas sp. strain kswiii and a 7.5-kb sali fragment from methylomonas sp. strain kspiii which contained the smmo gene clusters were cloned and sequenced. the sequences of these two fragments were almost identical. the smmo gene clusters in the fragment consisted of six open reading frames which were 52 to 79% similar to the corresponding genes of previously described smmo gene c ... | 1999 | 10583965 |
| bacterial triterpenoids of the hopane series from the methanotrophic bacteria methylocaldum spp.: phylogenetic implications and first evidence for an unsaturated aminobacteriohopanepolyol. | the hopanoid content of the two methanotrophic bacteria methylocaldum szegediense and methylocaldum tepidum was investigated. 35-aminobacteriohopane-30r,31r,32r,33s, 34s-pentol and its 3beta-methyl homologue were present in both strains. in m. tepidum, they were accompanied by 35-aminobacteriohopane-31r,32r,33s, 34s-tetrol and its 3beta-methyl homologue. the side chain structure was identical to those previously reported from two other obligate methanotrophs, methylococcus capsulatus and methylo ... | 2000 | 10620693 |
| primary structure of cytochrome c' of methylococcus capsulatus bath: evidence of a phylogenetic link between p460 and c'-type cytochromes. | cytochrome c' of methylococcus capsulatus bath is involved in electron flow from the enzyme responsible for hydroxylamine oxidation, cytochrome p460, to cytochrome c555. this cytochrome is spectrally similar to other cytochromes c' but is larger (16,000 da) and has a lower midpoint potential (-205 mv). by a combination of edman degradation, mass spectroscopy, and gene sequencing, we have obtained the primary structure of cytochrome c' from m. capsulatus bath. the cytochrome shows low sequence si ... | 2000 | 10648101 |
| molecular analysis of the pmo (particulate methane monooxygenase) operons from two type ii methanotrophs. | the particulate methane monooxygenase gene clusters, pmocab, from two representative type ii methanotrophs of the alpha-proteobacteria, methylosinus trichosporium ob3b and methylocystis sp. strain m, have been cloned and sequenced. primer extension experiments revealed that the pmo cluster is probably transcribed from a single transcriptional start site located 300 bp upstream of the start of the first gene, pmoc, for methylocystis sp. strain m. immediately upstream of the putative start site, c ... | 2000 | 10698759 |
| biomarker evidence for widespread anaerobic methane oxidation in mediterranean sediments by a consortium of methanogenic archaea and bacteria. the medinaut shipboard scientific party. | although abundant geochemical data indicate that anaerobic methane oxidation occurs in marine sediments, the linkage to specific microorganisms remains unclear. in order to examine processes of methane consumption and oxidation, sediment samples from mud volcanoes at two distinct sites on the mediterranean ridge were collected via the submersible nautile. geochemical data strongly indicate that methane is oxidized under anaerobic conditions, and compound-specific carbon isotope analyses indicate ... | 2000 | 10698781 |
| characterization of the gene cluster involved in isoprene metabolism in rhodococcus sp. strain ad45. | the genes involved in isoprene (2-methyl-1,3-butadiene) utilization in rhodococcus sp. strain ad45 were cloned and characterized. sequence analysis of an 8.5-kb dna fragment showed the presence of 10 genes of which 2 encoded enzymes which were previously found to be involved in isoprene degradation: a glutathione s-transferase with activity towards 1,2-epoxy-2-methyl-3-butene (isoi) and a 1-hydroxy-2-glutathionyl-2-methyl-3-butene dehydrogenase (isoh). furthermore, a gene encoding a second gluta ... | 2000 | 10715003 |
| effect of copper speciation on whole-cell soluble methane monooxygenase activity in methylosinus trichosporium ob3b. | soluble methane monooxygenase (smmo) activity in methylosinus trichosporium ob3b was found to be more strongly affected as copper-to-biomass ratios changed in a newly developed medium, m2m, which uses pyrophosphate for metal chelation, than in nitrate mineral salts (nms), which uses edta. when m2m medium was amended with edta, smmo activity was similar to that in nms medium, indicating that edta-bound copper had lower bioavailability than pyrophosphate-bound copper. edta did not limit the associ ... | 2000 | 10742271 |
| sequencing and analysis of the mmethylococcus capsulatus (bath) solublemethane monooxygenase genes. | the soluble methane monooxygenase (smmo) hydroxylase is a prototypical member of the class of proteins with non-heme carboxylate-bridged diiron sites. the smmo subclass of enzyme systems has several distinguishing characteristics, including the ability to catalyze hydroxylation or epoxidation chemistry, a multisubunit hydroxylase containing diiron centers in its alpha subunits, and the requirement of a coupling protein for optimal activity. sequence homology alignment of known members of the smm ... | 2000 | 10759840 |
| the trimethylamine methyltransferase gene and multiple dimethylamine methyltransferase genes of methanosarcina barkeri contain in-frame and read-through amber codons. | three different methyltransferases initiate methanogenesis from trimethylamine (tma), dimethylamine (dma) or monomethylamine (mma) by methylating different cognate corrinoid proteins that are subsequently used to methylate coenzyme m (com). here, genes encoding the dma and tma methyltransferases are characterized for the first time. a single copy of mttb, the tma methyltransferase gene, was cotranscribed with a copy of the dma methyltransferase gene, mtbb1. however, two other nearly identical co ... | 2000 | 10762254 |
| identification of intermediates of in vivo trichloroethylene oxidation by the membrane-associated methane monooxygenase. | the rate and products of trichloroethylene (tce) oxidation by methylomicrobium album bg8 expressing membrane-associated methane monooxygenase (pmmo) were determined using 14c radiotracer techniques. [(14)c]tce was degraded at a rate of 1.24 nmol (min mg protein)(-1) with the initial production of glyoxylate and then formate. radiolabeled co(2) was also found after incubating m. album bg8 for 5 h with [(14)c]tce. experiments with purified pmmo from methylococcus capsulatus bath showed that tce co ... | 2000 | 10779721 |
| effects of soil and water content on methyl bromide oxidation by the ammonia-oxidizing bacterium nitrosomonas europaea. | little information exists on the potential of nh(3)-oxidizing bacteria to cooxidize halogenated hydrocarbons in soil. a study was conducted to examine the cooxidation of methyl bromide (mebr) by an nh(3)-oxidizing bacterium, nitrosomonas europaea, under soil conditions. soil and its water content modified the availability of nh(4)(+) and mebr and influenced the relative rates of substrate (nh(3)) and cosubstrate (mebr) oxidations. these observations highlight the complexity associated with chara ... | 2000 | 10831449 |
| detection of methane oxidizing bacteria in forest soil by monooxygenase pcr amplification. | atmospheric methane oxidation by a spruce forest soil from norway at 15 degrees c was found to be maximal at a depth of ca 7 cm. examination of the kinetics of this methane oxidation revealed an apparent k(m) of 403.1 nm and a v(max) of 2.2 nmol g(-1) dry weight soil h(-1). the low apparent k(m) suggested the presence of active methane oxidizing bacteria with a high affinity for methane. dna was extracted from the 5-10 cm horizon, purified, and subjected to pcr amplification with primers directe ... | 2000 | 10882433 |
| molecular analysis of an outer membrane protein, mopb, of methylococcus capsulatus (bath) and structural comparisons with proteins of the ompa family. | the gene encoding a major outer membrane protein (mopb) of the methanotroph methylococcus capsulatus (bath) was cloned and sequenced. the cloned dna contained an open reading frame of 1044 bp coding for a 348-amino-acid polypeptide with a 21-amino-acid leader peptide. comparative sequence analysis of the predicted amino acid sequence revealed that the c-terminal part of mopb possessed sequences that are conserved in the ompa family of proteins. the n-terminal half of the protein had no significa ... | 2000 | 10896213 |
| characterization of methanotrophic bacteria on the basis of intact phospholipid profiles. | the intact phospholipid profiles (ipps) of seven species of methanotrophs from all three physiological groups, type i, ii and x, were determined using liquid chromatography/electrospray ionization/mass spectrometry. in these methanotrophs, two major classes of phospholipids were found, phosphatidylglycerol (pg) and phosphatidylethanolamine (pe) as well as its derivatives phosphatidylmethylethanolamine (pme) and phosphatidyldimethylethanolamine (pdme). specifically, the type i methanotrophs, meth ... | 2000 | 10913867 |
| characterization of an isolate that uses vinyl chloride as a growth substrate under aerobic conditions. | an aerobic enrichment culture was developed by using vinyl chloride (vc) as the sole organic carbon and electron donor source. vc concentrations as high as 7.3 mm were biodegraded without apparent inhibition. vc use did not occur when nitrate was provided as the electron acceptor. a gram-negative, rod-shaped, motile isolate was obtained from the enrichment culture and identified based on biochemical characteristics and the sequence of its 16s rrna gene as pseudomonas aeruginosa, designated strai ... | 2000 | 10919818 |
| comparison of epr-visible cu(2+) sites in pmmo from methylococcus capsulatus (bath) and methylomicrobium album bg8. | x-band (9.1 ghz) and s-band (3.4 ghz) electron paramagnetic resonance (epr) spectra for particulate methane monooxygenase (pmmo) in whole cells from methylococcus capsulatus (bath) grown on (63)cu and (15)n were obtained and compared with previously reported spectra for pmmo from methylomicrobium album bg8. for both m. capsulatus (bath) and m. album bg8, two nearly identical cu(2+) epr signals with resolved hyperfine coupling to four nitrogens are observed. the epr parameters for pmmo from m. ca ... | 2000 | 10920038 |
| [characteristics of hemagglutination reaction in methanotrophic bacteria]. | the reaction of hemagglutination with trypsin-treated rabbit erythrocytes was used to reveal lectins on the cell surface of methanotrophic bacteria and in their culture liquids. by this method, no lectins were detected on the cell surface of methylococcus capsulatus imv b-3001 and methylomonas rubra imv b-3075 or in the culture liquid of any of the species studied. with intact cells of methylocystis parvus imv b-3491, the positive hemagglutination reaction observed was nonspecific and most proba ... | 2000 | 10920812 |
| production and consumption of nitric oxide by three methanotrophic bacteria. | we studied nitrogen oxide production and consumption by methanotrophs methylobacter luteus (group i), methylosinus trichosporium ob3b (group ii), and an isolate from a hardwood swamp soil, here identified by 16s ribosomal dna sequencing as methylobacter sp. strain t20 (group i). all could consume nitric oxide (nitrogen monoxide, no), and produce small amounts of nitrous oxide (n(2)o). only methylobacter strain t20 produced large amounts of no (>250 parts per million by volume [ppmv] in the heads ... | 2000 | 10966405 |
| starvation alters the apparent half-saturation constant for methane in the type ii methanotroph methylocystis strain lr1. | when cells of a type ii methanotrophic bacterium (methylocystis strain lr1) were starved of methane, both the k(m(app)) and the v(max(app)) for methane decreased. the specific affinity (a(o)(s)) remained nearly constant. therefore, the decreased k(m(app)) in starved cells was probably not an adjustment to better utilize low-methane concentrations. | 2000 | 10966442 |
| possible interactions within a methanotrophic-heterotrophic groundwater community able to transform linear alkylbenzenesulfonates. | the relationships and interactions within a methanotrophic-heterotrophic groundwater community were studied in a closed system (shake culture) in the presence of methane as the primary carbon and energy source and with the addition of the pure linear alkylbenzenesulfonate (las) congener 2-[4-(sulfophenyl)]decan as a cometabolic substrate. when cultured under different conditions, this community was shown to be a stable association, consisting of one obligate type ii methanotroph and four or five ... | 2000 | 11010895 |
| pacific northwest marine sediments contain ammonia-oxidizing bacteria in the beta subdivision of the proteobacteria. | the diversity of ammonia-oxidizing bacteria in aquatic sediments was studied by retrieving ammonia monooxygenase and methane monooxygenase gene sequences. methanotrophs dominated freshwater sediments, while beta-proteobacterial ammonia oxidizers dominated marine sediments. these results suggest that gamma-proteobacteria such as nitrosococcus oceani are minor members of marine sediment ammonia-oxidizing communities. | 2000 | 11010911 |
| molecular characterization of methanotrophic isolates from freshwater lake sediment. | profiles of dissolved o(2) and methane with increasing depth were generated for lake washington sediment, which suggested the zone of methane oxidation is limited to the top 0.8 cm of the sediment. methane oxidation potentials were measured for 0.5-cm layers down to 1.5 cm and found to be relatively constant at 270 to 350 micromol/liter of sediment/h. approximately 65% of the methane was oxidized to cell material or metabolites, a signature suggestive of type i methanotrophs. eleven methanotroph ... | 2000 | 11097900 |
| the structure of the active center of beta-peptide membrane-bound methane monooxygenase (pmmo) from methylococcus capsulatus bath. | 2000 | 11109958 | |
| polyclonal antibodies recognizing the amob protein of ammonia oxidizers of the beta-subclass of the class proteobacteria. | a 41-kda protein of nitrosomonas eutropha was purified, and the n-terminal amino acid sequence was found to be nearly identical with the sequence of amob, a subunit of ammonia monooxygenase. this protein was used to develop polyclonal antibodies, which were highly specific for the detection of the four genera of ammonia oxidizers of the beta-subclass of proteobacteria (nitrosomonas, including nitrosococcus mobilis, which belongs phylogenetically to nitrosomonas; nitrosospira; nitrosolobus; and n ... | 2001 | 11133435 |
| chloromethane utilization gene cluster from hyphomicrobium chloromethanicum strain cm2(t) and development of functional gene probes to detect halomethane-degrading bacteria. | hyphomicrobium chloromethanicum cm2(t), an aerobic methylotrophic member of the alpha subclass of the class proteobacteria, can grow with chloromethane as the sole carbon and energy source. h. chloromethanicum possesses an inducible enzyme system for utilization of chloromethane, in which two polypeptides (67-kda cmua and 35-kda cmub) are expressed. previously, four genes, cmua, cmub, cmuc, and puru, were shown to be essential for growth of methylobacterium chloromethanicum on chloromethane. the ... | 2001 | 11133460 |
| expression of individual copies of methylococcus capsulatus bath particulate methane monooxygenase genes. | the expression of the two gene clusters encoding the particulate methane monooxygenase (pmmo) in methylococcus capsulatus bath was assessed by analysis of transcripts and by use of chromosomal gene fusions. the results suggest that the two clusters are functionally redundant but that relative expression alters depending on the copper levels available for growth. | 2001 | 11160118 |
| transcript analysis of multiple copies of amo (encoding ammonia monooxygenase) and hao (encoding hydroxylamine oxidoreductase) in nitrosomonas europaea. | the genes encoding ammonia monooxygenase (amocab), hydroxylamine oxidoreductase (hao), and the c-type cytochrome c-554 (hcy) are present in multiple copies in the genome of nitrosomonas europaea. the upstream regions of the two copies of amoc, the three copies of hao, and one copy of hcy were cloned and sequenced. primer extension reactions were done to identify transcription start sites for these genes, as well as for amoa. putative sigma(70) promoter sequences were found associated with all bu ... | 2001 | 11208810 |
| differential inhibition in vivo of ammonia monooxygenase, soluble methane monooxygenase and membrane-associated methane monoxygenase by phenylacetylene. | phenylacetylene was investigated as a differential inhibitor of ammonia monooxygenase (amo), soluble methane monooxygenase (smmo) and membrane-associated or particulate methane monooxygenase (pmmo) in vivo. at phenylacetylene concentrations > 1 microm, whole-cell amo activity in nitrosomonas europaea was completely inhibited. phenylacetylene concentrations above 100 microm inhibited more than 90% of smmo activity in methylococcus capsulatus bath and methylosinus trichosporium ob3b. in contrast, ... | 2000 | 11233157 |
| xenon and halogenated alkanes track putative substrate binding cavities in the soluble methane monooxygenase hydroxylase. | to investigate the role of protein cavities in facilitating movement of the substrates, methane and dioxygen, in the soluble methane monooxygenase hydroxylase (mmoh), we determined the x-ray structures of mmoh from methylococcus capsulatus (bath) cocrystallized with dibromomethane or iodoethane, or by using crystals pressurized with xenon gas. the halogenated alkanes bind in two cavities within the alpha-subunit that extend from one surface of the protein to the buried dinuclear iron active site ... | 2001 | 11297413 |
| solution structure of the toluene 4-monooxygenase effector protein (t4mod). | toluene 4-monooxygenase (t4mo) from pseudomonas mendocina catalyzes the nadh- and o(2)-dependent hydroxylation of toluene to form p-cresol. the complex consists of an nadh oxidoreductase (t4mof), a rieske ferredoxin (t4moc), a diiron hydroxylase [t4moh, with (alphabetagamma)(2) quaternary structure], and a catalytic effector protein (t4mod). the solution structure of the 102-amino acid t4mod effector protein has been determined from 2d and 3d (1)h, (13)c, and (15)n nmr spectroscopic data. the st ... | 2001 | 11297417 |
| changes in activity and community structure of methane-oxidizing bacteria over the growth period of rice. | the activity and community structure of methanotrophs in compartmented microcosms were investigated over the growth period of rice plants. in situ methane oxidation was important only during the vegetative growth phase of the plants and later became negligible. the in situ activity was not directly correlated with methanotrophic cell counts, which increased even after the decrease in in situ activity, possibly due to the presence of both vegetative cells and resting stages. by dividing the micro ... | 2001 | 11375143 |
| microbial diversity of the brine-seawater interface of the kebrit deep, red sea, studied via 16s rrna gene sequences and cultivation methods. | the brine-seawater interface of the kebrit deep, northern red sea, was investigated for the presence of microorganisms using phylogenetic analysis combined with cultivation methods. under strictly anaerobic culture conditions, novel halophiles were isolated. the new rod-shaped isolates belong to the halophilic genus halanaerobium and are the first representatives of the genus obtained from deep-sea, anaerobic brine pools. within the genus halanaerobium, they represent new species which grow chem ... | 2001 | 11425725 |
| crystal structures of the soluble methane monooxygenase hydroxylase from methylococcus capsulatus (bath) demonstrating geometrical variability at the dinuclear iron active site. | the oxidation of methane to methanol is performed at carboxylate-bridged dinuclear iron centers in the soluble methane monooxygenase hydroxylase (mmoh). previous structural studies of mmoh, and the related r2 subunit of ribonucleotide reductase, have demonstrated the occurrence of carboxylate shifts involving glutamate residues that ligate the catalytic iron atoms. these shifts are thought to have important mechanistic implications. recent kinetic and theoretical studies have also emphasized the ... | 2001 | 11456616 |
| methane oxidation and the competition for oxygen in the rice rhizosphere. | a mechanistic approach is presented to describe oxidation of the greenhouse gas methane in the rice rhizosphere of flooded paddies by obligate methanotrophic bacteria. in flooded rice paddies these methanotrophs compete for available o(2) with other types of bacteria. soil incubation studies and most-probable-number (mpn) counts of oxygen consumers show that microbial oxygen consumption rates were dominated by heterotrophic and methanotrophic respiration. mpn counts of methanotrophs showed large ... | 2001 | 11472935 |
| the c-terminal part of the surface-associated protein mope of the methanotroph methylococcus capsulatus (bath) is secreted into the growth medium. | a protein with an apparent molecular mass of 46 kda was detected as the major polypeptide in the culture medium of the biotechnologically important methanotrophic bacterium methylococcus capsulatus (bath). the protein cross-reacted with polyclonal antibodies raised against the outer-membrane-associated protein mope. the antiserum was used to identify a positive clone from a lambda gt11 library. the nucleotide sequence determined for the clone demonstrated that mope and the secreted protein are e ... | 2001 | 11511867 |
| comparison of pmoa pcr primer sets as tools for investigating methanotroph diversity in three danish soils. | three particulate methane monooxygenase pcr primer sets (a189-a682, a189-a650, and a189-mb661) were investigated for their ability to assess methanotroph diversity in soils from three sites, i.e., heath, oak, and sitka, each of which was capable of oxidizing atmospheric concentrations of methane. each pcr primer set was used to construct a library containing 50 clones from each soil type. the clones from each library were grouped by restriction fragment length polymorphism, and representatives f ... | 2001 | 11525970 |
| nifh sequences and nitrogen fixation in type i and type ii methanotrophs. | some methane-oxidizing bacteria (methanotrophs) are known to be capable of expressing nitrogenase and utilizing n2 as a nitrogen source. however, no sequences are available for nif genes in these strains, and the known nitrogen-fixing methanotrophs are confined mainly to a few genera. the purpose of this work was to assess the nitrogen-fixing capabilities of a variety of methanotroph strains. nifh gene fragments from four type i methanotrophs and seven type ii methanotrophs were pcr amplified an ... | 2001 | 11525998 |
| detection of methanotroph diversity on roots of submerged rice plants by molecular retrieval of pmoa, mmox, mxaf, and 16s rrna and ribosomal dna, including pmoa-based terminal restriction fragment length polymorphism profiling. | the diversity of methanotrophic bacteria associated with roots of submerged rice plants was assessed using cultivation-independent techniques. the research focused mainly on the retrieval of pmoa, which encodes the alpha subunit of the particulate methane monooxygenase. a novel methanotroph-specific community-profiling method was established using the terminal restriction fragment length polymorphism (t-rflp) technique. the t-rflp profiles clearly revealed a more complex root-associated methanot ... | 2001 | 11526021 |