Publications

total structure characterization of unsaturated acidic phospholipids provided by vicinal di-hydroxylation of fatty acid double bonds and negative electrospray ionization mass spectrometry.	in the present work, the unsaturated fatty acid substituents of some phosphatidic acid, phosphatidylserine, phosphatidylinositol, and phosphatidylglycerol species were converted to their 1,2-di-hydroxy derivatives by oso(4). the subsequent electrospray ionization tandem low-energy mass spectrometry analysis of the deprotonated species allowed positional determination of the double bonds by the production of specific product-ions. the product-ions are formed by charge-remote and charge-proximate ...	2005	15653363
crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane.	particulate methane monooxygenase (pmmo) is an integral membrane metalloenzyme that catalyses the conversion of methane to methanol. knowledge of how pmmo performs this extremely challenging chemistry may have an impact on the use of methane as an alternative energy source by facilitating the development of new synthetic catalysts. we have determined the structure of pmmo from the methanotroph methylococcus capsulatus (bath) to a resolution of 2.8 a. the enzyme is a trimer with an alpha3beta3gam ...	2005	15674245
a genomic view of methane oxidation by aerobic bacteria and anaerobic archaea.	recent sequencing of the genome and proteomic analysis of a model aerobic methanotrophic bacterium, methylococcus capsulatus (bath) has revealed a highly versatile metabolic potential. in parallel, environmental genomics has provided glimpses into anaerobic methane oxidation by certain archaea, further supporting the hypothesis of reverse methanogenesis.	2005	15693955
a new example of viral intein in mimivirus.	inteins are "protein introns" that remove themselves from their host proteins through an autocatalytic protein-splicing. after their discovery, inteins have been quickly identified in all domains of life, but only once to date in the genome of a eukaryote-infecting virus.	2005	15707490
fourier transform infrared characterization of the azido complex of methane monooxygenase hydroxylase from methylococcus capsulatus (bath).	the azido complex formed in oxidized methane monooxygenase from methylococcus capsulatus (bath) was investigated with resonance raman and ftir techniques. these experiments show the presence of a nuas(nnn) at approximately 2077 cm-1 which splits to two components at 2059 and 2073 cm-1 with 15n14n2. the vibrational data are assigned to an azido complex bound terminally to one iron(iii) at the diiron center. when the azido complex is illuminated at 15 k, a new nuas(nnn) is observed at 2136 cm-1 wh ...	2005	15783178
cloning, expression, and site-directed mutagenesis of the propene monooxygenase genes from mycobacterium sp. strain m156.	propene monooxygenase has been cloned from mycobacterium sp. strain m156, based on hybridization with the amoabcd genes of rhodococcus corallinus b276. sequencing indicated that the mycobacterial enzyme is a member of the binuclear nonheme iron monooxygenase family and, in gene order and sequence, is most similar to that from r. corallinus b-276. attempts were made to express the pmoabcd operon in escherichia coli and mycobacterium smegmatis mc(2)155. in the former, there appeared to be a proble ...	2005	15812019
ribonucleases j1 and j2: two novel endoribonucleases in b.subtilis with functional homology to e.coli rnase e.	many prokaryotic organisms lack an equivalent of rnase e, which plays a key role in mrna degradation in escherichia coli. in this paper, we report the purification and identification by mass spectrometry in bacillus subtilis of two paralogous endoribonucleases, here named rnases j1 and j2, which share functional homologies with rnase e but no sequence similarity. both enzymes are able to cleave the b.subtilis thrs leader at a site that can also be cleaved by e.coli rnase e. we have previously sh ...	2005	15831787
product bound structures of the soluble methane monooxygenase hydroxylase from methylococcus capsulatus (bath): protein motion in the alpha-subunit.	the soluble methane monooxygenase hydroxylase (mmoh) alpha-subunit contains a series of cavities that delineate the route of substrate entrance to and product egress from the buried carboxylate-bridged diiron center. the presence of discrete cavities is a major structural difference between mmoh, which can hydroxylate methane, and toluene/o-xylene monooxygenase hydroxylase (tomoh), which cannot. to understand better the functions of the cavities and to investigate how an enzyme designed for meth ...	2005	15839679
insights into the obligate methanotroph methylococcus capsulatus.	completion of the genome sequence of methylococcus capsulatus bath is an important event in molecular microbiology, and an achievement for which the authors deserve congratulation. m. capsulatus, along with other methanotrophs, has been the subject of intense biochemical and molecular study because of its role in the global carbon cycle: the conversion of biogenic methane to carbon dioxide. the methane monooxygenase enzymes that are central to this process also have high biotechnological potenti ...	2005	15866035
methane-oxidizing bacteria in a california upland grassland soil: diversity and response to simulated global change.	we investigated the diversity of methane-oxidizing bacteria (i.e., methanotrophs) in an annual upland grassland in northern california, using comparative sequence analysis of the pmoa gene. in addition to identifying type ii methanotrophs commonly found in soils, we discovered three novel pmoa lineages for which no cultivated members have been previously reported. these novel pmoa clades clustered together either with clone sequences related to "ra 14" or "wb5fh-a," which both represent clusters ...	2005	15870356
characterization of a prokaryotic haemerythrin from the methanotrophic bacterium methylococcus capsulatus (bath).	for a long time, the haemerythrin family of proteins was considered to be restricted to only a few phyla of marine invertebrates. when analysing differential protein expression in the methane-oxidizing bacterium, methylococcus capsulatus (bath), grown at a high and low copper-to-biomass ratio, respectively, we identified a putative prokaryotic haemerythrin expressed in high-copper cultures. haemerythrins are recognized by a conserved sequence motif that provides five histidines and two carboxyla ...	2005	15885093
an sos-regulated operon involved in damage-inducible mutagenesis in caulobacter crescentus.	dna polymerases of the y-family, such as escherichia coli umuc and dinb, are specialized enzymes induced by the sos response, which bypass lesions allowing the continuation of dna replication. umudc orthologs are absent in caulobacter crescentus and other bacteria, raising the question about the existence of sos mutagenesis in these organisms. here, we report that the c.crescentus dinb ortholog is not involved in damage-induced mutagenesis. however, an operon composed of two hypothetical genes a ...	2005	15886391
reactions of the peroxo intermediate of soluble methane monooxygenase hydroxylase with ethers.	soluble methane monooxygenase (smmo) isolated from methylococcus capsulatus (bath) utilizes a carboxylate-bridged diiron center and dioxygen to catalyze the conversion of methane to methanol. previous studies revealed that a di(mu-oxo)diiron(iv) intermediate termed q is responsible for the catalytic activity with hydrocarbons. in addition, the peroxodiiron(iii) intermediate (h(peroxo)) that precedes q formation in the catalytic cycle has been demonstrated to react with propylene, but its reactiv ...	2005	15898785
the archaeon pyrococcus horikoshii possesses a bifunctional enzyme for formaldehyde fixation via the ribulose monophosphate pathway.	pyrococcus horikoshii ot3, a hyperthermophilic and anaerobic archaeon, was found to have an open reading frame (ph1938) whose deduced amino acid sequence of the n-terminal and c-terminal halves showed significant similarity to two key enzymes of the ribulose monophosphate pathway for formaldehyde fixation in methylotrophic bacteria, 3-hexulose-6-phosphate synthase (hps) and 6-phospho-3-hexuloisomerase (phi), respectively. the organism constitutively produced the encoded protein and exhibited act ...	2005	15901685
the tetr family of transcriptional repressors.	we have developed a general profile for the proteins of the tetr family of repressors. the stretch that best defines the profile of this family is made up of 47 amino acid residues that correspond to the helix-turn-helix dna binding motif and adjacent regions in the three-dimensional structures of tetr, qacr, cprb, and ethr, four family members for which the function and three-dimensional structure are known. we have detected a set of 2,353 nonredundant proteins belonging to this family by scree ...	2005	15944459
facultative methanotrophs revisited.		2005	15968038
analysis of gene islands involved in methanopterin-linked c1 transfer reactions reveals new functions and provides evolutionary insights.	in this study, the occurrence and chromosomal clustering of genes encoding c(1) transfer reactions linked to tetrahydromethanopterin (h(4)mpt) were analyzed in a variety of proteobacteria and in representatives of the planctomycetes via genomic analysis or via partial sequencing by cosmid walking. although a tendency for clustering was found common for the genes of interest, significant variations in gene order and the degree of clustering were uncovered both between and within different groups ...	2005	15968072
methylocella species are facultatively methanotrophic.	all aerobic methanotrophic bacteria described to date are unable to grow on substrates containing carbon-carbon bonds. here we demonstrate that members of the recently discovered genus methylocella are an exception to this. these bacteria are able to use as their sole energy source the one-carbon compounds methane and methanol, as well as the multicarbon compounds acetate, pyruvate, succinate, malate, and ethanol. to conclusively verify facultative growth, acetate and methane were used as model ...	2005	15968078
regulation of a type iii and a putative secretion system in edwardsiella tarda by esrc is under the control of a two-component system, esra-esrb.	edwardsiella tarda is a gram-negative enteric pathogen that causes hemorrhagic septicemia in fish and gastro- and extraintestinal infections in humans. a type iii secretion system (ttss) and a putative secretion system (evp) have been found to play important roles in e. tarda pathogenesis. our previous studies suggested that the ttss and evp gene clusters were regulated by a two-component system of esra-esrb. in the present study, we characterized another regulator, esrc, which showed significan ...	2005	15972502
recent additions and improvements to the onto-tools.	the onto-tools suite is composed of an annotation database and six seamlessly integrated, web-accessible data mining tools: onto-express, onto-compare, onto-design, onto-translate, onto-miner and pathway-express. the onto-tools database has been expanded to include various types of data from 12 new databases. our database now integrates different types of genomic data from 19 sequence, gene, protein and annotation databases. additionally, our database is also expanded to include complete gene on ...	2005	15980579
origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members.	we report an in-depth computational study of the protein sequences and structures of the superfamily of archaeo-eukaryotic primases (aeps). this analysis greatly expands the range of diversity of the aeps and reveals the unique active site shared by all members of this superfamily. in particular, it is shown that eukaryotic nucleo-cytoplasmic large dna viruses, including poxviruses, asfarviruses, iridoviruses, phycodnaviruses and the mimivirus, encode aeps of a distinct family, which also includ ...	2005	16027112
molecular detection of cellulosimicrobium cellulans as the etiological agent of a chronic tongue ulcer in a human immunodeficiency virus-positive patient.	ulcerations appeared on the tongue of a 48-year-old human immunodeficiency virus-positive man. histological findings of the biopsy specimen and the fact that the patient had resided in louisiana led us to suspect "american histoplasmosis". a new ulcer appeared while the patient was being treated with itraconazole, and the gene for 16s rrna of cellulosimicrobium cellulans was amplified. the lesions healed during treatment with oral penicillin and azithromycin.	2005	16081997
characterization and structural analysis of an active particulate methane monooxygenase trimer from methylococcus capsulatus (bath).	the oxidation of methane to methanol in methanotrophs is catalyzed by the enzyme methane monooxygenase (mmo). two distinct forms of this enzyme exist, a soluble cytoplasmic mmo (smmo) and a membrane-bound particulate form (pmmo). we describe here the biochemical characterization of a stable and active purified pmmo hydroxylase (pmmo-h) and report a three-dimensional (3d) structure, determined by electron microscopy and single-particle analysis at 23 a resolution. both biochemical and structural ...	2005	16101279
e1 enzyme of the pyruvate dehydrogenase complex in corynebacterium glutamicum: molecular analysis of the gene and phylogenetic aspects.	the e1p enzyme is an essential part of the pyruvate dehydrogenase complex (pdhc) and catalyzes the oxidative decarboxylation of pyruvate with concomitant acetylation of the e2p enzyme within the complex. we analyzed the corynebacterium glutamicum acee gene, encoding the e1p enzyme, and constructed and characterized an e1p-deficient mutant. sequence analysis of the c. glutamicum acee gene and adjacent regions revealed that acee is not flanked by genes encoding other enzymes of the pdhc. transcrip ...	2005	16109942
strain variability in the dna immigration control region (icr) of xylella fastidiosa.	the genome of the bacterium xylella fastidiosa contains four orfs (xf2721, xf2725, xf2739 and xf0295) related to the restriction modification type i system, ordinarily named r-m. this system belongs to the dna immigration control region (icr). each orf is related to different operon structures, which are homologues among themselves and with subunit hsd r from the endonuclease coding genes. in addition, these orfs are highly homologous to genes in pseudomonas aeruginosa, methylococcus capsulatus ...	2006	16125907
the leeuwenhoek lecture 2000 the natural and unnatural history of methane-oxidizing bacteria.	methane gas is produced from many natural and anthropogenic sources. as such, methane gas plays a significant role in the earth's climate, being 25 times more effective as a greenhouse gas than carbon dioxide. as with nearly all other naturally produced organic molecules on earth, there are also micro-organisms capable of using methane as their sole source of carbon and energy. the microbes responsible (methanotrophs) are ubiquitous and, for the most part, aerobic. although anaerobic methanotrop ...	2005	16147517
structure and sequence conservation of hao cluster genes of autotrophic ammonia-oxidizing bacteria: evidence for their evolutionary history.	comparison of the organization and sequence of the hao (hydroxylamine oxidoreductase) gene clusters from the gammaproteobacterial autotrophic ammonia-oxidizing bacterium (aaob) nitrosococcus oceani and the betaproteobacterial aaob nitrosospira multiformis and nitrosomonas europaea revealed a highly conserved gene cluster encoding the following proteins: hao, hydroxylamine oxidoreductase; orf2, a putative protein; cyca, cytochrome c(554); and cycb, cytochrome c(m)(552). the deduced protein sequen ...	2005	16151127
a computational method to predict genetically encoded rare amino acids in proteins.	in several natural settings, the standard genetic code is expanded to incorporate two additional amino acids with distinct functionality, selenocysteine and pyrrolysine. these rare amino acids can be overlooked inadvertently, however, as they arise by recoding at certain stop codons. we report a method for such recoding prediction from genomic data, using read-through similarity evaluation. a survey across a set of microbial genomes identifies almost all the known cases as well as a number of no ...	2005	16168086
effect of methanobactin on the activity and electron paramagnetic resonance spectra of the membrane-associated methane monooxygenase in methylococcus capsulatus bath.	improvements in the purification of methanobactin (mb) from either methylosinus trichosporium ob3b(t) or methylococcus capsulatus bath resulted in preparations that stimulated methane-oxidation activity in both whole-cell and cell-free fractions of methylococcus capsulatus bath expressing the membrane-associated methane monooxygenase (pmmo). by using washed membrane factions with pmmo activities in the 290 nmol propylene oxidized min(-1) (mg protein)(-1) range, activities approaching 400 nmol pr ...	2005	16207923
stopped-flow fourier transform infrared spectroscopy of nitromethane oxidation by the diiron(iv) intermediate of methane monooxygenase.	the hydroxylase component (mmoh) of soluble methane monooxygenase from methylococcus capsulatus (bath) was reduced to the diiron(ii) form and then allowed to react with dioxygen to generate the diiron(iv) intermediate q in the first phase of a double-mixing stopped-flow experiment. cd3no2 was then introduced in the second phase of the experiment, which was carried out in d2o at 25 degrees c. the kinetics of the reaction of the substrate with q were monitored by stopped-flow fourier transform inf ...	2003	16220908
the incp island in the genome of brucella suis 1330 was acquired by site-specific integration.	an 18,228-bp region containing open reading frames predicted to be derived from the incp plasmid or phage ancestors is present in the genomes of brucella suis biovars 1 to 4, b. canis, b. neotomae, and strains isolated from marine mammals, but not in b. melitensis, b. abortus, b. ovis, and b. suis biovar 5. the presence of circular excision intermediates and the results of an analysis of sequenced bacterial genomes suggest that the region downstream of the guaa gene is a hotspot for site-specifi ...	2005	16239585
enzymatic and genetic characterization of carbon and energy metabolisms by deep-sea hydrothermal chemolithoautotrophic isolates of epsilonproteobacteria.	the carbon and energy metabolisms of a variety of cultured chemolithoautotrophic epsilonproteobacteria from deep-sea hydrothermal environments were characterized by both enzymatic and genetic analyses. all the epsilonproteobacteria tested had all three key reductive tricarboxylic acid (rtca) cycle enzymatic activities--atp-dependent citrate lyase, pyruvate:ferredoxin oxidoreductase, and 2-oxoglutarate:ferredoxin oxidoreductase--while they had no ribulose 1,5-bisphosphate carboxylase (rubisco) ac ...	2005	16269773
first genome data from uncultured upland soil cluster alpha methanotrophs provide further evidence for a close phylogenetic relationship to methylocapsa acidiphila b2 and for high-affinity methanotrophy involving particulate methane monooxygenase.	members of upland soil cluster alpha (usc alpha) are assumed to be methanotrophic bacteria (mb) adapted to the trace level of atmospheric methane. so far, these mb have eluded all cultivation attempts. while the 16s rrna phylogeny of usc alpha members is still not known, phylogenies constructed for the active-site polypeptide (encoded by pmoa) of particulate methane monooxygenase (pmmo) placed usc alpha next to the alphaproteobacterial methylocapsa acidiphila b2. to assess whether the pmoa tree ...	2005	16269789
a diet rich in phosphatidylethanolamine increases plasma homocysteine in mink: a comparison with a soybean oil diet.	the effects of high dietary levels of phosphatidylethanolamine (pe) on plasma concentrations of homocysteine (thcy) have not previously been studied. eighteen mink (mustela vison) studied were fed one of three diets during a 25 d period in a parallel-group design. the compared diets had 0, 17 and 67 % extracted lipids from natural gas-utilising bacteria (lngb), which were rich in pe. the group with 0 % lngb was fed a diet of 100 % soyabean oil (sb diet). phospholipids are the main lipid componen ...	2005	16277769
oxygen isotopes indicate most intracellular water in log-phase escherichia coli is derived from metabolism.	the transport of water into and out of unicellular organisms is a seemingly simple process in which water diffuses either through pores or directly across the membrane. because of the rates at which water can theoretically diffuse, it is generally accepted that intracellular water is indistinguishable from extracellular water. using stable isotope ratio mass spectrometry, we directly tested this assumption. here we demonstrate that under active growth, up to 70% of the intracellular water in log ...	2005	16301541
analysing the outer membrane subproteome of methylococcus capsulatus (bath) using proteomics and novel biocomputing tools.	high-resolution two-dimensional gel electrophoresis and mass spectrometry has been used to identify the outer membrane (om) subproteome of the gram-negative bacterium methylococcus capsulatus (bath). twenty-eight unique polypeptide sequences were identified from protein samples enriched in oms. only six of these polypeptides had previously been identified. the predictions from novel bioinformatic methods predicting beta-barrel outer membrane proteins (omps) and om lipoproteins were compared to p ...	2006	16311759
the copper chelator methanobactin from methylosinus trichosporium ob3b binds copper(i).	the oxidation state of copper bound to methanobactin, a small siderophore-like molecule from the methanotroph methylosinus trichosporium ob3b, was investigated. purified methanobactin loaded with cu(ii) exhibits a weak epr signal probably due to adventitious cu(ii). the epr signal intensity increases significantly upon addition of the strong oxidant nitric acid. features of the x-ray absorption near edge spectrum, including a 1s --> 4p transition at 8985 ev, further indicate the presence of cu(i ...	2005	16332035
intermolecular electron-transfer reactions in soluble methane monooxygenase: a role for hysteresis in protein function.	electron transfer from reduced nicotinamide adenine dinucleotide (nadh) to the hydroxylase component (mmoh) of soluble methane monooxygenase (smmo) primes its non-heme diiron centers for reaction with dioxygen to generate high-valent iron intermediates that convert methane to methanol. this intermolecular electron-transfer step is facilitated by a reductase (mmor), which contains [2fe-2s] and flavin adenine dinucleotide (fad) prosthetic groups. to investigate interprotein electron transfer, chem ...	2005	16332086
diversity and structure of bacterial chemolithotrophic communities in pine forest and agroecosystem soils.	obligate lithotrophs (e.g., ammonia oxidizers) and facultative lithotrophs (e.g., co and hydrogen oxidizers) collectively comprise a phylogenetically diverse functional group that contributes significantly to carbon and nitrogen cycles in soils and plays important roles in trace gas dynamics (e.g., carbon monoxide and nitrous and nitric oxides) that affect tropospheric chemistry and radiative forcing. in spite of their diverse physiologies, facultative and obligate lithotrophs typically possess ...	2005	16332829
genetic characterization of the bifidobacterium breve ucc 2003 hrca locus.	the bacterial heat shock response is characterized by the elevated expression of a number of chaperone complexes and transcriptional regulators, including the dnaj and the hrca proteins. genome analysis of bifidobacterium breve ucc 2003 revealed a second copy of a dnaj gene, named dnaj2, which is flanked by the hrca gene in a genetic constellation that appears to be unique to the actinobacteria. phylogenetic analysis using 53 bacterial dnaj sequences, including both dnaj1 and dnaj2 sequences, su ...	2005	16332909
identification of a copper-repressible c-type heme protein of methylococcus capsulatus (bath). a member of a novel group of the bacterial di-heme cytochrome c peroxidase family of proteins.	genomic sequencing of the methanotrophic bacterium, methylococcus capsulatus (bath), revealed an open reading frame (mca2590) immediately upstream of the previously described mope gene (mca2589). sequence analyses of the deduced amino acid sequence demonstrated that the mca2590-encoded protein shared significant, but restricted, sequence similarity to the bacterial di-heme cytochrome c peroxidase (bccp) family of proteins. two putative c-type heme-binding motifs were predicted, and confirmed by ...	2005	16336269
comparative genomic analyses of the bacterial phosphotransferase system.	we report analyses of 202 fully sequenced genomes for homologues of known protein constituents of the bacterial phosphoenolpyruvate-dependent phosphotransferase system (pts). these included 174 bacterial, 19 archaeal, and 9 eukaryotic genomes. homologues of pts proteins were not identified in archaea or eukaryotes, showing that the horizontal transfer of genes encoding pts proteins has not occurred between the three domains of life. of the 174 bacterial genomes (136 bacterial species) analyzed, ...	2005	16339738
microbial oxidation of gaseous hydrocarbons: production of methylketones from corresponding n-alkanes by methane-utilizing bacteria.	cell suspensions of methane-utilizing bacteria grown on methane oxidized n-alkanes (propane, butane, pentane, hexane) to their corresponding methylketones (acetone, 2-butanone, 2-pentanone, 2-hexanone). the product methylketones accumulated extracellularly. the rate of production of methylketones varied with the organism used for oxidation; however, the average rate of acetone, 2-butanone, 2-pentanone, and 2-hexanone production was 1.2, 1.0, 0.15, and 0.025 mumol/h per 5.0 mg of protein in cell ...	1980	16345538
evaluation of methyl fluoride and dimethyl ether as inhibitors of aerobic methane oxidation.	methyl fluoride (mf) and dimethyl ether (dme) were effective inhibitors of aerobic methanotrophy in a variety of soils. mf and dme blocked consumption of ch(4) as well as the oxidation of ch(4) to co(2), but neither mf nor dme affected the oxidation of [c]methanol or [c]formate to co(2). cooxidation of ethane and propane by methane-oxidizing soils was also inhibited by mf. nitrification (ammonia oxidation) in soils was inhibited by both mf and dme. production of n(2)o via nitrification was inhib ...	1992	16348771
methanol promotes atmospheric methane oxidation by methanotrophic cultures and soils.	two methanotrophic bacteria, methylobacter albus bg8 and methylosinus trichosporium ob3b, oxidized atmospheric methane during batch growth on methanol. methane consumption was rapidly and substantially diminished (95% over 9 days) when washed cell suspensions were incubated without methanol in the presence of atmospheric methane (1.7 ppm). methanotrophic activity was stimulated after methanol (10 mm) but not methane (1,000 ppm) addition. m. albus bg8 grown in continuous culture for 80 days with ...	1998	16349514
characterization of root-associated methanotrophs from three freshwater macrophytes: pontederia cordata, sparganium eurycarpum, and sagittaria latifolia.	root-associated methanotrophic bacteria were enriched from three common aquatic macrophytes: pontederia cordata, sparganium eurycarpum, and sagittaria latifolia. at least seven distinct taxa belonging to groups i and ii were identified and presumptively assigned to the genera methylosinus, methylocystis, methylomonas, and methylococcus. four of these strains appeared to be novel on the basis of partial 16s ribosomal dna sequence analysis. the root-methanotroph association did not appear to be hi ...	1998	16349515
methane and trichloroethylene degradation by methylosinus trichosporium ob3b expressing particulate methane monooxygenase.	whole-cell assays of methane and trichloroethylene (tce) consumption have been performed on methylosinus trichosporium ob3b expressing particulate methane monooxygenase (pmmo). from these assays it is apparent that varying the growth concentration of copper causes a change in the kinetics of methane and tce degradation. for m. trichosporium ob3b, increasing the copper growth concentration from 2.5 to 20 mum caused the maximal degradation rate of methane (v(max)) to decrease from 300 to 82 nmol o ...	1998	16349516
methanol improves methane uptake in starved methanotrophic microorganisms.	methanotrophs in enrichment cultures grew and sustained atmospheric methane oxidation when supplied with methanol. if they were not supplied with methanol or formate, their atmospheric methane oxidation came to a halt, but it was restored within hours in response to methanol or formate. indigenous forest soil methanotrophs were also dependent on a supply of methanol upon reduced methane access but only when exposed to a methane-free atmosphere. their immediate response to each methanol addition, ...	1998	16349519
the genome sequence of methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and h2 for methane formation and atp synthesis.	methanosphaera stadtmanae has the most restricted energy metabolism of all methanogenic archaea. this human intestinal inhabitant can generate methane only by reduction of methanol with h2 and is dependent on acetate as a carbon source. we report here the genome sequence of m. stadtmanae, which was found to be composed of 1,767,403 bp with an average g+c content of 28% and to harbor only 1,534 protein-encoding sequences (cds). the genome lacks 37 cds present in the genomes of all other methanoge ...	2006	16385054
distinguishing nitrous oxide production from nitrification and denitrification on the basis of isotopomer abundances.	the intramolecular distribution of nitrogen isotopes in n2o is an emerging tool for defining the relative importance of microbial sources of this greenhouse gas. the application of intramolecular isotopic distributions to evaluate the origins of n2o, however, requires a foundation in laboratory experiments in which individual production pathways can be isolated. here we evaluate the site preferences of n2o produced during hydroxylamine oxidation by ammonia oxidizers and by a methanotroph, ammoni ...	2006	16391101
dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain.	recently, a multiple gene cassette with mutagenic translation synthesis activity was identified and shown to be under lexa regulation in several proteobacteria species. in this work, we have traced down instances of this multiple gene cassette across the bacteria domain. phylogenetic analyses show that this cassette has undergone several reorganizations since its inception in the actinobacteria, and that it has dispersed across the bacterial domain through a combination of vertical inheritance, ...	2006	16407325
diversity of soluble methane monooxygenase-containing methanotrophs isolated from polluted environments.	methanotrophs were enriched and isolated from polluted environments in canada and germany. enrichments in low copper media were designed to specifically encourage growth of soluble methane monooxygenase (smmo) containing organisms. the 10 isolates were characterized physiologically and genetically with one type i and nine type ii methanotrophs being identified. three key genes: 16s rrna; pmoa and mmox, encoding for the particulate and soluble methane monooxygenases respectively, were cloned from ...	2006	16448499
the genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium thiobacillus denitrificans.	the complete genome sequence of thiobacillus denitrificans atcc 25259 is the first to become available for an obligately chemolithoautotrophic, sulfur-compound-oxidizing, beta-proteobacterium. analysis of the 2,909,809-bp genome will facilitate our molecular and biochemical understanding of the unusual metabolic repertoire of this bacterium, including its ability to couple denitrification to sulfur-compound oxidation, to catalyze anaerobic, nitrate-dependent oxidation of fe(ii) and u(iv), and to ...	2006	16452431
phenylacetylene reversibly inhibits the phenol hydroxylase of pseudomonas sp. cf600 at high concentrations but is oxidized at lower concentrations.	alkynes are mechanism-based inhibitors of several bacterial monooxygenases, including the soluble methane monooxygenase (smmo) of methylococcus capsulatus and the toluene o-monooxygenase (tom) of burkholderia cepacia g4. in this paper, we investigated the inhibition of the phenol hydroxylase of pseudomonas sp. cf600 by the alkyne phenylacetylene. growth of cf600 on phenol and phenol hydroxylase activity were inhibited by phenylacetylene concentrations greater than 1.0 mm. unlike other alkynes, w ...	2006	16485115
inhibition of methane oxidation by methylococcus capsulatus with hydrochlorofluorocarbons and fluorinated methanes.	the inhibition of methane oxidation by cell suspensions of methylococcus capsulatus (bath) exposed to hydrochlorofluorocarbon 21 (hcfc-21; difluorochloromethane [chf(inf2)cl]), hcfc-22 (fluorodichloromethane [chfcl(inf2)]), and various fluorinated methanes was investigated. hcfc-21 inhibited methane oxidation to a greater extent than hcfc-22, for both the particulate and soluble methane monooxygenases. among the fluorinated methanes, both methyl fluoride (ch(inf3)f) and difluoromethane (ch(inf2) ...	1997	16535662
expression, purification, crystallization and preliminary x-ray diffraction of a novel nitrosomonas europaea cytochrome, cytochrome p460.	cytochrome p460 from nitrosomonas europaea, a novel mono-heme protein containing an unusual cross-link between a conserved lysine and the porphyrin ring, has been recombinantly expressed and purified from escherichia coli. the protein crystallizes readily and diffraction to 1.7 angstroms has been obtained in-house. the crystals belong to the trigonal space group p3(1/2)21, with unit-cell parameters a = b = 53.3, c = 127.1 angstroms, and contain one monomer in the asymmetric unit.	2006	16582494
a database of bacterial lipoproteins (dolop) with functional assignments to predicted lipoproteins.	lipid modification of the n-terminal cys residue (n-acyl-s-diacylglyceryl-cys) has been found to be an essential, ubiquitous, and unique bacterial posttranslational modification. such a modification allows anchoring of even highly hydrophilic proteins to the membrane which carry out a variety of functions important for bacteria, including pathogenesis. hence, being able to identify such proteins is of great value. to this end, we have created a comprehensive database of bacterial lipoproteins, c ...	2006	16585737
use of a variable amplicon typing scheme reveals considerable variation in the accessory genomes of isolates of burkholderia pseudomallei.	melioidosis, a disease caused by the bacterium burkholderia pseudomallei, is endemic in southeast asia and northern australia. we used suppression subtractive hybridization (ssh) to identify sequences that varied between two b. pseudomallei isolates from australia and determined the distribution of 45 ssh-derived sequences among a panel of b. pseudomallei and b. thailandensis isolates. sequences exhibiting variable prevalence were included in a variable amplicon typing (vat) scheme designed to s ...	2006	16597858
a phylogenomic profile of globins.	globins occur in all three kingdoms of life: they can be classified into single-domain globins and chimeric globins. the latter comprise the flavohemoglobins with a c-terminal fad-binding domain and the gene-regulating globin coupled sensors, with variable c-terminal domains. the single-domain globins encompass sequences related to chimeric globins and "truncated" hemoglobins with a 2-over-2 instead of the canonical 3-over-3 alpha-helical fold.	2006	16600051
mekhla, a novel domain with similarity to pas domains, is fused to plant homeodomain-leucine zipper iii proteins.	homeodomain (hd) proteins play important roles in the development of plants, fungi, and animals. here we identify a novel domain, mekhla, in the c terminus of hd-leu zipper (hd-zip) iii plant hd proteins that shares similarity with a group of bacterial proteins and a protein from the green alga chlamydomonas reinhardtii. the group of bacterial mekhla proteins is found in cyanobacteria and other bacteria often found associated with plants. phylogenetic analysis suggests that a mekhla protein tran ...	2006	16607028
phylogenomic analysis of the giy-yig nuclease superfamily.	the giy-yig domain was initially identified in homing endonucleases and later in other selfish mobile genetic elements (including restriction enzymes and non-ltr retrotransposons) and in enzymes involved in dna repair and recombination. however, to date no systematic search for novel members of the giy-yig superfamily or comparative analysis of these enzymes has been reported.	2006	16646971
fluorescence in situ hybridization-flow cytometry-cell sorting-based method for separation and enrichment of type i and type ii methanotroph populations.	a fluorescence in situ hybridization-flow cytometry (fish/fc)-based method was optimized using artificial mixtures of pure cultures of methanotrophic bacteria. traditional oligonucleotide probes targeting 16s rrnas of type i (mg84/705 probe) and type ii (ma450 probe) methanotrophs were labeled with fluorescein or alexa fluor and used for fish, followed by fluorescence-activated fc analysis and cell sorting (facs). the method resulted in efficient separation of target cells (type i or type ii met ...	2006	16751544
steroids, triterpenoids and molecular oxygen.	there is a close connection between modern-day biosynthesis of particular triterpenoid biomarkers and presence of molecular oxygen in the environment. thus, the detection of steroid and triterpenoid hydrocarbons far back in earth history has been used to infer the antiquity of oxygenic photosynthesis. this prompts the question: were these compounds produced similarly in the past? in this paper, we address this question with a review of the current state of knowledge surrounding the oxygen requir ...	2006	16754609
site-directed amino acid substitutions in the hydroxylase alpha subunit of butane monooxygenase from pseudomonas butanovora: implications for substrates knocking at the gate.	butane monooxygenase (bmo) from pseudomonas butanovora has high homology to soluble methane monooxygenase (smmo), and both oxidize a wide range of hydrocarbons; yet previous studies have not demonstrated methane oxidation by bmo. studies to understand the basis for this difference were initiated by making single-amino-acid substitutions in the hydroxylase alpha subunit of butane monooxygenase (bmoh-alpha) in p. butanovora. residues likely to be within hydrophobic cavities, adjacent to the diiron ...	2006	16788204
cyp153a6, a soluble p450 oxygenase catalyzing terminal-alkane hydroxylation.	the first and key step in alkane metabolism is the terminal hydroxylation of alkanes to 1-alkanols, a reaction catalyzed by a family of integral-membrane diiron enzymes related to pseudomonas putida gpo1 alkb, by a diverse group of methane, propane, and butane monooxygenases and by some membrane-bound cytochrome p450s. recently, a family of cytoplasmic p450 enzymes was identified in prokaryotes that allow their host to grow on aliphatic alkanes. one member of this family, cyp153a6 from mycobacte ...	2006	16816194
distinguishing features of delta-proteobacterial genomes.	we analyzed several features of five currently available delta-proteobacterial genomes, including two aerobic bacteria exhibiting predatory behavior and three anaerobic sulfate-reducing bacteria. the delta genomes are distinguished from other bacteria by several properties: (i) the delta genomes contain two "giant" s1 ribosomal protein genes in contrast to all other bacterial types, which encode a single or no s1; (ii) in most delta-proteobacterial genomes the major ribosomal protein (rp) gene c ...	2006	16844781
[comparative characterization of cultured methane-oxidizing bacteria by serological and molecular methods].	three stable methane-oxidizing enrichment cultures, sb26, sb31, and sb31a were analyzed by transmission electron microscopy and by serological and molecular techniques. electron microscopy revealed the presence of both type i and type ii methanotrophs in sb31 and sb31a enrichments; only type ii methanotrophs were found in sb26 enrichment. methylosinus trichosporium was detected in all three enrichments by the application of species-specific antibodies. additionally, methylocystis echinoides was ...	2006	16871808
biochemical characterization of mmos, a sensor protein involved in copper-dependent regulation of soluble methane monooxygenase.	methane monooxygenase (mmo) enzymes catalyze the oxidation of methane to methanol in methanotrophic bacteria. several strains of methanotrophs, including methylococcus capsulatus (bath), express a membrane-bound or particulate mmo (pmmo) at high copper-to-biomass ratios and a soluble mmo (smmo) form when copper is limited. the mechanism of this "copper switch" is not understood. the mmos gene, located downstream of the smmo operon, encodes a sensor protein that is part of a two-component signali ...	2006	16922494
evolution of vitamin b2 biosynthesis: 6,7-dimethyl-8-ribityllumazine synthases of brucella.	the penultimate step in the biosynthesis of riboflavin (vitamin b2) involves the condensation of 3,4-dihydroxy-2-butanone 4-phosphate with 5-amino-6-ribitylamino-2,4(1h,3h)-pyrimidinedione, which is catalyzed by 6,7-dimethyl-8-ribityllumazine synthase (lumazine synthase). pathogenic brucella species adapted to an intracellular lifestyle have two genes involved in riboflavin synthesis, ribh1 and ribh2, which are located on different chromosomes. the ribh2 gene was shown previously to specify a lu ...	2006	16923880
genome characterization of lipid-containing marine bacteriophage pm2 by transposon insertion mutagenesis.	bacteriophage pm2 presently is the only member of the corticoviridae family. the virion consists of a protein-rich lipid vesicle, which is surrounded by an icosahedral protein capsid. the lipid vesicle encloses a supercoiled circular double-stranded dna genome of 10,079 bp. pm2 belongs to the marine phage community and is known to infect two gram-negative pseudoalteromonas species. in this study, we present a characterization of the pm2 genome made using the in vitro transposon insertion mutagen ...	2006	16940538
complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium nitrosococcus oceani atcc 19707.	the gammaproteobacterium nitrosococcus oceani (atcc 19707) is a gram-negative obligate chemolithoautotroph capable of extracting energy and reducing power from the oxidation of ammonia to nitrite. sequencing and annotation of the genome revealed a single circular chromosome (3,481,691 bp; g+c content of 50.4%) and a plasmid (40,420 bp) that contain 3,052 and 41 candidate protein-encoding genes, respectively. the genes encoding proteins necessary for the function of known modes of lithotrophy and ...	2006	16957257
sterol 14alpha-demethylase cytochrome p450 (cyp51), a p450 in all biological kingdoms.	the cyp51 family is an intriguing subject for fundamental p450 structure/function studies and is also an important clinical drug target. this review updates information on the variety of the cyp51 family members, including their physiological roles, natural substrates and substrate preferences, and catalytic properties in vitro. we present experimental support for the notion that specific conserved regions in the p450 sequences represent a cyp51 signature. two possible roles of cyp51 in p450 evo ...	2007	16963187
sterol 14alpha-demethylase cytochrome p450 (cyp51), a p450 in all biological kingdoms.	the cyp51 family is an intriguing subject for fundamental p450 structure/function studies and is also an important clinical drug target. this review updates information on the variety of the cyp51 family members, including their physiological roles, natural substrates and substrate preferences, and catalytic properties in vitro. we present experimental support for the notion that specific conserved regions in the p450 sequences represent a cyp51 signature. two possible roles of cyp51 in p450 evo ...	2007	16963187
genetic characterization of the phenylacetyl-coenzyme a oxygenase from the aerobic phenylacetic acid degradation pathway of escherichia coli.	we show here that the paaabcde genes of the paa cluster responsible for phenylacetate degradation in escherichia coli w encode a five-component oxygenase that hydroxylates phenylacetyl-coenzyme a (coa), the first intermediate of the pathway. the primary structure of the subunits of bacterial phenylacetyl-coa oxygenases revealed that these enzymes constitute the prototype of a new and distinct group of the large bacterial diiron multicomponent oxygenase family.	2006	16997993
characterization of the particulate methane monooxygenase metal centers in multiple redox states by x-ray absorption spectroscopy.	the integral membrane enzyme particulate methane monooxygenase (pmmo) converts methane, the most inert hydrocarbon, to methanol under ambient conditions. the 2.8-a resolution pmmo crystal structure revealed three metal sites: a mononuclear copper center, a dinuclear copper center, and a nonphysiological mononuclear zinc center. although not found in the crystal structure, solution samples of pmmo also contain iron. we have used x-ray absorption spectroscopy to analyze the oxidation states and co ...	2006	16999437
three-dimensional structure determination of a protein supercomplex that oxidizes methane to formaldehyde in methylococcus capsulatus (bath).	the oxidation of methane to methanol in methanotrophs is catalyzed by the enzyme methane monooxygenase (mmo). two distinct forms of this enzyme exist, a soluble cytoplasmic mmo (smmo) and a membrane-bound particulate form (pmmo). the active protein complex termed pmmo-c was purified recently from methylococcus capsulatus (bath). the complex consists of pmmo hydroxylase and an additional component pmmo-r, which was proposed to be the reductase for the pmmo complex. further study of this complex h ...	2006	17002291
duplication of the mmox gene in methylosinus sporium: cloning, sequencing and mutational analysis.	the soluble methane monooxygenase (smmo) is a key enzyme for methane oxidation, and is found in only some methanotrophs, including methylosinus sporium 5. smmo expression is regulated at the level of transcription from a sigma(54) promoter by a copper-switch, and is only expressed when the copper-to-biomass ratio during growth is low. extensive phylogenetic and genetic analyses of smmos and other soluble di-iron monooxygenases reveal that these enzymes have only been acquired relatively recently ...	2006	17005974
highly prevalent coxiella sp. bacterium in the tick vector amblyomma americanum.	laboratory-reared and field-collected amblyomma americanum ticks were hosts of a coxiella sp. and a rickettsia sp. while the coxiella sp. was detected in 50 of 50 field-collected ticks, the rickettsia sp. was absent from 32% of ticks. the coxiella sp. showed evidence of a reduced genome and may be an obligate endosymbiont.	2007	17085709
highly prevalent coxiella sp. bacterium in the tick vector amblyomma americanum.	laboratory-reared and field-collected amblyomma americanum ticks were hosts of a coxiella sp. and a rickettsia sp. while the coxiella sp. was detected in 50 of 50 field-collected ticks, the rickettsia sp. was absent from 32% of ticks. the coxiella sp. showed evidence of a reduced genome and may be an obligate endosymbiont.	2007	17085709
communities of archaea and bacteria in a subsurface radioactive thermal spring in the austrian central alps, and evidence of ammonia-oxidizing crenarchaeota.	scanning electron microscopy revealed great morphological diversity in biofilms from several largely unexplored subterranean thermal alpine springs, which contain radium 226 and radon 222. a culture-independent molecular analysis of microbial communities on rocks and in the water of one spring, the "franz-josef-quelle" in bad gastein, austria, was performed. four hundred fifteen clones were analyzed. one hundred thirty-two sequences were affiliated with 14 bacterial operational taxonomic units ( ...	2007	17085711
communities of archaea and bacteria in a subsurface radioactive thermal spring in the austrian central alps, and evidence of ammonia-oxidizing crenarchaeota.	scanning electron microscopy revealed great morphological diversity in biofilms from several largely unexplored subterranean thermal alpine springs, which contain radium 226 and radon 222. a culture-independent molecular analysis of microbial communities on rocks and in the water of one spring, the "franz-josef-quelle" in bad gastein, austria, was performed. four hundred fifteen clones were analyzed. one hundred thirty-two sequences were affiliated with 14 bacterial operational taxonomic units ( ...	2007	17085711
the genome of deep-sea vent chemolithoautotroph thiomicrospira crunogena xcl-2.	presented here is the complete genome sequence of thiomicrospira crunogena xcl-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. this gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. it has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. a ...	2006	17105352
the glycolytic pathway of trimastix pyriformis is an evolutionary mosaic.	glycolysis and subsequent fermentation is the main energy source for many anaerobic organisms. the glycolytic pathway consists of ten enzymatic steps which appear to be universal amongst eukaryotes. however, it has been shown that the origins of these enzymes in specific eukaryote lineages can differ, and sometimes involve lateral gene transfer events. we have conducted an expressed sequence tag (est) survey of the anaerobic flagellate trimastix pyriformis to investigate the nature of the evolut ...	2006	17123440
whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium methylibium petroleiphilum pm1.	methylibium petroleiphilum pm1 is a methylotroph distinguished by its ability to completely metabolize the fuel oxygenate methyl tert-butyl ether (mtbe). strain pm1 also degrades aromatic (benzene, toluene, and xylene) and straight-chain (c(5) to c(12)) hydrocarbons present in petroleum products. whole-genome analysis of pm1 revealed an approximately 4-mb circular chromosome and an approximately 600-kb megaplasmid, containing 3,831 and 646 genes, respectively. aromatic hydrocarbon and alkane deg ...	2007	17158667
whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium methylibium petroleiphilum pm1.	methylibium petroleiphilum pm1 is a methylotroph distinguished by its ability to completely metabolize the fuel oxygenate methyl tert-butyl ether (mtbe). strain pm1 also degrades aromatic (benzene, toluene, and xylene) and straight-chain (c(5) to c(12)) hydrocarbons present in petroleum products. whole-genome analysis of pm1 revealed an approximately 4-mb circular chromosome and an approximately 600-kb megaplasmid, containing 3,831 and 646 genes, respectively. aromatic hydrocarbon and alkane deg ...	2007	17158667
biochemical characterization of isocitrate dehydrogenase from methylococcus capsulatus reveals a unique nad+-dependent homotetrameric enzyme.	the gene encoding isocitrate dehydrogenase (idh) of methylococcus capsulatus (mcidh) was cloned and overexpressed in escherichia coli. the purified enzyme was nad+-dependent with a thermal optimum for activity at 55-60 degrees c and an apparent midpoint melting temperature (tm) of 70 degrees c. analytical ultracentrifugation (auc) revealed a homotetrameric state, and mcidh thus represents the first homotetrameric nad+-dependent idh that has been characterized. based on a structural alignment of ...	2007	17160675
characterization of the thermotoga maritima chemotaxis methylation system that lacks pentapeptide-dependent methyltransferase cher:mcp tethering.	sensory adaptation in bacterial chemotaxis is mediated by covalent modifications of specific glutamate and glutamine residues within the cytoplasmic domains of methyl-accepting chemotaxis proteins (mcps). in escherichia coli and salmonella enterica, efficient methylation of mcps depends on the localization of methyltransferase cher to mcp clusters through an interaction between the cher beta-subdomain and a pentapeptide sequence (nwetf or nwesf) at the c-terminus of the mcp. in vitro methylation ...	2007	17163981
characterization of the thermotoga maritima chemotaxis methylation system that lacks pentapeptide-dependent methyltransferase cher:mcp tethering.	sensory adaptation in bacterial chemotaxis is mediated by covalent modifications of specific glutamate and glutamine residues within the cytoplasmic domains of methyl-accepting chemotaxis proteins (mcps). in escherichia coli and salmonella enterica, efficient methylation of mcps depends on the localization of methyltransferase cher to mcp clusters through an interaction between the cher beta-subdomain and a pentapeptide sequence (nwetf or nwesf) at the c-terminus of the mcp. in vitro methylation ...	2007	17163981
high precision multi-genome scale reannotation of enzyme function by eficaz.	the functional annotation of most genes in newly sequenced genomes is inferred from similarity to previously characterized sequences, an annotation strategy that often leads to erroneous assignments. we have performed a reannotation of 245 genomes using an updated version of eficaz, a highly precise method for enzyme function prediction.	2006	17166279
isolation of a multiheme protein with features of a hydrazine-oxidizing enzyme from an anaerobic ammonium-oxidizing enrichment culture.	a multiheme protein having hydrazine-oxidizing activity was purified from enriched culture from a reactor in which an anammox bacterium, strain ksu-1, was dominant. the enzyme has oxidizing activity toward hydrazine but not hydroxylamine and is a 130-kda homodimer composed of a 62-kda polypeptide containing eight hemes. it was therefore named hydrazine-oxidizing enzyme (hzo). with cytochrome c as an electron acceptor, the v(max) and k(m) for hydrazine are 6.2 +/- 0.3 micromol/min.mg and 5.5 +/- ...	2007	17172456
isolation of a multiheme protein with features of a hydrazine-oxidizing enzyme from an anaerobic ammonium-oxidizing enrichment culture.	a multiheme protein having hydrazine-oxidizing activity was purified from enriched culture from a reactor in which an anammox bacterium, strain ksu-1, was dominant. the enzyme has oxidizing activity toward hydrazine but not hydroxylamine and is a 130-kda homodimer composed of a 62-kda polypeptide containing eight hemes. it was therefore named hydrazine-oxidizing enzyme (hzo). with cytochrome c as an electron acceptor, the v(max) and k(m) for hydrazine are 6.2 +/- 0.3 micromol/min.mg and 5.5 +/- ...	2007	17172456
x-ray structure of a hydroxylase-regulatory protein complex from a hydrocarbon-oxidizing multicomponent monooxygenase, pseudomonas sp. ox1 phenol hydroxylase.	phenol hydroxylase (ph) belongs to a family of bacterial multicomponent monooxygenases (bmms) with carboxylate-bridged diiron active sites. included are toluene/o-xylene (tomo) and soluble methane (smmo) monooxygenase. ph hydroxylates aromatic compounds, but unlike smmo, it cannot oxidize alkanes despite having a similar dinuclear iron active site. important for activity is formation of a complex between the hydroxylase and a regulatory protein component. to address how structural features of bm ...	2006	17176061
identification of important regions for ethylene binding and signaling in the transmembrane domain of the etr1 ethylene receptor of arabidopsis.	the ethylene binding domain (ebd) of the arabidopsis thaliana etr1 receptor is modeled as three membrane-spanning helices. we surveyed ethylene binding activity in different kingdoms and performed a bioinformatic analysis of the ebd. ethylene binding is confined to land plants, chara, and a group of cyanobacteria but is largely absent in other organisms, consistent with our finding that ebd-like sequences are overrepresented among plant and cyanobacterial species. we made amino acid substitution ...	2006	17189345
a novel protein, ttpc, is a required component of the tonb2 complex for specific iron transport in the pathogens vibrio anguillarum and vibrio cholerae.	active transport across the outer membrane in gram-negative bacteria requires the energy that is generated by the proton motive force in the inner membrane. this energy is transduced to the outer membrane by the tonb protein in complex with the proteins exbb and exbd. in the pathogen vibrio anguillarum we have identified two tonb systems, tonb1 and tonb2, the latter is used for ferric-anguibactin transport and is transcribed as part of an operon that consists of orf2, exbb2, exbd2, and tonb2. th ...	2007	17189363
a novel protein, ttpc, is a required component of the tonb2 complex for specific iron transport in the pathogens vibrio anguillarum and vibrio cholerae.	active transport across the outer membrane in gram-negative bacteria requires the energy that is generated by the proton motive force in the inner membrane. this energy is transduced to the outer membrane by the tonb protein in complex with the proteins exbb and exbd. in the pathogen vibrio anguillarum we have identified two tonb systems, tonb1 and tonb2, the latter is used for ferric-anguibactin transport and is transcribed as part of an operon that consists of orf2, exbb2, exbd2, and tonb2. th ...	2007	17189363
laba: a novel gene required for negative feedback regulation of the cyanobacterial circadian clock protein kaic.	in the cyanobacterium synechococcus elongatus pcc 7942, circadian timing is transmitted from the kaiabc-based central oscillator to the transcription factor rpaa via the kaic-interacting histidine kinase sasa to activate transcription, thereby generating rhythmic circadian gene expression. however, kaic can also repress circadian gene expression, including its own. the mechanism and significance of this negative feedback regulation have been unclear. here, we report a novel gene, laba (low-ampli ...	2007	17210789
optimization of solubilization and purification procedures for the hydroxylase component of membrane-bound methane monooxygenase from methylococcus capsulatus strain m.	the hydroxylase component of membrane-bound (particulate) methane monooxygenase (pmmo) from methylococcus capsulatus strain m was isolated and purified to homogeneity. the pmmo molecule comprises three subunits of molecular masses 47, 26, and 23 kd and contains three copper atoms and one iron atom. in solution the protein exists as a stable oligomer of 660 kd with possible subunit composition (alpha beta gamma)6. mass spectroscopy shows high homology of the purified protein with methane monooxyg ...	2006	17223785
[effect of substances which change the proton-motive force on activity of methane microbe oxygenation].	high extracellular concentration of k+ stimulated methane oxygenation with methylomonas rubra 15 [russian character: see text], methylococcus thermophilus 111 [russian character: see text] and methylococcus capsulatus 494 at neutral value of ph. that was determined by k+ arrival to the cells at neutral medium ph that resulted in the increase of ph difference between the exterior and interior sides of the membrane (aph) and, respectively, in the increase of the methane oxygenation rate. thus, met ...	2006	17243361
desaturase reactions complicate the use of norcarane as a mechanistic probe. unraveling the mixture of twenty-plus products formed in enzyme-catalyzed oxidations of norcarane.	norcarane, bicyclo[4.1.0]heptane, has been widely used as a mechanistic probe in studies of oxidations catalyzed by several iron-containing enzymes. we report here that, in addition to oxygenated products, norcarane is also oxidized by iron-containing enzymes in desaturase reactions that give 2-norcarene and 3-norcarene. furthermore, secondary products from further oxidation reactions of the norcarenes are produced in yields that are comparable to those of the minor products from oxidation of th ...	2007	17288366
products from enzyme-catalyzed oxidations of norcarenes.	recent studies revealed that norcarane (bicyclo[4.1.0]heptane) is oxidized to 2-norcarene (bicyclo[4.1.0]-hept-2-ene) and 3-norcarene (bicyclo[4.1.0]hept-3-ene) by iron-containing enzymes and that secondary oxidation products from the norcarenes complicate mechanistic probe studies employing norcarane as the substrate (newcomb, m.; chandrasena, r. e. p.; lansakara-p., d. s. p.; kim, h.-y.; lippard, s. j.; beauvais, l. g.; murray, l. j.; izzo, v.; hollenberg, p. f.; coon, m. j. j. org. chem. 2007 ...	2007	17288367