Publications

protein engineering of toluene-o-xylene monooxygenase from pseudomonas stutzeri ox1 for synthesizing 4-methylresorcinol, methylhydroquinone, and pyrogallol.	toluene-o-xylene monooxygenase (tomo) from pseudomonas stutzeri ox1 oxidizes toluene to 3- and 4-methylcatechol and oxidizes benzene to form phenol; in this study tomo was found to also form catechol and 1,2,3-trihydroxybenzene (1,2,3-thb) from phenol. to synthesize novel dihydroxy and trihydroxy derivatives of benzene and toluene, dna shuffling of the alpha-hydroxylase fragment of tomo (toua) and saturation mutagenesis of the toua active site residues i100, q141, t201, and f205 were used to gen ...	2004	15184119
distribution of rubisco genotypes along a redox gradient in mono lake, california.	partial sequences of ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) (ec 4.1.1.39) genes were retrieved from samples taken along a redox gradient in alkaline, hypersaline mono lake, calif. the form i gene (cbbl) was found in all samples, whereas form ii (cbbm) was not retrieved from any of the samples. none of the rubisco sequences we obtained were closely related (nucleotide similarity, <90%) to sequences in the database. some could be attributed to organisms isolated from the lake (c ...	2004	15184142
comparative genomics of rice and arabidopsis. analysis of 727 cytochrome p450 genes and pseudogenes from a monocot and a dicot.	data mining methods have been used to identify 356 cyt p450 genes and 99 related pseudogenes in the rice (oryza sativa) genome using sequence information available from both the indica and japonica strains. because neither of these genomes is completely available, some genes have been identified in only one strain, and 28 genes remain incomplete. comparison of these rice genes with the 246 p450 genes and 26 pseudogenes in the arabidopsis genome has indicated that most of the known plant p450 fam ...	2004	15208422
altering toluene 4-monooxygenase by active-site engineering for the synthesis of 3-methoxycatechol, methoxyhydroquinone, and methylhydroquinone.	wild-type toluene 4-monooxygenase (t4mo) of pseudomonas mendocina kr1 oxidizes toluene to p-cresol (96%) and oxidizes benzene sequentially to phenol, to catechol, and to 1,2,3-trihydroxybenzene. in this study t4mo was found to oxidize o-cresol to 3-methylcatechol (91%) and methylhydroquinone (9%), to oxidize m-cresol and p-cresol to 4-methylcatechol (100%), and to oxidize o-methoxyphenol to 4-methoxyresorcinol (87%), 3-methoxycatechol (11%), and methoxyhydroquinone (2%). apparent vmax values of ...	2004	15231803
determination by x-ray absorption spectroscopy of the fe-fe separation in the oxidized form of the hydroxylase of methane monooxygenase alone and in the presence of mmod.	the diiron active site in the hydroxylase of methylococcus capsulatus (bath) methane monooxygenase (mmoh) has been studied in the oxidized form by x-ray absorption spectroscopy (xas). previous investigations by xas and x-ray crystallography have identified two different distances (3.0 and 3.4 angstroms) between the two fe atoms in the dinuclear site. the present study has employed a systematic extended x-ray absorption fine structure (exafs) fitting methodology, utilizing known and simulated act ...	2004	15257585
nmr structure of the flavin domain from soluble methane monooxygenase reductase from methylococcus capsulatus (bath).	soluble methane monooxygenase (smmo) catalyzes the hydroxylation of methane by dioxygen to methanol, the first step in carbon assimilation by methanotrophs. this multicomponent system transfers electrons from nadh through a reductase component to the non-heme diiron center in the hydroxylase where o(2) is activated. the reductase component comprises three distinct domains, a [2fe-2s] ferredoxin domain along with fad- and nadh-binding domains. we report the solution structure of the reduced 27.6 ...	2004	15379538
genomic insights into methanotrophy: the complete genome sequence of methylococcus capsulatus (bath).	methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular, substantially reducing emissions of biologically generated methane to the atmosphere. despite their importance, and in contrast to organisms that play roles in other major parts of the carbon cycle such as photosynthesis, no genome-level studies have been published on the biology of methanotrophs. we repo ...	2004	15383840
domain engineering of the reductase component of soluble methane monooxygenase from methylococcus capsulatus (bath).	soluble methane monooxygenase (smmo) from methylococcus capsulatus (bath) is a three-component enzyme system that catalyzes the conversion of methane to methanol. a reductase (mmor), which contains [2fe-2s] and fad cofactors, facilitates electron transfer from nadh to the hydroxylase diiron active sites where dioxygen activation and substrate hydroxylation take place. by separately expressing the ferredoxin (mmorfd, mmor residues 1-98) and fad/nadh (mmor-fad, mmor residues 99-348) domains of the ...	2004	14613937
analysis of facultative lithotroph distribution and diversity on volcanic deposits by use of the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase.	a 492- to 495-bp fragment of the gene coding for the large subunit of the form i ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco) (rbcl) was amplified by pcr from facultatively lithotrophic aerobic co-oxidizing bacteria, colorless and purple sulfide-oxidizing microbial mats, and genomic dna extracts from tephra and ash deposits from kilauea volcano, for which atmospheric co and hydrogen have been previously documented as important substrates. pcr products from the mats and volcanic site ...	2004	15066819
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
facultative methanotrophs revisited.		2005	15968038
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
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
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
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
characterization of ichthyocidal activity of pfiesteria piscicida: dependence on the dinospore cell density.	the ichthyocidal activity of pfiesteria piscicida dinospores was examined in an aquarium bioassay format by exposing fish to either pfiesteria-containing environmental sediments or clonal p. piscicida. the presence of pfiesteria spp. and the complexity of the microbial assemblage in the bioassay were assessed by molecular approaches. cell-free water from bioassays that yielded significant fish mortality failed to show ichthyocidal activity. histopathological examination of moribund and dead fish ...	2005	15640229
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
[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
improved analysis of membrane protein by pvdf-aided, matrix-assisted laser desorption/ionization mass spectrometry.	characterization of membrane proteins remains an analytical challenge because of difficulties associated with tedious isolation and purification. this study presents the utility of the polyvinylidene difluoride (pvdf) membrane for direct sub-proteome profiling and membrane protein characterization by matrix-assisted laser desorption/ionization mass spectrometry (maldi-ms). the hydrophobic adsorption of protein, particularly membrane proteins, on the pvdf surface enables efficient on-pvdf washing ...	2006	17723354
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
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
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
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
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
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
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
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
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
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
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
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
facile o-atom insertion into c-c and c-h bonds by a trinuclear copper complex designed to harness a singlet oxene.	two trinuclear copper [cu(i)cu(i)cu(i)(l)](1+) complexes have been prepared with the multidentate ligands (l) 3,3'-(1,4-diazepane-1,4-diyl)bis(1-((2-(dimethylamino)ethyl)(methyl)amino)propan-2-ol) (7-me) and (3,3'-(1,4-diazepane-1,4-diyl)bis(1-((2-(diethylamino) ethyl)(ethyl) amino)propan-2-ol) (7-et) as models for the active site of the particulate methane monooxygenase (pmmo). the ligands were designed to form the proper spatial and electronic geometry to harness a "singlet oxene," according t ...	2007	17804786
crispr recognition tool (crt): a tool for automatic detection of clustered regularly interspaced palindromic repeats.	clustered regularly interspaced palindromic repeats (crisprs) are a novel type of direct repeat found in a wide range of bacteria and archaea. crisprs are beginning to attract attention because of their proposed mechanism; that is, defending their hosts against invading extrachromosomal elements such as viruses. existing repeat detection tools do a poor job of identifying crisprs due to the presence of unique spacer sequences separating the repeats. in this study, a new tool, crt, is introduced ...	2007	17577412
cryoradiolytic reduction of heme proteins: maximizing dose dependent yield.	radiolytic reduction in frozen solutions and crystals is a useful method for generation of trapped intermediates in protein based radical reactions. in this communication we define the conditions which provide the maximum yield of one electron reduced myoglobin at 77 k using (60)co γ-irradiation in aqueous glycerol glass. the yield reached 50% after 20 kgy, was almost complete at ∼160 kgy total dose, and does not depend on the protein concentration in the range 0.01 - 5 mm.	2007	18379640
intermediates in dioxygen activation by methane monooxygenase: a qm/mm study.	protein effects in the activation of dioxygen by methane monooxygenase (mmo) were investigated by using combined qm/mm and broken-symmetry density functional theory (dft) methods. the effects of a novel empirical scheme recently developed by our group on the relative dft energies of the various intermediates in the catalytic cycle are investigated. inclusion of the protein leads to much better agreement between the experimental and computed geometric structures for the reduced form (mmoh(red)). ...	2007	17326634
classification and regression tree (cart) analyses of genomic signatures reveal sets of tetramers that discriminate temperature optima of archaea and bacteria.	classification and regression tree (cart) analysis was applied to genome-wide tetranucleotide frequencies (genomic signatures) of 195 archaea and bacteria. although genomic signatures have typically been used to classify evolutionary divergence, in this study, convergent evolution was the focus. temperature optima for most of the organisms examined could be distinguished by cart analyses of tetranucleotide frequencies. this suggests that pervasive (nonlinear) qualities of genomes may reflect cer ...	2007	19054742
classification and regression tree (cart) analyses of genomic signatures reveal sets of tetramers that discriminate temperature optima of archaea and bacteria.	classification and regression tree (cart) analysis was applied to genome-wide tetranucleotide frequencies (genomic signatures) of 195 archaea and bacteria. although genomic signatures have typically been used to classify evolutionary divergence, in this study, convergent evolution was the focus. temperature optima for most of the organisms examined could be distinguished by cart analyses of tetranucleotide frequencies. this suggests that pervasive (nonlinear) qualities of genomes may reflect cer ...	2007	19054742
molecular ecology techniques for the study of aerobic methanotrophs.		2007	18165358
molecular ecology techniques for the study of aerobic methanotrophs.		2007	18165358
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
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
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
transcriptional regulatory network discovery via multiple method integration: application to e. coli k12.	transcriptional regulatory network (trn) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete trns. we develop a methodology, trnd, that integrates a preliminary trn, microarray data, gene ontology and phylogenic similarity to accurately discover trns and apply the method to e. coli k12. the approach can easily be extended to include other me ...	2007	17397539