Publications

cytochromes p460 and c'-beta; a new family of high-spin cytochromes c.	cytochromes-p460 of nitrosomonas europaea and methylococcus capsulatus (bath), and the cytochrome c' of m. capsulatus, believed to be involved in binding or transformation of n-oxides, are shown to represent an evolutionarily related new family of monoheme, approximately 17kda, cytochromes c found in the genomes of diverse proteobacteria. all members of this family have a predicted secondary structure predominantly of beta-sheets in contrast to the predominantly alpha-helical cytochromes c' foun ...	2007	17292891
complement activation and cytokine response by bioprotein, a bacterial single cell protein.	the bacterial single cell protein (bscp), bioprotein, is dried bacterial mass derived from fermentation of the gram negative bacteria methylococcus capsulatus, used for animal and fish feed. workers in this industry suffer frequently from pulmonary and systemic symptoms which may be induced by an inflammatory reaction. the aim of the present study was to examine the effect of bscp on inflammation in vitro as evaluated by complement activation and cytokine production. human serum was incubated wi ...	2007	17302729
isolation of methylophaga spp. from marine dimethylsulfide-degrading enrichment cultures and identification of polypeptides induced during growth on dimethylsulfide.	dimethylsulfide (dms)-degrading enrichment cultures were established from samples of coastal seawater, nonaxenic emiliania huxleyi cultures, and mixed marine methyl halide-degrading enrichment cultures. bacterial populations from a broad phylogenetic range were identified in the mixed dms-degrading enrichment cultures by denaturing gradient gel electrophoresis (dgge). sequences of dominant dgge bands were similar to those of members of the genera methylophaga and alcanivorax. several closely rel ...	2007	17322322
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
the biochemistry of methane oxidation.	methanotrophic bacteria oxidize methane to methanol in the first step of their metabolic pathway. two forms of methane monooxygenase (mmo) enzymes catalyze this reaction: soluble mmo (smmo) and membrane-bound or particulate mmo (pmmo). pmmo is expressed when copper is available, and its active site is believed to contain copper. whereas smmo is well characterized, most aspects of pmmo biochemistry remain unknown and somewhat controversial. this review emphasizes advances in the past two to three ...	2007	17328677
linear array of conserved sequence motifs to discriminate protein subfamilies: study on pyridine nucleotide-disulfide reductases.	the pyridine nucleotide disulfide reductase (pndr) is a large and heterogeneous protein family divided into two classes (i and ii), which reflect the divergent evolution of its characteristic disulfide redox active site. however, not all the pndr members fit into these categories and this suggests the need of further studies to achieve a more comprehensive classification of this complex family.	2007	17367536
a streamlined metabolic pathway for the biosynthesis of moenomycin a.	moenomycin a (mma) is a member of the phosphoglycolipid family of antibiotics, which are the only natural products known to directly target the extracellular peptidoglycan glycosyltransferases involved in bacterial cell wall biosynthesis. the structural and biological uniqueness of mma make it an attractive starting point for the development of new antibacterial drugs. in order both to elucidate the biosynthesis of this unusual compound and to develop tools to manipulate its structure, we have i ...	2007	17379141
transcription of all amoc copies is associated with recovery of nitrosomonas europaea from ammonia starvation.	the chemolithotrophic ammonia-oxidizing bacterium nitrosomonas europaea is known to be highly resistant to starvation conditions. the transcriptional response of n. europaea to ammonia addition following short- and long-term starvation was examined by primer extension and s1 nuclease protection analyses of genes encoding enzymes for ammonia oxidation (amocab operons) and co(2) fixation (cbbls), a third, lone copy of amoc (amoc(3)), and two representative housekeeping genes (glya and rpsj). prime ...	2007	17384196
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
genome of methylobacillus flagellatus, molecular basis for obligate methylotrophy, and polyphyletic origin of methylotrophy.	along with methane, methanol and methylated amines represent important biogenic atmospheric constituents; thus, not only methanotrophs but also nonmethanotrophic methylotrophs play a significant role in global carbon cycling. the complete genome of a model obligate methanol and methylamine utilizer, methylobacillus flagellatus (strain kt) was sequenced. the genome is represented by a single circular chromosome of approximately 3 mbp, potentially encoding a total of 2,766 proteins. based on genom ...	2007	17416667
on the origin and evolution of biosynthetic pathways: integrating microarray data with structure and organization of the common pathway genes.	the lysine, threonine, and methionine biosynthetic pathways share the three initial enzymatic steps, which are referred to as the common pathway (cp). in escherichia coli three different aspartokinases (aki, akii, akiii, the products of thra, metl and lysc, respectively) can perform the first step of the cp. moreover, two of them (aki and akii) are bifunctional, carrying also homoserine dehydrogenasic activity (hom product). the second step of the cp is catalyzed by a single aspartate semialdehy ...	2007	17430556
structural and mechanistic insights into methane oxidation by particulate methane monooxygenase.	particulate methane monooxygense (pmmo) is an integral membrane copper-containing enzyme that converts methane to methanol. knowledge of how pmmo selectively oxidizes methane under ambient conditions could impact the development of new catalysts. the crystal structure of methylococcus capsulatus (bath) pmmo reveals the composition and location of three metal centers. spectroscopic data provide insight into the coordination environments and oxidation states of these metal centers. these results, ...	2007	17444606
comparative genome analysis of four magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function.	magnetotactic bacteria (mtb) are a heterogeneous group of aquatic prokaryotes with a unique intracellular organelle, the magnetosome, which orients the cell along magnetic field lines. magnetotaxis is a complex phenotype, which depends on the coordinate synthesis of magnetosomes and the ability to swim and orient along the direction caused by the interaction with the earth's magnetic field. although a number of putative magnetotaxis genes were recently identified within a conserved genomic magne ...	2007	17449609
lanosterol biosynthesis in the prokaryote methylococcus capsulatus: insight into the evolution of sterol biosynthesis.	a putative operon containing homologues of essential eukaryotic sterol biosynthetic enzymes, squalene monooxygenase and oxidosqualene cyclase, has been identified in the genome of the prokaryote methylococcus capsulatus. expression of the squalene monooxygenase yielded a protein associated with the membrane fraction, while expression of oxidosqualene cyclase yielded a soluble protein, contrasting with the eukaryotic enzyme forms. activity studies with purified squalene monooxygenase revealed a c ...	2007	17567593
effect of afforestation and reforestation of pastures on the activity and population dynamics of methanotrophic bacteria.	we investigated the effect of afforestation and reforestation of pastures on methane oxidation and the methanotrophic communities in soils from three different new zealand sites. methane oxidation was measured in soils from two pine (pinus radiata) forests and one shrubland (mainly kunzea ericoides var. ericoides) and three adjacent permanent pastures. the methane oxidation rate was consistently higher in the pine forest or shrubland soils than in the adjacent pasture soils. a combination of pho ...	2007	17574997
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
the crystal structure of cytochrome p460 of nitrosomonas europaea reveals a novel cytochrome fold and heme-protein cross-link.	we have determined the 1.8 a x-ray crystal structure of a monoheme c-type cytochrome, cytochrome p460, from nitrosomonas europea. the chromophore possesses unusual spectral properties analogous to those of the catalytic heme p460 of hydroxylamine oxidoreductase (hao), the only known heme in biology to withdraw electrons from an iron-coordinated substrate. the analysis reveals a homodimeric structure and elucidates a new c-type cytochrome fold that is predominantly beta-sheet. in addition to the ...	2007	17583915
three putative cation/proton antiporters from the soda lake alkaliphile alkalimonas amylolytica n10 complement an alkali-sensitive escherichia coli mutant.	attempts to identify members of the antiporter complement of the alkali- and saline-adapted soda lake alkaliphile alkalimonas amylolytica n10 have used screens of dna libraries in antiporter-deficient escherichia coli knabc. earlier screens used na(+) or li(+) for selection but only identified one nhad-type antiporter whose properties were inconsistent with a robust role in ph homeostasis. here, new screens using elevated ph for selection identified three other putative antiporter genes that con ...	2007	17600061
a manganese(iv)/iron(iv) intermediate in assembly of the manganese(iv)/iron(iii) cofactor of chlamydia trachomatis ribonucleotide reductase.	we recently showed that the class ic ribonucleotide reductase from the human pathogen chlamydia trachomatis uses a mn(iv)/fe(iii) cofactor to generate protein and substrate radicals in its catalytic mechanism [jiang, w., yun, d., saleh, l., barr, e. w., xing, g., hoffart, l. m., maslak, m.-a., krebs, c., and bollinger, j. m., jr. (2007) science 316, 1188-1191]. here, we have dissected the mechanism of formation of this novel heterobinuclear redox cofactor from the mn(ii)/fe(ii) cluster and o2. a ...	2007	17616152
protein abundance ratios for global studies of prokaryotes.	the use of multidimensional capillary hplc combined with ms/ms has allowed high qualitative and quantitative proteome coverage of prokaryotic organisms. the determination of protein abundance change between two or more conditions has matured to the point that false discovery rates can be very low and for smaller proteomes coverage is sufficiently high to explicitly consider false negative error. selected aspects of using these methods for global protein abundance assessments are reviewed. these ...	2007	17639608
biochemical and molecular characterization of methanotrophs in soil from a pristine new zealand beech forest.	methane (ch4) oxidation and the methanotrophic community structure of a pristine new zealand beech forest were investigated using biochemical and molecular methods. phospholipid-fatty acid-stable-isotope probing (plfa-sip) was used to identify the active population of methanotrophs in soil beneath the forest floor, while terminal-restriction fragment length polymorphism (t-rflp) and cloning and sequencing of the pmoa gene were used to characterize the methanotrophic community. plfa-sip suggested ...	2007	17696992
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
insights into the genome of large sulfur bacteria revealed by analysis of single filaments.	marine sediments are frequently covered by mats of the filamentous beggiatoa and other large nitrate-storing bacteria that oxidize hydrogen sulfide using either oxygen or nitrate, which they store in intracellular vacuoles. despite their conspicuous metabolic properties and their biogeochemical importance, little is known about their genetic repertoire because of the lack of pure cultures. here, we present a unique approach to access the genome of single filaments of beggiatoa by combining whole ...	2007	17760503
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
biosynthesis of 2-methylbacteriohopanepolyols by an anoxygenic phototroph.	sedimentary 2-methyhopanes have been used as biomarker proxies for cyanobacteria, the only known bacterial clade capable of oxygenic photosynthesis and the only group of organisms found thus far to produce abundant 2-methylbacteriohopanepolyols (2-mebhps). here, we report the identification of significant quantities of 2-mebhp in two strains of the anoxygenic phototroph rhodopseudomonas palustris. biosynthesis of 2-mebhp can occur in the absence of o(2), deriving the c-2 methyl group from methio ...	2007	17848515
metagenomics of the deep mediterranean, a warm bathypelagic habitat.	metagenomics is emerging as a powerful method to study the function and physiology of the unexplored microbial biosphere, and is causing us to re-evaluate basic precepts of microbial ecology and evolution. most marine metagenomic analyses have been nearly exclusively devoted to photic waters.	2007	17878949
periplasmic proteins of the extremophile acidithiobacillus ferrooxidans: a high throughput proteomics analysis.	acidithiobacillus ferrooxidans is a chemolithoautotrophic acidophile capable of obtaining energy by oxidizing ferrous iron or sulfur compounds such as metal sulfides. some of the proteins involved in these oxidations have been described as forming part of the periplasm of this extremophile. the detailed study of the periplasmic components constitutes an important area to understand the physiology and environmental interactions of microorganisms. proteomics analysis of the periplasmic fraction of ...	2007	17911085
response of desulfovibrio vulgaris to alkaline stress.	the response of exponentially growing desulfovibrio vulgaris hildenborough to ph 10 stress was studied using oligonucleotide microarrays and a study set of mutants with genes suggested by microarray data to be involved in the alkaline stress response deleted. the data showed that the response of d. vulgaris to increased ph is generally similar to that of escherichia coli but is apparently controlled by unique regulatory circuits since the alternative sigma factors (sigma s and sigma e) contribut ...	2007	17921288
sterol biosynthesis by a prokaryote: first in vitro identification of the genes encoding squalene epoxidase and lanosterol synthase from methylococcus capsulatus.	sterol biosynthesis by prokaryotic organisms is very rare. squalene epoxidase and lanosterol synthase are prerequisite to cyclic sterol biosynthesis. these two enzymes, from the methanotrophic bacterium methylococcus capsulatus, were functionally expressed in escherichia coli. structural analyses of the enzymatic products indicated that the reactions proceeded in a complete regio- and stereospecific fashion to afford (3s)-2,3-oxidosqualene from squalene and lanosterol from (3s)-2,3-oxidosqualene ...	2007	17928701
soluble expression and purification of the oxidoreductase component of toluene 4-monooxygenase.	toluene 4-monooxygenase (t4mo) is a member of the bacterial multicomponent monooxygenases, an enzyme family that utilizes a soluble diiron hydroxylase to oxidize a variety of hydrocarbons as the initial step in their metabolism. the hydroxylases obtain reducing equivalents from nad(p)h via an electron transfer chain that is initiated by an oxidoreductase containing an n-terminal ferredoxin domain and c-terminal flavin- and nad-binding domains. t4mof, the nadh oxidoreductase of t4mo, was expresse ...	2008	17964805
soluble expression and purification of the oxidoreductase component of toluene 4-monooxygenase.	toluene 4-monooxygenase (t4mo) is a member of the bacterial multicomponent monooxygenases, an enzyme family that utilizes a soluble diiron hydroxylase to oxidize a variety of hydrocarbons as the initial step in their metabolism. the hydroxylases obtain reducing equivalents from nad(p)h via an electron transfer chain that is initiated by an oxidoreductase containing an n-terminal ferredoxin domain and c-terminal flavin- and nad-binding domains. t4mof, the nadh oxidoreductase of t4mo, was expresse ...	2008	17964805
the c-terminal aqueous-exposed domain of the 45 kda subunit of the particulate methane monooxygenase in methylococcus capsulatus (bath) is a cu(i) sponge.	the crystal structure of the particulate methane monooxygenase (pmmo) from methylococcus capsulatus (bath) has been reported recently [lieberman, r. l., and rosenzweig, a. c. (2005) crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane, nature 434, 177-182]. subsequent work has shown that the preparation on which the x-ray analysis is based might be missing many of the important metal cofactors, including the putative trinuclear copper cluster at ...	2007	17985930
blood parameters in growing pigs fed increasing levels of bacterial protein meal.	the experiment investigated the effects of increasing dietary levels of bacterial protein meal (bpm) on various blood parameters reflecting protein and fat metabolism, liver function, and purine base metabolism in growing pigs. sixteen barrows were allocated to four different experimental diets. the control diet was based on soybean meal. in the other three diets soybean meal was replaced with increasing levels of bpm, approximately 17%, 35%, and 50% of the nitrogen being derived from bpm. blood ...	2007	17996082
the [fefe] hydrogenase of nyctotherus ovalis has a chimeric origin.	the hydrogenosomes of the anaerobic ciliate nyctotherus ovalis show how mitochondria can evolve into hydrogenosomes because they possess a mitochondrial genome and parts of an electron-transport chain on the one hand, and a hydrogenase on the other hand. the hydrogenase permits direct reoxidation of nadh because it consists of a [fefe] hydrogenase module that is fused to two modules, which are homologous to the 24 kda and the 51 kda subunits of a mitochondrial complex i.	2007	18021395
dioxygen activation at non-heme diiron centers: oxidation of a proximal residue in the i100w variant of toluene/o-xylene monooxygenase hydroxylase.	at its carboxylate-bridged diiron active site, the hydroxylase component of toluene/o-xylene monooxygenase activates dioxygen for subsequent arene hydroxylation. in an i100w variant of this enzyme, we characterized the formation and decay of two species formed by addition of dioxygen to the reduced, diiron(ii) state by rapid-freeze quench (rfq) epr, mössbauer, and endor spectroscopy. the dependence of the formation and decay rates of this mixed-valent transient on ph and the presence of phenol, ...	2007	18044971
mössbauer studies of the membrane-associated methane monooxygenase from methylococcus capsulatus bath: evidence for a diiron center.	two methane monooxygenase (mmo) systems have been identified in methanotrophic bacteria, namely, a soluble or cytoplasmic mmo and a membrane-associated or particulate mmo. the active site of the well-characterized soluble mmo contains a bis-mu-hydroxo-bridged diiron cluster. x-ray crystallographic studies of the particulate enzyme, pmmo, have identified two copper centers on the alpha subunit (pmob) of the alphabetagamma trimer and a site at the interface of the betagamma subunits filled by a zn ...	2007	18052283
evolution of the chaperone/usher assembly pathway: fimbrial classification goes greek.	many proteobacteria use the chaperone/usher pathway to assemble proteinaceous filaments on the bacterial surface. these filaments can curl into fimbrial or nonfimbrial surface structures (e.g., a capsule or spore coat). this article reviews the phylogeny of operons belonging to the chaperone/usher assembly class to explore the utility of establishing a scheme for subdividing them into clades of phylogenetically related gene clusters. based on usher amino acid sequence comparisons, our analysis s ...	2007	18063717
genome of the epsilonproteobacterial chemolithoautotroph sulfurimonas denitrificans.	sulfur-oxidizing epsilonproteobacteria are common in a variety of sulfidogenic environments. these autotrophic and mixotrophic sulfur-oxidizing bacteria are believed to contribute substantially to the oxidative portion of the global sulfur cycle. in order to better understand the ecology and roles of sulfur-oxidizing epsilonproteobacteria, in particular those of the widespread genus sulfurimonas, in biogeochemical cycles, the genome of sulfurimonas denitrificans dsm1251 was sequenced. this genom ...	2008	18065616
genome of the epsilonproteobacterial chemolithoautotroph sulfurimonas denitrificans.	sulfur-oxidizing epsilonproteobacteria are common in a variety of sulfidogenic environments. these autotrophic and mixotrophic sulfur-oxidizing bacteria are believed to contribute substantially to the oxidative portion of the global sulfur cycle. in order to better understand the ecology and roles of sulfur-oxidizing epsilonproteobacteria, in particular those of the widespread genus sulfurimonas, in biogeochemical cycles, the genome of sulfurimonas denitrificans dsm1251 was sequenced. this genom ...	2008	18065616
glycerate 2-kinase of thermotoga maritima and genomic reconstruction of related metabolic pathways.	members of a novel glycerate-2-kinase (gk-ii) family were tentatively identified in a broad range of species, including eukaryotes and archaea and many bacteria that lack a canonical enzyme of the gark (gk-i) family. the recently reported three-dimensional structure of gk-ii from thermotoga maritima (tm1585; pdb code 2b8n) revealed a new fold distinct from other known kinase families. here, we verified the enzymatic activity of tm1585, assessed its kinetic characteristics, and used directed muta ...	2008	18156253
glycerate 2-kinase of thermotoga maritima and genomic reconstruction of related metabolic pathways.	members of a novel glycerate-2-kinase (gk-ii) family were tentatively identified in a broad range of species, including eukaryotes and archaea and many bacteria that lack a canonical enzyme of the gark (gk-i) family. the recently reported three-dimensional structure of gk-ii from thermotoga maritima (tm1585; pdb code 2b8n) revealed a new fold distinct from other known kinase families. here, we verified the enzymatic activity of tm1585, assessed its kinetic characteristics, and used directed muta ...	2008	18156253
molecular ecology techniques for the study of aerobic methanotrophs.		2007	18165358
molecular ecology techniques for the study of aerobic methanotrophs.		2007	18165358
methane oxidation at 55 degrees c and ph 2 by a thermoacidophilic bacterium belonging to the verrucomicrobia phylum.	methanotrophic bacteria constitute a ubiquitous group of microorganisms playing an important role in the biogeochemical carbon cycle and in control of global warming through natural reduction of methane emission. these bacteria share the unique ability of using methane as a sole carbon and energy source and have been found in a great variety of habitats. phylogenetically, known methanotrophs constitute a rather limited group and have so far only been affiliated with the proteobacteria. here, we ...	2008	18172218
copper methanobactin: a molecule whose time has come.	copper plays a key role in the physiology of methanotrophs. one way that these bacteria meet their high copper requirement is by the biosynthesis and release of high affinity copper binding compounds called methanobactins. recent advances in methanobactin characterization include the first crystal structure, detailed spectroscopic analyses, and studies of metal ion specificity. methanobactin may function in copper uptake, regulation of methane monooxygenase expression, protection against copper ...	2008	18313412
cohesion group approach for evolutionary analysis of tyra, a protein family with wide-ranging substrate specificities.	many enzymes and other proteins are difficult subjects for bioinformatic analysis because they exhibit variant catalytic, structural, regulatory, and fusion mode features within a protein family whose sequences are not highly conserved. however, such features reflect dynamic and interesting scenarios of evolutionary importance. the value of experimental data obtained from individual organisms is instantly magnified to the extent that given features of the experimental organism can be projected u ...	2008	18322033
an oxidized tryptophan facilitates copper binding in methylococcus capsulatus-secreted protein mope.	proteins can coordinate metal ions with endogenous nitrogen and oxygen ligands through backbone amino and carbonyl groups, but the amino acid side chains coordinating metals do not include tryptophan. here we show for the first time the involvement of the tryptophan metabolite kynurenine in a protein metal-binding site. the crystal structure to 1.35 angstroms of mope* from the methane-oxidizing methylococcus capsulatus (bath) provided detailed information about its structure and mononuclear copp ...	2008	18348978
the dawn of synthetic genomics.		2008	18353151
purification of two putative type ii nadh dehydrogenases with different substrate specificities from alkaliphilic bacillus pseudofirmus of4.	a putative type ii nadh dehydrogenase from halobacillus dabanensis was recently reported to have na+/h+ antiport activity (and called nap), raising the possibility of direct coupling of respiration to antiport-dependent ph homeostasis. this study characterized a homologous type ii nadh dehydrogenase of genetically tractable alkaliphilic bacillus pseudofirmus of4, in which evidence supports antiport-based ph homeostasis that is mediated entirely by secondary antiport. two candidate type ii nadh d ...	2008	18359284
impact of transcription units rearrangement on the evolution of the regulatory network of gamma-proteobacteria.	in the past years, several studies begun to unravel the structure, dynamical properties, and evolution of transcriptional regulatory networks. however, even those comparative studies that focus on a group of closely related organisms are limited by the rather scarce knowledge on regulatory interactions outside a few model organisms, such as e. coli among the prokaryotes.	2008	18366643
oxidase, superoxide dismutase, and hydrogen peroxide reductase activities of methanobactin from types i and ii methanotrophs.	methanobactin (mb) is a copper-binding chromopeptide that appears to be involved in oxidation of methane by the membrane-associated or particulate methane monooxygenase (pmmo). to examine this potential physiological role, the redox and catalytic properties of mb from three different methanotrophs were examined in the absence and presence of o(2). metal free mb from the type ii methanotroph methylosinus trichosporium ob3b, but not from the type i methanotrophs methylococcus capsulatus bath or me ...	2008	18372044
hemozoin: oil versus water.	because the quinolines inhibit heme crystallization within the malaria parasite much work has focused on mechanism of formation and inhibition of hemozoin. here we review the recent evidence for heme crystallization within lipids in diverse parasites and the new implications of a lipid site of crystallization for drug targeting. within leukocytes hemozoin can generate toxic radical lipid metabolites, which may alter immune function or reduce deformability of uninfected erythrocytes.	2008	18373972
hemozoin: oil versus water.	because the quinolines inhibit heme crystallization within the malaria parasite much work has focused on mechanism of formation and inhibition of hemozoin. here we review the recent evidence for heme crystallization within lipids in diverse parasites and the new implications of a lipid site of crystallization for drug targeting. within leukocytes hemozoin can generate toxic radical lipid metabolites, which may alter immune function or reduce deformability of uninfected erythrocytes.	2008	18373972
cloning, solubilization, and characterization of squalene synthase from thermosynechococcus elongatus bp-1.	squalene synthase (sqs) is a bifunctional enzyme that catalyzes the condensation of two molecules of farnesyl diphosphate (fpp) to give presqualene diphosphate (pspp) and the subsequent rearrangement of pspp to squalene. these reactions constitute the first pathway-specific steps in hopane biosynthesis in bacteria and sterol biosynthesis in eukarya. the genes encoding sqs were isolated from the hopane-producing bacteria thermosynechococcus elongatus bp-1, bradyrhizobium japonicum, and zymomonas ...	2008	18375558
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
probing the hydrophobic pocket of the active site in the particulate methane monooxygenase (pmmo) from methylococcus capsulatus (bath) by variable stereoselective alkane hydroxylation and olefin epoxidation.	pmmo from m. capsulatus (bath) oxidizes straight-chain c1-c5 alkanes and alkenes to form their corresponding 2-alcohols and epoxides. according to experiments performed with cryptically chiral ethane and d,l-[2-(2)h(1),3-(2)h(1)]butane, the reactions proceed through the concerted o-atom insertion mechanism. however, when propene and but-1-ene are used as epoxidation substrates, the enantiomeric excesses (ees) of the enzymatic products are only 18 and 37 %, respectively. this relatively poor ster ...	2008	18383583
complete genome sequence of nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment.	the complete genome of the ammonia-oxidizing bacterium nitrosospira multiformis (atcc 25196(t)) consists of a circular chromosome and three small plasmids totaling 3,234,309 bp and encoding 2,827 putative proteins. of the 2,827 putative proteins, 2,026 proteins have predicted functions and 801 are without conserved functional domains, yet 747 of these have similarity to other predicted proteins in databases. gene homologs from nitrosomonas europaea and nitrosomonas eutropha were the best match f ...	2008	18390676
isolation, purification and characterization of hemerythrin from methylococcus capsulatus (bath).	earlier work from our laboratory has indicated that a hemerythrin-like protein was over-produced together with the particulate methane monooxygenase (pmmo) when methylococcus capsulatus (bath) was grown under high copper concentrations. a homologue of hemerythrin had not previously been found in any prokaryote. to confirm its identity as a hemerythrin, we have isolated and purified this protein by ion-exchange, gel-filtration and hydrophobic interaction chromatography, and characterized it by ma ...	2008	18397812
genome sequence and rapid evolution of the rice pathogen xanthomonas oryzae pv. oryzae pxo99a.	xanthomonas oryzae pv. oryzae causes bacterial blight of rice (oryza sativa l.), a major disease that constrains production of this staple crop in many parts of the world. we report here on the complete genome sequence of strain pxo99a and its comparison to two previously sequenced strains, kacc10331 and maff311018, which are highly similar to one another.	2008	18452608
prediction of membrane-protein topology from first principles.	the current best membrane-protein topology-prediction methods are typically based on sequence statistics and contain hundreds of parameters that are optimized on known topologies of membrane proteins. however, because the insertion of transmembrane helices into the membrane is the outcome of molecular interactions among protein, lipids and water, it should be possible to predict topology by methods based directly on physical data, as proposed >20 years ago by kyte and doolittle. here, we present ...	2008	18477697
unraveling the evolutionary history of the phosphoryl-transfer chain of the phosphoenolpyruvate:phosphotransferase system through phylogenetic analyses and genome context.	the phosphoenolpyruvate phosphotransferase system (pts) plays a major role in sugar transport and in the regulation of essential physiological processes in many bacteria. the pts couples solute transport to its phosphorylation at the expense of phosphoenolpyruvate (pep) and it consists of general cytoplasmic phosphoryl transfer proteins and specific enzyme ii complexes which catalyze the uptake and phosphorylation of solutes. previous studies have suggested that the evolution of the constituents ...	2008	18485189
planktonic and sediment-associated aerobic methanotrophs in two seep systems along the north american margin.	methane vents are of significant geochemical and ecological importance. notable progress has been made toward understanding anaerobic methane oxidation in marine sediments; however, the diversity and distribution of aerobic methanotrophs in the water column are poorly characterized. both environments play an essential role in regulating methane release from the oceans to the atmosphere. in this study, the diversity of particulate methane monooxygenase (pmoa) and 16s rrna genes from two methane v ...	2008	18487407
[the binuclear iron site of the membrane-bound methane hydroxylase from methylococcus capsulatus (strain m)].	the particulate membrane-bound methane hydroxylase (pmmoh) was isolated from methane-oxidizing cells of methylococcus capsulatus (strain m). at sds page, pmmoh displays three bands: 47 (alpha), 27 (beta), and 25 kda (gamma). the esr spectrum of pmmoh incubated with hydrogen peroxide (final concentration 20 mm) at 4 degrees c exhibited, along with the copper signal of type i with g = 2.05, signals of cytochrome with g = 3.0 and of high-spin ferriheme with g = 6.00. after incubation at -30 degrees ...	2008	18522275
highly plastic genome of microcystis aeruginosa pcc 7806, a ubiquitous toxic freshwater cyanobacterium.	the colonial cyanobacterium microcystis proliferates in a wide range of freshwater ecosystems and is exposed to changing environmental factors during its life cycle. microcystis blooms are often toxic, potentially fatal to animals and humans, and may cause environmental problems. there has been little investigation of the genomics of these cyanobacteria.	2008	18534010
the metal centers of particulate methane monooxygenase from methylosinus trichosporium ob3b.	particulate methane monooxygenase (pmmo) is a membrane-bound metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. the nature of the pmmo active site and the overall metal content are controversial, with spectroscopic and crystallographic data suggesting the presence of a mononuclear copper center, a dinuclear copper center, a trinuclear center, and a diiron center or combinations thereof. most studies have focused on pmmo from methylococcus capsulatus (bath). pmmo from a s ...	2008	18540635
effect of temperature and pressure on growth and methane utilization by several methanotrophic cultures.	several methanotrophic microorganisms, i.e., methylococcus capsulatus (bath), methylomonas albus (bg-8), methylosinus trichosporium ob3b, and methylocystis parvus (obbp), were evaluated for growth and methane utilization. the effect of temperature was examined in the range of 25 to 45 degrees c for growth and methane utilization. the temperature variations (25-35 degrees c) had minimal effect on growth of m. albus and m. parvus. methane consumption varied at different temperatures with a maximum ...	1998	18576037
complete genome sequence of the extremely acidophilic methanotroph isolate v4, methylacidiphilum infernorum, a representative of the bacterial phylum verrucomicrobia.	the phylum verrucomicrobia is a widespread but poorly characterized bacterial clade. although cultivation-independent approaches detect representatives of this phylum in a wide range of environments, including soils, seawater, hot springs and human gastrointestinal tract, only few have been isolated in pure culture. we have recently reported cultivation and initial characterization of an extremely acidophilic methanotrophic member of the verrucomicrobia, strain v4, isolated from the hell's gate ...	2008	18593465
high accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using mycobacterium tuberculosis as an example.	while the genomic annotations of diverse lineages of the mycobacterium tuberculosis complex are available, divergences between gene prediction methods are still a challenge for unbiased protein dataset generation. m. tuberculosis gene annotation is an example, where the most used datasets from two independent institutions (sanger institute and institute of genomic research-tigr) differ up to 12% in the number of annotated open reading frames, and 46% of the genes contained in both annotations ha ...	2008	18597682
salmonella enterica serovar typhimurium nife uptake-type hydrogenases are differentially expressed in vivo.	salmonella enterica serovar typhimurium, a common enteric pathogen, possesses three nife uptake-type hydrogenases. the results from mouse infection studies suggest that the h(2) oxidation capacity provided by these hydrogenases is important for virulence. since the three enzymes are similar in structure and function, it may be expected that they are utilized under different locations and times during an infection. a recombination-based method to examine promoter activity in vivo (rivet) was used ...	2008	18625729
cd and mcd studies of the effects of component b variant binding on the biferrous active site of methane monooxygenase.	the multicomponent soluble form of methane monooxygenase (smmo) catalyzes the oxidation of methane through the activation of o 2 at a nonheme biferrous center in the hydroxylase component, mmoh. reactivity is limited without binding of the smmo effector protein, mmob. past studies show that mutations of specific mmob surface residues cause large changes in the rates of individual steps in the mmoh reaction cycle. to define the structural and mechanistic bases for these observations, cd, mcd, and ...	2008	18627173
the fine structure of methylococcus capsulatus.	the fine structure of methylococcus capsulatus is described. particular emphasis is focused on the intracytoplasmic membrane system which is organized as a stacked array of flattened saccules. each saccule is limited by a 75 a unit membrane and lies in close apposition to adjacent saccules. methylococcus capsulatus is an obligate methylotroph whose sole source of carbon and energy is methane (or methanol). in this study methane oxidation is demonstrated for the first time in a cell-free system. ...	1970	18631529
two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in methylocystis sp. strain sc2.	methane-oxidizing bacteria (methanotrophs) attenuate methane emission from major sources, such as wetlands, rice paddies, and landfills, and constitute the only biological sink for atmospheric methane in upland soils. their key enzyme is particulate methane monooxygenase (pmmo), which converts methane to methanol. it has long been believed that methane at the trace atmospheric mixing ratio of 1.75 parts per million by volume (ppmv) is not oxidized by the methanotrophs cultured to date, but rathe ...	2008	18632585
transcription of nitrification genes by the methane-oxidizing bacterium, methylococcus capsulatus strain bath.	methylococcus capsulatus strain bath, a methane-oxidizing bacterium, and ammonia-oxidizing bacteria (aob) carry out the first step of nitrification, the oxidation of ammonia to nitrite, through the intermediate hydroxylamine. aob use hydroxylamine oxidoreductase (hao) to produce nitrite. m. capsulatus bath was thought to oxidize hydroxylamine with cytochrome p460 (cytl), until the recent discovery of an hao gene in its genome. we used quantitative pcr analyses of cdna from m. capsulatus bath inc ...	2008	18650926
the presence of multiple c-type cytochromes at the surface of the methanotrophic bacterium methylococcus capsulatus (bath) is regulated by copper.	identification of surface proteins is essential to understand bacterial communication with its environment. analysis of the surface-associated proteins of methylococcus capsulatus (bath) revealed a highly dynamic structure responding closely to the availability of copper in the medium in the range from approximately 0 to 10 microm. several c-type cytochromes, including three novel multihaem proteins, are present at the cellular surface, a feature that is otherwise a peculiarity of dissimilatory ...	2008	18681943
insight into the coupling mechanism of the vitamin k-dependent carboxylase: mutation of histidine 160 disrupts glutamic acid carbanion formation and efficient coupling of vitamin k epoxidation to glutamic acid carboxylation.	vitamin k-dependent (vkd) proteins become activated by the vkd carboxylase, which converts glu's to carboxylated glu's (gla's) in their gla domains. the carboxylase uses vitamin k epoxidation to drive glu carboxylation, and the two half-reactions are coupled in 1:1 stoichiometry by an unknown mechanism. we now report the first identification of a residue, his160, required for coupling. a h160a mutant showed wild-type levels of epoxidation but substantially less carboxylation. monitoring proton a ...	2008	18717596
a phylogenomic profile of hemerythrins, the nonheme diiron binding respiratory proteins.	hemerythrins, are the non-heme, diiron binding respiratory proteins of brachiopods, priapulids and sipunculans; they are also found in annelids and bacteria, where their functions have not been fully elucidated.	2008	18764950
resilience of the iron environment in heme proteins.	conformational flexibility is essential to the functional behavior of proteins. we use an effective force constant introduced by zaccai, the resilience, to quantify this flexibility. site-selective experimental and computational methods allow us to determine the resilience of heme protein active sites. the vibrational density of states of the heme fe determined using nuclear resonance vibrational spectroscopy provides a direct experimental measure of the resilience of the fe environment, which w ...	2008	18835904
[purification and properties of membrane-bound methane hydroxylase from methylococcus capsulatus (strain m)].	membrane fraction of methylococcus capsulatus (strain m) were treated with [14c]acetylene, an affinity label binding to the active center of membrane-bound methane monooxygenase (mmo). high-purity particulate form of methane hydroxylase (pmh) was obtained by ion exchange and hydrophobic chromatography. according to sds-page data, the enzyme contained three polypeptides with molecular weights of 47 (alpha), 27 (beta), and 25 (gamma) kda in the ratio 1:1:1. the radiolabel was contained in the beta ...	2008	18946992
using shotgun sequence data to find active restriction enzyme genes.	whole genome shotgun sequence analysis has become the standard method for beginning to determine a genome sequence. the preparation of the shotgun sequence clones is, in fact, a biological experiment. it determines which segments of the genome can be cloned into escherichia coli and which cannot. by analyzing the complete set of sequences from such an experiment, it is possible to identify genes lethal to e. coli. among this set are genes encoding restriction enzymes which, when active in e. col ...	2009	18988632
pdbsum new things.	pdbsum (http://www.ebi.ac.uk/pdbsum) provides summary information about each experimentally determined structural model in the protein data bank (pdb). here we describe some of its most recent features, including figures from the structure's key reference, citation data, pfam domain diagrams, topology diagrams and protein-protein interactions. furthermore, it now accepts users' own pdb format files and generates a private set of analyses for each uploaded structure.	2008	18996896
pdbsum new things.	pdbsum (http://www.ebi.ac.uk/pdbsum) provides summary information about each experimentally determined structural model in the protein data bank (pdb). here we describe some of its most recent features, including figures from the structure's key reference, citation data, pfam domain diagrams, topology diagrams and protein-protein interactions. furthermore, it now accepts users' own pdb format files and generates a private set of analyses for each uploaded structure.	2008	18996896
the metal centres of particulate methane mono-oxygenase.	pmmo (particulate methane mono-oxygenase) is an integral membrane metalloenzyme that catalyses the oxidation of methane to methanol. the pmmo metal active site has not been identified, precluding detailed investigation of the reaction mechanism. models for the metal centres proposed by various research groups have evolved as crystallographic and spectroscopic data have become available. the present review traces the evolution of these active-site models before and after the 2005 methylococcus ca ...	2008	19021511
the methane monooxygenase intrinsic activity of kinds of methanotrophs.	methanotrophs have promising applications in the epoxidation of some alkenes and some chlorinated hydrocarbons and in the production of a biopolymer, poly-beta-hydroxybutyrate (poly-3-hydroxybutyrate; phb). in contrast with methane monooxygenase (mmo) activity and ability of phb synthesis of four kinds of methanotrophic bacteria methylosinus trichosporium ob3b, m. trichosporium imv3011, methylococcus capsulatus hd6t, methylomonas sp. gyj3, and the mixture of the four kinds of strains, m. trichos ...	2009	19052919
characterization of the pyrophosphate-dependent 6-phosphofructokinase from methylococcus capsulatus bath.	an active pyrophosphate-dependent 6-phosphofructokinase (ppi-pfk) from the thermotolerant methanotroph methylococcus capsulatus bath, containing a six-residue polyhistidine tag, was characterized. the enzyme was homodimeric (2 x 45 kda), nonallosteric and most active at ph 7.0. ppi-pfk catalyzed reactions of ppi-dependent phosphorylation of fructose-6-phosphate (f-6-p) (k(m) 2.27 mm and v(max) 7.6 u mg(-1) of protein), sedoheptulose-7-phosphate (k(m) 0.027 mm and v(max) 31 u mg(-1)) and ribulose ...	2008	19054082
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
formation and function of the manganese(iv)/iron(iii) cofactor in chlamydia trachomatis ribonucleotide reductase.	the beta(2) subunit of a class ia or ib ribonucleotide reductase (rnr) is activated when its carboxylate-bridged fe(2)(ii/ii) cluster reacts with o(2) to oxidize a nearby tyrosine (y) residue to a stable radical (y()). during turnover, the y() in beta(2) is thought to reversibly oxidize a cysteine (c) in the alpha(2) subunit to a thiyl radical (c()) by a long-distance ( approximately 35 a) proton-coupled electron-transfer (pcet) step. the c() in alpha(2) then initiates reduction of the 2' po ...	2008	19061340
electrochemical evidence for multiple peroxidatic heme states of the diheme cytochrome c peroxidase of pseudomonas aeruginosa.	the enzyme cytochrome c peroxidase from pseudomonas aeruginosa and its catalytic mechanism were investigated using protein film voltammetry. monolayers of the diheme bacterial enzyme were immobilized on both pyrolytic graphite edge and alkanethiol-modified au electrodes. the redox couple associated with the low potential heme could be detected on both electrode surfaces at a reduction potential of -234 mv vs she. the midpoint potential displays a distinct ph dependence at acidic ph values, indic ...	2009	19072039
acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications.	acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). it is a chemolithoautrophic, gamma-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. it thrives at extremely low ph (ph 1-2) and fixes both carbon and nitrogen from the atmosphere. it solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemica ...	2008	19077236
spectroscopic definition of the biferrous and biferric sites in de novo designed four-helix bundle dfsc peptides: implications for o2 reactivity of binuclear non-heme iron enzymes.	dfsc is a single chain de novo designed four-helix bundle peptide that mimics the core protein fold and primary ligand set of various binuclear non-heme iron enzymes. dfsc and the e11d, y51l, and y18f single amino acid variants have been studied using a combination of near-ir circular dichroism (cd), magnetic circular dichroism (mcd), variable temperature variable field mcd (vtvh mcd), and x-ray absorption (xas) spectroscopies. the biferrous sites are all weakly antiferromagnetically coupled wit ...	2009	19090676
trypanosoma cruzi cyp51 inhibitor derived from a mycobacterium tuberculosis screen hit.	the two front-line drugs for chronic trypanosoma cruzi infections are limited by adverse side-effects and declining efficacy. one potential new target for chagas' disease chemotherapy is sterol 14alpha-demethylase (cyp51), a cytochrome p450 enzyme involved in biosynthesis of membrane sterols.	2009	19190730
structure and dynamics of metalloproteins in live cells.	x-ray absorption spectroscopy (xas) has emerged as one of the premier tools for investigating the structure and dynamic properties of metals in cells and in metal containing biomolecules. utilizing the high flux and broad energy range of x-rays supplied by synchrotron light sources, one can selectively excite core electronic transitions in each metal. spectroscopic signals from these electronic transitions can be used to dissect the chemical architecture of metals in cells, in cellular component ...	2008	19195552
adaptations to submarine hydrothermal environments exemplified by the genome of nautilia profundicola.	submarine hydrothermal vents are model systems for the archaean earth environment, and some sites maintain conditions that may have favored the formation and evolution of cellular life. vents are typified by rapid fluctuations in temperature and redox potential that impose a strong selective pressure on resident microbial communities. nautilia profundicola strain am-h is a moderately thermophilic, deeply-branching epsilonproteobacterium found free-living at hydrothermal vents and is a member of ...	2009	19197347
development and validation of promoter-probe vectors for the study of methane monooxygenase gene expression in methylococcus capsulatus bath.	a series of integrative and versatile broad-host-range promoter-probe vectors carrying reporter genes encoding green fluorescent protein (gfp), catechol 2,3-dioxygenase (xyle) or beta-galactosidase (lacz) were constructed for use in methanotrophs. these vectors facilitated the measurement of in vivo promoter activity in methanotrophs under defined growth conditions. they were tested by constructing transcriptional fusions between the soluble methane monooxygenase (smmo) sigma(54) promoter or par ...	2009	19246747
new plasmid-mediated quinolone resistance gene, qnrc, found in a clinical isolate of proteus mirabilis.	since the discovery of qnra in 1998, two additional qnr genes, qnrb and qnrs, have been described. these three plasmid-mediated genes contribute to quinolone resistance in gram-negative pathogens worldwide. a clinical strain of proteus mirabilis was isolated from an outpatient with a urinary tract infection and was susceptible to most antimicrobials but resistant to ampicillin, sulfamethoxazole, and trimethoprim. plasmid phs10, harbored by this strain, was transferred to azide-resistant escheric ...	2009	19258263
structural model studies for the high-valent intermediate q of methane monooxygenase from broken-symmetry density functional calculations.	mössbauer isomer shift parameters have been obtained for both density functional theory (dft) opbe and olyp functionals by linear regressions between the measured isomer shifts and calculated electron densities at fe nuclei for a number of fe(2+,2.5+) and fe(2.5+,3+,3.5+,4+) complexes grouped separately. the calculated isomer shifts and quadrupole splittings on the sample fe complexes from opbe and olyp functionals are similar to those of pw91 calculations (j. comput. chem. 27 (2006) 1292), howe ...	2008	19262682
structure of the redox sensor domain of methylococcus capsulatus (bath) mmos.	mmos from methylococcus capsulatus (bath) is the multidomain sensor protein of a two-component signaling system proposed to play a role in the copper-mediated regulation of soluble methane monooxygenase (smmo). mmos binds an fad cofactor within its n-terminal tandem per-arnt-sim (pas) domains, suggesting that it functions as a redox sensor. the crystal structure of the mmos tandem pas domains, designated pas-a and pas-b, has been determined to 2.34 a resolution. both domains adopt the typical pa ...	2009	19271777
diversity and transcription of proteases involved in the maturation of hydrogenases in nostoc punctiforme atcc 29133 and nostoc sp. strain pcc 7120.	the last step in the maturation process of the large subunit of [nife]-hydrogenases is a proteolytic cleavage of the c-terminal by a hydrogenase specific protease. contrary to other accessory proteins these hydrogenase proteases are believed to be specific whereby one type of hydrogenases specific protease only cleaves one type of hydrogenase. in cyanobacteria this is achieved by the gene product of either hupw or hoxw, specific for the uptake or the bidirectional hydrogenase respectively. the f ...	2009	19284580
copper-dioxygen complex mediated c-h bond oxygenation: relevance for particulate methane monooxygenase (pmmo).	particulate methane monooxygenase (pmmo), an integral membrane protein found in methanotrophic bacteria, catalyzes the oxidation of methane to methanol. expression and greater activity of the enzyme in the presence of copper ion suggest that pmmo is a cuprous metalloenzyme. recent advances - especially the first crystal structures of pmmo - have energized the field, but the nature of the active site(s) and the mechanism of methane oxidation remain poorly understood-yet hotly contested. herein th ...	2009	19286415
evidence that the intra-amoebal legionella drancourtii acquired a sterol reductase gene from eukaryotes.	free-living amoebae serve as a natural reservoir for some bacteria that have evolved into "amoeba-resistant" bacteria. among these, some are strictly intra-amoebal, such as candidatus "protochlamydia amoebophila" (candidatus "p. amoebophila"), whose genomic sequence is available. we sequenced the genome of legionella drancourtii (l. drancourtii), another recently described intra-amoebal bacterium. by comparing these two genomes with those of their closely related species, we were able to study t ...	2009	19327142