Publications

cleavage of the iron-methionine bond in c-type cytochromes: crystal structure of oxidized and reduced cytochrome c(2) from rhodopseudomonas palustris and its ammonia complex.	the three-dimensional structures of the native cytochrome c(2) from rhodopseudomonas palustris and of its ammonia complex have been obtained at ph 4.4 and ph 8.5, respectively. the structure of the native form has been refined in the oxidized state at 1.70 a and in the reduced state at 1.95 a resolution. these are the first high-resolution crystal structures in both oxidation states of a cytochrome c(2) with relatively high redox potential (+350 mv). the differences between the two oxidation sta ...	2002	11742117
glyoxylate regeneration pathway in the methylotroph methylobacterium extorquens am1.	most serine cycle methylotrophic bacteria lack isocitrate lyase and convert acetyl coenzyme a (acetyl-coa) to glyoxylate via a novel pathway thought to involve butyryl-coa and propionyl-coa as intermediates. in this study we have used a genome analysis approach followed by mutation to test a number of genes for involvement in this novel pathway. we show that methylmalonyl-coa mutase, an r-specific crotonase, isobutyryl-coa dehydrogenase, and a gtpase are involved in glyoxylate regeneration. we a ...	2002	11872727
ania regulates reserve polymer accumulation and global protein expression in rhizobium etli.	previously, it was reported that the oxidative capacity and ability to grow on carbon sources such as pyruvate and glucose were severely diminished in the rhizobium etli phac::omegasm(r)/sp(r) mutant car1, which is unable to synthesize poly-beta-hydroxybutyric acid (phb) (m. a. cevallos, s. encarnación, a. leija, y. mora, and j. mora, j. bacteriol. 178:1646-1654, 1996). by random tn5 mutagenesis of the phac strain, we isolated the mutants vem57 and vem58, both of which contained single tn5 inser ...	2002	11914361
trna is the source of low-level trans-zeatin production in methylobacterium spp.	pink-pigmented facultatively methylotrophic bacteria (ppfms), classified as methylobacterium spp., are persistent colonizers of plant leaf surfaces. reports of ppfm-plant dialogue led us to examine cytokinin production by ppfms. using immunoaffinity and high-performance liquid chromatography (hplc) purification, we obtained 22 to 111 ng of trans-zeatin per liter from culture filtrates of four ppfm leaf isolates (from arabidopsis, barley, maize, and soybean) and of a methylobacterium extorquens t ...	2002	11889088
stoichiometric model for evaluating the metabolic capabilities of the facultative methylotroph methylobacterium extorquens am1, with application to reconstruction of c(3) and c(4) metabolism.	a stoichiometric model of central metabolism was developed based on new information regarding metabolism in this bacterium to evaluate the steady-state growth capabilities of the serine cycle facultative methylotroph methylobacterium extorquens am1 during growth on methanol, succinate, and pyruvate. the model incorporates 20 reversible and 47 irreversible reactions, 65 intracellular metabolites, and experimentally-determined biomass composition. the flux space for this underdetermined system of ...	2002	11920446
a review of bacterial methyl halide degradation: biochemistry, genetics and molecular ecology.	methyl halide-degrading bacteria are a diverse group of organisms that are found in both terrestrial and marine environments. they potentially play an important role in mitigating ozone depletion resulting from methyl chloride and methyl bromide emissions. the first step in the pathway(s) of methyl halide degradation involves a methyltransferase and, recently, the presence of this pathway has been studied in a number of bacteria. this paper reviews the biochemistry and genetics of methyl halide ...	2002	12010126
generation of formate by the formyltransferase/hydrolase complex (fhc) from methylobacterium extorquens am1.	methylobacterium extorquens am1 possesses a formyltransferase (ftr) complex that is essential for growth in the presence of methanol and involved in formaldehyde oxidation to co(2). one of the subunits of the complex carries the catalytic site for transfer of the formyl group from tetrahydromethanopterin to methanofuran (mfr). we now found via nuclear magnetic resonance-based studies that the ftr complex also catalyzes the hydrolysis of formyl-mfr and generates formate. the enzyme was therefore ...	2002	12123819
structure of methylene-tetrahydromethanopterin dehydrogenase from methylobacterium extorquens am1.	nadp-dependent methylene-h(4)mpt dehydrogenase, mtda, from methylobacterium extorquens am1 catalyzes the dehydrogenation of methylene-tetrahydromethanopterin and methylene-tetrahydrofolate with nadp(+) as cosubstrate. the x-ray structure of mtda with and without nadp bound was established at 1.9 a resolution. the enzyme is present as a homotrimer. the alpha,beta fold of the monomer is related to that of methylene-h(4)f dehydrogenases, suggesting a common evolutionary origin. the position of the ...	2002	12176390
lateral gene transfer and parallel evolution in the history of glutathione biosynthesis genes.	glutathione is found primarily in eukaryotes and in gram-negative bacteria. it has been proposed that eukaryotes acquired the genes for glutathione biosynthesis from the alpha-proteobacterial progenitor of mitochondria. to evaluate this, we have used bioinformatics to analyze sequences of the biosynthetic enzymes gamma-glutamylcysteine ligase and glutathione synthetase.	2002	12049666
a new modified ortho cleavage pathway of 3-chlorocatechol degradation by rhodococcus opacus 1cp: genetic and biochemical evidence.	the 4-chloro- and 2,4-dichlorophenol-degrading strain rhodococcus opacus 1cp has previously been shown to acquire, during prolonged adaptation, the ability to mineralize 2-chlorophenol. in addition, homogeneous chlorocatechol 1,2-dioxygenase from 2-chlorophenol-grown biomass has shown relatively high activity towards 3-chlorocatechol. based on sequences of the n terminus and tryptic peptides of this enzyme, degenerate pcr primers were now designed and used for cloning of the respective gene from ...	2002	12218013
diversity of endophytic bacterial populations and their interaction with xylella fastidiosa in citrus plants.	citrus variegated chlorosis (cvc) is caused by xylella fastidiosa, a phytopathogenic bacterium that can infect all citrus sinensis cultivars. the endophytic bacterial communities of healthy, resistant, and cvc-affected citrus plants were studied by using cultivation as well as cultivation-independent techniques. the endophytic communities were assessed in surface-disinfected citrus branches by plating and denaturing gradient gel electrophoresis (dgge). dominant isolates were characterized by fat ...	2002	12324338
the aquatic budding bacterium blastobacter denitrificans is a nitrogen-fixing symbiont of aeschynomene indica.	blastobacter spp. are freshwater bacteria that form rosette structures by cellular attachment to a common base. comparative analyses of ribosomal 16s rrna gene and internally transcribed spacer region sequences indicated that b. denitrificans is a member of the alpha-subdivision of proteobacteria. among the alpha-proteobacteria, b. denitrificans was related to a cluster of genera, including rhodopseudomonas palustris, afipia felis, nitrobacter hamburgensis, and bradyrhizobium spp. although the p ...	2002	11872460
thirteen years of building constraint-based in silico models of escherichia coli.		2003	12700248
novel methylotrophy genes of methylobacterium extorquens am1 identified by using transposon mutagenesis including a putative dihydromethanopterin reductase.	ten novel methylotrophy genes of the facultative methylotroph methylobacterium extorquens am1 were identified from a transposon mutagenesis screen. one of these genes encodes a product having identity with dihydrofolate reductase (dhfr). this mutant has a c(1)-defective and methanol-sensitive phenotype that has previously only been observed for strains defective in tetrahydromethanopterin (h(4)mpt)-dependent formaldehyde oxidation. these results suggest that this gene, dmra, may encode dihydrome ...	2003	12511515
differential growth response of colony-forming alpha- and gamma-proteobacteria in dilution culture and nutrient addition experiments from lake kinneret (israel), the eastern mediterranean sea, and the gulf of eilat.	even though it is widely accepted that bacterioplankton growth in lakes and marine ecosystems is determined by the trophic status of the systems, knowledge of the relationship between nutrient concentrations and growth of particular bacterial species is almost nonexistent. to address this question, we performed a series of culture experiments with water from lake kinneret (israel), the eastern mediterranean sea, and the gulf of eilat (northern red sea). in the initial water samples, the proporti ...	2003	12513996
alanine aminotransferase homologs catalyze the glutamate:glyoxylate aminotransferase reaction in peroxisomes of arabidopsis.	plant peroxisomal glyoxylate aminotransferases play central roles within the photorespiratory pathway. genes encoding glyoxylate aminotransferases have been isolated from several animals and microbes, but only recently have plant homologs been identified. three arabidopsis homologs of alanine (ala):glyoxylate aminotransferase 2 (agt2) contain a putative type 1 peroxisomal targeting signal (pts1), but the metabolic significance of these agt2 homologs is unknown. ggt1 and ggt2 are ala aminotransfe ...	2003	12529529
quantitative detection of methanotrophs in soil by novel pmoa-targeted real-time pcr assays.	methane oxidation in soils is mostly accomplished by methanotrophic bacteria. little is known about the abundance of methanotrophs in soils, since quantification by cultivation and microscopic techniques is cumbersome. comparison of 16s ribosomal dna and pmoa (alpha subunit of the particulate methane monooxygenase) phylogenetic trees showed good correlation and revealed five distinct groups of methanotrophs within the alpha and gamma subclasses of proteobacteria: the methylococcus group, the met ...	2003	12732507
archaea and their potential role in human disease.		2003	12540534
application of a colorimetric assay to identify putative ribofuranosylaminobenzene 5'-phosphate synthase genes expressed with activity in escherichia coli.	tetrahydromethanopterin (h(4)mpt) is a tetrahydrofolate analog originally discovered in methanogenic archaea, but later found in other archaea and bacteria. the extent to which h(4)mpt occurs among living organisms is unknown. the key enzyme which distinguishes the biosynthetic pathways of h(4)mpt and tetrahydrofolate is ribofuranosylaminobenzene 5'-phosphate synthase (rfap synthase). given the importance of rfap synthase in h(4)mpt biosynthesis, the identification of putative rfap synthase gene ...	2003	12734554
the tungsten-containing formate dehydrogenase from methylobacterium extorquens am1: purification and properties.	nad-dependent formate dehydrogenase (fdh1) was isolated from the alpha-proteobacterium methylobacterium extorquens am1 under oxic conditions. the enzyme was found to be a heterodimer of two subunits (alpha1beta1) of 107 and 61 kda, respectively. the purified enzyme contained per mol enzyme approximately 5 mol nonheme iron and acid-labile sulfur, 0.6 mol noncovalently bound fmn, and approximately 1.8 mol tungsten. the genes encoding the two subunits of fdh1 were identified on the m. extorquens am ...	2003	12605683
qscr, a lysr-type transcriptional regulator and cbbr homolog, is involved in regulation of the serine cycle genes in methylobacterium extorquens am1.	a new gene, qscr, encoding a lysr-type transcriptional regulator that is a homolog of cbbr, has been characterized from the facultative methylotroph methylobacterium extorquens am1 and shown to be the major regulator of the serine cycle, the specific c1 assimilation pathway. the qscr mutant was shown to be unable to grow on c1 compounds, and it lacked the activity of serine-glyoxylate aminotransferase, a key enzyme of the serine cycle. activities of other serine cycle enzymes were decreased duri ...	2003	12562792
reconstruction of c(3) and c(4) metabolism in methylobacterium extorquens am1 using transposon mutagenesis.	the growth of methylobacterium extorquens am1 on c(1) compounds has been well-studied, but little is known about how this methylotroph grows on multicarbon compounds. a tn5 transposon mutagenesis procedure was performed to identify genes involved in the growth of m. extorquens am1 on succinate and pyruvate. of the 15000 insertion colonies screened, 71 mutants were found that grew on methanol but either grew slowly or were unable to grow on one or both of the multicarbon substrates. for each of t ...	2003	12634329
the role of the mxad protein in the respiratory chain of methylobacterium extorquens during growth on methanol.	the largest of the gene clusters coding for proteins involved in methanol oxidation is the cluster mxafjgir(s)ackldehb. disruption of most of these genes leads to lack of growth on methanol. the previous results showed that the mutant lacking mxad grows on methanol although at a low rate. this is explained by the low rate of methanol oxidation by whole cells. the specific activity of methanol dehydrogenase (mdh) is higher in the mutant but its electron acceptor (cytochrome c(l)) is unchanged. us ...	2003	12686160
promoters and transcripts for genes involved in methanol oxidation in methylobacterium extorquens am1.	twenty-five genes are involved in methanol oxidation to formaldehyde by the methanol dehydrogenase system in the facultative methylotroph methylobacterium extorquens am1 organized in five gene clusters. rt-pcr was used to assess the transcripts for the main gene clusters that encode methanol dehydrogenase and proteins required for its activity (mxafgjirsackldehb), and the enzymes that are required for the synthesis of the methanol dehydrogenase prosthetic group, pyrroloquinoline quinone (pqqabc/ ...	2003	12686645
methylotrophy in methylobacterium extorquens am1 from a genomic point of view.		2003	12730156
overexpression of a heterologous protein, haloalkane dehalogenase, in a poly-beta-hydroxybutyrate-deficient strain of the facultative methylotroph methylobacterium extorquens am1.	using an expression vector containing p(mxaf'), a strong native promoter, expression of a model heterologous protein, haloalkane dehalogenase, from xanthobacter autotrophicus gj10 was achieved in the methylotrophic bacterium, methylobacterium extorquens am1. although expression using the wild-type strain was <5% of total cell protein, expression at a level of 10% of the total cell protein was achieved in a mutant unable to synthesize poly-beta-hydroxybutyrate granules. two other tested heterolog ...	2003	12474248
growth of mycobacteria on carbon monoxide and methanol.	several mycobacterial strains, such as mycobacterium flavescens, mycobacterium gastri, mycobacterium neoaurum, mycobacterium parafortuitum, mycobacterium peregrinum, mycobacterium phlei, mycobacterium smegmatis, mycobacterium tuberculosis, and mycobacterium vaccae, were found to grow on carbon monoxide (co) as the sole source of carbon and energy. these bacteria, except for m. tuberculosis, also utilized methanol as the sole carbon and energy source. a co dehydrogenase (co-dh) assay, staining by ...	2003	12486050
detection and diversity assessment of xylella fastidiosa in field-collected plant and insect samples by using 16s rrna and gyrb sequences.	the causal agent of diseases in many economically important plants is attributed to the xylem-limited bacterium xylella fastidiosa. the detection of this plant pathogen has been hampered due to its difficult isolation and slow growth on plates. nearly complete nucleotide sequences of the 16s rrna gene and partial sequences of the gyrb gene were determined for 18 strains of x. fastidiosa isolated from different plant hosts. a phylogenetic analysis, based on gyrb, grouped strains in three clusters ...	2003	12839807
[the fractionation of chlorine isotopes by the aerobic methylotrophic bacterium methylobacterium dichloromethanicum grown on dichloromethane].	methylobacterium dichloromethanicum was found to be able to utilize dichloromethane (dcm) as the source of carbon and energy with the production of biomass, co2, and hcl. a comparative analysis of abundances of the major dcm isotopomers 35cl(2)12c1h2, 35cl37cl12c1h2 and 37cl(2)12ch2 made it possible to estimate the fractionation of chlorine isotopes during the bacterial metabolism of dcm. the kinetic chlorine isotope effects for 35cl37cl12c1h2 (m/z 86) and 37cl(2)12c1h2 (m/z 88) relative to 35cl ...	2003	12901015
formaldehyde-detoxifying role of the tetrahydromethanopterin-linked pathway in methylobacterium extorquens am1.	the facultative methylotroph methylobacterium extorquens am1 possesses two pterin-dependent pathways for c(1) transfer between formaldehyde and formate, the tetrahydrofolate (h(4)f)-linked pathway and the tetrahydromethanopterin (h(4)mpt)-linked pathway. both pathways are required for growth on c(1) substrates; however, mutants defective for the h(4)mpt pathway reveal a unique phenotype of being inhibited by methanol during growth on multicarbon compounds such as succinate. it has been previousl ...	2003	14645276
purification of the formate-tetrahydrofolate ligase from methylobacterium extorquens am1 and demonstration of its requirement for methylotrophic growth.	the serine cycle methylotroph methylobacterium extorquens am1 contains two pterin-dependent pathways for c(1) transfers, the tetrahydrofolate (h(4)f) pathway and the tetrahydromethanopterin (h(4)mpt) pathway, and both are required for growth on c(1) compounds. with the exception of formate-tetrahydrofolate ligase (ftfl, alternatively termed formyl-h(4)f synthetase), all of the genes encoding the enzymes comprising these two pathways have been identified, and the corresponding gene products have ...	2003	14645277
genetic characterization of the carotenoid biosynthetic pathway in methylobacterium extorquens am1 and isolation of a colorless mutant.	genomic searches were used to reconstruct the putative carotenoid biosynthesis pathway in the pink-pigmented facultative methylotroph methylobacterium extorquens am1. four genes for putative phytoene desaturases were identified. a colorless mutant was obtained by transposon mutagenesis, and the insertion was shown to be in one of the putative phytoene desaturase genes. mutations in the other three did not affect color. the tetracycline marker was removed from the original transposon mutant, resu ...	2003	14660416
quantification of central metabolic fluxes in the facultative methylotroph methylobacterium extorquens am1 using 13c-label tracing and mass spectrometry.	the metabolic fluxes of central carbon metabolism were measured in chemostat-grown cultures of methylobacterium extorquens am1 with methanol as the sole organic carbon and energy source and growth-limiting substrate. label tracing experiments were carried out using 70% (13)c-methanol in the feed, and the steady-state mass isotopomer distributions of amino acids derived from total cell protein were measured by gas chromatography coupled to mass spectrometry. fluxes were calculated from the isotop ...	2003	12910542
oxidative folding intermediates with nonnative disulfide bridges between adjacent cysteine residues.	the oxidative folding of the amaranthus alpha-amylase inhibitor, a 32-residue cystine-knot protein with three disulfide bridges, was studied in vitro in terms of the disulfide content of the intermediate species. a nonnative vicinal disulfide bridge between cysteine residues 17 and 18 was found in three of five fully oxidized intermediates. one of these, the most abundant folding intermediate (mfi), was further analyzed by (1)h nmr spectroscopy and photochemically induced dynamic nuclear polariz ...	2003	12724517
compound library development guided by protein structure similarity clustering and natural product structure.	to identify biologically relevant and drug-like protein ligands for medicinal chemistry and chemical biology research the grouping of proteins according to evolutionary relationships and conservation of molecular recognition is an established method. we propose to employ structure similarity clustering of the ligand-sensing cores of protein domains (pssc) in conjunction with natural product guided compound library development as a synergistic approach for the identification of biologically preva ...	2004	15548605
expression profiling-based identification of co2-responsive genes regulated by ccm1 controlling a carbon-concentrating mechanism in chlamydomonas reinhardtii.	photosynthetic acclimation to co2-limiting stress is associated with control of genetic and physiological responses through a signal transduction pathway, followed by integrated monitoring of the environmental changes. although several co2-responsive genes have been previously isolated, genome-wide analysis has not been applied to the isolation of co2-responsive genes that may function as part of a carbon-concentrating mechanism (ccm) in photosynthetic eukaryotes. by comparing expression profile ...	2004	15235119
shear rate moderates community diversity in freshwater biofilms.	the development of freshwater multispecies biofilms at solid-liquid interfaces occurs both in quiescent waters and under conditions of high shear rates. however, the influence of hydrodynamic shear rates on bacterial biofilm diversity is poorly understood. we hypothesized that different shear rates would significantly influence biofilm diversity and alter the relative proportions of coaggregating and autoaggregating community isolates. in order to study this hypothesis, freshwater biofilms were ...	2004	15574945
optstrain: a computational framework for redesign of microbial production systems.	this paper introduces the hierarchical computational framework optstrain aimed at guiding pathway modifications, through reaction additions and deletions, of microbial networks for the overproduction of targeted compounds. these compounds may range from electrons or hydrogen in biofuel cell and environmental applications to complex drug precursor molecules. a comprehensive database of biotransformations, referred to as the universal database (with >5700 reactions), is compiled and regularly upda ...	2004	15520298
bacterial communities associated with flowering plants of the ni hyperaccumulator thlaspi goesingense.	thlaspi goesingense is able to hyperaccumulate extremely high concentrations of ni when grown in ultramafic soils. recently it has been shown that rhizosphere bacteria may increase the heavy metal concentrations in hyperaccumulator plants significantly, whereas the role of endophytes has not been investigated yet. in this study the rhizosphere and shoot-associated (endophytic) bacteria colonizing t. goesingense were characterized in detail by using both cultivation and cultivation-independent te ...	2004	15128517
quinone biogenesis: structure and mechanism of pqqc, the final catalyst in the production of pyrroloquinoline quinone.	the biosynthesis of pyrroloquinoline quinone (pqq), a vitamin and redox cofactor of quinoprotein dehydrogenases, is facilitated by an unknown pathway that requires the expression of six genes, pqqa to -f. pqqc, the protein encoded by pqqc, catalyzes the final step in the pathway in a reaction that involves ring cyclization and eight-electron oxidation of 3a-(2-amino-2-carboxyethyl)-4,5-dioxo-4,5,6,7,8,9-hexahydroquinoline-7,9-dicarboxylic-acid to pqq. herein, we describe the crystal structures o ...	2004	15148379
characterization of two methanopterin biosynthesis mutants of methylobacterium extorquens am1 by use of a tetrahydromethanopterin bioassay.	an enzymatic assay was developed to measure tetrahydromethanopterin (h(4)mpt) levels in wild-type and mutant cells of methylobacterium extorquens am1. h(4)mpt was detectable in wild-type cells but not in strains with a mutation of either the orf4 or the dmra gene, suggesting a role for these two genes in h(4)mpt biosynthesis. the protein encoded by orf4 catalyzed the reaction of ribofuranosylaminobenzene 5'-phosphate synthase, the first committed step of h(4)mpt biosynthesis. these results provi ...	2004	14973120
production of heterologous protein by methylobacterium extorquens in high cell density fermentation.	the green fluorescent protein (gfp) was used as a model protein to study the recombinant protein production by the strain methylobacterium extorquens atcc 55366. scale-up from shake flasks to 20 l fed-batch fermentation was achieved using methanol as a sole carbon and energy source and a completely minimal culture medium. two different expression vectors were used to express gfp. clone pcm-gfp containing the vector pcm110 with native promoter of the methanol dehydrogenase pmxaf produced approxim ...	2004	14987765
biochemical characterization of a dihydromethanopterin reductase involved in tetrahydromethanopterin biosynthesis in methylobacterium extorquens am1.	during growth on one-carbon (c1) compounds, the aerobic alpha-proteobacterium methylobacterium extorquens am1 synthesizes the tetrahydromethanopterin (h4mpt) derivative dephospho-h4mpt as a c1 carrier in addition to tetrahydrofolate. the enzymes involved in dephospho-h4mpt biosynthesis have not been identified in bacteria. in archaea, the final step in the proposed pathway of h4mpt biosynthesis is the reduction of dihydromethanopterin (h2mpt) to h4mpt, a reaction analogous to the reaction of the ...	2004	15028691
unraveling the function of the rhodospirillum rubrum activator of polyhydroxybutyrate (phb) degradation: the activator is a phb-granule-bound protein (phasin).	efficient hydrolysis of native poly(3-hydroxybutyrate) (nphb) granules in vitro by soluble phb depolymerase of rhodospirillum rubrum requires pretreatment of nphb with an activator compound present in r. rubrum cells (j. m. merrick and m. doudoroff, j. bacteriol. 88:60-71, 1964). edman sequencing of the purified activator (17.4 kda; matrix-assisted laser desorption ionization-time of flight mass spectrometry) revealed identity to a hypothetical protein deduced from a partially sequenced r. rubru ...	2004	15060050
molecular detection and isolation of facultatively methylotrophic bacteria, including methylobacterium podarium sp. nov., from the human foot microflora.	this is the first study to demonstrate that diverse methylotrophic bacteria occur in the human foot microflora. polymerase chain reaction (pcr) amplification of dna from the soles and toe clefts of feet of five subjects indicated methylobacterium strains to be present in all cases. polymerase chain reaction amplification also showed the gene for the alpha-subunit of methanol dehydrogenase (mxaf) to be present in all samples. two types of mxaf were recovered, one closest to that of methylobacteri ...	2004	15250884
methylobacterium populi sp. nov., a novel aerobic, pink-pigmented, facultatively methylotrophic, methane-utilizing bacterium isolated from poplar trees (populus deltoides x nigra dn34).	a pink-pigmented, aerobic, facultatively methylotrophic bacterium, strain bj001t, was isolated from internal poplar tissues (populus deltoidesxnigra dn34) and identified as a member of the genus methylobacterium. phylogenetic analyses showed that strain bj001t is related to methylobacterium thiocyanatum, methylobacterium extorquens, methylobacterium zatmanii and methylobacterium rhodesianum. however, strain bj001t differed from these species in its carbon-source utilization pattern, particularly ...	2004	15280290
characterization and heterologous gene expression of a novel esterase from lactobacillus casei cl96.	a novel esterase gene (esti) of lactobacillus casei cl96 was localized on a 3.3-kb bamhi dna fragment containing an open reading frame (orf) of 1,800 bp. the orf of esti was isolated by pcr and expressed in escherichia coli, the methylotrophic bacterium methylobacterium extorquens, and the methylotrophic yeast pichia pastoris under the control of t7, methanol dehydrogenase (p(mxaf)), and alcohol oxidase (aox1) promoters, respectively. the amino acid sequence of esti indicated that the esterase i ...	2004	15184114
comparison of the proteome of methylobacterium extorquens am1 grown under methylotrophic and nonmethylotrophic conditions.	methylobacterium extorquens am1 is a facultative methylotrophic bacterium that is capable of growing in the presence of methanol as the sole carbon and energy source, but is also able to grow on a limited number of c(2), c(3), and c(4) compounds, for example succinate. this study provides a proteomic view of the cellular adaptation of m. extorquens am1 to growth on methanol and succinate, respectively. cytosolic proteins were separated by two-dimensional gel electrophoresis employing overlapping ...	2004	15188393
the principle of flux minimization and its application to estimate stationary fluxes in metabolic networks.	cellular functions are ultimately linked to metabolic fluxes brought about by thousands of chemical reactions and transport processes. the synthesis of the underlying enzymes and membrane transporters causes the cell a certain 'effort' of energy and external resources. considering that those cells should have had a selection advantage during natural evolution that enabled them to fulfil vital functions (such as growth, defence against toxic compounds, repair of dna alterations, etc.) with minima ...	2004	15233787
chloromethane-dependent expression of the cmu gene cluster of hyphomicrobium chloromethanicum.	the methylotrophic bacterium hyphomicrobium chloromethanicum cm2 can utilize chloromethane (ch(3)cl) as the sole carbon and energy source. previously genes cmub, cmuc, cmua, and fold were shown to be essential for the growth of methylobacterium chloromethanicum on ch(3)cl. these ch(3)cl-specific genes were subsequently detected in h. chloromethanicum. transposon and marker exchange mutagenesis studies were carried out to identify the genes essential for ch(3)cl metabolism in h. chloromethanicum. ...	2004	15240299
change in bacterial community structure during in situ biostimulation of subsurface sediment cocontaminated with uranium and nitrate.	previous studies have demonstrated that metal-reducing microorganisms can effectively promote the precipitation and removal of uranium from contaminated groundwater. microbial communities were stimulated in the acidic subsurface by ph neutralization and addition of an electron donor to wells. in single-well push-pull tests at a number of treated sites, nitrate, fe(iii), and uranium were extensively reduced and electron donors (glucose, ethanol) were consumed. examination of sediment chemistry in ...	2004	15294831
meab is a component of the methylmalonyl-coa mutase complex required for protection of the enzyme from inactivation.	adenosylcobalamin-dependent methylmalonyl-coa mutase catalyzes the interconversion of methylmalonyl-coa and succinyl-coa. in humans, deficiencies in the mutase lead to methylmalonic aciduria, a rare disease that is fatal in the first year of life. such inherited deficiencies can result from mutations in the mutase structural gene or from mutations that impair the acquisition of cobalamins. recently, a human gene of unknown function, mmaa, has been implicated in methylmalonic aciduria (dobson, c. ...	2004	14734568
biphenyl and benzoate metabolism in a genomic context: outlining genome-wide metabolic networks in burkholderia xenovorans lb400.	we designed and successfully implemented the use of in situ-synthesized 45-mer oligonucleotide dna microarrays (xeochips) for genome-wide expression profiling of burkholderia xenovorans lb400, which is among the best aerobic polychlorinated biphenyl degraders known so far. we conducted differential gene expression profiling during exponential growth on succinate, benzoate, and biphenyl as sole carbon sources and investigated the transcriptome of early-stationary-phase cells grown on biphenyl. ba ...	2004	15294836
multiple formate dehydrogenase enzymes in the facultative methylotroph methylobacterium extorquens am1 are dispensable for growth on methanol.	formate dehydrogenase has traditionally been assumed to play an essential role in energy generation during growth on c(1) compounds. however, this assumption has not yet been experimentally tested in methylotrophic bacteria. in this study, a whole-genome analysis approach was used to identify three different formate dehydrogenase systems in the facultative methylotroph methylobacterium extorquens am1 whose expression is affected by either molybdenum or tungsten. a complete set of single, double, ...	2004	14679220
development of an insertional expression vector system for methylobacterium extorquens am1 and generation of null mutants lacking mtda and/or fch.	over the past few years, the genetic 'toolkit' available for use with methylobacterium extorquens am1 has expanded significantly. here a further advance is presented and demonstrated, an insertional expression system that allows expression of genes from a stable, unmarked chromosomal locus. this system has been used to better understand the role of the tetrahydrofolate (h4f) pathway in methylotrophy. previously, it has not been possible to generate null mutants lacking either mtda (encoding an n ...	2004	14702393
phylogenetic and physiological diversity of microorganisms isolated from a deep greenland glacier ice core.	we studied a sample from the gisp 2 (greenland ice sheet project) ice core to determine the diversity and survival of microorganisms trapped in the ice at least 120,000 years ago. previously, we examined the phylogenetic relationships among 16s ribosomal dna (rdna) sequences in a clone library obtained by pcr amplification from genomic dna extracted from anaerobic enrichments. here we report the isolation of nearly 800 aerobic organisms that were grouped by morphology and amplified rdna restrict ...	2004	14711643
subtilosin production by two bacillus subtilis subspecies and variance of the sbo-alb cluster.	eight different bacillus subtilis strains and bacillus atrophaeus were found to produce the bacteriocin subtilosin a. on the basis of the subtilosin gene (sbo) sequences two distinct classes of b. subtilis strains were distinguished, and they fell into the two b. subtilis subspecies (b. subtilis subsp. subtilis and b. subtilis subsp. spizizenii). the entire sequence of the subtilosin gene cluster of a b. subtilis subsp. spizizenii strain, b. subtilis atcc 6633, was determined. this sequence exhi ...	2004	15066831
[physiological and biochemical analysis of the transformants of aerobic methylobacteria expressing the dcm a gene of dichloromethane dehydrogenase].	the transformants of methylobacterium dichloromethanicum dm4 (dm4-2cr-/pme8220 and dm4-2cr-/pme8221) and of methylobacterium extorquens am1 (am1/pme8220 and am1/pme8221) that express the dcm a gene of dichloromethane dehalogenase undergo lysis when incubated in the presence of dichloromethane and are sensitive to acidic shock. the lysis of the transformants was found to be related neither to the accumulation of cl- ions, ch2o, and hcooh, nor to the impairment of glutathione synthesis or to the m ...	2004	15074037
isolation of microorganisms for biological detoxification of lignocellulosic hydrolysates.	acid pretreatment of lignocellulosic biomass releases furan and phenolic compounds, which are toxic to microorganisms used for subsequent fermentation. in this study, we isolated new microorganisms for depletion of inhibitors in lignocellulosic acid hydrolysates. a sequential enrichment strategy was used to isolate microorganisms from soil. selection was carried out in a defined mineral medium containing a mixture of ferulic acid (5 mm), 5-hydroxymethylfurfural (5-hmf, 15 mm), and furfural (20 m ...	2004	12908085
[effect of uv-radiation and drying on bacterium diversity in soil].	it has been shown that after dna-injuring factors (uv irradiation or drying) action on soil one could observe the decrease of the total quantity of bacteria and the number of species, i.e., the decrease of microbe diversity. at the same time not numerous species were found in soils after their action. thus the drying or uv-irradiation makes it possible to estimate more completely the microbe diversity in soils as well as to find resistant bacteria. it has been established that the strain methylo ...	2004	15104058
molecular analysis of shower curtain biofilm microbes.	households provide environments that encourage the formation of microbial communities, often as biofilms. such biofilms constitute potential reservoirs for pathogens, particularly for immune-compromised individuals. one household environment that potentially accumulates microbial biofilms is that provided by vinyl shower curtains. over time, vinyl shower curtains accumulate films, commonly referred to as "soap scum," which microscopy reveals are constituted of lush microbial biofilms. to determi ...	2004	15240300
geomicrobiology of high-level nuclear waste-contaminated vadose sediments at the hanford site, washington state.	sediments from a high-level nuclear waste plume were collected as part of investigations to evaluate the potential fate and migration of contaminants in the subsurface. the plume originated from a leak that occurred in 1962 from a waste tank consisting of high concentrations of alkali, nitrate, aluminate, cr(vi), (137)cs, and (99)tc. investigations were initiated to determine the distribution of viable microorganisms in the vadose sediment samples, probe the phylogeny of cultivated and uncultiva ...	2004	15240306
anaerobic growth of methanosarcina acetivorans c2a on carbon monoxide: an unusual way of life for a methanogenic archaeon.	all methanogenic archaea examined to date rely on methanogenesis as their sole means of energy conservation. among these are ones that use carbon monoxide as a growth substrate, producing methane via a pathway that involves hydrogen as an intermediate. to further examine the role of hydrogen in this process, we tested the ability of methanosarcina acetivorans c2a, a metabolically versatile methanogen devoid of significant hydrogen metabolism, to use co as a growth substrate. m. acetivorans grew ...	2004	15550538
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
computational design of reduced metabolic networks.	cellular functions are based on thousands of chemical reactions and transport processes, most of them being catalysed and regulated by specific proteins. systematic gene knockouts have provided evidence that this complex reaction network possesses considerable redundancy, that is, alternative routes exist along which signals and metabolic fluxes may be directed to accomplish an identical output behaviour. this property is of particular importance in cases where parts of the reaction network are ...	2004	15457535
engineering of chimeric class ii polyhydroxyalkanoate synthases.	pha synthase is a key enzyme involved in the biosynthesis of polyhydroxyalkanoates (phas). using a combinatorial genetic strategy to create unique chimeric class ii pha synthases, we have obtained a number of novel chimeras which display improved catalytic properties. to engineer the chimeric pha synthases, we constructed a synthetic phac gene from pseudomonas oleovorans (phac1po) that was devoid of an internal 540-bp fragment. randomly amplified pcr products (created with primers based on conse ...	2004	15528546
the atomic resolution structure of methanol dehydrogenase from methylobacterium extorquens.	the crystal structure of methanol dehydrogenase (mdh) from methylobacterium extorquens has been refined without stereochemical restraints at a resolution of 1.2 a. the high-resolution data have defined the conformation of the tricyclic pyrroloquinoline quinone (pqq) cofactor ring as entirely planar. the detailed definition of the active-site geometry has shown many features that are similar to the quinohaemo-protein alcohol dehydrogenases from comamonas testosteroni and pseudomonas putida, both ...	2004	15608378
automated metabolic reconstruction for methanococcus jannaschii.	we present the computational prediction and synthesis of the metabolic pathways in methanococcus jannaschii from its genomic sequence using the pathologic software. metabolic reconstruction is based on a reference knowledge base of metabolic pathways and is performed with minimal manual intervention. we predict the existence of 609 metabolic reactions that are assembled in 113 metabolic pathways and an additional 17 super-pathways consisting of one or more component pathways. these assignments r ...	2004	15810431
automated metabolic reconstruction for methanococcus jannaschii.	we present the computational prediction and synthesis of the metabolic pathways in methanococcus jannaschii from its genomic sequence using the pathologic software. metabolic reconstruction is based on a reference knowledge base of metabolic pathways and is performed with minimal manual intervention. we predict the existence of 609 metabolic reactions that are assembled in 113 metabolic pathways and an additional 17 super-pathways consisting of one or more component pathways. these assignments r ...	2004	15810431
enhanced sensitivity of dna- and rrna-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients.	stable isotope probing (sip) of nucleic acids allows the detection and identification of active members of natural microbial populations that are involved in the assimilation of an isotopically labelled compound into nucleic acids. sip is based on the separation of isotopically labelled dna or rrna by isopycnic density gradient centrifugation. we have developed a highly sensitive protocol for the detection of 'light' and 'heavy' nucleic acids in fractions of centrifugation gradients. it involves ...	2004	14686943
amoebae-resisting bacteria isolated from human nasal swabs by amoebal coculture.	amoebae feed on bacteria, and few bacteria can resist their microbicidal ability. amoebal coculture could therefore be used to selectively grow these amoebae-resisting bacteria (arb), which may be human pathogens. to isolate new arb, we performed amoebal coculture from 444 nasal samples. we recovered 7 (1.6%) arb from 444 nasal swabs, including 4 new species provisionally named candidatus roseomonas massiliae, c. rhizobium massiliae, c. chryseobacterium massiliae, and c. amoebinatus massiliae. t ...	2004	15109415
multiple formaldehyde oxidation/detoxification pathways in burkholderia fungorum lb400.	burkholderia species are free-living bacteria with a versatile metabolic lifestyle. the genome of b. fungorum lb400 is predicted to encode three different pathways for formaldehyde oxidation: an nad-linked, glutathione (gsh)-independent formaldehyde dehydrogenase; an nad-linked, gsh-dependent formaldehyde oxidation system; and a tetrahydromethanopterin-methanofuran-dependent formaldehyde oxidation system. the other burkholderia species for which genome sequences are available, b. mallei, b. pseu ...	2004	15028703
interaction between endophytic bacteria from citrus plants and the phytopathogenic bacteria xylella fastidiosa, causal agent of citrus-variegated chlorosis.	to isolate endophytic bacteria and xylella fastidiosa and also to evaluate whether the bacterial endophyte community contributes to citrus-variegated chlorosis (cvc) status in sweet orange (citrus sinensis [l.] osbeck cv. pera).	2004	15189288
[the aeration-dependent effect of vitamin b12 on dna biosynthesis in methylobacterium dichloromethanicum].	the effect of vitamin b12 (cobalamin) on dna biosynthesis in methylobacterium dichloromethanicum was studied. when cultivated in media with methanol or dichloromethane, the bacterium produced approximately 10 micrograms corrinoids per g dry biomass, compared to about 7 micrograms/g when cultivated on ethanol or succinate. exogenous adenosylcobalamin (adocbl) stimulated dna biosynthesis in m. dichloromethanicum cells grown under poor aeration, the effect being mediated by adocb1-linked ribonucleo ...	2004	15198026
bud endophytes of scots pine produce adenine derivatives and other compounds that affect morphology and mitigate browning of callus cultures.	endophytes are found in meristematic bud tissues of scots pine (pinus sylvestris l.) especially prior to growth, which would suggest their involvement in growth of the bud. to test this hypothesis, production of phytohormones by two bacterial (methylobacterium extorquens, pseudomonas synxantha) and one fungal endophyte (rhodotorula minuta) was studied by mass spectrometry. the most common gibberellins, auxins, or cytokinins were not detected in the fractions studied. instead, m. extorquens and r ...	2004	15153198
determination of enzyme mechanisms by molecular dynamics: studies on quinoproteins, methanol dehydrogenase, and soluble glucose dehydrogenase.	molecular dynamics (md) simulations have been carried out to study the enzymatic mechanisms of quinoproteins, methanol dehydrogenase (mdh), and soluble glucose dehydrogenase (sgdh). the mechanisms of reduction of the orthoquinone cofactor (pqq) of mdh and sgdh involve concerted base-catalyzed proton abstraction from the hydroxyl moiety of methanol or from the 1-hydroxyl of glucose, and hydride equivalent transfer from the substrate to the quinone carbonyl carbon c5 of pqq. the products of methan ...	2004	15273299
metacyc: a multiorganism database of metabolic pathways and enzymes.	metacyc is a database of metabolic pathways and enzymes located at http://metacyc.org/. its goal is to serve as a metabolic encyclopedia, containing a collection of non-redundant pathways central to small molecule metabolism, which have been reported in the experimental literature. most of the pathways in metacyc occur in microorganisms and plants, although animal pathways are also represented. metacyc contains metabolic pathways, enzymatic reactions, enzymes, chemical compounds, genes and revie ...	2005	16381923
metacyc: a multiorganism database of metabolic pathways and enzymes.	metacyc is a database of metabolic pathways and enzymes located at http://metacyc.org/. its goal is to serve as a metabolic encyclopedia, containing a collection of non-redundant pathways central to small molecule metabolism, which have been reported in the experimental literature. most of the pathways in metacyc occur in microorganisms and plants, although animal pathways are also represented. metacyc contains metabolic pathways, enzymatic reactions, enzymes, chemical compounds, genes and revie ...	2005	16381923
growth substrate- and phase-specific expression of biphenyl, benzoate, and c1 metabolic pathways in burkholderia xenovorans lb400.	recent microarray experiments suggested that burkholderia xenovorans lb400, a potent polychlorinated biphenyl (pcb)-degrading bacterium, utilizes up to three apparently redundant benzoate pathways and a c(1) metabolic pathway during biphenyl and benzoate metabolism. to better characterize the roles of these pathways, we performed quantitative proteome profiling of cells grown on succinate, benzoate, or biphenyl and harvested during either mid-logarithmic growth or the transition between the loga ...	2005	16291673
reclassification of methylobacterium chloromethanicum and methylobacterium dichloromethanicum as later subjective synonyms of methylobacterium extorquens and of methylobacterium lusitanum as a later subjective synonym of methylobacterium rhodesianum.	phylogenetic analysis based on 16s rdna sequences was performed on all type strains of the 14 validly described methylobacterium species to ascertain the genealogic relationships among these species. the results showed that type strains of methylobacterium were divided into two monophyletic groups whose members were distinct species with sequence similarity values greater than 97.0% between any two of the members in the same group. only m. organophilum jcm 2833(t) and atcc 27886(t) were not divi ...	2005	16314683
molecular cloning of the dna gyrase genes from methylovorus sp. strain ss1 and the mechanism of intrinsic quinolone resistance in methylotrophic bacteria.	the genes encoding the dna gyrase a (gyra) and b subunits (gyrb) of methylovorus sp. strain ss1 were cloned and sequenced. gyra and gyrb coded for proteins of 846 and 799 amino acids with calculated molecular weights of 94,328 and 88,714, respectively, and complemented escherichia coli gyra and gyrb temperature sensitive (ts) mutants. to analyze the role of type ii topoisomerases in the intrinsic quinolone resistance of methylotrophic bacteria, the sequences of the quinolone resistance-determini ...	2005	16404155
community structure and diversity of biofilms from a beer bottling plant as revealed using 16s rrna gene clone libraries.	the microbial composition of biofilms from a beer bottling plant was analyzed by a cultivation independent analysis of the 16s rrna genes. clone libraries were differentiated by amplified 16s rrna gene restriction analysis and representative clones from each group were sequenced. the diversity of the clone libraries was comparable with the diversity found for environmental samples. no evidences for the presence of strictly anaerobic taxa or important beer spoilers were found, indicating that bio ...	2005	16204578
description of toluene inhibition of methyl bromide biodegradation in seawater and isolation of a marine toluene oxidizer that degrades methyl bromide.	methyl bromide (ch3br) and methyl chloride (ch3cl) are important precursors for destruction of stratospheric ozone, and oceanic uptake is an important component of the biogeochemical cycle of these methyl halides. in an effort to identify and characterize the organisms mediating halocarbon biodegradation, we surveyed the effect of potential cometabolic substrates on ch3br biodegradation using a 13ch3br incubation technique. toluene (160 to 200 nm) clearly inhibited ch3br and ch3cl degradation in ...	2005	16000753
loss of the mtr operon in methanosarcina blocks growth on methanol, but not methanogenesis, and reveals an unknown methanogenic pathway.	in the methanogenic archaeon methanosarcina barkeri fusaro, the n5-methyl-tetrahydrosarcinapterin (ch3-h4spt):coenzyme m (com) methyltransferase, encoded by the mtr operon, catalyzes the energy-conserving (sodium-pumping) methyl transfer from ch3-h4spt to com during growth on h2/co2 or acetate. however, in the disproportionation of c-1 compounds, such as methanol, to methane and carbon dioxide, it catalyzes the reverse, endergonic transfer from methyl-com to h4spt, which is driven by sodium upta ...	2005	16024727
characterization of the gallate dioxygenase gene: three distinct ring cleavage dioxygenases are involved in syringate degradation by sphingomonas paucimobilis syk-6.	sphingomonas paucimobilis syk-6 converts vanillate and syringate to protocatechuate (pca) and 3-o-methylgallate (3mga) in reactions with the tetrahydrofolate-dependent o-demethylases ligm and desa, respectively. pca is further degraded via the pca 4,5-cleavage pathway, whereas 3mga is metabolized via three distinct pathways in which pca 4,5-dioxygenase (ligab), 3mga 3,4-dioxygenase (desz), and 3mga o-demethylase (ligm) are involved. in the 3mga o-demethylation pathway, ligm converts 3mga to gall ...	2005	16030198
adaptation and acclimatization to formaldehyde in methylotrophs capable of high-concentration formaldehyde detoxification.	formaldehyde is a highly toxic chemical common in industrial effluents, and it is also an intermediate in bacterial metabolism of one-carbon growth substrates, although its role as a bacterial growth substrate per se has not been extensively reported. this study investigated two highly formaldehyde-resistant formaldehyde utilizers, strains bip and ros1; the former strain has been used for industrial remediation of formaldehyde-containing effluents. the two strains were shown by means of 16s rrna ...	2005	16079340
mtdc, a novel class of methylene tetrahydromethanopterin dehydrogenases.	novel methylene tetrahydromethanopterin (h4mpt) dehydrogenase enzymes, named mtdc, were purified after expressing in escherichia coli genes from, respectively, gemmata sp. strain wa1-1 and environmental dna originating from unidentified microbial species. the mtdc enzymes were shown to possess high affinities for methylene-h4mpt and nadp but low affinities for methylene tetrahydrofolate or nad. the substrate range and the kinetic properties revealed by mtdc enzymes distinguish them from the prev ...	2005	16109948
evidence for the presence of a cmua methyltransferase pathway in novel marine methyl halide-oxidizing bacteria.	marine bacteria that oxidized methyl bromide and methyl chloride were enriched and isolated from seawater samples. six methyl halide-oxidizing enrichments were established from which 13 isolates that grew on methyl bromide and methyl chloride as sole sources of carbon and energy were isolated and maintained. all isolates belonged to three different clades in the roseobacter group of the alpha subdivision of the proteobacteria and were distinct from leisingera methylohalidivorans, the only other ...	2005	15892703
kinetic isotope effects and ligand binding in pqq-dependent methanol dehydrogenase.	the reaction of pqq (2,7,9-tricarboxypyrroloquinoline quinone)-dependent mdh (methanol dehydrogenase) from methylophilus methylotrophus has been studied under steady-state conditions in the presence of an alternative activator [gee (glycine ethyl ester)] and compared with similar reactions performed with ammonium (used more generally as an activator in steady-state analysis of mdh). studies of initial velocity with methanol (protiated methanol, c1h3o1h) and [2h]methanol (deuteriated methanol, c2 ...	2005	15617516
how an enzyme binds the c1 carrier tetrahydromethanopterin. structure of the tetrahydromethanopterin-dependent formaldehyde-activating enzyme (fae) from methylobacterium extorquens am1.	tetrahydromethanopterin (h4 mpt) is a tetrahydrofolate analogue involved as a c1 carrier in the metabolism of various groups of microorganisms. how h4mpt is bound to the respective c1 unit converting enzymes remained elusive. we describe here the structure of the homopentameric formaldehyde-activating enzyme (fae) from methylobacterium extorquens am1 established at 2.0 angstrom without and at 1.9 angstrom with methylene-h4mpt bound. methylene-h4mpt is bound in an "s"-shaped conformation into the ...	2005	15632161
methylobacterium hispanicum sp. nov. and methylobacterium aquaticum sp. nov., isolated from drinking water.	members of the genus methylobacterium are ubiquitous in nature and can be isolated from almost any freshwater environment where dissolved oxygen exists. this genus is composed of a variety of pink-pigmented, facultatively methylotrophic (ppfm) bacteria. during a screening programme to monitor the bacterial population present in the drinking water of a municipal water supply in seville (spain) during the year 2003, five strains of ppfm bacteria were isolated and characterized. analysis of their c ...	2005	15653888
flux analysis uncovers key role of functional redundancy in formaldehyde metabolism.	genome-scale analysis of predicted metabolic pathways has revealed the common occurrence of apparent redundancy for specific functional units, or metabolic modules. in many cases, mutation analysis does not resolve function, and instead, direct experimental analysis of metabolic flux under changing conditions is necessary. in order to use genome sequences to build models of cellular function, it is important to define function for such apparently redundant systems. here we describe direct flux m ...	2005	15660163
l-malyl-coenzyme a/beta-methylmalyl-coenzyme a lyase is involved in acetate assimilation of the isocitrate lyase-negative bacterium rhodobacter capsulatus.	cell extracts of rhodobacter capsulatus grown on acetate contained an apparent malate synthase activity but lacked isocitrate lyase activity. therefore, r. capsulatus cannot use the glyoxylate cycle for acetate assimilation, and a different pathway must exist. it is shown that the apparent malate synthase activity is due to the combination of a malyl-coenzyme a (coa) lyase and a malyl-coa-hydrolyzing enzyme. malyl-coa lyase activity was 20-fold up-regulated in acetate-grown cells versus glucose- ...	2005	15687206
a comprehensive update of the sequence and structure classification of kinases.	a comprehensive update of the classification of all available kinases was carried out. this survey presents a complete global picture of this large functional class of proteins and confirms the soundness of our initial kinase classification scheme.	2005	15771780
heterologous extracellular production of enterocin p from enterococcus faecium p13 in the methylotrophic bacterium methylobacterium extorquens.	enterocin p (entp), a strong antilisterial pediocin-like bacteriocin from enterococcus faecium p13, was produced by methylobacterium extorquens. for heterologous expression of entp in the methylotrophic bacterium m. extorquens, a recombinant plasmid was constructed. the gene encoding the entp structural gene (entp) was cloned into the plasmid vector pcm80, under control of the methanol dehydrogenase promoter (p(mxaf)), to generate plasmid ps25. when m. extorquens atcc 55366 was transformed with ...	2005	15950402
methylotrophic metabolism is advantageous for methylobacterium extorquens during colonization of medicago truncatula under competitive conditions.	facultative methylotrophic bacteria of the genus methylobacterium are commonly found in association with plants. inoculation experiments were performed to study the importance of methylotrophic metabolism for colonization of the model legume medicago truncatula. competition experiments with methylobacterium extorquens wild-type strain am1 and methylotrophy mutants revealed that the ability to use methanol as a carbon and energy source provides a selective advantage during colonization of m. trun ...	2005	16269765
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
biosynthesis of ribose-5-phosphate and erythrose-4-phosphate in archaea: a phylogenetic analysis of archaeal genomes.	a phylogenetic analysis of the genes encoding enzymes in the pentose phosphate pathway (ppp), the ribulose monophosphate (rump) pathway, and the chorismate pathway of aromatic amino acid biosynthesis, employing data from 13 complete archaeal genomes, provides a potential explanation for the enigmatic phylogenetic patterns of the ppp genes in archaea. genomic and biochemical evidence suggests that three archaeal species (methanocaldococcus jannaschii, thermoplasma acidophilum and thermoplasma vol ...	2005	15876568
biosynthesis of ribose-5-phosphate and erythrose-4-phosphate in archaea: a phylogenetic analysis of archaeal genomes.	a phylogenetic analysis of the genes encoding enzymes in the pentose phosphate pathway (ppp), the ribulose monophosphate (rump) pathway, and the chorismate pathway of aromatic amino acid biosynthesis, employing data from 13 complete archaeal genomes, provides a potential explanation for the enigmatic phylogenetic patterns of the ppp genes in archaea. genomic and biochemical evidence suggests that three archaeal species (methanocaldococcus jannaschii, thermoplasma acidophilum and thermoplasma vol ...	2005	15876568
qscr-mediated transcriptional activation of serine cycle genes in methylobacterium extorquens am1.	qscr, a lysr-type regulator, is the major regulator of assimilatory c1 metabolism in methylobacterium extorquens am1. it has been shown to interact with the promoters of the two operons that encode the majority of the serine cycle enzymes (sga-hpr-mtda-fch for the qsc1 operon and mtka-mtkb-ppc-mcla for the qsc2 operon), as well as with the promoter of glya and its own promoter. to obtain further insights into the mechanisms of this regulation, we mapped transcriptional start sites for the qsc1 a ...	2005	16237034