| purification and characterization of methylmalonyl-coa mutase from a methanol-utilizing bacterium, methylobacterium extorquens nr-1. | high activity (about 50 mu x mg protein(-1)) of methylmalonyl-coa mutase (82-95% apo-enzyme) was constantly found during the cell growth of a methanol-utilizing bacterium, methylobacterium extorquens nr-1. the apo-enzyme was purified to homogeneity and characterized. the purified enzyme was colorless. an apparent mr of m. extorquens nr-1 enzyme was calculated to be 150,000 +/- 5,000 by superdex 200 hr gel filtration. sds-polyacrylamide gel electrophoresis of the purified enzyme gave two protein ... | 2002 | 12350084 |
| 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 |
| 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 |
| l-malyl-coenzyme a lyase/beta-methylmalyl-coenzyme a lyase from chloroflexus aurantiacus, a bifunctional enzyme involved in autotrophic co(2) fixation. | the 3-hydroxypropionate cycle is a bicyclic autotrophic co(2) fixation pathway in the phototrophic chloroflexus aurantiacus (bacteria), and a similar pathway is operating in autotrophic members of the sulfolobaceae (archaea). the proposed pathway involves in a first cycle the conversion of acetyl-coenzyme a (acetyl-coa) and two bicarbonates to l-malyl-coa via 3-hydroxypropionate and propionyl-coa; l-malyl-coa is cleaved by l-malyl-coa lyase into acetyl-coa and glyoxylate. in a second cycle, glyo ... | 2002 | 12374834 |
| 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 |
| 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 |
| [consumption of oxalic acid by pseudomonas extorquens bassalik in relation to the starting number of cells]. | | 1950 | 14815272 |
| 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 |
| protein sequences and cellular factors required for polar localization of a histidine kinase in caulobacter crescentus. | the caulobacter crescentus sensor kinase divj is required for an early cell division step and localizes at the base of the newly formed stalk during the g1-to-s-phase transition when the protein is synthesized. to identify sequences within divj that are required for polar localization, we examined the ability of mutagenized divj sequences to direct localization of the green fluorescent protein. the effects of overlapping c-terminal deletions of divj established that the n-terminal 326 residues, ... | 2002 | 12374838 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| pqqc/d, which converts a biosynthetic intermediate to pyrroloquinoline quinone. | pqqc/d was purified from escherichia coli transformant. the purified enzyme converted an intermediate that accumulated in a pqqc mutant of methylobacterium extorquens am1 to pqq. the reaction did not show any dependence of nad(p)h that was observed in the crude extract before purification. pqqc/d reacted with the intermediate stoichiometrically, but not catalytically. when partially purified proteins from the crude extract of e. coli were added to the reaction mixture, the rate of pqq production ... | 2002 | 12437981 |
| 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 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 |
| 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 |
| 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 |
| [the effect of gamma-radiation and desiccation on the viability of the soil bacteria isolated from the alienated zone around the chernobyl nuclear power plant]. | methylobacterium extorquens, m. mesophilicum, and bacillus subtilis strains were found to be resistant to gamma-radiation, irrespective of whether they were isolated from the alienated zone around the chernobyl nuclear power plant or outside this zone. the ld90 of methylobacterium and b. subtilis strains with respect to gamma-radiation was 2.0-3.4 and 3.7-4.4 kgy, respectively, whereas their ld99.99 values were 4.5-6.9 and more than 10 kgy, respectively. the high threshold levels of gamma-radiat ... | 2002 | 12449639 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| archaea and their potential role in human disease. | | 2003 | 12540534 |
| 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 |
| 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 |
| identification of genes involved in the glyoxylate regeneration cycle in methylobacterium extorquens am1, including two new genes, meac and mead. | the glyoxylate regeneration cycle (grc) operates in serine cycle methylotrophs to effect the net conversion of acetyl coenzyme a to glyoxylate. mutants have been generated in several genes involved in the grc, and phenotypic analysis has been carried out to clarify their role in this cycle. | 2005 | 15687219 |
| 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 |
| genome-scale reconstruction of the metabolic network in staphylococcus aureus n315: an initial draft to the two-dimensional annotation. | several strains of bacteria have sequenced and annotated genomes, which have been used in conjunction with biochemical and physiological data to reconstruct genome-scale metabolic networks. such reconstruction amounts to a two-dimensional annotation of the genome. these networks have been analyzed with a constraint-based formalism and a variety of biologically meaningful results have emerged. staphylococcus aureus is a pathogenic bacterium that has evolved resistance to many antibiotics, represe ... | 2005 | 15752426 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| [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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| e1 enzyme of the pyruvate dehydrogenase complex in corynebacterium glutamicum: molecular analysis of the gene and phylogenetic aspects. | the e1p enzyme is an essential part of the pyruvate dehydrogenase complex (pdhc) and catalyzes the oxidative decarboxylation of pyruvate with concomitant acetylation of the e2p enzyme within the complex. we analyzed the corynebacterium glutamicum acee gene, encoding the e1p enzyme, and constructed and characterized an e1p-deficient mutant. sequence analysis of the c. glutamicum acee gene and adjacent regions revealed that acee is not flanked by genes encoding other enzymes of the pdhc. transcrip ... | 2005 | 16109942 |
| 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 |
| [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 |
| 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 |
| enzymatic synthesis of l-[4-13c]aspartic acid. | an efficient procedure for the production of l-[4-13c]aspartic acid (4-13c-asp) was investigated. in this procedure, phosphoenolpyruvate carboxylase originating from the methanol-assimilating microbe, methylobacterium extorquens jcm 2805, was used for the production of labeled oxaloacetic acid from phosphoenolpyruvate (pep) and nah13co3; the oxaloacetic acid was then converted to 4-13c-asp with glutamic-oxaloacetic transaminase. in this reaction, with starting concentrations of 10 mm pep, 10 mm ... | 2000 | 16232766 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| refined crystal structure of pseudoazurin from methylobacterium extorquens am1 at 1.5 a resolution. | the crystal structure of pseudoazurin from methylobacterium extorquens am1 (pazam1) has been solved by the molecular replacement method using copper-copper distances as translation parameters, which were obtained from difference patterson maps calculated with the synchrotron radiation data containing the multiwavelength anomalous-dispersion effect. the structure refinement was carried out by the use of molecular dynamics optimization and the restrained least-squares method. the final crystallogr ... | 1994 | 15299445 |
| 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 |
| 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 |
| 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 |
| multicopy integration and expression of heterologous genes in methylobacterium extorquens atcc 55366. | high-level expression of chromosomally integrated genes in methylobacterium extorquens atcc 55366 was achieved under the control of the strong m. extorquens am1 methanol dehydrogenase promoter (pmxaf) using the mini-tn7 transposon system. stable maintenance and expression of the integrated genes were obtained in the absence of antibiotic selective pressure. furthermore, using this technology, a multicopy integration protocol for m. extorquens was also developed. chromosomal integration of one to ... | 2006 | 16391115 |
| 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 |
| 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 |
| measurement of respiration rates of methylobacterium extorquens am1 cultures by use of a phosphorescence-based sensor. | respiration rates of bacterial cultures can be a powerful tool in gauging the effects of genetic manipulation and environmental changes affecting overall metabolism. we present an optical method for measuring respiration rates using a robust phosphorescence lifetime-based sensor and off-the-shelf technology. this method was tested with the facultative methylotroph methylobacterium extorquens am1 to demonstrate subtle mutant phenotypes. | 2006 | 16461730 |
| a genomic view of methane oxidation by aerobic bacteria and anaerobic archaea. | recent sequencing of the genome and proteomic analysis of a model aerobic methanotrophic bacterium, methylococcus capsulatus (bath) has revealed a highly versatile metabolic potential. in parallel, environmental genomics has provided glimpses into anaerobic methane oxidation by certain archaea, further supporting the hypothesis of reverse methanogenesis. | 2005 | 15693955 |
| novel dephosphotetrahydromethanopterin biosynthesis genes discovered via mutagenesis in methylobacterium extorquens am1. | methylobacterium extorquens am1 was used to explore the genetics of dephosphotetrahydromethanopterin (dh(4)mpt) biosynthesis. strains with mutations in eight "archaeal-type" genes linked on the chromosome of m. extorquens am1 were analyzed for the ability to synthesize dh(4)mpt, and six were found to be dh(4)mpt negative. putative functions of these genes in dh(4)mpt biosynthesis are discussed. | 2005 | 15774894 |
| methylotrophic autotrophy in beijerinckia mobilis. | representatives of the genus beijerinckia are known as heterotrophic, dinitrogen-fixing bacteria which utilize a wide range of multicarbon compounds. here we show that at least one of the currently known species of this genus, i.e., beijerinckia mobilis, is also capable of methylotrophic metabolism coupled with the ribulose bisphosphate (rubp) pathway of c1 assimilation. a complete suite of dehydrogenases commonly involved in the sequential oxidation of methanol via formaldehyde and formate to c ... | 2005 | 15901717 |
| upregulated transcription of plasmid and chromosomal ribulose monophosphate pathway genes is critical for methanol assimilation rate and methanol tolerance in the methylotrophic bacterium bacillus methanolicus. | the natural plasmid pbm19 carries the key mdh gene needed for the oxidation of methanol into formaldehyde by bacillus methanolicus. five more genes, glpx, fba, tkt, pfk, and rpe, with deduced roles in the cell primary metabolism, are also located on this plasmid. by using real-time pcr, we show that they are transcriptionally upregulated (6- to 40-fold) in cells utilizing methanol; a similar induction was shown for two chromosomal genes, hps and phi. these seven genes are involved in the fructos ... | 2006 | 16585766 |
| 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 |
| fast, easy and efficient: site-specific insertion of transgenes into enterobacterial chromosomes using tn7 without need for selection of the insertion event. | inserting transgenes into bacterial chromosomes is generally quite involved, requiring a selection for cells carrying the insertion, usually for drug-resistance, or multiple cumbersome manipulations, or both. several approaches use phage lambda red recombination, which allows for the possibility of mutagenesis of the transgene during a pcr step. | 2006 | 16646962 |
| 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 |
| identification of oxalotrophic bacteria by neural network analysis of numerical phenetic data. | a new approach with artificial neural network (ann) was applied to numerical taxonomy of bacteria using the oxalate as carbon and energy source. for this aim the characters effective in differentiating separate groups were selected from morphological, physiological and biochemical test results. fourteen aerobic, gram-negative, oxalate-utilizing isolates and four oxalate-utilizing reference strains (ralstonia eutropha dsm 428, methylobacterium extorquens dsm 1337t, ralstonia oxalatica dsm 1105t, ... | 2006 | 16821716 |
| 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 |
| a rapid method for the purification of methanol dehydrogenase from methylobacterium extorquens. | methanol dehydrogenase (mdh) is a water soluble quinoprotein that catalyzes the oxidation of methanol as an important carbon source in methylotrophic bacteria. a rapid method for the purification of mdh from methylobacterium extorquens am1 was developed using a single cation exchange chromatographic step, followed by ultrafiltration for final purification, enzyme concentration, and buffer exchange. mdh was obtained in an excellent overall yield with a final enzyme purity of greater than 97%. sto ... | 2006 | 16139516 |
| 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 |
| a plasmid-borne truncated luxi homolog controls quorum-sensing systems and extracellular carbohydrate production in methylobacterium extorquens am1. | a cryptic plasmid of methylobacterium extorquens am1 was found to encode tsli, a truncated luxi homolog. tsli was shown to be expressed and to control transcription of the acyl-homoserine lactone (hsl) synthase gene msai and thus, indirectly, acyl-hsl production. in addition, tsli was found to positively regulate extracellular polysaccharide production. | 2006 | 17015673 |
| bestowing inducibility on the cloned methanol dehydrogenase promoter (pmxaf) of methylobacterium extorquens by applying regulatory elements of pseudomonas putida f1. | pmxaf is a strong methanol-inducible promoter in methylobacterium extorquens. when this promoter is cloned in expression vectors and used to drive heterologous gene expression, methanol inducibility is either greatly reduced or entirely lost. in order to bestow inducibility upon the cloned pmxaf promoter in expression vectors, we adopted combinational methods (regulatory elements of the pseudomonas putida f1 cym and cmt operons and tn7 transposon system) to control reporter gene expression at th ... | 2006 | 17041156 |
| purification and molecular characterization of a quinoprotein alcohol dehydrogenase from pseudogluconobacter saccharoketogenes ifo 14464. | we have cloned and verified a gene for a novel quinoprotein alcohol dehydrogenase (adh) from pseudogluconobacter saccharoketogenes ifo 14464 that has the ability to oxidize l-sorbose to 2-keto-l-gulonic acid (2-klga). the enzyme was purified from the soluble fraction of the bacterium and was estimated to be a monomeric protein with a molecular weight of 65 kda from the analyses of sds-page and gel-filtration chromatography. an open reading frame of 1824 bp for 608 amino acid residues was estimat ... | 2001 | 16233140 |
| [effect of dna-damaging agents on the aerobic methylobacteria capable and incapable of utilizing dichloromethane]. | methylobacterium dichloromethanicum dm4, a degrader of dichloromethane (dcm), was more tolerant to the effect of h2o2 and uv irradiation than methylobacterium extorquens am1, which does not consume dcm. addition of ch2cl2 to methylobacteria with active serine, ribulose monophosphate, and ribulose bisphosphate pathways of c1 metabolism, grown on methanol, resulted in a 1.1- to 2.5-fold increase in the incorporation of [alpha-32p]datp into dna klenow fragment (exo-). as dcm dehalogenase was not in ... | 2005 | 16240654 |