| 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 |
| methylobacterium extorquens am1 produces a novel type of acyl-homoserine lactone with a double unsaturated side chain under methylotrophic growth conditions. | acyl-homoserine lactones (acyl-hsls) have emerged as important regulatory molecules for many gram-negative bacteria. we have found that methylobacterium extorquens am1, a member of the pink-pigmented facultative methylotrophs commonly present on plant surfaces, produces several acyl-hsls depending upon the carbon source. a novel hsl was discovered with a double unsaturated carbon chain (n-(tetradecenoyl)) (c14:2) and characterized by ms and proton nmr. this long-chain acyl-hsl is synthesized by ... | 2006 | 16412429 |
| 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 |
| characterization of ni-tolerant methylobacteria associated with the hyperaccumulating plant thlaspi goesingense and description of methylobacterium goesingense sp. nov. | various pink-pigmented facultative methylotrophic (ppfm) bacteria (strains ieii3, ieiv1, iei6, ieii1, ieiii3 ieiii4, ieiii5, irii1, irii2, iriii1, iriv1 and iriv2) were obtained from the rhizosphere and endosphere of hyperaccumulating plant thlaspi goesingense grown in redschlag, austria [r. idris, r. trifonova, m. puschenreiter, w.w. wenzel, a. sessitsch, bacterial communities associated with flowering plants of the ni hyperaccumulator thlaspi goesingense, appl. environ. microbiol. 70 (2004) 26 ... | 2006 | 16488569 |
| direct methanol biocatalytic fuel cell--considerations of restraints on electron transfer. | in this paper structure and operational principles of a novel type direct methanol biocatalytic fuel cell (dmbfc) system is introduced. in addition observed restraints in the energy generation are discussed. the operational principle of the biofuel cell is enzymatic breakdown of methanol by methanol dehydrogenase (mdh) from methylobacterium extorquens at the anode. the terminal electron acceptor at the cathode is potassium permanganate. performance characteristics of the system are the following ... | 2006 | 16554148 |
| substrate binding in quinoprotein ethanol dehydrogenase from pseudomonas aeruginosa studied by electron-nuclear double resonance. | binding of methanol to the quinoprotein ethanol dehydrogenase from pseudomonas aeruginosa has been studied by pulsed electron-nuclear double resonance at 9 ghz. shifts in the hyperfine couplings of the pyrroloquinoline quinone radical provide direct evidence for a change in the environment of the cofactor when substrate is present. by performing experiments with deuteriated methanol, we confirmed that methanol was the cause of the effect. density functional theory calculations show that these sh ... | 2006 | 16567634 |
| phylogenomic analysis of proteins that are distinctive of archaea and its main subgroups and the origin of methanogenesis. | the archaea are highly diverse in terms of their physiology, metabolism and ecology. presently, very few molecular characteristics are known that are uniquely shared by either all archaea or the different main groups within archaea. the evolutionary relationships among different groups within the euryarchaeota branch are also not clearly understood. | 2007 | 17394648 |
| 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 |
| genome of methylobacillus flagellatus, molecular basis for obligate methylotrophy, and polyphyletic origin of methylotrophy. | along with methane, methanol and methylated amines represent important biogenic atmospheric constituents; thus, not only methanotrophs but also nonmethanotrophic methylotrophs play a significant role in global carbon cycling. the complete genome of a model obligate methanol and methylamine utilizer, methylobacillus flagellatus (strain kt) was sequenced. the genome is represented by a single circular chromosome of approximately 3 mbp, potentially encoding a total of 2,766 proteins. based on genom ... | 2007 | 17416667 |
| 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 |
| physiological analysis of methylobacterium extorquens am1 grown in continuous and batch cultures. | chemostat cultures of methylobacterium extorquens am1 grown on methanol or succinate at a range of dilution rates were compared to batch cultures in terms of enzyme levels, poly-beta-hydroxybutyrate content, and intracellular concentrations of adenine and pyridine nucleotides. in both chemostat and batch cultures, enzymes specific to c1 metabolism were up-regulated during growth on methanol and down-regulated during growth on succinate, polyhydroxybutyrate levels were higher on succinate, intrac ... | 2006 | 16821027 |
| identification of bacteria on the surface of clinically infected and non-infected prosthetic hip joints removed during revision arthroplasties by 16s rrna gene sequencing and by microbiological culture. | it has been postulated that bacteria attached to the surface of prosthetic hip joints can cause localised inflammation, resulting in failure of the replacement joint. however, diagnosis of infection is difficult with traditional microbiological culture methods, and evidence exists that highly fastidious or non-cultivable organisms have a role in implant infections. the purpose of this study was to use culture and culture-independent methods to detect the bacteria present on the surface of prosth ... | 2007 | 17501992 |
| disruption of suca, which encodes the e1 subunit of alpha-ketoglutarate dehydrogenase, affects the survival of nitrosomonas europaea in stationary phase. | although nitrosomonas europaea lacks measurable alpha-ketoglutarate dehydrogenase activity, the recent completion of the genome sequence revealed the presence of the genes encoding the enzyme. a knockout mutation was created in the suca gene encoding the e1 subunit. compared to wild-type cells, the mutant strain showed an accelerated loss of ammonia monooxygenase and hydroxylamine oxidoreductase activities upon entering stationary phase. in addition, unlike wild-type cells, the mutant strain sho ... | 2006 | 16352852 |
| the genome sequence of methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and h2 for methane formation and atp synthesis. | methanosphaera stadtmanae has the most restricted energy metabolism of all methanogenic archaea. this human intestinal inhabitant can generate methane only by reduction of methanol with h2 and is dependent on acetate as a carbon source. we report here the genome sequence of m. stadtmanae, which was found to be composed of 1,767,403 bp with an average g+c content of 28% and to harbor only 1,534 protein-encoding sequences (cds). the genome lacks 37 cds present in the genomes of all other methanoge ... | 2006 | 16385054 |
| characterizing nad-dependent alcohol dehydrogenase enzymes of methylobacterium extorquens and strawberry (fragaria x ananassa cv. elsanta). | the methylotroph methylobacterium extorquens (strain with cabi registration number imi 369321), which has been isolated from strawberry (fragaria x ananassa cv. elsanta) callus cultures, was grown on a mixture of methanol (0.25% v/v) and 1,2-propanediol (0.75% v/v). the microbial biotransformation of 1,2-propanediol to 2-hydroxypropanal (lactaldehyde) was studied. the bacterial alcohol dehydrogenase (adh) enzymatic activities were assessed, and the optimum ph for adh activity was found to be ph ... | 2006 | 16390205 |
| isolation of poly-3-hydroxybutyrate metabolism genes from complex microbial communities by phenotypic complementation of bacterial mutants. | the goal of this study was to initiate investigation of the genetics of bacterial poly-3-hydroxybutyrate (phb) metabolism at the community level. we constructed metagenome libraries from activated sludge and soil microbial communities in the broad-host-range incp cosmid prk7813. several unique clones were isolated from these libraries by functional heterologous complementation of a sinorhizobium meliloti bdha mutant, which is unable to grow on the phb cycle intermediate d-3-hydroxybutyrate due t ... | 2006 | 16391068 |
| identifying conditions for inducible protein production in e. coli: combining a fed-batch and multiple induction approach. | in the interest of generating large amounts of recombinant protein, inducible systems have been studied to maximize both the growth of the culture and the production of foreign proteins. even though thermo-inducible systems were developed in the late 1970's, the number of studies that focus on strategies for the implementation at bioreactor scale is limited. in this work, the bacteriophage lambda pl promoter is once again investigated as an inducible element but for the production of green fluor ... | 2006 | 16911799 |
| a proteomic study of methylobacterium extorquens reveals a response regulator essential for epiphytic growth. | aerial plant surfaces are colonized by diverse bacteria such as the ubiquitous methylobacterium spp. the specific physiological traits as well as the underlying regulatory mechanisms for bacterial plant colonization are largely unknown. the purpose of this study was to identify proteins produced specifically in the phyllosphere by comparing the proteome of methylobacterium extorquens colonizing the leaves either with that of bacteria colonizing the roots or with that of bacteria growing on synth ... | 2006 | 16926146 |
| 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 |
| 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 |
| whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium methylibium petroleiphilum pm1. | methylibium petroleiphilum pm1 is a methylotroph distinguished by its ability to completely metabolize the fuel oxygenate methyl tert-butyl ether (mtbe). strain pm1 also degrades aromatic (benzene, toluene, and xylene) and straight-chain (c(5) to c(12)) hydrocarbons present in petroleum products. whole-genome analysis of pm1 revealed an approximately 4-mb circular chromosome and an approximately 600-kb megaplasmid, containing 3,831 and 646 genes, respectively. aromatic hydrocarbon and alkane deg ... | 2007 | 17158667 |
| 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 |
| molecular interaction between methylobacterium extorquens and seedlings: growth promotion, methanol consumption, and localization of the methanol emission site. | four methylobacterium extorquens strains were isolated from strawberry (fragaria x ananassa cv. elsanta) leaves, and one strain, called me4, was tested for its ability to promote the growth of various plant seedlings. seedling weight and shoot length of nicotiana tabacum, lycopersicon esculentum, sinapis alba, and fragaria vesca increased significantly in the presence of the pink-pigmented facultative methylotroph (ppfm), but the germination behaviour of seeds from six other plants was not affec ... | 2006 | 17043084 |
| whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium methylibium petroleiphilum pm1. | methylibium petroleiphilum pm1 is a methylotroph distinguished by its ability to completely metabolize the fuel oxygenate methyl tert-butyl ether (mtbe). strain pm1 also degrades aromatic (benzene, toluene, and xylene) and straight-chain (c(5) to c(12)) hydrocarbons present in petroleum products. whole-genome analysis of pm1 revealed an approximately 4-mb circular chromosome and an approximately 600-kb megaplasmid, containing 3,831 and 646 genes, respectively. aromatic hydrocarbon and alkane deg ... | 2007 | 17158667 |
| isolation of methylophaga spp. from marine dimethylsulfide-degrading enrichment cultures and identification of polypeptides induced during growth on dimethylsulfide. | dimethylsulfide (dms)-degrading enrichment cultures were established from samples of coastal seawater, nonaxenic emiliania huxleyi cultures, and mixed marine methyl halide-degrading enrichment cultures. bacterial populations from a broad phylogenetic range were identified in the mixed dms-degrading enrichment cultures by denaturing gradient gel electrophoresis (dgge). sequences of dominant dgge bands were similar to those of members of the genera methylophaga and alcanivorax. several closely rel ... | 2007 | 17322322 |
| [adaptation of aerobic methylobacteria to dichloromethane degradation]. | a shortening of the lag phase in dichloromethane (dcm) consumption was observed in the methylobacteria methylopila helvetica dm6 and albibacter methylovorans dm10 after prior growth on methanol with the presence of 1.5% naci. neither heat nor acid stress accelerated methylobacterium adaptation to dcm consumption. sodium azide (1 mm) and potassium cyanide (1 mm) inhibited consumption of dcm by these degraders but not by transconjugants methylobacterium extorquens am1, expressing dcm dehalogenase ... | 2007 | 17345859 |
| metabolic modeling of a mutualistic microbial community. | the rate of production of methane in many environments depends upon mutualistic interactions between sulfate-reducing bacteria and methanogens. to enhance our understanding of these relationships, we took advantage of the fully sequenced genomes of desulfovibrio vulgaris and methanococcus maripaludis to produce and analyze the first multispecies stoichiometric metabolic model. model results were compared to data on growth of the co-culture on lactate in the absence of sulfate. the model accurate ... | 2007 | 17353934 |
| an extracytoplasmic function sigma factor acts as a general stress response regulator in sinorhizobium meliloti. | sinorhizobium meliloti genes transcriptionally up-regulated after heat stress, as well as upon entry into stationary phase, were identified by microarray analyses. sixty stress response genes were thus found to be up-regulated under both conditions. one of them, rpoe2 (smc01506), encodes a putative extracytoplasmic function (ecf) sigma factor. we showed that this sigma factor controls its own transcription and is activated by various stress conditions, including heat and salt, as well as entry i ... | 2007 | 17400745 |
| a tale of two oxidation states: bacterial colonization of arsenic-rich environments. | microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. finding a means of preserving natural environments-including ground and surface waters-from arsenic constitutes a major challenge facing modern society. although this metalloid is ubiquitous on earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. in-depth exploration of the genome of the beta ... | 2007 | 17432936 |
| engineering of the methylmalonyl-coa metabolite node of saccharopolyspora erythraea for increased erythromycin production. | engineering of the methylmalonyl-coa (mmcoa) metabolite node of the saccharopolyspora erythraea wild-type strain through duplication of the mmcoa mutase (mcm) operon led to a 50% increase in erythromycin production in a high-performance oil-based fermentation medium. the mcm operon was carried on a 6.8kb dna fragment in a plasmid which was inserted by homologous recombination into the s. erythraea chromosome. the fragment contained one uncharacterized gene, orf1; three mcm related genes, muta, m ... | 2007 | 17482861 |
| composition of metabolic flux distributions by functionally interpretable minimal flux modes (minmodes). | all cellular functions are ultimately linked to the metabolism which constitutes a highly branched network of thousands of enzyme-catalyzed chemical reactions and carrier-mediated transport processes. depending on the prevailing functions (e.g. detoxification of a toxin or accumulation of biomass) the distribution of fluxes in the metabolic network may vary considerably. to better reveal and quantify this flux-function relationship we propose a novel computational approach which identifies disti ... | 2006 | 17503369 |
| cre-lox-based system for multiple gene deletions and selectable-marker removal in lactobacillus plantarum. | the classic strategy to achieve gene deletion variants is based on double-crossover integration of nonreplicating vectors into the genome. in addition, recombination systems such as cre-lox have been used extensively, mainly for eukaryotic organisms. this study presents the construction of a cre-lox-based system for multiple gene deletions in lactobacillus plantarum that could be adapted for use on gram-positive bacteria. first, an effective mutagenesis vector (pnz5319) was constructed that allo ... | 2007 | 17142375 |
| autoregulator protein phar for biosynthesis of polyhydroxybutyrate [p(3hb)] possibly has two separate domains that bind to the target dna and p(3hb): functional mapping of amino acid residues responsible for dna binding. | phar from paracoccus denitrificans functions as a repressor or autoregulator of the expression of genes encoding phasin protein (phap) and phar itself, both of which are components of polyhydroxyalkanoate (pha) granules (a. maehara, s. taguchi, t. nishiyama, t. yamane, and y. doi, j. bacteriol. 184:3992-4002, 2002). phar is a unique regulatory protein in that it also has the ability to bind tightly to an effector molecule, pha polyester. in this study, by using a quartz crystal microbalance, we ... | 2007 | 17122335 |
| biodegradation of methyl tert-butyl ether by cold-adapted mixed and pure bacterial cultures. | an aerobic mixed bacterial culture (cl-emc-1) capable of utilizing methyl tert-butyl ether (mtbe) as the sole source of carbon and energy with a growth temperature range of 3 to 30 degrees c and optimum of 18 to 22 degrees c was enriched from activated sludge. transient accumulation of tert-butanol (tba) occurred during utilization of mtbe at temperatures from 3 degrees c to 14 degrees c, but tba did not accumulate above 18 degrees c. the culture utilized mtbe at a concentration of up to 1.5 g l ... | 2007 | 17146651 |
| autoregulator protein phar for biosynthesis of polyhydroxybutyrate [p(3hb)] possibly has two separate domains that bind to the target dna and p(3hb): functional mapping of amino acid residues responsible for dna binding. | phar from paracoccus denitrificans functions as a repressor or autoregulator of the expression of genes encoding phasin protein (phap) and phar itself, both of which are components of polyhydroxyalkanoate (pha) granules (a. maehara, s. taguchi, t. nishiyama, t. yamane, and y. doi, j. bacteriol. 184:3992-4002, 2002). phar is a unique regulatory protein in that it also has the ability to bind tightly to an effector molecule, pha polyester. in this study, by using a quartz crystal microbalance, we ... | 2007 | 17122335 |
| 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 |
| 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 |
| the 1.6a x-ray structure of the unusual c-type cytochrome, cytochrome cl, from the methylotrophic bacterium methylobacterium extorquens. | the structure of cytochrome cl from methylobacterium extorquens has been determined by x-ray crystallography to a resolution of 1.6 a. this unusually large, acidic cytochrome is the physiological electron acceptor for the quinoprotein methanol dehydrogenase in the periplasm of methylotrophic bacteria. its amino acid sequence is completely different from that of other cytochromes but its x-ray structure reveals a core that is typical of class i cytochromes c, having alpha-helices folded into a co ... | 2006 | 16414073 |
| cre-lox-based system for multiple gene deletions and selectable-marker removal in lactobacillus plantarum. | the classic strategy to achieve gene deletion variants is based on double-crossover integration of nonreplicating vectors into the genome. in addition, recombination systems such as cre-lox have been used extensively, mainly for eukaryotic organisms. this study presents the construction of a cre-lox-based system for multiple gene deletions in lactobacillus plantarum that could be adapted for use on gram-positive bacteria. first, an effective mutagenesis vector (pnz5319) was constructed that allo ... | 2007 | 17142375 |
| functional characterization of the sinorhizobium meliloti acetate metabolism genes acea, smc00767, and glcb. | the genes encoding malate synthase (glcb) and isocitrate lyase (acea) and a 240-bp open reading frame (smc00767) located downstream of acea were isolated and functionally characterized in sinorhizobium meliloti. independent and double interposon mutants of each gene were constructed, and the corresponding phenotypes were analyzed. acea mutants failed to grow on acetate, and mutants deficient in smc00767 were also affected in acetate utilization. in contrast, mutants deficient in glcb grew on ace ... | 2007 | 17526694 |
| including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks. | in recent years, constrained optimization - usually referred to as flux balance analysis (fba) - has become a widely applied method for the computation of stationary fluxes in large-scale metabolic networks. the striking advantage of fba as compared to kinetic modeling is that it basically requires only knowledge of the stoichiometry of the network. on the other hand, results of fba are to a large degree hypothetical because the method relies on plausible but hardly provable optimality principle ... | 2007 | 17543097 |
| synthesis of c5-dicarboxylic acids from c2-units involving crotonyl-coa carboxylase/reductase: the ethylmalonyl-coa pathway. | fifty years ago, kornberg and krebs established the glyoxylate cycle as the pathway for the synthesis of cell constituents from c2-units. however, since then, many bacteria have been described that do not contain isocitrate lyase, the key enzyme of this pathway. here, a pathway termed the ethylmalonyl-coa pathway operating in such organisms is described. isotopically labeled acetate and bicarbonate were transformed to ethylmalonyl-coa by cell extracts of acetate-grown, isocitrate lyase-negative ... | 2007 | 17548827 |
| investigating the metabolic capabilities of mycobacterium tuberculosis h37rv using the in silico strain inj661 and proposing alternative drug targets. | mycobacterium tuberculosis continues to be a major pathogen in the third world, killing almost 2 million people a year by the most recent estimates. even in industrialized countries, the emergence of multi-drug resistant (mdr) strains of tuberculosis hails the need to develop additional medications for treatment. many of the drugs used for treatment of tuberculosis target metabolic enzymes. genome-scale models can be used for analysis, discovery, and as hypothesis generating tools, which will ho ... | 2007 | 17555602 |
| cell-to-cell heterogeneity in growth rate and gene expression in methylobacterium extorquens am1. | cell-to-cell heterogeneity in gene expression and growth parameters was assessed in the facultative methylotroph methylobacterium extorquens am1. a transcriptional fusion between a well-characterized methylotrophy promoter (p(mxaf)) and gfp(uv) (encoding a variant of green fluorescent protein [gfpuv]) was used to assess single-cell gene expression. using a flowthrough culture system and laser scanning microscopy, data on fluorescence and cell size were obtained over time through several growth c ... | 2007 | 17644598 |
| glycerate kinase of the hyperthermophilic archaeon thermoproteus tenax: new insights into the phylogenetic distribution and physiological role of members of the three different glycerate kinase classes. | the presence of the branched entner-doudoroff (ed) pathway in two hyperthermophilic crenarchaea, the anaerobe thermoproteus tenax and the aerobe sulfolobus solfataricus, was suggested. however, so far no enzymatic information of the non-phosphorylative ed branch and especially its key enzyme - glycerate kinase - was available. in the t. tenax genome, a gene homolog with similarity to putative hydroxypyruvate reductase/glycerate dehydrogenase and glycerate kinase was identified. | 2007 | 17764545 |
| knockout and overexpression of pyrroloquinoline quinone biosynthetic genes in gluconobacter oxydans 621h. | in gluconobacter oxydans, pyrroloquinoline quinone (pqq) serves as the cofactor for various membrane-bound dehydrogenases that oxidize sugars and alcohols in the periplasm. proteins for the biosynthesis of pqq are encoded by the pqqabcde gene cluster. our reverse transcription-pcr and promoter analysis data indicated that the pqqa promoter represents the only promoter within the pqqabcde cluster of g. oxydans 621h. pqq overproduction in g. oxydans was achieved by transformation with the plasmid- ... | 2006 | 16936032 |
| influence of the poly-3-hydroxybutyrate (phb) granule-associated proteins (phap1 and phap2) on phb accumulation and symbiotic nitrogen fixation in sinorhizobium meliloti rm1021. | sinorhizobium meliloti cells store excess carbon as intracellular poly-3-hydroxybutyrate (phb) granules that assist survival under fluctuating nutritional conditions. phb granule-associated proteins (phasins) are proposed to regulate phb synthesis and granule formation. although the enzymology and genetics of phb metabolism in s. meliloti have been well characterized, phasins have not yet been described for this organism. comparison of the protein profiles of the wild type and a phb synthesis mu ... | 2007 | 17921298 |
| identification of a fourth formate dehydrogenase in methylobacterium extorquens am1 and confirmation of the essential role of formate oxidation in methylotrophy. | a mutant of methylobacterium extorquens am1 with lesions in genes for three formate dehydrogenase (fdh) enzymes was previously described by us (l. chistoserdova, m. laukel, j.-c. portais, j. a. vorholt, and m. e. lidstrom, j. bacteriol. 186:22-28, 2004). this mutant had lost its ability to grow on formate but still maintained the ability to grow on methanol. in this work, we further investigated the phenotype of this mutant. nuclear magnetic resonance experiments with [13c]formate, as well as 14 ... | 2007 | 17921299 |
| phyr is involved in the general stress response of methylobacterium extorquens am1. | phyr represents a novel alphaproteobacterial family of response regulators having a structure consisting of two domains; a predicted amino-terminal extracytoplasmic function (ecf) sigma factor-like domain and a carboxy-terminal receiver domain. phyr was first described in methylobacterium extorquens am1, in which it has been shown to be essential for plant colonization, probably due to its suggested involvement in the regulation of a number of stress proteins. here we investigated the phyr regul ... | 2008 | 18024517 |
| pyrroloquinoline quinone is a plant growth promotion factor produced by pseudomonas fluorescens b16. | pseudomonas fluorescens b16 is a plant growth-promoting rhizobacterium. to determine the factors involved in plant growth promotion by this organism, we mutagenized wild-type strain b16 using omegakm elements and isolated one mutant, k818, which is defective in plant growth promotion, in a rockwool culture system. a cosmid clone, pok40, which complements the mutant k818, was isolated from a genomic library of the parent strain. tn3-gusa mutagenesis of pok40 revealed that the genes responsible fo ... | 2008 | 18055583 |
| mesaconyl-coenzyme a hydratase, a new enzyme of two central carbon metabolic pathways in bacteria. | the coenzyme a (coa)-activated c5-dicarboxylic acids mesaconyl-coa and beta-methylmalyl-coa play roles in two as yet not completely resolved central carbon metabolic pathways in bacteria. first, these compounds are intermediates in the 3-hydroxypropionate cycle for autotrophic co2 fixation in chloroflexus aurantiacus, a phototrophic green nonsulfur bacterium. second, mesaconyl-coa and beta-methylmalyl-coa are intermediates in the ethylmalonyl-coa pathway for acetate assimilation in various bacte ... | 2008 | 18065535 |
| degradation of glyoxylate and glycolate with atp synthesis by a thermophilic anaerobic bacterium, moorella sp. strain huc22-1. | the thermophilic homoacetogenic bacterium moorella sp. strain huc22-1 ferments glyoxylate to acetate roughly according to the reaction 2 glyoxylate --> acetate + 2 co(2). a batch culture with glyoxylate and yeast extract yielded 11.7 g per mol of cells per substrate, which was much higher than that obtained with h(2) plus co(2). crude extracts of glyoxylate-grown cells catalyzed the adp- and nadp-dependent condensation of glyoxylate and acetyl coenzyme a (acetyl-coa) to pyruvate and co(2) and co ... | 2008 | 18083850 |
| degradation of glyoxylate and glycolate with atp synthesis by a thermophilic anaerobic bacterium, moorella sp. strain huc22-1. | the thermophilic homoacetogenic bacterium moorella sp. strain huc22-1 ferments glyoxylate to acetate roughly according to the reaction 2 glyoxylate --> acetate + 2 co(2). a batch culture with glyoxylate and yeast extract yielded 11.7 g per mol of cells per substrate, which was much higher than that obtained with h(2) plus co(2). crude extracts of glyoxylate-grown cells catalyzed the adp- and nadp-dependent condensation of glyoxylate and acetyl coenzyme a (acetyl-coa) to pyruvate and co(2) and co ... | 2008 | 18083850 |
| implementation of microarrays for methylobacterium extorquens am1. | microarrays are an important tool for understanding global gene expression changes, and the resulting data sets can be used to direct physiologic and metabolic studies. to take advantage of this technology, 60-mer oligonucleotide microarrays were designed for methylobacterium extorquens am1 to study gene expression changes that occur under differing physiological conditions. the carbon utilization pathways for methanol and succinate have been well characterized, and growth with these substrates ... | 2007 | 18092906 |
| glycerate 2-kinase of thermotoga maritima and genomic reconstruction of related metabolic pathways. | members of a novel glycerate-2-kinase (gk-ii) family were tentatively identified in a broad range of species, including eukaryotes and archaea and many bacteria that lack a canonical enzyme of the gark (gk-i) family. the recently reported three-dimensional structure of gk-ii from thermotoga maritima (tm1585; pdb code 2b8n) revealed a new fold distinct from other known kinase families. here, we verified the enzymatic activity of tm1585, assessed its kinetic characteristics, and used directed muta ... | 2008 | 18156253 |
| glycerate 2-kinase of thermotoga maritima and genomic reconstruction of related metabolic pathways. | members of a novel glycerate-2-kinase (gk-ii) family were tentatively identified in a broad range of species, including eukaryotes and archaea and many bacteria that lack a canonical enzyme of the gark (gk-i) family. the recently reported three-dimensional structure of gk-ii from thermotoga maritima (tm1585; pdb code 2b8n) revealed a new fold distinct from other known kinase families. here, we verified the enzymatic activity of tm1585, assessed its kinetic characteristics, and used directed muta ... | 2008 | 18156253 |
| [changes of chlorine isotope composition characterize bacterial dehalogenation of dichloromethane]. | fractionation of dichloromethane (dcm) molecules with different chlorine isotopes by aerobic methylobacteria methylobacterium dichloromethanicum dm4 and albibacter nethylovorans dm10; cell-free extract of strain dm4; and transconjugant methylobacterium evtorquens al1/pme 8220, expressing the dcma gene for dcm dehalogenase but unable to grow on dcm, was studied. kinetic indices of dcm isotopomers for chlorine during bacterial dehalogenation and diffusion were compared. a two-step model is propose ... | 2007 | 18173108 |
| identification of proteins involved in formaldehyde metabolism by rhodobacter sphaeroides. | formaldehyde is an intermediate formed during the metabolism of methanol or other methylated compounds. many gram-negative bacteria generate formaldehyde from methanol via a periplasmic pyrroloquinoline quinone (pqq)-dependent dehydrogenase in which the alpha subunit of an alpha(2)beta(2) tetramer has catalytic activity. the genome of the facultative formaldehyde-oxidizing bacterium rhodobacter sphaeroides encodes xoxf, a homologue of the catalytic subunit of a proposed pqq-containing dehydrogen ... | 2008 | 18174148 |
| mutagenesis of the c1 oxidation pathway in methanosarcina barkeri: new insights into the mtr/mer bypass pathway. | a series of methanosarcina barkeri mutants lacking the genes encoding the enzymes involved in the c1 oxidation/reduction pathway were constructed. mutants lacking the methyl-tetrahydromethanopterin (h4mpt):coenzyme m (com) methyltransferase-encoding operon (delta mtr), the methylene-h4mpt reductase-encoding gene (delta mer), the methylene-h4mpt dehydrogenase-encoding gene (delta mtd), and the formyl-methanofuran:h4mpt formyl-transferase-encoding gene (delta ftr) all failed to grow using either m ... | 2008 | 18178739 |
| improved prediction of malaria degradomes by supervised learning with svm and profile kernel. | the spread of drug resistance through malaria parasite populations calls for the development of new therapeutic strategies. however, the seemingly promising genomics-driven target identification paradigm is hampered by the weak annotation coverage. to identify potentially important yet uncharacterized proteins, we apply support vector machines using profile kernels, a supervised discriminative machine learning technique for remote homology detection, as a complement to the traditional alignment ... | 2009 | 19057851 |
| phylogenomic and functional analysis of pterin-4a-carbinolamine dehydratase family (cog2154) proteins in plants and microorganisms. | pterin-4a-carbinolamine dehydratases (pcds) recycle oxidized pterin cofactors generated by aromatic amino acid hydroxylases (aahs). pcds are known biochemically only from animals and one bacterium, but pcd-like proteins (cog2154 in the clusters of orthologous groups [cogs] database) are encoded by many plant and microbial genomes. because these genomes often encode no aah homologs, the annotation of their cog2154 proteins as pcds is questionable. moreover, some cog2154 proteins lack canonical re ... | 2008 | 18245455 |
| cultivation-independent characterization of methylobacterium populations in the plant phyllosphere by automated ribosomal intergenic spacer analysis. | bacteria of the genus methylobacterium are widespread in the environment, but their ecological role in ecosystems, such as the plant phyllosphere, is not very well understood. to gain better insight into the distribution of different methylobacterium species in diverse ecosystems, a rapid and specific cultivation-independent method for detection of these organisms and analysis of their community structure is needed. therefore, 16s rrna gene-targeted primers specific for this genus were designed ... | 2008 | 18263752 |
| delivery of tailor-made cobalamin to methylmalonyl-coa mutase. | | 2008 | 18277972 |
| influence of the sigmab stress factor and yxab, the gene for a putative exopolysaccharide synthase under sigmab control, on biofilm formation. | bacillus subtilis forms structured communities of biofilms encased in an exopolysaccharide matrix on solid surfaces and at the air-liquid interface. it is postulated that nonoptimal growth conditions induce this multicellular behavior. we showed that under laboratory conditions a strain deleted for sigb was unable to form a floating pellicle on the surface of a liquid medium. however, overexpression of yxab, encoding a putative exopolysaccharide synthase, from a p(spac) promoter in a sigb-delete ... | 2008 | 18326573 |
| the pyrroloquinoline quinone biosynthesis pathway revisited: a structural approach. | the biosynthesis pathway of pyrroloquinoline quinone, a bacterial redox active cofactor for numerous alcohol and aldose dehydrogenases, is largely unknown, but it is proven that at least six genes in klebsiella pneumoniae (pqqa-f) are required, all of which are located in the pqq-operon. | 2008 | 18371220 |
| genome sequence analysis of the emerging human pathogenic acetic acid bacterium granulibacter bethesdensis. | chronic granulomatous disease (cgd) is an inherited immune deficiency characterized by increased susceptibility to infection with staphylococcus, certain gram-negative bacteria, and fungi. granulibacter bethesdensis, a newly described genus and species within the family acetobacteraceae, was recently isolated from four cgd patients residing in geographically distinct locales who presented with fever and lymphadenitis. we sequenced the genome of the reference strain of granulibacter bethesdensis, ... | 2007 | 17827295 |
| metabolite profiling analysis of methylobacterium extorquens am1 by comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry. | methylobacterium extorquens am1 is a facultative methylotroph, which is a potential candidate to be used in commercial processes to convert simple one-carbon compounds to a variety of multicarbon chemicals and products. to better understand c(1) metabolism in m. extorquens am1 at the systems level, metabolite profiling tools were developed and applied in this bacterium. comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (gc x gc-tofms) was used to obta ... | 2008 | 17879968 |
| methylotrophy in freshwater beggiatoa alba strains. | two freshwater strains of the gammaproteobacterium beggiatoa alba, b18ld and oh75-2a, are able to use methanol as a sole carbon and energy source under microoxic conditions. genes encoding a methanol dehydrogenase large-subunit homolog and four enzymes of the tetrahydromethanopterin-dependent c(1) oxidation pathway were identified in b18ld. no evidence of methanotrophy was detected. | 2008 | 18621874 |
| crystal structure of human edc3 and its functional implications. | edc3 is an enhancer of decapping and serves as a scaffold that aggregates mrna ribonucleoproteins together for p-body formation. edc3 forms a network of interactions with the components of the mrna decapping machinery and has a modular domain architecture consisting of an n-terminal lsm domain, a central fdf domain, and a c-terminal yjef-n domain. we have determined the crystal structure of the n-terminally truncated human edc3 at a resolution of 2.2 a. the structure reveals that the yjef-n doma ... | 2008 | 18678652 |
| comprehensive proteomics of methylobacterium extorquens am1 metabolism under single carbon and nonmethylotrophic conditions. | in order to validate a gel free quantitative proteomics assay for the model methylotrophic bacterium methylobacterium extorquens am1, we examined the m. extorquens am1 proteome under single carbon (methanol) and multicarbon (succinate) growth, conditions that have been studied for decades and for which extensive corroborative data have been compiled. in total, 4447 proteins from a database containing 7556 putative orfs from m. extorquens am1 could be identified with two or more peptide sequences ... | 2008 | 18686303 |
| quantitative metabolome analysis using liquid chromatography-high-resolution mass spectrometry. | in this report, we introduce a liquid chromatography single-mass spectrometry method for metabolome quantification, using the ltq orbitrap high-resolution mass spectrometer. analytes were separated with hydrophilic interaction liquid chromatography. at a working resolution of 30,000 (at m/z 400), the limit of detection varied from 50 fmol to 5 pmol for 25 metabolites tested. in terms of metabolite concentration, the linearity was about 2 to 3 orders of magnitude for most compounds (r(2)>0.99). t ... | 2008 | 18694716 |
| development of a broad-host-range sacb-based vector for unmarked allelic exchange. | although genome sequences are available for an ever-increasing number of bacterial species, the availability of facile genetic tools for physiological analysis have generally lagged substantially behind traditional genetic models. | 2008 | 18710539 |
| conservation and variability of west nile virus proteins. | west nile virus (wnv) has emerged globally as an increasingly important pathogen for humans and domestic animals. studies of the evolutionary diversity of the virus over its known history will help to elucidate conserved sites, and characterize their correspondence to other pathogens and their relevance to the immune system. we describe a large-scale analysis of the entire wnv proteome, aimed at identifying and characterizing evolutionarily conserved amino acid sequences. this study, which used ... | 2009 | 19401763 |
| towards kinetic modeling of global metabolic networks: methylobacterium extorquens am1 growth as validation. | here we report a systematic method for constructing a large scale kinetic metabolic model and its initial application to the modeling of central metabolism of methylobacterium extorquens am1, a methylotrophic and environmental important bacterium. its central metabolic network includes formaldehyde metabolism, serine cycle, citric acid cycle, pentose phosphate pathway, gluconeogensis, phb synthesis and acetyl-coa conversion pathway, respiration and energy metabolism. through a systematic and con ... | 2008 | 18807980 |
| frequent homologous recombination events in mycobacterium tuberculosis pe/ppe multigene families: potential role in antigenic variability. | the pe and ppe (pe/ppe) multigene families of mycobacterium tuberculosis are particularly gc-rich and share extensive homologous repetitive sequences. we hypothesized that they may undergo homologous recombination events, a mechanism rarely described in the natural evolution of mycobacteria. to test our hypothesis, we developed a specific oligonucleotide-based microarray targeting nearly all of the pe/ppe genes, aimed at detecting signals for homologous recombination. such a microarray has never ... | 2008 | 18820012 |
| the bet v 1 fold: an ancient, versatile scaffold for binding of large, hydrophobic ligands. | the major birch pollen allergen, bet v 1, is a member of the ubiquitous pr-10 family of plant pathogenesis-related proteins. in recent years, a number of diverse plant proteins with low sequence similarity to bet v 1 was identified. in addition, determination of the bet v 1 structure revealed the existence of a large superfamily of structurally related proteins. in this study, we aimed to identify and classify all bet v 1-related structures from the protein data bank and all bet v 1-related sequ ... | 2008 | 18922149 |
| sleeping beauty mutase (sbm) is expressed and interacts with ygfd in escherichia coli. | in escherichia coli, a four-gene operon, sbm-ygfd-ygfg-ygfh, has been shown to encode a putative cobalamin-dependent pathway with the ability to produce propionate from succinate in vitro [haller t, buckel t, retey j, gerlt ja. discovering new enzymes and metabolic pathways: conversion of succinate to propionate by escherichia coli. biochemistry 2000;39:4622-4629]. however, the operon was thought to be silent in vivo, illustrated by the eponym describing its first gene, "sleeping beauty mutase" ... | 2009 | 18950999 |
| sleeping beauty mutase (sbm) is expressed and interacts with ygfd in escherichia coli. | in escherichia coli, a four-gene operon, sbm-ygfd-ygfg-ygfh, has been shown to encode a putative cobalamin-dependent pathway with the ability to produce propionate from succinate in vitro [haller t, buckel t, retey j, gerlt ja. discovering new enzymes and metabolic pathways: conversion of succinate to propionate by escherichia coli. biochemistry 2000;39:4622-4629]. however, the operon was thought to be silent in vivo, illustrated by the eponym describing its first gene, "sleeping beauty mutase" ... | 2009 | 18950999 |
| a genome survey of moniliophthora perniciosa gives new insights into witches' broom disease of cacao. | the basidiomycete fungus moniliophthora perniciosa is the causal agent of witches' broom disease (wbd) in cacao (theobroma cacao). it is a hemibiotrophic pathogen that colonizes the apoplast of cacao's meristematic tissues as a biotrophic pathogen, switching to a saprotrophic lifestyle during later stages of infection. m. perniciosa, together with the related species m. roreri, are pathogens of aerial parts of the plant, an uncommon characteristic in the order agaricales. a genome survey (1.9x c ... | 2008 | 19019209 |
| improved prediction of malaria degradomes by supervised learning with svm and profile kernel. | the spread of drug resistance through malaria parasite populations calls for the development of new therapeutic strategies. however, the seemingly promising genomics-driven target identification paradigm is hampered by the weak annotation coverage. to identify potentially important yet uncharacterized proteins, we apply support vector machines using profile kernels, a supervised discriminative machine learning technique for remote homology detection, as a complement to the traditional alignment ... | 2009 | 19057851 |
| statistical media optimization for growth and phb production from methanol by a methylotrophic bacterium. | media components were optimized by statistical design for cell growth and phb production of methylobacterium extorquens dsmz 1340. four important components of growth media were optimized by central composite design. the growth increased from an od=1.35 for choi medium as control to an od=2.15 for optimal medium. then media components for phb production were optimized. optimization of five important factors was conducted by response surface method. the optimal composition of phb production mediu ... | 2009 | 19121581 |
| sigma factor mimicry involved in regulation of general stress response. | bacteria have evolved regulatory traits to rapidly adapt to changing conditions. two principal regulatory mechanisms to modulate gene expression consist of regulation via alternative sigma factors and phosphorylation-dependent response regulators. phyr represents a recently discovered protein family combining parts of both systems: a sigma factor-like domain of the extracytoplasmic function (ecf) subfamily linked to a receiver domain of a response regulator. here we investigated the mode of acti ... | 2009 | 19218445 |
| thiopeptide biosynthesis featuring ribosomally synthesized precursor peptides and conserved posttranslational modifications. | thiopeptides, with potent activity against various drug-resistant pathogens, contain a characteristic macrocyclic core consisting of multiple thiazoles, dehydroamino acids, and a 6-membered nitrogen heterocycle. their biosynthetic pathways remain elusive, in spite of great efforts by in vivo feeding experiments. here, cloning, sequencing, and characterization of the thiostrepton and siomycin a gene clusters unveiled a biosynthetic paradigm for the thiopeptide specific core formation, featuring r ... | 2009 | 19246004 |
| demonstration of the ethylmalonyl-coa pathway by using 13c metabolomics. | the assimilation of one-carbon (c1) compounds, such as methanol, by serine cycle methylotrophs requires the continuous regeneration of glyoxylate. instead of the glyoxylate cycle, this process is achieved by a not yet established pathway where coa thioesters are known to play a key role. we applied state-of-the-art metabolomics and (13)c metabolomics strategies to demonstrate how glyoxylate is generated during methylotrophic growth in the isocitrate lyase-negative methylotroph methylobacterium e ... | 2009 | 19261854 |
| characterization of a novel methanol dehydrogenase in representatives of burkholderiales: implications for environmental detection of methylotrophy and evidence for convergent evolution. | some members of burkholderiales are able to grow on methanol but lack the genes (mxafi) responsible for the well-characterized two-subunit pyrroloquinoline quinone-dependent quinoprotein methanol dehydrogenase that is widespread in methylotrophic proteobacteria. here, we characterized novel, mono-subunit enzymes responsible for methanol oxidation in four strains, methyloversatilis universalis fam5, methylibium petroleiphilum pm1, and unclassified burkholderiales strains rz18-153 and fam1. the en ... | 2008 | 18390659 |
| tightly regulated and heritable division control in single bacterial cells. | the robust surface adherence property of the aquatic bacterium caulobacter crescentus permits visualization of single cells in a linear microfluidic culture chamber over an extended number of generations. the division rate of caulobacter in this continuous-flow culture environment is substantially faster than in other culture apparati and is independent of flow velocity. analysis of the growth and division of single isogenic cells reveals that the cell cycle control network of this bacterium gen ... | 2008 | 18469083 |
| pantothenate kinase from the thermoacidophilic archaeon picrophilus torridus. | pantothenate kinase (coaa) catalyzes the first step of the coenzyme a (coa) biosynthetic pathway and controls the intracellular concentrations of coa through feedback inhibition in bacteria. an alternative enzyme found in archaea, pantoate kinase, is missing in the order thermoplasmatales. the pto0232 gene from picrophilus torridus, a thermoacidophilic euryarchaeon, is shown to be a distant homologue of the prokaryotic type i coaa. the cloned gene clearly complements the poor growth of the tempe ... | 2010 | 19854913 |
| formate as the main branch point for methylotrophic metabolism in methylobacterium extorquens am1. | in serine cycle methylotrophs, methylene tetrahydrofolate (h4f) is the entry point of reduced one-carbon compounds into the serine cycle for carbon assimilation during methylotrophic metabolism. in these bacteria, two routes are possible for generating methylene h4f from formaldehyde during methylotrophic growth: one involving the reaction of formaldehyde with h4f to generate methylene h4f and the other involving conversion of formaldehyde to formate via methylene tetrahydromethanopterin-depende ... | 2008 | 18502865 |
| production of an insecticidal crystal protein from bacillus thuringiensis by the methylotroph methylobacterium extorquens. | the cry1aa protein from bacillus thuringiensis is an insecticidal protein that is highly active against several species of lepidoptera. we cloned and expressed the cry1aa gene in a plant-colonizing methylotroph, methylobacterium extorquens, under the control of the strong m. extorquens am1 methanol dehydrogenase promoter, p(mxaf). transmission electron microscopy revealed characteristic bipyramidal intracellular delta-endotoxin crystals similar to the crystalline inclusions formed by b. thuringi ... | 2008 | 18552184 |
| complete genome sequence of the extremely acidophilic methanotroph isolate v4, methylacidiphilum infernorum, a representative of the bacterial phylum verrucomicrobia. | the phylum verrucomicrobia is a widespread but poorly characterized bacterial clade. although cultivation-independent approaches detect representatives of this phylum in a wide range of environments, including soils, seawater, hot springs and human gastrointestinal tract, only few have been isolated in pure culture. we have recently reported cultivation and initial characterization of an extremely acidophilic methanotrophic member of the verrucomicrobia, strain v4, isolated from the hell's gate ... | 2008 | 18593465 |
| enhancing production of l-serine by increasing the glya gene expression in methylobacterium sp. mb200. | microbial fermentation using methylotrophic bacteria is one of the most promising methods for l-serine production. here we describe the metabolic engineering of a methylobacterium strain to increase the production of l-serine. the glya gene, encoding serine hydroxymethyltransferase (shmt), was isolated from the genomic dna of methylobacterium sp. mb200, using a dna fragment encoding methylobacterium extorquens am1 shmt as a probe, and inserted into the vector plafr3. the resulting construct was ... | 2010 | 19266321 |
| liquid chromatography-tandem quadrupole mass spectrometry and comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry measurement of targeted metabolites of methylobacterium extorquens am1 grown on two different carbon sources. | complementary methods using liquid chromatography-tandem quadrupole mass spectrometry (lc-ms/ms) and comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (gcxgc-tof-ms) were developed and applied to determine targeted metabolites involved in central carbon metabolism [including tricarboxylic acid cycle, serine cycle, ethylmalonyl-coenzyme a (ethylmalonyl-coa) pathway and poly-beta-hydroxybutyrate cycle] of the bacterium methylobacterium extorquens am1 grown on two ca ... | 2009 | 19268957 |
| c(1) compounds as auxiliary substrate for engineered pseudomonas putida s12. | the solvent-tolerant bacterium pseudomonas putida s12 was engineered to efficiently utilize the c(1) compounds methanol and formaldehyde as auxiliary substrate. the hps and phi genes of bacillus brevis, encoding two key steps of the ribulose monophosphate (rump) pathway, were introduced to construct a pathway for the metabolism of the toxic methanol oxidation intermediate formaldehyde. this approach resulted in a remarkably increased biomass yield on the primary substrate glucose when cultured i ... | 2009 | 19280184 |
| constraint-based analysis of metabolic capacity of salmonella typhimurium during host-pathogen interaction. | infections with salmonella cause significant morbidity and mortality worldwide. replication of salmonella typhimurium inside its host cell is a model system for studying the pathogenesis of intracellular bacterial infections. genome-scale modeling of bacterial metabolic networks provides a powerful tool to identify and analyze pathways required for successful intracellular replication during host-pathogen interaction. | 2009 | 19356237 |
| proteomic and transcriptomic analyses reveal genes upregulated by cis-dichloroethene in polaromonas sp. strain js666. | polaromonas sp. strain js666 is the only bacterial isolate capable of using cis-dichloroethene (cdce) as a sole carbon and energy source. studies of cdce degradation in this novel organism are of interest because of potential bioremediation and biocatalysis applications. the primary cellular responses of js666 to growth on cdce were explored using proteomics and transcriptomics to identify the genes upregulated by cdce. two-dimensional gel electrophoresis revealed upregulation of genes annotated ... | 2009 | 19363075 |
| role of the extracytoplasmic function sigma factor rpoe4 in oxidative and osmotic stress responses in rhizobium etli. | the aims of this study were to functionally characterize and analyze the transcriptional regulation and transcriptome of the rhizobium etli rpoe4 gene. an r. etli rpoe4 mutant was sensitive to oxidative, saline, and osmotic stresses. using transcriptional fusions, we determined that rpoe4 controls its own transcription and that it is negatively regulated by rsef (regulator of sigma rpoe4; ch03274), which is cotranscribed with rpoe4. rpoe4 expression was induced not only after oxidative, saline, ... | 2009 | 19376852 |
| improving protein extraction and separation methods for investigating the metaproteome of anaerobic benzene communities within sediments. | btex compounds such as benzene are frequent soil and groundwater contaminants that are easily biodegraded under oxic conditions by bacteria. in contrast, benzene is rather recalcitrant under anaerobic conditions. the analysis of anoxic degradation is often hampered by difficult sampling conditions, limited amounts of biomass and interference of matrix compounds with proteomic approaches. in order to improve the procedure for protein extraction we established a scheme consisting of the following ... | 2009 | 19381451 |
| population heterogeneity in methylobacterium extorquens am1. | heterogeneity of cells within exponentially growing populations was addressed in a bacterium, the facultative methylotroph methylobacterium extorquens am1. a transcriptional fusion between a well-characterized methanol-inducible promoter (p(mxaf)) and gfp(uv) was used with flow cytometry to analyse the distribution of gene expression in populations grown on either succinate or methanol, correlated with forward scatter as a measure of cell size. these cell populations were found to consist of thr ... | 2009 | 19383691 |
| a rotary mechanism for coenzyme b(12) synthesis by adenosyltransferase. | adenosyltransferases (atrs) catalyze the synthesis of the reactive cobalt-carbon bond found in coenzyme b(12) or 5'-deoxyadenosylcobalamin (adocbl), which serves as a cofactor for a number of isomerases. the reaction involves a reductive adenosylation of cob(ii)alamin in which an electron delivered by a reductase reduces cob(ii)alamin to cob(i)alamin, which attacks the 5'-carbon of atp to form adocbl and inorganic triphosphate. of the three classes of atrs found in nature, the pduo type, which i ... | 2009 | 19413290 |
| methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of c1 compounds from natural and industrial sources. | methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. the genomes of two pink-pigmented facultative methylotrophic bacteria of the alpha-proteobacterial genus methylobacterium, the reference species methylobacterium extorquens strain am1 and the dichloromethane-degrading strain dm4, were compared. | 2009 | 19440302 |