Publications
| Title | Abstract | Year(sorted descending) Filter | PMID Filter |
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| the enzymatic reaction-induced configuration change of the prosthetic group pqq of methanol dehydrogenase. | methanol dehydrogenase is a heterotetrameric enzyme containing the prosthetic group pyrroloquinoline quinone (pqq), which catalyzes the oxidation of methanol to formaldehyde. the crystal structure of methanol dehydrogenase from methylophilus w3a1, previously determined at high resolution, exhibits a non-planar configuration of the pqq ring system and lends support for a hydride transfer mechanism of the enzymatic reaction catalyzed by the enzyme. to investigate why pqq is in the c5-reduced form ... | 2011 | 21356200 |
| methylophilus glucosoxydans sp. nov., a restricted facultative methylotroph from rice rhizosphere. | two restricted facultative methylotrophic strains, designed bt and p, were isolated from the rice roots and characterized. the isolates were strictly aerobic, gram negative, asporogenous, motile rods multiplying by binary fission, mesophilic and neutrophilic, syntheized indole-3-acetate. the cellular fatty acid profile is dominated by c16:0, c16:1?7c and 2-oh c16:0 fatty acids. the major ubiquinone is q8. the predominant phospholipids were phosphatidylethanolamine and phosphatidylglycerol. cardi ... | 2011 | 21378135 |
| highly selective ligand binding by methylophilus methylotrophus cytochrome c'' | cytochrome c'' (cyt c'') from methylophilus methylotrophus is unusual insofar as the heme has two axial histidine ligands in the oxidized form but one is detached when the protein is reduced. despite cyt c'' having an axial site available for binding small ligands, we show here that only no binds readily to the ferrous cyt c''. binding of co, as well as cn(-), on the other hand requires considerable structural reorganization, or reduction of the disulfide bridge close to the heme. standard free ... | 2011 | 21599015 |
| an integrated proteomics/transcriptomics approach points to oxygen as the main electron sink for methanol metabolism in methylotenera mobilis. | methylotenera species, unlike their close relatives in the genera of methylophilus, methylobacillus and methylovorus neither exhibit the activity of methanol dehydrogenase, nor possess mxafi genes encoding this enzyme, yet they are able to grow on methanol. in this work, we integrated two genome-wide -omics approaches, shotgun proteomics and shotgun transcriptome sequencing (rna-seq) of methylotenera mobilis jlw8 to identify genes and enzymes potentially involved in methanol oxidation, with spec ... | 2011 | 21764938 |
| application of the bacteriophage mu-driven system for the integration/amplification of target genes in the chromosomes of engineered gram-negative bacteria--mini review. | the advantages of phage mu transposition-based systems for the chromosomal editing of plasmid-less strains are reviewed. the cis and trans requirements for mu phage-mediated transposition, which include the l/r ends of the mu dna, the transposition factors mua and mub, and the cis/trans functioning of the e element as an enhancer, are presented. mini-mu(lr)/(ler) units are mu derivatives that lack most of the mu genes but contain the l/r ends or a properly arranged e element in cis to the l/r en ... | 2011 | 21698377 |
| phyllosphere bacterial communities of trichome-bearing and trichomeless arabidopsis thaliana leaves. | this study aimed to investigate whether the presence of trichomes as conspicuous physical attributes of the leaf surface affects the microbial community composition on arabidopsis thaliana leaves. the a. thaliana ecotype col-0 and its trichomeless gl1 mutant were grown in growth cabinets under climate-controlled conditions. the gl1 mutant showed a similar wax composition as the col-0 wild type with slightly reduced amounts of c(29), c(31) and c(33) alkanes by gc/ms and gc/fid analyses. 120 bacte ... | 2011 | 22080429 |
| diversity and biogeography of selected phyllosphere bacteria with special emphasis on methylobacterium spp. | on the basis of cultivation-dependent (isolation on mineral salt medium supplemented with 0.5% methanol) and -independent (dgge analysis) methods, we investigated the influence of the host plant species trifolium repens and cerastium holosteoides, three geographic locations and the land-use types meadow, mown pasture and pasture on the abundance and community composition of selected phyllosphere bacteria with emphasis on methylobacterium species. methylobacterium abundance was significantly high ... | 2011 | 22000032 |
| Impact of anthracene addition on microbial community structure in soil microcosms from contaminated and uncontaminated sites. | This paper aims to investigate the impact of anthracene addition on microbial community in agricultural soil irrigated with tap water or reclaimed wastewater. | 2011 | 22108422 |
| Changes in bacterial community of anthracene bioremediation in municipal solid waste composting soil. | Polycyclic aromatic hydrocarbons (PAHs) are common contaminants in a municipal solid waste (MSW) composting site. Knowledge of changes in microbial structure is useful to identify particular PAH degraders. However, the microbial community in the MSW composting soil and its change associated with prolonged exposure to PAHs and subsequent biodegradation remain largely unknown. In this study, anthracene was selected as a model compound. The bacterial community structure was investigated using termi ... | 2011 | 21887852 |
| bacterial communities constructed in artificial consortia of bacteria and chlorella vulgaris. | we established artificial consortia of bacteria inoculated from soil and a green alga, chlorella vulgaris nies-227. the bacteria and the alga were mixed in a tube or partitioned in a dialysing culture vessel, and the bacterial composition was examined after cultivation. the community of bacteria formed in the consortia included those phylogenetically closely related to the genera phenylobacterium, brevundimonas, phyllobacterium, afipia, sphingomonas, sandaracinobacter, ramlibacter, ralstonia, ce ... | 2010 | 21576850 |
| aromatic amino acid auxotrophs constructed by recombinant marker exchange in methylophilus methylotrophus as1 cells expressing the arop-encoded transporter of escherichia coli. | the isolation of auxotrophic mutants, which is a prerequisite for a substantial genetic analysis and metabolic engineering of obligate methylotrophs, remains a rather complicated task. we describe a novel method of constructing mutants of the bacterium methylophilus methylotrophus as1 that are auxotrophic for aromatic amino acids. the procedure begins with the mu-driven integration of the escherichia coli gene arop, which encodes the common aromatic amino acid transporter, into the genome of m. ... | 2010 | 19880640 |
| methylophilus flavus sp. nov. and methylophilus luteus sp. nov., aerobic, methylotrophic bacteria associated with plants. | novel yellow, obligately methylotrophic and restricted facultatively methylotrophic bacteria, respectively designated strains ship(t) and mim(t), with the ribulose monophosphate pathway of c(1) assimilation are described. cells were strictly aerobic, gram-negative, asporogenous, non-motile rods that multiply by binary fission, were mesophilic and neutrophilic and synthesized indole-3-acetic acid and exopolysaccharide. the predominant cellular fatty acids were c(16 : 0) and c(16 : 1). the major u ... | 2010 | 20023062 |
| enrichment and cultivation of pelagic bacteria from a humic lake using phenol and humic matter additions. | abstract individual bacterial populations are known to respond differently toward substrate availability. to test how the availability of either pure phenol or natural humic matter (hm) selects for specific pelagic bacteria phylotypes from a humic lake (lake grosse fuchskuhle, northeastern germany), we used culture-dependent and -independent approaches. using a batch approach, the bacterial community composition (bcc) differed depending on both the quantity and the quality of added substrates. u ... | 2010 | 20100184 |
| [stearic acid methyl ether: a new extracellular metabolite of the obligate methylotrophic bacterium methylophilus quaylei]. | methyl esters of fatty acids, free fatty acids, and hydrocarbons were found in the culture liquid and in the cellular lipids of the obligate methylotrophic bacterium methylophilus quaylei under optimal growth conditions and osmotic stress. the main extracellular hydrophobic metabolite was methyl stearate. exogenous free fatty acids c16-c18 and their methyl esters stimulated the m. quaylei growth and survivability, as well as production of exopolysaccharide under osmotic and oxidative stress, pla ... | 2010 | 20391761 |
| enrichment and cultivation of pelagic bacteria from a humic lake using phenol and humic matter additions. | individual bacterial populations are known to respond differently toward substrate availability. to test how the availability of either pure phenol or natural humic matter (hm) selects for specific pelagic bacteria phylotypes from a humic lake (lake grosse fuchskuhle, northeastern germany), we used culture-dependent and -independent approaches. using a batch approach, the bacterial community composition (bcc) differed depending on both the quantity and the quality of added substrates. using a di ... | 2010 | 20459514 |
| crystal structure of histamine dehydrogenase from nocardioides simplex. | histamine dehydrogenase (hadh) isolated from nocardioides simplex catalyzes the oxidative deamination of histamine to imidazole acetaldehyde. hadh is highly specific for histamine, and we are interested in understanding the recognition mode of histamine in its active site. we describe the first crystal structure of a recombinant form of hadh (hadh) to 2.7-a resolution. hadh is a homodimer, where each 76-kda subunit contains an iron-sulfur cluster ([4fe-4s](2+)) and a 6-s-cysteinyl flavin mononuc ... | 2010 | 20538584 |
| endosymbionts of acanthamoeba isolated from domestic tap water in korea. | in a previous study, we reported our discovery of acanthamoeba contamination in domestic tap water; in that study, we determined that some acanthamoeba strains harbor endosymbiotic bacteria, via our molecular characterization by mitochondrial dna restriction fragment length polymorphism (mt dna rflp). five (29.4%) among 17 acanthamoeba isolates contained endosymbionts in their cytoplasm, as demonstrated via orcein staining. in order to estimate their pathogenicity, we conducted a genetic charact ... | 2009 | 19967080 |
| functional analysis of mmei from methanol utilizer methylophilus methylotrophus, a subtype iic restriction-modification enzyme related to type i enzymes. | mmei from methylophilus methylotrophus belongs to the type ii restriction-modification enzymes. it recognizes an asymmetric dna sequence, 5'-tccrac-3' (r indicates g or a), and cuts both strands at fixed positions downstream of the specific site. this particular feature has been exploited in transcript profiling of complex genomes (using serial analysis of gene expression technology). we have shown previously that the endonucleolytic activity of mmei is strongly dependent on the presence of s-ad ... | 2009 | 18997032 |
| fluorescence lifetimes of tyrosine residues in cytochrome c'' as local probes to study protein unfolding. | time-resolved fluorescence spectroscopy was used to show that multiple tyrosine residues of a protein can serve as localized probes of structural changes during thermal unfolding. cytochrome c'' from methylophilus methylotrophus, which has four tyrosine residues, was chosen as a model protein. the procedure involved, first, the assignment of the experimental decay times to the tyrosine residues, followed by the interpretation of the changes in the decay times and pre-exponential coefficients wit ... | 2009 | 19249841 |
| life without light: microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in movile cave. | microbial diversity in movile cave (romania) was studied using bacterial and archaeal 16s rrna gene sequence and functional gene analyses, including ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco), soxb (sulfate thioesterase/thiohydrolase) and amoa (ammonia monooxygenase). sulfur oxidizers from both gammaproteobacteria and betaproteobacteria were detected in 16s rrna, soxb and rubisco gene libraries. dna-based stable-isotope probing analyses using 13c-bicarbonate showed that thiobacill ... | 2009 | 19474813 |
| methanol removal efficiency and bacterial diversity of an activated carbon biofilter. | motivated by the need to establish an economical and environmentally friendly methanol control technology for the pulp and paper industry, a bench-scale activated carbon biofiltration system was developed. this system was evaluated for its performance in removing methanol from an artificially contaminated air stream and characterized for its bacterial diversity over time, under varied methanol loading rates, and in different spatial regions of the filter. the biofilter system, composed of a nove ... | 2009 | 19665889 |
| biphenyl-metabolizing bacteria in the rhizosphere of horseradish and bulk soil contaminated by polychlorinated biphenyls as revealed by stable isotope probing. | dna-based stable isotope probing in combination with terminal restriction fragment length polymorphism was used in order to identify members of the microbial community that metabolize biphenyl in the rhizosphere of horseradish (armoracia rusticana) cultivated in soil contaminated with polychlorinated biphenyls (pcbs) compared to members of the microbial community in initial, uncultivated bulk soil. on the basis of early and recurrent detection of their 16s rrna genes in clone libraries construct ... | 2009 | 19700551 |
| identification and cloning of a gene encoding dichloromethane dehalogenase from a methylotrophic bacterium, bacillus circulans wz-12 cctcc m 207006. | the gene dehala encoding a novel dichloromethane dehalogenases (dehala), has been cloned from bacillus circulans wz-12 cctcc m 207006. the open reading frame of dehala, spanning 864 bp, encoded a 288-amino acid protein that showed 85.76% identity to the dichloromethane dehalogenases of hyphomicrobium sp. gj21 with several commonly conserved sequences. these sequences could not be found in putative dichloromethane (dcm) dehalogenases reported from other bacteria and fungi. dehala was expressed in ... | 2009 | 19277720 |
| methylophilus rhizosphaerae sp. nov., a restricted facultative methylotroph isolated from rice rhizosphere soil. | three facultative methylotrophic bacterial strains, designated cbmb127(t), cbmb145 and cbmb147, were isolated from the rhizosphere soil of rice and characterized. the strains produced indole-3-acetic acid and siderophores, had 1-aminocyclopropane-1-carboxylate deaminase activity and sulfur oxidation property and also methanol dehydrogenase. phylogenetic analysis based on the 16s rrna and methanol dehydrogenase (mxaf) gene sequences showed that methylophilus methylotrophus was their close relativ ... | 2009 | 19628595 |
| medium composition suitable for l-lysine production by methylophilus methylotrophus in fed-batch cultivation. | l-lysine production was investigated in fed-batch fermentation using l-lysine producer of methylophilus methylotrophus. by the addition of nutrient composition, containing l-methionine, k(2)hpo(4), nah(2)po(4), cuso(4).5aq, mnso(4).5aq, znso(4).7aq, fecl(3), mgso(4).7aq and cacl(2).2aq, in the feed medium, cell growth could be maintained through the cultivation, and l-lysine production reached to 7.86 g. in addition, the effect of counter ion for nh(4)(+) (cl(-), so(4)(2-), glutamate, succinate ... | 2008 | 19134554 |
| phage mu-driven two-plasmid system for integration of recombinant dna in the methylophilus methylotrophus genome. | a phage mu-driven two-plasmid system for dna integration in escherichia coli genome has been adjusted for methylophilus methylotrophus. constructed helper plasmids with broad-host-range replicons carry thermo-inducible genes for transposition factors mua and mub. integrative plasmids that are only replicated in e. coli could be mobilized to m. methylotrophus and contained mini-mu unit with a short terminus of mu dna, mu-attl/r. mini-mu unit was integrated in the m. methylotrophus genome via mobi ... | 2008 | 18820908 |
| improvement of l-lysine production by methylophilus methylotrophus from methanol via the entner-doudoroff pathway, originating in escherichia coli. | to improve the amino acid production by metabolic engineering, eliminating the pathway bottleneck is known to be very effective. the metabolic response of methylophilus methylotrophus upon the addition of glucose and of pyruvate was investigated in batch cultivation. we found that the supply of pyruvate is a bottleneck in l-lysine production in m. methylotrophus from methanol as carbon source. m. methylotrophus has a ribulose monophosphate (rump) pathway for methanol assimilation, and consequent ... | 2008 | 18838820 |
| mmei: a minimal type ii restriction-modification system that only modifies one dna strand for host protection. | mmei is an unusual type ii restriction enzyme that is useful for generating long sequence tags. we have cloned the mmei restriction-modification (r-m) system and found it to consist of a single protein having both endonuclease and dna methyltransferase activities. the protein comprises an amino-terminal endonuclease domain, a central dna methyltransferase domain and c-terminal dna recognition domain. the endonuclease cuts the two dna strands at one site simultaneously, with enzyme bound at two s ... | 2008 | 18931376 |
| probing the dynamic interface between trimethylamine dehydrogenase (tmadh) and electron transferring flavoprotein (etf) in the tmadh-2etf complex: role of the arg-alpha237 (etf) and tyr-442 (tmadh) residue pair. | we have used multiple solution state techniques and crystallographic analysis to investigate the importance of a putative transient interaction formed between arg-alpha237 in electron transferring flavoprotein (etf) and tyr-442 in trimethylamine dehydrogenase (tmadh) in complex assembly, electron transfer, and structural imprinting of etf by tmadh. we have isolated four mutant forms of etf altered in the identity of the residue at position 237 (alphar237a, alphar237k, alphar237c, and alphar237e) ... | 2008 | 18407658 |
| spatio-temporal niche separation of planktonic betaproteobacteria in an oligo-mesotrophic lake. | we investigated the diversity of planktonic betaproteobacteria and the seasonal population changes of betaproteobacterial taxa in an oligo-mesotrophic lake (piburger see, austria). focus was put on the vertical distribution of the investigated populations and on differences between their respective cell fractions with apparent amino acid incorporation. on average, 66% of betaproteobacterial cells and 73% of their diversity could be attributed to four clades within three lineages that were furthe ... | 2008 | 18430016 |
| disruption of metf increased l-lysine production by methylophilus methylotrophus from methanol. | methionine auxotrophic mutants of methylophilus methylotrophus as1 expressing a mutant form of dapa (dapa24) encoding a dihydrodipicolinate synthase desensitized from feedback inhibition by l-lysine, and mutated lyse (lyse24) encoding the l-lysine exporter from corynebacterium glutamicum 2256, produced higher amounts of l-lysine from methanol as sole carbon source than did other amino acid auxotrophic mutants. especially, the m. methylotrophus 102 strain, carrying both dapa24 and lyse24, produce ... | 2008 | 18460806 |
| community structures and activities of nitrifying and denitrifying bacteria in industrial wastewater-treating biofilms. | the bacterial community structure, in situ spatial distributions and activities of nitrifying and denitrifying bacteria in biofilms treating industrial wastewater were investigated by combination of the 16s rrna gene clone analysis, fluorescence in situ hybridization (fish) and microelectrodes. these results were compared with the nitrogen removal capacity of the industrial wastewater treatment plant (iwtp). both nitrification and denitrification occurred in the primary denitrification (pd) tank ... | 2006 | 16477661 |
| l-lysine biosynthetic pathway of methylophilus methylotrophus and construction of an l-lysine producer. | previously, we showed that the enzymes aspartokinase (ak) and dihydrodipicolinate synthase (ddps), which are involved in l-lysine biosynthesis in the gram-negative obligate methylotroph methylophilus methylotrophus as1, were inhibited by allosteric effectors, including l-lysine. to elucidate further the regulation of l-lysine biosynthesis in m. methylotrophus, we cloned the genes encoding three other enzymes involved in this pathway, l-aspartate-beta-semialdehyde dehydrogenase, dihydrodipicolina ... | 2006 | 16483680 |
| enhancement of l-lysine production in methylotroph methylophilus methylotrophus by introducing a mutant lyse exporter. | the obligate methylotroph methylophilus methylotrophus as1 expressing a mutant form of dapa (dapa24) encoding a dihydrodipicolinate synthase desensitized from feedback inhibition by l-lysine could secrete l-lysine into the medium, but also maintained a high concentration of intracellular l-lysine. to improve the yield from excretion, we attempted to introduce an l-lysine/l-arginine exporter (lyse) from corynebacterium glutamicum 2256 into m. methylotrophus. we were unable to stably transform m. ... | 2006 | 16870294 |
| identification of acetate- or methanol-assimilating bacteria under nitrate-reducing conditions by stable-isotope probing. | stable-isotope probing (sip) was used to identify acetate- or methanol-assimilating bacteria under nitrate-reducing conditions in activated sludge. a sludge sample obtained from wastewater treatment systems was incubated in a denitrifying batch reactor fed with synthetic wastewater containing [(13)c]acetate or [(13)c]methanol as the main carbon source and nitrate as the electron acceptor. we analyzed how growth of bacterial populations was stimulated by acetate or methanol as the external carbon ... | 2006 | 16897304 |
| characterization of a unique mutant lyse gene, originating from corynebacterium glutamicum, encoding a product that induces l-lysine production in methylophilus methylotrophus. | lyse24 is an allele of lyse encoding an l-lysine exporter of corynebacterium glutamicum. the mutant gene is able to induce l-lysine production in methylophilus methylotrophus. although lyse24 has a mutation in the middle of lyse that results in chain termination, the entire lyse locus, including the region downstream of the short open reading frame, is necessary for l-lysine production. we propose that separate polypeptides are synthesized from the lyse24 locus due to reinitiation of translation ... | 2006 | 17151474 |
| structural evidence for a proton transfer pathway coupled with haem reduction of cytochrome c" from methylophilus methylotrophus. | the crystal structures of the oxidized and reduced forms of cytochrome c" from methylophilus methylotrophus were solved from x-ray synchrotron data to atomic resolution. the overall fold of the molecule in the two redox states is very similar and is comparable to that of the oxygen-binding protein from the purple phototrophic bacterium rhodobacter sphaeroides. however, significant modifications occur near the haem group, in particular the detachment from axial binding of his95 observed upon redu ... | 2006 | 16341897 |
| stable carbon isotope fractionation during degradation of dichloromethane by methylotrophic bacteria. | stable carbon isotope fractionation during dichloromethane (dcm) degradation by methylotrophic bacteria was investigated under aerobic and nitrate-reducing conditions. the strains studied comprise several hyphomicrobium strains, methylobacterium, methylopila, methylophilus and methylorhabdus spp. that are considered to degrade dcm by a glutathione (gsh)-dependent dehalogenase enzyme system in the initial step. the stable carbon isotope fractionation factors (alphac) of the strains varied under a ... | 2006 | 16343330 |
| 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 |
| the interaction of trimethylamine dehydrogenase and electron-transferring flavoprotein. | the interaction between the physiological electron transfer partners trimethylamine dehydrogenase (tmadh) and electron-transferring flavoprotein (etf) from methylophilus methylotrophus has been examined with particular regard to the proposal that the former protein "imprints" a conformational change on the latter. the results indicate that the absorbance change previously attributed to changes in the environment of the fad of etf upon binding to tmadh is instead caused by electron transfer from ... | 2005 | 15760891 |
| histamine dehydrogenase from rhizobium sp.: gene cloning, expression in escherichia coli, characterization and application to histamine determination. | the gene encoding histamine dehydrogenase in rhizobium sp. 4--9 has been cloned and overexpressed in escherichia coli. the coding region of the gene was 2,079 bp and encoded a protein of 693 amino acids with a calculated molecular mass of 76,732 da. this histamine dehydrogenase was related to histamine dehydrogenase from nocardioides simplex (54.5% identical), trimethylamine dehydrogenase from methylophilus methylotrophus (39.3% identical) and dimethylamine dehydrogenase from hyphomicrobium x (3 ... | 2005 | 15964650 |
| methylophilus quaylei sp. nov., a new aerobic obligately methylotrophic bacterium. | a new obligately methylotrophic bacterium (strain mtt) with the ribulose monophosphate pathway of carbon assimilation is described. the isolate, utilizing only methanol, is an aerobic, gram-negative, asporogenous, non-motile short rod multiplying by binary fission. its cellular fatty acids profile consists primarily of straight-chain saturated c16:0 and unsaturated c16:l acids. the major ubiquinone is q-8. the dominant phospholipids are phosphatidylethanolamine and phosphatidylglycerol. diphosph ... | 2005 | 15997702 |
| bacterial populations active in metabolism of c1 compounds in the sediment of lake washington, a freshwater lake. | active members of the bacterial community in the sediment of lake washington, with special emphasis on c1 utilizers, were identified by employing two complementary culture-independent approaches: reverse transcription of environmental mrna and 16s rrna combined with pcr (rt-pcr) and stable-isotope probing (sip) of dna with the 13c-labeled c1 substrates methanol, methylamine, formaldehyde, and formate. analysis of rt-pcr-amplified fragments of 16s rrna-encoding genes revealed that gammaproteobact ... | 2005 | 16269723 |
| detection of potentially novel bacterial components of the human skin microbiota using culture-independent molecular profiling. | although the micro-organisms forming the cutaneous microbiota are considered to play important roles in the modification and prevention of skin diseases, a comprehensive analysis of their composition has not yet been carried out because of difficulties in determining yet-to-be-cultured micro-organisms in the samples. swab-scrubbed forehead skin samples of five healthy volunteers were analysed by profiling 16s rrna genes, as well as by conventional culture methods, to provide a profile of the cut ... | 2005 | 16278439 |
| 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 |
| use of stable-isotope probing, full-cycle rrna analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community. | a denitrifying microbial consortium was enriched in an anoxically operated, methanol-fed sequencing batch reactor (sbr) fed with a mineral salts medium containing methanol as the sole carbon source and nitrate as the electron acceptor. the sbr was inoculated with sludge from a biological nutrient removal activated sludge plant exhibiting good denitrification. the sbr denitrification rate improved from less than 0.02 mg of no(3)(-)-n mg of mixed-liquor volatile suspended solids (mlvss)(-1) h(-1) ... | 2004 | 14711691 |
| [deuterium oxide as a stress factor to the methylotrophic bacterium methylophilus sp]. | the adaptation of the methylotrophic bacterium methylophilus sp. b-7741 to growth in highly deuterated media was studied. for the first time, we showed the cross adaptation of bacterial cells to deuterated media and oxidative and osmotic stresses. the activity at catalase in deuterated cells was higher than in the control cells. deuterated cell-free culture liquids showed protective effects on the growth of methylophilus sp. b-7741 in deuterated media, which was manifested as an increase in the ... | 2004 | 15198027 |
| characterization of the l-lysine biosynthetic pathway in the obligate methylotroph methylophilus methylotrophus. | the l-lysine biosynthetic pathway of the gram-negative obligate methylotroph methylophilus methylotrophus as1 was examined through characterization of the enzymes aspartokinase (ak), aspartsemialdehyde dehydrogenase, dihydrodipicolinate synthase (ddps), dihydrodipicolinate reductase, and diaminopimelate decarboxylase. the ak was inhibited by l-threonine and by a combination of l-threonine and l-lysine, but not by l-lysine alone, and the activity of ddps was moderately reduced by l-lysine. in an ... | 2004 | 15277749 |
| [the release of flavin adenine dinucleotide upon local conformational transition in electron-transferring flavoprotein induced by trimethylamine dehydrogenase]. | the electron-transferring proteins, trimethylamine dehydrogenase (tmad) and electron-transferring flavoprotein (etf) from the bacterium methylophilius methylotrophus, were studied in vitro by fluorescence spectroscopy. flavin adenine dinucleotide (fad) was found to be capable of a slow and spontaneous release from etf, which is accompanied by an increase in flavin fluorescence. at a rather high ionic strength (0.1 m nacl or 50 mm phosphate), the fad release is sharply activated by tmad preparati ... | 2004 | 15344654 |
| detection of ectoin biosynthesis genes in halotolerant aerobic methylotrophic bacteria. | 2004 | 15378927 | |
| [effect of deuteration on methanol dehydrogenase activity in methylophilus sp. b-7741]. | we studied the effect of deuterium oxide present in the medium on the activity of methanol dehydrogenase (ec 1.1.99.8) from methylotrophic bacteria methylophilus sp. b-7741. methanol dehydrogenase activity in extracts of the biomass obtained in a highly deuterated medium (2h-enzyme) was 34-47% of enzyme activity in the control biomass, which depended on reaction conditions. the isotopic effects of substrate deuterium (methanol) for 1h-enzyme and 2h-enzyme were 1.37 +/- 0.05 and 1.38 +/- 0.01, re ... | 2004 | 15029692 |
| extensive conformational sampling in a ternary electron transfer complex. | here we report the crystal structures of a ternary electron transfer complex showing extensive motion at the protein interface. this physiological complex comprises the iron-sulfur flavoprotein trimethylamine dehydrogenase and electron transferring flavoprotein (etf) from methylophilus methylotrophus. in addition, we report the crystal structure of free etf. in the complex, electron density for the fad domain of etf is absent, indicating high mobility. positions for the fad domain are revealed b ... | 2003 | 12567183 |
| crystallization and preliminary x-ray characterization of cytochrome c" from the obligate methylotroph methylophilus methylotrophus. | cytochrome c" from the obligate methylotroph methylophilus methylotrophus is a 15 kda monohaem protein which has a c-type haem covalently linked to the protein chain. two histidine residues are the axial ligands of the fe atom in the oxidized form. this cytochrome is one of the few known haem proteins which undergoes a change of spin state of the fe atom upon reduction, with the detachment of an axial histidine ligand. initial crystallization conditions involved the utilization of cadmium chlori ... | 2003 | 12595732 |
| effects of multiple ligand binding on kinetic isotope effects in pqq-dependent methanol dehydrogenase. | the reaction of pqq-dependent methanol dehydrogenase (mdh) from methylophilus methylotrophus has been studied by steady-state and stopped-flow kinetic methods, with particular reference to multiple ligand binding and the kinetic isotope effect (kie) for pqq reduction. phenazine ethosulfate (pes; an artificial electron acceptor) and cyanide (a suppressant of endogenous activity), but not ammonium (an activator of mdh), compete for binding at the catalytic methanol-binding site. cyanide does not a ... | 2003 | 12667088 |
| catalytic mechanism of dichloromethane dehalogenase from methylophilus sp. strain dm11. | the glutathione (gsh)-dependent dichloromethane dehalogenase from methylophilus sp. strain dm11 catalyzes the dechlorination of ch(2)cl(2) to formaldehyde via a highly reactive, genotoxic intermediate, s-(chloromethyl)glutathione (gs-ch(2)cl). the catalytic mechanism of the enzyme toward a series of dihalomethane and monohaloethane substrates suggests that the initial addition of gsh to the alkylhalides is fast and that the rate-limiting step in turnover is the release of either the peptide prod ... | 2003 | 12974641 |
| x-ray structure of methanol dehydrogenase from paracoccus denitrificans and molecular modeling of its interactions with cytochrome c-551i. | the x-ray structure of methanol dehydrogenase (medh) from paracoccus denitrificans (medh-pd) was determined at 2.5 a resolution using molecular replacement based on the structure of medh from methylophilus methylotrophus w3a1 (medh-wa). the overall structures from the two bacteria are similar to each other except that the former has a longer c-terminal tail in each subunit and shows local differences in several insertion regions. the "x-ray sequence" of the segment alphagly444-alphaleu452 was es ... | 2003 | 14505072 |
| a mechanism for substrate-induced formation of 6-hydroxyflavin mononucleotide catalyzed by c30a trimethylamine dehydrogenase. | experiments are described to determine the origin of the 6-hydroxyl group of 6-hydroxyfmn produced by the substrate-induced transformation of fmn in the c30a mutant of trimethylamine dehydrogenase. the conversion of fmn to 6-hydroxyfmn is carried out in the presence of h(2)(18)o and 18o(2), and the results clearly show that the 6-hydroxyl group is derived from molecular oxygen and not from water. | 2003 | 14592522 |
| enzymes of dimethylsulfone metabolism and the phylogenetic characterization of the facultative methylotrophs arthrobacter sulfonivorans sp. nov., arthrobacter methylotrophus sp. nov., and hyphomicrobium sulfonivorans sp. nov. | novel methylotrophic arthrobacter and hyphomicrobium species are described. constitutive membrane-associated dimethylsulfone- and dimethylsulfoxide-reductases were found in arthrobacter methylotrophus strain tga and hyphomicrobium sulfonivorans strain s1. enzyme activities increased during growth with dimethylsulfone or dimethylsulfoxide, respectively, and different ratios of activity with different growth substrates indicated that they are separate enzymes. sds-page showed some membrane-associa ... | 2002 | 11807567 |
| identification of klebsiella pneumoniae genes involved in intestinal colonization and adhesion using signature-tagged mutagenesis. | klebsiella pneumoniae is an opportunistic pathogen responsible for nosocomial infections that initially colonize the intestinal tract of patients. signature-tagged mutagenesis was used to identify genes required for this function. a library of 2,200 mutants was analyzed for the inability of the mutants to survive in a murine model of intestinal colonization and to adhere to human intestinal cells (int-407) in vitro. twenty-nine attenuated mutants were selected for further analyses after competit ... | 2002 | 12117993 |
| sequence variation in dichloromethane dehalogenases/glutathione s-transferases. | dichloromethane dehalogenase/glutathione s-transferase allows methylotrophic bacteria to grow with dichloromethane (dcm), a predominantly man-made compound. bacteria growing with dcm by virtue of this enzyme have been readily isolated in the past. so far, the sequence of the dcma gene encoding dcm dehalogenase has been determined for methylobacterium dichloromethanicum dm4 and methylophilus sp. dm11. dcm dehalogenase genes closely related to that of strain dm4 were amplified by pcr and cloned fr ... | 2001 | 11238968 |
| alpha arg-237 in methylophilus methylotrophus (sp. w3a1) electron-transferring flavoprotein affords approximately 200-millivolt stabilization of the fad anionic semiquinone and a kinetic block on full reduction to the dihydroquinone. | the midpoint reduction potentials of the fad cofactor in wild-type methylophilus methylotrophus (sp. w3a1) electron-transferring flavoprotein (etf) and the alphar237a mutant were determined by anaerobic redox titration. the fad reduction potential of the oxidized-semiquinone couple in wild-type etf (e'(1)) is +153 +/- 2 mv, indicating exceptional stabilization of the flavin anionic semiquinone species. conversion to the dihydroquinone is incomplete (e'(2) < -250 mv), because of the presence of b ... | 2001 | 11285259 |
| solution structure of methylophilus methylotrophus cytochrome c": insights into the structural basis of haem-ligand detachment. | cytochrome c" from methylophilus methylotrophus is a monohaem protein with 124 amino acid residues. the iron has two histidine ligands in the oxidised form, one of which detaches and picks up a proton when the protein is reduced. thus, both forms are paramagnetic. the structure of the oxidised form in solution, determined from nmr data is presented. the family of structures has an average backbone rmsd value of 0.53 a, and a heavy atom rmsd value of 0.95 a, within a target function range of 32 % ... | 2001 | 11327772 |
| catalytic mechanism of quinoprotein methanol dehydrogenase: a theoretical and x-ray crystallographic investigation. | the catalytic mechanism of the reductive half reaction of the quinoprotein methanol dehydrogenase (mdh) is believed to proceed either through a hemiketal intermediate or by direct transfer of a hydride ion from the substrate methyl group to the cofactor, pyrroloquinoline quinone (pqq). a crystal structure of the enzyme-substrate complex of a similar quinoprotein, glucose dehydrogenase, has recently been reported that strongly favors the hydride transfer mechanism in that enzyme. a theoretical an ... | 2001 | 11149955 |
| [phylogenetic analysis of aerobic methylotrophic bacteria, using dichloromethane]. | the phylogenetic relationships of 12 aerobic dichloromethane-degrading bacteria that implement different c1-assimilation pathways was determined based on 16s ribosomal rna sequences and dna-dna hybridization data. the restricted facultative methylotroph "methylophilus leisingerii" dm11 with the ribulose monophosphate pathway was found to belong to the genus methylophilus cluster of the beta subdivision of the phylogenetic kingdom proteobacteria. the facultative methylotroph methylorhabdus multiv ... | 2001 | 11338843 |
| inactivation of c30a trimethylamine dehydrogenase by n-cyclopropyl-alpha-methylbenzylamine, 1-phenylcyclopropylamine, and phenylhydrazine. | trimethylamine dehydrogenase (tmadh) from the bacterium methylophilus methylotrophus (sp. w(3)a(1)) and its c30a mutant were inactivated with three known inactivators of monoamine oxidase, namely, phenylhydrazine, n-cyclopropyl-alpha-methylbenzylamine, and 1-phenylcyclopropylamine. all three compounds irreversibly inactivated both the wild-type and c30a mutant enzymes, although phenylhydrazine was 10 times more potent than n-cyclopropyl-alpha-methylbenzylamine, which was much more potent than 1- ... | 2001 | 11456490 |
| crystal structures of an oxygen-binding cytochrome c from rhodobacter sphaeroides. | the photosynthetic bacterium rhodobacter sphaeroides produces a heme protein (shp), which is an unusual c-type cytochrome capable of transiently binding oxygen during autooxidation. similar proteins have not only been observed in other photosynthetic bacteria but also in the obligate methylotroph methylophilus methylotrophus and the metal reducing bacterium shewanella putrefaciens. a three-dimensional structure of shp was derived using the multiple isomorphous replacement phasing method. besides ... | 2000 | 10821858 |
| radiolytic studies of trimethylamine dehydrogenase. spectral deconvolution of the neutral and anionic flavin semiquinone, and determination of rate constants for electron transfer in the one-electron reduced enzyme. | trimethylamine dehydrogenase from the pseudomonad methylophilus methylotrophus has been examined using the technique of pulse radiolysis to rapidly introduce a single reducing equivalent into the enzyme. using enzyme that has had its iron-sulfur center rendered redox-inert by prior reaction with ferricenium hexafluorophosphate, we determined the spectral change associated with formation of both the anionic and neutral forms that were generated at high and low ph, respectively, of the unique 6-cy ... | 2000 | 10859304 |
| structural and biochemical characterization of recombinant wild type and a c30a mutant of trimethylamine dehydrogenase from methylophilus methylotrophus (sp. w(3)a(1)). | trimethylamine dehydrogenase (tmadh) is an iron-sulfur flavoprotein that catalyzes the oxidative demethylation of trimethylamine to form dimethylamine and formaldehyde. it contains a unique flavin, in the form of a 6-s-cysteinyl fmn, which is bent by approximately 25 degrees along the n5-n10 axis of the flavin isoalloxazine ring. this unusual conformation is thought to modulate the properties of the flavin to facilitate catalysis, and has been postulated to be the result of covalent linkage to c ... | 2000 | 10869173 |
| differential coupling through val-344 and tyr-442 of trimethylamine dehydrogenase in electron transfer reactions with ferricenium ions and electron transferring flavoprotein. | modeling studies of the trimethylamine dehydrogenase-electron transferring flavoprotein (tmadh-etf) electron transfer complex have suggested potential roles for val-344 and tyr-442, found on the surface of tmadh, in electronic coupling between the 4fe-4s center of tmadh and the fad of etf. the importance of these residues in electron transfer, both to etf and to the artificial electron acceptor, ferricenium (fc(+)), has been studied by site-directed mutagenesis and stopped-flow spectroscopy. red ... | 2000 | 10924112 |
| solution structure and metal-ion binding of the p4 element from bacterial rnase p rna. | we determined the solution structure of two 27-nt rna hairpins and their complexes with cobalt(iii)-hexammine (co(nh3)3+(6)) by nmr spectroscopy. the rna hairpins used in this study are the p4 region from escherichia coli rnase p rna and a c-to-u mutant that confers altered divalent metal-ion specificity (ca2+ replaces mg2+) for catalytic activity of this ribozyme. co(nh3)3+(6) is a useful spectroscopic probe for mg(h2o)2+(6)-binding sites because both complexes have octahedral symmetry and have ... | 2000 | 10999599 |
| high yield of methylophilus methylotrophus cytochrome c by coexpression with cytochrome c maturation gene cluster from escherichia coli. | heterologous expression of c-type cytochromes in the periplasm of escherichia coli often results in low soluble product yield, apoprotein formation, or protein degradation. we have expressed cytochrome c from methylophilus methylotrophus in e. coli by coexpression of the gene encoding the cytochrome (cyca) with the host-specific cytochrome c maturation elements, within the ccma-h gene cluster. aerobic cultures produced up to 10 mg holoprotein per liter after induction with iptg. in the absence o ... | 2000 | 11087684 |
| [methylovorus mays--novel species of aerobic, obligatory methylotrophic bacteria associated with plants]. | a bacterial strain utilizing methanol as the sole source of carbon and energy was isolated from the maize phyllosphere. cells are nonpigmented gram-negative motile rods that do not form spores or prosthecae and reproduce by binary fission. the strain does not require vitamins or supplementary growth factors. it is obligately aerobic and urease-, oxidase-, and catalase-positive. the optimum growth temperature is 35-40 degrees c; the optimum ph is 7.0-7.5. the doubling time is 2 h. the bacterium i ... | 2000 | 11315676 |
| x-ray structure of the quinoprotein ethanol dehydrogenase from pseudomonas aeruginosa: basis of substrate specificity. | the homodimeric enzyme form of quinoprotein ethanol dehydrogenase from pseudomonas aeruginosa atcc 17933 crystallizes readily with the space group r3. the x-ray structure was solved at 2.6 a resolution by molecular replacement. aside from differences in some loops, the folding of the enzyme is very similar to the large subunit of the quinoprotein methanol dehydrogenases from methylobacterium extorquens or methylophilus w3a1. eight w-shaped beta-sheet motifs are arranged circularly in a propeller ... | 2000 | 10736230 |
| x-ray scattering studies of methylophilus methylotrophus (sp. w3a1) electron-transferring flavoprotein. evidence for multiple conformational states and an induced fit mechanism for assembly with trimethylamine dehydrogenase. | small angle x-ray solution scattering has been used to generate a low resolution, model-independent molecular envelope structure for electron-transferring flavoprotein (etf) from methylophilus methylotrophus (sp. w(3)a(1)). analysis of both the oxidized and 1-electron-reduced (anionic flavin semiquinone) forms of the protein revealed that the solution structures of the protein are similar in both oxidation states. comparison of the molecular envelope of etf from the x-ray scattering data with pr ... | 2000 | 10766748 |
| formation of w(3)a(1) electron-transferring flavoprotein (etf) hydroquinone in the trimethylamine dehydrogenase x etf protein complex. | the electron-transferring flavoprotein (etf) from methylophilus methylotrophus (sp. w(3)a(1)) exhibits unusual oxidation-reduction properties and can only be reduced to the level of the semiquinone under most circumstances (including turnover with its physiological reductant, trimethylamine dehydrogenase (tmadh), or reaction with strong reducing reagents such as sodium dithionite). in the present study, we demonstrate that etf can be reduced fully to its hydroquinone form both enzymatically and ... | 2000 | 10777543 |
| effect of ph on axial ligand coordination of cytochrome c" from methylophilus methylotrophus and horse heart cytochrome c. | the effect of protons on the axial ligand coordination and on structural aspects of the protein moiety of cytochrome c' ' from methylophilus methylotrophus, an obligate methylotroph, has been investigated down to very low ph (i.e., 0.3). the unusual resistance of this cytochrome to very low ph values has been exploited to carry out this study in comparison with horse heart cytochrome c. the experiments were undertaken at a constant phosphate concentration to minimize the variation of ionic stren ... | 2000 | 10889031 |
| the reaction of trimethylamine dehydrogenase with trimethylamine. | the reductive half-reaction of trimethylamine dehydrogenase with its physiological substrate trimethylamine has been examined by stopped-flow spectroscopy over the ph range 6.0-11.0, with attention focusing on the fastest of the three kinetic phases of the reaction, the flavin reduction/substrate oxidation process. as in previous work with the slow substrate diethylmethylamine, the reaction is found to consist of three well resolved kinetic phases. the observed rate constant for the fast phase e ... | 1999 | 10224069 |
| enzyme-mediated dichloromethane toxicity and mutagenicity of bacterial and mammalian dichloromethane-active glutathione s-transferases. | the kinetic properties of bacterial and rat liver glutathione s-transferases (gst) active with dichloromethane (dcm) were compared. the theta class glutathione s-transferase (rgstti-1) from rat liver had an affinity for dihalomethanes lower by three orders of magnitude (k(app) > 50 mm) than the bacterial dcm dehalogenase/gst from methylophilus sp. dm11. unlike the bacterial dcm dehalogenase, the rat enzyme was unable to support growth of the dehalogenase minus methylobacterium sp. dm4-2cr mutant ... | 1999 | 10350186 |
| cytochrome c" from the obligate methylotroph methylophilus methylotrophus, an unexpected homolog of sphaeroides heme protein from the phototroph rhodobacter sphaeroides. | the complete primary structure of an unusual soluble cytochrome c isolated from the obligate methylotrophic bacterium methylophilus methylotrophus has been determined to contain 124 amino acids and to have an average molecular mass of 14293.0 da. the sequence has two unusual features: firstly, the location of the heme-binding cysteines is far downstream from the n-terminus, namely at positions 49 and 52; secondly, an extra pair of cysteine residues is present near the c-terminus. in both respect ... | 1999 | 10354493 |
| cloning and sequence analysis of the gene encoding methylophilus methylotrophus cytochrome c", a unique protein with a perpendicular orientation of the histidinyl ligands. | cytochrome c" from methylophilus methylotrophus is an unusual monohaem protein that undergoes a major redox-linked spin-state transition: one of the two axial histidines bound to the iron in the oxidised form is detached upon reduction and a proton is taken up. a 3.5-kb dna fragment, containing the gene encoding cytochrome c" (cyca), has been cloned and sequenced. the cytochrome c" gene codes for a pre-protein with a typical prokaryotic 20-residue signal sequence, suggesting that the protein is ... | 1999 | 10524262 |
| crystallization and preliminary diffraction studies of two quinoprotein alcohol dehydrogenases (adhs): a soluble monomeric adh from pseudomonas putida hk5 (adh-iib) and a heterotrimeric membrane-bound adh from gluconobacter suboxydans (adh-gs). | crystals of a soluble monomeric quinocytochrome alcohol dehydrogenase (adh-iib) and of a trimeric membrane-associated quinocytochrome alcohol dehydrogenase (adh-gs) have been obtained. the adh-iib crystals are triclinic, with one monomer in the unit cell, and were obtained in the presence of peg 8000, sodium citrate, hepes buffer and 2-propanol. x-ray data were collected at 110 k to 1. 9 a resolution (r(merge) = 6.4%) and the orientation of a methanol dehydrogenase search molecule (from methylop ... | 1999 | 10531500 |
| structure of the phylogenetically most conserved domain of srp rna. | the signal recognition particle (srp) is a phylogenetically conserved ribonucleoprotein required for cotranslational targeting of proteins to the membrane of the endoplasmic reticulum of the bacterial plasma membrane. domain iv of srp rna consists of a short stem-loop structure with two internal loops that contain the most conserved nucleotides of the molecule. all known essential interactions of srp occur in that moiety containing domain iv. the solution structure of a 43-nt rna comprising the ... | 1999 | 10580470 |
| enzymatic h-transfer requires vibration-driven extreme tunneling. | enzymatic breakage of the substrate c-h bond by methylophilus methyltrophus (sp. w3a1) methylamine dehydrogenase (madh) has been studied by stopped-flow spectroscopy. the rate of reduction of the tryptophan tryptophylquinone (ttq) cofactor has a large kinetic isotope effect (kie = 16.8 +/- 0.5), and the kie is independent of temperature. analysis of the temperature dependence of c-h bond breakage revealed that extreme (ground state) quantum tunneling is responsible for the transfer of the hydrog ... | 1999 | 10074378 |
| detailed active site configuration of a new crystal form of methanol dehydrogenase from methylophilus w3a1 at 1.9 a resolution. | the three-dimensional structure of a new crystal form of methanol dehydrogenase from methylophilus w3a1 has been obtained in the presence of substrate using data recorded at a synchrotron. the structure of this approximately 140 kda heterotetramer, refined at 1. 9 a resolution, reveals the detailed configuration of its redox cofactor, pyrroloquinoline quinone (pqq). c4, one of the oxygen-bearing atoms of this orthoquinone is in a planar configuration while c5, which bears the other quinone oxyge ... | 1999 | 9930981 |
| homology model of the quinohaemoprotein alcohol dehydrogenase from comamonas testosteroni. | a molecular model of qh-adh, the quinohaemoprotein alcohol dehydrogenase from comamonas testosteroni, has been built by homology modelling. sequence similarity of n-terminal residues 1-570 with the alpha-subunit of quinoprotein methanol dehydrogenases (mdhs) from methylophilus methylotrophus w3a1 and methylobacterium extorquens provided a basis for the design of the pqq-binding domain of qh-adh. minimal sequence similarity with cytochrome c551 from ectothiorhodospira halophila and cytochrome c5 ... | 1998 | 9613842 |
| two intertwined methylation activities of the mmei restriction-modification class-iis system from methylophilus methylotrophus. | the class-iis restriction endonuclease, r.mmei, was isolated from methylophilus methylotrophus. it was originally described as a monomeric enzyme, with the native mr 105000+/-7000, which did not cleave dna efficiently [boyd et al. (1986) nucleic acids res. 14, 5255-5274; tucholski et al. (1995) gene 157, 87-92]. however, it was discovered that r.mmei endonucleolytic activity is enhanced by s-adenosyl-l-methionine (adomet) and sinefungin, an analogue of adomet. surprisingly, the purified r.mmei e ... | 1998 | 9858752 |
| [site-directed mutagenesis of the dichloromethane dehalogenase gene from methylophilus sp. strain dm11]. | in order to investigate the role of different residues of methylophilus sp. strain dm11 dichloromethane dehalogenase for substrate binding, glutathione affinity, and catalytic activity, site-directed mutagenesis studies of the gene encoding the enzyme were carried out. the conserved tryptophane residue at 103 region was respectively substituted by phenylalanine, valine or asparagine. the conserved arginine residue at 109 region was substituted by leucine. the conserved tryptophane residue at 117 ... | 1998 | 12549326 |
| purification and characterization of the mutant enzyme w117y of the dichloromethane dehalogenase from methylophilus sp. strain dm11. | 1998 | 10075637 | |
| characterisation of a binding-protein-dependent, active transport system for short-chain amides and urea in the methylotrophic bacterium methylophilus methylotrophus. | three genes (fmdcab) encoding an outer-membrane porin for short-chain amides and urea, formamidase, and a putative regulatory protein in methylophilus methylotrophus have previously been cloned and characterised. three genes have now been identified downstream of fmdb, viz fmdd encoding a hydrophilic protein containing an n-terminal signal sequence, and fmdef encoding hydrophobic transmembrane proteins. the derived amino acid sequence of mature fmdd (predicted molecular mass 41,870 da) was simil ... | 1998 | 9492267 |
| effects of bacterial host and dichloromethane dehalogenase on the competitiveness of methylotrophic bacteria growing with dichloromethane. | methylobacterium sp. strain dm4 and methylophilus sp. strain dm11 can grow with dichloromethane (dcm) as the sole source of carbon and energy by virtue of homologous glutathione-dependent dcm dehalogenases with markedly different kinetic properties (the kcat values of the enzymes of these strains are 0.6 and 3.3 s-1, respectively, and the km values are 9 and 59 microm, respectively). these strains, as well as transconjugant bacteria expressing the dcm dehalogenase gene (dcma) from dm11 or dm4 on ... | 1998 | 9546153 |
| knowledge-based modeling of a bacterial dichloromethane dehalogenase. | a three-dimensional structural model of the dichloromethane dehalogenase (dcmd) from methylophilus sp. dm11 is constructed based on sequence similarities to the glutathione s-transferases (gsts). to maximize sequence identity and minimize gaps in the alignment, a hybrid approach is used that takes advantage of the increased homology found between dm11 and domain i of the sheep blowfly theta class gst (residues 1-79) and domain ii of the human alpha class gst (residues 81-222). the resulting stru ... | 1997 | 9188739 |
| an outer-membrane porin inducible by short-chain amides and urea in the methylotrophic bacterium methylophilus methylotrophus. | the fmda and fmdb genes encoding formamidase and a putative regulatory protein, respectively, from the methylotrophic bacterium methylophilus methylotrophus were recloned with additional flanking dna (psw1). fmdc, encoding a weakly hydrophilic protein containing an n-terminal signal sequence, was identified upstream of fmdab. the derived amino acid sequence of mature fmdc (m(r) 39204) showed that it was rich in beta-sheet and aromatic amino acids, and exhibited significant similarities to severa ... | 1997 | 9245819 |
| creating auxotrophic mutants in methylophilus methylotrophus as1 by combining electroporation and chemical mutagenesis. | stable auxotrophic mutants of the methylotroph methylophilus methylotrophus as1 were obtained by a novel mutagenesis technique in which electroporation is used to transport the chemical mutagen n-methyl-n'-nitro-n-nitrosoguanidine (mnng) across the cell membrane. by combining chemical mutagenesis with electroporation and screening single colonies for auxotrophy in 36 different amino acids and growth factors, 3 auxotrophs per 156 colonies screened were obtained, whereas no auxotrophs were found w ... | 1997 | 9274053 |
| identification of a novel determinant of glutathione affinity in dichloromethane dehalogenases/glutathione s-transferases. | bacterial dichloromethane dehalogenases catalyze the glutathione-dependent hydrolysis of dichloromethane to formaldehyde and are members of the enzyme superfamily of glutathione s-transferases involved in the detoxification of electrophilic compounds. numerous protein engineering studies have addressed questions pertaining to the substrate specificity, the reaction mechanism, and the kinetic pathway of glutathione s-transferases. in contrast, the molecular determinants for binding of the glutath ... | 1997 | 9299530 |
| cloning and analysis of methanol oxidation genes in the methylotroph hyphomicrobium methylovorum gm2. | the gene encoding the alpha-subunit of methanol dehydrogenase (mxaf) and its flanking region was isolated from a methylotrophic bacterium, hyphomicrobium methylovorum gm2. the deduced amino acid sequence of mxaf showed 80, 80, 74 and 66% identity with those of methylobacterium extorquens am1, m. organophilum xx, paracoccus denitrificans and methylophilus methylotrophus, respectively. the putative mxaf promoter sequence (-35 -aaagaca-, -10 -tagaa-) observed in other methylotrophs was not found in ... | 1997 | 9311140 |
| ph dependence of structural and functional properties of oxidized cytochrome c" from methylophilus methylotrophus. | cytochrome c" from methylophilus methylotrophus is an unusual monoheme protein that undergoes a major redox-linked change in the heme arrangement: one of the two axial histidines bound to the iron in the oxidized form is detached upon reduction and a proton is taken up. the kinetics of reduction by sodium dithionite and the spectroscopic properties of the oxidized cytochrome c" have been investigated over the ph range between 1.4 and 10.0. the rate of reduction displays proton-linked transitions ... | 1997 | 9312076 |
| transformation of methylotrophic bacteria by electroporation. | an efficient system for electroporation of the methylotrophic bacteria hyphomicrobium facilis, hyphomicrobium denitrificans, methylobacillus glycogenes, methylobacterium extorquens, and methylophilus methylotrophus is described. it could be demonstrated that vectors based on the broad-host-range plasmid pbbr1 could be transferred into these strains. plasmid pbbr1kan (3.9 kb), a kanamycin-resistant derivative of pbbr1, was suitable for transformation experiments in these methylotrophic bacteria. ... | 1997 | 9090108 |
| a high-potential soluble cytochrome c-551 from the purple phototrophic bacterium chromatium vinosum is homologous to cytochrome c8 from denitrifying pseudomonads. | a minor cytochrome c-551 component of chromatium vinosum was previously found to efficiently couple electron transfer between the cytochrome bc1 complex and the photosynthetic reaction center. we have now determined the amino acid sequence of this cytochrome c-551 and find that it is homologous to cytochrome c8 (formerly called pseudomonas cytochrome c-551). it is most similar to methylophilus methylotrophus, rhodocyclus tenuis, and azotobacter vinelandii cytochromes c8 (respectively, 57%, 52% a ... | 1996 | 8612646 |
| physical, biochemical, and immunological characterization of a thermostable amidase from klebsiella pneumoniae nctr 1. | an amidase capable of degrading acrylamide and aliphatic amides was purified to apparent homogeneity from klebsiella pneumoniae nctr 1. the enzyme is a monomer with an apparent molecular weight of 62,000. the ph and temperature optima of the enzyme were 7.0 and 65 degrees c, respectively. the purified amidase contained 11 5,5-dithiobis(2-nitrobenzoate) (dtnb)-titratable sulfhydryl (sh) groups. in the native enzyme 1.0 sh group readily reacted with dtnb with no detectable loss of activity. titrat ... | 1996 | 8636044 |
| determination of the gene sequence and the three-dimensional structure at 2.4 angstroms resolution of methanol dehydrogenase from methylophilus w3a1. | the dna sequences for the genes encoding the heavy and light subunits of methanol dehydrogenase from methylophilus methylotrophus w3a1 have been determined. the deduced amino acid sequence has enabled the structure of the enzyme to be refined at 2.4 angstrom resolution against x-ray data collected on a hamlin area detector. the structure was refined using the programs profft and x-plor with several model building step interspersed. the final model contains two heavy chains (571 amino acids), two ... | 1996 | 8676383 |