Publications

effect of initial carbon sources on the electrochemical detection of glucose by gluconobacter oxydans.	an electrochemical system consisted of gluconobacter oxydans as a microorganism and 2-hydroxy-1,4-naphthoquinone (hnq) as a mediator has been setup to examine the effect of initial carbon sources on the detection of glucose. catalytic current due to the oxidation of glucose was observed only when both g. oxydans and hnq were present. from amperometric measurements, it was found that the sensitivity strongly depended on the initial carbon sources. the sensitivity was highest for the cells culture ...	2002	12160615
gluconobacter asaii mason and claus 1989 is a junior subjective synonym of gluconobacter cerinus yamada and akita 1984.	five strains received as gluconobacter cerinus and gluconobacter asaii were examined for dna base composition, dna-dna similarity, 16s rrna gene sequences and phenotypic characteristics, including acid production from ethanol, growth on l-arabitol and meso-ribitol and requirement for nicotinic acid. the five strains showed dna base compositions ranging from 54 to 56 mol% g+c. g. cerinus ifo 3267t and iam 1832 and g. asaii ifo 3276t and ifo 3275 showed high levels of dna-dna similarity (70-100%) ...	2002	12361267
continuous production of high-content fructooligosaccharides by a complex cell system.	a complex biocatalyst system with a bioreactor equipped with a microfiltration (mf) module was employed to produce high-content fructooligosaccharides (fos) in a continuous process initiated by a batch process. the system used mycelia of aspergillus japonicus ccrc 93007 or aureobasidium pullulans atcc 9348 with beta-fructofuranosidase activity and gluconobacter oxydans atcc 23771 with glucose dehydrogenase activity. calcium carbonate slurry was used to control ph to 5.5, and gluconic acid in the ...	2002	12467463
productivity improvement in l-sorbose biosynthesis by fedbatch cultivation of gluconobacter oxydans.	the effect of increased (100, 200 and 300 gl(-1)) initial sorbitol concentrations (s0) was investigated in the sorbitol to sorbose bioconversion process. batch cultivations with a s0 of 100, 200 and 300 gl(-1) were completed at 10, 14 and 24 h with a corresponding overall sorbose productivity of 10.1, 14.3 and 12.4 gl(-1) h(-1) respectively. the decrease in sorbose productivity at s0=300 gl(-1) was attributed to the inhibition by sorbitol of culture growth and product formation. in order to elim ...	2002	16233266
manufacture of a beverage from cheese whey using a "tea fungus" fermentation.	kombucha is a sour beverage reported to have potential health effects prepared from the fermentation of black tea and sugar with a "tea fungus", a symbiotic culture of acetic acid bacteria and yeasts. although black tea is the preferred substrate for kombucha fermentation, other beverages have also been tested as substrates with fair results. cheese whey is a by-product with a good amount of fermentable lactose that has been used before in the production of beverages, so the objective of this st ...	2003	17061515
construction of a vector plasmid for use in gluconobacter oxydans.	a host vector system in gluconobacter oxydans was constructed. an acetobacter-escherichia coli shuttle vector was introduced with the efficiency of 10(4) transformants/microg of dna. next, aiming for a self-cloning vector, we found a cryptic plasmid (which we named pag5) of 5648 bp in g. oxydans strain ifo 3171, and sequenced the nucleotides. the plasmid seemed to have only one open reading flame (orf) for a possible replication protein. shuttle vectors of gluconobacter-e. coli were constructed ...	2003	12619700
5-keto-d-gluconate production is catalyzed by a quinoprotein glycerol dehydrogenase, major polyol dehydrogenase, in gluconobacter species.	acetic acid bacteria, especially gluconobacter species, have been known to catalyze the extensive oxidation of sugar alcohols (polyols) such as d-mannitol, glycerol, d-sorbitol, and so on. gluconobacter species also oxidize sugars and sugar acids and uniquely accumulate two different keto-d-gluconates, 2-keto-d-gluconate and 5-keto-d-gluconate, in the culture medium by the oxidation of d-gluconate. however, there are still many controversies regarding their enzyme systems, especially on d-sorbit ...	2003	12676670
membrane-bound d-sorbitol dehydrogenase of gluconobacter suboxydans ifo 3255--enzymatic and genetic characterization.	gluconobacter strains effectively produce l-sorbose from d-sorbitol because of strong activity of the d-sorbitol dehydrogenase (sldh). l-sorbose is one of the important intermediates in the industrial vitamin c production process. two kinds of membrane-bound sldhs, which consist of three subunits, were reportedly found in gluconobacter strains [agric. biol. chem. 46 (1982) 135,fems microbiol. lett. 125 (1995) 45]. we purified a one-subunit-type sldh (80 kda) from the membrane fraction of glucono ...	2003	12686146
cloning of the xylitol dehydrogenase gene from gluconobacter oxydans and improved production of xylitol from d-arabitol.	xylitol dehydrogenase (xdh) was purified from the cytoplasmic fraction of gluconobacter oxydans atcc 621. the purified enzyme reduced d-xylulose to xylitol in the presence of nadh with an optimum ph of around 5.0. based on the determined nh2-terminal amino acid sequence, the gene encoding xdh was cloned, and its identity was confirmed by expression in escherichia coli. the xdh gene encodes a polypeptide composed of 262 amino acid residues, with an estimated molecular mass of 27.8 kda. the deduce ...	2003	12723607
improved selectivity of microbial biosensor using membrane coating. application to the analysis of ethanol during fermentation.	a ferricyanide mediated microbial biosensor for ethanol detection was prepared by surface modification of a glassy carbon electrode. the selectivity of the whole gluconobacter oxydans cell biosensor for ethanol determination was greatly enhanced by the size exclusion effect of a cellulose acetate (ca) membrane. the use of a ca membrane increased the ethanol to glucose sensitivity ratio by a factor of 58.2 and even the ethanol to glycerol sensitivity ratio by a factor of 7.5 compared with the use ...	2003	12788555
glucose oxidation by gluconobacter oxydans: characterization in shaking-flasks, scale-up and optimization of the ph profile.	in this study, the advantage of a novel measuring device for the online determination of oxygen and carbon dioxide transfer rates in shaking-flasks is reported for glucose oxidation by gluconobacter oxydans. in this fermentation process, this device was used for the characterization of the oxidation pattern of different strains. g. oxydans ncimb 8084 forms 2,5-diketogluconate from d-glucose in a multi-stage process via three different membrane-bound dehydrogenases. this strain was chosen for a s ...	2003	12835926
cloning and expression of the gene encoding catalytic subunit of thermostable glucose dehydrogenase from burkholderia cepacia in escherichia coli.	we have cloned a 1620-nucleotide gene encoding the catalytic subunit (alpha subunit) of a thermostable glucose dehydrogenase (gdh) from burkholderia cepacia. the fad binding motif was found in the n-terminal region of the alpha subunit. the deduced primary structure of the alpha subunit showed about 48% identity to the catalytic subunits of sorbitol dehydrogenase (sdh) from gluconobacter oxydans and 2-keto-d-gluconate dehydrogenases (2kgdh) from erwinia herbicola and pantoea citrea. the alpha su ...	2003	12573242
optimization of the microbial synthesis of dihydroxyacetone from glycerol with gluconobacter oxydans.	an optimized repeated-fed-batch fermentation process for the synthesis of dihydroxyacetone (dha) from glycerol utilizing gluconobacter oxydans is presented. cleaning, sterilization, and inoculation procedures could be reduced significantly compared to the conventional fed-batch process. a stringent requirement was that the product concentration was kept below a critical threshold level at all times in order to avoid irreversible product inhibition of the cells. on the basis of experimentally val ...	2003	14598160
design and evaluation of pcr primers for analysis of bacterial populations in wine by denaturing gradient gel electrophoresis.	denaturing gradient gel electrophoresis (dgge) of pcr-amplified ribosomal dna (rdna) is routinely used to compare levels of diversity of microbial communities and to monitor population dynamics. while using pcr-dgge to examine the bacteria in wine fermentations, we noted that several commonly used pcr primers for amplifying bacterial 16s rdna also coamplified yeast, fungal, or plant dna present in samples. unfortunately, amplification of nonbacterial dna can result in a masking of bacterial popu ...	2003	14602643
transaldolase/glucose-6-phosphate isomerase bifunctional enzyme and ribulokinase as factors to increase xylitol production from d-arabitol in gluconobacter oxydans.	xylitol production from d-arabitol by the membrane and soluble fractions of gluconobacter oxydans was investigated. two proteins in the soluble fraction were found to have the ability to increase xylitol production. both of these xylitol-increasing factors were purified, and on the basis of their nh(2)-terminal amino acid sequences the genes encoding both of the factors were cloned. expression of the cloned genes in escherichia coli showed that one of the xylitol-increasing factors is the bifunc ...	2003	14730129
coenzyme specificity of enzymes in the oxidative pentose phosphate pathway of gluconobacter oxydans.	the coenzyme specificity of enzymes in the oxidative pentose phosphate pathway of gluconobacter oxydans was investigated. by investigation of the activities of glucose-6-phosphate dehydrogenase (g6pdh) and 6-phosphogluconate dehydrogenase (6pgdh) in the soluble fraction of g. oxydans, and cloning and expression of genes in escherichia coli, it was found that both g6pdh and 6pgdh have nad/nadp dual coenzyme specificities. it was suggested that the pentose phosphate pathway is responsible for nadh ...	2003	14730146
application of nad-dependent polyol dehydrogenases for enzymatic mannitol/sorbitol production with coenzyme regeneration.	d-mannitol and d-sorbitol were produced enzymatically from d-fructose using nad-dependent polyol dehydrogenases. for the production of d-mannitol the leuconostoc mesenteroides mannitol dehydrogenase could be used. gluconobacter oxydans cell extract contained however both mannitol and sorbitol dehydrogenase. when this cell extract was used, the reduction of d-fructose resulted in a mixture of d-sorbitol and d-mannitol. to determine the optimal bioconversion conditions the polyol dehydrogenases we ...	2003	15296174
gluconobacter thailandicus sp. nov., an acetic acid bacterium in the alpha-proteobacteria.	four strains of acetic acid bacteria were isolated from flowers collected in thailand. in phylogenetic trees based on 16s rrna gene sequences and 16s-23s rdna internal transcribed spacer (its) region sequences, the four isolates were located in the lineage of the genus gluconobacter and constituted a separate cluster from the known gluconobacter species, gluconobacter oxydans, gluconobacter cerinus, and gluconobacter frateurii. in addition, the isolates were distinguished from the known species ...	2004	15486825
quinate oxidation in gluconobacter oxydans ifo3244: purification and characterization of quinoprotein quinate dehydrogenase.	quinoprotein quinate dehydrogenase (qdh) is a membrane-bound enzyme containing pyrroloquinoline quinone (pqq) as the prosthetic group. qdh in gluconobacter oxydans ifo3244 was found to be inducible by quinate and it is not constitutively expressed in the absence of quinate. the purification of holo-form of qdh to nearly homogeneity was achieved. the purified qdh appears to have two subunits of approximately 65 and 21 kda, which could be the result of proteolysis of single polypeptide. kinetic an ...	2004	15598527
a gluconobacter oxydans mutant converting glucose almost quantitatively to 5-keto-d-gluconic acid.	gluconobacter oxydans converts glucose to gluconic acid and subsequently to 2-keto-d-gluconic acid (2-kga) and 5-keto-d-gluconic acid (5-kga) by membrane-bound periplasmic pyrroloquinoline quinone-dependent and flavin-dependent dehydrogenases. the product pattern obtained with several strains differed significantly. to increase the production of 5-kga, which can be converted to industrially important l-(+)-tartaric acid, growth parameters were optimized. whereas resting cells of g. oxydans atcc ...	2004	15735967
application of molecular methods for the differentiation of acetic acid bacteria in a red wine fermentation.	to apply rapid and reliable molecular techniques for typing acetic acid bacteria and studying their population dynamics during wine-making processes.	2004	15012825
identification of strains assigned to the genus gluconobacter asai 1935 based on the sequence and the restriction analyses of the 16s-23s rdna internal transcribed spacer regions.	thirteen reference strains, including the type strains of the type species of the genus gluconobacter, gluconobacter oxydans (nbrc 14819t), gluconobacter cerinus (nbrc 3267t), and gluconobacter frateurii (ifo 3264t) were examined for their species identification based on the sequence and the restriction analyses of the 16s-23s rdna internal transcribed spacer (its) regions. a phylogenetic tree constructed by the neighbor-joining method represented three clusters corresponding respectively to the ...	2004	15057706
mutation of gluconobacter oxydans and bacillus megaterium in a two-step process of l-ascorbic acid manufacture by ion beam.	to increase the transformation rate of l-sorbose to 2-keto-l-gulonic (2-klg) acid in a two-step process of l-ascrobic acid manufacture by ion beam.	2004	15139924
characterization of bacterial diversity in pulque, a traditional mexican alcoholic fermented beverage, as determined by 16s rdna analysis.	the bacterial diversity in pulque, a traditional mexican alcoholic fermented beverage, was studied in 16s rdna clone libraries from three pulque samples. sequenced clones identified as lactobacillus acidophilus, lactobacillus strain asf360, l. kefir, l. acetotolerans, l. hilgardii, l. plantarum, leuconostoc pseudomesenteroides, microbacterium arborescens, flavobacterium johnsoniae, acetobacter pomorium, gluconobacter oxydans, and hafnia alvei, were detected for the first time in pulque. identity ...	2004	15183874
biotransformation of glucose to 5-keto-d-gluconic acid by recombinant gluconobacter oxydans dsm 2343.	for the conversion of glucose to 5-keto-d-gluconate (5-kga), a precursor of the industrially important l-(+)-tartaric acid, gluconobacter strains were genetically engineered. in order to increase 5-kga formation, a plasmid-encoded copy of the gene encoding the gluconate:nadp-5 oxidoreductase (gno) was overexpressed in g. oxydans strain dsm 2434. this enzyme is involved in the nonphosphorylative ketogenic oxidation of glucose and oxidizes gluconate to 5-kga. as the 5-kga reductase activity depend ...	2004	14564486
purification and characterization of inducible cephalexin synthesizing enzyme in gluconobacter oxydans.	cephalexin synthesizing enzyme (cse) of gluconobacter oxydans atcc 9324 was purified up to about 940-fold at a yield of 12%. cse biosynthesis in g. oxydans was found inducible in the presence of d-phenylglycine but not its substrate phenylglycine methyl ester. the purified enzyme was shown homogeneous on sds-page and exhibited a specific activity of 440 u per mg protein. the apparent molecular mass of the native enzyme was estimated to be 70 kda over a superdex 200 gel filtration column and 68 k ...	2005	15784972
gluconobacter oxydans nad-dependent, d-fructose reducing, polyol dehydrogenases activity: screening, medium optimisation and application for enzymatic polyol production.	gluconobacter oxydans lmg 1489 was selected as the best strain for nad(p)-dependent polyol dehydrogenase production. the highest enzyme activities were obtained when this strain was cultivated on a medium consisting of 30 g glycerol l(-1), 7.2 g peptone l(-1) and 1.8 g yeast extract l(-1). two d-fructose reducing, nad-dependent intracellular enzymes were present in the g. oxydans cell-free extract: sorbitol dehydrogenase, and mannitol dehydrogenase. substrate reduction occurred optimally at a lo ...	2005	15834790
microbial dextran-hydrolyzing enzymes: fundamentals and applications.	dextran is a chemically and physically complex polymer, breakdown of which is carried out by a variety of endo- and exodextranases. enzymes in many groups can be classified as dextranases according to function: such enzymes include dextranhydrolases, glucodextranases, exoisomaltohydrolases, exoisomaltotriohydrases, and branched-dextran exo-1,2-alpha-glucosidases. cycloisomalto-oligosaccharide glucanotransferase does not formally belong to the dextranases even though its side reaction produces hy ...	2005	15944458
complete genome sequence of the acetic acid bacterium gluconobacter oxydans.	gluconobacter oxydans is unsurpassed by other organisms in its ability to incompletely oxidize a great variety of carbohydrates, alcohols and related compounds. furthermore, the organism is used for several biotechnological processes, such as vitamin c production. to further our understanding of its overall metabolism, we sequenced the complete genome of g. oxydans 621h. the chromosome consists of 2,702,173 base pairs and contains 2,432 open reading frames. in addition, five plasmids were identi ...	2005	15665824
dextran dextrinase and dextran of gluconobacter oxydans.	certain strains of gluconobacter oxydans have been known since the 1940s to produce the enzyme dextran dextrinase (ddase; ec2.4.1.2)-a transglucosidase converting maltodextrins into (oligo)dextran. the enzyme catalyses the transfer of an alpha1,4 linked glucosyl unit from a donor to an acceptor molecule, forming an alpha1,6 linkage: consecutive glucosyl transfers result in the formation of high molecular weight dextran from maltodextrins. in the early 1990s, the group of k. yamamoto in japan rev ...	2005	15973532
study of the inhibitory effect of the product dihydroxyacetone on gluconobacter oxydans in a semi-continuous two-stage repeated-fed-batch process.	the influence of the product inhibition by dihydroxyacetone (dha) on gluconobacter oxydans for a novel semi-continuous two-stage repeated-fed-batch process was examined quantitatively. it was shown that the culture was able to grow up to a dha concentration of 80 kg m(-3) without any influence of product inhibition. the regeneration capability of the reversibly product inhibited culture from a laboratory-scale bioreactor system was observed up to a dha concentration of about 160 kg m(-3). at hig ...	2005	16044287
molecular cloning and functional expression of d-arabitol dehydrogenase gene from gluconobacter oxydans in escherichia coli.	a nadp-dependent d-arabitol dehydrogenase gene was cloned from gluconobacter oxydans cgmcc 1.110 and functionally expressed in escherichia coli. with d-arabitol as sole carbon source, e. coli transformants grew rapidly in minimal medium, and produced d-xylulose. the enzymatic properties of the 29kda enzyme were documented. the dna sequence surrounding the gene suggested that it is part of an operon with several components of a sugar alcohol transporter system, and the d-arabitol dehydrogenase ge ...	2005	16165327
production of l-ribulose by dehydrogenation of ribitol with gluconobacter oxydans.		2005	16366284
differential real-time pcr assay for enumeration of lactic acid bacteria in wine.	oenococcus oeni is often employed to perform the malolactic fermentation in wine production, while nonoenococcal lactic acid bacteria often contribute to wine spoilage. two real-time pcr assays were developed to enumerate the total, and nonoenococcal, lactic acid bacterial populations in wine. used together, these assays can assess the spoilage risk of juice or wine from lactic acid bacteria.	2005	16332898
health considerations regarding horizontal transfer of microbial transgenes present in genetically modified crops.	the potential effects of horizontal gene transfer on human health are an important item in the safety assessment of genetically modified organisms. horizontal gene transfer from genetically modified crops to gut microflora most likely occurs with transgenes of microbial origin. the characteristics of microbial transgenes other than antibiotic-resistance genes in market-approved genetically modified crops are reviewed. these characteristics include the microbial source, natural function, function ...	2005	16489267
micheck: a web tool for fast checking of syntactic annotations of bacterial genomes.	the annotation of newly sequenced bacterial genomes begins with running several automatic analysis methods, with major emphasis on the identification of protein-coding genes. dna sequences are heterogeneous in local nucleotide composition and this leads sometimes to sequences being annotated as authentic genes when they are not protein-coding genes or are true but uncharacterized protein-coding genes. this first annotation step is generally followed by an expert manual annotation of the predicte ...	2005	15980515
biofilm reactors for industrial bioconversion processes: employing potential of enhanced reaction rates.	this article describes the use of biofilm reactors for the production of various chemicals by fermentation and wastewater treatment. biofilm formation is a natural process where microbial cells attach to the support (adsorbent) or form flocs/aggregates (also called granules) without use of chemicals and form thick layers of cells known as "biofilms." as a result of biofilm formation, cell densities in the reactor increase and cell concentrations as high as 74 gl(-1) can be achieved. the reactor ...	2005	16122390
a database of bacterial lipoproteins (dolop) with functional assignments to predicted lipoproteins.	lipid modification of the n-terminal cys residue (n-acyl-s-diacylglyceryl-cys) has been found to be an essential, ubiquitous, and unique bacterial posttranslational modification. such a modification allows anchoring of even highly hydrophilic proteins to the membrane which carry out a variety of functions important for bacteria, including pathogenesis. hence, being able to identify such proteins is of great value. to this end, we have created a comprehensive database of bacterial lipoproteins, c ...	2006	16585737
the prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains.	ubiquitin (ub)-mediated signaling is one of the hallmarks of all eukaryotes. prokaryotic homologs of ub (this and moad) and e1 ligases have been studied in relation to sulfur incorporation reactions in thiamine and molybdenum/tungsten cofactor biosynthesis. however, there is no evidence for entire protein modification systems with ub-like proteins and deconjugation by deubiquitinating enzymes in prokaryotes. hence, the evolutionary assembly of the eukaryotic ub-signaling apparatus remains unclea ...	2006	16859499
structure-guided engineering of xylitol dehydrogenase cosubstrate specificity.	xylitol dehydrogenase (xdh) is one of several enzymes responsible for assimilating xylose into eukaryotic metabolism and is useful for fermentation of xylose contained in agricultural byproducts to produce ethanol. for efficient xylose utilization at high flux rates, cosubstrates should be recycled between the nad+-specific xdh and the nadph-preferring xylose reductase, another enzyme in the pathway. to understand and alter the cosubstrate specificity of xdh, we determined the crystal structure ...	2006	16531240
evolution of the yellow/major royal jelly protein family and the emergence of social behavior in honey bees.	the genomic architecture underlying the evolution of insect social behavior is largely a mystery. eusociality, defined by overlapping generations, parental brood care, and reproductive division of labor, has most commonly evolved in the hymenopteran insects, including the honey bee apis mellifera. in this species, the major royal jelly protein (mrjp) family is required for all major aspects of eusocial behavior. here, using data obtained from the a. mellifera genome sequencing project, we demons ...	2006	17065613
real-time quantitative pcr (qpcr) and reverse transcription-qpcr for detection and enumeration of total yeasts in wine.	real-time pcr, or quantitative pcr (qpcr), has been developed to rapidly detect and quantify the total number of yeasts in wine without culturing. universal yeast primers were designed from the variable d1/d2 domains of the 26s rrna gene. these primers showed good specificity with all the wine yeasts tested, and they did not amplify the most representative wine species of acetic acid bacteria and lactic acid bacteria. numerous standard curves were constructed with different strains and species g ...	2006	17088381
purification and properties of nadp-dependent shikimate dehydrogenase from gluconobacter oxydans ifo 3244 and its application to enzymatic shikimate production.	nadp-dependent shikimate dehydrogenae (skdh, ec 1.1.1.25) was purified from gluconobacter oxydans ifo 3244. skdh showed a single protein band on native-page accompanying enzyme activity. it required nadp exclusively and catalyzed only the shuttle reaction between shikimate and 3-dehydroshikimate. the optimum ph for shikimate oxidation and 3-dehydroshikimate reduction was found at ph 10 and 7 respectively. skdh proved to be a useful catalyst for shikimate production from 3-dehydroshikimate.	2006	17090918
function and evolution of plasmid-borne genes for pyrimidine biosynthesis in borrelia spp.	the thyx gene for thymidylate synthase of the lyme borreliosis (lb) agent borrelia burgdorferi is located in a 54-kb linear plasmid. in the present study, we identified an orthologous thymidylate synthase gene in the relapsing fever (rf) agent borrelia hermsii, located it in a 180-kb linear plasmid, and demonstrated its expression. the functions of the b. hermsii and b. burgdorferi thyx gene products were evaluated both in vivo, by complementation of a thymidylate synthase-deficient escherichia ...	2006	16428394
asymmetric oxidation by gluconobacter oxydans.	asymmetric oxidation is of great value and a major interest in both research and application. this review focuses on asymmetric oxidation of organic compounds by gluconobacter oxydans. the microbe can be used for bioproduction of several kinds of important chiral compounds, such as vitamin c, 6-(2-hydroxyethyl)amino-6-deoxy-alpha-l-sorbofuranose, (s)-2-methylbutanoic acid, (r)-2-hydroxy-propionic acid and 5-keto-d-gluconic acid. characteristics of the bacteria and research progress on the enanti ...	2006	16432743
pyrroloquinoline quinone-dependent dehydrogenases from ketogulonicigenium vulgare catalyze the direct conversion of l-sorbosone to l-ascorbic acid.	a novel enzyme, l-sorbosone dehydrogenase 1 (sndh1), which directly converts l-sorbosone to l-ascorbic acid (l-aa), was isolated from ketogulonicigenium vulgare dsm 4025 and characterized. this enzyme was a homooligomer of 75-kda subunits containing pyrroloquinoline quinone (pqq) and heme c as the prosthetic groups. two isozymes of sndh, sndh2 consisting of 75-kda and 55-kda subunits and sndh3 consisting of 55-kda subunits, were also purified from the bacterium. all of the sndhs produced l-aa, a ...	2006	16461703
enhanced benzaldehyde tolerance in zymomonas mobilis biofilms and the potential of biofilm applications in fine-chemical production.	biotransformation plays an increasingly important role in the industrial production of fine chemicals due to its high product specificity and low energy requirement. one challenge in biotransformation is the toxicity of substrates and/or products to biocatalytic microorganisms and enzymes. biofilms are known for their enhanced tolerance of hostile environments compared to planktonic free-living cells. zymomonas mobilis was used in this study as a model organism to examine the potential of surfac ...	2006	16461720
tfam detects co-evolution of trna identity rules with lateral transfer of histidyl-trna synthetase.	we present tfam, an automated, statistical method to classify the identity of trnas. tfam, currently optimized for bacteria, classifies initiator trnas and predicts the charging identity of both typical and atypical trnas such as suppressors with high confidence. we show statistical evidence for extensive variation in trna identity determinants among bacterial genomes due to variation in overall tdna base content. with tfam we have detected the first case of eukaryotic-like trna identity rules i ...	2006	16473847
in vitro fermentation of mixed linkage glucooligosaccharides produced by gluconobacter oxydans ncimb 4943 by the human colonic microflora.	the aim of this study was to develop selectively fermented (prebiotic) carbohydrate molecules which would also result in the generation of butyric acid. gluco-oligosaccharides produced by gluconobacter oxydans ncimb 4943 from various types of maltodextrins were evaluated for their fermentation by mixed cultures of human colonic microflora. the selectivity of growth of desirable bacteria (bifidobacteria, lactobacilli) was studied in stirred ph-controlled (6.8) batch cultures. bacterial population ...	2006	16570694
in vitro three-stage continuous fermentation of gluco-oligosaccharides produced by gluconobacter oxydans ncimb 4943 by the human colonic microflora.	gluco-oligosaccharides produced by gluconobacter oxydans ncimb 4943 from maltodextrin as the source, were evaluated for their fermentability by the human colonic microflora. the selectivity of growth of desirable bacteria in the human colon was studied in a three-stage continuous model of the human large intestine. populations of bacteria, and their fluctuations as a response to the fermentation, were enumerated using fluorescent in situ hybridization (fish). the gluco-oligosaccharides resulted ...	2006	16570695
a novel bacterium associated with lymphadenitis in a patient with chronic granulomatous disease.	chronic granulomatous disease (cgd) is a rare inherited disease of the phagocyte nadph oxidase system causing defective production of toxic oxygen metabolites, impaired bacterial and fungal killing, and recurrent life-threatening infections. we identified a novel gram-negative rod in excised lymph nodes from a patient with cgd. gram-negative rods grew on charcoal-yeast extract, but conventional tests could not identify it. the best 50 matches of the 16s rrna (using blast) were all members of the ...	2006	16617373
[use of nmr spectroscopy in studies of sorbitol and glucose transformation by gluconobacter oxydans].	nmr spectroscopy was applied for studying the products of glucose and sorbitol oxidation by cells of gluconobacter oxydans. an analysis of 1h nmr spectra showed that the transformation of glucose results in the formation of diketogluconic acid, and sorbitol is oxidized to sorbose. in the 32p nmr spectra, only a signal of inorganic phosphate was detected, which accumulated in the medium as a result of cell lysis.	2006	16637338
dehydrogenation of ribitol with gluconobacter oxydans: production and stability of l-ribulose.	l-ribulose is an important chiral lead molecule used for the synthesis of, among others, l-ribose, a high-value rare sugar used in the preparation of antiviral drugs. these drugs--nucleoside-analogues--gain importance in the treatment of severe viral diseases, like those caused by the hiv or hepatitis virus. in this study, factors that may have an impact on l-ribulose production with gluconobacter oxydans and on the stability of l-ribulose were investigated. a bioconversion-type process, using w ...	2006	16650498
an outer membrane enzyme encoded by salmonella typhimurium lpxr that removes the 3'-acyloxyacyl moiety of lipid a.	the salmonella and related bacteria modify the structure of the lipid a portion of their lipopolysaccharide in response to environmental stimuli. some lipid a modifications are required for virulence and resistance to cationic antimicrobial peptides. we now demonstrate that membranes of salmonella typhimurium contain a novel hydrolase that removes the 3'-acyloxyacyl residue of lipid a in the presence of 5 mm ca2+. we have identified the gene encoding the s. typhimurium lipid a 3'-o-deacylase, de ...	2006	16704973
production of xylitol from d-xylose by a xylitol dehydrogenase gene-disrupted mutant of candida tropicalis.	xylitol dehydrogenase (xdh) is one of the key enzymes in d-xylose metabolism, catalyzing the oxidation of xylitol to d-xylulose. two copies of the xyl2 gene encoding xdh in the diploid yeast candida tropicalis were sequentially disrupted using the ura-blasting method. the xyl2-disrupted mutant, bsxdh-3, did not grow on a minimal medium containing d-xylose as a sole carbon source. an enzyme assay experiment indicated that bsxdh-3 lost apparently all xdh activity. xylitol production by bsxdh-3 was ...	2006	16751533
a model system for increasing the intensity of whole-cell biocatalysis: investigation of the rate of oxidation of d-sorbitol to l-sorbose by thin bi-layer latex coatings of non-growing gluconobacter oxydans.	we developed a novel <50-microm thick nano-porous bi-layer latex coating for preserving gluconobacter oxydans, a strict aerobe, as a whole cell biocatalyst. g. oxydans was entrapped in an acrylate/vinyl acetate co-polymer matrix (t (g) approximately 10 degrees c) and cast into 12.7-mm diameter patch coatings (cellcoat) containing approximately 10(9) cfu covered by a nano-porous topcoat. the oxidation of d-sorbitol to l-sorbose was used to investigate the coating catalytic properties. intrinsic k ...	2006	16804947
high-yield 5-keto-d-gluconic acid formation is mediated by soluble and membrane-bound gluconate-5-dehydrogenases of gluconobacter oxydans.	gluconobacter oxydans dsm 2343 is known to catalyze the oxidation of glucose to gluconic acid, and subsequently, to 2-keto-d-gluconic acid (2-kga) and 5-keto-d-gluconic acid (5-kga), by membrane-bound and soluble dehydrogenases. in g. oxydans mf1, in which the membrane-bound gluconate-2-dehydrogenase complex was inactivated, formation of the undesired 2-kga was absent. this mutant strain uniquely accumulates high amounts of 5-kga in the culture medium. to increase the production rate of 5-kga, w ...	2006	16820953
engineering escherichia coli for xylitol production from glucose-xylose mixtures.	the range of value-added chemicals produced by escherichia coli from simple sugars has been expanded to include xylitol. this was accomplished by screening the in vivo activity of a number of heterologous xylitol-producing enzymes. xylose reductases from candida boidinii (cbxr), candida tenuis (ctxr), pichia stipitis (psxr), and saccharmoyces cerivisiae (scxr), and xylitol dehydrogenases from gluconobacter oxydans (goxdh) and pichia stipitis (psxdh) were all functional in e. coli to varying exte ...	2006	16838379
modification of the membrane-bound glucose oxidation system in gluconobacter oxydans significantly increases gluconate and 5-keto-d-gluconic acid accumulation.	gluconobacter oxydans dsm 2343 (atcc 621h)catalyzes the oxidation of glucose to gluconic acid and subsequently to 5-keto-d-gluconic acid (5-kga), a precursor of the industrially important l-(+)-tartaric acid. to further increase 5-kga production in g. oxydans, the mutant strain mf1 was used. in this strain the membrane-bound gluconate-2-dehydrogenase activity, responsible for formation of the undesired by-product 2-keto-d-gluconic acid, is disrupted. therefore, high amounts of 5-kga accumulate i ...	2006	16892291
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
complete nucleotide sequence of an exogenously isolated plasmid, plb1, involved in gamma-hexachlorocyclohexane degradation.	the alpha-proteobacterial strain sphingobium japonicum ut26 utilizes a highly chlorinated pesticide, gamma-hexachlorocyclohexane (gamma-hch), as a sole source of carbon and energy, and haloalkane dehalogenase linb catalyzes the second step of gamma-hch degradation in ut26. functional complementation of a linb mutant of ut26, ut26db, was performed by the exogenous plasmid isolation technique using hch-contaminated soil, leading to our successful identification of a plasmid, plb1, carrying the lin ...	2006	16963556
high precision multi-genome scale reannotation of enzyme function by eficaz.	the functional annotation of most genes in newly sequenced genomes is inferred from similarity to previously characterized sequences, an annotation strategy that often leads to erroneous assignments. we have performed a reannotation of 245 genomes using an updated version of eficaz, a highly precise method for enzyme function prediction.	2006	17166279
the sphingomonas plasmid pcar3 is involved in complete mineralization of carbazole.	we determined the complete 254,797-bp nucleotide sequence of the plasmid pcar3, a carbazole-degradative plasmid from sphingomonas sp. strain ka1. a region of about 65 kb involved in replication and conjugative transfer showed similarity to a region of plasmid pnl1 isolated from the aromatic-degrading novosphingobium aromaticivorans strain f199. the presence of many insertion sequences, transposons, repeat sequences, and their remnants suggest plasticity of this plasmid in genetic structure. alth ...	2007	17172338
the sphingomonas plasmid pcar3 is involved in complete mineralization of carbazole.	we determined the complete 254,797-bp nucleotide sequence of the plasmid pcar3, a carbazole-degradative plasmid from sphingomonas sp. strain ka1. a region of about 65 kb involved in replication and conjugative transfer showed similarity to a region of plasmid pnl1 isolated from the aromatic-degrading novosphingobium aromaticivorans strain f199. the presence of many insertion sequences, transposons, repeat sequences, and their remnants suggest plasticity of this plasmid in genetic structure. alth ...	2007	17172338
a novel ferredoxin-dependent glutamate synthase from the hydrogen-oxidizing chemoautotrophic bacterium hydrogenobacter thermophilus tk-6.	glutamate synthases are classified according to their specificities for electron donors. ferredoxin-dependent glutamate synthases had been found only in plants and cyanobacteria, whereas many bacteria have nadph-dependent glutamate synthases. in this study, hydrogenobacter thermophilus, a hydrogen-oxidizing chemoautotrophic bacterium, was shown to possess a ferredoxin-dependent glutamate synthase like those of phototrophs. this is the first observation, to our knowledge, of a ferredoxin-dependen ...	2007	17237175
identification of membrane-bound quinoprotein inositol dehydrogenase in gluconobacter oxydans atcc 621h.	the gox1857 gene, which encodes a putative membrane-bound pyrroloquinoline quinone (pqq)-dependent dehydrogenase in gluconobacter oxydans atcc 621h, was characterized. gox1857 was disrupted and the oxidizing potential of the resulting mutant strain was compared to that of the wild-type. in contrast to the wild-type, the mutant was unable to grow with myo-inositol as the sole energy source and did not show any myo-inositol dehydrogenase activity in vitro, indicating that gox1857 encodes an inosit ...	2007	17259621
application of molecular methods for analysing the distribution and diversity of acetic acid bacteria in chilean vineyards.	the presence of acetic acid bacteria populations on grape surfaces from several chilean valleys is reported. the bacteria were analysed at both the species and the strain level by molecular methods such as rflp-pcr 16s rrna gene, rflp-pcr its 16s-23s rrna gene regions and arbitrary primed (ap) pcr. our results show that there are limited numbers of species of acetic acid bacteria in the grapes and that there is a need for an enrichment medium before plating to recover the individual colonies. in ...	2007	17289199
genome analysis of dna repair genes in the alpha proteobacterium caulobacter crescentus.	the integrity of dna molecules is fundamental for maintaining life. the dna repair proteins protect organisms against genetic damage, by removal of dna lesions or helping to tolerate them. dna repair genes are best known from the gamma-proteobacterium escherichia coli, which is the most understood bacterial model. however, genome sequencing raises questions regarding uniformity and ubiquity of these dna repair genes and pathways, reinforcing the need for identifying genes and proteins, which may ...	2007	17352799
a novel microbial biosensor based on cells of gluconobacter oxydans for the selective determination of 1,3-propanediol in the presence of glycerol and its application to bioprocess monitoring.	novel and selective microbial amperometric biosensors that use gluconobacter oxydans cells to monitor the bacterial bioconversion of glycerol (gly) to 1,3-propanediol (1,3-pd) are described. two different mediators, ferricyanide and flexible polyvinylimidazole osmium functionalized polymer (os-polymer), were employed to prepare two different microbial biosensors, both of which gave high detection performance. the good operational stabilities of both types of biosensor were underlined by the abil ...	2007	17393157
sampling for metabolome analysis of microorganisms.	in the present work we investigated the most commonly applied methods used for sampling of microorganisms in the field of metabolomics in order to unravel potential sources of error previously ignored but of utmost importance for accurate metabolome analysis. to broaden the significance of our study, we investigated different gram-negative and gram-positive bacteria, i.e., bacillus subtilis, corynebacterium glutamicum, escherichia coli, gluconobacter oxydans, pseudomonas putida, and zymononas mo ...	2007	17411014
production of gluconobacter oxydans cells from low-cost culture medium for conversion of glycerol to dihydroxyacetone.	gluconobacter oxydans could be immobilized as a biocatalyst for the conversion of glycerol to dihydroxyacetone. to reduce the production cost, the cells were produced from agricultural byproducts. corn meal hydrolysate and corn steep liquor were employed to replace of sorbitol and yeast extract as medium for g. oxydans cell production. the optimal medium contained 80 g/l reducing sugar, 25 g/l corn steep liquor, and 10 g/l glycerol. the cell mass was about 4.22 g/l and the glycerol dehydrogenase ...	2007	17454822
l-sorbose reductase and its transcriptional regulator involved in l-sorbose utilization of gluconobacter frateurii.	upstream of the gene for flavin adenine dinucleotide (fad)-dependent d-sorbitol dehydrogenase (sldh), sldslc, a putative transcriptional regulator was found in gluconobacter frateurii thd32 (nbrc 101656). in this study, the whole sbor gene and the adjacent gene, sboa, were cloned and analyzed. sbor mutation did not affect fad-sldh activity in the membrane fractions. the sboa enzyme expressed and purified from an escherichia coli transformant showed nadph-dependent l-sorbose reductase (nadph-sr) ...	2007	17468249
biotransformation of glycerol to dihydroxyacetone by recombinant gluconobacter oxydans dsm 2343.	the genus gluconobacter is well known for its rapid and incomplete oxidation of a wide range of substrates. therefore, gluconobacter oxydans especially is used for several biotechnological applications, e.g., the efficient oxidation of glycerol to dihydroxyacetone (dha). for this reaction, g. oxydans is equipped with a membrane-bound glycerol dehydrogenase that is also described to oxidize sorbitol, gluconate, and arabitol. here, we demonstrated the impact of sldab overexpression on glycerol oxi ...	2007	17497148
purification and properties of nad(p)-independent polyol dehydrogenase complex from the plasma membrane of gluconobacter oxydans.	gluconobacter oxydans rapidly oxidizes many different polyhydroxy alcohols (polyols). polyol oxidations are catalyzed by constitutively synthesized membrane-bound dehydrogenases directly linked to the electron transport chain. a polyol-oxidizing enzyme was isolated from the membranes of g. oxydans and tested for its ability to oxidize various substrates. the enzyme was composed of three subunits: a 67 kda catalytic unit, a 46 kda c-type cytochrome, and a 15 kda subunit. the enzyme oxidized compo ...	2007	17612605
overproduction and characterization of two distinct aldehyde-oxidizing enzymes from gluconobacter oxydans 621h.	the gluconobacter oxydans 621h genome contains two genes (gox1122 and gox0499) that encode putative cytosolic nad(p)-dependent aldehyde dehydrogenases. each gene was expressed in escherichia coli, and the recombinant enzymes were purified and characterized. the native protein gox1122 exhibited an apparent molecular mass of 50.1 kda, and the subunit mass was 50.5 kda, indicating a monomeric structure of the native enzyme. the preferred substrates were acetaldehyde and nadp. the enzyme also oxidiz ...	2007	17693722
membrane-bound, 2-keto-d-gluconate-yielding d-gluconate dehydrogenase from "gluconobacter dioxyacetonicus" ifo 3271: molecular properties and gene disruption.	most gluconobacter species produce and accumulate 2-keto-d-gluconate (2kga) and 5kga simultaneously from d-glucose via ga in culture medium. 2kga is produced by membrane-bound flavin adenine dinucleotide-containing ga 2-dehydrogenase (fad-gadh). fad-gadh was purified from "gluconobacter dioxyacetonicus" ifo 3271, and n-terminal sequences of the three subunits were analyzed. pcr primers were designed from the n-terminal sequences, and part of the fad-gadh genes was cloned as a pcr product. using ...	2007	17720837
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
the genus gluconobacter oxydans: comprehensive overview of biochemistry and biotechnological applications.	the genus gluconobacter comprises some of the most frequently used microorganisms when it comes to biotechnological applications. not only has it been involved in "historical" production processes, such as vinegar production, but in the last decades many bioconversion routes for special and rare sugars involving gluconobacter have been developed. among the most recent are the biotransformations involved in the production of l-ribose and miglitol, both very promising pharmaceutical lead molecules ...	2007	17849259
metabolic engineering of lactobacillus plantarum for production of l-ribulose.	l-ribulose is a rare and expensive sugar that can be used as a precursor for the production of other rare sugars of high market value such as l-ribose. in this work we describe a production process for l-ribulose using l-arabinose, a common component of polymers of lignocellulosic materials, as the starting material. a ribulokinase-deficient mutant of the heterofermentative lactic acid bacterium lactobacillus plantarum ncimb8826 was constructed. expression of araa, which encodes the critical enz ...	2007	17873078
preparation of enzymes required for enzymatic quantification of 5-keto-d-gluconate and 2-keto-d-gluconate.	for easy measurement of 5-keto d-gluconate (5kga) and 2-keto d-gluconate (2kga), two enzymes, 5kga reductase (5kgr) and 2kga reductase (2kgr) are useful. the gene for 5kgr has been reported, and a corresponding gene was found in the genome of gluconobacter oxydans 621h and was identified as gox2187. on the other hand, the gene for 2kgr was identified in this study as gox0417 from the n-terminal amino acid sequence of the partially purified enzyme. several plasmids were constructed to express gox ...	2007	17928715
the complete genome sequence of roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism.	purple aerobic anoxygenic phototrophs (aaps) are the only organisms known to capture light energy to enhance growth only in the presence of oxygen but do not produce oxygen. the highly adaptive aaps compose more than 10% of the microbial community in some euphotic upper ocean waters and are potentially major contributors to the fixation of the greenhouse gas co2. we present the complete genomic sequence and feature analysis of the aap roseobacter denitrificans, which reveal clues to its physiolo ...	2007	17098896
the complete genome sequence of roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism.	purple aerobic anoxygenic phototrophs (aaps) are the only organisms known to capture light energy to enhance growth only in the presence of oxygen but do not produce oxygen. the highly adaptive aaps compose more than 10% of the microbial community in some euphotic upper ocean waters and are potentially major contributors to the fixation of the greenhouse gas co2. we present the complete genomic sequence and feature analysis of the aap roseobacter denitrificans, which reveal clues to its physiolo ...	2007	17098896
biotransformation of patulin by gluconobacter oxydans.	a bacterium isolated from patulin-contaminated apples was capable of degrading patulin to a less-toxic compound, ascladiol. the bacterium was identified as gluconobacter oxydans by 16s rrna gene sequencing, whereas ascladiol was identified by liquid chromatography-tandem mass spectrometry and proton and carbon nuclear magnetic resonance. degradation of up to 96% of patulin was observed in apple juices containing up to 800 microg/ml of patulin and incubated with g. oxydans.	2007	17114325
biotransformation of patulin by gluconobacter oxydans.	a bacterium isolated from patulin-contaminated apples was capable of degrading patulin to a less-toxic compound, ascladiol. the bacterium was identified as gluconobacter oxydans by 16s rrna gene sequencing, whereas ascladiol was identified by liquid chromatography-tandem mass spectrometry and proton and carbon nuclear magnetic resonance. degradation of up to 96% of patulin was observed in apple juices containing up to 800 microg/ml of patulin and incubated with g. oxydans.	2007	17114325
repeated use of immobilized gluconobacter oxydans cells for conversion of glycerol to dihydroxyacetone.	dihydroxyacetone (dha) is of great interest in the fine chemical and pharmaceutical industry; therefore, the discovery of suitable biocatalysts for the efficient production of it is very necessary. in the experiment, gluconobacter oxydans was immobilized in polyvinyl alcohol (pva). various parameters of the immobilized cells were investigated. the results have shown that the optimal conversion conditions by the immobilized cells were at 30 degrees c and ph 6.0. the immobilized cells remained ver ...	2007	17134984
denoising inferred functional association networks obtained by gene fusion analysis.	gene fusion detection - also known as the 'rosetta stone' method - involves the identification of fused composite genes in a set of reference genomes, which indicates potential interactions between its un-fused counterpart genes in query genomes. the precision of this method typically improves with an ever-increasing number of reference genomes.	2007	18081932
use of cyanobacterial gas vesicles as oxygen carriers in cell culture.	the gas vesicles isolated from the cells of filamentous cyanobacterium anabaena flos-aquae were treated and sterilized with glutaraldehyde and then evaluated for their effectiveness as gas carriers in cell culture. anchorage-dependent vero cells were grown in a packed bed of microcarrier beads under the perfusion of dulbecco's modified eagle's medium with 1% serum. the culture medium supplemented with 1.8% (v/v) gas vesicles was found to support a 30% higher maximum glucose utilization rate than ...	2007	19002872
use of cyanobacterial gas vesicles as oxygen carriers in cell culture.	the gas vesicles isolated from the cells of filamentous cyanobacterium anabaena flos-aquae were treated and sterilized with glutaraldehyde and then evaluated for their effectiveness as gas carriers in cell culture. anchorage-dependent vero cells were grown in a packed bed of microcarrier beads under the perfusion of dulbecco's modified eagle's medium with 1% serum. the culture medium supplemented with 1.8% (v/v) gas vesicles was found to support a 30% higher maximum glucose utilization rate than ...	2007	19002872
mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach.	selenocysteine and pyrrolysine are the 21st and 22nd amino acids, which are genetically encoded by stop codons. since a number of microbial genomes have been completely sequenced to date, it is tempting to ask whether the 23rd amino acid is left undiscovered in these genomes. recently, a computational study addressed this question and reported that no trna gene for unknown amino acid was found in genome sequences available. however, performance of the trna prediction program on an unknown trna f ...	2007	17597547
transcriptional regulatory network discovery via multiple method integration: application to e. coli k12.	transcriptional regulatory network (trn) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete trns. we develop a methodology, trnd, that integrates a preliminary trn, microarray data, gene ontology and phylogenic similarity to accurately discover trns and apply the method to e. coli k12. the approach can easily be extended to include other me ...	2007	17397539
phylogenomics and signature proteins for the alpha proteobacteria and its main groups.	alpha proteobacteria are one of the largest and most extensively studied groups within bacteria. however, for these bacteria as a whole and for all of its major subgroups (viz. rhizobiales, rhodobacterales, rhodospirillales, rickettsiales, sphingomonadales and caulobacterales), very few or no distinctive molecular or biochemical characteristics are known.	2007	18045498
origins of flagellar gene operons and secondary flagellar systems.	forty-one flagellated species representing 11 bacterial phyla were used to investigate the origin of secondary flagellar systems and the structure and formation of flagellar gene operons over the course of bacterial evolution. secondary (i.e., lateral) flagellar systems, which are harbored by five of the proteobacterial species considered, originated twice, once in the alphaproteobacterial lineage and again in the common ancestor of the beta- and gammaproteobacteria. the order and organization o ...	2007	17644605
metabolic regulation and overproduction of primary metabolites.	overproduction of microbial metabolites is related to developmental phases of microorganisms. inducers, effectors, inhibitors and various signal molecules play a role in different types of overproduction. biosynthesis of enzymes catalysing metabolic reactions in microbial cells is controlled by well-known positive and negative mechanisms, e.g. induction, nutritional regulation (carbon or nitrogen source regulation), feedback regulation, etc. the microbial production of primary metabolites contri ...	2008	21261849
anatomy of the e2 ligase fold: implications for enzymology and evolution of ubiquitin/ub-like protein conjugation.	the configuration of the active site of e2 ligases, central enzymes in the ubiquitin/ubiquitin-like protein (ub/ubl) conjugation systems, has long puzzled researchers. taking advantage of the wealth of newly available structures and sequences of e2s from diverse organisms, we performed a large-scale comparative analysis of these proteins. as a result we identified a previously under-appreciated diversity in the active site of these enzymes, in particular, the spatial location of the catalytic cy ...	2008	18276160
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
expression of two old yellow enzyme homologues from gluconobacter oxydans and identification of their citral hydrogenation abilities.	two genes that encode proteins which share 30-35% sequence identity with yeast oye (old yellow enzyme, an nad(p)h fmn-oxidoreductase), the well-studied archetype of the oye protein family, have been identified in gluconobacter oxydans m5. the two genes are localized in the chromosome and plasmid, respectively. comparison of the deduced amino acid sequences of the enzymes with database entries revealed 75.1% similarity and 64.9% identity to that of the pseudomonas syringae pv. glycinea nad(p)h-de ...	2008	18064575
wine genomics.		2008	21261827
cohesion group approach for evolutionary analysis of tyra, a protein family with wide-ranging substrate specificities.	many enzymes and other proteins are difficult subjects for bioinformatic analysis because they exhibit variant catalytic, structural, regulatory, and fusion mode features within a protein family whose sequences are not highly conserved. however, such features reflect dynamic and interesting scenarios of evolutionary importance. the value of experimental data obtained from individual organisms is instantly magnified to the extent that given features of the experimental organism can be projected u ...	2008	18322033
microbial iron management mechanisms in extremely acidic environments: comparative genomics evidence for diversity and versatility.	iron is an essential nutrient but can be toxic at high intracellular concentrations and organisms have evolved tightly regulated mechanisms for iron uptake and homeostasis. information on iron management mechanisms is available for organisms living at circumneutral ph. however, very little is known about how acidophilic bacteria, especially those used for industrial copper bioleaching, cope with environmental iron loads that can be 1018 times the concentration found in ph neutral environments. t ...	2008	19025650
vinyl ketone reduction by three distinct gluconobacter oxydans 621h enzymes.	three cytosolic nadph-dependent flavin-associated proteins (gox2107, gox0502, and gox2684) from gluconobacter oxydans 621h were overproduced in escherichia coli, and the recombinant enzymes were purified and characterized. apparent native molecular masses of 65.2, 78.2, and 78.4 kda were observed for gox2107, gox0502, and gox2684, corresponding to a trimeric structure for gox2107 and dimers for gox0502 and gox2684. analysis of flavin content revealed gox2107 was flavin adenine dinucleotide depen ...	2008	18629490