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an ompa family protein, a target of the gini/ginr quorum-sensing system in gluconacetobacter intermedius, controls acetic acid fermentation.via n-acylhomoserine lactones, the gini/ginr quorum-sensing system in gluconacetobacter intermedius nci1051, a gram-negative acetic acid bacterium, represses acetic acid and gluconic acid fermentation. two-dimensional polyacrylamide gel electrophoretic analysis of protein profiles of strain nci1051 and gini and ginr mutants identified a protein that was produced in response to the gini/ginr regulatory system. cloning and nucleotide sequencing of the gene encoding this protein revealed that it en ...200818487322
a specialized citric acid cycle requiring succinyl-coenzyme a (coa):acetate coa-transferase (aarc) confers acetic acid resistance on the acidophile acetobacter aceti.microbes tailor macromolecules and metabolism to overcome specific environmental challenges. acetic acid bacteria perform the aerobic oxidation of ethanol to acetic acid and are generally resistant to high levels of these two membrane-permeable poisons. the citric acid cycle (cac) is linked to acetic acid resistance in acetobacter aceti by several observations, among them the oxidation of acetate to co2 by highly resistant acetic acid bacteria and the previously unexplained role of a. aceti citr ...200818502856
membrane-bound pyrroloquinoline quinone-dependent dehydrogenase in gluconobacter oxydans m5, responsible for production of 6-(2-hydroxyethyl) amino-6-deoxy-l-sorbose.a membrane-bound protein purified from gluconobacter oxydans m5 was confirmed to be a pyrroloquinoline quinone-dependent d-sorbitol dehydrogenase. gene disruption and complementation experiments demonstrated that this enzyme is responsible for the oxidation of 1-(2-hydroxyethyl) amino-1-deoxy-d-sorbitol (1nsl) to 6-(2-hydroxyethyl) amino-6-deoxy-l-sorbose (6nse), which is the precursor of an antidiabetic drug, miglitol.200818502922
a novel 3-dehydroquinate dehydratase catalyzing extracellular formation of 3-dehydroshikimate by oxidative fermentation of gluconobacter oxydans ifo 3244.in addition to the cytoplasmic soluble form of 3-dehydroquinate dehydratase (sdqd) (ec 4.1.2.10), a novel form of dqd occurring in the periplasmic space was found in gluconobacter oxydans ifo 3244. the novel dqd, tentatively designated as pdqd, appeared to have a practical function involved in oxidative fermentation extracellularly coupling with membrane-bound quinoprotein quinate dehydrogenase (qdh) yielding 3-dehydroshikimate from quinate via 3-dehydroquinate. pdqd was not detached from the me ...200818540103
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 ...200818629490
complete genome of phenylobacterium zucineum--a novel facultative intracellular bacterium isolated from human erythroleukemia cell line k562.phenylobacterium zucineum is a recently identified facultative intracellular species isolated from the human leukemia cell line k562. unlike the known intracellular pathogens, p. zucineum maintains a stable association with its host cell without affecting the growth and morphology of the latter.200818700039
phylogenetic characterization of two novel commensal bacteria involved with innate immune homeostasis in drosophila melanogaster.during a previous study on the molecular interaction between commensal bacteria and host gut immunity, two novel bacterial strains, a911(t) and g707(t), were isolated from the gut of drosophila melanogaster. in this study, these strains were characterized in a polyphasic taxonomic study using phenotypic, genetic, and chemotaxonomic analyses. we show that the strains represent novel species in the family acetobacteraceae. strain g707(t), a highly pathogenic organism, represents a new species in t ...200818723651
a novel thermostable arylesterase from the archaeon sulfolobus solfataricus p1: purification, characterization, and expression.a novel thermostable arylesterase, a 35-kda monomeric enzyme, was purified from the thermoacidophilic archaeon sulfolobus solfataricus p1. the optimum temperature and ph were 94 degrees c and 7.0, respectively. the enzyme displayed remarkable thermostability: it retained 52% of its activity after 50 h of incubation at 90 degrees c. in addition, the purified enzyme showed high stability against denaturing agents, including various detergents, urea, and organic solvents. the enzyme has broad subst ...200818931117
metabolic function of corynebacterium glutamicum aminotransferases alat and avta and impact on l-valine production.aminotransferases (ats) interacting with l-alanine are the least studied bacterial ats. whereas alat converts pyruvate to l-alanine in a glutamate-dependent reaction, avta is able to convert pyruvate to l-alanine in an l-valine-dependent manner. we show here that the wild type of corynebacterium glutamicum with a deletion of either of the corresponding genes does not exhibit an explicit growth deficiency. however, a double mutant was auxotrophic for l-alanine, showing that both ats can provide l ...200818931286
acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications.acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). it is a chemolithoautrophic, gamma-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. it thrives at extremely low ph (ph 1-2) and fixes both carbon and nitrogen from the atmosphere. it solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemica ...200819077236
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 ...200818322033
whole-cell bioreduction of aromatic alpha-keto esters using candida tenuis xylose reductase and candida boidinii formate dehydrogenase co-expressed in escherichia coli.abstract:200819077192
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 ...200818055583
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 ...200818064575
an easy cloning and expression vector system for gluconobacter oxydans.gluconobacter oxydans is known for causing rapid and incomplete oxidation of a wide range of sugars, sugar acids and sugar alcohols. therefore, this microorganism is already employed in several biotechnological processes that involve incomplete oxidation of a substrate, e.g. vitamin c or dihydroxyacetone production. to fully exploit the oxidative potential of g. oxydans, characterization of the biological role of gene products is essential. to take advantage of the genome sequence of g. oxydans ...200817976848
genomics of plant-associated microbes. 200921255272
characterisation of a recombinant nadp-dependent glycerol dehydrogenase from gluconobacter oxydans and its application in the production of l-glyceraldehyde.the acetic acid bacterium gluconobacter oxydans has a high potential for oxidoreductases with a variety of different catalytic abilities. one putative oxidoreductase gene codes for an enzyme with a high similarity to the nadp+-dependent glycerol dehydrogenase (glydh) from hypocrea jecorina. due to this homology, the glydh (gox1615) has been cloned, over-expressed in escherichia coli, purified and characterised. gox1615 shows an apparent native molecular mass of 39 kda, which corresponds well to ...200919579248
screening of thermotolerant gluconobacter strains for production of 5-keto-d-gluconic acid and disruption of flavin adenine dinucleotide-containing d-gluconate dehydrogenase.we isolated thermotolerant gluconobacter strains that are able to produce 5-keto-d-gluconic acid (5kga) at 37 degrees c, a temperature at which regular mesophilic 5kga-producing strains showed much less growth and 5kga production. the thermotolerant strains produced 2kga as the major product at both 30 and 37 degrees c. the amount of ketogluconates produced at 37 degrees c was slightly less than the amount produced at 30 degrees c. to improve the yield of 5kga in these strains, we disrupted flav ...200919411430
optimising the inactivation of grape juice spoilage organisms by pulse electric fields.the effect of some pulsed electric field (pef) processing parameters (electric field strength, pulse frequency and treatment time), on a mixture of microorganisms (kloeckera apiculata, saccharomyces cerevisiae, lactobacillus plantarum, lactobacillus hilgardii and gluconobacter oxydans) typically present in grape juice and wine were evaluated. an experimental design based on response surface methodology (rsm) was used and results were also compared with those of a factorially designed experiment. ...200919246114
gluconobacter japonicus sp. nov., an acetic acid bacterium in the alphaproteobacteria.five strains, nbrc 3271(t), nbrc 3272, nbrc 3263, nbrc 3260 and nbrc 3269 were examined genetically, phylogenetically, phenotypically and chemotaxonomically. the dna g+c contents of the five strains were 55.1-56.4 mol%. the five strains had low levels of dna-dna hybridization of 13-51 % to the type strains of gluconobacter frateurii, gluconobacter thailandicus, gluconobacter oxydans, gluconobacter cerinus, gluconobacter albidus and gluconobacter kondonii and formed a cluster that was separate fr ...200919244423
origin of an alternative genetic code in the extremely small and gc-rich genome of a bacterial symbiont.the genetic code relates nucleotide sequence to amino acid sequence and is shared across all organisms, with the rare exceptions of lineages in which one or a few codons have acquired novel assignments. recoding of uga from stop to tryptophan has evolved independently in certain reduced bacterial genomes, including those of the mycoplasmas and some mitochondria. small genomes typically exhibit low guanine plus cytosine (gc) content, and this bias in base composition has been proposed to drive ug ...200919609354
physiology of acetic acid bacteria in light of the genome sequence of gluconobacter oxydans.acetic acid bacteria are a distinct group of microorganisms within the family acetobacteriaceae. they are characterized by their ability to incompletely oxidize a wide range of carbohydrates and alcohols. the great advantage of these reactions is that many substrates are regio- and stereoselectively oxidized. this feature is already exploited in several combined biotechnological-chemical procedures for the synthesis of sugar derivatives. therefore, it is important to understand the basic concept ...200918957863
recombinant organisms for production of industrial products.a revolution in industrial microbiology was sparked by the discoveries of ther double-stranded structure of dna and the development of recombinant dna technology. traditional industrial microbiology was merged with molecular biology to yield improved recombinant processes for the industrial production of primary and secondary metabolites, protein biopharmaceuticals and industrial enzymes. novel genetic techniques such as metabolic engineering, combinatorial biosynthesis and molecular breeding te ...200921326937
recombinant organisms for production of industrial products.a revolution in industrial microbiology was sparked by the discoveries of ther double-stranded structure of dna and the development of recombinant dna technology. traditional industrial microbiology was merged with molecular biology to yield improved recombinant processes for the industrial production of primary and secondary metabolites, protein biopharmaceuticals and industrial enzymes. novel genetic techniques such as metabolic engineering, combinatorial biosynthesis and molecular breeding te ...200921326937
quantification of natural populations of gluconacetobacter diazotrophicus and herbaspirillum spp. in sugar cane (saccharum spp.) using differente polyclonal antibodies.the species gluconacetobacter diazotrophicus, herbaspirillum seropedicae and h. rubrisubalbicans are endophytic n2-fixing [diazotrophic] bacteria which colonise not only roots, but also the aerial tissue of sugar cane. however, the technique most commonly used to quantify the populations of these microbes in plants is by culturing serial dilutions of macerates of plant tissues in n free semi-solid media which are only semi-selective for the species/genera [the most probable number (mpn) techniqu ...200924031435
solubilization, purification, and properties of membrane-bound d-glucono-delta-lactone hydrolase from gluconobacter oxydans.membrane-bound glucono-delta-lactonase (mgl) was purified to homogeneity from the membrane fraction of gluconobacter oxydans ifo 3244. after solubilization with 1 m cacl2, mgl was purified in the presence of ca2+ and detergent. a single band corresponding to 60 kda appeared in sds-page. the molecular weight of mgl was judged to be 120 k. differently from cytoplasmic lactonases, mgl showed optimum ph in an acidic range of 5-5.5. it was highly sensitive to metal-chelating agents such as edta, and ...200919129636
structural insight into the catalytic mechanism of gluconate 5-dehydrogenase from streptococcus suis: crystal structures of the substrate-free and quaternary complex enzymes.gluconate 5-dehydrogenase (ga5dh) is an nadp(h)-dependent enzyme that catalyzes a reversible oxidoreduction reaction between d-gluconate and 5-keto-d-gluconate, thereby regulating the flux of this important carbon and energy source in bacteria. despite the considerable amount of physiological and biochemical knowledge of ga5dh, there is little physical or structural information available for this enzyme. to this end, we herein report the crystal structures of ga5dh from pathogenic streptococcus ...200919177572
a microbial biosensor based on bacterial cells immobilized on chitosan matrix.a bio-electrochemical system consisting of gluconobacter oxydans dsm 2343 cells as a biological material and carbon nanotube (cnt)-free and cnt-modified chitosan as immobilizing matrices has been developed. the measurement was based on the respiratory activity of the cells estimated by the oxygen consumption at -0.7 v (versus the ag|agcl reference electrode) due to the metabolic activity in the presence of substrates. the system was calibrated and dependence of signal amplitude on the measuring ...200919196553
quantification of the expression of reference and alcohol dehydrogenase genes of some acetic acid bacteria in different growth conditions.the aim of this study was to develop a reliable system to analyse the expression of the pyrroloquinoline quinone (pqq)-alcohol dehydrogenase (adh) and test its ability to predict the growth and oxidative activity of some acetic acid bacteria (aab).200919200331
irre, a global regulator of extreme radiation resistance in deinococcus radiodurans, enhances salt tolerance in escherichia coli and brassica napus.globally, about 20% of cultivated land is now affected by salinity. salt tolerance is a trait of importance to all crops in saline soils. previous efforts to improve salt tolerance in crop plants have met with only limited success. bacteria of the genus deinococcus are known for their ability to survive highly stressful conditions, and therefore possess a unique pool of genes conferring extreme resistance. in deinococcus radiodurans, the irre gene encodes a global regulator responsible for extre ...200919204796
a new plasmid vector for dna delivery using lactococci.the use of food-grade lactococci as bacterial carriers to dna delivery into epithelial cells is a new strategy to develop live oral dna vaccine. our goal was to develop a new plasmid, named pvalac, for antigen delivery for use in lactococci. the pvalac plasmid was constructed by the fusion of: i) a eukaryotic region, allowing the cloning of an antigen of interest under the control of the pcmv eukaryotic promoter to be expressed by a host cell and ii) a prokaryotic region allowing replication and ...200919208231
membrane-bound dehydrogenases from gluconobacter sp.: interfacial electrochemistry and direct bioelectrocatalysis.although membrane-bound dehydrogenases isolated from gluconobacter sp. (mainly pqq-dependent alcohol and fructose dehydrogenase) have been used for preparing diverse forms of bioelectronic interfaces for almost 2 decades, it is not an easy task to interpret an electrochemical behaviour correctly. recent discoveries regarding redox properties of membrane-bound dehydrogenases along with extensive investigations of direct electron transfer (det) or direct bioelectrocatalysis with these enzymes are ...200919329366
process development in hansenula polymorpha and arxula adeninivorans, a re-assessment.abstract: a range of industrial h. polymorpha-based processes exist, most of them for the production of pharmaceuticals. the established industrial processes lean on the use of promoters derived from mox and fmd, genes of the methanol metabolism pathway. in hansenula polymorpha these promoters are de-repressed upon depletion of a range of carbon sources like glucose and glycerol instead of being induced by methanol as reported for other methylotrophs. due to these characteristics screening and f ...200919368732
biochemical and spectroscopic properties of cyanide-insensitive quinol oxidase from gluconobacter oxydans.cyanide-insensitive quinol oxidase (cioab), a relative of cytochrome bd, has no spectroscopic features of hemes b(595) and d in the wild-type bacteria and is difficult to purify for detailed characterization. here we studied enzymatic and spectroscopic properties of cioab from the acetic acid bacterium gluconobacter oxydans. gluconobacter oxydans cioab showed the k(m) value for ubiquinol-1 comparable to that of escherichia coli cytochrome bd but it was more resistant to kcn and quinone-analogue ...200919416958
high cell density fermentation of gluconobacter oxydans dsm 2003 for glycolic acid production.gluconobacter oxydans has a lower biomass yield. uniform design (ud) was applied to determine the optimum composition of the critical media and their mutual interactions for increased biomass yield of gluconobacter oxydans dsm 2003 in shake flasks. fed-batch fermentation process for biomass was optimized in a 3.7-l fermentor. by undertaking a preliminary and improved fed-batch fermentation-process strategy, a cell density of 6.0 g/l (dcw) was achieved in 22 h and 14.1 g/l (dcw) in 35 h, which is ...200919434434
annotating enzymes of uncertain function: the deacylation of d-amino acids by members of the amidohydrolase superfamily.the catalytic activities of three members of the amidohydrolase superfamily were discovered using amino acid substrate libraries. bb3285 from bordetella bronchiseptica, gox1177 from gluconobacter oxidans, and sco4986 from streptomyces coelicolor are currently annotated as d-aminoacylases or n-acetyl-d-glutamate deacetylases. these three enzymes are 22-34% identical to one another in amino acid sequence. substrate libraries containing nearly all combinations of n-formyl-d-xaa, n-acetyl-d-xaa, n-s ...200919518059
electrochemical polymerization of 1-(4-nitrophenyl)-2,5-di(2-thienyl)-1 h-pyrrole as a novel immobilization platform for microbial sensing.two types of bacterial biosensor were constructed by immobilization of gluconobacter oxydans and pseudomonas fluorescens cells on graphite electrodes modified with the conducting polymer; poly(1-(4-nitrophenyl)-2,5-di(2-thienyl)-1 h-pyrrole) [sns(no(2))]. the measurement was based on the respiratory activity of cells estimated by the oxygen consumption at -0.7 v due to the metabolic activity in the presence of substrate. as well as analytical characterization, the linear detection ranges, effect ...200919520619
whole-genome analyses reveal genetic instability of acetobacter pasteurianus.acetobacter species have been used for brewing traditional vinegar and are known to have genetic instability. to clarify the mutability, acetobacter pasteurianus nbrc 3283, which forms a multi-phenotype cell complex, was subjected to genome dna sequencing. the genome analysis revealed that there are more than 280 transposons and five genes with hyper-mutable tandem repeats as common features in the genome consisting of a 2.9-mb chromosome and six plasmids. there were three single nucleotide muta ...200919638423
mutations that disrupt either the pqq or the gdh gene of rahnella aquatilis abolish the production of an antibacterial substance and result in reduced biological control of grapevine crown gall.rahnella aquatilis hx2, a biocontrol agent for grapevine crown gall caused by agrobacterium vitis, produces an antibacterial substance that inhibits the growth of a. vitis in vitro. in this study, we show that mh15 and mh16, two tn5-induced mutants of hx2, have lost their abilities to inhibit a. vitis and have reduced biocontrol activities; they grow in logarithmic phase at a rate similar to that of the wild type and have single tn5 insertions. they are also impaired in producing pyrroloquinolin ...200919734331
complete genome sequence of the sugarcane nitrogen-fixing endophyte gluconacetobacter diazotrophicus pal5.gluconacetobacter diazotrophicus pal5 is an endophytic diazotrophic bacterium that lives in association with sugarcane plants. it has important biotechnological features such as nitrogen fixation, plant growth promotion, sugar metabolism pathways, secretion of organic acids, synthesis of auxin and the occurrence of bacteriocins.200919775431
[advance in dihydroxyacetone production by microbial fermentation].we reviewed the fermentation for dihydroxyacetone production. microbial fermentation is better for dihydroxyacetone production as compared to chemical methods. gluconobacter oxydans was recognized as the most important strain for industrial production of dihydroxyacetone. the dihydroxyacetone yield is associated with many factors such as substrate, product, oxygen and biomass concentration. repeated fed-batch fermentation and immobilization fermentation were recognized as the most potential proc ...200919777820
microbial production of glyceric acid, an organic acid that can be mass produced from glycerol.glyceric acid (ga), an unfamiliar biotechnological product, is currently produced as a small by-product of dihydroxyacetone production from glycerol by gluconobacter oxydans. we developed a method for the efficient biotechnological production of ga as a target compound for new surplus glycerol applications in the biodiesel and oleochemical industries. we investigated the ability of 162 acetic acid bacterial strains to produce ga from glycerol and found that the patterns of productivity and enant ...200919837846
glycerol conversion to d-xylulose by a two-stage microbial reaction using candida parapsilosis and gluconobacter oxydans.a yeast strain, 25n-2b, that produces d-arabitol from glycerol, was identified as candida parapsilosis based on phylogenetic, morphological, physiological, and biochemical analyses. it produced 32.2 g/l d-arabitol from 170 g/l glycerol in a jar fermentor. the d-arabitol in the reaction mixture was then completely converted to d-xylulose using gluconobacter oxydans nbrc3293. the product was isolated from the reaction mixture and confirmed to be d-xylulose by (1)h and (13)c-nmr and optical rotatio ...200919844074
cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways.aspartokinase (ask) exists within a variable network that supports the synthesis of 9 amino acids and a number of other important metabolites. lysine, isoleucine, aromatic amino acids, and dipicolinate may arise from the ask network or from alternative pathways. ask proteins were subjected to cohesion group analysis, a methodology that sorts a given protein assemblage into groups in which evolutionary continuity is assured. two subhomology divisions, ask(alpha) and ask(beta), have been recognize ...200919946135
glucose oxidation and pqq-dependent dehydrogenases in gluconobacter oxydans.gluconobacter oxydans is famous for its rapid and incomplete oxidation of a wide range of sugars and sugar alcohols. the organism is known for its efficient oxidation of d-glucose to d-gluconate, which can be further oxidized to two different keto-d-gluconates, 2-keto-d-gluconate and 5-keto-d-gluconate, as well as 2,5-di-keto-d-gluconate. for this oxidation chain and for further oxidation reactions, g. oxydans possesses a high number of membrane-bound dehydrogenases. in this review, we focus on ...200918957858
identification of new inhibitors for alternative nadh dehydrogenase (ndh-ii).in bacterial membranes and plant, fungus and protist mitochondria, nadh dehydrogenase (ndh-ii) serves as an alternative nadh : quinone reductase, a non-proton-pumping single-subunit enzyme bound to the membrane surface. because ndh-ii is absent in mammalian mitochondria, it is a promising target for new antibiotics. however, inhibitors for ndh-ii are rare and unspecific. taking advantage of the simple organization of the respiratory chain in gluconobacter oxydans, we carried out screening of nat ...200919076229
computational design of candida boidinii xylose reductase for altered cofactor specificity.in this study we introduce a computationally-driven enzyme redesign workflow for altering cofactor specificity from nadph to nadh. by compiling and comparing data from previous studies involving cofactor switching mutations, we show that their effect cannot be explained as straightforward changes in volume, hydrophobicity, charge, or blosum62 scores of the residues populating the cofactor binding site. instead, we find that the use of a detailed cofactor binding energy approximation is needed to ...200919693930
unsupervised statistical clustering of environmental shotgun sequences.the development of effective environmental shotgun sequence binning methods remains an ongoing challenge in algorithmic analysis of metagenomic data. while previous methods have focused primarily on supervised learning involving extrinsic data, a first-principles statistical model combined with a self-training fitting method has not yet been developed.200919799776
bioreactor mixing efficiency modulates the activity of a prpos::gfp reporter gene in e. coli.extensive studies have shown that up-scaling of bioprocesses has a significant impact on the physiology of the microorganisms. among the factors associated with the fluid dynamics of the bioreactor, concentration gradients induced by loss of the global mixing efficiency associated with the increasing scale is the main phenomena leading to strong physiological modifications at the level of the microbial population. these changes are not fully understood since they involve complex physiological me ...200919243588
escherichia coli, an intestinal microorganism, as a biosensor for quantification of amino acid bioavailability.in animal diets optimal amino acid quantities and balance among amino acids is of great nutritional importance. essential amino acid deficiencies have negative impacts on animal physiology, most often expressed in sub-optimal body weight gains. over supplementation of diets with amino acids is costly and can increase the nitrogen emissions from animals. although in vivo animal assays for quantification of amino acid bioavailability are well established, escherichia coli-based bioassays are viabl ...200922399985
potential for development of an escherichia coli-based biosensor for assessing bioavailable methionine: a review.methionine is an essential amino acid for animals and is typically considered one of the first limiting amino acids in animal feed formulations. methionine deficiency or excess in animal diets can lead to sub-optimal animal performance and increased environmental pollution, which necessitates its accurate quantification and proper dosage in animal rations. animal bioassays are the current industry standard to quantify methionine bioavailability. however, animal-based assays are not only time con ...201022319312
the three-dimensional structure of akr11b4, a glycerol dehydrogenase from gluconobacter oxydans, reveals a tryptophan residue as an accelerator of reaction turnover.the nadp-dependent glycerol dehydrogenase (ec 1.1.1.72) from gluconobacter oxydans is a member of family 11 of the aldo-keto reductase (akr) enzyme superfamily; according to the systematic nomenclature within the akr superfamily, the term akr11b4 has been assigned to the enzyme. akr11b4 is a biotechnologically attractive enzyme because of its broad substrate spectrum, combined with its distinctive regioselectivity and stereoselectivity. these features can be partially rationalized based on a 2-å ...201020887732
[isolation pqq biosynthesis gene cluster from gluconobacter oxydans based on sorbose-dehydrogenase activity].to isolate pqq biosynthesis gene cluster from gluconobacter oxydans h24 based on sorbose-dehydrogenase activity.201020931881
an easy and efficient fluorescent method for detecting aldehydes and its application in biotransformation.water-soluble aldehydes (acetaldehyde, propionaldehyde) and non-water-soluble aldehydes (butyraldehyde and phenylacetaldehyde) were easily detected by an efficient fluorescent method with 5-aminofluorescein as probe. under optimal detection conditions, 5-aminofluorescein could selectively respond to aldehydes with high sensitivity in comparison with other carbonyl compounds like ketones and acids. thus, the proposed method was used to monitor microbial oxidation and succeeded in trapping transie ...201020953822
identification of diverse antimicrobial resistance determinants carried on bacterial, plasmid, or viral metagenomes from an activated sludge microbial assemblage.using both sequence- and function-based metagenomic approaches, multiple antibiotic resistance determinants were identified within metagenomic libraries constructed from dna extracted from bacterial chromosomes, plasmids, or viruses within an activated sludge microbial assemblage. metagenomic clones and a plasmid that in escherichia coli expressed resistance to chloramphenicol, ampicillin, or kanamycin were isolated, with many cloned dna sequences lacking any significant homology to known antibi ...201020382816
characterization of a novel nadph-dependent oxidoreductase from gluconobacter oxydans.a novel protein from gluconobacter oxydans dsm2003 which shows 60-70% similarity with members of aldo-keto reductase (akr) superfamily was overexpressed in escherichia coli bl21 (de3) and purified by one step affinity chromatography with a ni-nta agarose column. the recombinant protein (named gox0644) consists of 279 amino acids with an apparent molecular mass of 32 kda in the soluble fraction, and the gene sequence encoding the protein gox0644 is 100% identical to the orf of gox0644 in g. oxyda ...201020411365
characterization of two aldo-keto reductases from gluconobacter oxydans 621h capable of regio- and stereoselective alpha-ketocarbonyl reduction.two cytosolic nadph-dependent carbonyl reductases from gluconobacter oxydans 621h, gox0644 and gox1615, were heterologously produced in escherichia coli. the recombinant proteins were purified to homogeneity and characterized. gox0644 and gox1615 were dimers with native molecular masses of 66.1 and 74.5 kda, respectively. the enzymes displayed broad substrate specificities and reduced alpha-ketocarbonyls at the keto moiety most proximal to the terminus of the alkyl chain to produce alpha-hydroxy ...201020414648
metabolic engineering of gluconobacter oxydans for improved growth rate and growth yield on glucose by elimination of gluconate formation.gluconobacter oxydans n44-1, an obligatory aerobic acetic acid bacterium, oxidizes glucose primarily in the periplasm to the end products 2-ketogluconate and 2,5-diketogluconate, with intermediate formation of gluconate. only a minor part of the glucose (less than 10%) is metabolized in the cytoplasm after conversion to gluconate or after phosphorylation to glucose-6-phosphate via the only functional catabolic routes, the pentose phosphate pathway and the entner-doudoroff pathway. this unusual m ...201020453146
purification and characterization of membrane-bound 3-dehydroshikimate dehydratase from gluconobacter oxydans ifo 3244, a new enzyme catalyzing extracellular protocatechuate formation.3-dehydroshikimate dehydratase (dsd) is the first known enzyme catalyzing aromatization from 3-dehydroshikimate (dsa) to protocatechuate (pca). differently from cytosolic dsd (sdsd), a membrane-bound 3-dehydroshikimate dehydratase (mdsd) was found for the first time in the membrane fraction of gluconobacter oxydans ifo 3244, and dsa was confirmed to be the direct precursor of pca. in contrast to weak and instable sdsd, the abundance of mdsd in the membrane fraction suggested the metabolic signif ...201020460715
magnetospirillum bellicus sp. nov., a novel dissimilatory perchlorate-reducing alphaproteobacterium isolated from a bioelectrical reactor.previously isolated dissimilatory perchlorate-reducing bacteria (dprb) have been primarily affiliated with the betaproteobacteria. enrichments from the cathodic chamber of a bioelectrical reactor (ber) inoculated from creek water in berkeley, ca, yielded a novel organism most closely related to a previously described strain, wd (99% 16s rrna gene identity). strain vdy(t) has 96% 16s rrna gene identity to both magnetospirillum gryphiswaldense and magnetospirillum magnetotacticum, and along with s ...201020495050
construction of a novel shuttle vector for use in gluconobacter oxydans.a shuttle vector pzl1 which can replicate both in gluconobacter oxydans and escherichia coli was constructed based on g. oxydans dsm2003 cryptic plasmid pgox3, a homology of g. oxydans 621h pgox3, and e. coli cloning vector puc18. it was found to be stably maintained in g. oxydans during the serial subcultures in the absence of antibiotic pressure for 144 h. with pgox3 as the reference sample, the relative copy number of pzl1 in g. oxydans is 13 determined by real-time fluorescence quantitative ...201020524160
enhanced production of dihydroxyacetone from glycerol by overexpression of glycerol dehydrogenase in an alcohol dehydrogenase-deficient mutant of gluconobacter oxydans.gluconobacter oxydans can rapidly and incompletely oxidize glycerol to dihydroxyacetone (dha), a versatile product extensively used in cosmetic, chemical and pharmaceutical industries. to improve dha production, the glycerol dehydrogenase (gdh) responsible for dha formation was overexpressed in g. oxydans m5am, in which the gene coding for the membrane-bound alcohol dehydrogenase (adh) was interrupted. real-time pcr and enzyme activity assay revealed that the absence of adh together with the ove ...201020576428
molecular characterization and heterologous expression of quinate dehydrogenase gene from gluconobacter oxydans ifo3244.the quinate dehydrogenase (qdh) from gluconobacter oxydans ifo3244 exhibits high affinity for quinate, suggesting its application in shikimate production. nucleotide sequence analysis of the qdh gene revealed a full-length of 2475-bp encoding an 824-amino acid protein. the qdh gene has the unusual ttg translation initiation codon. conserved regions and a signature sequence for the quinoprotein family were observed. phylogenetic analysis demonstrated relatedness of qdh from g. oxydans to other qu ...201020618134
disruption of the membrane-bound alcohol dehydrogenase-encoding gene improved glycerol use and dihydroxyacetone productivity in gluconobacter oxydans.dihydroxyacetone (dha) production from glycerol by gluconobacter oxydans is an industrial form of fermentation, but some problems exist related to microbial dha production. for example, glycerol inhibits dha production and affects its biological activity. g. oxydans produces both dha and glyceric acid (ga) from glycerol simultaneously, and membrane-bound glycerol dehydrogenase and membrane-bound alcohol dehydrogenases are involved in the two reactions, respectively. we discovered that the g. oxy ...201020622460
optimization of immobilization for selective oxidation of benzyl alcohol by gluconobacter oxydans using response surface methodology.this study used the box-behnken design and response surface methodology to optimize immobilization of gluconobacter oxydans in ca-alginate gel for the production of benzaldehyde in a biphasic system. immobilization parameters, such as na-alginate concentration, cell load, and bead diameter, were optimized. the mathematical model developed was validated and proven to be statistically adequate and accurate in predicting the response. for both activity and stability responses, the best results were ...201020667717
characterization of enzymes involved in the central metabolism of gluconobacter oxydans.gluconobacter oxydans is an industrially important bacterium that lacks a complete embden-meyerhof pathway (glycolysis). the organism instead uses the pentose phosphate pathway to oxidize sugars and their phosphorylated intermediates. however, the lack of glycolysis limits the amount of nadh as electron donor for electron transport phosphorylation. it has been suggested that the pentose phosphate pathway contributes to nadh production. six enzymes predicted to play central roles in intracellular ...201020676631
antioxidant pathways are up-regulated during biological nitrogen fixation to prevent ros-induced nitrogenase inhibition in gluconacetobacter diazotrophicus.gluconacetobacter diazotrophicus, an endophyte isolated from sugarcane, is a strict aerobe that fixates n(2). this process is catalyzed by nitrogenase and requires copious amounts of atp. nitrogenase activity is extremely sensitive to inhibition by oxygen and reactive oxygen species (ros). however, the elevated oxidative metabolic rates required to sustain biological nitrogen fixation (bnf) may favor an increased production of ros. here, we explored this paradox and observed that ros levels are, ...201020697694
inositol catabolism, a key pathway in sinorhizobium meliloti for competitive host nodulation.the nitrogen-fixing symbiont of alfalfa, sinorhizobium meliloti, is able to use myo-inositol as the sole carbon source. putative inositol catabolism genes (iola and iolrcdeb) have been identified in the s. meliloti genome based on their similarities with the bacillus subtilis iol genes. in this study, functional mutational analysis revealed that the iola and iolcdeb genes are required for growth not only with the myo-isomer but also for growth with scyllo- and d-chiro-inositol as the sole carbon ...201020971862
highly selective oxidation of benzyl alcohol using engineered gluconobacter oxydans in biphasic system.the gluconobacter oxydans m5 with disruption of the pyrroloquinoline quinine-dependent membrane-bound aldehyde dehydrogenase (aldh) was used for the oxidation of benzyl alcohol. the selectivity toward benzaldehyde showed an obvious increase for the engineered strain, which reached the 67.3%, while the wild strain had only 2.8%. meantime, the aqueous/isooctane (1:1) biphasic system was used for the further improvement of selectivity. by these methods, nearly 100% selectivity and conversion rate c ...201021140150
conversion of quinate to 3-dehydroshikimate by ca-alginate-immobilized membrane of gluconobacter oxydans ifo 3244 and subsequent asymmetric reduction of 3-dehydroshikimate to shikimate by immobilized cytoplasmic nadp-shikimate dehydrogenase.the membrane fraction of gluconobacter oxydans ifo 3244, involving membrane-bound quinoprotein quinate dehydrogenase and 3-dehydroquinate dehydratase, was immobilized into ca-alginate beads. the ca-alginate-immobilized bacterial membrane catalyzed a sequential reaction of quinate oxidation to 3-dehydroquinate and its spontaneous conversion to 3-dehydroshikimate under neutral ph. an almost 100% conversion rate from quinate to 3-dehydroshikimate was observed. nadp-dependent cytoplasmic enzymes fro ...201021150112
vitamin b(6) is required for full motility and virulence in helicobacter pylori.despite recent advances in our understanding of how helicobacter pylori causes disease, the factors that allow this pathogen to persist in the stomach have not yet been fully characterized. to identify new virulence factors in h. pylori, we generated low-infectivity variants of a mouse-colonizing h. pylori strain using the classical technique of in vitro attenuation. the resulting variants and their highly infectious progenitor bacteria were then analyzed by global gene expression profiling. the ...201021151756
bacterial communities associated with the lichen symbiosis.lichens are commonly described as a mutualistic symbiosis between fungi and "algae" (chlorophyta or cyanobacteria); however, they also have internal bacterial communities. recent research suggests that lichen-associated microbes are an integral component of lichen thalli and that the classical view of this symbiotic relationship should be expanded to include bacteria. however, we still have a limited understanding of the phylogenetic structure of these communities and their variability across li ...201021169444
bacterial communities associated with the lichen symbiosis.lichens are commonly described as a mutualistic symbiosis between fungi and "algae" (chlorophyta or cyanobacteria); however, they also have internal bacterial communities. recent research suggests that lichen-associated microbes are an integral component of lichen thalli and that the classical view of this symbiotic relationship should be expanded to include bacteria. however, we still have a limited understanding of the phylogenetic structure of these communities and their variability across li ...201021169444
capillary electrophoresis for the monitoring of carboxylic acid production by gluconobacter oxydans.determination of carboxylic acids in gluconobacter oxydans fermentations of wheat straw hydrolyzate was carried out. this matrix is of complex composition containing carbohydrates, organic compounds (e.g., amino acids, toxins), and inorganic salts making the analysis challenging even with separation techniques. a method based on capillary electrophoresis with indirect uv detection was developed for the simultaneous quantification of 18 carboxylic acids. the background electrolyte solution of amm ...201020074741
identification and quantification of acetic acid bacteria in wine and vinegar by taqman-mgb probes.a real-time pcr (rt-pcr) assay was developed using taqman minor groove binder (mgb) probes for the specific detection and quantification of five acetic acid bacteria (aab) species (acetobacter pasteurianus, acetobacter aceti, gluconacetobacter hansenii, gluconacetobacter europaeus and gluconobacter oxydans) in wine and vinegar. the primers and probes, designed from the 16s rrna gene, showed good specificity with the target aab species. the technique was tested on aab grown in glucose medium (gy) ...201020141944
characterization of a whole-cell catalyst co-expressing glycerol dehydrogenase and glucose dehydrogenase and its application in the synthesis of l-glyceraldehyde.a whole-cell catalyst using escherichia coli bl21(de3) as a host, co-expressing glycerol dehydrogenase (glydh) from gluconobacter oxydans and glucose dehydrogenase (gdh) from bacillus subtilis for cofactor regeneration, has been successfully constructed and used for the reduction of aliphatic aldehydes, such as hexanal or glyceraldehyde to the corresponding alcohols. this catalyst was characterized in terms of growth conditions, temperature and ph dependency, and regarding the influence of exter ...201020198657
production of 1,3-dihydroxyacetone from glycerol by gluconobacter oxydans zjb09112.the culture variables were optimized to increase 1,3-dihydroxyacetone (dha) production by gluconobacter oxydans zjb09112 in shake flask and bubble column bioreactor. after fermentation in the optimized medium (g/l: yeast extract 5, glycerol 2.5, mannitol 22.5, k(2)hpo(4) 0.5, kh(2)po(4) 0.5, mgso(4) x 7h(2)o 0.1, caco(3) 2.0, ph 5.0), when five times of glycerol feeding were made, 161.9 + or - 5.9 g/l of dha was attained at 88.7 + or - 3.2% conversion rate of glycerol to dha.201020208438
pyrroloquinoline quinone biosynthesis in escherichia coli through expression of the gluconobacter oxydans pqqabcde gene cluster.we have expressed the pqqabcde gene cluster from gluconobacter oxydans, which is involved in pyrroloquinoline quinone (pqq) biosynthesis, in escherichia coli, resulting in pqq accumulation in the medium. since the gene cluster does not include the tldd gene needed for pqq production, this result suggests that the e. coli tldd gene, which shows high homology to the g. oxydans tldd gene, carries out that function. the synthesis of pqq activated d-glucose dehydrogenase in e. coli and the growth of ...201020213113
bacterial biodiversity and dynamics during malolactic fermentation of tempranillo wines as determined by a culture-independent method (pcr-dgge).the bacterial population during malolactic fermentation of tempranillo wine was studied using the polymerase chain reaction-denaturing gradient gel electrophoresis, a culture-independent method successfully used for identification and monitoring of bacterial population in different habitats included food fermentations. the results showed that oenococcus oeni was the predominant species in the malolactic fermentation of tempranillo wines, although the presence of gluconobacter oxydans, asaia siam ...201020217079
characterization and inactivation of the membrane-bound polyol dehydrogenase in gluconobacter oxydans dsm 7145 reveals a role in meso-erythritol oxidation.the growth of gluconobacter oxydans dsm 7145 on meso-erythritol is characterized by two stages: in the first stage, meso-erythritol is oxidized almost stoichiometrically to l-erythrulose according to the bertrand-hudson rule. the second phase is distinguished from the first phase by a global metabolic change from membrane-bound meso-erythritol oxidation to l-erythrulose assimilation with concomitant accumulation of acetic acid. the membrane-associated erythritol-oxidizing enzyme was found to be ...201020223802
analysis of aldehyde reductases from gluconobacter oxydans 621h.two cytosolic nicotinamide adenine dinucleotide phosphate-dependent aldehyde reductases, gox1899 and gox2253, from gluconobacter oxydans 621h were overproduced and purified from escherichia coli. the purified proteins exhibited subunit masses of 26.4 (gox1899) and 36.7 kda (gox2253). both proteins formed homo-octamers exhibiting native masses of 210 and 280 kda, respectively. the substrate spectra, optimal reaction conditions, and kinetic constants were determined for gox1899 and gox2253. both e ...201019644687
intergenic transposable elements are not randomly distributed in bacteria.insertion sequences (iss) are mobile genetic elements in bacterial genomes. in general, intergenic is elements are probably less deleterious for their hosts than intragenic iss, simply because they have a lower likelihood of disrupting native genes. however, since promoters, shine-dalgarno sequences, and transcription factor binding sites are intergenic and upstream of genes, i hypothesized that not all neighboring gene orientations (ngos) are selectively equivalent for is insertion. to test thi ...201020697140
construction of expression vectors for protein production in gluconobacter oxydans.the characteristic ability of gluconobacter oxydans to incompletely oxidize numerous sugars, sugar acids, polyols, and alcohols has been exploited in several biotechnological processes, for example vitamin c production. the genome sequence of g. oxydans 621h is known but molecular tools are needed for the characterization of putative proteins and for the improvement of industrial strains by heterologous and homologous gene expression. to this end, promoter regions for the genes encoding g. oxyda ...201020969898
a rationally designed peptide enhances homologous recombination in vitro and resistance to dna damaging agents in vivo.the reca family of proteins is essential in homologous recombination, a critical step in dna repair. here, we report that a rationally-designed small peptide based on the crystal structure of escherichia coli reca-dna complex can promote homologous recombination through the enhancement of both reca-mediated strand assimilation and three-strand exchange activity. among 17 peptides tested, peptide #3 with the amino acid sequence of irfltarrr has the most potent activity in promoting the reca-media ...201020308162
characterization of enzymes in the oxidation of 1,2-propanediol to d: -(-)-lactic acid by gluconobacter oxydans dsm 2003.although gluconobacter oxydans can convert 1,2-propanediol to d: -(-)-lactic acid, the enzyme(s) responsible for the conversion has remain unknown. in this study, the membrane-bound alcohol dehydrogenase (adh) of gluconobacter oxydans dsm 2003 was purified and confirmed to be essential for the process of d: -(-)-lactic acid production by gene knockout and complementation studies. a 25 percent decrease in d: -(-)-lactic acid production was found for the aldehyde dehydrogenase (aldh) deficient str ...201020300886
expression of vitreoscilla hemoglobin enhances cell growth and dihydroxyacetone production in gluconobacter oxydans.dihydroxyacetone (dha) is an important ketose sugar, which is extensively used in the cosmetic, chemical, and pharmaceutical industries. dha has been industrially produced by gluconobacter oxydans with a high demand of oxygen. to improve the production of dha, the gene vgb encoding vitreoscilla hemoglobin (vhb) was successfully introduced into g. oxydans, where it was stably maintained, and expressed at about 76.0 nmol/g dry cell weight. results indicated that the constitutively expressed vhb im ...201020358375
ubiquitous presence of the hammerhead ribozyme motif along the tree of life.examples of small self-cleaving rnas embedded in noncoding regions already have been found to be involved in the control of gene expression, although their origin remains uncertain. in this work, we show the widespread occurrence of the hammerhead ribozyme (hhr) motif among genomes from the bacteria, chromalveolata, plantae, and metazoa kingdoms. intergenic hhrs were detected in three different bacterial genomes, whereas metagenomic data from galapagos islands showed the occurrence of similar ri ...201020705646
review of glucose oxidases and glucose dehydrogenases: a bird's eye view of glucose sensing enzymes.the evolution from first-generation through third-generation glucose sensors has witnessed the appearance of a number of very diverse oxidoreductases, which vary tremendously in terms of origin, structure, substrate specificity, cofactor used as primary electron acceptor, and acceptable final electron acceptor. this article summarizes our present knowledge of redox enzymes currently utilized in commercially available glucose monitoring systems to promote a fuller appreciation of enzymatic proper ...201122027299
gene cloning and biochemical characterization of a catalase from gluconobacter oxydans.gluconobacter oxydans has a large number of membrane-bound dehydrogenases linked to the respiratory chain that catalyze incomplete oxidation of a wide range of organic compounds by oxidative fermentation. because the respiratory chain is a primary site of reactive oxygen species (ros) production, the bacterium is expected to have a high capacity to detoxify nascent ros. in the present study, a gene that encodes a catalase of g. oxydans, which might act as a potential scavenger of h(2)o(2), was c ...201121317031
Efficient conversion of 1,2-butanediol to (R)-2-hydroxybutyric acid using whole cells of Gluconobacter oxydans.(R)-2-Hydroxybutyric acid ((R)-2-HBA) is an important building block for azinothricin family of antitumour antibiotics and biodegradable poly(2-hydroxybutyric acid). However, optically active (R)-2-HBA could not be produced through microbial fermentation or chemical synthesis. Several biocatalytic methods have been reported for the production of (R)-2-HBA. Those processes used expensive and scarce substrates and would not be suitable for practical application. In this work, Gluconobacter oxydans ...201122126977
Preclinical pharmacokinetics of the radiomitigator KZ-41 in rats.KZ-41, a quinic acid derivative, significantly reduces mortality in a murine model of hematopoietic acute radiation syndrome. The purpose of this study was to evaluate the systemic pharmacokinetics, elimination, and oral bioavailability of KZ-41 in rats. Male Sprague-Dawley rats (n?=?6 per group) received a single dose (10 mg/kg) of KZ-41 administered either intravenously via the jugular vein or orally via gavage. In vitro stability was determined using both rat liver microsomes and the bacteria ...201121864202
use of glycerol for producing 1,3-dihydroxyacetone by gluconobacter oxydans in an airlift bioreactor.1,3-dihydroxyacetone can be produced by biotransformation of glycerol with glycerol dehydrogenase from gluconobacter oxydans cells. firstly, improvement the activity of glycerol dehydrogenase was carried out by medium optimization. the optimal medium for cell cultivation was composed of 5.6g/l yeast extract, 4.7g/l glycerol, 42.1g/l mannitol, 0.5g/l k(2)hpo(4), 0.5g/l kh(2)po(4), 0.1g/l mgso(4)·7h(2)o, and 2.0g/l caco(3) with the initial ph of 4.9. secondly, an internal loop airlift bioreactor w ...201121592784
enhancement of 1,3-dihydroxyacetone production by a uv-induced mutant of gluconobacter oxydans with do control strategy.the 1,3-dihydroxyacetone (dha)-overproducing mutant of gluconobacter oxydans was screened via uv mutagenesis to enhance the dha production, and the dha fermentation condition was optimized using the dissolved oxygen (do) control strategy. the stable mutant g. oxydans zjb11001 exhibits high dha productivity and can tolerate high dha concentrations. the optimal condition for dha production by g. oxydans zjb11001 in a 15-l fermentor required an initial medium containing 5-ág/l yeast extract, 20-ág/ ...201121833510
influence of oxygen limitation, absence of the cytochrome bc(1) complex and low ph on global gene expression in gluconobacter oxydans 621h using dna microarray technology.the genome-wide transcriptional responses of the strictly aerobic α-proteobacterium gluconobacter oxydans 621h to oxygen limitation, to the absence of the cytochrome bc(1) complex, and to low ph were studied using dna microarray analyses. oxygen limitation caused expression changes of 486 genes, representing 20% of the chromosomal genes. genes with an increased mrna level included those for terminal oxidases, the cytochrome bc(1) complex, transhydrogenase, two alcohol dehydrogenases, heme biosyn ...201122226911
evolution of the oligopeptide transporter family.the oligopeptide transporter (opt) family of peptide and iron-siderophore transporters includes members from both prokaryotes and eukaryotes but with restricted distribution in the latter domain. eukaryotic members were found only in fungi and plants with a single slime mold homologue clustering with the fungal proteins. all functionally characterized eukaryotic peptide transporters segregate from the known iron-siderophore transporters on a phylogenetic tree. prokaryotic members are widespread, ...201121347612
distribution of genes encoding nucleoid-associated protein homologs in plasmids.bacterial nucleoid-associated proteins (naps) form nucleoprotein complexes and influence the expression of genes. recent studies have shown that some plasmids carry genes encoding nap homologs, which play important roles in transcriptional regulation networks between plasmids and host chromosomes. in this study, we determined the distributions of the well-known naps fis, h-ns, hu, ihf, and lrp and the newly found naps mvat and ndpa among the whole-sequenced 1382 plasmids found in gram-negative b ...201121350637
across bacterial phyla, distantly-related genomes with similar genomic gc content have similar patterns of amino acid usage.the gc content of bacterial genomes ranges from 16% to 75% and wide ranges of genomic gc content are observed within many bacterial phyla, including both gram negative and gram positive phyla. thus, divergent genomic gc content has evolved repeatedly in widely separated bacterial taxa. since genomic gc content influences codon usage, we examined codon usage patterns and predicted protein amino acid content as a function of genomic gc content within eight different phyla or classes of bacteria. w ...201121423704
species diversity, community dynamics, and metabolite kinetics of the microbiota associated with traditional ecuadorian spontaneous cocoa bean fermentations.traditional fermentations of the local ecuadorian cocoa type nacional, with its fine flavor, are carried out in boxes and on platforms for a short time. a multiphasic approach, encompassing culture-dependent and -independent microbiological analyses of fermenting cocoa pulp-bean samples, metabolite target analyses of both cocoa pulp and beans, and sensory analysis of chocolates produced from the respective fermented dry beans, was applied for the investigation of the influence of these fermentat ...201121926224
optimization of culture conditions to produce high yields of active acetobacter sp. cctcc m209061 cells for anti-prelog reduction of prochiral ketones.chiral alcohols are widely used in the synthesis of chiral pharmaceuticals, flavors and functional materials and appropriate whole-cell biocatalysts offer a highly enantioselective, minimally polluting route to these valuable compounds. the recently isolated strain acetobacter sp. cctcc m209061 showed exclusive anti-prelog stereoselectivity for the reduction of prochiral ketones, but the low biomass has limited its commercialization and industrial applications. to tackle this problem, the effect ...201122099947
Innate immunity against Granulibacter bethesdensis, an emerging Gram-negative bacterial pathogen.Acetic acid bacteria were previously considered non-pathogenic in humans. However, over the past decade, five genera of Acetobacteraceae have been isolated from patients with inborn or iatrogenic immunodeficiencies. Here, we describe the first studies of the interactions of the human innate immune system with a member of this bacterial family, Granulibacter bethesdensis, an emerging pathogen in patients with chronic granulomatous disease (CGD). Efficient phagocytosis of G. bethesdensis by normal ...201122184421
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