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complete genomic dna sequence of the east asian spotted fever disease agent rickettsia japonica.rickettsia japonica is an obligate intracellular alphaproteobacteria that causes tick-borne japanese spotted fever, which has spread throughout east asia. we determined the complete genomic dna sequence of r. japonica type strain yh (vr-1363), which consists of 1,283,087 base pairs (bp) and 971 protein-coding genes. comparison of the genomic dna sequence of r. japonica with other rickettsiae in the public databases showed that 2 regions (4,323 and 216 bp) were conserved in a very narrow range of ...201324039725
construction of an in vitro bypassed pyruvate decarboxylation pathway using thermostable enzyme modules and its application to n-acetylglutamate production.metabolic engineering has emerged as a practical alternative to conventional chemical conversion particularly in biocommodity production processes. however, this approach is often hampered by as yet unidentified inherent mechanisms of natural metabolism. one of the possible solutions for the elimination of the negative effects of natural regulatory mechanisms on artificially engineered metabolic pathway is to construct an in vitro pathway using a limited number of enzymes. employment of thermost ...201324099461
frequent replenishment sustains the beneficial microbiome of drosophila melanogaster.we report that establishment and maintenance of the drosophila melanogaster microbiome depend on ingestion of bacteria. frequent transfer of flies to sterile food prevented establishment of the microbiome in newly emerged flies and reduced the predominant members, acetobacter and lactobacillus spp., by 10- to 1,000-fold in older flies. flies with a normal microbiome were less susceptible than germfree flies to infection by serratia marcescens and pseudomonas aeruginosa. augmentation of the norma ...201324194543
plasmids of carotenoid-producing paracoccus spp. (alphaproteobacteria) - structure, diversity and evolution.plasmids are components of many bacterial genomes. they enable the spread of a large pool of genetic information via lateral gene transfer. many bacterial strains contain mega-sized replicons and these are particularly common in alphaproteobacteria. considerably less is known about smaller alphaproteobacterial plasmids. we analyzed the genomes of 14 such plasmids residing in 4 multireplicon carotenoid-producing strains of the genus paracoccus (alphaproteobacteria): p. aestuarii dsm 19484, p. hae ...201324260361
detailed analysis of the microbial population in malaysian spontaneous cocoa pulp fermentations reveals a core and variable microbiota.the fermentation of cocoa pulp is one of the few remaining large-scale spontaneous microbial processes in today's food industry. the microbiota involved in cocoa pulp fermentations is complex and variable, which leads to inconsistent production efficiency and cocoa quality. despite intensive research in the field, a detailed and comprehensive analysis of the microbiota is still lacking, especially for the expanding asian production region. here, we report a large-scale, comprehensive analysis of ...201324358116
effects of growth medium on matrix-assisted laser desorption-ionization time of flight mass spectra: a case study of acetic acid bacteria.the effect of the growth medium used on the matrix-assisted laser desorption ionization-time of flight (maldi-tof) mass spectra generated and its consequences for species and strain level differentiation of acetic acid bacteria (aab) were determined by using a set of 25 strains. the strains were grown on five different culture media that yielded a total of more than 600 mass spectra, including technical and biological replicates. the results demonstrate that the culture medium can have a profoun ...201424362425
influence of acetobacter pasteurianus sku1108 asps gene expression on escherichia coli morphology.the asps gene encoding aspartyl-trna synthetase (asprs) from a thermotolerant acetic acid bacterium, acetobacter pasteurianus sku1108, has been cloned and characterized. the open reading frame (orf) of the asps gene consists of 1,788 bp, encoding 595 amino acid residues. the highly conserved gly-val-asp-arg atp binding motif (motif 3) is located at the position 537-540 in the c-terminus. deletion analysis of the asps gene upstream region suggested that the promoter is around 173 bp upstream from ...201324385356
experimental evolution reveals habitat-specific fitness dynamics among wolbachia clades in drosophila melanogaster.the diversity and infection dynamics of the endosymbiont wolbachia can be influenced by many factors, such as transmission rate, cytoplasmic incompatibility, environment, selection and genetic drift. the interplay of these factors in natural populations can result in heterogeneous infection patterns with substantial differences between populations and strains. the causes of these heterogeneities are not yet understood, partly due to the complexity of natural environments. we present experimental ...201424387805
oxidation of metabolites highlights the microbial interactions and role of acetobacter pasteurianus during cocoa bean fermentation.four cocoa-specific acetic acid bacterium (aab) strains, namely, acetobacter pasteurianus 386b, acetobacter ghanensis lmg 23848(t), acetobacter fabarum lmg 24244(t), and acetobacter senegalensis 108b, were analyzed kinetically and metabolically during monoculture laboratory fermentations. a cocoa pulp simulation medium (cpsm) for aab, containing ethanol, lactic acid, and mannitol, was used. all aab strains differed in their ethanol and lactic acid oxidation kinetics, whereby only a. pasteurianus ...201424413595
3d structure modeling of alpha-amino acid ester hydrolase from xanthomonas rubrilineans.alpha-amino acid ester hydrolase (ec 3.1.1.43, aeh) is a promising biocatalyst for the production of semi-synthetic β-lactam antibiotics, penicillins and cephalosporins. the aeh gene from xanthomonas rubrilineans (xraeh) was recently cloned in this laboratory. the three-dimensional structure of xraeh was simulated using the homology modeling method for rational design experiments. the analysis of the active site was performed, and its structure was specified. the key amino acid residues in the a ...201324455184
yeasts are essential for cocoa bean fermentation.cocoa beans (theobroma cacao) are the major raw material for chocolate production and fermentation of the beans is essential for the development of chocolate flavor precursors. in this study, a novel approach was used to determine the role of yeasts in cocoa fermentation and their contribution to chocolate quality. cocoa bean fermentations were conducted with the addition of 200ppm natamycin to inhibit the growth of yeasts, and the resultant microbial ecology and metabolism, bean chemistry and c ...201424462702
pellicle of thermotolerant acetobacter pasteurianus strains: characterization of the polysaccharides and of the induction patterns.acetobacter species are well known to have the ability to grow floating on the surface of the medium by producing pellicle, which consists of cells and a self-produced matrix of cell-attached polysaccharide. we previously isolated three thermotolerant strains (sl13e-2, sl13e-3, and sl13e-4) from sri lankan coconut vinegar and identified all these strains as acetobacter pasteurianus. the pellicle polysaccharides of these three strains and of a. pasteurianus sku1108, which was originally isolated ...201424559734
acetic acid bacteria and the production and quality of wine vinegar.the production of vinegar depends on an oxidation process that is mainly performed by acetic acid bacteria. despite the different methods of vinegar production (more or less designated as either "fast" or "traditional"), the use of pure starter cultures remains far from being a reality. uncontrolled mixed cultures are normally used, but this review proposes the use of controlled mixed cultures. the acetic acid bacteria species determine the quality of vinegar, although the final quality is a com ...201424574887
mechanical properties, biocompatibility, and biodegradation of cross-linked cellulose acetate-reinforced polyester composites.composites of treated (cross-linked) cellulose acetate (t-ca) and acrylic acid-grafted poly(hydroxyalkanoate) (pha-g-aa/t-ca) exhibited noticeably superior mechanical properties compared with pha/ca composites due to greater compatibility between the two components. the dispersion covering of t-ca in the pha-g-aa matrix was highly homogeneous as a result of condensation reactions. human lung fibroblasts (fbs) were seeded on these two series of composites to characterize the biocompatibility prop ...201424708950
annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms.the functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. the molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden markov models of structural recognition. here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. we find ...201124710297
a novel carbonyl reductase with anti-prelog stereospecificity from acetobacter sp. cctcc m209061: purification and characterization.a novel carbonyl reductase (accr) catalyzing the asymmetric reduction of ketones to enantiopure alcohols with anti-prelog stereoselectivity was found in acetobacter sp. cctcc m209061 and enriched 27.5-fold with an overall yield of 0.4% by purification. the enzyme showed a homotetrameric structure with an apparent molecular mass of 104 kda and each subunit of 27 kda. the gene sequence of accr was cloned and sequenced, and a 762 bp gene fragment was obtained. either nad(h) or nadp(h) can be used a ...201424740089
nickel-resistance determinants in acidiphilium sp. pm identified by genome-wide functional screening.acidiphilium spp. are conspicuous dwellers of acidic, metal-rich environments. indeed, they are among the most metal-resistant organisms; yet little is known about the mechanisms behind the metal tolerance in this genus. acidiphilium sp. pm is an environmental isolate from rio tinto, an acidic, metal-laden river located in southwestern spain. the characterization of its metal resistance revealed a remarkable ability to tolerate high ni concentrations. here we report the screening of a genomic li ...201424740277
evolution of mitochondria reconstructed from the energy metabolism of living bacteria.the ancestors of mitochondria, or proto-mitochondria, played a crucial role in the evolution of eukaryotic cells and derived from symbiotic α-proteobacteria which merged with other microorganisms - the basis of the widely accepted endosymbiotic theory. however, the identity and relatives of proto-mitochondria remain elusive. here we show that methylotrophic α-proteobacteria could be the closest living models for mitochondrial ancestors. we reached this conclusion after reconstructing the possibl ...201424804722
the key to acetate: metabolic fluxes of acetic acid bacteria under cocoa pulp fermentation-simulating conditions.acetic acid bacteria (aab) play an important role during cocoa fermentation, as their main product, acetate, is a major driver for the development of the desired cocoa flavors. here, we investigated the specialized metabolism of these bacteria under cocoa pulp fermentation-simulating conditions. a carefully designed combination of parallel 13c isotope labeling experiments allowed the elucidation of intracellular fluxes in the complex environment of cocoa pulp, when lactate and ethanol were inclu ...201424837393
metagenomic analyses reveal phylogenetic diversity of carboxypeptidase gene sequences in activated sludge of a wastewater treatment plant in shanghai, china.activated sludge of wastewater treatment plants carries a diverse microflora. however, up to 80-90 % of microorganisms in activated sludge cannot be cultured by current laboratory techniques, leaving an enzyme reservoir largely unexplored. in this study, we investigated carboxypeptidase diversity in activated sludge of a wastewater treatment plant in shanghai, china, by a culture-independent metagenomic approach. three sets of consensus degenerate hybrid oligonucleotide primers (codehops) target ...201324860282
metagenomic analyses reveal phylogenetic diversity of carboxypeptidase gene sequences in activated sludge of a wastewater treatment plant in shanghai, china.activated sludge of wastewater treatment plants carries a diverse microflora. however, up to 80-90 % of microorganisms in activated sludge cannot be cultured by current laboratory techniques, leaving an enzyme reservoir largely unexplored. in this study, we investigated carboxypeptidase diversity in activated sludge of a wastewater treatment plant in shanghai, china, by a culture-independent metagenomic approach. three sets of consensus degenerate hybrid oligonucleotide primers (codehops) target ...201324860282
replacement of a terminal cytochrome c oxidase by ubiquinol oxidase during the evolution of acetic acid bacteria.the bacterial aerobic respiratory chain has a terminal oxidase of the heme-copper oxidase superfamily, comprised of cytochrome c oxidase (cox) and ubiquinol oxidase (uox); uox evolved from cox. acetobacter pasteurianus, an α-proteobacterial acetic acid bacterium (aab), produces uox but not cox, although it has a partial cox gene cluster, ctabd and ctaa, in addition to the uox operon cyabacd. we expressed ctab and ctaa genes of a. pasteurianus in escherichia coli and demonstrated their function a ...201424862920
microbiota-induced changes in drosophila melanogaster host gene expression and gut morphology.to elucidate mechanisms underlying the complex relationships between a host and its microbiota, we used the genetically tractable model drosophila melanogaster. consistent with previous studies, the microbiota was simple in composition and diversity. however, analysis of single flies revealed high interfly variability that correlated with differences in feeding. to understand the effects of this simple and variable consortium, we compared the transcriptome of guts from conventionally reared flie ...201424865556
draft genome sequence of acetobacter aceti strain 1023, a vinegar factory isolate.the genome sequence of acetobacter aceti 1023, an acetic acid bacterium adapted to traditional vinegar fermentation, comprises 3.0 mb (chromosome plus plasmids). a. aceti 1023 is closely related to the cocoa fermenter acetobacter pasteurianus 386b but possesses many additional insertion sequence elements.201424903876
biocatalytic anti-prelog reduction of prochiral ketones with whole cells of acetobacter pasteurianus gim1.158.enantiomerically pure alcohols are important building blocks for production of chiral pharmaceuticals, flavors, agrochemicals and functional materials and appropriate whole-cell biocatalysts offer a highly enantioselective, minimally polluting route to these valuable compounds. at present, most of these biocatalysts follow prelog's rule, and thus the (s)-alcohols are usually obtained when the smaller substituent of the ketone has the lower cip priority. only a few anti-prelog (r)-specific whole ...201424916156
pyrosequencing analysis of the microbial diversity of airag, khoormog and tarag, traditional fermented dairy products of mongolia.here, we used pyrosequencing to obtain a detailed analysis of the microbial diversities of traditional fermented dairy products of mongolia. from 22 airag (fermented mare's milk), 5 khoormog (fermented camel's milk) and 26 tarag (fermented milk of cows, goats and yaks) samples collected in the mongolian provinces of arhangai, bulgan, dundgobi, tov, uburhangai and umnugobi, we obtained a total of 81 operational taxonomic units, which were assigned to 15 families, 21 genera and 41 species in 3 phy ...201425003019
identification and characterization of thermotolerant acetic acid bacteria strains isolated from coconut water vinegar in sri lanka.from the pellicle formed on top of brewing coconut water vinegar in sri lanka, three acetobacter strains (sl13e-2, sl13e-3, and sl13e-4) that grow at 42 °c and four gluconobacter strains (sl13-5, sl13-6, sl13-7, and sl13-8) grow at 37 °c were identified as acetobacter pasteurianus and gluconobacter frateurii, respectively. acetic acid production by the isolated acetobacter strains was examined. all three strains gave 4% acetic acid from 6% initial ethanol at 37 °c, and 2.5% acetic acid from 4% i ...201425036846
effects of ensiling fermentation and aerobic deterioration on the bacterial community in italian ryegrass, guinea grass, and whole-crop maize silages stored at high moisture content.the effects of storage period and aerobic deterioration on the bacterial community were examined in italian ryegrass (ir), guinea grass (gg), and whole-crop maize (wm) silages. direct-cut forages were stored in a laboratory silo for 3, 7, 14, 28, 56, and 120 d without any additives; live counts, content of fermentation products, and characteristics of the bacterial community were determined. 2,3-butanediol, acetic acid, and lactic acid were the dominant fermentation products in the ir, gg, and w ...201325049913
microbial diversity and flavor formation in onion fermentation.fermented onion products are popular in many countries. we conducted fermentation with and without salt to identify the microorganisms responsible for onion fermentation and the unique taste of fermented onion. the results of pcr-dgge (polymerase chain reaction-denaturing gradient gel electrophoresis) revealed that lactic acid bacteria (lactobacillus zymae, l. malefermentans, l. plantarum), acetic acid bacteria (acetobacter pasteurianus, a. orientalis), citric acid bacteria (citrobacter sp., c. ...201425088041
impact of next generation sequencing techniques in food microbiology.understanding the maxam-gilbert and sanger sequencing as the first generation, in recent years there has been an explosion of newly-developed sequencing strategies, which are usually referred to as next generation sequencing (ngs) techniques. ngs techniques have high-throughputs and produce thousands or even millions of sequences at the same time. these sequences allow for the accurate identification of microbial taxa, including uncultivable organisms and those present in small numbers. in speci ...201425132799
metagenome-wide association of microbial determinants of host phenotype in drosophila melanogaster.animal-associated bacteria (microbiota) affect host behaviors and physiological traits. to identify bacterial genetic determinants of microbiota-responsive host traits, we employed a metagenome-wide association (mgwa) approach in two steps. first, we measured two microbiota-responsive host traits, development time and triglyceride (tag) content, in drosophila melanogaster flies monoassociated with each of 41 bacterial strains. the effects of monoassociation on host traits were not confined to pa ...201425271286
p2cs: updates of the prokaryotic two-component systems database.the p2cs database (http://www.p2cs.org/) is a comprehensive resource for the analysis of prokaryotic two-component systems (tcss). tcss are comprised of a receptor histidine kinase (hk) and a partner response regulator (rr) and control important prokaryotic behaviors. the latest incarnation of p2cs includes 164,651 tcs proteins, from 2758 sequenced prokaryotic genomes. several important new features have been added to p2cs since it was last described. users can search p2cs via blast, adding hits ...201425324303
p2cs: updates of the prokaryotic two-component systems database.the p2cs database (http://www.p2cs.org/) is a comprehensive resource for the analysis of prokaryotic two-component systems (tcss). tcss are comprised of a receptor histidine kinase (hk) and a partner response regulator (rr) and control important prokaryotic behaviors. the latest incarnation of p2cs includes 164,651 tcs proteins, from 2758 sequenced prokaryotic genomes. several important new features have been added to p2cs since it was last described. users can search p2cs via blast, adding hits ...201425324303
structure and functional characterization of pyruvate decarboxylase from gluconacetobacter diazotrophicus.bacterial pyruvate decarboxylases (pdc) are rare. their role in ethanol production and in bacterially mediated ethanologenic processes has, however, ensured a continued and growing interest. pdcs from zymomonas mobilis (zmpdc), zymobacter palmae (zppdc) and sarcina ventriculi (svpdc) have been characterized and zmpdc has been produced successfully in a range of heterologous hosts. pdcs from the acetobacteraceae and their role in metabolism have not been characterized to the same extent. examples ...201425369873
in vivo function and comparative genomic analyses of the drosophila gut microbiota identify candidate symbiosis factors.symbiosis is often characterized by co-evolutionary changes in the genomes of the partners involved. an understanding of these changes can provide insight into the nature of the relationship, including the mechanisms that initiate and maintain an association between organisms. in this study we examined the genome sequences of bacteria isolated from the drosophila melanogaster gut with the objective of identifying genes that are important for function in the host. we compared microbiota isolates ...201425408687
enzymatic strategies and biocatalysts for amide bond formation: tricks of the trade outside of the ribosome.amide bond-containing (abc) biomolecules are some of the most intriguing and functionally significant natural products with unmatched utility in medicine, agriculture and biotechnology. the enzymatic formation of an amide bond is therefore a particularly interesting platform for engineering the synthesis of structurally diverse natural and unnatural abc molecules for applications in drug discovery and molecular design. as such, efforts to unravel the mechanisms involved in carboxylate activation ...201425418915
enzymatic strategies and biocatalysts for amide bond formation: tricks of the trade outside of the ribosome.amide bond-containing (abc) biomolecules are some of the most intriguing and functionally significant natural products with unmatched utility in medicine, agriculture and biotechnology. the enzymatic formation of an amide bond is therefore a particularly interesting platform for engineering the synthesis of structurally diverse natural and unnatural abc molecules for applications in drug discovery and molecular design. as such, efforts to unravel the mechanisms involved in carboxylate activation ...201425418915
conservation analysis of the cydx protein yields insights into small protein identification and evolution.the reliable identification of proteins containing 50 or fewer amino acids is difficult due to the limited information content in short sequences. the 37 amino acid cydx protein in escherichia coli is a member of the cytochrome bd oxidase complex, an enzyme found throughout eubacteria. to investigate the extent of cydx conservation and prevalence and evaluate different methods of small protein homologue identification, we surveyed 1095 eubacteria species for the presence of the small protein.201425475368
multitasking secb chaperones in bacteria.protein export in bacteria is facilitated by the canonical secb chaperone, which binds to unfolded precursor proteins, maintains them in a translocation competent state and specifically cooperates with the translocase motor seca to ensure their proper targeting to the sec translocon at the cytoplasmic membrane. besides its key contribution to the sec pathway, secb chaperone tasking is critical for the secretion of the sec-independent heme-binding protein hasa and actively contributes to the cell ...201425538690
the oxidative fermentation of ethanol in gluconacetobacter diazotrophicus is a two-step pathway catalyzed by a single enzyme: alcohol-aldehyde dehydrogenase (adha).gluconacetobacter diazotrophicus is a n2-fixing bacterium endophyte from sugar cane. the oxidation of ethanol to acetic acid of this organism takes place in the periplasmic space, and this reaction is catalyzed by two membrane-bound enzymes complexes: the alcohol dehydrogenase (adh) and the aldehyde dehydrogenase (aldh). we present strong evidence showing that the well-known membrane-bound alcohol dehydrogenase (adha) of ga. diazotrophicus is indeed a double function enzyme, which is able to use ...201525574602
change in the plasmid copy number in acetic acid bacteria in response to growth phase and acetic acid concentration.plasmids pge1 (2.5 kb), pge2 (7.2 kb), and pge3 (5.5 kb) were isolated from gluconacetobacter europaeus kgma0119, and sequence analyses revealed they harbored 3, 8, and 4 genes, respectively. plasmid copy numbers (pcns) were determined by real-time quantitative pcr at different stages of bacterial growth. when kgma0119 was cultured in medium containing 0.4% ethanol and 0.5% acetic acid, pcn of pge1 increased from 7 copies/genome in the logarithmic phase to a maximum of 12 copies/genome at the be ...201525575969
comparative genomic and phylogenetic analyses of gammaproteobacterial glg genes traced the origin of the escherichia coli glycogen glgbxcap operon to the last common ancestor of the sister orders enterobacteriales and pasteurellales.production of branched α-glucan, glycogen-like polymers is widely spread in the bacteria domain. the glycogen pathway of synthesis and degradation has been fairly well characterized in the model enterobacterial species escherichia coli (order enterobacteriales, class gammaproteobacteria), in which the cognate genes (branching enzyme glgb, debranching enzyme glgx, adp-glucose pyrophosphorylase glgc, glycogen synthase glga, and glycogen phosphorylase glgp) are clustered in a glgbxcap operon arrang ...201525607991
a novel pyrroloquinoline quinone-dependent 2-keto-d-glucose dehydrogenase from pseudomonas aureofaciens.a gene encoding an enzyme similar to a pyrroloquinoline quinone (pqq)-dependent sugar dehydrogenase from filamentous fungi, which belongs to new auxiliary activities (aa) family 12 in the cazy database, was cloned from pseudomonas aureofaciens. the deduced amino acid sequence of the cloned enzyme showed only low homology to previously characterized pqq-dependent enzymes, and multiple-sequence alignment analysis showed that the enzyme lacks one of the three conserved arginine residues that functi ...201525645559
protein profile of acetobacter pasteurianus hsz3-21.acetobacter pasteurianus plays an important role in the process of traditional vinegar production and is also essential for the fermentation of zhenjiang aromatic vinegar. in this study, we utilized the proteomic approach to analyze the proteomic profile of a. pasteurianus hsz3-21, and 258 proteins were successfully identified by maldi-tof-ms and database search. the hydropathy and go analyse combined with cog results of the identified proteins revealed the molecular biological characteristics o ...201525648427
variable active site loop conformations accommodate the binding of macrocyclic largazole analogues to hdac8.the macrocyclic depsipeptide largazole is a potent inhibitor of metal-dependent histone deacetylases (hdacs), some of which are drug targets for cancer chemotherapy. indeed, largazole partially resembles romidepsin (fk228), a macrocyclic depsipeptide already approved for clinical use. each inhibitor contains a pendant side chain thiol that coordinates to the active site zn(2+) ion, as observed in the x-ray crystal structure of the hdac8-largazole complex [cole, k. e., dowling, d. p., boone, m. a ...201525793284
isolation and characterization of plant growth-promoting rhizobacteria from wheat rhizosphere and their effect on plant growth promotion.the present study was conducted to characterize the native plant growth promoting (pgp) bacteria from wheat rhizosphere and root-endosphere in the himalayan region of rawalakot, azad jammu and kashmir (ajk), pakistan. nine bacterial isolates were purified, screened in vitro for pgp characteristics and evaluated for their beneficial effects on the early growth of wheat (triticum aestivum l.). among nine bacterial isolates, seven were able to produce indole-3- acetic acid in tryptophan-supplemente ...201525852661
a comprehensive genomic, transcriptomic and proteomic analysis of a hyperosmotic stress sensitive α-proteobacterium.with the aim of remaining viable, bacteria must deal with changes in environmental conditions, including increases in external osmolarity. while studies concerning bacterial response to this stress condition have focused on soil, marine and enteric species, this report is about caulobacter crescentus, a species inhabiting freshwater oligotrophic habitats.201525879753
the effect of lactic acid bacteria on cocoa bean fermentation.cocoa beans (theobroma cacao l.) are the raw material for chocolate production. fermentation of cocoa pulp by microorganisms is crucial for developing chocolate flavor precursors. yeasts conduct an alcoholic fermentation within the bean pulp that is essential for the production of good quality beans, giving typical chocolate characters. however, the roles of bacteria such as lactic acid bacteria and acetic acid bacteria in contributing to the quality of cocoa bean and chocolate are not fully und ...201525889523
alpinia calcarata roscoe: a potential phytopharmacological source of natural medicine.alpinia calcarata roscoe (family: zingiberaceae), is a rhizomatous perennial herb, which is commonly used in the traditional medicinal systems in sri lanka. alpinia calcarata is cultivated in tropical countries, including sri lanka, india, and malaysia. experimentally, rhizomes of alpinia calcarata are shown to possess antibacterial, antifungal, anthelmintic, antinociceptive, anti-inflammatory, antioxidant, aphrodisiac, gastroprotective, and antidiabetic activities. phytochemical screening revea ...201526009694
new aminopeptidase from "microbial dark matter" archaeon.marine sediments host a large population of diverse, heterotrophic, uncultured microorganisms with unknown physiologies that control carbon flow through organic matter decomposition. recently, single-cell genomics uncovered new key players in these processes, such as the miscellaneous crenarchaeotal group. these widespread archaea encode putative intra- and extracellular proteases for the degradation of detrital proteins present in sediments. here, we show that one of these enzymes is a self-com ...201526062601
breeding strategy to generate robust yeast starter cultures for cocoa pulp fermentations.cocoa pulp fermentation is a spontaneous process during which the natural microbiota present at cocoa farms is allowed to ferment the pulp surrounding cocoa beans. because such spontaneous fermentations are inconsistent and contribute to product variability, there is growing interest in a microbial starter culture that could be used to inoculate cocoa pulp fermentations. previous studies have revealed that many different fungi are recovered from different batches of spontaneous cocoa pulp fermen ...201526150457
pqqe from methylobacterium extorquens am1: a radical s-adenosyl-l-methionine enzyme with an unusual tolerance to oxygen.methylobacterium extorquens am1 is an aerobic facultative methylotroph known to secrete pyrroloquinoline quinone (pqq), a cofactor of a number of bacterial dehydrogenases, into the culture medium. to elucidate the molecular mechanism of pqq biosynthesis, we are focusing on pqqe which is believed to be the enzyme catalysing the first reaction of the pathway. pqqe belongs to the radical s-adenosyl-l-methionine (sam) superfamily, in which most, if not all, enzymes are very sensitive to dissolved ox ...201526188050
pqqe from methylobacterium extorquens am1: a radical s-adenosyl-l-methionine enzyme with an unusual tolerance to oxygen.methylobacterium extorquens am1 is an aerobic facultative methylotroph known to secrete pyrroloquinoline quinone (pqq), a cofactor of a number of bacterial dehydrogenases, into the culture medium. to elucidate the molecular mechanism of pqq biosynthesis, we are focusing on pqqe which is believed to be the enzyme catalysing the first reaction of the pathway. pqqe belongs to the radical s-adenosyl-l-methionine (sam) superfamily, in which most, if not all, enzymes are very sensitive to dissolved ox ...201526188050
simultaneous production of acetic and gluconic acids by a thermotolerant acetobacter strain during acetous fermentation in a bioreactor.the activity of bacterial strains significantly influences the quality and the taste of vinegar. previous studies of acetic acid bacteria have primarily focused on the ability of bacterial strains to produce high amounts of acetic acid. however, few studies have examined the production of gluconic acid during acetous fermentation at high temperatures. the production of vinegar at high temperatures by two strains of acetic acid bacteria isolated from apple and cactus fruits, namely af01 and cv01, ...201626253254
assessing the genetic diversity of cu resistance in mine tailings through high-throughput recovery of full-length copa genes.characterizing the genetic diversity of microbial copper (cu) resistance at the community level remains challenging, mainly due to the polymorphism of the core functional gene copa. in this study, a local blastn method using a copa database built in this study was developed to recover full-length putative copa sequences from an assembled tailings metagenome; these sequences were then screened for potentially functioning copa using conserved metal-binding motifs, inferred by evolutionary trace an ...201526286020
complete genome and gene expression analyses of asaia bogorensis reveal unique responses to culture with mammalian cells as a potential opportunistic human pathogen.asaia bogorensis, a member of acetic acid bacteria (aab), is an aerobic bacterium isolated from flowers and fruits, as well as an opportunistic pathogen that causes human peritonitis and bacteraemia. here, we determined the complete genomic sequence of the as. bogorensis type strain nbrc 16594, and conducted comparative analyses of gene expression under different conditions of co-culture with mammalian cells and standard aab culture. the genome of as. bogorensis contained 2,758 protein-coding ge ...201526358298
comparative proteome of acetobacter pasteurianus ab3 during the high acidity rice vinegar fermentation.as a traditional asian food for several centuries, vinegar is known to be produced by acetic acid bacteria. the acetobacter species is the primary starter for vinegar fermentation and has evolutionarily acquired acetic acid resistance, in which acetobacter pasteurianus ab3 is routinely used for industrial production of rice vinegar with a high acidity (9 %, w/v). in contrast to the documented short-term and low acetic acid effects on a. pasteurianus, here we investigated the molecular and cellul ...201526369782
sdhe-dependent formation of a functional acetobacter pasteurianus succinate dehydrogenase in gluconobacter oxydans--a first step toward a complete tricarboxylic acid cycle.the obligatory aerobic α-proteobacterium gluconobacter oxydans 621h possesses an unusual metabolism in which the majority of the carbohydrate substrates are incompletely oxidized in the periplasm and only a small fraction is metabolized in the cytoplasm. the cytoplasmic oxidation capabilities are limited due to an incomplete tricarboxylic acid (tca) cycle caused by the lack of succinate dehydrogenase (sdh) and succinyl-coa synthetase. as a first step to test the consequences of a functional tca ...201526399411
molecular identification and physiological characterization of yeasts, lactic acid bacteria and acetic acid bacteria isolated from heap and box cocoa bean fermentations in west africa.yeast, lactic acid bacteria (lab) and acetic acid bacteria (aab) populations, isolated from cocoa bean heap and box fermentations in west africa, have been investigated. the fermentation dynamicswere determined by viable counts, and 106 yeasts, 105 lab and 82 aab isolateswere identified by means of rep-pcr grouping and sequencing of the rrna genes. during the box fermentations, the most abundant species were saccharomyces cerevisiae, candida ethanolica, lactobacillus fermentum, lactobacillus pla ...201626425801
comparative genome analysis of the candidate functional starter culture strains lactobacillus fermentum 222 and lactobacillus plantarum 80 for controlled cocoa bean fermentation processes.lactobacillus fermentum 222 and lactobacillus plantarum 80, isolates from a spontaneous ghanaian cocoa bean fermentation process, proved to be interesting functional starter culture strains for cocoa bean fermentations. lactobacillus fermentum 222 is a thermotolerant strain, able to dominate the fermentation process, thereby converting citrate and producing mannitol. lactobacillus plantarum 80 is an acid-tolerant and facultative heterofermentative strain that is competitive during cocoa bean fer ...201526459565
genomic analyses of thermotolerant microorganisms used for high-temperature fermentations.environmental adaptation is considered as one of the most challenging subjects in biology to understand evolutionary or ecological diversification processes and in biotechnology to obtain useful microbial strains. temperature is one of the important environmental stresses; however, microbial adaptation to higher temperatures has not been studied extensively. for industrial purposes, the use of thermally adapted strains is important, not only to reduce the cooling expenses of the fermentation sys ...201626566045
milk kefir: composition, microbial cultures, biological activities, and related products.in recent years, there has been a strong focus on beneficial foods with probiotic microorganisms and functional organic substances. in this context, there is an increasing interest in the commercial use of kefir, since it can be marketed as a natural beverage that has health promoting bacteria. there are numerous commercially available kefir based-products. kefir may act as a matrix in the effective delivery of probiotic microorganisms in different types of products. also, the presence of kefir' ...201526579086
tuning chocolate flavor through development of thermotolerant saccharomyces cerevisiae starter cultures with increased acetate ester production.microbial starter cultures have extensively been used to enhance the consistency and efficiency of industrial fermentations. despite the advantages of such controlled fermentations, the fermentation involved in the production of chocolate is still a spontaneous process that relies on the natural microbiota at cocoa farms. however, recent studies indicate that certain thermotolerant saccharomyces cerevisiae cultures can be used as starter cultures for cocoa pulp fermentation. in this study, we in ...201626590272
bacterial ecology of fermented cucumber rising ph spoilage as determined by nonculture-based methods.fermented cucumber spoilage (fcs) characterized by rising ph and the appearance of manure- and cheese-like aromas is a challenge of significant economical impact for the pickling industry. previous culture-based studies identified the yeasts pichia manshurica and issatchenkia occidentalis, 4 gram-positive bacteria, lactobacillus buchneri, lactobacillus parrafaraginis, clostridium sp., and propionibacterium and 1 gram-negative genus, pectinatus, as relevant in various stages of fcs given their ab ...201526605993
bacterial ecology of fermented cucumber rising ph spoilage as determined by nonculture-based methods.fermented cucumber spoilage (fcs) characterized by rising ph and the appearance of manure- and cheese-like aromas is a challenge of significant economical impact for the pickling industry. previous culture-based studies identified the yeasts pichia manshurica and issatchenkia occidentalis, 4 gram-positive bacteria, lactobacillus buchneri, lactobacillus parrafaraginis, clostridium sp., and propionibacterium and 1 gram-negative genus, pectinatus, as relevant in various stages of fcs given their ab ...201526605993
evaluation of thermotolerant acetobacter pasteurianus strains isolated from moroccan fruits catalyzing oxidative fermentation at high temperature.six strains of acetic acid bacteria were isolated from moroccan local products and their potential as industrial strains was evaluated in lab-bioreactor. three of them, namely tav01, af01 and cv01, isolated from traditional apple vinegar, apple and cactus fruit, respectively were selected and their responses to high temperature were assessed. morphological and biochemical identification confirmed that these strains belong to acetobacter species. their growth and acetic acid production were compa ...201526630753
microbial community, and biochemical and physiological properties of korean traditional black raspberry (robus coreanus miquel) vinegar.the aim of this study was to elucidate the changes in microbial community and biochemical and physiological properties of traditional muju black raspberry (robus coreanus miquel) vinegar (tmbv) during fermentation by culture-independent methods.201626676481
global insights into acetic acid resistance mechanisms and genetic stability of acetobacter pasteurianus strains by comparative genomics.acetobacter pasteurianus (ap) cicc 20001 and cgmcc 1.41 are two acetic acid bacteria strains that, because of their strong abilities to produce and tolerate high concentrations of acetic acid, have been widely used to brew vinegar in china. to globally understand the fermentation characteristics, acid-tolerant mechanisms and genetic stabilities, their genomes were sequenced. genomic comparisons with 9 other sequenced ap strains revealed that their chromosomes were evolutionarily conserved, where ...201526691589
screening and characterization of ethanol-tolerant and thermotolerant acetic acid bacteria from chinese vinegar pei.acetic acid bacteria (aab) are important microorganisms in the vinegar industry. however, aab have to tolerate the presence of ethanol and high temperatures, especially in submerged fermentation (sf), which inhibits aab growth and acid yield. in this study, seven aab that are tolerant to temperatures above 40 °c and ethanol concentrations above 10% (v/v) were isolated from chinese vinegar pei. all the isolated aab belong to acetobacter pasteurianus according to 16s rdna analysis. among all aab, ...201626712629
reconciling differences in pool-gwas between populations: a case study of female abdominal pigmentation in drosophila melanogaster.the degree of concordance between populations in the genetic architecture of a given trait is an important issue in medical and evolutionary genetics. here, we address this problem, using a replicated pooled genome-wide association study approach (pool-gwas) to compare the genetic basis of variation in abdominal pigmentation in female european and south african drosophila melanogaster. we find that, in both the european and the south african flies, variants near the tan and bric-à-brac 1 (bab1) ...201526715669
reconciling differences in pool-gwas between populations: a case study of female abdominal pigmentation in drosophila melanogaster.the degree of concordance between populations in the genetic architecture of a given trait is an important issue in medical and evolutionary genetics. here, we address this problem, using a replicated pooled genome-wide association study approach (pool-gwas) to compare the genetic basis of variation in abdominal pigmentation in female european and south african drosophila melanogaster. we find that, in both the european and the south african flies, variants near the tan and bric-à-brac 1 (bab1) ...201526715669
redirection of the reaction specificity of a thermophilic acetolactate synthase toward acetaldehyde formation.acetolactate synthase and pyruvate decarboxylase are thiamine pyrophosphate-dependent enzymes that convert pyruvate into acetolactate and acetaldehyde, respectively. although the former are encoded in the genomes of many thermophiles and hyperthermophiles, the latter has been found only in mesophilic organisms. in this study, the reaction specificity of acetolactate synthase from thermus thermophilus was redirected to catalyze acetaldehyde formation to develop a thermophilic pyruvate decarboxyla ...201626731734
microbial diversity and metabolite composition of belgian red-brown acidic ales.belgian red-brown acidic ales are sour and alcoholic fermented beers, which are produced by mixed-culture fermentation and blending. the brews are aged in oak barrels for about two years, after which mature beer is blended with young, non-aged beer to obtain the end-products. the present study evaluated the microbial community diversity of belgian red-brown acidic ales at the end of the maturation phase of three subsequent brews of three different breweries. the microbial diversity was compared ...201626802571
bacteria isolated from korean black raspberry vinegar with low biogenic amine production in wine.a high concentration of histamine, one of the biogenic amines (bas) usually found in fermented foods, can cause undesirable physiological side effects in sensitive humans. the objective of this study is to isolate indigenous acetobacter strains from naturally fermented bokbunja vinegar in korea with reduced histamine production during starter fermentation. further, we examined its physiological and biochemical properties, including ba synthesis. the obtained strain mba-77, identified as acetobac ...201626991285
lvtree viewer: an interactive display for the all-species living tree incorporating automatic comparison with prokaryotic systematics.we describe an interactive viewer for the all-species living tree (lvtree). the viewer incorporates treeing and lineage information from the arb-silva website. it allows collapsing the tree branches at different taxonomic ranks and expanding the collapsed branches as well, keeping the overall topology of the tree unchanged. it also enables the user to observe the consequence of trial lineage modifications by re-collapsing the tree. the system reports taxon statistics at all ranks automatically a ...201627018315
review: diversity of microorganisms in global fermented foods and beverages.culturalable and non-culturable microorganisms naturally ferment majority of global fermented foods and beverages. traditional food fermentation represents an extremely valuable cultural heritage in most regions, and harbors a huge genetic potential of valuable but hitherto undiscovered strains. holistic approaches for identification and complete profiling of both culturalable and non-culturable microorganisms in global fermented foods are of interest to food microbiologists. the application of ...201627047484
accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes.metagenomics, the application of shotgun sequencing, facilitates the reconstruction of the genomes of individual species from natural environments. a major challenge in the genome recovery domain is to agglomerate or 'bin' sequences assembled from metagenomic reads into individual groups. metagenomic binning without consideration of reference sequences enables the comprehensive discovery of new microbial organisms and aids in the microbial genome reconstruction process. here we present mycc, an ...201627067514
evolutionary relationships between heme-binding ferredoxin α + β barrels.the α + β barrel superfamily of the ferredoxin-like fold consists of a functionally diverse group of evolutionarily related proteins. the barrel architecture of these proteins is formed by either homo-/hetero-dimerization or duplication and fusion of ferredoxin-like domains. several members of this superfamily bind heme in order to carry out their functions.201627089923
cocobiota: implications for human health.manufacturing of dark chocolate and other cocoa-based products is a complex multistage process beginning with spontaneous cocoa bean fermentation driven in the postharvest period by different microorganisms derived from the environment. cocobiota defined as the association of microbial species involved in cocoa bean fermentation may have considerable impact on the medicinal properties of cocoa products via various primary and secondary metabolites, whose presence in dark chocolate and other coco ...201627144019
engineering escherichia coli to convert acetic acid to β-caryophyllene.under aerobic conditions, acetic acid is the major byproduct produced by e. coli during the fermentation. and acetic acid is detrimental to cell growth as it destroys transmembrane ph gradients. hence, how to reduce the production of acetic acid and how to utilize it as a feedstock are of intriguing interest. in this study, we provided an evidence to produce β-caryophyllene by the engineered e. coli using acetic acid as the only carbon source.201627149950
the impact of yeast starter cultures on the microbial communities and volatile compounds in cocoa fermentation and the resulting sensory attributes of chocolate.theobroma cacao seeds are the main raw material for chocolate production. during their fermentation, a succession of microorganisms are responsible for the physicochemical changes occurring in the pulp and inside the beans. the aim of this study was to investigate the effects of yeast inoculation (saccharomyces cerevisiae ufla ca11, pichia kluivery ccma0237, and hanseniaspora uvarum ccma0236) on the profile of the volatile compounds and microbial communities in cocoa fermentation. the resulting ...201527162390
the impact of yeast starter cultures on the microbial communities and volatile compounds in cocoa fermentation and the resulting sensory attributes of chocolate.theobroma cacao seeds are the main raw material for chocolate production. during their fermentation, a succession of microorganisms are responsible for the physicochemical changes occurring in the pulp and inside the beans. the aim of this study was to investigate the effects of yeast inoculation (saccharomyces cerevisiae ufla ca11, pichia kluivery ccma0237, and hanseniaspora uvarum ccma0236) on the profile of the volatile compounds and microbial communities in cocoa fermentation. the resulting ...201527162390
combination of deep eutectic solvent and ionic liquid to improve biocatalytic reduction of 2-octanone with acetobacter pasteurianus gim1.158 cell.the efficient anti-prelog asymmetric reduction of 2-octanone with acetobacter pasteurianus gim1.158 cells was successfully performed in a biphasic system consisting of deep eutectic solvent (des) and water-immiscible ionic liquid (il). various dess exerted different effects on the synthesis of (r)-2-octanol. choline chloride/ethylene glycol (chcl/eg) exhibited good biocompatibility and could moderately increase the cell membrane permeability thus leading to the better results. adding chcl/eg inc ...201627185089
gqqa, a novel protein in komagataeibacter europaeus involved in bacterial quorum quenching and cellulose formation.we report on the functional screening and identification of an active quorum quenching (qq) gene in the komagataeibacter europaeus strain cect 8546, which is a member of the acetic acid bacteria (aab).201627221658
genomic analysis unravels reduced inorganic sulfur compound oxidation of heterotrophic acidophilic acidicaldus sp. strain dx-1.although reduced inorganic sulfur compound (risc) oxidation in many chemolithoautotrophic sulfur oxidizers has been investigated in recent years, there is little information about risc oxidation in heterotrophic acidophiles. in this study, acidicaldus sp. strain dx-1, a heterotrophic sulfur-oxidizing acidophile, was isolated. its genome was sequenced and then used for comparative genomics. furthermore, real-time quantitative pcr was performed to identify the expression of genes involved in the r ...201627239474
design and performance testing of a dna extraction assay for sensitive and reliable quantification of acetic acid bacteria directly in red wine using real time pcr.although strategies exist to prevent aab contamination, the increased interest for wines with low sulfite addition leads to greater aab spoilage. hence, there is a real need for a rapid, specific, sensitive, and reliable method for detecting these spoilage bacteria. all these requirements are met by real time polymerase chain reaction (or quantitative pcr; qpcr). here, we compare existing methods of isolating dna and their adaptation to a red wine matrix. two different protocols for isolating dn ...201627313572
draft genome sequence of acetobacter malorum cect 7742, a strain isolated from strawberry vinegar.the present article reports the draft genome sequence of the strain acetobacter malorum cect 7742, an acetic acid bacterium isolated from strawberry vinegar. this species is characterized by the production of d-gluconic acid from d-glucose, which it further metabolizes to keto-d-gluconic acids.201627340078
enzymes responsible for acetate oxidation by acetic acid bacteria.several acetic acid bacteria of the genus acetobacter oxidize much acetate oxidation, which is not desired in vinegar manufacturing. acetobacter rancens sku 1111, a strong acetate oxidant, grew rapidly with a biphasic growth curve while consuming acetate in the second growth phase. acetobacter aceti ifo 3284 did not show extensive acetate oxidation. addition of glycerol to the culture medium of acetobacter rancens sku 1111 increased acetate oxidation and resulted in more biomass in the second gr ...199927373914
characterization of the enantioselective properties of the quinohemoprotein alcohol dehydrogenase of acetobacter pasteurianus lmg 1635. 1. different enantiomeric ratios of whole cells and purified enzyme in the kinetic resolution of racemic glycidol.resting cells of acetobacter pasteurianus lmg 1635 (atcc 12874) show appreciable enantioselectivity (e=16-18) in the oxidative kinetic resolution of racemic 2,3-epoxy-1-propanol, glycidol. distinctly lower values (e=7-9) are observed for the ferricyanide-coupled oxidation of glycidol by the isolated quinohemoprotein alcohol dehydrogenase, qh-adh, which is responsible for the enantiospecific oxidation step in whole cells. the accuracy of e-values from conversion experiments could be verified usin ...199927392873
building bridges: biocatalytic c-c-bond formation toward multifunctional products.carbon-carbon bond formation is the key reaction for organic synthesis to construct the carbon framework of organic molecules. the review gives a selection of biocatalytic c-c-bond-forming reactions which have been investigated during the last 5 years and which have already been proven to be applicable for organic synthesis. in most cases, the reactions lead to products functionalized at the site of c-c-bond formation (e.g., α-hydroxy ketones, aminoalcohols, diols, 1,4-diketones, etc.) or allow ...201627398261
characterization of newly identified dnaa and dnab proteins from acetobacter.although chromosomal replication is an essential feature of the bacterial life cycle, the replication mechanism and involved molecular players have never been properly characterized in the acetobacter genera. thanks to whole-genome sequencing, the unknown replication proteins from acetobacter pasteurianus and acetobacter orleanensis, dnaa-like and dnab-like, could be identified. despite the low nucleotide or amino acid similarity to the respective orthologs from escherichia coli, their involveme ...201627404460
microbial diversity and biochemical characteristics of borassus akeassii wine.palm wine produced traditionally and consumed by many people in the south-west of burkina faso is subject to alteration. in this study, we carried out a follow-up of two palm wines' fermentation during the 10 days in which palm wines are classically produced and consumed. we monitored biochemical characteristics of fermenting wines as well as followed the microflora kinetics using culture-dependent and culture-independent methods. the analysis of the acid content and the bacterial population rev ...201627450560
elucidating and regulating the acetoin production role of microbial functional groups in multispecies acetic acid fermentation.acetoin (3-hydroxy-2-butanone) formation in vinegar microbiota is crucial for the flavor quality of zhenjiang aromatic vinegar, a traditional vinegar produced from cereals. however, the specific microorganisms responsible for acetoin formation in this centuries-long repeated batch fermentation have not yet been clearly identified. here, the microbial distribution discrepancy in the diacetyl/acetoin metabolic pathway of vinegar microbiota was revealed at the species level by a combination of meta ...201627451452
high-throughput identification of the microbial biodiversity of cocoa bean fermentation by maldi-tof ms.matrix-assisted laser desorption ionization time-of-flight mass spectrometry (maldi-tof ms) is a powerful biotyping tool increasingly used for high-throughput identification of clinical microbial isolates, however, in food fermentation research this approach is still not well established. this study examines the microbial biodiversity of cocoa bean fermentation based on the isolation of micro-organisms in cocoa-producing regions, followed by maldi-tof ms in switzerland. a preceding 6-week storag ...201627454854
comparative evaluation of the genomes of three common drosophila-associated bacteria.drosophila melanogaster is an excellent model to explore the molecular exchanges that occur between an animal intestine and associated microbes. previous studies in drosophila uncovered a sophisticated web of host responses to intestinal bacteria. the outcomes of these responses define critical events in the host, such as the establishment of immune responses, access to nutrients, and the rate of larval development. despite our steady march towards illuminating the host machinery that responds t ...201627493201
fermented foods: are they tasty medicines for helicobacter pylori associated peptic ulcer and gastric cancer?more than a million people die every year due to gastric cancer and peptic ulcer. helicobacter pylori infection in stomach is the most important reason for these diseases. interestingly, only 10-20% of the h. pylori infected individuals suffer from these gastric diseases and rest of the infected individuals remain asymptomatic. the genotypes of h. pylori, host genetic background, lifestyle including smoking and diet may determine clinical outcomes. people from different geographical regions have ...201627504109
regio- and stereoselective aliphatic-aromatic cross-benzoin reaction: enzymatic divergent catalysis.the catalytic asymmetric synthesis of chiral 2-hydroxy ketones by using different thiamine diphosphate dependent enzymes, namely benzaldehyde lyase from pseudomonas fluorescens (pfbal), a variant of benzoylformate decarboxylase from pseudomonas putida (ppbfd-l461a), branched-chain 2-keto acid decarboxylase from lactococcus lactis (llkdca) and a variant of pyruvate decarboxylase from acetobacter pasteurianus (appdc-e469g), was studied. starting with the same set of substrates, substituted benzald ...201627515897
characterization of a novel d-glycero-d-talo-oct-2-ulosonic acid-substituted lipid a moiety in the lipopolysaccharide produced by the acetic acid bacterium acetobacter pasteurianus nbrc 3283.acetobacter pasteurianus is an aerobic gram-negative rod that is used in the fermentation process used to produce the traditional japanese black rice vinegar kurozu. previously, we found that a hydrophobic fraction derived from kurozu stimulates toll-like receptors to produce cytokines. lpss, particularly lps from a. pasteurianus, are strong candidates for the immunostimulatory component of kurozu. the lps of a. pasteurianus remains stable in acidic conditions during the 2 years of the abovement ...201627539854
crystal structure of pyruvate decarboxylase from zymobacter palmae.pyruvate decarboxylase (pdc; ec 4.1.1.1) is a thiamine pyrophosphate- and mg(2+) ion-dependent enzyme that catalyses the non-oxidative decarboxylation of pyruvate to acetaldehyde and carbon dioxide. it is rare in bacteria, but is a key enzyme in homofermentative metabolism, where ethanol is the major product. here, the previously unreported crystal structure of the bacterial pyruvate decarboxylase from zymobacter palmae is presented. the crystals were shown to diffract to 2.15 å resolution. they ...201627599861
comparative genomics of acetobacterpasteurianus ab3, an acetic acid producing strain isolated from chinese traditional rice vinegar meiguichu.acetobacter pasteurianus, an acetic acid resistant bacterium belonging to alpha-proteobacteria, has been widely used to produce vinegar in the food industry. to understand the mechanism of its high tolerance to acetic acid and robust ability of oxidizing ethanol to acetic acid (> 12%, w/v), we described the 3.1 mb complete genome sequence (including 0.28 m plasmid sequence) with a g+c content of 52.4% of a. pasteurianus ab3, which was isolated from the traditional chinese rice vinegar (meiguichu ...201627611790
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