| relaxed specificity of the r1162 nickase: a model for evolution of a system for conjugative mobilization of plasmids. | the primary dna processing protein for conjugative mobilization of the plasmid r1162 is the transesterase moba, which acts at a unique site on the plasmid, the origin of transfer (orit). both moba and orit are members of a large family of related elements that are widely distributed among bacteria. each orit consists of a highly conserved core and an adjacent region that is required for binding by its cognate moba. the sequence of the adjacent region is important in determining the specificity o ... | 2003 | 12775691 |
| influence of turning and environmental contamination on the dynamics of populations of lactic acid and acetic acid bacteria involved in spontaneous cocoa bean heap fermentation in ghana. | the influence of turning and environmental contamination on six spontaneous cocoa bean heap fermentations performed in ghana was studied through a multiphasic approach, encompassing both microbiological (culture-dependent and culture-independent techniques) and metabolite target analyses. a sensory analysis of chocolate made from the fermented, dried beans was performed as well. only four clusters were found among the isolates of acetic acid bacteria (aab) identified: acetobacter pasteurianus, a ... | 2008 | 17993565 |
| transposable modules generated by a single copy of insertion sequence ispme1 and their influence on structure and evolution of natural plasmids of paracoccus methylutens dm12. | we demonstrated that a single copy of insertion sequence ispme1 can mobilize adjacent segments of genomic dna of paracoccus methylutens dm12, which leads to the generation of diverse transposable elements of various size and dna contents. all elements (named transposable modules [tmos]) contain ispme1 (placed at the 5' ends of the elements) and have variable 3'-end regions of between 0.5 and 5 kb. ispme1 was shown to encode an outwardly oriented promoter, which may activate the transcription of ... | 2008 | 18296518 |
| application of culture culture-independent molecular biology based methods to evaluate acetic acid bacteria diversity during vinegar processing. | acetic acid bacteria (aab) are considered fastidious microorganisms because they are difficult to isolate and cultivate. different molecular approaches were taken to detect aab diversity, independently of their capacity to grow in culture media. those methods were tested in samples that originated during traditional vinegar production. bacterial diversity was assessed by analysis of 16s rrna gene, obtained by pcr amplifications of dna extracted directly from the acetification container. bacteria ... | 2008 | 18571262 |
| necessary corrections to the approved lists of bacterial names according to rule 40d (formerly rule 46). opinion 86. | the judicial commission affirms that, according to rule 40d, formerly rule 46, of the bacteriological code, the authorship of a number of subspecies names included on the approved lists of bacterial names must be corrected. these names are acetobacter aceti subsp. aceti, acetobacter pasteurianus subsp. pasteurianus, bacteroides melaninogenicus subsp. melaninogenicus, campylobacter fetus subsp. fetus, mycobacterium chelonae subsp. chelonae, propionibacterium freudenreichii subsp. freudenreichii, ... | 2008 | 18676492 |
| acetobacter turbidans alpha-amino acid ester hydrolase: how a single mutation improves an antibiotic-producing enzyme. | the alpha-amino acid ester hydrolase (aeh) from acetobacter turbidans is a bacterial enzyme catalyzing the hydrolysis and synthesis of beta-lactam antibiotics. the crystal structures of the native enzyme, both unliganded and in complex with the hydrolysis product d-phenylglycine are reported, as well as the structures of an inactive mutant (s205a) complexed with the substrate ampicillin, and an active site mutant (y206a) with an increased tendency to catalyze antibiotic production rather than hy ... | 2006 | 16377627 |
| analysis of several methods for the extraction of high quality dna from acetic acid bacteria in wine and vinegar for characterization by pcr-based methods. | acetic acid bacteria (aab) are fastidious microorganisms with poor recovery in culture. culture-independent methods are currently under examination. good dna extraction is a strict requirement of these methods. we compared five methods for extracting the dna of aab directly from wine and vinegar samples. four matrices (white wine, red wine, superficial vinegar and submerged vinegar) contaminated with two aab strains belonging to acetobacter pasteurianus and gluconacetobacter hansenii were assaye ... | 2008 | 18950887 |
| 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). | 2009 | 19200331 |
| the calculation of information and organismal complexity. | it is difficult to measure precisely the phenotypic complexity of living organisms. here we propose a method to calculate the minimal amount of genomic information needed to construct organism (effective information) as a measure of organismal complexity, by using permutation and combination formulas and shannon's information concept. | 2010 | 20937149 |
| succession of selected strains of acetobacter pasteurianus and other acetic acid bacteria in traditional balsamic vinegar. | the application of a selected acetobacter pasteurianus strain for traditional balsamic vinegar production was assessed. genomic dna was extracted from biofilms after enrichment cultures on gyc medium (10% glucose, 1.0% yeast extract, 2.0% calcium carbonate) and used for pcr/denaturing gradient gel electrophoresis, 16s rrna gene sequencing, and enterobacterial repetitive intergenic consensus/pcr sequencing. results suggested that double-culture fermentation is suitable for traditional balsamic vi ... | 2009 | 19251897 |
| differentiation of species of the family acetobacteraceae by aflp dna fingerprinting: gluconacetobacter kombuchae is a later heterotypic synonym of gluconacetobacter hansenii. | amplified fragment length polymorphism (aflp) dna fingerprinting was investigated as a tool for fast and accurate identification of acetic acid bacteria (aab) to the species level. one hundred and thirty five reference strains and 15 additional strains, representing 50 recognized species of the family acetobacteraceae, were subjected to aflp analysis using the restriction enzyme combination apai/taqi and the primer combination a03/t03. the reference strains had been previously subjected to eithe ... | 2009 | 19542117 |
| main microorganisms involved in the fermentation of ugandan ghee. | ghee is widely produced from a traditional fermented butter-like product named mashita in western uganda. however, no detailed studies have been done to identify the microorganisms involved in mashita fermentation. the aim of this study was to identify the microorganisms present at the end of mashita ripening using culture-dependent and culture-independent techniques. the most commonly identified species of lactic acid bacteria (lab) in mashita using culture-dependent techniques were lactobacill ... | 2009 | 19577815 |
| complete genome sequence of the prototype lactic acid bacterium lactococcus lactis subsp. cremoris mg1363. | lactococcus lactis is of great importance for the nutrition of hundreds of millions of people worldwide. this paper describes the genome sequence of lactococcus lactis subsp. cremoris mg1363, the lactococcal strain most intensively studied throughout the world. the 2,529,478-bp genome contains 81 pseudogenes and encodes 2,436 proteins. of the 530 unique proteins, 47 belong to the cog (clusters of orthologous groups) functional category "carbohydrate metabolism and transport," by far the largest ... | 2007 | 17307855 |
| cloning and characterization of ethanol-regulated esterase genes in acetobacter pasteurianus. | the esterase encoding genes, est1 and est2, were cloned from acetobacter pasteurianus. nucleotide sequence analysis of est1 revealed a gene of 954 bp, and est1 coded for an arylesterase with a molecular weight of 34863 da consisting of 317 amino acids. the est2 gene contained an open reading frame composed of 1221 bp encoding an esterase with a molecular weight of 43389 da consisting of 406 amino acids. the est1 gene showed some similarity, but the est2 gene showed no significant homology to oth ... | 1999 | 16232420 |
| increased number of arginine-based salt bridges contributes to the thermotolerance of thermotolerant acetic acid bacteria, acetobacter tropicalis sku1100. | thermotolerant acetic acid bacteria (aab), acetobacter tropicalis sku1100, can grow above 40°c. to investigate the basis of its thermotolerance, we compared the genome of a. tropicalis sku1100 with that of mesophilic aab strain acetobacter pasteurianus ifo3283-01. the comparative genomic study showed that amino acid substitutions from large to small residue and lys to arg occur in many orthologous genes. furthermore, comparative modeling study was carried out with the orthologous proteins betwee ... | 2011 | 21554859 |
| 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 ... | 2009 | 19638423 |
| hydrogen peroxide resistance of acetobacter pasteurianus nbrc3283 and its relationship to acetic acid fermentation. | the bacterium acetobacter pasteurianus can ferment acetic acid, a process that proceeds at the risk of oxidative stress. to understand the stress response, we investigated catalase and oxyr in a. pasteurianus nbrc3283. this strain expresses only a kate homolog as catalase, which is monofunctional and growth dependent. disruption of the oxyr gene increased kate activity, but both the kate and oxyr mutant strains showed greater sensitivity to hydrogen peroxide as compared to the parental strain. t ... | 2008 | 18838821 |
| in vivo methylation of mtdna reveals the dynamics of protein-mtdna interactions. | to characterize the organization of mtdna-protein complexes (known as nucleoids) in vivo, we have probed the mtdna surface exposure using site-specific dna methyltransferases targeted to the mitochondria. we have observed that dna methyltransferases have different accessibility to different sites on the mtdna based on the levels of protein occupancy. we focused our studies on selected regions of mtdna that are believed to be major regulatory regions involved in transcription and replication. the ... | 2009 | 19740762 |
| diversity of acetobacter pasteurianus strains isolated from solid-state fermentation of cereal vinegars. | vinegar production is based on the acetification process by indigenous acetic acid bacteria (aab). among vinegar technologies, solid-state fermentation (ssf) processes are widespread in asian countries to produce vinegar at small-scale. in this study, 21 aab strains isolated from chinese cereal vinegars produced by ssf collected in different regions of china were characterized by enterobacterial repetitive intergenic consensus (eric)-pcr fingerprinting. isolates exhibited high degree of phenotyp ... | 2010 | 19924479 |
| cloning and functional analysis of adhs gene encoding quinoprotein alcohol dehydrogenase subunit iii from acetobacter pasteurianus sku1108. | the adhs gene which encodes the smallest subunit, subunit iii, of quinoprotein alcohol dehydrogenase (pqq-adh) from acetobacter pasteurianus sku1108 has been cloned and characterized. the role of this subunit on the function of pqq-adh was investigated by construction of adhs gene disruptant and mutants. the adhs gene disruptant completely lost its pqq-adh activity and acetate-producing ability but retained acetic acid toleration. in contrast, this disruptant grew well, even better than the wild ... | 2010 | 20096472 |
| the microbiology of ghanaian cocoa fermentations analysed using culture-dependent and culture-independent methods. | export of cocoa beans is of great economic importance in ghana and several other tropical countries. raw cocoa has an astringent unpleasant taste and a spontaneous fermentation is the first step in a process leading to cocoa beans with the characteristic cocoa flavour and taste. the microbiology of ghanaian cocoa fermentations was investigated using culture-dependent and culture-independent methods. samples were collected at 12 hour intervals during 96-144 hour tray and traditional heap fermenta ... | 2007 | 17161485 |
| microbial asymmetric oxidation of 2-butyl-1,3-propanediol. | microbial asymmetric oxidation of 2-butyl-1,3-propanediol was investigated for an efficient synthesis of s- and r-enantiomers of 2-hydroxymethylhexanoic acid (2-hmha). from an intensive survey of the stocked bacterial strains, acetobacter pasteurianus iam 12073 and pseudomonas putida ifo 3738 were found to show the highest s- and r-2-hmha-producing activity, respectively. under optimized conditions, a. pasteurianus (351 mg dry cell weight) and p. putida (642 mg dry cell weight) cells produced 12 ... | 2007 | 17453192 |
| increased internal and external bacterial load during drosophila aging without life-span trade-off. | the role of microbial load during aging of the adult fruit fly drosophila melanogaster is incompletely understood. here we show dramatic increases in aerobic and anaerobic bacterial load during aging, both inside the body and on the surface. scanning electron microscopy and cell staining analyses of the surface of aged flies detected structures resembling abundant small bacteria and bacterial biofilms. bacteria cultured from laboratory flies included aerobic species acetobacter aceti, acetobacte ... | 2007 | 17681150 |
| cloning and characterization of clpb in acetobacter pasteurianus nbrc 3283. | the clpb gene in acetobacter pasteurianus was cloned and characterized. although the clpb gene was transcribed in response to a temperature shift and exposure to ethanol, the clpb disruption mutant was only affected by high temperature, suggesting that the clpb protein is closely associated with heat resistance in a. pasteurianus. | 2010 | 20541119 |
| enhanced production of bacterial cellulose by using a biofilm reactor and its material property analysis. | bacterial cellulose has been used in the food industry for applications such as low-calorie desserts, salads, and fabricated foods. it has also been used in the paper manufacturing industry to enhance paper strength, the electronics industry in acoustic diaphragms for audio speakers, the pharmaceutical industry as filtration membranes, and in the medical field as wound dressing and artificial skin material. in this study, different types of plastic composite support (pcs) were implemented separa ... | 2009 | 19630969 |
| acetic acid fermentation of acetobacter pasteurianus: relationship between acetic acid resistance and pellicle polysaccharide formation. | acetobacter pasteurianus strains ifo3283, sku1108, and msu10 were grown under acetic acid fermentation conditions, and their growth behavior was examined together with their capacity for acetic acid resistance and pellicle formation. in the fermentation process, the cells became aggregated and covered by amorphous materials in the late-log and stationary phases, but dispersed again in the second growth phase (due to overoxidation). the morphological change in the cells was accompanied by changes ... | 2010 | 20699583 |
| characterization of thermotolerant acetobacter pasteurianus strains and their quinoprotein alcohol dehydrogenases. | we isolated several thermotolerant acetobacter species of which msu10 strain, identified as acetobacter pasteurianus, could grow well on agar plates at 41 degrees c, tolerate to 1.5% acetic acid or 4% ethanol at 39 degrees c, similarly seen with a. pasteurianus sku1108 previously isolated. the msu10 strain showed higher acetic acid productivity in a medium containing 6% ethanol at 37 degrees c than sku1108 while sku1108 strain could accumulate more acetic acid in a medium supplemented with 4-5% ... | 2010 | 19711069 |
| thermostable lipases from the extreme thermophilic anaerobic bacteria thermoanaerobacter thermohydrosulfuricus sol1 and caldanaerobacter subterraneus subsp. tengcongensis. | two novel genes encoding for heat and solvent stable lipases from strictly anaerobic extreme thermophilic bacteria thermoanaerobacter thermohydrosulfuricus (liptth) and caldanaerobacter subterraneus subsp. tengcongensis (lipcst) were successfully cloned and expressed in e. coli. recombinant proteins were purified to homogeneity by heat precipitation, hydrophobic interaction, and gel filtration chromatography. unlike the enzymes from mesophile counterparts, enzymatic activity was measured at a br ... | 2009 | 19579003 |
| kinetic analysis of strains of lactic acid bacteria and acetic acid bacteria in cocoa pulp simulation media toward development of a starter culture for cocoa bean fermentation. | the composition of cocoa pulp simulation media (psm) was optimized with species-specific strains of lactic acid bacteria (psm-lab) and acetic acid bacteria (psm-aab). also, laboratory fermentations were carried out in psm to investigate growth and metabolite production of strains of lactobacillus plantarum and lactobacillus fermentum and of acetobacter pasteurianus isolated from ghanaian cocoa bean heap fermentations, in view of the development of a defined starter culture. in a first step, a se ... | 2010 | 20889778 |
| development of a sequence-characterized amplified region marker-targeted quantitative pcr assay for strain-specific detection of oenococcus oeni during wine malolactic fermentation. | control over malolactic fermentation (mlf) is a difficult goal in winemaking and needs rapid methods to monitor oenococcus oeni malolactic starters (mls) in a stressful environment such as wine. in this study, we describe a novel quantitative pcr (qpcr) assay enabling the detection of an o. oeni strain during mlf without culturing. o. oeni strain lb221 was used as a model to develop a strain-specific sequence-characterized amplified region (scar) marker derived from a discriminatory opa20-based ... | 2010 | 20935116 |
| the bacterial community in 'taberna' a traditional beverage of southern mexico. | to characterize the bacterial community of taberna, an alcoholic traditional beverage from the southern part of mexico produced by the fermentation of the coyol palm sap (acrocomia aculeate). | 2010 | 21039665 |
| double duty for a conserved glutamate in pyruvate decarboxylase: evidence of the participation in stereoelectronically controlled decarboxylation and in protonation of the nascent carbanion/enamine intermediate . | pyruvate decarboxylase (pdc) catalyzes the nonoxidative decarboxylation of pyruvate into acetaldehyde and carbon dioxide and requires thiamin diphosphate (thdp) and a divalent cation as cofactors. recent studies have permitted the assignment of functional roles of active site residues; however, the underlying reaction mechanisms of elementary steps have remained hypothetical. here, a kinetic and thermodynamic single-step analysis in conjunction with x-ray crystallographic studies of pdc from zym ... | 2010 | 20715795 |
| 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 ... | 2011 | 24710297 |
| dynamics and species diversity of communities of lactic acid bacteria and acetic acid bacteria during spontaneous cocoa bean fermentation in vessels. | to speed up research on the usefulness and selection of bacterial starter cultures for cocoa bean fermentation, a benchmark cocoa bean fermentation process under natural fermentation conditions was developed successfully. therefore, spontaneous fermentations of cocoa pulp-bean mass in vessels on a 20 kg scale were tried out in triplicate. the community dynamics and kinetics of these fermentations were studied through a multiphasic approach. microbiological analysis revealed a limited bacterial s ... | 2010 | 21356451 |
| genome sequences of the high-acetic acid-resistant bacteria gluconacetobacter europaeus lmg 18890t and g. europaeus lmg 18494 (reference strains), g. europaeus 5p3, and gluconacetobacter oboediens 174bp2 (isolated from vinegar). | bacteria of the genus gluconacetobacter are usually involved in the industrial production of vinegars with high acetic acid concentrations. we describe here the genome sequence of three gluconacetobacter europaeus strains, a very common bacterial species from industrial fermentors, as well as of a gluconacetobacter oboediens strain. | 2011 | 21441523 |
| 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 ... | 2014 | 24740277 |
| monitoring the bacterial community of maize silage stored in a bunker silo inoculated with enterococcus faecium, lactobacillus plantarum and lactobacillus buchneri. | to monitor variations in the bacterial community and fermentation products of maize silage within and between bunker silos. | 2011 | 21447012 |
| spontaneous organic cocoa bean box fermentations in brazil are characterized by a restricted species diversity of lactic acid bacteria and acetic acid bacteria. | spontaneous organic cocoa bean box fermentations were carried out on two different farms in brazil. physical parameters, microbial growth, bacterial species diversity [mainly lactic acid bacteria (lab) and acetic acid bacteria (aab)], and metabolite kinetics were monitored, and chocolates were produced from the fermented dry cocoa beans. the main end-products of the catabolism of the pulp substrates (glucose, fructose, and citric acid) by yeasts, lab, and aab were ethanol, lactic acid, mannitol, ... | 2011 | 21839382 |
| molecular cloning and characterization of two inducible nad(+)-adh genes encoding nad(+)-dependent alcohol dehydrogenases from acetobacter pasteurianus sku1108. | the cytosolic nad(+)-dependent alcohol dehydrogenases (nad(+)-adhs) are induced in the quinoprotein adh-(pqq-adh) defective acetobacter pasteurianus sku1108 mutant during growth in an ethanol medium. the adhi and adhii genes, which encode nad(+)-adh i and adh ii, respectively, of this strain have been cloned and characterized. sequence analyses have revealed that the adhi gene consists of 1029bp coding for 342 amino acids, which share 99.71% identity with the same protein from a. pasteurianus if ... | 2011 | 21843965 |
| microbial dynamics during aerobic exposure of corn silage stored under oxygen barrier or polyethylene films. | the aims were to compare the effects of sealing forage maize with a new oxygen barrier film or with a conventional polyethylene film. this comparison would be during both ensilage and subsequent exposure of silage to air, and would include chemical, microbiological and molecular (dna and rna) assessments. the forage was inoculated with a mixture of lactobacillus buchneri, lb. plantarum, and enterococcus faecium and ensiled in polyethylene (pe) and oxygen barrier (ob) plastic bags. the oxygen per ... | 2011 | 21821764 |
| Biochemical and Mutational Studies of the Bacillus cereus CECT 5050T Formamidase Support the Existence of a C-E-E-K Tetrad in Several Members of the Nitrilase Superfamily. | Formamidases (EC 3.5.1.49) are poorly characterized proteins. In spite of this scarce knowledge, ammonia has been described as playing a central role in the pathogenesis of human pathogens such as Helicobacter pylori, for which formamidase has been shown to participate in the nitrogen metabolic pathway. Sequence analysis has revealed that at least two different groups of formamidases are classified as EC 3.5.1.49: on the one hand, the derivatives of the FmdA-AmdA superfamily, which are the best ... | 2011 | 21705545 |
| proteome analysis of acetobacter pasteurianus during acetic acid fermentation. | acetic acid bacteria (aab) are gram-negative, strictly aerobic microorganisms that show a unique resistance to ethanol (etoh) and acetic acid (ach). members of the acetobacter and gluconacetobacter genera are capable of transforming etoh into ach via the alcohol dehydrogenase (adh) and aldehyde dehydrogenase (aldh) enzymes and are used for the industrial production of vinegar. several mechanisms have been proposed to explain how aab resist high concentrations of ach, such as the assimilation of ... | 2011 | 22155126 |
| 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 ... | 2011 | 22099947 |
| population dynamics of acetic acid bacteria during traditional wine vinegar production. | the population dynamics of acetic acid bacteria in traditional vinegar production was determined in two independent vinegar plants at both the species and strain level. the effect of barrels made of four different woods upon the population dynamics was also determined. acetic acid bacteria were isolated on solid media and the species were identified by rflp-pcr of 16s rrna genes and confirmed by 16s rrna gene sequencing, while strains were typed by eric-pcr and (gtg)(5)-rep-pcr. the most widely ... | 2010 | 20117853 |
| cloning and characterization of grpe in acetobacter pasteurianus nbrc 3283. | the grpe gene in acetobacter pasteurianus nbrc 3283 was cloned and characterized, to elucidate the mechanism underlying the resistance of acetic acid bacteria to the stressors existing during acetic acid fermentation. this gene was found to be located in tandem with two related genes, appearing on the genome in the order grpe-dnak-dnaj. a sigma(32)-type promoter sequence was found in the upstream region of grpe. the relative transcription levels of grpe, dnak, and dnaj mrna were in the ratio of ... | 2010 | 20129077 |
| 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) ... | 2010 | 20141944 |
| effect of barrel design and the inoculation of acetobacter pasteurianus in wine vinegar production. | the traditional production of wine vinegar is a lengthy process with little or no microbiological control. the aim of this study was to shorten the acetification process via three different strategies: changes in wood type; barrel shape; and the inoculation of an acetobacter pasteurianus pure culture. the barrel shape was modified by constructing two prototypes with higher liquid-air interface. we compared the changes in acetic acid bacteria (aab) population dynamics in these barrels with those ... | 2010 | 20478638 |
| 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 ... | 2010 | 20495050 |
| assessment of bacterial diversity in selected philippine fermented food products through pcr-dgge. | the bacterial population in several philippine fermented food preparations was assessed by pcr-denaturing gradient gel electrophoresis (pcr-dgge) of the 16s rrna gene (16s rdna). genomic dna was isolated directly from alamang (fermented shrimp paste), burong isda (fermented fish and rice), burong hipon (fermented shrimp and rice), burong mustasa (fermented mustard leaves), tuba (sugar cane wine), suka (vinegar) and sinamak (spiced vinegar) using one of two protocols, namely - mobio dna extractio ... | 2011 | 22146687 |
| Genome-wide phylogenetic analysis of differences in thermotolerance among closely related Acetobacter pasteurianus strains. | Acetobacter pasteurianus is a Gram-negative strictly aerobic bacterium that is widely used for the industrial production of vinegar. Three Acetobacter pasteurianus strains, SKU1108, NBRC 3283 and IFO 3191, have the same 16S rRNA sequence (100?% sequence identity) but show differences in thermotolerance. To clarify the relationships between phylogeny and thermotolerance of these strains, genome-wide analysis of these three strains was performed. Concatenated phylogenetic analysis of a dataset of ... | 2012 | 22016572 |
| 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 ... | 2011 | 21926224 |
| identification of yeast and acetic acid bacteria isolated from the fermentation and acetification of persimmon (diospyros kaki). | persimmon (diospyros kaki) is a seasonal fruit with important health benefits. in this study, persimmon use in wine and condiment production was investigated using molecular methods to identify the yeast and acetic acid bacteria (aab) isolated from the alcoholic fermentation and acetification of the fruit. alcoholic fermentation was allowed to occur either spontaneously, or by inoculation with a commercial saccharomyces cerevisiae wine strain, while acetification was always spontaneous; all thes ... | 2012 | 22265289 |
| azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments. | fossil records indicate that life appeared in marine environments ∼3.5 billion years ago (gyr) and transitioned to terrestrial ecosystems nearly 2.5 gyr. sequence analysis suggests that "hydrobacteria" and "terrabacteria" might have diverged as early as 3 gyr. bacteria of the genus azospirillum are associated with roots of terrestrial plants; however, virtually all their close relatives are aquatic. we obtained genome sequences of two azospirillum species and analyzed their gene origins. while m ... | 2011 | 22216014 |
| on-farm implementation of a starter culture for improved cocoa bean fermentation and its influence on the flavour of chocolates produced thereof. | cocoa bean fermentations controlled by means of starter cultures were introduced on several farms in two different cocoa-producing regions (west africa and southeast asia). two starter culture mixtures were tested, namely one composed of saccharomyces cerevisiae h5s5k23, lactobacillus fermentum 222, and acetobacter pasteurianus 386b (three heaps and one box), and another composed of l. fermentum 222 and a. pasteurianus 386b (seven heaps and one box). in all starter culture-added cocoa bean ferme ... | 2011 | 22365351 |
| amino ester hydrolase from xanthomonas campestris pv. campestris, atcc 33913 for enzymatic synthesis of ampicillin. | a-amino ester hydrolases (aeh) are a small class of proteins, which are highly specific for hydrolysis or synthesis of a-amino containing amides and esters including ß-lactam antibiotics such as ampicillin, amoxicillin, and cephalexin. a blast search revealed the sequence of a putative glutaryl 7-aminocephalosporanic acid (gl-7-aca) acylase 93% identical to a known aeh from xanthomonas citri. the gene, termed gaa, was cloned from the genomic dna of xanthomonas campestris pv. campestris sp. strai ... | 2010 | 22087071 |
| 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 ... | 2015 | 25607991 |
| comparative analysis of two phenotypically-similar but genomically-distinct burkholderia cenocepacia-specific bacteriophages. | genomic analysis of bacteriophages infecting the burkholderia cepacia complex (bcc) is an important preliminary step in the development of a phage therapy protocol for these opportunistic pathogens. the objective of this study was to characterize kl1 (vb_bces_kl1) and ah2 (vb_bces_ah2), two novel burkholderia cenocepacia-specific siphoviruses isolated from environmental samples. | 2012 | 22676492 |
| 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 ... | 2014 | 24804722 |
| 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 ... | 2015 | 25645559 |
| insertion sequences. | insertion sequences (iss) constitute an important component of most bacterial genomes. over 500 individual iss have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. the last 10 years have also seen some striking advances in our understanding of the transposition process itself. not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic e ... | 1998 | 9729608 |
| 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 ... | 2011 | 21350637 |
| 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. | 2014 | 25475368 |
| 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 ... | 2015 | 25852661 |
| molecular determinants for substrate selectivity of ω-transaminases. | ω-transaminase (ω-ta) is an industrially important enzyme for production of chiral amines. about 20 (s)-specific ω-tas known to date show remarkably similar substrate selectivity characterized by stringent steric constraint precluding entry of a substituent larger than an ethyl group in the small binding pocket (s) and dual recognition of an aromatic substituent as well as a carboxylate group in the large pocket (l). the strictly defined substrate selectivity of the available ω-tas remains a lim ... | 2011 | 21983703 |
| diversity of acetic acid bacteria present in healthy grapes from the canary islands. | the identification of acetic acid bacteria (aab) from sound grapes from the canary islands is reported in the present study. no direct recovery of bacteria was possible in the most commonly used medium, so microvinifications were performed on grapes from tenerife, la palma and lanzarote islands. up to 396 aab were isolated from those microvinifications and identified by 16s rrna gene sequencing and phylogenetic analysis. with this method, acetobacter pasteurianus, acetobacter tropicalis, glucono ... | 2011 | 21903289 |
| 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, ... | 2010 | 20697694 |
| saccharomyces cerevisiae metabolism in ecological context. | the architecture and regulation of saccharomyces cerevisiae metabolic network are among the best studied owing to its widespread use in both basic research and industry. yet, several recent studies have revealed notable limitations in explaining genotype-metabolic phenotype relations in this yeast, especially when concerning multiple genetic/environmental perturbations. apparently unexpected genotype-phenotype relations may originate in the evolutionarily shaped cellular operating principles bei ... | 2016 | 27634775 |
| 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 ... | 2014 | 25538690 |
| 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 ... | 2013 | 24099461 |
| 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 ... | 2013 | 24039725 |
| ehrlichia chaffeensis tandem repeat proteins and ank200 are type 1 secretion system substrates related to the repeats-in-toxin exoprotein family. | ehrlichia chaffeensis has type 1 and 4 secretion systems (t1ss and t4ss), but the substrates have not been identified. potential substrates include secreted tandem repeat protein (trp) 47, trp120, and trp32, and the ankyrin repeat protein, ank200, that are involved in molecular host-pathogen interactions including dna binding and a network of protein-protein interactions with host targets associated with signaling, transcriptional regulation, vesicle trafficking, and apoptosis. in this study we ... | 2011 | 22919588 |
| 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 ... | 2014 | 25418915 |
| 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 ... | 2014 | 24740089 |
| 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. | 2016 | 27089923 |
| 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 ... | 2016 | 26731734 |
| structural studies of pseudomonas and chromobacterium ω-aminotransferases provide insights into their differing substrate specificity. | the crystal structures and inhibitor complexes of two industrially important ω-aminotransferase enzymes from pseudomonas aeruginosa and chromobacterium violaceum have been determined in order to understand the differences in their substrate specificity. the two enzymes share 30% sequence identity and use the same amino acceptor, pyruvate; however, the pseudomonas enzyme shows activity towards the amino donor β-alanine, whilst the chromobacterium enzyme does not. both enzymes show activity toward ... | 2013 | 23519665 |
| Gene cloning and characterization of a-amino acid ester acyl transferase in Empedobacter brevis ATCC14234 and Sphingobacterium siyangensis AJ2458. | The gene encoding a-amino acid ester acyl transferase (AET), the enzyme that catalyzes the peptide-forming reaction from amino acid methyl esters and amino acids, was cloned from Empedobacter brevis ATCC14234 and Sphingobacterium siyangensis AJ2458 and expressed in Escherichia coli. This is the first report on the aet gene. It encodes a polypeptide composed of 616 (ATCC14234) and 619 (AJ2458) amino acids residues. The V(max) values of these recombinant enzymes during the catalysis of L-alanyl-L- ... | 2011 | 22056425 |
| characterization of rpoh in acetobacter pasteurianus nbrc3283. | the rpoh in acetobacter pasteurianus nbrc3283 was characterized. it was revealed that the rpoh controls the expression of groel, dnakj, grpe, and clpb to different extents. in addition, the rpoh disruption mutant became apt to be affected by heat, ethanol, and acetic acid, indicating its importance in acetic acid fermentation. | 2011 | 21239225 |
| 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 ... | 2016 | 27398261 |
| 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 ... | 2014 | 25132799 |
| 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 ... | 2014 | 24916156 |
| isolation and preliminary characterization of amino acid substitution mutations that increase the activity of the osmoregulated prop protein of salmonella enterica serovar typhimurium. | in enterobacteriaceae, the prop protein, which takes up proline and glycine betaine, is subject to a post-translational control mechanism that increases its activity at high osmolarity. in order to investigate the osmoregulatory mechanism of the salmonella enterica prop, we devised a positive selection for mutations that conferred increased activity on this protein at low osmolarity. the selection involved the isolation of mutations in a proline auxotroph that resulted in increased accumulation ... | 2012 | 22360681 |
| 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 ... | 2014 | 25369873 |
| 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 ... | 2014 | 25408687 |
| 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 ... | 2013 | 24860282 |
| 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 ... | 2013 | 24860282 |
| the clpb gene is involved in the stress response of myxococcus xanthus during vegetative growth and development. | the clp/hsp100 family of molecular chaperones is ubiquitous in both prokaryotes and eukaryotes. these proteins play important roles in refolding, disaggregating and degrading proteins damaged by stress. as a subclass of the clp/hsp100 family, clpb has been shown to be involved in various stress responses as well as other functions in bacteria. in the present study, we investigated the role of a predicted clpb-encoding gene, mxan5092, in the stress response during vegetative growth and developmen ... | 2012 | 22790397 |
| 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 ... | 2014 | 25271286 |
| 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 ... | 2015 | 26188050 |
| 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 ... | 2015 | 26188050 |
| 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 ... | 2016 | 27047484 |
| 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 ... | 2013 | 24455184 |
| valorization of date palm (phoenix dactylifera) fruit processing by-products and wastes using bioprocess technology - review. | the date palm phoenix dactylifera has played an important role in the day-to-day life of the people for the last 7000 years. today worldwide production, utilization and industrialization of dates are continuously increasing since date fruits have earned great importance in human nutrition owing to their rich content of essential nutrients. tons of date palm fruit wastes are discarded daily by the date processing industries leading to environmental problems. wastes such as date pits represent an ... | 2013 | 23961227 |
| 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 ... | 2014 | 25418915 |
| 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 ... | 2015 | 26009694 |
| 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. | 2015 | 25879753 |
| combined fluxomics and transcriptomics analysis of glucose catabolism via a partially cyclic pentose phosphate pathway in gluconobacter oxydans 621h. | in this study, the distribution and regulation of periplasmic and cytoplasmic carbon fluxes in gluconobacter oxydans 621h with glucose were studied by (13)c-based metabolic flux analysis ((13)c-mfa) in combination with transcriptomics and enzyme assays. for (13)c-mfa, cells were cultivated with specifically (13)c-labeled glucose, and intracellular metabolites were analyzed for their labeling pattern by liquid chromatography-mass spectrometry (lc-ms). in growth phase i, 90% of the glucose was oxi ... | 2013 | 23377928 |
| oasis: an automated program for global investigation of bacterial and archaeal insertion sequences. | insertion sequences (iss) are simple transposable elements present in most bacterial and archaeal genomes and play an important role in genomic evolution. the recent expansion of sequenced genomes offers the opportunity to study iss comprehensively, but this requires efficient and accurate tools for is annotation. we have developed an open-source program called oasis, or optimized annotation system for insertion sequences, which automatically annotates iss within sequenced genomes. oasis annotat ... | 2012 | 22904081 |
| 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 ... | 2013 | 24260361 |
| gut-associated microbes of drosophila melanogaster. | there is growing interest in using drosophila melanogaster to elucidate mechanisms that underlie the complex relationships between a host and its microbiota. in addition to the many genetic resources and tools drosophila provides, its associated microbiota is relatively simple (1-30 taxa), in contrast to the complex diversity associated with vertebrates (> 500 taxa). these attributes highlight the potential of this system to dissect the complex cellular and molecular interactions that occur betw ... | 2012 | 22572876 |