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structural and kinetic characterization of the 4-carboxy-2-hydroxymuconate hydratase from the gallate and protocatechuate 4,5-cleavage pathways of pseudomonas putida kt2440.the bacterial catabolism of lignin and its breakdown products is of interest for applications in industrial processing of ligno-biomass. the gallate degradation pathway ofpseudomonas putidakt2440 requires a 4-carboxy-2-hydroxymuconate (chm) hydratase (galb), which has a 12% sequence identity to a previously identified chm hydratase (ligj) fromsphingomonassp. syk-6. the structure of galb was determined and found to be a member of the pig-ln-acetylglucosamine deacetylase family; galb is structural ...201626867578
high resolution structures of periplasmic glucose-binding protein of pseudomonas putida csv86 reveal structural basis of its substrate specificity.periplasmic substrate-binding proteins (sbps) bind to the specific ligand with high affinity and mediate their transport into the cytoplasm via the cognate inner membrane atp-binding cassette proteins. because of low sequence identities, understanding the structural basis of substrate recognition by sbps has remained very challenging. there are several structures available for the ligand-bound sugar sbps, but very few unliganded structures are reported. no structural data are available for sugar ...201626861882
metabolic engineering of pseudomonas putida kt2440 for complete mineralization of methyl parathion and γ-hexachlorocyclohexane.agricultural soils are often cocontaminated with multiple pesticides. unfortunately, microorganisms isolated from natural environments do not possess the ability to simultaneously degrade different classes of pesticides. currently, we can use the approaches of synthetic biology to create a strain endowed with various catabolic pathways that do not exist in a natural microorganism. here, we describe the metabolic engineering of a biosafety pseudomonas putida strain kt2440 for complete mineralizat ...201626854500
biodegradation of chlorpyrifos by bacterial genus pseudomonas.chlorpyrifos is an organophosphorus pesticide commonly used in agriculture. it is noxious to a variety of organisms that include living soil biota along with beneficial arthropods, fish, birds, humans, animals, and plants. exposure to chlorpyrifos may cause detrimental effects as delayed seedling emergence, fruit deformities, and abnormal cell division. contamination of chlorpyrifos has been found about 24 km from the site of its application. there are many physico-chemical and biological approa ...201626837064
the toxin grat inhibits ribosome biogenesis.most bacteria encode numerous chromosomal toxin-antitoxin (ta) systems that are proposed to contribute to stress tolerance, as they are able to shift the cells to a dormant state. toxins act on a variety of targets with the majority attacking the translational apparatus. intriguingly, the toxicity mechanisms of even closely related toxins may differ essentially. here, we report on a new type of ta toxin that inhibits ribosome biogenesis. grat of the grata system has previously been described in ...201626833678
a pseudomonas putida double mutant deficient in butanol assimilation: a promising step for engineering a biological biofuel production platform.biological production in heterologous hosts is of interest for the production of the c4 alcohol (butanol) and other chemicals. however, some hurdles need to be overcome in order to achieve an economically viable process; these include avoiding the consumption of butanol and maintaining tolerance to this solvent during production. pseudomonas putida is a potential host for solvent production; in order to further adapt p. putida to this role, we generated mini-tn5 mutant libraries in strain bird-1 ...201626818251
mechanistic understanding of reduced agnp phytotoxicity induced by extracellular polymeric substances.a knowledge gap concerning the potential effects of extracellular polymeric substances (eps), a common organic material but highly variable in their composition of microbial origin, on the fate and phytotoxicity of silver nanoparticles (agnp) still remains. a 48-h root elongation toxicity test showed that agnp toxicity to wheat triticum aestivum l. was dramatically alleviated by eps isolated from pseudomonas putida, as revealed by 7-59% increase in relative root elongation (rre), 8-99% increase ...201626808239
comparisons of the transferability of plasmids pcar1, pb10, r388, and nah7 among pseudomonas putida at different cell densities.the transferability of plasmids pcar1, pb10, r388, and nah7 was compared using the same donor-recipient system at different cell density combinations in liquid or on a solid surface. pcar1 was efficiently transferred in liquid, whereas the other plasmids were preferentially transferred on a solid surface. difference of liquid or solid affected the transfer frequency especially at lower cell densities.201626806196
influence of oxygen transfer on pseudomonas putida effects on growth rate and biodesulfurization capacity.the growth rate and desulfurization capacity accumulated by the cells during the growth of pseudomonas putida kth2 under different oxygen transfer conditions in a stirred and sparged tank bioreactor have been studied. hydrodynamic conditions were changed using different agitation conditions. during the culture, several magnitudes associated to growth, such as the specific growth rate, the dissolved oxygen concentration and the carbon source consumption have been measured. experimental results in ...201626762940
pseudomonas putida attunes morphophysiological, biochemical and molecular responses in cicer arietinum l. during drought stress and recovery.drought is one of the most important abiotic stresses that adversely affect plant growth and yield potential. however, some drought resistant rhizosphere competent bacteria are known to improve plant health and promote growth during abiotic stresses. present study showed the role of pseudomonas putida mtcc5279 (ra) in ameliorating drought stress on cv. bg-362 (desi) and cv. bg-1003 (kabuli) chickpea cultivars under in vitro and green house conditions. polyethylene glycol-induced drought stress s ...201626744996
the response of aggregated pseudomonas putida cp1 cells to uv-c and uv-a/b disinfection.uv radiation is a spread method used worldwide for the disinfection of water. however, much of the research on the disinfection of bacterial cells by uv has focused on planktonic cells. many bacterial cells in nature are present in clumps or aggregates, and these aggregates, which are more resistant to disinfection than their planktonic counterparts, can be problematic in engineered water systems. the current research used pseudomonas putida (p. putida) cp1, an environmental and non-pathogenic m ...201627655528
in silico analysis for prediction of degradative capacity of pseudomonas putida sf1.the study employs draft genome sequence data to explore p-nitrophenol (pnp) degradation activity of pseudomonas putida strain sf-1 at a genomic scale. annotation analysis proposes that the strain sf1 not only possesses the gene cluster for pnp utilization but also for the utilization of benzoate, catechol, hydroxybenzoate, protocatechuate, and homogentisate. further, the analysis was carried out to understand more details of pnp 4-monooxygenase and its regulator. a comparative analysis of pnp 4- ...201627317892
signaling states of a short blue-light photoreceptor protein ppsb1-lov revealed from crystal structures and solution nmr spectroscopy.light-oxygen-voltage (lov) domains represent the photo-responsive domains of various blue-light photoreceptor proteins and are widely distributed in plants, algae, fungi, and bacteria. here, we report the dark-state crystal structure of ppsb1-lov, a slow-reverting short lov protein from pseudomonas putida that is remarkably different from our previously published "fully light-adapted" structure [1]. a direct comparison of the two structures provides insight into the light-activated signaling mec ...201627291287
a pseudo-outbreak of pseudomonas putida and stenotrophomonas maltophilia in a bronchoscopy unit.endoscopes represent the medical devices most commonly linked to health care-associated outbreaks and pseudo-outbreaks. most of the recent outbreaks and pseudo-outbreaks have resulted from contaminated automated endoscope reprocessors (aer) or the use of damaged or malfunctioning bronchoscopes or contaminated equipment.201627627819
a rapid method to estimate nadh regeneration rates in living cells.we introduce a rapid whole cell assay for the estimation of nadh regeneration rates based on the fluorescent dye resazurin. a co-feed of formate and glucose, known to increase the intrinsic nadh regeneration rate of p. putida kt2440, was chosen as model system for the validation of this assay.201627592588
structural and kinetic properties of the aldehyde dehydrogenase nahf, a broad substrate specificity enzyme for aldehyde oxidation.the salicylaldehyde dehydrogenase (nahf) catalyzes the oxidation of salicylaldehyde to salicylate using nad(+) as a cofactor, the last reaction of the upper degradation pathway of naphthalene in pseudomonas putida g7. the naphthalene is an abundant and toxic compound in oil and has been used as a model for bioremediation studies. the steady-state kinetic parameters for oxidation of aliphatic or aromatic aldehydes catalyzed by 6xhis-nahf are presented. the 6xhis-nahf catalyzes the oxidation of ar ...201627580341
recombineering and i-scei-mediated pseudomonas putida kt2440 scarless gene deletion.pseudomonas putida kt2440 is a saprophytic, generally recognized as safe microorganism that plays important roles in the biodegradation and production of value-added chemicals. chromosomal gene deletion of p. putida kt2440 usually involves time-consuming gene coning, conjugal transfer and counterselection. recently, we developed a p. putida kt2440 markerless gene deletion method based on recombineering and cre/loxp site-specific recombination. pcr-based λ red recombineering circumvents the tedio ...201627765807
a broad mercury resistant strain of pseudomonas putida secretes pyoverdine under limited iron conditions and high mercury concentrations.the pseudomonas putida fb1, known as a broad-spectrum mercury resistant strain, becomes yellow-green due to the secretion of pyoverdine (pvds) under limited iron conditions and high mercury concentrations. different modified nelson's media were obtained by adding mercury, iron, and the complexing agent nitrilotriacetic acid to demonstrate that the strain produces only the highest concentrations of pvds due to the induction with 25 µm hg(2+). an amount of 250 mg pvds was purified from the superna ...201627848043
effect of crc and hfq proteins on the transcription, processing, and stability of the pseudomonas putida crcz srna.in pseudomonas putida, the hfq and crc proteins regulate the expression of many genes in response to nutritional and environmental cues, by binding to mrnas that bear specific target motifs and inhibiting their translation. the effect of these two proteins is antagonized by the crcz and crcy small rnas (srnas), the levels of which vary greatly according to growth conditions. the crcz and crcy genes are transcribed from promoters pcrcz and pcrcy, respectively, a process that relies on the cbrb tr ...201627777366
production of encapsulated creatinase using yeast spores.yeast spores can be used as a carrier to produce enzyme capsules. in the present study, this technique was applied to a diagnostic enzyme named creatinase. we found that a secretory form of pseudomonas putida creatinase could be entrapped in the spore wall, and such spores were used as creatinase capsules. the activity of the encapsulated creatinase was largely improved by mild spore wall defective mutations, such as dit1 or osw2 deletions. the advantages of this method include the following: en ...201627791465
biofilm removal using carbon dioxide aerosols without nitrogen purge.biofilms can cause serious concerns in many applications. not only can they cause economic losses, but they can also present a public health hazard. therefore, it is highly desirable to remove biofilms from surfaces. many studies on co2 aerosol cleaning have employed nitrogen purges to increase biofilm removal efficiency by reducing the moisture condensation generated during the cleaning. however, in this study, periodic jets of co2 aerosols without nitrogen purges were used to remove pseudomona ...201627842343
responses of pseudomonas putida to zinc excess determined at the proteome level: pathways dependent and independent of colrs.zinc is an important micronutrient for bacteria, but its excess is toxic. recently, the colrs two-component system was shown to detect and respond to zinc excess and to contribute to zinc tolerance of pseudomonas putida. here, we applied a label-free whole-cell proteome analysis to compare the zinc-induced responses of p. putida and colr knockout. we identified dozens of proteins that responded to zinc in a colr-independent manner, among others, known metal efflux systems czccba1, czccba2, cada2 ...201627797207
elimination of persistent emerging micropollutants in a suspended-bed photocatalytic reactor: influence of operating conditions and combination with aerobic biological treatment.a larger, lab-scale photocatalytic suspended-bed reactor using tio2 sol-gel-coated expanded clay granules as a bed material was evaluated for oxidative removal of the persistent pharmaceuticals doxycycline, prednisolone, amoxicillin, and sulfamethizole, as well as their mixture, in ppm concentrations. the photocatalytic degradation potential of drug molecules increases as their adsorption affinity increases towards tio2-containing coatings. the performance of the photocatalytic reactor in the re ...201627830220
development and evaluation of an experimental protocol for 3-d visualization and characterization of the structure of bacterial biofilms in porous media using laboratory x-ray tomography.the development of a reliable model allowing accurate predictions of biofilm growth in porous media relies on a good knowledge of the temporal evolution of biofilm structure within the porous network. since little is known about the real 3-d structure of biofilms in porous media, this work was aimed at developing a new experimental protocol to visualize the 3-d microstructure of the inside of a porous medium using laboratory x-ray microtomography. a reliable and reproducible methodology is propo ...201627827532
toxicity testing of pristine and aged silver nanoparticles in real wastewaters using bioluminescent pseudomonas putida.impact of aging on nanoparticle toxicity in real matrices is scarcely investigated due to a lack of suitable methodologies. herein, the toxicity of pristine and aged silver nanoparticles (ag nps) to a bioluminescent pseudomonas putida bioreporter was measured in spiked crude and final wastewater samples (cws and fws, respectively) collected from four wastewater treatment plants (wwtps). results showed lower toxicity of pristine ag nps in cws than in fws. the effect of the matrix on the eventual ...201628344306
isolation and characterization of bacteria that use furans as the sole carbon source.five bacterial strains were isolated from wastewater treatment facilities which were able to use furfural as the sole carbon source. based on 16s rrna phylogenetic analysis, these strains were identified as cupriavidus pinatubonensis (designated als1280), pigmentiphaga sp. (als1172), pseudomonas sp. bwdy (als1279), pseudomonas mendocina (als1131), and pseudomonas putida (als1267). in all cases, growth under oxygenated conditions on furfural was accompanied by the transient accumulation of 2-furo ...201626419660
use of response surface method for maximizing the production of arginine deiminase by pseudomonas putida.statistically designed experiments were used to optimize the production of arginine deiminase (adi) by pseudomonas putida kt2440 in batch culture. a plackett-burman design involving eleven factors showed that adi production was most influenced by the initial ph and the initial concentrations of glucose and yeast extract. a central composite experimental design showed that the optimal values of these factors were 8.0, 10 g/l and 12.5 g/l, respectively. the other components of the optimal culture ...201628352521
potential of pseudomonas putida pci2 for the protection of tomato plants against fungal pathogens.tomato is one of the most economically attractive vegetable crops due to its high yields. diseases cause significant losses in tomato production worldwide. we carried out polymerase chain reaction studies to detect the presence of genes encoding antifungal compounds in the dna of pseudomonas putida strain pci2. we also used liquid chromatography-electrospray tandem mass spectrometry to detect and quantify the production of compounds that increase the resistance of plants to diseases from culture ...201627246499
two-step bioleaching of copper and gold from discarded printed circuit boards (pcb).an effective strategy for environmentally sound biological recovery of copper and gold from discarded printed circuit boards (pcb) in a two-step bioleaching process was experimented. in the first step, chemolithotrophic acidophilic acidithiobacillus ferrivorans and acidithiobacillus thiooxidans were used. in the second step, cyanide-producing heterotrophic pseudomonas fluorescens and pseudomonas putida were used. results showed that at a 1% pulp density (10g/l pcb concentration), 98.4% of the co ...201626704063
hydrogen isotope fractionation as a tool to identify aerobic and anaerobic pah biodegradation.aerobic and anaerobic polycyclic aromatic hydrocarbon (pah) biodegradation was characterized by compound specific stable isotope analysis (csia) of the carbon and hydrogen isotope effects of the enzymatic reactions initiating specific degradation pathways, using naphthalene and 2-methylnaphtalene as model compounds. aerobic activation of naphthalene and 2-methylnaphthalene by pseudomonas putida ncib 9816 and pseudomonas fluorescens atcc 17483 containing naphthalene dioxygenases was associated wi ...201626855125
expression of the diguanylate cyclase gcba is regulated by fleq in response to cyclic di-gmp in pseudomonas putida kt2440.cyclic di-gmp (c-di-gmp), a ubiquitous bacterial second messenger that regulates diverse cellular processes, is synthesized by diguanylate cyclase (dgc) and degraded by phosphodiesterase (pde). gcba is a well conserved dgc among pseudomonas species, and has been reported to influence biofilm formation and flagellar motility in pseudomonas fluorescens and pseudomonas aeruginosa. here we confirm the function of gcba in pseudomonas putida and reveal that expression of gcba is regulated by fleq in r ...201627701843
interference competition among household strains of pseudomonas.bacterial species exhibit biogeographical patterns like those observed in larger organisms. the distribution of bacterial species is driven by environmental selection through abiotic and biotic factors as well dispersal limitations. we asked whether interference competition, a biotic factor, could explain variability in habitat use by pseudomonas species in the human home. to answer this question, we screened almost 8000 directional, pairwise interactions between 89 pseudomonas strains including ...201626276409
a novel papillation assay for the identification of genes affecting mutation rate in pseudomonas putida and other pseudomonads.formation of microcolonies (papillae) permits easy visual screening of mutational events occurring in single colonies of bacteria. in this study, we have established a novel papillation assay employable in a wide range of pseudomonads including pseudomonas aeruginosa and pseudomonas putida for monitoring mutation frequency in distinct colonies. with the aid of this assay, we conducted a genome-wide search for the factors affecting mutation frequency in p. putida. screening ∼27,000 transposon mut ...201627447898
the cryptic dsda gene encodes a functional d-serine dehydratase in pseudomonas aeruginosa pao1.d-serine, an important neurotransmitter, also contributes to bacterial adaptation and virulence in humans. it was reported that pseudomonas aeruginosa pao1 can grow on d-serine as the sole nitrogen source, and growth was severely reduced in the dada mutant devoid of the d-alanine dehydrogenase with broad substrate specificity. in this study, the dsda gene (pa3357) encoding a putative d-serine dehydratase was subjected to further characterization. growth on d-serine as the sole source of nitrogen ...201626957519
assessment of the contribution of chemoreceptor-based signalling to biofilm formation.although it is well established that one- and two-component regulatory systems participate in regulating biofilm formation, there also exists evidence suggesting that chemosensory pathways are also involved. however, little information exists about which chemoreceptors and signals modulate this process. here we report the generation of the complete set of chemoreceptor mutants of pseudomonas putida kt2440 and the identification of four mutants with significantly altered biofilm phenotypes. these ...201626662997
removal of 2-butoxyethanol gaseous emissions by biotrickling filtration packed with polyurethane foam.the removal of 2-butoxyethanol from gaseous emissions was studied using two biotrickling filters (btf1 and btf2) packed with polyurethane foam. two different inoculum sources were used: a pure culture of pseudomonas sp. boe200 (btf1) and activated sludge from a municipal wastewater treatment plant (btf2). the bioreactors were operated at inlet loads (ils) of 130 and 195 g m(-3) hour(-1) and at an empty bed residence time (ebrt) of 12.5s. under an il of ∼130 g m(-3) hour(-1), btf1 presented highe ...201626596886
analysis of the core genome and pangenome of pseudomonas putida.pseudomonas putida are strict aerobes that proliferate in a range of temperate niches and are of interest for environmental applications due to their capacity to degrade pollutants and ability to promote plant growth. furthermore solvent-tolerant strains are useful for biosynthesis of added-value chemicals. we present a comprehensive comparative analysis of nine strains and the first characterization of the pseudomonas putida pangenome. the core genome of p. putida comprises approximately 3386 g ...201626261031
the expression of many chemoreceptor genes depends on the cognate chemoeffector as well as on the growth medium and phase.chemoreceptor-based signaling is a major bacterial signal transduction mechanism. escherichia coli, the traditional model, has five chemoreceptors. recent genome analyses have shown that many bacteria have a much higher number of chemoreceptors. pseudomonas putida kt2440 is an alternative model that has 27 chemoreceptors and the cognate chemoeffector is known for many of them. here, we address the question whether and which factors modulate chemoreceptor gene expression. we report reverse transc ...201627632030
esterase estk from pseudomonas putida mt-2: an enantioselective acetylesterase with activity for deacetylation of xylan and poly(vinylacetate).an extracellular esterase gene estk was identified in pseudomonas putida mt-2, and was overexpressed to high levels in escherichia coli. the recombinant estk enzyme was purified and characterised kinetically against p-nitrophenyl ester and other aryl-alkyl ester substrates, and was found to be selective for hydrolysis of acetyl ester substrates, with high activity for p-nitrophenyl acetate (kcat 5.5 s(-1) , km 285 μm). recombinant estk was found to catalyse deacetylation of acetylated beech xyla ...201627696534
on-chip cell lysis by antibacterial non-leaching reusable quaternary ammonium monolithic column.reusable antibacterial non-leaching monolithic columns polymerized in microfluidic channels designed for on-chip cell lysis applications were obtained by the photoinitiated free radical copolymerization of diallyldimethylammonium chloride (dadmac) and ethylene glycol diacrylate (egda) in the presence of a porogenic solvent. the microfluidic channels were fabricated in cross-linked poly(methyl methacrylate) (x-pmma) substrates by laser micromachining. the monolithic columns have the ability to in ...201626671610
integrated acoustic separation, enrichment, and microchip polymerase chain reaction detection of bacteria from blood for rapid sepsis diagnostics.this paper describes an integrated microsystem for rapid separation, enrichment, and detection of bacteria from blood, addressing the unmet clinical need for rapid sepsis diagnostics. the blood sample is first processed in an acoustophoresis chip, where red blood cells are focused to the center of the channel by an acoustic standing wave and sequentially removed. the bacteria-containing plasma proceeds to a glass capillary with a localized acoustic standing wave field where the bacteria are trap ...201627264110
nitrile-synthesizing enzyme: gene cloning, overexpression and application for the production of useful compounds.one of the nitrile-synthesizing enzymes, β-cyano-l-alanine synthase, catalyzes β-cyano-l-alanine (β-cnala) from potassium cyanide and o-acetyl-l-serine or l-cysteine. we have identified this enzyme from pseudomonas ovalis no. 111. in this study, we cloned the β-cnala synthase gene and expressed it in escherichia coli and rhodococcus rhodochrous. furthermore, we carried out co-expression of β-cnala synthase with nitrilase or nitrile hydratases in order to synthesize aspartic acid and asparagine f ...201627250664
regulation of hydroxylation and nitroreduction pathways during metabolism of the neonicotinoid insecticide imidacloprid by pseudomonas putida.imidacloprid (imi) is mainly metabolized via nitroreduction and hydroxylation pathways, which produce different metabolites that are toxic to mammals and insects. however, regulation of imi metabolic flux between nitroreduction and hydroxylation pathways is still unclear. in this study, pseudomonas putida was found to metabolize imi to 5-hydroxy and nitroso imi and was therefore used for investigating the regulation of imi metabolic flux. the cell growth time, cosubstrate, dissolved oxygen conce ...201627230024
synthesis of chiral 2-alkanols from n-alkanes by a p. putida whole-cell biocatalyst.the cytochrome p450 monooxygenase cyp154a8 from nocardia farcinica was previously found to catalyze hydroxylation of linear alkanes (c7 -c9 ) with a high regio- and stereoselectivity. the objective of this study was to integrate cyp154a8 along with suitable redox partners into a whole-cell system for the production of chiral 2-alkanols starting from alkanes. both recombinant escherichia coli and pseudomonas putida whole-cell biocatalysts tested for this purpose showed the ability to produce chir ...201626887569
design of inducible expression vectors for improved protein production in ralstonia eutropha h16 derived host strains.ralstonia eutropha h16 (cupriavidus necator h16) is a gram-negative, facultative chemolithoautotrophic bacterium which can use h2 and co2 as sole energy and carbon sources in the absence of organic substrates. the biotechnological use of r. eutropha h16 on an industrial scale has already been established; however, only a small number of tools promoting inducible gene expression is available. within this study two systems promoting inducible expression were designed on the basis of the strong j5 ...201627085887
genetic programming of catalytic pseudomonas putida biofilms for boosting biodegradation of haloalkanes.bacterial biofilms outperform planktonic counterparts in whole-cell biocatalysis. the transition between planktonic and biofilm lifestyles of the platform strain pseudomonas putida kt2440 is ruled by a regulatory network controlling the levels of the trigger signal cyclic di-gmp (c-di-gmp). this circumstance was exploited for designing a genetic device that over-runs the synthesis or degradation of c-di-gmp--thus making p. putida to form biofilms at user's will. for this purpose, the transcripti ...201626620533
metabolic engineering of pseudomonas putida for production of docosahexaenoic acid based on a myxobacterial pufa synthase.long-chain polyunsaturated fatty acids (lc-pufas) can be produced de novo via polyketide synthase-like enzymes known as pufa synthases, which are encoded by pfa biosynthetic gene clusters originally discovered from marine microorganisms. recently similar gene clusters were detected and characterized in terrestrial myxobacteria revealing several striking differences. as the identified myxobacterial producers are difficult to handle genetically and grow very slowly we aimed to establish heterologo ...201626617065
impact of nanoscale zero valent iron on bacteria is growth phase dependent.the toxic effect of nanoscale zero valent iron (nzvi) particles on bacteria from different growth phases was studied. four bacterial strains namely escherichia coli strains jm109 and bw25113, and pseudomonas putida strains kt2440 and f1 were experimented. the growth curves of these strains were determined. bacterial cells were harvested based on the predetermined time points, and exposed to nzvi. cell viability was determined by the plate count method. bacterial cells in lag and stationary phase ...201626378872
structural similarities and differences in h-ns family proteins revealed by the n-terminal structure of turb in pseudomonas putida kt2440.h-ns family proteins play key roles in bacterial nucleoid compaction and global transcription. mvat homologues in pseudomonas have almost negligible amino acid sequence identity with h-ns, but can complement an hns-related phenotype of escherichia coli. here, we report the crystal structure of the n-terminal dimerization/oligomerization domain of turb, an mvat homologue in pseudomonas putida kt2440. our data identify two dimerization sites; the structure of the central dimerization site is almos ...201627709616
the ssr protein (t1e_1405) from pseudomonas putida dot-t1e enables oligonucleotide-based recombineering in platform strain p. putida em42.some strains of the soil bacterium pseudomonas putida have become in recent years platforms of choice for hosting biotransformations of industrial interest. despite availability of many genetic tools for this microorganism, genomic editing of the cell factory p. putida em42 (a derivative of reference strain kt2440) is still a time-consuming endeavor. in this work we have investigated the in vivo activity of the ssr protein encoded by the open reading frame t1e_1405 from pseudomonas putida dot-t1 ...201627367544
stereochemical consequences of vinylpyruvate hydratase-catalyzed reactions.a stereochemical analysis has been carried out on two vinylpyruvate hydratases (vph), which convert 2-hydroxy-2,4-pentadienoate to 2-keto-4s-hydroxypentanoate in meta-fission pathways. bacterial strains with this pathway can use aromatic compounds as sole sources of energy and carbon. the analysis was carried out using the 5-methyl and 5-chloro derivatives of 2-hydroxy-2,4-pentadienoate with the enzymes from pseudomonas putida mt-2 (pp) and leptothrix cholodnii sp-6 (lc). in both organisms, vph ...201627362840
investigation of plasmid-induced growth defect in pseudomonas putida.genetic engineering in bacteria mainly relies on the use of plasmids. but despite their pervasive use for physiological studies as well as for the design and optimization of industrially used production strains, only limited information about plasmid induced growth defects is available for different replicons and organisms. here, we present the identification and characterization of such a phenomenon for pseudomonas putida transformants carrying the pbbr1-derived plasmid pmis1. we identified the ...201627287537
two novel sets of genes essential for nicotine degradation by sphingomonas melonis ty.nicotine is a type of environmental pollutant present in the tobacco waste that is generated during tobacco manufacturing. sphingomonas melonis ty can utilize nicotine as a sole source of carbon, nitrogen and energy via a variant of the pyridine and pyrrolidine pathway (the vpp pathway). in this study, we report the identification of two novel sets of genes, ndra1a2a3, and ndrb1b2b3b4, which are crucial for nicotine degradation by strain ty. ndra1a2a3 and ndrb1b2b3b4 exhibit similarity with both ...201628144232
extraction method plays critical role in antibacterial activity of propolis-loaded hydrogels.extracted propolis has been used for a long time as a remedy. however, if the release rate of propolis is not controlled, the efficacy is reduced. to overcome this issue, extracted propolis was added to a cryogel system. propolis collected from southern brazil was extracted using different methods and loaded at different concentrations into polyvinyl alcohol (pva) and polyacrylic acid hydrogels as carrier systems. the material properties were investigated with a focus on the propolis release pro ...201626886307
screening through the plicable promoter toolbox enhances protein production in escherichia coli.escherichia coli is a common host for recombinant protein production in which production titers are highly dependent on the employed expression system. promoters are thereby a key element to control gene expression levels. in this study, a novel plicable promoter toolbox was developed which enables in a single cloning step and after a screening experiment to identify out of ten iptg-inducible promoters (t7, a3, lpp, tac, pac, sp6, lac, npr, trc and syn) the most suitable one for high level prote ...201627753230
dna sequence-selective c8-linked pyrrolobenzodiazepine-heterocyclic polyamide conjugates show anti-tubercular-specific activities.new chemotherapeutic agents with novel mechanisms of action are in urgent need to combat the tuberculosis pandemic. a library of 12 c8-linked pyrrolo[2,1-c][1,4]benzodiazepine (pbd)-heterocyclic polyamide conjugates (1-12) was evaluated for anti-tubercular activity and dna sequence selectivity. the pbd conjugates were screened against slow-growing mycobacterium bovis bacillus calmette-guérin and m. tuberculosis h37rv, and fast-growing escherichia coli, pseudomonas putida and rhodococcus sp. rha1 ...201627168314
identification of a chemoreceptor that specifically mediates chemotaxis toward metabolizable purine derivatives.chemotaxis is an essential mechanism that enables bacteria to move toward favorable ecological niches. escherichia coli, the historical model organism for studying chemotaxis, has five well-studied chemoreceptors. however, many bacteria with different lifestyle have more chemoreceptors, most of unknown function. using a high throughput screening approach, we identified a chemoreceptor from pseudomonas putida kt2440, named mcph, which specifically recognizes purine and its derivatives, adenine, g ...201626355499
unusual poly-3-hydroxyalkanoates (phas) biosynthesis behavior of pseudomonas putida bet001 and delftia tsuruhatensis bet002 isolated from palm oil mill effluent.pseudomonas putida bet001 and delftia tsuruhatensis bet002, isolated from palm oil mill effluent, accumulated poly (3-hydroxyalkanoates) (pha) when grown on aliphatic fatty acids, sugars and glycerol. the substrates were supplied at 20:1 c/n mole ratio. among c-even n-alkanoic acids, myristic acid gave the highest pha content 26 and 28 wt% in p. putida and d. tsuruhatensis respectively. among c-odd n-alkanoic acids, undecanoic gave the highest pha content at 40 wt% in p. putida and 46 wt% in d. ...201626800648
cyp101j2, cyp101j3, and cyp101j4, 1,8-cineole-hydroxylating cytochrome p450 monooxygenases from sphingobium yanoikuyae strain b2.we report the isolation and characterization of three new cytochrome p450 monooxygenases: cyp101j2, cyp101j3, and cyp101j4. these p450s were derived from sphingobium yanoikuyae b2, a strain that was isolated from activated sludge based on its ability to fully mineralize 1,8-cineole. genome sequencing of this strain in combination with purification of native 1,8-cineole-binding proteins enabled identification of 1,8-cineole-binding p450s. the p450 enzymes were cloned, heterologously expressed (n- ...201627590809
efficient hydroxylation of 1,8-cineole with monoterpenoid-resistant recombinant pseudomonas putida gs1.in this work, monoterpenoid hydroxylation with pseudomonas putida gs1 and kt2440 were investigated as host strains, and the cytochrome p450 monooxygenase cyp176a1 (p450cin) and its native redox partner cindoxin (cinc) from citrobacter braakii were introduced in p. putida to catalyze the stereoselective hydroxylation of 1,8-cineole to (1r)-6β-hydroxy-1,8-cineole. growth experiments in the presence of 1,8-cineole confirmed pseudomonads' superior resilience compared to e. coli. whole-cell p. putida ...201627263007
biotechnological production of aromatic compounds of the extended shikimate pathway from renewable biomass.aromatic chemicals that contain an unsaturated ring with alternating double and single bonds find numerous applications in a wide range of industries, e.g. paper and dye manufacture, as fuel additives, electrical insulation, resins, pharmaceuticals, agrochemicals, in food, feed and cosmetics. their chemical production is based on petroleum (btx; benzene, toluene, and xylene), but they can also be obtained from plants by extraction. due to petroleum depletion, health compliance, or environmental ...201627871872
activity enhancement based on the chemical equilibrium of multiple-subunit nitrile hydratase from bordetella petrii.the maturation mechanism of nitrile hydratase (nhase) of pseudomonas putida nrrl-18668 was discovered and named as "self-subunit swapping." since the nhase of bordetella petrii dsm 12804 is similar to that of p. putida, the nhase maturation of b. petrii is proposed to be the same as that of p. putida. however, there is no further information on the application of nhase according to these findings. we successfully rapidly purified nhase and its activator through affinity his tag, and found that t ...201627075457
identification and characterization of a novel (+)-γ-lactamase from microbacterium hydrocarbonoxydans.2-azabicyclo[2.2.1]hept-5-en-3-one (γ-lactam) is an important precursor of many carbocyclic nucleoside analogs and pharmaceuticals. (-)-γ-lactam has attracted much attention because of its role as an intermediate of antiviral drugs such as abacavir and carbovir. (+)-γ-lactamase can be used for the kinetic resolution of γ-lactam to obtain (-)-γ-lactam. in this study, a novel (+)-γ-lactamase (mh33h4-5540) was discovered from the gene library of microbacterium hydrocarbonoxydans based on a colorime ...201627255489
a novel enterocin t1 with anti-pseudomonas activity produced by enterococcus faecium t1 from chinese tibet cheese.an enterocin-producing enterococcus faecium t1 was isolated from chinese tibet cheese. the enterocin was purified by sp-sepharose and reversed phase hplc. it was identified as unique from other reported bacteriocins based on molecular weight (4629 da) and amino acid compositions; therefore it was subsequently named enterocin t1. enterocin t1 was stable at 80-100 °c and over a wide ph range, ph 3.0-10.0. protease sensitivity was observed to trypsin, pepsin, papain, proteinase k, and pronase e. im ...201626745981
structure of methionine γ-lyase from clostridium sporogenes.methionine γ-lyase (mgl) is a pyridoxal 5'-phosphate-dependent enzyme that catalyzes the γ-elimination reaction of l-methionine. the enzyme is a promising target for therapeutic intervention in some anaerobic pathogens and has attracted interest as a potential cancer treatment. the crystal structure of mgl from clostridium sporogenes has been determined at 2.37 å resolution. the fold of the protein is similar to those of homologous enzymes from citrobacter freundii, entamoeba histolytica, pseudo ...201626750487
bacteria induce pigment formation in the basidiomycete serpula lacrymans.basidiomycete fungi are characterized ecologically for their vital functional role in ecosystem carbon recycling and chemically for their capacity to produce a diverse array of small molecules. chromophoric natural products derived from the quinone precursor atromentin, such as variegatic acid and involutin, have been shown to function in redox cycling. yet, in the context of an inter-kingdom natural system these pigments are still elusive. here, we co-cultured the model saprotrophic basidiomyce ...201627699944
evaluation of the catalytic contribution from a positioned general base in ketosteroid isomerase.proton transfer reactions are ubiquitous in enzymes and utilize active site residues as general acids and bases. crystal structures and site-directed mutagenesis are routinely used to identify these residues, but assessment of their catalytic contribution remains a major challenge. in principle, effective molarity measurements, in which exogenous acids/bases rescue the reaction in mutants lacking these residues, can estimate these catalytic contributions. however, these exogenous moieties can be ...201627410422
nutrition effects on the biofilm immobilization and 3,5-dnba degradation of comamonas testosteroni a3 during bioaugmentation treatment.the survival of inoculated microbes is critical for successful bioaugmentation in wastewater treatment. the influence of readily available nutrients (rans) on the colonization of two functional bacteria, pseudomonas putida m9, a strong biofilm-forming strain, and comamonas testosteroni a3, a 3,5-dinitrobenzoic acid (3,5-dnba)-degrading strain, in biofilms was studied with 3,5-dinitrobenoic acid synthetic wastewater (dcmm) complemented with various ratios of luria-bertani broth (lb). with the inc ...201625345550
direct detection of burkholderia cepacia in susceptible pharmaceutical products using semi-nested pcr.burkholderia cepaciahas recently received a considerable attention as one of the major risks in susceptible pharmaceutical products. this microorganism can easily propagate and cause vast and severe contamination, especially to the water supplies for pharmaceutical companies. moreover, it proliferates within the products and can cause severe infections for humans. therefore, fast and sensitive detection of these bacteria is of a great demand. the present study introduces improved application of ...201626797972
a preliminary study on the antibacterial mechanism of tegillarca granosa hemoglobin by derived peptides and peroxidase activity.the blood clam, tegillarca granosa, is one of the few bivalve molluscs containing hemoglobin (hb). in the present study, we purified two types of t. granosa hemoglobin, tg-hbi and tg-hbii, using size exclusion chromatography and measured their antibacterial and peroxidase activities. we also tested antibacterial activities of peptides prepared by trypsin digestion of purified tg-hb and reversed-phase high-performance liquid chromatography purification. purified tg-hbi and tg-hbii showed antibact ...201626876330
preparation and biological activity of new collagen composites, part i: collagen/zinc titanate nanocomposites.the aim of this investigation was to develop new antimicrobial collagen/zinc titanate (zntio3) biomaterials using a sol-gel cryogenic draying technology in keeping the native collagen activity. broad-spectrum antimicrobial activity was demonstrated against firmicutes (staphylococcus epidermidis, bacillus cereus, and candida lusitaniae) and gracilicutes (escherichia coli, salmonella enterica, and pseudomonas putida) microorganisms. the antimicrobial activity as well as the cytotoxicity were speci ...201627138724
rational design, synthesis, anti-hiv-1 rt and antimicrobial activity of novel 3-(6-methoxy-3,4-dihydroquinolin-1(2h)-yl)-1-(piperazin-1-yl)propan-1-one derivatives.in the present study, fifteen novel 3-(6-methoxy-3,4-dihydroquinolin-1(2h)-yl)-1-(piperazin-1-yl)propan-1-one (6a-o) derivatives were designed as inhibitor of hiv-1 rt using ligand based drug design approach and in-silico evaluated for drug-likeness properties. designed compounds were synthesized, characterized and in-vitro evaluated for rt inhibitory activity against wild hiv-1 rt strain. among the tested compounds, four compounds (6a, 6b, 6j and 6o) exhibited significant inhibition of hiv-1 rt ...201627288643
molecular and spectroscopic characterization of aspergillus flavipes and pseudomonas putida l-methionine γ-lyase in vitro.pseudomonas putida l-methionine γ-lyase (ppmgl) has been recognized as an efficient anticancer agent, however, its antigenicity and stability remain as critical challenges for its clinical use. from our studies, aspergillus flavipes l-methionine γ-lyase (afmgl) displayed more affordable biochemical properties than ppmgl. thus, the objective of this work was to comparatively assess the functional properties of afmgl and ppmgl via stability of their internal aldimine linkage, tautomerism of pyrido ...201627796875
mcpq is a specific citrate chemoreceptor that responds preferentially to citrate/metal ion complexes.chemoreceptors are at the beginning of chemosensory pathways that mediate chemotaxis. pseudomonas putida kt2440 is predicted to have 27 chemoreceptors, most of which uncharacterized. we have previously identified mcps as chemoreceptor for krebs cycle intermediates. citrate is primarily present in the environment as metal complex, which, however, is not recognized by mcps. we show here that the mcps paralogue mcpq recognizes specifically citrate and citrate/metal(2+) complexes. the mcpq ligand bi ...201626463109
mechanism-specific and whole-organism ecotoxicity of mono-rhamnolipids.biosurfactants like rhamnolipids are promising alternatives to chemical surfactants in a range of applications. a wider use requires an analysis of their environmental fate and their ecotoxicological potential. in the present study mono-rhamnolipids produced by a recombinant pseudomonas putida strain were analyzed using the green toxicology concept for acute and mechanism-specific toxicity in an ecotoxicological test battery. acute toxicity tests with the invertebrate daphnia magna and with zebr ...201626802344
silver nanoparticles formation by extracellular polymeric substances (eps) from electroactive bacteria.microbial extracellular polymeric substances (eps) excreted from microorganisms were a complex natural biological polymer mixture of proteins and polysaccharides, which played an important roles in the transport of metals, such as ag(+). electroactive bacteria, is an important class of environmental microorganisms, which can use iron or manganese mineral as terminal electron acceptors to generate energy for biosynthesis and cell maintenance. in this work, the eps extracted of three electroactive ...201626797954
[microbial composition of various surfaces of skin during develop- ment of atopic dermatitis based on data from maldi-tof mass-spectrometry identification method].study transformation of skin microflora during development of atopic dermatitis.201627228668
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
effect of fermented broth from lactic acid bacteria on pathogenic bacteria proliferation.in this study, the effect that 5 fermented broths of lactic acid bacteria (lab) strains have on the viability or proliferation and adhesion of 7 potentially pathogenic microorganisms was tested. the fermented broth from lactococcus lactis c660 had a growth inhibitory effect on escherichia coli k92 that reached of 31%, 19% to pseudomonas fluorescens, and 76% to staphylococcus epidermidis. the growth of staph. epidermidis was negatively affected to 90% by lc. lactis 11454 broth, whereas the growth ...201626851857
isolation and characterization of bacterial endophytes of curcuma longa l.fourteen endophytic bacterial isolates were isolated from the rhizome of curcuma longa l. were characterized on the basis of morphology, biochemical characteristics and 16s rrna gene sequence analysis. the isolates were identified to six strains namely bacillus cereus (ecl1), bacillus thuringiensis (ecl2), bacillus sp. (ecl3), bacillus pumilis (ecl4), pseudomonas putida (ecl5), and clavibacter michiganensis (ecl6). all the strains produced iaa and solubilized phosphate and only two strains produ ...201628330130
application of cinder gel-beads/reeds combination strategy for bioremediation of pyrene- and indeno(1,2,3-cd)pyrene-contaminated estuarine wetlands.pseudomonas putida pyr1 and acinetobacter baumannii inp1 isolated from liaohe estuarine wetlands were entrapped in cinder beads to make cinder gel-beads. they were combined with reeds for bioremediation of pyrene- and indeno(1,2,3-cd)pyrene-contaminated estuarine wetlands. the results showed that the removal percentages of pyrene and indeno(1,2,3-cd)pyrene (69.2 and 89.8 % respectively) in 40 days using cinder gel-beads/reeds were obviously higher than those using cinder gel-beads(52.6 and 70.0  ...201626897584
comparative genomics between two xenorhabdus bovienii strains highlights differential evolutionary scenarios within an entomopathogenic bacterial species.bacteria of the genus xenorhabdus are symbionts of soil entomopathogenic nematodes of the genus steinernema. this symbiotic association constitutes an insecticidal complex active against a wide range of insect pests. within xenorhabdus bovienii species, the x. bovienii cs03 strain (xb cs03) is nonvirulent when directly injected into lepidopteran insects, and displays a low virulence when associated with its steinernema symbiont. the genome of xb cs03 was sequenced and compared with the genome of ...201626769959
diffusion of bacterial cells in porous media.the chemotaxis signal transduction network regulates the biased random walk of many bacteria in favorable directions and away from harmful ones through modulating the frequency of directional reorientations. in mutants of diverse bacteria lacking the chemotaxis response, migration in classic motility agar, which constitutes a fluid-filled porous medium, is compromised; straight-swimming cells unable to tumble become trapped within the agar matrix. spontaneous mutations that restore spreading hav ...201626745427
efficient and automated large-scale detection of structural relationships in proteins with a flexible aligner.the total number of known three-dimensional protein structures is rapidly increasing. consequently, the need for fast structural search against complete databases without a significant loss of accuracy is increasingly demanding. recently, topsearch, an ultra-fast method for finding rigid structural relationships between a query structure and the complete protein data bank (pdb), at the multi-chain level, has been released. however, comparable accurate flexible structural aligners to perform effi ...201626732380
detection of substrate-dependent conformational changes in the p450 fold by nuclear magnetic resonance.cytochrome p450 monooxygenases typically catalyze the insertion of one atom of oxygen from o2 into unactivated carbon-hydrogen and carbon-carbon bonds, with concomitant reduction of the other oxygen atom to h2o by nad(p)h. comparison of the average structures of the camphor hydroxylase cytochrome p450(cam) (cyp101) obtained from residual dipolar coupling (rdc)-restrained molecular dynamics (md) in the presence and absence of substrate camphor shows structural displacements resulting from the ess ...201626911901
characterization of triclosan metabolism in sphingomonas sp. strain yl-jm2c.triclosan (tcs) is one of the most widespread emerging contaminants and has adverse impact on aquatic ecosystem, yet little is known about its complete biodegradation mechanism in bacteria. sphingomonas sp, strain yl-jm2c, isolated from activated sludge of a wastewater treatment plant, was very effective on degrading tcs. response surface methodology (rsm) was applied to optimize the conditions like temperature and ph. from rsm, the optimal tcs degradation conditions were found to be 30 °c and p ...201626912101
terpene arms race in the seiridium cardinale - cupressus sempervirens pathosystem.the canker-causing fungus seiridium cardinale is the major threat to cupressus sempervirens worldwide. we investigated the production of terpenes by canker-resistant and susceptible cypresses inoculated with s. cardinale, the effect of these terpenes on fungal growth, and the defensive biotransformation of the terpenes conducted by the fungus. all infected trees produced de novo terpenes and strongly induced terpenic responses, but the responses were stronger in the canker-resistant than the sus ...201626796122
mvat family proteins encoded on incp-7 plasmid pcar1 and the host chromosome regulate the host transcriptome cooperatively but differently.mvat proteins are members of the h-ns family of proteins in pseudomonads. the incp-7 conjugative plasmid pcar1 carries an mvat-homologous gene, pmr. in pseudomonas putida kt2440 bearing pcar1, pmr and the chromosomally carried homologous genes, tura and turb, are transcribed at high levels, and pmr interacts with tura and turb in vitro. in the present study, we clarified how the three mvat proteins regulate the transcriptome of p. putida kt2440(pcar1). analyses performed by a modified chromatin ...201626590283
engineering cell factories for producing building block chemicals for bio-polymer synthesis.synthetic polymers are widely used in daily life. due to increasing environmental concerns related to global warming and the depletion of oil reserves, the development of microbial-based fermentation processes for the production of polymer building block chemicals from renewable resources is desirable to replace current petroleum-based methods. to this end, strains that efficiently produce the target chemicals at high yields and productivity are needed. recent advances in metabolic engineering h ...201626794242
highly active and stable large catalase isolated from a hydrocarbon degrading aspergillus terreus mtcc 6324.a hydrocarbon degrading aspergillus terreus mtcc 6324 produces a high level of extremely active and stable cellular large catalase (cat) during growth on n-hexadecane to combat the oxidative stress caused by the hydrocarbon degrading metabolic machinery inside the cell. a 160-fold purification with specific activity of around 66 × 10(5) u mg(-1) protein was achieved. the native protein molecular mass was 368 ± 5 kda with subunit molecular mass of nearly 90 kda, which indicates that the native ca ...201627057351
construction of a subunit-fusion nitrile hydratase and discovery of an innovative metal ion transfer pattern.metallochaperones are metal-binding proteins designed to deliver the appropriate metal to a target protein. the metal is usually transferred between different proteins. in this study, we discovered that metal was transferred between the same subunit of a mutant nitrile hydratase (nhase). various "activator proteins" mediate the trafficking of metal ions into nhases. we constructed fusion nhases by fusing the β- and α-subunits and/or the "activator proteins" of the nhase from pseudomonas putida. ...201626755342
lignin engineering in field-grown poplar trees affects the endosphere bacterial microbiome.cinnamoyl-coa reductase (ccr), an enzyme central to the lignin biosynthetic pathway, represents a promising biotechnological target to reduce lignin levels and to improve the commercial viability of lignocellulosic biomass. however, silencing of the ccr gene results in considerable flux changes of the general and monolignol-specific lignin pathways, ultimately leading to the accumulation of various extractable phenolic compounds in the xylem. here, we evaluated host genotype-dependent effects of ...201626755604
diversity and interactions of microbial functional genes under differing environmental conditions: insights from a membrane bioreactor and an oxidation ditch.the effect of environmental conditions on the diversity and interactions of microbial communities has caused tremendous interest in microbial ecology. here, we found that with identical influents but differing operational parameters (mainly mixed liquor suspended solid (mlss) concentrations, solid retention time (srt) and dissolved oxygen (do) concentrations), two full-scale municipal wastewater treatment systems applying oxidation ditch (od) and membrane bioreactor (mbr) processes harbored a ma ...201626743465
characterization of the vibrio fischeri fatty acid chemoreceptors, vfcb and vfcb2.bacteria use a wide variety of methyl-accepting chemotaxis proteins (mcps) to mediate their attraction to or repulsion from different chemical signals in their environment. the bioluminescent marine bacterium vibrio fischeri is the monospecific symbiont of the hawaiian bobtail squid, euprymna scolopes, and encodes a large repertoire of mcps that are hypothesized to be used during different parts of its complex, multistage lifestyle. here, we report the initial characterization of two such mcps f ...201626567312
rice-field drowning-associated pneumonia in which pseudomonas spp., aspergillus fumigatus, and cunninghamella sp. are isolated.we herein report the case of an 84-year-old who developed pneumonia after drowning in a rice field. besides aspergillus fumigatus, many pathogens previously not reported in drowning-associated pneumonia (such as pseudomonas fluorescens, pseudomonas putida, nocardia niigatensis, and cunninghamella sp.) were isolated from his sputum. he received sulbactam/ampicillin, trimethoprim/sulfamethoxazole, voriconazole, levofloxacin and liposomal amphotericin b, but died due to respiratory failure. because ...201627041173
understanding butanol tolerance and assimilation in pseudomonas putida bird-1: an integrated omics approach.pseudomonas putida bird-1 has the potential to be used for the industrial production of butanol due to its solvent tolerance and ability to metabolize low-cost compounds. however, the strain has two major limitations: it assimilates butanol as sole carbon source and butanol concentrations above 1% (v/v) are toxic. with the aim of facilitating bird-1 strain design for industrial use, a genome-wide mini-tn5 transposon mutant library was screened for clones exhibiting increased butanol sensitivity ...201626986205
identification of genes conferring tolerance to lignocellulose-derived inhibitors by functional selections in soil metagenomes.the production of fuels or chemicals from lignocellulose currently requires thermochemical pretreatment to release fermentable sugars. these harsh conditions also generate numerous small-molecule inhibitors of microbial growth and fermentation, limiting production. we applied small-insert functional metagenomic selections to discover genes that confer microbial tolerance to these inhibitors, identifying both individual genes and general biological processes associated with tolerance to multiple ...201626546427
a microbial transformation using bacillus subtilis b7-s to produce natural vanillin from ferulic acid.bacillus subtilis strain b7-s screened from18 strains is an aerobic, endospore-forming, model organism of gram-positive bacteria which is capable to form vanillin during ferulic acid bioconversion. the bioconversion of ferulic acid to vanillin by bacillus subtilis b7-s (b. subtilis b7-s) was investigated. based on our results, the optimum bioconversion conditions for the production of vanillin by b. subtilis b7-s can be summarized as follows: temperature 35 °c; initial ph 9.0; inoculum volume 5% ...201626841717
comparative transcriptomics elucidates adaptive phenol tolerance and utilization in lipid-accumulating rhodococcus opacus pd630.lignin-derived (e.g. phenolic) compounds can compromise the bioconversion of lignocellulosic biomass to fuels and chemicals due to their toxicity and recalcitrance. the lipid-accumulating bacterium rhodococcus opacus pd630 has recently emerged as a promising microbial host for lignocellulose conversion to value-added products due to its natural ability to tolerate and utilize phenolics. to gain a better understanding of its phenolic tolerance and utilization mechanisms, we adaptively evolved r. ...201626837573
study on wastewater toxicity using toxtrak™ method.toxtrak™ method is an analytical tool for the measurement of toxicity of drinking water, wastewater and natural water. it is based upon the estimation of the inhibitive effect on bacterial respiration processes. the main aim of this work was to test the applicability of toxtrak™ method in the assessment of wastewater toxicity in a full-scale wwtp in poland. in order to achieve it, the study was divided into two parts. first, the validation of toxtrak™ method was performed. second, wastewater tox ...201626832868
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