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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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
structural analysis provides mechanistic insight into nicotine oxidoreductase from pseudomonas putida.the first structure of nicotine oxidoreductase (nica2) was determined by x-ray crystallography. pseudomonas putida has evolved nicotine-degrading activity to provide a source of carbon and nitrogen. the structure establishes nica2 as a member of the monoamine oxidase family. residues 1-50 are disordered and may play a role in localization. the nicotine-binding site proximal to the isoalloxazine ring of flavin shows an unusual composition of the classical aromatic cage (w427 and n462). the active ...201627933790
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
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
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
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
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
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
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
interactive effects of phosphorus and pseudomonas putida on chickpea (cicer arietinum l.) growth, nutrient uptake, antioxidant enzymes and organic acids exudation.phosphorus (p) availability in alkaline soils of arid and semi-arid regions is a major constraint for decreased crop productivity. use of plant growth promoting rhizobacteria (pgpr) may enhance plant growth through the increased plant antioxidation activity. additionally, pgpr may increase nutrient uptake by plants as a result of induced root exudation and rhizosphere acidification. the current study was aimed to investigate combined effects of p and pesudomonas putida (pgpr) on chickpea growth ...201627485620
robust at-line quantification of poly(3-hydroxyalkanoate) biosynthesis by flow cytometry using a bodipy 493/503-syto 62 double-staining.poly(3-hydroxyalkanoates) (phas) are bio-based and biodegradable polyesters which have been considered as a promising alternative to petrol-based plastics. their bacterial production is a dynamic process in which intracellular polymerization and depolymerization are closely linked and depend on the availability of carbon substrates and other nutrients. these dynamics require a fast and quantitative method to determine the optimal harvest-time of pha containing cells or to adjust carbon supply. i ...201627720900
identification and validation of novel small proteins in pseudomonas putida.small proteins of 50 amino acids or less have been understudied due to difficulties that impede their annotation and detection. in order to obtain information on small open reading frames (sorfs) in pseudomonas putida, bioinformatic and proteomic approaches were used to identify putative sorfs in the well-characterized strain kt2440. a plasmid-based system was established for sorf validation, enabling expression of c-terminal sequential peptide affinity tagged variants and their detection via pr ...201627717237
stepwise simulation of 3,5-dihydro-5-methylidene-4h-imidazol-4-one (mio) biogenesis in histidine ammonia-lyase.a 3,5-dihydro-5-methylidene-4h-imidazol-4-one (mio) electrophilic moiety is post-translationally and autocatalytically generated in homotetrameric histidine ammonia-lyase (hal) and other enzymes containing the tripeptide ala-ser-gly in a suitably positioned loop. the backbone cyclization step is identical to that taking place during fluorophore formation in green fluorescent protein from the tripeptide ser-tyr-gly, but dehydration, rather than dehydrogenation by molecular oxygen, is the reaction ...201627682658
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
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
competitive adsorption of pb and cd on bacteria-montmorillonite composite.the characteristics and mechanisms of competitive adsorption of trace metals on bacteria-associated clay mineral composites have never been studied, despite their being among the most common organic-mineral complexes in geological systems. herein, competitive adsorption of pb and cd on pseudomonas putida-montmorillonite composite was investigated through adsorption-desorption experiment, isothermal titration calorimetry (itc), and synchrotron micro x-ray fluorescence (μ-xrf). from the experiment ...201627566847
spatial pattern of copper phosphate precipitation involves in copper accumulation and resistance of unsaturated pseudomonas putida cz1 biofilm.bacterial biofilms are spatially structured communities that contain bacterial cells with a wide range of physiological states. the spatial distribution and speciation of copper in unsaturated pseudomonas putida cz1 biofilms that accumulated 147.0 mg copper per g dry weight were determined by transmission electron microscopy coupled with energy dispersive x-ray analysis, and micro-x-ray fluorescence microscopy coupled with micro-x-ray absorption near edge structure (micro-xanes) analysis. it was ...201627558435
rhizosphere selection of pseudomonas putida kt2440 variants with increased fitness associated to changes in gene expression.as the interface between plant roots and soil, the rhizosphere is a complex environment where nutrients released by the plant promote microbial growth. increasing evidences indicate that the plant also exerts a selective pressure on microbial populations in the rhizosphere, favouring colonization by certain groups. in this work, we have designed an experimental setup to begin analysing the evolution of a specific bacterial population in the rhizosphere, using pseudomonas putida kt2440 as model o ...201627487165
biosorption of aluminum through the use of non-viable biomass of pseudomonas putida.living and non-living biomass of pseudomonas putida a (atcc 12633) was used as biosorbent for the removing of al(3+) from aqueous solutions. the process was stable with time, efficient at ph 4.3 and between 15°c and 42°c. two isotherms models were applied to describe the interaction between the biosorbent and al(3+). non-living biomass of p. putida a (atcc 12633) was found to be the most efficient at adsorbing al(3+) with a maximum sorption capacity of 0.55mg al(3+)/gr adsorbent and with 36×10(5 ...201627485814
proteome analysis of pseudomonas putida f1 genes induced in soil environments.knowledge of the gene expression dynamics of a single soil bacterial strain contributes to the understanding of its behaviour, physiological state and surrounding microenvironment. genes expressed in soil environments rather than in laboratory media are considered to particularly relevant. here, we compared genome-wide gene expression profiles of the bacterium pseudomonas putida f1 inoculated in three different types of nonsterile soils deduced using proteome analysis via sodium dodecyl sulfate- ...201627452675
production of glucaric acid from myo-inositol in engineered pichia pastoris.a potential myo-inositol oxygenase (ppmiox) was identified as a functional enzyme and a glucaric acid synthetic pathway was firstly constructed in pichia pastoris. coexpression of the native ppmiox and the urinate dehydrogenase (udh) from pseudomonas putida kt2440 led to obvious accumulation of glucaric acid (90.46±0.04mg/l) from myo-inositol whereas no glucaric acid was detected from glucose. in comparison, coexpression of the heterologous mouse miox (mmiox) and udh resulted in higher titers of ...201627444324
content of cardiolipin of the membrane and sensitivity to cationic surfactants in pseudomonas putida.to establish the role of cardiolipin (cl) of the membrane in response to the presence of tetradecyltrimethylammonium in pseudomonas putida a (atcc 12633).201627442261
self-regulation and interplay of rsm family proteins modulate the lifestyle of pseudomonas putida.in the plant-beneficial bacterium pseudomonas putida kt2440, three genes have been identified that encode posttranscriptional regulators of the csra/rsma family. their regulatory roles in the motile and sessile lifestyles of p. putida have been investigated by generating single-, double-, and triple-null mutants and by overexpressing each protein (rsma, rsme, and rsmi) in different genetic backgrounds. the rsm triple mutant shows reduced swimming and swarming motilities and increased biofilm for ...201627422830
pseudomonas putida as a platform for the synthesis of aromatic compounds.aromatic compounds such as l-phenylalanine, 2-phenylethanol and trans-cinnamate are aromatic compounds of industrial interest. current trends support replacement of chemical synthesis of these compounds by 'green' alternatives produced in microbial cell factories. the solvent-tolerant pseudomonas putida dot-t1e strain was genetically modified to produce up to 1 g l-1 of l-phenylalanine. in order to engineer this strain, we carried out the following stepwise process: (1) we selected random mutant ...201627417954
biofilm adaptation to iron availability in the presence of biotite and consequences for chemical weathering.bacteria in nature often live within biofilms, exopolymeric matrices that provide a favorable environment that can differ markedly from their surroundings. biofilms have been found growing on mineral surfaces and are expected to play a role in weathering those surfaces, but a clear understanding of how environmental factors, such as trace-nutrient limitation, influence this role is lacking. here, we examine biofilm development by pseudomonas putida in media either deficient or sufficient in fe d ...201627384343
role of conserved met112 residue in the catalytic activity and stability of ketosteroid isomerase.ketosteroid isomerase (3-oxosteroid δ(5)-δ(4)-isomerase, ksi) from pseudomonas putida catalyzes allylic rearrangement of the 5,6-double bond of δ(5)-3-ketosteroid to 4,5-position by stereospecific intramolecular transfer of a proton. the active site of ksi is formed by several hydrophobic residues and three catalytic residues (tyr14, asp38, and asp99). in this study, we investigated the role of a hydrophobic met112 residue near the active site in the catalysis, steroid binding, and stability of ...201627375051
3-fluorophenmetrazine, a fluorinated analogue of phenmetrazine: studies on in vivo metabolism in rat and human, in vitro metabolism in human cyp isoenzymes and microbial biotransformation in pseudomonas putida and wastewater using gc and lc coupled to (hr)-ms techniques.wastewater-based epidemiology (wbe) as means to estimate illicit drug and new psychoactive substance (nps) consumption with spatial and temporal resolution is gaining increasing attention. in order to evaluate a given nps using wbe, in vivo metabolism and microbial biotransformation of excretion products and unchanged compounds need evaluation. the aims of this study were to identify in vivo phase i and ii metabolites of the nps 3-fluorophenmetrazine (3-fpm) in human and rat urine and study the ...201627372653
pyridine nucleotide transhydrogenases enable redox balance of pseudomonas putida during biodegradation of aromatic compounds.the metabolic versatility of the soil bacterium pseudomonas putida is reflected by its ability to execute strong redox reactions (e.g., mono- and di-oxygenations) on aromatic substrates. biodegradation of aromatics occurs via the pathway encoded in the archetypal tol plasmid pww0, yet the effect of running such oxidative route on redox balance against the background metabolism of p. putida remains unexplored. to answer this question, the activity of pyridine nucleotide transhydrogenases (that ca ...201627348295
novel polyhydroxyalkanoate copolymers produced in pseudomonas putida by metagenomic polyhydroxyalkanoate synthases.bacterially produced biodegradable polyhydroxyalkanoates (phas) with versatile properties can be achieved using different pha synthases (phacs). this work aims to expand the diversity of known phacs via functional metagenomics and demonstrates the use of these novel enzymes in pha production. complementation of a pha synthesis-deficient pseudomonas putida strain with a soil metagenomic cosmid library retrieved 27 clones expressing either class i, class ii, or unclassified pha synthases, and many ...201627333909
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
first chemo-enzymatic synthesis of the (r)-taniguchi lactone and substrate profiles of camo and otemo, two new baeyer-villiger monooxygenases.this study investigates the substrate profile of cycloalkanone monooxygenase and 2-oxo-δ(3)-4,5,5-trimethylcyclopentenylacetyl-coenzyme a monooxygenase, two recently discovered enzymes of the baeyer-villiger monooxygenase family, used as whole-cell biocatalysts. biooxidations of a diverse set of ketones were performed on analytical scale: desymmetrization of substituted prochiral cyclobutanones and cyclohexanones, regiodivergent oxidation of terpenones and bicyclic ketones, as well as kinetic re ...201628127101
the detoxification and degradation of benzothiazole from the wastewater in microbial electrolysis cells.in this study, the high-production-volume chemical benzothiazole (bth) from synthetic water was fully degraded into less toxic intermediates of simple organic acids using an up-flow internal circulation microbial electrolysis reactor (uicmer) under the hydraulic retention time (hrt) of 24 h. the bioelectrochemical system was operated at 25 ± 2 °c and continuous-flow mode. the bth loading rate varied during experiments from 20 g·m(-3)·day(-1) to 110 g·m(-3)·day(-1). bth and soluble cod (chemical ...201627999421
advances and challenges in logical modeling of cell cycle regulation: perspective for multi-scale, integrative yeast cell models.the eukaryotic cell cycle is robustly designed, with interacting molecules organized within a definite topology that ensures temporal precision of its phase transitions. its underlying dynamics are regulated by molecular switches, for which remarkable insights have been provided by genetic and molecular biology efforts. in a number of cases, this information has been made predictive, through computational models. these models have allowed for the identification of novel molecular mechanisms, lat ...201627993914
advances and challenges in logical modeling of cell cycle regulation: perspective for multi-scale, integrative yeast cell models.the eukaryotic cell cycle is robustly designed, with interacting molecules organized within a definite topology that ensures temporal precision of its phase transitions. its underlying dynamics are regulated by molecular switches, for which remarkable insights have been provided by genetic and molecular biology efforts. in a number of cases, this information has been made predictive, through computational models. these models have allowed for the identification of novel molecular mechanisms, lat ...201627993914
redox properties of extracellular polymeric substances (eps) from electroactive bacteria.although the capacity for electroactive bacteria to convert environmental metallic minerals and organic pollutants is well known, the role of the redox properties of microbial extracellular polymeric substances (eps) in this process is poorly understood. in this work, the redox properties of eps from two widely present electroactive bacterial strains (shewanella oneidensis and pseudomonas putida) were explored. electrochemical analysis demonstrates that the eps extracted from the two strains exh ...201627991531
genes encoding norcoclaurine synthase occur as tandem fusions in the papaveraceae.norcoclaurine synthase (ncs) catalyzes the enantioselective pictet-spengler condensation of dopamine and 4-hydroxyphenylacetaldehyde as the first step in benzylisoquinoline alkaloid (bia) biosynthesis. ncs orthologs in available transcriptome databases were screened for variants that might improve the low yield of bias in engineered microorganisms. databases for 21 bia-producing species from four plant families yielded 33 assembled contigs with homology to characterized ncs genes. predicted tran ...201627991536
copy number variability of expression plasmids determined by cell sorting and droplet digital pcr.plasmids are widely used for molecular cloning or production of proteins in laboratory and industrial settings. constant modification has brought forth countless plasmid vectors whose characteristics in terms of average plasmid copy number (pcn) and stability are rarely known. the crucial factor determining the pcn is the replication system; most replication systems in use today belong to a small number of different classes and are available through repositories like the standard european vector ...201627993152
inoculation of soil with plant growth promoting bacteria producing 1-aminocyclopropane-1-carboxylate deaminase or expression of the corresponding acds gene in transgenic plants increases salinity tolerance in camelina sativa.camelina sativa (camelina) is an oilseed crop touted for use on marginal lands; however, it is no more tolerant of soil salinity than traditional crops, such as canola. plant growth-promoting bacteria (pgpb) that produce 1-aminocyclopropane-1-carboxylate deaminase (acc deaminase) facilitate plant growth in the presence of abiotic stresses by reducing stress ethylene. rhizospheric and endophytic pgpb and the corresponding acds- mutants of the latter were examined for their ability to enhance tole ...201628018305
arsenic resistance strategy in pantoea sp. imh: organization, function and evolution of ars genes.pantoea sp. imh is the only bacterium found in genus pantoea with a high as resistance capacity, but its molecular mechanism is unknown. herein, the organization, function, and evolution of ars genes in imh are studied starting with analysis of the whole genome. two ars systems - ars1 (arsr1b1c1h1) and ars2 (arsr2b2c2h2) - with low sequence homology and two arsc-like genes, were found in the imh genome. both ars1 and ars2 are involved in the as resistance, where ars1 is the major contributor at ...201627966630
high titer heterologous rhamnolipid production.heterologous mono-rhamnolipid production by pseudomonas putida kt2440 psynpro8ot_rhlab using glucose as the single carbon source was characterized in fed-batch bioreactor cultivations. for the described experiments, a defined mineral salt medium was used, and a two phase glucose feeding profile was applied, which yielded a final rhamnolipid concentration of 14.9 g/l. applying the feeding profile, glucose stayed almost constant until 28 h of cultivation and decreased afterwards to limiting levels ...201627957724
systemic responses of barley to the 3-hydroxy-decanoyl-homoserine lactone producing plant beneficial endophyte acidovorax radicis n35.quorum sensing auto-inducers of the n-acyl homoserine lactone (ahl) type produced by gram-negative bacteria have different effects on plants including stimulation on root growth and/or priming or acquirement of systemic resistance in plants. in this communication the influence of ahl production of the plant growth promoting endophytic rhizosphere bacterium acidovorax radicis n35 on barley seedlings was investigated. a. radicis n35 produces 3-hydroxy-c10-homoserine lactone (3-oh-c10-hsl) as the m ...201628018401
identification of electrode respiring, hydrocarbonoclastic bacterial strain stenotrophomonas maltophilia mk2 highlights the untapped potential for environmental bioremediation.electrode respiring bacteria (erb) possess a great potential for many biotechnological applications such as microbial electrochemical remediation systems (mers) because of their exoelectrogenic capabilities to degrade xenobiotic pollutants. very few erb have been isolated from mers, those exhibited a bioremediation potential toward organic contaminants. here we report once such bacterial strain, stenotrophomonas maltophilia mk2, a facultative anaerobic bacterium isolated from a hydrocarbon fed m ...201628018304
functional characterization of aconitase x as a cis-3-hydroxy-l-proline dehydratase.in the aconitase superfamily, which includes the archetypical aconitase, homoaconitase, and isopropylmalate isomerase, only aconitase x is not functionally annotated. the corresponding gene (lhpi) was often located within the bacterial gene cluster involved in l-hydroxyproline metabolism. screening of a library of (hydroxy)proline analogues revealed that this protein catalyzes the dehydration of cis-3-hydroxy-l-proline to δ(1)-pyrroline-2-carboxylate. furthermore, electron paramagnetic resonance ...201627929065
insights into functional and evolutionary analysis of carbaryl metabolic pathway from pseudomonas sp. strain c5pp.carbaryl (1-naphthyl n-methylcarbamate) is a most widely used carbamate pesticide in the agriculture field. soil isolate, pseudomonas sp. strain c5pp mineralizes carbaryl via 1-naphthol, salicylate and gentisate, however the genetic organization and evolutionary events of acquisition and assembly of pathway have not yet been studied. the draft genome analysis of strain c5pp reveals that the carbaryl catabolic genes are organized into three putative operons, 'upper', 'middle' and 'lower'. the seq ...201627924916
a metabolic widget adjusts the phosphoenolpyruvate-dependent fructose influx in pseudomonas putida.fructose uptake in the soil bacterium pseudomonas putida occurs through a canonical phosphoenolpyruvate (pep)-dependent sugar transport system (pts(fru)). the logic of the genetic circuit that rules its functioning is puzzling: the transcription of the frubka operon, encoding all the components of pts(fru), can escape the repression exerted by the catabolite repressor/activator protein cra solely in the presence of intracellular fructose-1-p, an agonist formed only when fructose has been already ...201627933319
properties of alternative microbial hosts used in synthetic biology: towards the design of a modular chassis.the chassis is the cellular host used as a recipient of engineered biological systems in synthetic biology. they are required to propagate the genetic information and to express the genes encoded in it. despite being an essential element for the appropriate function of genetic circuits, the chassis is rarely considered in their design phase. consequently, the circuits are transferred to model organisms commonly used in the laboratory, such as escherichia coli, that may be suboptimal for a requir ...201627903818
synthesis and functions of jasmonates in maize.of the over 600 oxylipins present in all plants, the phytohormone jasmonic acid (ja) remains the best understood in terms of its biosynthesis, function and signaling. much like their eicosanoid analogues in mammalian system, evidence is growing for the role of the other oxylipins in diverse physiological processes. ja serves as the model plant oxylipin species and regulates defense and development. for several decades, the biology of ja has been characterized in a few dicot species, yet the func ...201627916835
microscope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes.the annotation of genomes from ngs platforms needs to be automated and fully integrated. however, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. this shortcoming limits the knowledge that can be extracted from genomes and metabolic models. launched in 2005, the microscope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and ...201627899624
microscope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes.the annotation of genomes from ngs platforms needs to be automated and fully integrated. however, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. this shortcoming limits the knowledge that can be extracted from genomes and metabolic models. launched in 2005, the microscope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and ...201627899624
salicylic acid is involved in the basal resistance of tomato plants to citrus exocortis viroid and tomato spotted wilt virus.tomato plants expressing the nahg transgene, which prevents accumulation of endogenous salicylic acid (sa), were used to study the importance of the sa signalling pathway in basal defence against citrus exocortis viroid (cevd) or tomato spotted wilt virus (tswv). the lack of sa accumulation in the cevd- or tswv-infected nahg tomato plants led to an early and dramatic disease phenotype, as compared to that observed in the corresponding parental money maker. addition of acibenzolar-s-methyl, a ben ...201627893781
metabolic engineering of pseudomonas putida kt2440 for the production of para-hydroxy benzoic acid.para-hydroxy benzoic acid (phba) is the key component for preparing parabens, a common preservatives in food, drugs, and personal care products, as well as high-performance bioplastics such as liquid crystal polymers. pseudomonas putida kt2440 was engineered to produce phba from glucose via the shikimate pathway intermediate chorismate. to obtain the phba production strain, chorismate lyase ubic from escherichia coli and a feedback resistant 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase e ...201627965953
multiple and variable nhej-like genes are involved in resistance to dna damage in streptomyces ambofaciens.non-homologous end-joining (nhej) is a double strand break (dsb) repair pathway which does not require any homologous template and can ligate two dna ends together. the basic bacterial nhej machinery involves two partners: the ku protein, a dna end binding protein for dsb recognition and the multifunctional ligd protein composed a ligase, a nuclease and a polymerase domain, for end processing and ligation of the broken ends. in silico analyses performed in the 38 sequenced genomes of streptomyce ...201627965636
initiation of chromosomal replication in predatory bacterium bdellovibrio bacteriovorus.bdellovibrio bacteriovorus is a small gram-negative predatory bacterium that attacks other gram-negative bacteria, including many animal, human, and plant pathogens. this bacterium exhibits a peculiar biphasic life cycle during which two different types of cells are produced: non-replicating highly motile cells (the free-living phase) and replicating cells (the intracellular-growth phase). the process of chromosomal replication in b. bacteriovorus must therefore be temporally and spatially regul ...201627965633
whole-genome sequences of two manganese(ii)-oxidizing bacteria, bosea sp. strain biwako-01 and alphaproteobacterium strain u9-1i.this report describes the whole-genome sequences of two mn(ii)-oxidizing bacteria, filamentous mn oxide microparticle-forming bosea sp. strain biwako-01 and alphaproteobacterium strain u9-1i.201627881541
enhancing poly(3-hydroxyalkanoate) production in escherichia coli by the removal of the regulatory gene arca.recombinant escherichia coli is a desirable platform for the production of many biological compounds including poly(3-hydroxyalkanoates), a class of naturally occurring biodegradable polyesters with promising biomedical and material applications. although the controlled production of desirable polymers is possible with the utilization of fatty acid feedstocks, a central challenge to this biosynthetic route is the improvement of the relatively low polymer yield, a necessary factor of decreasing t ...201627878786
draft genome sequence of pseudomonas mosselii gil3, isolated from catfish and antagonistic against hypervirulent aeromonas hydrophila.pseudomonas mosselii gil3 was isolated from a catfish that survived from lethal challenge with hypervirulent aeromonas hydrophila (vah). when assayed in vitro, the bacterium showed antagonism against vah. sequence analysis revealed that the genome of p. mosselii gil3 encodes numerous aromatic metabolism pathways and proteins for biosynthesis of antimicrobial compounds.201627856595
two-step production of phenylpyruvic acid from l-phenylalanine by growing and resting cells of engineered escherichia coli: process optimization and kinetics modeling.phenylpyruvic acid (ppa) is widely used in the pharmaceutical, food, and chemical industries. here, a two-step bioconversion process, involving growing and resting cells, was established to produce ppa from l-phenylalanine using the engineered escherichia coli constructed previously. first, the biotransformation conditions for growing cells were optimized (l-phenylalanine concentration 20.0 g·l-1, temperature 35°c) and a two-stage temperature control strategy (keep 20°c for 12 h and increase the ...201627851793
mutation of the streptococcus gordonii thiol-disulfide oxidoreductase sdba leads to enhanced biofilm formation mediated by the ciarh two-component signaling system.streptococcus gordonii is a commensal inhabitant of human oral biofilms. previously, we identified an enzyme called sdba that played an important role in biofilm formation by s. gordonii. sdba is thiol-disulfide oxidoreductase that catalyzes disulfide bonds in secreted proteins. surprisingly, inactivation of sdba results in enhanced biofilm formation. in this study we investigated the basis for biofilm formation by the δsdba mutant. the results revealed that biofilm formation was mediated by the ...201627846284
adaptive evolution of phosphorus metabolism in prochlorococcus.inorganic phosphorus is scarce in the eastern mediterranean sea, where the high-light-adapted ecotype hli of the marine picocyanobacterium prochlorococcus marinus thrives. physiological and regulatory control of phosphorus acquisition and partitioning has been observed in hli both in culture and in the field; however, the optimization of phosphorus metabolism and associated gains for its phosphorus-limited-growth (plg) phenotype have not been studied. here, we reconstructed a genome-scale metabo ...201627868089
novel culturing techniques select for heterotrophs and hydrocarbon degraders in a subantarctic soil.the soil substrate membrane system (ssms) is a novel micro-culturing technique targeted at terrestrial soil systems. we applied the ssms to pristine and diesel fuel spiked polar soils, along with traditional solid media culturing and culture independent 454 tag pyrosequencing to elucidate the effects of diesel fuel on the soil community. the ssms enriched for up to 76% of the total soil diversity within high diesel fuel concentration soils, in contrast to only 26% of the total diversity for the ...201627827405
draft genome sequence of a multi-metal resistant bacterium pseudomonas putida ath-43 isolated from greenwich island, antarctica. 201627877169
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