Publications

isolation and characterization of polyacrylamide-degrading bacteria from dewatered sludge.	polyacrylamide (pam) is a water-soluble polymer that is widely used as a flocculant in sewage treatment. the accumulation of pam affects the formation of dewatered sludge and potentially produces hazardous monomers. in the present study, the bacterial strain hi47 was isolated from dewatered sludge. this strain could metabolize pam as its sole nutrient source and was subsequently identified as pseudomonas putida. the efficiency of pam degradation was 31.1% in 7 days and exceeded 45% under optimum ...	2015	25893998
draft genome sequence of lysinibacillus fusiformis strain sw-b9, a novel strain for biotransformation of isoeugenol to vanillin.	lysinibacillus fusiformis sw-b9 was the first reported strain in l. fusiformis showing effective biotransformation of isoeugenol to vanillin. here, we report the annotated genome of strain sw-b9, which has special pathways for producing vanillin. the genome will provide a genetic basis for better understanding the physiology of this species.	2015	25883291
engineering mediator-based electroactivity in the obligate aerobic bacterium pseudomonas putida kt2440.	pseudomonas putida strains are being developed as microbial production hosts for production of a range of amphiphilic and hydrophobic biochemicals. p. putida's obligate aerobic growth thereby can be an economical and technical challenge because it requires constant rigorous aeration and often causes reactor foaming. here, we engineered a strain of p. putida kt2440 that can produce phenazine redox-mediators from pseudomonas aeruginosa to allow partial redox balancing with an electrode under oxyge ...	2015	25914687
sensor kinase pa4398 modulates swarming motility and biofilm formation in pseudomonas aeruginosa pa14.	pseudomonas aeruginosa is an opportunistic human pathogen that is able to sense and adapt to numerous environmental stimuli by the use of transcriptional regulators, including two-component regulatory systems. in this study, we demonstrate that the sensor kinase pa4398 is involved in the regulation of swarming motility and biofilm formation in p. aeruginosa pa14. apa4398 mutant strain was considerably impaired in swarming motility, while biofilm formation was increased by approximately 2-fold. t ...	2015	25501476
novel reporter for identification of interference with acyl homoserine lactone and autoinducer-2 quorum sensing.	two reporter strains were established to identify novel biomolecules interfering with bacterial communication (quorum sensing [qs]). the basic design of these escherichia coli-based systems comprises a gene encoding a lethal protein fused to promoters induced in the presence of qs signal molecules. consequently, these e. coli strains are unable to grow in the presence of the respective qs signal molecules unless a nontoxic qs-interfering compound is present. the first reporter strain designed to ...	2015	25527543
cell surface-based sensing with metallic nanoparticles.	metallic nanoparticles provide versatile scaffolds for biosensing applications. in this review, we focus on the use of metallic nanoparticles for cell surface sensings. examples of the use of both specific recognition and array-based "chemical nose" approaches to cell surface sensing will be discussed.	2015	25853985
comparative ser/thr/tyr phosphoproteomics between two mycobacterial species: the fast growing mycobacterium smegmatis and the slow growing mycobacterium bovis bcg.	ser/thr/tyr protein phosphorylation plays a critical role in regulating mycobacterial growth and development. understanding the mechanistic link between protein phosphorylation signaling network and mycobacterial growth rate requires a global view of the phosphorylation events taking place at a given time under defined conditions. in the present study we employed a phosphopeptide enrichment and high throughput mass spectrometry-based strategy to investigate and qualitatively compare the phosphop ...	2015	25904896
cysb negatively affects the transcription of pqsr and pseudomonas quinolone signal production in pseudomonas aeruginosa.	pseudomonas aeruginosa is a gram-negative bacterium that is ubiquitous in the environment, and it is an opportunistic pathogen that can infect a variety of hosts, including humans. during the process of infection, p. aeruginosa coordinates the expression of numerous virulence factors through the production of multiple cell-to-cell signaling molecules. the production of these signaling molecules is linked through a regulatory network, with the signal n-(3-oxododecanoyl) homoserine lactone and its ...	2015	25845844
a moonlighting metabolic protein influences repair at dna double-stranded breaks.	catalytically active proteins with divergent dual functions are often described as 'moonlighting'. in this work we characterize a new, chromatin-based function of lys20, a moonlighting protein that is well known for its role in metabolism. lys20 was initially described as homocitrate synthase (hcs), the first enzyme in the lysine biosynthetic pathway in yeast. its nuclear localization led to the discovery of a key role for lys20 in dna damage repair through its interaction with the myst family h ...	2015	25628362
the lipid-modifying multiple peptide resistance factor is an oligomer consisting of distinct interacting synthase and flippase subunits.	phospholipids are synthesized at the inner leaflet of the bacterial cytoplasmic membrane but have to be translocated to the outer leaflet to maintain membrane lipid bilayer composition and structure. even though phospholipid flippases have been proposed to exist in bacteria, only one such protein, mprf, has been described. mprf is a large integral membrane protein found in several prokaryotic phyla, whose c terminus modifies phosphatidylglycerol (pg), the most common bacterial phospholipid, with ...	2015	25626904
proteomics as the final step in the functional metagenomics study of antimicrobial resistance.	the majority of clinically applied antimicrobial agents are derived from natural products generated by soil microorganisms and therefore resistance is likely to be ubiquitous in such environments. this is supported by the fact that numerous clinically important resistance mechanisms are encoded within the genomes of such bacteria. advances in genomic sequencing have enabled the in silico identification of putative resistance genes present in these microorganisms. however, it is not sufficient to ...	2015	25784907
a reusable immobilization matrix for the biodegradation of phenol at 5000 mg/l.	bacteria-mediated degradation of toxins has been reported as a practical technique for the innocuous removal of toxic organic compounds from water. specifically, immobilized and pre-acclimatized pseudomonas putida has been shown to clear low levels of contaminants (less than 2000 mg/l) from wastewater, wherein the bacteria consumes toxic aromatic compounds as the only source of carbon and energy. here we report the preparation of a high-capacity composite adsorbent as an immobilization matrix fo ...	2015	25733015
quorum sensing triggers the stochastic escape of individual cells from pseudomonas putida biofilms.	the term 'quorum sensing' (qs) is generally used to describe the phenomenon that bacteria release and perceive signal molecules to coordinate cooperative behaviour in response to their population size. qs-based communication has therefore been considered a social trait. here we show that qs signals (n-acyl-homoserine lactones, ahls) are stochastically produced in young biofilms of pseudomonas putida and act mainly as self-regulatory signals rather than inducing neighbouring cells. we demonstrate ...	2015	25592773
production of cinnamic and p-hydroxycinnamic acid from sugar mixtures with engineered escherichia coli.	the aromatic compounds cinnamic acid (ca) and p-hydroxycinnamic acid (phca) are used as flavoring agents as well as precursors of chemicals. these compounds are present in plants at low concentrations, therefore, complex purification processes are usually required to extract the product. an alternative production method for these aromatic acids is based on the use of microbial strains modified by metabolic engineering. these biotechnological processes are usually based on the use of simple sugar ...	2015	25592545
expression of extra-cellular levansucrase in pseudomonas syringae is controlled by the in planta fitness-promoting metabolic repressor hexr.	pseudomonas syringae pv. glycinea pg4180 causes bacterial blight on soybean plants and enters the leaf tissue through stomata or open wounds, where it encounters a sucrose-rich milieu. sucrose is utilized by invading bacteria via the secreted enzyme, levansucrase (lsc), liberating glucose and forming the polyfructan levan. p. syringae pg4180 possesses two functional lsc alleles transcribed at virulence-promoting low temperatures.	2015	25886911
structural studies on laz, a promiscuous anticancer neisserial protein.	azurin and laz (lipidated azurin) are 2 bacterial proteins with anticancer, anti-viral and anti-parasitic activities. azurin, isolated from the bacterium pseudomonas aeruginosa, termed paz, demonstrates anticancer activity against a range of cancers but not against brain tumors. in contrast, laz is produced by members of gonococci/meningococci, including neisseria meningitides which can cross the blood-brain barrier to infect brain meninges. it has been previously reported that laz has an additi ...	2015	25714335
diabetic foot gangrene patient with multi-drug resistant pseudomonas putida infection in karawaci district, indonesia.	pseudomonas putida is a rod-shaped, non fermenting gram-negative organism frequently found in the environment that utilizes aerobic metabolism, previously thought to be of low pathogenicity. it had been reported as cause of skin and soft tissue infection, especially in immunocompromised patients. a female green grocer, 51 year-old came to internal medicine out-patient clinic with gangrene and osteomyelitis on her 1(st), 2(nd) and 3(rd) digit and wound on the sole of the right foot since 1 month ...	2015	25722620
escherichia coli overexpressing a baeyer-villiger monooxygenase from acinetobacter radioresistens becomes resistant to imipenem.	antimicrobial resistance is a global issue currently resulting in the deaths of hundreds of thousands of people a year worldwide. data present in the literature illustrate the emergence of many bacterial species that display resistance to known antibiotics; acinetobacter spp. are a good example of this. we report here that acinetobacter radioresistens has a baeyer-villiger monooxygenase (ar-bvmo) with 100% amino acid sequence identity to the ethionamide monooxygenase of multidrug-resistant (mdr) ...	2015	26459905
escherichia coli overexpressing a baeyer-villiger monooxygenase from acinetobacter radioresistens becomes resistant to imipenem.	antimicrobial resistance is a global issue currently resulting in the deaths of hundreds of thousands of people a year worldwide. data present in the literature illustrate the emergence of many bacterial species that display resistance to known antibiotics; acinetobacter spp. are a good example of this. we report here that acinetobacter radioresistens has a baeyer-villiger monooxygenase (ar-bvmo) with 100% amino acid sequence identity to the ethionamide monooxygenase of multidrug-resistant (mdr) ...	2015	26459905
assay of blood and synovial fluid of patients with rheumatoid arthritis for staphylococcus aureus enterotoxin d: absence of bacteria but presence of its toxin.	rheumatoid arthritis (ra) is the most common chronic inflammatory disease. the staphylococcal superantigens are considered as the causative agent of ra disease.	2015	26870313
metabolic engineering and comparative performance studies of synechocystis sp. pcc 6803 strains for effective utilization of xylose.	wood sugars such as xylose can be used as an inexpensive carbon source for biotechnological applications. the model cyanobacterium synechocystis sp. pcc 6803 lacks the ability to catabolize wood sugars as an energy source. here, we generated four synechocystis strains that heterologously expressed xylab enzymes, which mediate xylose catabolism, either in combination with or without one of three xylose transporters, namely xyle, galp, or glf. except for glf, which is derived from the bacterium zy ...	2015	26732758
prevalence and antimicrobial resistance of microbes causing bloodstream infections in unguja, zanzibar.	bloodstream infections (bsi) are frequent and cause high case-fatality rates. urgent antibiotic treatment can save patients' lives, but antibiotic resistance can render antibiotic therapy futile. this study is the first to collect epidemiological data on bsi from unguja, zanzibar.	2015	26700032
role of burkholderia pseudomallei sigma n2 in amino acids utilization and in regulation of catalase e expression at the transcriptional level.	burkholderia pseudomallei is the causative agent of melioidosis. the complete genome sequences of this pathogen have been revealed, which explain some pathogenic mechanisms. in various hostile conditions, for example, during nitrogen and amino acid starvation, bacteria can utilize alternative sigma factors such as rpos and rpon to modulate genes expression for their adaptation and survival. in this study, we demonstrate that mutagenesis of rpon2, which lies on chromosome 2 of b. pseudomallei and ...	2015	26904748
anodes stimulate anaerobic toluene degradation via sulfur cycling in marine sediments.	hydrocarbons released during oil spills are persistent in marine sediments due to the absence of suitable electron acceptors below the oxic zone. here, we investigated an alternative bioremediation strategy to remove toluene, a model monoaromatic hydrocarbon, using a bioanode. bioelectrochemical reactors were inoculated with sediment collected from a hydrocarbon-contaminated marine site, and anodes were polarized at 0 mv and +300 mv (versus an ag/agcl [3 m kcl] reference electrode). the degradat ...	2015	26497463
anodes stimulate anaerobic toluene degradation via sulfur cycling in marine sediments.	hydrocarbons released during oil spills are persistent in marine sediments due to the absence of suitable electron acceptors below the oxic zone. here, we investigated an alternative bioremediation strategy to remove toluene, a model monoaromatic hydrocarbon, using a bioanode. bioelectrochemical reactors were inoculated with sediment collected from a hydrocarbon-contaminated marine site, and anodes were polarized at 0 mv and +300 mv (versus an ag/agcl [3 m kcl] reference electrode). the degradat ...	2015	26497463
functional coexistence of twin arsenic resistance systems in pseudomonas putida kt2440.	the genome of the soil bacterium pseudomonas putida kt2440 bears two virtually identical arsrbch operons putatively encoding resistance to inorganic arsenic species. single and double chromosomal deletions in each of these ars clusters of this bacterium were tested for arsenic sensitivity and found that the contribution of each operon to the resistance to the metalloid was not additive, as either cluster sufficed to endow cells with high-level resistance. however, otherwise identical traits link ...	2015	24673935
the differential response of the pben promoter of pseudomonas putida mt-2 to benr and xyls prevents metabolic conflicts in m-xylene biodegradation.	pseudomonas putida mt-2 encompasses two alternative and potentially conflicting routes for benzoate metabolism, one meta pathway encoded by xyl genes of the pww0 plasmid and mastered by the pm promoter and xyls, and one chromosomally encoded ortho pathway initiated by pben and the benr protein. any cross-activation of pben promoter by xyls ought to cause a metabolic conflict during the degradation of m-xylene because 3-methylbenzoate (3mbz) generated as an intermediate can be channelled through ...	2015	24588992
purification and characterization of carbon-phosphorus bond-cleavage enzyme from glyphosate degrading pseudomonas putida t5.	an inducible, carbon-phosphorus bond-cleavage enzyme was purified from cells of pseudomonas putida t5 grown on n-phosphonomethyl glycine. the native enzyme had a molecular mass of approximately 70 kd and upon sodium dodecyl sulfate polyacrylamide gel electrophoresis (sds-page), yielded a homogeneous protein band with an apparent molecular mass of about 70 kd. activity of purified enzyme was increased by 627-fold compared to the crude extract and showed ph and temperature optima of approximately ...	2015	24840030
functional analyses of three acyl-coa synthetases involved in bile acid degradation in pseudomonas putida doc21.	pseudomonas putida doc21, a soil-dwelling proteobacterium, catabolizes a variety of steroids and bile acids. transposon mutagenesis and bioinformatics analyses identified four clusters of steroid degradation (std) genes encoding a single catabolic pathway. the latter includes three predicted acyl-coa synthetases encoded by stda1, stda2 and stda3 respectively. the δstda1 and δstda2 deletion mutants were unable to assimilate cholate or other bile acids but grew well on testosterone or 4-androstene ...	2015	24428272
abatement of styrene waste gas emission by biofilter and biotrickling filter: comparison of packing materials and inoculation procedures.	the removal of styrene was studied using two biofilters packed with peat and coconut fibre (bf1-p and bf2-c, respectively) and one biotrickling filter (btf) packed with plastic rings. two inoculation procedures were applied: an enriched culture with strain pseudomonas putida cect 324 for bfs and activated sludge from a municipal wastewater treatment plant for the btf. inlet loads (ils) between 10 and 45 g m(-3) h(-1) and empty bed residence times (ebrts) from 30 to 120 s were applied. at inlet c ...	2015	24797312
the crc and hfq proteins of pseudomonas putida cooperate in catabolite repression and formation of ribonucleic acid complexes with specific target motifs.	the crc protein is a global regulator that has a key role in catabolite repression and optimization of metabolism in pseudomonads. crc inhibits gene expression post-transcriptionally, preventing translation of mrnas bearing an aanaanaa motif [the catabolite activity (ca) motif] close to the translation start site. although crc was initially believed to bind rna by itself, this idea was recently challenged by results suggesting that a protein co-purifying with crc, presumably the hfq protein, cou ...	2015	24803210
freeing pseudomonas putida kt2440 of its proviral load strengthens endurance to environmental stresses.	2.6% of the genome of the soil bacterium pseudomonas putida kt2440 encodes phage-related functions, but the burden of such opportunistic dna on the host physiology is unknown. each of the four apparently complete prophages borne by this strain was tested for stability, spontaneous excision and ability to cause lysis under various stressing conditions. while prophages p3 (pp2266-pp2297) and p4 (pp1532-1584) were discharged from the genome at a detectable rate, their induction failed otherwise to ...	2015	24762028
high cell density cultivation of pseudomonas putida kt2440 using glucose without the need for oxygen enriched air supply.	high cell density (hcd) cultivation of bacteria is essential for the majority of industrial processes to achieve high volumetric productivity (g l(-1) h(-1) ) of a bioproduct of interest. this study developed a fed batch bioprocess using glucose as sole carbon and energy source for the hcd of the well described biocatalyst pseudomonas putida kt2440 without the supply of oxygen enriched air. growth kinetics data from batch fermentations were used for building a bioprocess model and designing feed ...	2015	25311981
near-zero growth kinetics of pseudomonas putida deduced from proteomic analysis.	intensive microbial growth typically observed in laboratory rarely occurs in nature. because of severe nutrient deficiency, natural populations exhibit near-zero growth (nzg). there is a long-standing controversy about sustained nzg, specifically whether there is a minimum growth rate below which cells die or whether cells enter a non-growing maintenance state. using chemostat with cell retention (ccr) of pseudomonas putida, we resolve this controversy and show that under nzg conditions, bacteri ...	2015	25088710
the potential of the ni-resistant tce-degrading pseudomonas putida w619-tce to reduce phytotoxicity and improve phytoremediation efficiency of poplar cuttings on a ni-tce co-contamination.	to examine the potential of pseudomonas putida w619-tce to improve phytoremediation of ni-tce co-contamination, the effects of inoculation of a ni-resistant, tce-degrading root endophyte on ni-tce phytotoxicity, ni uptake and trichloroethylene (tce) degradation of ni-tce-exposed poplar cuttings are evaluated. after inoculation with p. putida w619-tce, root weight of non-exposed poplar cuttings significantly increased. further, inoculation induced a mitigation of the ni-tce phytotoxicity, which w ...	2015	25174423
experimental and kinetic study on the cometabolic biodegradation of phenol and 4-chlorophenol by psychrotrophic pseudomonas putida ly1.	this study investigated the kinetics of phenol and 4-chlorophenol (4-cp) biodegradation by a cold-adapted bacteria, pseudomonas putida ly1, isolated from songhua river sediment. the results showed that p. putida ly1 cannot grow on 4-cp as a sole carbon source. p. putida ly1 had the potential to cometabolic biodegrade phenol and 4-cp in a wide range of temperature (varying from 5 to 35 °c) with the optimal temperature around 25 °c. mixture of phenol and 4-cp were completely removed at two 4-cp co ...	2015	25091164
biocatalytic coatings for air pollution control: a proof of concept study on voc biodegradation.	although biofilm-based biotechnologies exhibit a large potential as solutions for off-gas treatment, the high water content of biofilms often causes pollutant mass transfer limitations, which ultimately limit their widespread application. the present study reports on the proof of concept of the applicability of bioactive latex coatings for air pollution control. toluene vapors served as a model volatile organic compound (voc). the results showed that pseudomonas putida f1 cells could be successf ...	2015	25115963
transcriptional and translational control through the 5'-leader region of the dmpr master regulatory gene of phenol metabolism.	expression of pathways for dissimilation of toxic aromatic compounds such as (methyl)phenols interfaces both stress-response and carbon catabolite repression control cascades. in pseudomonas putida, carbon catabolite repression is mediated by the protein crc - a translational repressor that counteracts utilization of less-preferred carbon sources as growth substrates until they are needed. in this work we dissect the regulatory role of the 5'-leader region (5'-lr) of the dmpr gene that encodes t ...	2015	24889314
singlet oxygen photosensitisation by the fluorescent protein pp2fbfp l30m, a novel derivative of pseudomonas putida flavin-binding pp2fbfp.	flavin-binding fluorescent proteins (fbfps) are a class of fluorescent reporters that have been increasingly used as reporters in the study of cellular structures and dynamics. flavin's intrinsic high singlet oxygen ((1)o2) quantum yield (φδ = 0.51) provides a basis for the development of new fbfp mutants capable of photosensitising (1)o2 for mechanistic and therapeutic applications, as recently exemplified by the fbfp minisog. in the present work we report an investigation on the (1)o2 photopro ...	2015	25375892
formulation of microbial cocktails for btex biodegradation.	btex biodegradation by a mixed community of micro-organisms offers a promising approach in terms of cost-effectiveness and elimination of secondary pollution. two bacterial strains, pseudomonas putida f1 and pseudomonas stutzeri ox1 were chosen to formulate synthetic consortia based on their ability to biodegrade the mono-aromatic compounds. benzene and toluene supported the growth of both the strains; while ethyl benzene and o-xylene were only utilized as growth substrates by p. putida f1 and p ...	2015	25331771
toxicity of fungal-generated silver nanoparticles to soil-inhabiting pseudomonas putida kt2440, a rhizospheric bacterium responsible for plant protection and bioremediation.	silver nanoparticles have attracted considerable attention due to their beneficial properties. but toxicity issues associated with them are also rising. the reports in the past suggested health hazards of silver nanoparticles at the cellular, molecular, or whole organismal level in eukaryotes. whereas, there is also need to examine the exposure effects of silver nanoparticle to the microbes, which are beneficial to humans as well as environment. the available literature suggests the harmful effe ...	2015	25562807
widening functional boundaries of the σ(54) promoter pu of pseudomonas putida by defeating extant physiological constraints.	the extant layout of the σ(54) promoter pu, harboured by the catabolic tol plasmid, pww0, of pseudomonas putida is one of the most complex instances of endogenous and exogenous signal integration known in the prokaryotic domain. in this regulatory system, all signal inputs are eventually translated into occupation of the promoter sequence by either of two necessary components: the m-xylene responsive transcriptional factor xylr and the σ(54) containing form of rna polymerase. modelling of these ...	2015	25560994
the potential of using low cost naturally available biogenic substrates for biological removal of chlorophenol.	this study details the application of naturally available biogenic substrates (nabs) in microbial degradation of 2-chlorophenol (cp). jatropha deoiled cakes (jdc) and karanja deoiled cakes (kdc) are used as nabs. the potential of nabs is compared with standard biogenic substrate, glucose. the study was carried out with both acclimatized mixed culture and pure culture, pseudomonas putida. microbial activity of the culture was monitored by measuring reduction in chlorophenol concentration, cod, to ...	2015	26238237
effect of trace metals and electron shuttle on simultaneous reduction of reactive black-5 azo dye and hexavalent chromium in liquid medium by pseudomonas sp.	this study demonstrates the role of electron shuttles and trace metals in the biotransformation of azo dye reactive black-5 and hexavalent chromium (crvi) that are released simultaneously in tannery effluent. previously isolated bacterial strain pseudomonas putida ki was used for the simultaneous reduction of the dye (100 mg l(-1)) and crvi (2 mg l(-1)) in a mineral salts medium (msm). among various trace metals, only cu(ii) had a stimulating effect on the bacterial-mediated reduction process. a ...	2015	25556007
genotypic and phenotypic diversity of polyhydroxybutyrate (phb) producing pseudomonas putida isolates of chhattisgarh region and assessment of its phosphate solubilizing ability.	a diverse and versatile spectrum of metabolic activities among isolates of fluorescent pseudomonas putida indicates their adaptability to various niches. these polyhydroxybutyrate producing and phosphate solubilizing isolates showed a high level of functional and genetic versatility among themselves. one of the potential p. putida isolate p132 can contribute as a candidate agent for both biocontrol and pgpr applications. identified as one of the most efficient phb producer and phosphate solubili ...	2015	28324359
removing selected steroid hormones, biocides and pharmaceuticals from water by means of biogenic manganese oxide nanoparticles in situ at ppb levels.	the oxidation of organic micro-pollutants by biogenic manganese oxide nanoparticles (biomnox) has been studied with respect to possible implementation of biomnox in wastewater treatment. for this it would be prerequisite that microbial mn(2+) oxidation and biomnox-driven pollutant removal can occur in situ, i.e. in the same reactor as the removal. here we present the in situ reactivity of biomnox produced by pseudomonas putida towards a range of micro-pollutants at environmentally relevant conce ...	2015	25532770
evaluation of metal biouptake from the analysis of bulk metal depletion kinetics at various cell concentrations: theory and application.	bioavailability of trace metals is a key parameter for assessment of toxicity on living organisms. proper evaluation of metal bioavailability requires monitoring the various interfacial processes that control metal partitioning dynamics at the biointerface, which includes metal transport from solution to cell membrane, adsorption at the biosurface, internalization, and possible excretion. in this work, a methodology is proposed to quantitatively describe the dynamics of cd(ii) uptake by pseudomo ...	2015	25525993
aromatic catabolic pathway selection for optimal production of pyruvate and lactate from lignin.	lignin represents an untapped feedstock for the production of fuels and chemicals, but its intrinsic heterogeneity makes lignin valorization a significant challenge. in nature, many aerobic organisms degrade lignin-derived aromatic molecules through conserved central intermediates including catechol and protocatechuate. harnessing this microbial approach offers potential for lignin upgrading in modern biorefineries, but significant technical development is needed to achieve this end. catechol an ...	2015	25617773
development of eukaryotic zoospores within polycyclic aromatic hydrocarbon (pah)-polluted environments: a set of behaviors that are relevant for bioremediation.	in this study, we assessed the development (formation, taxis and settlement) of eukaryotic zoospores under different regimes of exposure to polycyclic aromatic hydrocarbons (pahs), which imitated environmental scenarios of pollution and bioremediation. with this aim, we used an oomycete, pythium aphanidermatum, as a source of zoospores and two pah-degrading bacteria (mycobacterium gilvum vm552 and pseudomonas putida g7). the oomycete and both bacteria were not antagonistic, and zoospore formatio ...	2015	25617701
effect of heavy-metal-resistant bacteria on enhanced metal uptake and translocation of the cu-tolerant plant, elsholtzia splendens.	a hydroponics trial was employed to study the effects of pseudomonas putida cz1 (cz1), a heavy-metal-resistant bacterial strain isolated from the rhizosphere of elsholtzia splendens (e. splendens), on the uptake and translocation of copper (cu) in e. splendens. significant promotion of plant growth coupled with the obvious plant-growth-promoting (pgp) characters of the bacteria suggested that cz1 would be a plant-growth-promoting rhizobacterium (pgpr) to e. splendens under cu stress condition. t ...	2015	25510610
fringe-controlled biodegradation under dynamic conditions: quasi 2-d flow-through experiments and reactive-transport modeling.	biodegradation in contaminated aquifers has been shown to be most pronounced at the fringe of contaminant plumes, where mixing of contaminated water and ambient groundwater, containing dissolved electron acceptors, stimulates microbial activity. while physical mixing of contaminant and electron acceptor by transverse dispersion has been shown to be the major bottleneck for biodegradation in steady-state plumes, so far little is known on the effect of flow and transport dynamics (caused, e.g., by ...	2015	25496820
the ppui-rsal-ppur quorum-sensing system regulates cellular motility, pectate lyase activity, and virulence in potato opportunistic pathogen pseudomonas sp. stflb209.	pseudomonas sp. stflb209 was isolated from potato leaf as an n-acylhomoserine lactone (ahl)-producing bacterium and showed a close phylogenetic relationship with p. cichorii, a known plant pathogen. although there are no reports of potato disease caused by pseudomonads in japan, stflb209 was pathogenic to potato leaf. in this study, we reveal the complete genome sequence of stflb209, and show that the strain possesses a ppui-rsal-ppur quorum-sensing system, the sequence of which shares a high si ...	2015	25485871
the quest for a practical synthesis of morphine alkaloids and their derivatives by chemoenzymatic methods.	we became interested in approaches to morphine in the early 1990s following our immersion into the new program on the enzymatic dihydroxylation of aromatics. larry kwart, a former classmate of one of us at rice university, who worked with our group at virginia tech in the mid-1980s, introduced to us the use of blocked mutants of pseudomonas putida (pp39d) for the production of arene-cis-dihydrodiols. larry had gained expertise in microbiology from a postdoctoral stay with david gibson, who disco ...	2015	25730681
personal care product preservatives: risk assessment and mixture toxicities with an industrial wastewater.	the aquatic toxicity of eight preservatives frequently used in personal care products (pcps) (iodopropynyl butylcarbamate, bronopol, diazolidinyl urea, benzalkonium chloride, zinc pyrithione, propylparaben, triclosan and a mixture of methylchloroisothiazolinone and methylisothiazolinone) was assessed by means of two different approaches: a battery of bioassays composed of single species tests of bacteria (vibrio fischeri and pseudomonas putida) and protozoa (tetrahymena thermophila), and a whole ...	2015	25585550
integration of chemotaxis, transport and catabolism in pseudomonas putida and identification of the aromatic acid chemoreceptor pcay.	aromatic and hydroaromatic compounds that are metabolized through the β-ketoadipate catabolic pathway serve as chemoattractants for pseudomonas putida f1. a screen of p. putida f1 mutants, each lacking one of the genes encoding the 18 putative methyl-accepting chemotaxis proteins (mcps), revealed that pcay encodes the mcp required for metabolism-independent chemotaxis to vanillate, vanillin, 4-hydroxybenzoate, benzoate, protocatechuate, quinate, shikimate, as well as 10 substituted benzoates tha ...	2015	25582673
molecular dynamics investigation of the substrate binding mechanism in carboxylesterase.	a recombinant carboxylesterase, cloned from pseudomonas putida and designated as rppe, is capable of catalyzing the bioresolution of racemic 2-acetoxy-2-(2'-chlorophenyl)acetate (rac-aco-cpa) with excellent (s)-enantioselectivity. semirational design of the enzyme showed that the w187h variant could increase the activity by ∼100-fold compared to the wild type (wt) enzyme. in this study, we performed all-atom molecular dynamics (md) simulations of both apo-rppe and rppe in complex with (s)-aco-cp ...	2015	25711934
the crc/crcz-crcy global regulatory system helps the integration of gluconeogenic and glycolytic metabolism in pseudomonas putida.	in metabolically versatile bacteria, carbon catabolite repression (ccr) facilitates the preferential assimilation of the most efficient carbon sources, improving growth rates and fitness. in pseudomonas putida, the crc and hfq proteins and the crcz and crcy small rnas, which are believed to antagonize crc/hfq, are key players in ccr. unlike that seen in other bacterial species, succinate and glucose elicit weak ccr in this bacterium. in the present work, metabolic, transcriptomic and constraint- ...	2015	25711694
ner enzymes maintain genome integrity and suppress homologous recombination in the absence of exogenously induced dna damage in pseudomonas putida.	in addition to its prominence in producing genetic diversity in bacterial species, homologous recombination (hr) plays a key role in dna repair and damage tolerance. the frequency of hr depends on several factors, including the efficiency of dna repair systems as hr is involved in recovery of replication forks perturbed by dna damage. nucleotide excision repair (ner) is one of the major dna repair pathways involved in repair of a broad range of dna lesions generally induced by exogenous chemical ...	2015	25463394
integrated micro-biochemical approach for phytoremediation of cadmium and zinc contaminated soils.	the integrated potential of oilcake manure (om), elemental sulphur (s(0)), glomus fasciculatum and pseudomonas putida by growing helianthus annuus l for phytoremediation of cadmium and zinc contaminated soils was investigated under pot experiment. the integrated treatment (2.5 g kg(-1) om, 0.8 g kg(-1) s(0) and co-inoculation with g. fasciculatum and p. putida promoted the dry biomass of the plant. the treatment was feasible for enhanced cadmium accumulation up to 6.56 and 5.25 mg kg(-1) and zin ...	2015	25450919
genome-wide investigation of the genes involved in nicotine metabolism in pseudomonas putida j5 by tn5 transposon mutagenesis.	pseudomonas putida j5 is an efficient nicotine-degrading bacterial strain isolated from the tobacco rhizosphere. we successfully performed a comprehensive whole-genome analysis of nicotine metabolism-associated genes by tn5 transposon mutagenesis in p. putida j5. a total of 18 mutants with unique insertions screened from 16,324 tn5-transformants failed to use nicotine as the sole carbon source. flanking sequences of the tn5 transposon were cloned with a shotgun method from all of the nicotine-gr ...	2015	25808517
an integrated view of redox and catalytic properties of b-type ppdyp from pseudomonas putida met94 and its distal variants.	ppdyp from pseudomonas putida met94 is an extremely versatile b-type dye-decolourising peroxidase (dyp) capable of efficient oxidation of a wide range of anthraquinonic and azo dyes, phenolic substrates, the non-phenolic veratryl alcohol and even manganese and ferrous ions. in reaction with h2o2 it forms a stable compound i at a rate of (1.4±0.3)×10(6)m(-1)s(-1), comparable to those of classical peroxidases and other dyps. we provide the first report of standard redox potential (e(0')) of the co ...	2015	25797439
effect of silver nanoparticles on pseudomonas putida biofilms at different stages of maturity.	this study determined the effect of silver nanoparticles (agnps) on pseudomonas putida kt2440 biofilms at different stages of maturity. three biofilm stages (1-3, representing early to late stages of development) were identified from bacterial adenosine triphosphate (atp) activity under static (96-well plate) and dynamic conditions (center for disease control and prevention biofilm reactor). extracellular polymeric substance (eps) levels, measured using crystal violet and total carbohydrate assa ...	2015	25756827
plant growth-promoting effects of native pseudomonas strains on mentha piperita (peppermint): an in vitro study.	plant growth-promoting rhizobacteria (pgpr) affect growth of host plants through various direct and indirect mechanisms. three native pgpr (pseudomonas putida) strains isolated from rhizospheric soil of a mentha piperita (peppermint) crop field near córdoba, argentina, were characterised and screened in vitro for plant growth-promoting characteristics, such as indole-3-acetic acid (iaa) production, phosphate solubilisation and siderophore production, effects of direct inoculation on plant growth ...	2015	26012535
dynamics of suspended and attached aerobic toluene degraders in small-scale flow-through sediment systems under growth and starvation conditions.	the microbially mediated reactions, that are responsible for field-scale natural attenuation of organic pollutants, are governed by the concurrent presence of a degrading microbial community, suitable energy and carbon sources, electron acceptors, as well as nutrients. the temporal lack of one of these essential components for microbial activity, arising from transient environmental conditions, might potentially impair in situ biodegradation. this study presents results of small scale flow-throu ...	2015	26009808
continuous ozonation treatment of ofloxacin: transformation products, water matrix effect and aquatic toxicity.	the continuous ozonation of the antibiotic ofloxacin (ofx) has been performed using a synthetic water matrix and in a sewage treatment plant (stp) effluent. the aim was to study the effect of the water matrix on the ozonation with particular emphasis on the aquatic toxicity of treated water. ofx was completely removed in both water matrices, although the amount of ozone consumed for its depletion was strongly matrix-dependent. the extent of mineralization was limited and a number of intermediate ...	2015	25796038
5-methyl phenazine-1-carboxylic acid: a novel bioactive metabolite by a rhizosphere soil bacterium that exhibits potent antimicrobial and anticancer activities.	a new rhizosphere soil bacterium that exhibits antimicrobial potential against human pathogens was isolated. on the basis of 16s ribosomal rna nucleotide sequence homology and subsequent phylogenetic tree analysis, the strain puw5 was identified as pseudomonas putida. a bioactive metabolite was extracted and purified using silica gel column chromatography and preparative hplc. characterization of metabolite was done by employing fourier transform infrared spectroscopy (ftir), nuclear magnetic re ...	2015	25765238
engineering biological approaches for detection of toxic compounds: a new microbial biosensor based on the pseudomonas putida ttgr repressor.	environmental contamination by toxic organic compounds and antimicrobials is one of the causes for the recent surge of multidrug-resistant pathogenic bacteria. monitoring contamination is therefore the first step in containment of antimicrobial resistance and requires the development of simple, sensitive, and quantitative tools that detect a broad spectrum of toxic compounds. in this study, we have engineered a new microbial biosensor based on the ttgr-regulated promoter that controls expression ...	2015	25731724
impact of dissolved organic matter on bacterial tactic motility, attachment, and transport.	bacterial dispersal is a key driver of the ecology of microbial contaminant degradation in soils. this work investigated the role of dissolved organic matter (dom) in the motility, attachment, and transport of the soil bacterium pseudomonas putida g7 in saturated porous media. the study is based on the hypothesis that dom quality is critical to triggering tactic motility and, consequently, affects bacterial transport and dispersal. sunflower root exudates, humic acids (ha), and the synthetic ole ...	2015	25734420
engineering pseudomonas putida kt2440 for simultaneous degradation of organophosphates and pyrethroids and its application in bioremediation of soil.	agricultural soils are usually co-contaminated with organophosphate (op) and pyrethroid pesticides. to develop a stable and marker-free pseudomonas putida for co-expression of two pesticide-degrading enzymes, we constructed a suicide plasmid with expression cassettes containing a constitutive promoter j23119, an op-degrading gene (mpd), a pyrethroid-hydrolyzing carboxylesterase gene (pyth) that utilizes the upp gene as a counter-selectable marker for upp-deficient p. putida. by introduction of s ...	2015	25917649
thiamethoxam degradation by pseudomonas and bacillus strains isolated from agricultural soils.	twelve bacterial species were evaluated to know the degradation pattern of thiamethoxam in liquid medium. all the bacterial species could actively degrade phorate in a mineral salt medium containing phorate (50 μg ml(-1)) as sole carbon source. as these species have ability to degrade, we used these for the degradation of thiamethoxam--a neonicoitinoids. screening of 12 active phorate-metabolizing bacterial species resulted in selection of bacillus aeromonas strain imbl 4.1 and pseudomonas putid ...	2015	25917187
analysis of the molecular response of pseudomonas putida kt2440 to the next-generation biofuel n-butanol.	to increase the efficiency of biocatalysts a thorough understanding of the molecular response of the biocatalyst to precursors, products and environmental conditions applied in bioconversions is essential. here we performed a comprehensive proteome and phospholipid analysis to characterize the molecular response of the potential biocatalyst pseudomonas putida kt2440 to the next-generation biofuel n-butanol. using complementary quantitative proteomics approaches we were able to identify and quant ...	2015	25829261
repeated batch and continuous degradation of chlorpyrifos by pseudomonas putida.	the present study was undertaken with the objective of studying repeated batch and continuous degradation of chlorpyrifos (o,o-diethyl o-3,5,6-trichloropyridin-2-yl phosphorothioate) using ca-alginate immobilized cells of pseudomonas putida isolated from an agricultural soil, and to study the genes and enzymes involved in degradation. the study was carried out to reduce the toxicity of chlorpyrifos by degrading it to less toxic metabolites. long-term stability of pesticide degradation was studie ...	2015	25826103
integrated engineering of β-oxidation reversal and ω-oxidation pathways for the synthesis of medium chain ω-functionalized carboxylic acids.	an engineered reversal of the β-oxidation cycle was exploited to demonstrate its utility for the synthesis of medium chain (6-10-carbons) ω-hydroxyacids and dicarboxylic acids from glycerol as the only carbon source. a redesigned β-oxidation reversal facilitated the production of medium chain carboxylic acids, which were converted to ω-hydroxyacids and dicarboxylic acids by the action of an engineered ω-oxidation pathway. the selection of a key thiolase (bktb) and thioesterase (ydii) in combinat ...	2015	25638687
a comparison of the sorption reactivity of bacteriogenic and mycogenic mn oxide nanoparticles.	biogenic mno2 minerals affect metal fate and transport in natural and engineered systems by strongly sorbing metals ions. the ability to produce mno2 is widely dispersed in the microbial tree of life, leading to potential differences in the minerals produced by different organisms. in this study, we compare the structure and reactivity of biogenic mn oxides produced by the biofilm-forming bacterium pseudomonas putida gb-1 and the white-rot fungus coprinellus sp. the rate of mn(ii) oxidation, and ...	2015	25668070
the phasin phaf controls bacterial shape and size in a network-forming strain of pseudomonas putida.	pseudomonas putida n, a poly-3-hydroxyalkonate (pha)-producing bacterium, showing ampicillin resistance, is an unusual strain. in the presence of this antibiotic, it grows as giant cells (25-50μm) forming complex networks inter-connected by micro-tubular structures. the transformation of this bacterium with a plasmid containing the gene phaf, which encodes a phasin involved in the molecular architecture of the pha-granules, (i) restores the wild-type phenotype by reducing both bacterial size and ...	2015	25661838
effects of impurities in biodiesel-derived glycerol on growth and expression of heavy metal ion homeostasis genes and gene products in pseudomonas putida ls46.	biodiesel production-derived waste glycerol (wg) was previously investigated as potential carbon source for medium chain length polyhydroxyalkanoate (mcl-pha) production by pseudomonas putida ls46. in this study, we evaluated the effect of impurities in the wg on p. putida ls46 physiology during exponential growth and corresponding changes in transcription and protein expression profiles compared with cells grown on pure, reagent grade glycerol. high concentration of metal ions, such as na(+), a ...	2015	26002633
crude oil biodegradation aided by biosurfactants from pseudozyma sp. nii 08165 or its culture broth.	the aim of this work was to evaluate the biosurfactants produced by the yeast pseudozyma sp. nii 08165 for enhancing the degradation of crude oil by a model hydrocarbon degrading strain, pseudomonas putida mtcc 1194. pseudozyma biosurfactants were supplemented at various concentrations to the p. putida culture medium containing crude oil as sole carbon source. supplementation of the biosurfactants enhanced the degradation of crude oil by p. putida; the maximum degradation of hydrocarbons was obs ...	2015	25985416
oxidative stress in bacteria (pseudomonas putida) exposed to nanostructures of silicon carbide.	silicon carbide (sic) nanostructures produced by combustion synthesis can cause oxidative stress in the bacterium pseudomonas putida. the results of this study showed that sic nanostructures damaged the cell membrane, which can lead to oxidative stress in living cells and to the loss of cell viability. as a reference, micrometric sic was also used, which did not exhibit toxicity toward cells. oxidative stress was studied by analyzing the activity of peroxidases, and the expression of the glucose ...	2015	25965002
a new p. putida instrumental toxicity bioassay.	here, we present a new toxicity bioassay (co2-tox), able to detect toxic or inhibitory compounds in water samples, based on the quantification of pseudomonas putida kt2440 co2 production. the metabolically produced co2 was measured continuously and directly in the liquid assay media, with a potentiometric gas electrode. the optimization studies were performed using as a model toxicant 3,5-dcp (3,5-dichlorophenol); later, heavy metals (pb(2+), cu(2+), or zn(2+)) and a metalloid (as(5+)) were assa ...	2015	25910719
[influence of microcystin-lr on cell viability and surface characteristics of pseudomonas putida].	in microcystin-lr (mc-lr) degradation system, the change in surface characteristics and cell viability of pseudomonas putida was studied. the purpose of this study was to reveal the influence of mc-lr on p. putida and elucidate the toxicity of mc-lr on microorganisms. the result demonstrated that mc-lr enhanced the cytoplasmic membrane permeability, as well as affected the ion metabolism and protein release of p. putida. the soluble sugar and na+, cl-release increased with the rising concentrati ...	2015	25898672
the c-di-gmp phosphodiesterase bifa regulates biofilm development in pseudomonas putida.	we previously showed the isolation of biofilmpersistent pseudomonas putida mutants that fail to undergo biofilm dispersal upon entry in stationary phase. two such mutants were found to bear insertions in pp0914, encoding a ggdef/eal domain protein with high similarity to pseudomon asaeruginosa bifa. here we show the phenotypic characterization of a δbifa mutant in p. putida kt2442.this mutant displayed increased biofilm and pellicle formation, cell aggregation in liquid medium and decreased star ...	2015	25870874
quantitative analysis of cellular proteome alterations of pseudomonas putida to naphthalene-induced stress.	to investigate whether genes other than the operons nahaaabacadbfced and nahgthinlomkj of pseudomonas putida are involved in the tolerance of the bacterium to naphthalene.	2015	25868532
genes involved in nutrient competition by pseudomonas putida jbc17 to suppress green mold in postharvest satsuma mandarin.	understanding the mechanisms underlying biocontrol activity in biocontrol agents is indispensable to implement biological control. however, the understanding of specific mechanisms for nutrient competition in nutrient limited environments is still limited. this study was performed to control green mold of postharvest satsuma mandarin (mandarin) using pseudomonas putida jbc17 (jbc17), and identify the genes involved in nutrient competition. treatment with jbc17 on wounded mandarin fruits at a con ...	2015	25707389
hormetic effect of ionic liquid 1-ethyl-3-methylimidazolium acetate on bacteria.	the biological effect of ionic liquids (ils) is one of the highly debated topics as they are being contemplated for various industrial applications. 1-ethyl-3-methylimidazolium acetate ([emim][ac]) showed remarkable hormesis on anaerobic clostridium sp. and aerobic pseudomonas putida. bacterial growth was stimulated at up to 2.5 g l(-1) and inhibited at >2.5 g l(-1) of [emim][ac]. the growth of clostridium sp. and p. putida were higher by 0.4 and 4-fold respectively, in the presence of 0.5 g l(- ...	2015	25703901
engineering towards nitroreductase functionality in ene-reductase scaffolds.	nitroreductases (nrs) and ene-reductases (ers) both utilize flavin mononucleotide cofactors but catalyze distinct reactions. nrs reduce nitroaromatics, whereas ers reduce unsaturated c=c double bonds, and these functionalities are known to somewhat overlap. recent studies on the er xenobiotic reductase a (xena) from pseudomonas putida demonstrated the possibility of increasing nr activity with active site modifications. structural comparison between nrs and ers led us to hypothesize that active ...	2015	25703443
a new strategy for smoking cessation: characterization of a bacterial enzyme for the degradation of nicotine.	smoking is the leading cause of preventable diseases; thus, effective smoking cessation aids are crucial for reducing the prevalence of cigarette smoking and smoking-related illnesses. in our current campaign we offer a nicotine-degrading enzyme from pseudomonas putida, nica2, a flavin-containing protein. to explore its potential, a kinetic evaluation of the enzyme was conducted, which included determination of k(m), k(cat), buffer/serum half-life, and thermostability. additionally, the cataboli ...	2015	26237398
interplay of the ptsn (eiia(ntr)) protein of pseudomonas putida with its target sensor kinase kdpd.	the nitrogen phosphotransferase system (pts(ntr) ) of pseudomonas putida is a multi-component regulatory device that participates in controlling a variety of physiological processes in a post-translational fashion. a general survey of genes regulated by ptsn exposed transcription of the kdpfabc operon is most conspicuously affected. measurements of kdpfp promoter activity in different pts mutants showed that ptsn is responsible for repression of kdpfabc transcription. this effect could be assign ...	2015	26224366
phenolic wastewater treatment through extractive recovery coupled with biodegradation in a two-phase partitioning membrane bioreactor.	a two-phase partitioning membrane bioreactor (tppmb) was designed and operated for treatment of high strength phenolic wastewater through extraction/stripping and concomitant biodegradation. tributyl phosphate dissolved in kerosene was used as the organic phase, sodium hydroxide as the stripping phase and pseudomonas putida for biodegradation. in a semi-dispersive approach, organic phase dispersed in the stripping solution was contacted with wastewater through semi-permeable membranes for remova ...	2015	26210322
modeling the interplay of pseudomonas putida eiia with the potassium transporter kdpfabc.	the nitrogen phosphotransferase system (pts(ntr)) of pseudomonas putida is a key regulatory device that participates in controlling many physiological processes in a posttranscriptional fashion. one of the target functions of the pts(ntr) is the regulation of potassium transport. this is mediated by the direct interaction of one of its components with the sensor kinase kdpd of the two-component system controlling transcription of the kdpfabc genes. from a detailed experimental analysis of the ac ...	2015	26159078
heterofunctional magnetic metal-chelate-epoxy supports for the purification and covalent immobilization of benzoylformate decarboxylase from pseudomonas putida and its carboligation reactivity.	in this study, the combined use of the selectivity of metal chelate affinity chromatography with the capacity of epoxy supports to immobilize poly-his-tagged recombinant benzoylformate decarboxylase from pseudomonas putida (bfd, e.c. 4.1.1.7) via covalent attachment is shown. this was achieved by designing tailor-made magnetic chelate-epoxy supports. in order to selectively adsorb and then covalently immobilize the poly-his-tagged bfd, the epoxy groups (300 µmol epoxy groups/g support) and a ver ...	2015	26147067
tn7-based device for calibrated heterologous gene expression in pseudomonas putida.	the soil bacterium pseudomonas putida is increasingly attracting considerable interest as a platform for advanced metabolic engineering through synthetic biology approaches. however, genomic context, gene copy number, and transcription/translation interplay often introduce considerable uncertainty to the design of reliable genetic constructs. in this work, we have established a standardized heterologous expression device in which the promoter strength is the only variable; the remaining paramete ...	2015	26133359
a quick rhizobacterial selection tests for the remediation of copper contaminated soils.	the main objective of the study is to develop and improve quick bacterial tests to select the best candidates for the bioaugmentation of metal-contaminated soil, coupled with phytoextraction.	2015	26042640
biocompatibility of low molecular weight polymers for two-phase partitioning bioreactors.	two phase partitioning bioreactors (tppbs) improve the efficiency of fermentative processes by limiting the exposure of microorganisms to toxic solutes by sequestering them into a non-aqueous phase (nap). a potential limitation of this technology, when using immiscible organic solvents as the nap, is the cytoxicity that these materials may exert on the microbes. an improved tppb configuration is one in which polymeric naps are used to replace organic solvents in order to take advantage of their ...	2015	26032439
[the role of mineral phosphorus compounds in naphthalene biodegradation by pseudomonas putida].	the effect of phosphate concentration in the culture medium on the growth and naphthalene degradation by pseudomonas putida bs 3701 was studied. the limiting concentration of phosphate was 0.4 mm and 0.1 mm under cultivation in media with naphthalene and glucose, respectively the phosphate deficiency correlated with a decrease in the activities of naphthalene dioxygenase and salicylate hydroxylase and with salicylate accumulation in the culture medium. we suggest that this fact indicates the imp ...	2015	26027355
complete genome sequence of solvent-tolerant pseudomonas putida s12 including megaplasmid ptts12.	pseudomonas putida s12 is a solvent-tolerant gamma-proteobacterium with an extensive track record for production of industrially relevant chemicals. here we report the annotated complete genome sequence of this organism, including the megaplasmid ptts12 which encodes many of the unique features of the s12 strain.	2015	25746905
systematic profiling of indole-3-acetic acid biosynthesis in bacteria using lc-ms/ms.	indole-3-acetic acid (iaa) is produced from tryptophan through five synthesis pathways. a comprehensive method for the quantification of iaa and biosynthesis-related intermediates in a culture medium was developed. sample preparation was simple with protein precipitation. the analytes were separated on a superficially porous c18 silica column and detected by electrospray ionization-tandem mass spectrometry in the positive ion multiple reaction monitoring mode. the limit of detection was 0.05 μm, ...	2015	25746752
nhej enzymes ligd and ku participate in stationary-phase mutagenesis in pseudomonas putida.	under growth-restricting conditions bacterial populations can rapidly evolve by a process known as stationary-phase mutagenesis. bacterial nonhomologous end-joining (nhej) system which consists of the dna-end-binding enzyme ku and the multifunctional dna ligase ligd has been shown to be important for survival of bacteria especially during quiescent states, such as late stationary-phase populations or sporulation. in this study we provide genetic evidence that nhej enzymes participate in stationa ...	2015	25942369
mechanisms of solvent resistance mediated by interplay of cellular factors in pseudomonas putida.	a number of microorganisms have the ability to thrive in the presence of a range of toxic solvents. tolerance to these chemicals is a multifactorial process, meaning that bacterial cells use a set of physiological and gene expression changes to overcome the damage imparted by these chemicals. this review focuses mainly on issues related to tolerance to aromatic hydrocarbons and butanol in pseudomonas, although other microorganisms are also discussed. pseudomonas putida strains contain a circular ...	2015	25934123
detection and location of op-degrading activity: a model to integrate education and research.	the environmental sampling research module (esrm) is an investigative/discovery module that provides undergraduate research experiences for students as part of an interdisciplinary research-based biotechnology curriculum at the university of houston campus. as part of the esrm, students collect soil samples from various locations to test for the presence of organophosphorous (op) degrading bacteria. at the end of this research project students submit a research paper on their field and laborator ...	2015	25863354
cometabolism of methyl tert-butyl ether by a new microbial consortium ers.	the release of methyl tert-butyl-ether (mtbe) into the environment has increased the worldwide concern about the pollution of mtbe. in this paper, a microbial consortium was isolated from the soil sample near an oil station, which can degrade mtbe directly with a low biomass yield and mtbe degrading efficiency. further research has indicated that this consortium can degrade mtbe efficiently when grown on n-octane as the cometabolic substrate. the results of 16s rdna based on phylogenetic analysi ...	2015	25697553