Publications

three pseudomonas putida fnr family proteins with different sensitivities to o2.	the escherichia coli fumarate-nitrate reduction regulator (fnr) protein is the paradigm for bacterial o2-sensing transcription factors. however, unlike e. coli, some bacterial species possess multiple fnr proteins that presumably have evolved to fulfill distinct roles. here, three fnr proteins (anr, pp_3233, and pp_3287) from a single bacterial species, pseudomonas putida kt2440, have been analyzed. under anaerobic conditions, all three proteins had spectral properties resembling those of [4fe-4 ...	2015	25971977
microbial community in high arsenic shallow groundwater aquifers in hetao basin of inner mongolia, china.	a survey was carried out on the microbial community of 20 groundwater samples (4 low and 16 high arsenic groundwater) and 19 sediments from three boreholes (two high arsenic and one low arsenic boreholes) in a high arsenic groundwater system located in hetao basin, inner mongolia, using the 454 pyrosequencing approach. a total of 233,704 sequence reads were obtained and classified into 12-267 operational taxonomic units (otus). groundwater and sediment samples were divided into low and high arse ...	2015	25970606
development of biological oxygen demand biosensor for monitoring the fermentation industry effluent.	a biosensor was developed for the determination of bod value of fermentation industry effluent. the developed biosensor was fabricated by immobilizing the microbial consortium on cellulose acetate (ca) membrane in close proximity to a do probe electrode. the microbial consortium was harvested from the fermentation industry effluent. the bod biosensor was calibrated by using a solution containing the equivalent amount of glucose/glutamic acid (gga) as a standard sample solution. the response time ...	2012	25969770
development of biological oxygen demand biosensor for monitoring the fermentation industry effluent.	a biosensor was developed for the determination of bod value of fermentation industry effluent. the developed biosensor was fabricated by immobilizing the microbial consortium on cellulose acetate (ca) membrane in close proximity to a do probe electrode. the microbial consortium was harvested from the fermentation industry effluent. the bod biosensor was calibrated by using a solution containing the equivalent amount of glucose/glutamic acid (gga) as a standard sample solution. the response time ...	2012	25969770
carbapenemase producing bacteria in the food supply escaping detection.	carbapenem antimicrobials are critically important to human health and they are often the only remaining effective antibiotics for treating serious infections. resistance to these drugs mediated by acquired carbapenemase enzymes is increasingly encountered in gram-negative bacteria and is considered a public health emergency. animal origin food products are recognized as a potential source of resistant organisms, although carbapenem resistance has only recently been reported. in western countrie ...	2015	25966303
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
what it takes to be a pseudomonas aeruginosa? the core genome of the opportunistic pathogen updated.	pseudomonas aeruginosa is an opportunistic bacterial pathogen able to thrive in highly diverse ecological niches and to infect compromised patients. its genome exhibits a mosaic structure composed of a core genome into which accessory genes are inserted en bloc at specific sites. the size and the content of the core genome are open for debate as their estimation depends on the set of genomes considered and the pipeline of gene detection and clustering. here, we redefined the size and the content ...	2015	25961859
the production of ω-hydroxy palmitic acid using fatty acid metabolism and cofactor optimization in escherichia coli.	hydroxylated fatty acids (hfas) are used as important precursors for bulk and fine chemicals in the chemical industry. here, to overproduce long-chain (c16-c18) fatty acids and hydroxy fatty acid, their biosynthetic pathways including thioesterase (lreu_0335) from lactobacillus reuteri dsm20016, β-hydroxyacyl-acp dehydratase (fabz) from escherichia coli, and a p450 system (i.e., cyp153a from marinobacter aquaeolei vt8 and cama/camb from pseudomonas putida atcc17453) were overexpressed. acyl-coa ...	2015	25957153
metabolism of doubly para-substituted hydroxychlorobiphenyls by bacterial biphenyl dioxygenases.	in this work, we examined the profile of metabolites produced from the doubly para-substituted biphenyl analogs 4,4'-dihydroxybiphenyl, 4-hydroxy-4'-chlorobiphenyl, 3-hydroxy-4,4'-dichlorobiphenyl, and 3,3'-dihydroxy-4,4'-chlorobiphenyl by biphenyl-induced pandoraea pnomenusa b356 and by its biphenyl dioxygenase (bpdo). 4-hydroxy-4'-chlorobiphenyl was hydroxylated principally through a 2,3-dioxygenation of the hydroxylated ring to generate 2,3-dihydro-2,3,4-trihydroxy-4'-chlorobiphenyl and 3,4-d ...	2015	25956777
enterocin f4-9, a novel o-linked glycosylated bacteriocin.	enterococcus faecalis f4-9 isolated from egyptian salted-fermented fish produces a novel bacteriocin, termed enterocin f4-9. enterocin f4-9 was purified from the culture supernatant by three steps, and its molecular mass was determined to be 5,516.6 da by mass spectrometry. amino acid and dna sequencing showed that the propeptide consists of 67 amino acid residues, with a leader peptide containing a double glycine cleavage site to produce a 47-amino-acid mature peptide. enterocin f4-9 is modifie ...	2015	25956765
draft genome sequence of se(iv)-reducing bacterium pseudomonas migulae es3-33.	pseudomonas migulae es3-33 is a gram-negative strain that strongly reduces se(iv) and was isolated from a selenium mining area in enshi, southwest china. here we present the draft genome of this strain containing potential genes involved in selenite reduction and a large number of genes encoding resistances to copper and antibiotics.	2015	25953191
enhanced horizontal transfer of antibiotic resistance genes in freshwater microcosms induced by an ionic liquid.	the spread and propagation of antibiotic resistance genes (args) is a worldwide public health concern. ionic liquids (ils), considered as "environmentally friendly" replacements for industrial organic solvents, have been widely applied in modern industry. however, few data have been collected regarding the potential ecological and environmental risks of ils, which are important for preparing for their potential discharge into the environment. in this paper, the il 1-butyl-3-methylimidazolium hex ...	2015	25951456
contribution of a low-barrier hydrogen bond to catalysis is not significant in ketosteroid isomerase.	low-barrier hydrogen bonds (lbhbs) have been proposed to have important influences on the enormous reaction rate increases achieved by many enzymes. δ(5)-3-ketosteroid isomerase (ksi) catalyzes the allylic isomerization of δ(5)-3-ketosteroid to its conjugated δ(4)-isomers at a rate that approaches the diffusion limit. tyr14, a catalytic residue of ksi, has been hypothesized to form an lbhb with the oxyanion of a dienolate steroid intermediate generated during the catalysis. the unusual chemical ...	2015	25947291
high quality draft genome sequence of the heavy metal resistant bacterium halomonas zincidurans type strain b6(t).	halomonas zincidurans strain b6(t) was isolated from a deep-sea heavy metal rich sediment from the south atlantic mid-ocean ridge. the strain showed significant resistance to heavy metals, especially to zinc. here we describe the genome sequence and annotation, as well as the features, of the organism. the genome contains 3,325 protein-coding genes (2,848 with predicted functions), 61 trna genes and 6 rrna genes. h. zincidurans strain b6(t) encodes 31 genes related to heavy metal resistance. and ...	2014	25945155
re-evaluation of dioxygenase gene phylogeny for the development and validation of a quantitative assay for environmental aromatic hydrocarbon degraders.	rieske non-heme iron oxygenases enzymes have been widely studied, as they catalyse essential reactions initiating the bacterial degradation of organic compounds, for instance aromatic hydrocarbons. the genes encoding these enzymes offer a potential target for studying aromatic hydrocarbon-degrading organisms in the environment. however, previously reported primer sets that target dioxygenase gene sequences or the common conserved rieske centre of aromatics dioxygenases have limited specificity a ...	2015	25944871
cosmetics-triggered percutaneous remote control of transgene expression in mice.	synthetic biology has significantly advanced the rational design of trigger-inducible gene switches that program cellular behavior in a reliable and predictable manner. capitalizing on genetic componentry, including the repressor pmer and its cognate operator opmer, that has evolved in pseudomonas syringae pathovar tomato dc3000 to sense and resist plant-defence metabolites of the paraben class, we have designed a set of inducible and repressible mammalian transcription-control devices that coul ...	2015	25943548
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
nonphotosynthetic pigments as potential biosignatures.	previous work on possible surface reflectance biosignatures for earth-like planets has typically focused on analogues to spectral features produced by photosynthetic organisms on earth, such as the vegetation red edge. although oxygenic photosynthesis, facilitated by pigments evolved to capture photons, is the dominant metabolism on our planet, pigmentation has evolved for multiple purposes to adapt organisms to their environment. we present an interdisciplinary study of the diversity and detect ...	2015	25941875
the kinetic characterization and x-ray structure of a putative benzoylformate decarboxylase from m. smegmatis highlights the difficulties in the functional annotation of thdp-dependent enzymes.	benzoylformate decarboxylase (bfdc) is a thiamin diphosphate (thdp)-dependent enzyme that catalyzes the nonoxidative decarboxylation of benzoylformate. it is the penultimate enzyme in both the mandelate pathway and the d-phenylglycine degradation pathway. the thdp-dependent enzyme engineering database (teed) now lists more than 800 sequences annotated as bfdcs, including one from mycobacterium smegmatis (msbfdc). however, there is no evidence that either pathway for benzoylformate formation exis ...	2015	25936776
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
immobilized laccase mediated dye decolorization and transformation pathway of azo dye acid red 27.	laccases have good potential as bioremediating agents and can be used continuously in the immobilized form like many other enzymes.	2015	25932329
use of taguchi methodology to enhance the yield of caffeine removal with growing cultures of pseudomonas pseudoalcaligenes.	microbial caffeine removal is a green solution for treatment of caffeinated products and agro-industrial effluents. we directed this investigation to optimizing a bio-decaffeination process with growing cultures of pseudomonas pseudoalcaligenes through taguchi methodology which is a structured statistical approach that can be lowered variations in a process through design of experiments (doe).	2014	25926962
plant-microbe cross-talk in the rhizosphere: insight and biotechnological potential.	rhizosphere, the interface between soil and plant roots, is a chemically complex environment which supports the development and growth of diverse microbial communities. the composition of the rhizosphere microbiome is dynamic and controlled by multiple biotic and abiotic factors that include environmental parameters, physiochemical properties of the soil, biological activities of the plants and chemical signals from the plants and bacteria which inhabit the soil adherent to root-system. recent a ...	2015	25926899
specific gamma-aminobutyrate chemotaxis in pseudomonads with different lifestyle.	the pctc chemoreceptor of pseudomonas aeruginosa mediates chemotaxis with high specificity to gamma-aminobutyric acid (gaba). this compound is present everywhere in nature and has multiple functions, including being a human neurotransmitter or plant signaling compound. because p. aeruginosa is ubiquitously distributed in nature and able to infect and colonize different hosts, the physiological relevance of gaba taxis is unclear, but it has been suggested that bacterial attraction to neurotransmi ...	2015	25921834
rhizobium leguminosarum bv. viciae 3841 adapts to 2,4-dichlorophenoxyacetic acid with "auxin-like" morphological changes, cell envelope remodeling and upregulation of central metabolic pathways.	there is a growing need to characterize the effects of environmental stressors at the molecular level on model organisms with the ever increasing number and variety of anthropogenic chemical pollutants. the herbicide 2,4-dichlorophenoxyacetic acid (2,4-d), as one of the most widely applied pesticides in the world, is one such example. this herbicide is known to have non-targeted undesirable effects on humans, animals and soil microbes, but specific molecular targets at sublethal levels are unkno ...	2015	25919284
nad-independent l-lactate dehydrogenase required for l-lactate utilization in pseudomonas stutzeri a1501.	nad-independent l-lactate dehydrogenases (l-ildhs) play important roles in l-lactate utilization of different organisms. all of the previously reported l-ildhs were flavoproteins that catalyze the oxidation of l-lactate by the flavin mononucleotide (fmn)-dependent mechanism. based on comparative genomic analysis, a gene cluster with three genes (llda, lldb, and lldc) encoding a novel type of l-ildh was identified in pseudomonas stutzeri a1501. when the gene cluster was expressed in escherichia c ...	2015	25917905
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
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
photoautotrophic polyhydroxybutyrate granule formation is regulated by cyanobacterial phasin phap in synechocystis sp. strain pcc 6803.	cyanobacteria are photoautotrophic microorganisms which fix atmospheric carbon dioxide via the calvin-benson cycle to produce carbon backbones for primary metabolism. fixed carbon can also be stored as intracellular glycogen, and in some cyanobacterial species like synechocystis sp. strain pcc 6803, polyhydroxybutyrate (phb) accumulates when major nutrients like phosphorus or nitrogen are absent. so far only three enzymes which participate in phb metabolism have been identified in this organism, ...	2015	25911471
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
characterization of chromosomal and megaplasmid partitioning loci in thermus thermophilus hb27.	in low-copy-number plasmids, the partitioning loci (par) act to ensure proper plasmid segregation and copy number maintenance in the daughter cells. in many bacterial species, par gene homologues are encoded on the chromosome, but their function is much less understood. in the two-replicon, polyploid genome of the hyperthermophilic bacterium thermus thermophilus, both the chromosome and the megaplasmid encode par gene homologues (parabc and parabm, respectively). the mode of partitioning of the ...	2015	25909452
identification of nasal colonization with β-lactamase-producing enterobacteriaceae in patients, health care workers and students in madagascar.	this study assesses the nasal occurrence of β-lactamase-producing enterobacteriaceae both in patients in a hospital department of infectious diseases at admission and in healthy madagascan students and health care workers. nasal swabs from 681 students, 824 health care workers, and 169 patients were obtained in antananarivo, madagascar, and transferred to germany. screening for β-lactamase (esbl, ampc) producing enterobacteriaceae was performed by cultural and molecular approaches, comprising br ...	2015	25908994
laboratory diagnosis of melioidosis: past, present and future.	melioidosis is an emerging, potentially fatal disease caused by burkholderia pseudomallei, which requires prolonged antibiotic treatment to prevent disease relapse. however, difficulties in laboratory diagnosis of melioidosis may delay treatment and affect disease outcomes. isolation of b. pseudomallei from clinical specimens has been improved with the use of selective media. however, even with positive cultures, identification of b. pseudomallei can be difficult in clinical microbiology laborat ...	2015	25908634
multiple antibiotic susceptibility of polyphosphate kinase mutants (ppk1 and ppk2) from pseudomonas aeruginosa pao1 as revealed by global phenotypic analysis.	pseudomonas aeruginosa is known to be a multidrug resistant opportunistic pathogen. particularly, p. aeruginosa pao1 polyphosphate kinase mutant (ppk1) is deficient in motility, quorum sensing, biofilm formation and virulence.	2015	25907584
lucy: a versatile new fluorescent reporter protein.	we report on the discovery, isolation, and use of a novel yellow fluorescent protein. lucigen yellow (lucy) binds one fad molecule within its core, thus shielding it from water and maintaining its structure so that fluorescence is 10-fold higher than freely soluble fad. lucy displays excitation and emission spectra characteristic of fad, with 3 excitation peaks at 276 nm, 377 nm, and 460 nm and a single emission peak at 530 nm. these excitation and emission maxima provide the large stokes shift ...	2015	25906065
crystal structure of x-prolyl aminopeptidase from caenorhabditis elegans: a cytosolic enzyme with a di-nuclear active site.	eukaryotic aminopeptidase p1 (app1), also known as x-prolyl aminopeptidase (xpnpep1) in human tissues, is a cytosolic exopeptidase that preferentially removes amino acids from the n-terminus of peptides possessing a penultimate n-terminal proline residue. the enzyme has an important role in the catabolism of proline containing peptides since peptide bonds adjacent to the imino acid proline are resistant to cleavage by most peptidases. we show that recombinant and catalytically active caenorhabdi ...	2015	25905034
perception of pathogenic or beneficial bacteria and their evasion of host immunity: pattern recognition receptors in the frontline.	plants are continuously monitoring the presence of microorganisms to establish an adapted response. plants commonly use pattern recognition receptors (prrs) to perceive microbe- or pathogen-associated molecular patterns (mamps/pamps) which are microorganism molecular signatures. located at the plant plasma membrane, the prrs are generally receptor-like kinases (rlks) or receptor-like proteins (rlps). mamp detection will lead to the establishment of a plant defense program called mamp-triggered i ...	2015	25904927
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
pan-genome dynamics of pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite.	phylogenetic heterogeneity across pseudomonas genus is complemented by its diverse genome architecture enriched by accessory genetic elements (plasmids, transposons, and integrons) conferring resistance across this genus. here, we sequenced a stress tolerant genotype i.e. pseudomonas sp. strain rl isolated from a hexachlorocyclohexane (hch) contaminated pond (45 mg of total hch g(-1) sediment) and further compared its gene repertoire with 17 reference ecotypes belonging to p. stutzeri, p. mendoc ...	2015	25898829
[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
quantitatively predicting bacterial adhesion using surface free energy determined with a spectrophotometric method.	bacterial adhesion onto solid surfaces is of importance in a wide spectrum of problems, including environmental microbiology, biomedical research, and various industrial applications. despite many research efforts, present thermodynamic models that rely on the evaluation of the adhesion energy are often elusive in predicting the bacterial adhesion behavior. here, we developed a new spectrophotometric method to determine the surface free energy (sfe) of bacterial cells. the adhesion behaviors of ...	2015	25898026
bacterial modulation of plant ethylene levels.	a focus on the mechanisms by which acc deaminase-containing bacteria facilitate plant growth.bacteria that produce the enzyme 1-aminocyclopropane-1-carboxylate (acc) deaminase, when present either on the surface of plant roots (rhizospheric) or within plant tissues (endophytic), play an active role in modulating ethylene levels in plants. this enzyme activity facilitates plant growth especially in the presence of various environmental stresses. thus, plant growth-promoting bacteria that express ...	2015	25897004
structural characterization of multiple pyoverdines secreted by two pseudomonas strains using liquid chromatography-high resolution tandem mass spectrometry with varying dissociation energies.	high-affinity iron (fe)-scavenging molecules, or siderophores, are secreted by microorganisms to acquire and compete for fe. pyoverdine (pvd), the primary siderophore produced by pseudomonas, consists of a dihydroxyquinoline-type chromophore, a peptide chain of variable length and conformation, and a side chain composed of a dicarboxylic acid or its monoamide derivative. elucidation of the pvd structures secreted by different pseudomonas strains is an important step toward understanding their fe ...	2015	25895945
determination of zinc, cadmium and lead bioavailability in contaminated soils at the single-cell level by a combination of whole-cell biosensors and flow cytometry.	zinc, lead and cadmium are metallic trace elements (mtes) that are widespread in the environment and tend to accumulate in soils because of their low mobility and non-degradability. the purpose of this work is to evaluate the applicability of biosensors as tools able to provide data about the bioavailability of such mtes in contaminated soils. here, we tested the genetically-engineered strain escherichia coli pp(znta)gfp as a biosensor applicable to the detection of zinc, lead and cadmium by the ...	2015	25894939
reactions of cg10062, a cis-3-chloroacrylic acid dehalogenase homologue, with acetylene and allene substrates: evidence for a hydration-dependent decarboxylation.	cg10062 is a cis-3-chloroacrylic acid dehalogenase (cis-caad) homologue from corynebacterium glutamicum with an unknown function and an uninformative genomic context. it shares 53% pairwise sequence similarity with cis-caad including the six active site amino acids (pro-1, his-28, arg-70, arg-73, tyr-103, and glu-114) that are critical for cis-caad activity. however, cg10062 is a poor cis-caad: it lacks catalytic efficiency and isomer specificity. two acetylene compounds (propiolate and 2-butyno ...	2015	25894805
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
isolation of ndm-1-producing multidrug-resistant pseudomonas putida from a paediatric case of acute gastroenteritis, india.	pseudomonas putida is an uncommon opportunistic pathogen, usually susceptible to antimicrobial agents. data concerning resistance to antimicrobial agents in clinical p. putida isolates are limited. to the best of our knowledge we report for the first time the isolation of ndm-1-producing multidrug-resistant p. putida from a case of acute gastroenteritis. the isolate showed resistance to a wide range of antimicrobials, including fluoroquinolones, third-generation cephalosporins and carbapenems. t ...	2015	25893095
genome reduction boosts heterologous gene expression in pseudomonas putida.	the implementation of novel platform organisms to be used as microbial cell factories in industrial applications is currently the subject of intense research. ongoing efforts include the adoption of pseudomonas putida kt2440 variants with a reduced genome as the functional chassis for biotechnological purposes. in these strains, dispensable functions removed include flagellar motility (1.1% of the genome) and a number of open reading frames expected to improve genotypic and phenotypic stability ...	2015	25890048
biobutanol from cheese whey.	at present, due to environmental and economic concerns, it is urgent to evolve efficient, clean and secure systems for the production of advanced biofuels from sustainable cheap sources. biobutanol has proved better characteristics than the more widely used bioethanol, however the main disadvantage of biobutanol is that it is produced in low yield and titer by abe (acetone-butanol-ethanol) fermentation, this process being not competitive from the economic point of view. in this review we summari ...	2015	25889728
conjunctival flora of clinically normal and diseased turtles and tortoises.	in captive breed turtles and tortoises conjunctival disease is common. our aim was to investigate the bacterial and fungal flora present in the eyes of healthy and pathological chelonians and to compare findings in turtles with those in tortoises.	2015	25889261
structure and function of a short lov protein from the marine phototrophic bacterium dinoroseobacter shibae.	light, oxygen, voltage (lov) domains are widely distributed in plants, algae, fungi, bacteria, and represent the photo-responsive domains of various blue-light photoreceptor proteins. their photocycle involves the blue-light triggered adduct formation between the c(4a) atom of a non-covalently bound flavin chromophore and the sulfur atom of a conserved cysteine in the lov sensor domain. lov proteins show considerable variation in the structure of n- and c-terminal elements which flank the lov co ...	2015	25887755
phenotypic knockouts of selected metabolic pathways by targeting enzymes with camel-derived nanobodies (v(hh)s).	surveying the dynamics of metabolic networks of gram-negative bacteria often requires the conditional shutdown of enzymatic activities once the corresponding proteins have been produced. we show that given biochemical functions can be entirely suppressed in vivo with camel antibodies (vhhs, nanobodies) that target active sites of cognate enzymes expressed in the cytoplasm. as a proof of principle, we raised vhhs against 2,5-dihydroxypyridine dioxygenase (nicx) of pseudomonas putida, involved in ...	2015	25887637
microbiological characteristics of sepsis in a university hospital.	microbiological characteristics of sepsis and antimicrobial resistance are well studied, although in state university of campinas, no data has been published yet.	2015	25887416
clear distinction between burkholderia mallei and burkholderia pseudomallei using fluorescent motb primers.	a frame-shift mutation in the flagellum motor gene motb coding for the chemotaxis motb protein of burkholderia mallei has been utilized to design a conventional duplex pcr assay with fluorescent labelled primers.	2015	25887130
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
essential role of the a'α/aβ gap in the n-terminal upstream of lov2 for the blue light signaling from lov2 to kinase in arabidopsis photototropin1, a plant blue light receptor.	phototropin (phot) is a blue light (bl) receptor in plants and is involved in phototropism, chloroplast movement, stomata opening, etc. a phot molecule has two photo-receptive domains named lov (light-oxygen-voltage) 1 and 2 in its n-terminal region and a serine/threonine kinase (stk) in its c-terminal region. stk activity is regulated mainly by lov2, which has a cyclic photoreaction, including the transient formation of a flavin mononucleotide (fmn)-cysteinyl adduct (s390). one of the key event ...	2015	25886203
lipopeptide biosynthesis in pseudomonas fluorescens is regulated by the protease complex clpap.	lipopeptides (lp) are structurally diverse compounds with potent surfactant and broad-spectrum antibiotic activities. in pseudomonas and other bacterial genera, lp biosynthesis is governed by large multimodular nonribosomal peptide synthetases (nrps). to date, relatively little is known about the regulatory genetic network of lp biosynthesis.	2015	25885431
the crystal structure of d-threonine aldolase from alcaligenes xylosoxidans provides insight into a metal ion assisted plp-dependent mechanism.	threonine aldolases catalyze the pyridoxal phosphate (plp) dependent cleavage of threonine into glycine and acetaldehyde and play a major role in the degradation of this amino acid. in nature, l- as well as d-specific enzymes have been identified, but the exact physiological function of d-threonine aldolases (dtas) is still largely unknown. both types of enantio-complementary enzymes have a considerable potential in biocatalysis for the stereospecific synthesis of various β-hydroxy amino acids, ...	2015	25884707
characterization of uronate dehydrogenases catalysing the initial step in an oxidative pathway.	uronate dehydrogenases catalyse the oxidation of uronic acids to aldaric acids, which represent 'top value-added chemicals' that have the potential to substitute petroleum-derived chemicals. the identification and annotation of three uronate dehydrogenases derived from fulvimarina pelagi htcc2506, streptomyces viridochromogenes dsm 40736 and oceanicola granulosus dsm 15982 via sequence analysis is described. characterization and comparison with two known uronate dehydrogenases in regard to subst ...	2015	25884328
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
competition between burkholderia pseudomallei and b. thailandensis.	burkholderia pseudomallei is a gram-negative bacterium that causes melioidosis, an often fatal disease in tropical countries. burkholderia thailandensis is a non-virulent but closely related species. both species are soil saprophytes but are almost never isolated together.	2015	25879538
agriculture and food animals as a source of antimicrobial-resistant bacteria.	one of the major breakthroughs in the history of medicine is undoubtedly the discovery of antibiotics. their use in animal husbandry and veterinary medicine has resulted in healthier and more productive farm animals, ensuring the welfare and health of both animals and humans. unfortunately, from the first use of penicillin, the resistance countdown started to tick. nowadays, the infections caused by antibiotic-resistant bacteria are increasing, and resistance to antibiotics is probably the major ...	2015	25878509
making variability less variable: matching expression system and host for oxygenase-based biotransformations.	variability in whole-cell biocatalyst performance represents a critical aspect for stable and productive bioprocessing. in order to investigate whether and how oxygenase-catalyzed reactions are affected by such variability issues in solvent-tolerant pseudomonas, different inducers, expression systems, and host strains were tested for the reproducibility of xylene and styrene monooxygenase catalyzed hydroxylation and epoxidation reactions, respectively. significantly higher activity variations we ...	2015	25877162
marine hydrocarbonoclastic bacteria as whole-cell biosensors for n-alkanes.	whole-cell biosensors offer potentially useful, cost-effective systems for the in-situ monitoring of seawater for hydrocarbons derived from accidental spills. the present work compares the performance of a biosensor system for the detection of alkanes in seawater, hosted in either escherichia coli (commonly employed in whole-cell biosensors but not optimized for alkane assimilation) or different marine bacteria specialized in assimilating alkanes. the sensor system was based on the pseudomonas p ...	2015	25874658
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
nitrogen removal from micro-polluted reservoir water by indigenous aerobic denitrifiers.	treatment of micro-polluted source water is receiving increasing attention because of environmental awareness on a global level. we isolated and identified aerobic denitrifying bacteria zoogloea sp. n299, acinetobacter sp. g107, and acinetobacter sp. 81y and used these to remediate samples of their native source water. we first domesticated the isolated strains in the source water, and the 48-h nitrate removal rates of strains n299, g107, and 81y reached 33.69%, 28.28%, and 22.86%, respectively, ...	2015	25867475
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
biphenyl 4-hydroxylases involved in aucuparin biosynthesis in rowan and apple are cytochrome p450 736a proteins.	upon pathogen attack, fruit trees such as apple (malus spp.) and pear (pyrus spp.) accumulate biphenyl and dibenzofuran phytoalexins, with aucuparin as a major biphenyl compound. 4-hydroxylation of the biphenyl scaffold, formed by biphenyl synthase (bis), is catalyzed by a cytochrome p450 (cyp). the biphenyl 4-hydroxylase (b4h) coding sequence of rowan (sorbus aucuparia) was isolated and functionally expressed in yeast (saccharomyces cerevisiae). sab4h was named cyp736a107. no catalytic function ...	2015	25862456
biodegradation of naphthalene using pseudomonas aeruginosa by up flow anoxic-aerobic continuous flow combined bioreactor.	naphthalene is a poly aromatic hydrocarbon (pah) present in many sediment-water systems. the aim of this study was to evaluate the applicability of an anoxic/aerobic system for the biological treatment of water polluted by naphthalene by pseudomonas aeruginosa ptcc 1707 to utilize naphthalene. the naphthalene elimination from wastewater was determined in anoxic-aerobic continuous flow combined bioreactor under continuously oxic and anoxic conditions. experiments were conducted in continues mode, ...	2015	25859393
improved n-butanol tolerance in escherichia coli by controlling membrane related functions.	as the increasing demand from both chemical and fuel markets, the interest in producing n-butanol using biological route has been rejuvenated to engineer an economical fermentation process, competing with the currently-dominant chemical synthesis. n-butanol has been traditionally produced from the abe fermentation of clostridium acetobutylicum. this system, however, is not economically feasible due to its limited efficiency and the lack of genetic modification tools for further improvements. alt ...	2015	25858152
identification of novel mycobacterium tuberculosis cd4 t-cell antigens via high throughput proteome screening.	elicitation of cd4 ifn-gamma t cell responses to mycobacterium tuberculosis (mtb) is a rational vaccine strategy to prevent clinical tuberculosis. diagnosis of mtb infection is based on t-cell immune memory to mtb antigens. the mtb proteome contains over four thousand open reading frames (orfs). we conducted a pilot antigen identification study using 164 mtb proteins and mtb-specific t-cells expanded in vitro from 12 persons with latent mtb infection. enrichment of mtb-reactive t-cells from pbmc ...	2015	25857935
antibiotic-free selection in biotherapeutics: now and forever.	the continuously improving sophistication of molecular engineering techniques gives access to novel classes of bio-therapeutics and new challenges for their production in full respect of the strengthening regulations. among these biologic agents are dna based vaccines or gene therapy products and to a lesser extent genetically engineered live vaccines or delivery vehicles. the use of antibiotic-based selection, frequently associated with genetic manipulation of microorganism is currently undergo ...	2015	25854922
above-belowground interactions govern the course and impact of biological invasions.	introduction of exotic organisms that subsequently become invasive is considered a serious threat to global biodiversity, and both scientists and nature-conservationists attempt to find explanations and means to meet this challenge. this requires a thorough analysis of the invasion phenomenon in an evolutionary and ecological context; in the case of invasive plants, we must have a major focus on above-belowground interactions. thus, we discuss different theories that have been proposed to explai ...	2015	25854693
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
recent functional insights into the role of (p)ppgpp in bacterial physiology.	the alarmones guanosine tetraphosphate and guanosine pentaphosphate (collectively referred to as (p)ppgpp) are involved in regulating growth and several different stress responses in bacteria. in recent years, substantial progress has been made in our understanding of the molecular mechanisms of (p)ppgpp metabolism and (p)ppgpp-mediated regulation. in this review, we summarize these recent insights, with a focus on the molecular mechanisms governing the activity of the rela/spot homologue (rsh) ...	2015	25853779
characterization of kfra proteins encoded by a plasmid of paenibacillus popilliae atcc 14706(t).	a scaffold obtained from whole-genome shotgun sequencing of paenibacillus popilliae atcc 14706(t) shares partial homology with plasmids found in other strains of p. popilliae. pcr and sequencing for gap enclosure indicated that the scaffold originated from a 15,929-bp circular dna. the restriction patterns of a plasmid isolated from p. popilliae atcc 14706(t) were identical to those expected from the sequence; thus, this circular dna was identified as a plasmid of atcc 14706(t) and designated pp ...	2015	25853059
strain and process development for poly(3hb-co-3hp) fermentation by engineered shimwellia blattae from glycerol.	poly(3-hydroxybytyrate-co-3-hydroxypropionate), poly(3hb-co-3hp), is a possible alternative to synthetic polymers such as polypropylene, polystyrene and polyethylene due to its low crystallinity and fragility. we already reported that recombinant strains of shimwellia blattae expressing 1,3-propanediol dehydrogenase dhat as well as aldehyde dehydrogenase aldd of pseudomonas putida kt2442, propionate-coa transferase pct of clostridium propionicum x2 and pha synthase phac1 of ralstonia eutropha h1 ...	2015	25852995
unraveling the kinetic diversity of microbial 3-dehydroquinate dehydratases of shikimate pathway.	3-dehydroquinate dehydratase (dhqase) catalyzes the conversion of 3-dehydroquinic acid to 3-dehydroshikimic acid of the shikimate pathway. in this study, 3180 prokaryotic genomes were examined and 459 dhqase sequences were retrieved. based on sequence analysis and their original hosts, 38 dhqase genes were selected for chemical synthesis. the selected dhqases were translated into new dna sequences according to the genetic codon usage bias by both escherichia coli and corynebacterium glutamicum. ...	2015	25852984
procalcitonin levels in gram-positive, gram-negative, and fungal bloodstream infections.	procalcitonin (pct) can discriminate bacterial from viral systemic infections and true bacteremia from contaminated blood cultures. the aim of this study was to evaluate pct diagnostic accuracy in discriminating gram-positive, gram-negative, and fungal bloodstream infections. a total of 1,949 samples from patients with suspected bloodstream infections were included in the study. median pct value in gram-negative (13.8 ng/ml, interquartile range (iqr) 3.4-44.1) bacteremias was significantly highe ...	2015	25852221
the pww0 plasmid imposes a stochastic expression regime to the chromosomal ortho pathway for benzoate metabolism in pseudomonas putida.	environmental plasmids often expand the metabolic repertoire of bacteria that carry them, but they also interfere with the biochemical and genetic network of the host. the pww0 plasmid born by pseudomonas putida mt-2 encodes the tol pathway for degradation of toluene/m-xylene through production of intermediate compounds benzoate/3-methylbenzoate. these can be also recognized as substrates by the chromosomally encoded ben and cat gene products, thereby creating a manifest regulatory and biochemic ...	2014	25848660
panoramic view of a superfamily of phosphatases through substrate profiling.	large-scale activity profiling of enzyme superfamilies provides information about cellular functions as well as the intrinsic binding capabilities of conserved folds. herein, the functional space of the ubiquitous haloalkanoate dehalogenase superfamily (hadsf) was revealed by screening a customized substrate library against >200 enzymes from representative prokaryotic species, enabling inferred annotation of ∼35% of the hadsf. an extremely high level of substrate ambiguity was revealed, with the ...	2015	25848029
x-ray and cryo-electron microscopy structures of monalysin pore-forming toxin reveal multimerization of the pro-form.	β-barrel pore-forming toxins (β-pft), a large family of bacterial toxins, are generally secreted as water-soluble monomers and can form oligomeric pores in membranes following proteolytic cleavage and interaction with cell surface receptors. monalysin has been recently identified as a β-pft that contributes to the virulence of pseudomonas entomophila against drosophila. it is secreted as a pro-protein that becomes active upon cleavage. here we report the crystal and cryo-electron microscopy stru ...	2015	25847242
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
bactericidal compounds controlling growth of the plant pathogen pseudomonas syringae pv. actinidiae, which forms biofilms composed of a novel exopolysaccharide.	pseudomonas syringae pv. actinidiae is the major cause of bacterial canker and is a severe threat to kiwifruit production worldwide. many aspects of the disease caused by p. syringae pv. actinidiae, such as the pathogenicity-relevant formation of a biofilm composed of extracellular polymeric substances (epss), are still unknown. here, a highly virulent strain of p. syringae pv. actinidiae, nz v-13, was studied with respect to biofilm formation and architecture using a flow cell system combined w ...	2015	25841017
draft genome sequence of pseudomonas sp. nov. h2.	we report the draft genome sequence of pseudomonas sp. nov. h2, isolated from creek sediment in moscow, id, usa. the strain is most closely related to pseudomonas putida. however, it has a slightly smaller genome that appears to have been impacted by horizontal gene transfer and poorly maintains incp-1 plasmids.	2015	25838493
draft genome sequence of pseudomonas toyotomiensis kf710, a polychlorinated biphenyl-degrading bacterium isolated from biphenyl-contaminated soil.	pseudomonas toyotomiensis kf710 utilizes biphenyl and degrades polychlorinated biphenyls (pcbs). here, we report the genome sequence of the kf710 strain, consisting of 5,596,721 bp with 5,155 coding sequences. the biphenyl catabolic genes were almost identical to those of pseudomonas pseudoalcaligenes kf707, one of the most well-characterized biphenyl-utilizing strains.	2015	25838482
role of cyanobacterial exopolysaccharides in phototrophic biofilms and in complex microbial mats.	exopolysaccharides (epss) are an important class of biopolymers with great ecological importance. in natural environments, they are a common feature of microbial biofilms, where they play key protective and structural roles. as the primary colonizers of constrained environments, such as desert soils and lithic and exposed substrates, cyanobacteria are the first contributors to the synthesis of the epss constituting the extracellular polymeric matrix that favors the formation of microbial associa ...	2015	25837843
characterization and structure prediction of partial length protein sequences of pcoa, pcor and chrb genes from heavy metal resistant bacteria from the klip river, south africa.	the klip river has suffered from severe anthropogenic effects from industrial activities such as mining. long-term exposure to heavy metal pollution has led to the development of heavy metal resistant strains of pseudomonas sp. kr23, lysinibacillus sp. kr25, and e. coli kr29. the objectives of this study were to characterize the genetics of copper and chromate resistance of the isolates. copper and chromate resistance determinants were cloned and sequenced. open reading frames (orfs) related to ...	2015	25837632
valvulopathy consistent with endocarditis in an argentine boa (boa constrictor occidentalis).	an argentine boa (boa constrictor occidentalis) of 5 yr 7 mo of age was presented for respiratory problems and regurgitation. radiographs revealed evidence of cardiomegaly and pneumonia. blood smear examination revealed the presence of intracytoplasmic inclusion bodies in peripheral lymphocytes, consistent with inclusion body disease. cultures of a tracheal wash sample resulted in growth of ochrobactrum intermedium and pseudomonas putida. echocardiographic examination revealed a large vegetative ...	2015	25831585
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
pseudomonads biodegradation of aromatic compounds in oil sands process-affected water.	aromatic naphthenic acids (nas) have been shown to be more toxic than the classical nas found in oil sands process-affected water (ospw). to reduce this toxicity, pseudomonas fluorescens and pseudomonas putida were used to determine their ability to biodegrade aromatic compounds including treatments considering the impacts of external carbon and iron addition. results showed that with added carbon p. fluorescens and p. putida have the capability of biodegrading these aromatics. in the presence o ...	2015	25828413
an upp-based markerless gene replacement method for genome reduction and metabolic pathway engineering in pseudomonas mendocina nk-01 and pseudomonas putida kt2440.	a markerless gene replacement method was adapted by combining a suicide plasmid, pex18tc, with a counterselectable marker, the upp gene encoding uracil phosphoribosyltransferase (uprtase), for the medium-chain length polyhydroxyalkanoates (pha(mcl))-producing strain pseudomonas mendocina nk-01. an nk-01 5-fluorouracil (5-fu) resistant background strain was first constructed by deleting the chromosomal upp gene. the suicide plasmid pex18tc, carrying a functional allele of the upp gene of p. mendo ...	2015	25828098
the glycerol-dependent metabolic persistence of pseudomonas putida kt2440 reflects the regulatory logic of the glpr repressor.	the growth of the soil bacterium pseudomonas putida kt2440 on glycerol as the sole carbon source is characterized by a prolonged lag phase, not observed with other carbon substrates. we examined the bacterial growth in glycerol cultures while monitoring the metabolic activity of individual cells. fluorescence microscopy and flow cytometry, as well as the analysis of the temporal start of growth in single-cell cultures, revealed that adoption of a glycerol-metabolizing regime was not the result o ...	2015	25827416
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
role of bacillus subtilis dna glycosylase mutm in counteracting oxidatively induced dna damage and in stationary-phase-associated mutagenesis.	reactive oxygen species (ros) promote the synthesis of the dna lesion 8-oxo-g, whose mutagenic effects are counteracted in distinct organisms by the dna glycosylase mutm. we report here that in bacillus subtilis, mutm is expressed during the exponential and stationary phases of growth. in agreement with this expression pattern, results of a western blot analysis confirmed the presence of mutm in both stages of growth. in comparison with cells of a wild-type strain, cells of b. subtilis lacking m ...	2015	25825434
inhibition of cell differentiation in bacillus subtilis by pseudomonas protegens.	interspecies interactions have been described for numerous bacterial systems, leading to the identification of chemical compounds that impact bacterial physiology and differentiation for processes such as biofilm formation. here, we identified soil microbes that inhibit biofilm formation and sporulation in the common soil bacterium bacillus subtilis. we did so by creating a reporter strain that fluoresces when the transcription of a biofilm-specific gene is repressed. using this reporter in a co ...	2015	25825426
dimeric c-di-gmp is required for post-translational regulation of alginate production in pseudomonas aeruginosa.	pseudomonas aeruginosa is an opportunistic human pathogen that secretes the exopolysaccharide alginate during infection of the respiratory tract of individuals afflicted with cystic fibrosis and chronic obstructive pulmonary disease. among the proteins required for alginate production, alg44 has been identified as an inner membrane protein whose bis-(3',5')-cyclic dimeric guanosine monophosphate (c-di-gmp) binding activity post-translationally regulates alginate secretion. in this study, we repo ...	2015	25817996
an s188v mutation alters substrate specificity of non-stereospecific α-haloalkanoic acid dehalogenase e (dehe).	the non-stereospecific α-haloalkanoic acid dehalogenase e (dehe) degrades many halogenated compounds but is ineffective against β-halogenated compounds such as 3-chloropropionic acid (3cp). using molecular dynamics (md) simulations and site-directed mutagenesis we show here that introducing the mutation s188v into dehe improves substrate specificity towards 3cp. md simulations showed that residues w34, f37, and s188 of dehe were crucial for substrate binding. dehe showed strong binding ability f ...	2015	25816329