Publications

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
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
next generation sequencing analysis reveals that the ribonucleases rnase ii, rnase r and pnpase affect bacterial motility and biofilm formation in e. coli.	the rna steady-state levels in the cell are a balance between synthesis and degradation rates. although transcription is important, rna processing and turnover are also key factors in the regulation of gene expression. in escherichia coli there are three main exoribonucleases (rnase ii, rnase r and pnpase) involved in rna degradation. although there are many studies about these exoribonucleases not much is known about their global effect in the transcriptome.	2015	25757888
high quality draft genome sequence and analysis of pontibacter roseus type strain src-1(t) (dsm 17521(t)) isolated from muddy waters of a drainage system in chandigarh, india.	pontibacter roseus is a member of genus pontibacter family cytophagaceae, class cytophagia. while the type species of the genus pontibacter actiniarum was isolated in 2005 from a marine environment, subsequent species of the same genus have been found in different types of habitats ranging from seawater, sediment, desert soil, rhizosphere, contaminated sites, solar saltern and muddy water. here we describe the features of pontibacter roseus strain src-1(t) along with its complete genome sequence ...	2015	26203325
dysbiosis of the gut microbiota in disease.	there is growing evidence that dysbiosis of the gut microbiota is associated with the pathogenesis of both intestinal and extra-intestinal disorders. intestinal disorders include inflammatory bowel disease, irritable bowel syndrome (ibs), and coeliac disease, while extra-intestinal disorders include allergy, asthma, metabolic syndrome, cardiovascular disease, and obesity.	2015	25651997
biotechnological applications of functional metagenomics in the food and pharmaceutical industries.	microorganisms are found throughout nature, thriving in a vast range of environmental conditions. the majority of them are unculturable or difficult to culture by traditional methods. metagenomics enables the study of all microorganisms, regardless of whether they can be cultured or not, through the analysis of genomic data obtained directly from an environmental sample, providing knowledge of the species present, and allowing the extraction of information regarding the functionality of microbia ...	2015	26175729
genome-wide gene order distances support clustering the gram-positive bacteria.	initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ...	2015	25653643
genome-wide gene order distances support clustering the gram-positive bacteria.	initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ...	2015	25653643
a novel quality measure and correction procedure for the annotation of microbial translation initiation sites.	the identification of translation initiation sites (tiss) constitutes an important aspect of sequence-based genome analysis. an erroneous tis annotation can impair the identification of regulatory elements and n-terminal signal peptides, and also may flaw the determination of descent, for any particular gene. we have formulated a reference-free method to score the tis annotation quality. the method is based on a comparison of the observed and expected distribution of all tiss in a particular gen ...	2015	26204119
carnitine in bacterial physiology and metabolism.	carnitine is a quaternary amine compound found at high concentration in animal tissues, particularly muscle, and is most well studied for its contribution to fatty acid transport into mitochondria. in bacteria, carnitine is an important osmoprotectant, and can also enhance thermotolerance, cryotolerance and barotolerance. carnitine can be transported into the cell or acquired from metabolic precursors, where it can serve directly as a compatible solute for stress protection or be metabolized thr ...	2015	25787873
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
alcohol selectivity in a synthetic thermophilic n-butanol pathway is driven by biocatalytic and thermostability characteristics of constituent enzymes.	n-butanol is generated as a natural product of metabolism by several microorganisms, but almost all grow at mesophilic temperatures. a synthetic pathway for n-butanol production from acetyl coenzyme a (acetyl-coa) that functioned at 70°c was assembled in vitro from enzymes recruited from thermophilic bacteria to inform efforts for engineering butanol production into thermophilic hosts. recombinant versions of eight thermophilic enzymes (β-ketothiolase [thl], 3-hydroxybutyryl-coa dehydrogenase [h ...	2015	26253677
a bioinformatic survey of distribution, conservation, and probable functions of luxr solo regulators in bacteria.	luxr solo transcriptional regulators contain both an autoinducer binding domain (abd; n-terminal) and a dna binding helix-turn-helix domain (hth; c-terminal), but are not associated with a cognate n-acyl homoserine lactone (ahl) synthase coding gene in the same genome. although a few luxr solos have been characterized, their distributions as well as their role in bacterial signal perception and other processes are poorly understood. in this study we have carried out a systematic survey of distri ...	2015	25759807
characterization of flavin-containing opine dehydrogenase from bacteria.	opines, in particular nopaline and octopine, are specific compounds found in crown gall tumor tissues induced by infections with agrobacterium species, and are synthesized by well-studied nad(p)h-dependent dehydrogenases (synthases), which catalyze the reductive condensation of α-ketoglutarate or pyruvate with l-arginine. the corresponding genes are transferred into plant cells via a tumor-inducing (ti) plasmid. in addition to the reverse oxidative reaction(s), the genes noxb-noxa and ooxb-ooxa ...	2015	26382958
influence of rhizobacterial volatiles on the root system architecture and the production and allocation of biomass in the model grass brachypodium distachyon (l.) p. beauv.	plant growth-promoting rhizobacteria are increasingly being seen as a way of complementing conventional inputs in agricultural systems. the effects on their host plants are diverse and include volatile-mediated growth enhancement. this study sought to assess the effects of bacterial volatiles on the biomass production and root system architecture of the model grass brachypodium distachyon (l.) beauv.	2015	26264238
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
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
identification and characterization of bifunctional proline racemase/hydroxyproline epimerase from archaea: discrimination of substrates and molecular evolution.	proline racemase (pror) is a member of the pyridoxal 5'-phosphate-independent racemase family, and is involved in the stickland reaction (fermentation) in certain clostridia as well as the mechanisms underlying the escape of parasites from host immunity in eukaryotic trypanosoma. hydroxyproline epimerase (hype), which is in the same protein family as pror, catalyzes the first step of the trans-4-hydroxy-l-proline metabolism of bacteria. their substrate specificities were previously considered to ...	2015	25786142
pgprs and nitrogen-fixing legumes: a perfect team for efficient cd phytoremediation?	cadmium (cd) is a toxic, biologically non-essential and highly mobile metal that has become an increasingly important environmental hazard to both wildlife and humans. in contrast to conventional remediation technologies, phytoremediation based on legume-rhizobia symbiosis has emerged as an inexpensive decontamination alternative which also revitalize contaminated soils due to the role of legumes in nitrogen cycling. in recent years, there is a growing interest in understanding symbiotic legume- ...	2015	25763004
resource niche overlap promotes stability of bacterial community metabolism in experimental microcosms.	decomposition of organic matter is an important ecosystem process governed in part by bacteria. the process of decomposition is expected to benefit from interspecific bacterial interactions such as resource partitioning and facilitation. however, the relative importance of resource niche breadth (metabolic diversity) and resource niche overlap (functional redundancy) on decomposition and the temporal stability of ecosystem processes received little scientific attention. therefore, this study aim ...	2015	25759686
colonization of lettuce rhizosphere and roots by tagged streptomyces.	beneficial microorganisms are increasingly used in agriculture, but their efficacy often fails due to limited knowledge of their interactions with plants and other microorganisms present in rhizosphere. we studied spatio-temporal colonization dynamics of lettuce roots and rhizosphere by genetically modified streptomyces spp. five streptomyces strains, strongly inhibiting in vitro the major soil-borne pathogen of horticultural crops, sclerotinia sclerotiorum, were transformed with pij8641 plasmid ...	2015	25705206
a flagellar glycan-specific protein encoded by campylobacter phages inhibits host cell growth.	we previously characterized a carbohydrate binding protein, gp047, derived from lytic campylobacter phage nctc 12673, as a promising diagnostic tool for the identification of campylobacter jejuni and campylobacter coli. we also demonstrated that this protein binds specifically to acetamidino-modified pseudaminic acid residues on host flagella, but the role of this protein in the phage lifecycle remains unknown. here, we report that gp047 is capable of inhibiting c. jejuni growth both on solid an ...	2015	26694450
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
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
living in an extremely polluted environment: clues from the genome of melanin-producing aeromonas salmonicida subsp. pectinolytica 34melt.	aeromonas salmonicida subsp. pectinolytica 34mel(t) can be considered an extremophile due to the characteristics of the heavily polluted river from which it was isolated. while four subspecies of a. salmonicida are known fish pathogens, 34mel(t) belongs to the only subspecies isolated solely from the environment. genome analysis revealed a high metabolic versatility, the capability to cope with diverse stress agents, and the lack of several virulence factors found in pathogenic aeromonas. the mo ...	2015	26025898
microbial toluene removal in hypoxic model constructed wetlands occurs predominantly via the ring monooxygenation pathway.	in the present study, microbial toluene degradation in controlled constructed wetland model systems, planted fixed-bed reactors (pfrs), was queried with dna-based methods in combination with stable isotope fractionation analysis and characterization of toluene-degrading microbial isolates. two pfr replicates were operated with toluene as the sole external carbon and electron source for 2 years. the bulk redox conditions in these systems were hypoxic to anoxic. the autochthonous bacterial communi ...	2015	26150458
characterization of para-nitrophenol-degrading bacterial communities in river water by using functional markers and stable isotope probing.	microbial degradation is a major determinant of the fate of pollutants in the environment. para-nitrophenol (pnp) is an epa-listed priority pollutant with a wide environmental distribution, but little is known about the microorganisms that degrade it in the environment. we studied the diversity of active pnp-degrading bacterial populations in river water using a novel functional marker approach coupled with [(13)c6]pnp stable isotope probing (sip). culturing together with culture-independent ter ...	2015	26209677
bacterial cellulose biosynthesis: diversity of operons, subunits, products, and functions.	recent studies of bacterial cellulose biosynthesis, including structural characterization of a functional cellulose synthase complex, provided the first mechanistic insight into this fascinating process. in most studied bacteria, just two subunits, bcsa and bcsb, are necessary and sufficient for the formation of the polysaccharide chain in vitro. other subunits - which differ among various taxa - affect the enzymatic activity and product yield in vivo by modulating (i) the expression of the bios ...	2015	26077867
pseudomonas induces salinity tolerance in cotton (gossypium hirsutum) and resistance to fusarium root rot through the modulation of indole-3-acetic acid.	abiotic stresses cause changes in the balance of phytohormones in plants and result in inhibited root growth and an increase in the susceptibility of plants to root rot disease. the aim of this work was to ascertain whether microbial indole-3-acetic acid (iaa) plays a role in the regulation of root growth and microbially mediated control of root rot of cotton caused by fusarium solani. seed germination and seedling growth were improved by both nacl and mg2so4 (100 mm) solutions when treated with ...	2015	26587006
metabolite profiling reveals abiotic stress tolerance in tn5 mutant of pseudomonas putida.	pseudomonas is an efficient plant growth-promoting rhizobacteria (pgpr); however, intolerance to drought and high temperature limit its application in agriculture as a bioinoculant. transposon 5 (tn5) mutagenesis was used to generate a stress tolerant mutant from a pgpr pseudomonas putida nbri1108 isolated from chickpea rhizosphere. a mutant nbri1108t, selected after screening of nearly 10,000 transconjugants, exhibited significant tolerance towards high temperature and drought. southern hybridi ...	2015	25629312
bacterial signal transduction by cyclic di-gmp and other nucleotide second messengers.	the first international symposium on c-di-gmp signaling in bacteria (22 to 25 march 2015, harnack-haus, berlin, germany)brought together 131 molecular microbiologists from 17 countries to discuss recent progress in our knowledge of bacterial nucleotide second messenger signaling. while the focus was on signal input, synthesis, degradation, and the striking diversity of the modes of action of the current second messenger paradigm, i.e., cyclic di-gmp (c-di-gmp), “classics” like camp and (p)ppgpp ...	2015	26055111
bacterial signal transduction by cyclic di-gmp and other nucleotide second messengers.	the first international symposium on c-di-gmp signaling in bacteria (22 to 25 march 2015, harnack-haus, berlin, germany)brought together 131 molecular microbiologists from 17 countries to discuss recent progress in our knowledge of bacterial nucleotide second messenger signaling. while the focus was on signal input, synthesis, degradation, and the striking diversity of the modes of action of the current second messenger paradigm, i.e., cyclic di-gmp (c-di-gmp), “classics” like camp and (p)ppgpp ...	2015	26055111
σ54-dependent regulome in desulfovibrio vulgaris hildenborough.	the σ(54) subunit controls a unique class of promoters in bacteria. such promoters, without exception, require enhancer binding proteins (ebps) for transcription initiation. desulfovibrio vulgaris hildenborough, a model bacterium for sulfate reduction studies, has a high number of ebps, more than most sequenced bacteria. the cellular processes regulated by many of these ebps remain unknown.	2015	26555820
reinvigorating natural product combinatorial biosynthesis with synthetic biology.	natural products continue to play a pivotal role in drug-discovery efforts and in the understanding if human health. the ability to extend nature's chemistry through combinatorial biosynthesis--altering functional groups, regiochemistry and scaffold backbones through the manipulation of biosynthetic enzymes--offers unique opportunities to create natural product analogs. incorporating emerging synthetic biology techniques has the potential to further accelerate the refinement of combinatorial bio ...	2015	26284672
allopatric integrations selectively change host transcriptomes, leading to varied expression efficiencies of exotic genes in myxococcus xanthus.	exotic genes, especially clustered multiple-genes for a complex pathway, are normally integrated into chromosome for heterologous expression. the influences of insertion sites on heterologous expression and allotropic expressions of exotic genes on host remain mostly unclear.	2015	26194479
pseudomonas putida-a versatile host for the production of natural products.	the biosynthesis of natural products by heterologous expression of biosynthetic pathways in amenable production strains enables biotechnological access to a variety of valuable compounds by conversion of renewable resources. pseudomonas putida has emerged as a microbial laboratory work horse, with elaborated techniques for cultivation and genetic manipulation available. beyond that, this bacterium offers several particular advantages with regard to natural product biosynthesis, notably a versati ...	2015	26099332
characterizations of two bacterial persulfide dioxygenases of the metallo-β-lactamase superfamily.	persulfide dioxygenases (pdos), also known as sulfur dioxygenases (sdos), oxidize glutathione persulfide (gssh) to sulfite and gsh. pdos belong to the metallo-β-lactamase superfamily and play critical roles in animals, plants, and microorganisms, including sulfide detoxification. the structures of two pdos from human and arabidopsis thaliana have been reported; however, little is known about the substrate binding and catalytic mechanism. the crystal structures of two bacterial pdos from pseudomo ...	2015	26082492
characteristics of dr1790 disruptant and its functional analysis in deinococcus radiodurans.	deinococcus radiodurans (dr) is an extremophile that is well known for its resistance to radiation, oxidants and desiccation. the gene dr1790 of d. radiodurans was predicted to encode a yellow-related protein. the primary objective of the present study was to characterize the biological function of the dr1790 protein, which is a member of the ancient yellow/major royal jelly (mrj) protein family, in prokaryotes. fluorescence labeling demonstrated that the yellow-related protein encoded by dr1790 ...	2015	26273280
biomineralization processes of calcite induced by bacteria isolated from marine sediments.	biomineralization is a known natural phenomenon associated with a wide range of bacterial species. bacterial-induced calcium carbonate precipitation by marine isolates was investigated in this study. three genera of ureolytic bacteria, sporosarcina sp., bacillus sp. and brevundimonas sp. were observed to precipitate calcium carbonate minerals. of these species, sporosarcina sp. dominated the cultured isolates. b. lentus cp28 generated higher urease activity and facilitated more efficient precipi ...	2015	26273260
environmental sensing in actinobacteria: a comprehensive survey on the signaling capacity of this phylum.	signal transduction is an essential process that allows bacteria to sense their complex and ever-changing environment and adapt accordingly. three distinct major types of signal-transducing proteins (stps) can be distinguished: one-component systems (1css), two-component systems (2css), and extracytoplasmic-function σ factors (ecfs). since actinobacteria are particularly rich in stps, we comprehensively investigated the abundance and diversity of stps encoded in 119 actinobacterial genomes, base ...	2015	25986905
chromosome organization and replisome dynamics in mycobacterium smegmatis.	subcellular organization of the bacterial nucleoid and spatiotemporal dynamics of dna replication and segregation have been studied intensively, but the functional link between these processes remains poorly understood. here we use quantitative time-lapse fluorescence microscopy for single-cell analysis of chromosome organization and dna replisome dynamics in mycobacterium smegmatis. we report that dna replication takes place near midcell, where, following assembly of the replisome on the replic ...	2015	25691587
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
2-(3'-indolyl)-n-arylthiazole-4-carboxamides: synthesis and evaluation of antibacterial and anticancer activities.	a new series of 2-(3'-indolyl)-n-arylthiazole-4-carboxamides 17a-p has been designed and synthesized. initial reaction of readily available thioamides 15 with bromopyruvic acid under refluxing conditions produced different thiazole carboxylic acids 16 which upon coupling with arylamines by using edci·hcl and hobt afforded diverse arylthiazole-4-carboxamides 17a-p in 78-87% yields. antibacterial activity evaluation against gram-positive and gram-negative bacterial strains led to compounds 17i-k a ...	2015	26298501
highly efficient cyp167a1 (epok) dependent epothilone b formation and production of 7-ketone epothilone d as a new epothilone derivative.	since their discovery in the soil bacterium sorangium cellulosum, epothilones have emerged as a valuable substance class with promising anti-tumor activity. because of their benefits in the treatment of cancer and neurodegenerative diseases, epothilones are targets for drug design and pharmaceutical research. the final step of their biosynthesis - a cytochrome p450 mediated epoxidation of epothilone c/d to a/b by cyp167a1 (epok) - needs significant improvement, in particular regarding the effici ...	2015	26445909
large-scale 13c flux profiling reveals conservation of the entner-doudoroff pathway as a glycolytic strategy among marine bacteria that use glucose.	marine bacteria form one of the largest living surfaces on earth, and their metabolic activity is of fundamental importance for global nutrient cycling. here, we explored the largely unknown intracellular pathways in 25 microbes representing different classes of marine bacteria that use glucose: alphaproteobacteria, gammaproteobacteria, and flavobacteriia of the bacteriodetes phylum. we used (13)c isotope experiments to infer metabolic fluxes through their carbon core pathways. notably, 90% of a ...	2015	25616803
preliminary investigation on the use of allyi isothiocyanate to increase the shelf-life of gilthead sea bream (sparus aurata) fillets.	the aim of this work is to evaluate the activity of allyl isothiocyanate (aitc) against fish spoilage bacteria (specific spoilage organisms; ssos) as well as its possible use in gilthead sea bream (sparus aurata) fillets to extend their shelf-life. in this regard, in vitro tests are carried out in order to evaluate the inhibitory activity of aitc and its vapours on several strains of ssos. the aitc effect on the shelf-life of sea bream fillets was made by putting them in plastic trays hermetical ...	2015	27800402
diverse reductive dehalogenases are associated with clostridiales-enriched microcosms dechlorinating 1,2-dichloroethane.	the achievement of successful biostimulation of active microbiomes for the cleanup of a polluted site is strictly dependent on the knowledge of the key microorganisms equipped with the relevant catabolic genes responsible for the degradation process. in this work, we present the characterization of the bacterial community developed in anaerobic microcosms after biostimulation with the electron donor lactate of groundwater polluted with 1,2-dichloroethane (1,2-dca). through a multilevel analysis, ...	2015	26273600
phenotypic heterogeneity, a phenomenon that may explain why quorum sensing does not always result in truly homogenous cell behavior.	phenotypic heterogeneity describes the occurrence of "nonconformist" cells within an isogenic population. the nonconformists show an expression profile partially different from that of the remainder of the population. phenotypic heterogeneity affects many aspects of the different bacterial lifestyles, and it is assumed that it increases bacterial fitness and the chances for survival of the whole population or smaller subpopulations in unfavorable environments. well-known examples for phenotypic ...	2015	26025903
relationship between heat-labile enterotoxin secretion capacity and virulence in wild type porcine-origin enterotoxigenic escherichia coli strains.	heat-labile enterotoxin (lt) is an important virulence factor secreted by some strains of enterotoxigenic escherichia coli (etec). the prototypic human-origin strain h10407 secretes lt via a type ii secretion system (t2ss). we sought to determine the relationship between the capacity to secrete lt and virulence in porcine-origin wild type (wt) etec strains. sixteen wt etec strains isolated from cases of severe diarrheal disease were analyzed by gm1ganglioside enzyme-linked immunosorbent assay to ...	2015	25768732
assessing the antimicrobial activity of polyisoprene based surfaces.	there has been an intense research effort in the last decades in the field of biofouling prevention as it concerns many aspects of everyday life and causes problems to devices, the environment, and human health. many different antifouling and antimicrobial materials have been developed to struggle against bacteria and other micro- and macro-organism attachment to different surfaces. however the "miracle solution" has still to be found. the research presented here concerns the synthesis of bio-ba ...	2015	25706513
individuality, phenotypic differentiation, dormancy and 'persistence' in culturable bacterial systems: commonalities shared by environmental, laboratory, and clinical microbiology.	for bacteria, replication mainly involves growth by binary fission. however, in a very great many natural environments there are examples of phenotypically dormant, non-growing cells that do not replicate immediately and that are phenotypically 'nonculturable' on media that normally admit their growth. they thereby evade detection by conventional culture-based methods. such dormant cells may also be observed in laboratory cultures and in clinical microbiology. they are usually more tolerant to s ...	2015	26629334
strategies and approaches in plasmidome studies-uncovering plasmid diversity disregarding of linear elements?	the term plasmid was originally coined for circular, extrachromosomal genetic elements. today, plasmids are widely recognized not only as important factors facilitating genome restructuring but also as vehicles for the dissemination of beneficial characters within bacterial communities. plasmid diversity has been uncovered by means of culture-dependent or -independent approaches, such as endogenous or exogenous plasmid isolation as well as pcr-based detection or transposon-aided capture, respect ...	2015	26074886
beyond iron: non-classical biological functions of bacterial siderophores.	bacteria secrete small molecules known as siderophores to acquire iron from their surroundings. for over 60 years, investigations into the bioinorganic chemistry of these molecules, including fundamental coordination chemistry studies, have provided insight into the crucial role that siderophores play in bacterial iron homeostasis. the importance of understanding the fundamental chemistry underlying bacterial life has been highlighted evermore in recent years because of the emergence of antibiot ...	2015	25764171
the challenge of efflux-mediated antibiotic resistance in gram-negative bacteria.	the global emergence of multidrug-resistant gram-negative bacteria is a growing threat to antibiotic therapy. the chromosomally encoded drug efflux mechanisms that are ubiquitous in these bacteria greatly contribute to antibiotic resistance and present a major challenge for antibiotic development. multidrug pumps, particularly those represented by the clinically relevant acrab-tolc and mex pumps of the resistance-nodulation-division (rnd) superfamily, not only mediate intrinsic and acquired mult ...	2015	25788514
evaluation of phosphate-solubilizing bacteria on the growth and grain yield of rice (oryza sativa l.) cropped in northern iran.	this study aimed to evaluate the efficiency of four phosphate-solubilizing bacteria (psb) on the growth and yield of rice under different soil conditions.	2015	26294004
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
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
comparison of biomass detachment from biofilms of two different pseudomonas spp. under constant shear conditions.	in the context of biofilm development, detachment is of practical importance when placed in a biofilm management perspective. the objective of the present study was to examine biofilm structure and biofilm detachment under controlled conditions for two distinct microorganisms grown under constant shear conditions. detached biofilm biomass was regularly collected and analysed over the course of 72 h biofilm growth by pseudomonas putida and pseudomonas fluorescens cells, and biofilm structural dev ...	2015	25563340
characterization of the ability to form biofilms by plant-associated pseudomonas species.	successful colonization is the initial step for plant-bacteria interactions; therefore, the development of strategies to improve adherence to plant surfaces is critically important for environmental bacteria. biofilm formation is thought to be one such strategy for bacteria to establish stable colonization on inert and living surfaces. although biofilms play potential roles in enabling persistent bacterial colonization, little attention has been paid to biofilms formed by plant-associated bacter ...	2015	25487118
application of internal standard method in recombinant luminescent bacteria test.	mercury and its organic compounds have been of severe concern worldwide due to their damage to the ecosystem and human health. the development of effective and affordable technology to monitor and signal the presence of bioavailable mercury is an urgent need. the mer gene is a mercury-responsive resistant gene, and a mercury-sensing recombinant luminescent bacterium using the mer gene was constructed in this study. the mer operon from marine pseudomonas putida strain sp1 was amplified and fused ...	2015	26354701
extracellular expression of natural cytosolic arginine deiminase from pseudomonas putida and its application in the production of l-citrulline.	the pseudomonas putida arginine deiminase (adi), a natural cytosolic enzyme, and thermobifida fusca cutinase were co-expressed in escherichia coli, and the optimized cutinase gene was used for increasing its expression level. 90.9% of the total adi protein was released into culture medium probably through a nonspecific leaking mechanism caused by the co-expressed cutinase. the enzymatic properties of the extracellular adi were found to be similar to those of adi prepared by conventional cytosoli ...	2015	26233330
quantitative polymerase chain reaction for microbial growth kinetics of mixed culture system.	microbial growth kinetics is often used to optimize environmental processes owing to its relation to the breakdown of substrate (contaminants). however, the quantification of bacterial populations in the environment is difficult owing to the challenges of monitoring a specific bacterial population within a diverse microbial community. conventional methods are unable to detect and quantify the growth of individual strains separately in the mixed culture reactor. this work describes a novel quanti ...	2015	26165316
solvent resistance pumps of pseudomonas putida s12: applications in 1-naphthol production and biocatalyst engineering.	the solvent resistance capacity of pseudomonas putida s12 was applied by using the organism as a host for biocatalysis and through cloning and expressing solvent resistant pump genes into escherichia coli. p. putida s12 expressing toluene ortho mononooxygenase (tom-green) was used for 1-naphthol production in a water-organic solvent biphasic system. application of p. putida s12 improved 1-naphthol production per gram cell dry weight by approximately 42% compared to e. coli. moreover, p. putida s ...	2015	26143210
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
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
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
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
construction of a novel phenol synthetic pathway in escherichia coli through 4-hydroxybenzoate decarboxylation.	phenol is a bulk chemical with lots of applications in the chemical industry. fermentative production of phenol had been realized in both pseudomonas putida and escherichia coli by recruiting tyrosine phenol-lyase (tpl). the tpl pathway needs tyrosine as the direct precursor for phenol production. in this work, a novel phenol synthetic pathway was created in e. coli by recruiting 4-hydroxybenzoate decarboxylase, which can convert 4-hydroxybenzoate to phenol and carbon dioxide. activating 3-deoxy ...	2015	25758959
biosynthesis of poly(3-hydroxybutyrate-co-3-hydroxyalkanoates) by recombinant escherichia coli from glucose.	the polyhydroxyalkanoate (pha) copolymers consisting of short-chain-length (scl) and medium-chain-length (mcl) monomers have various properties ranging from stiff to flexible depending on the molar fraction of the monomer compositions. it has been reported that phag, which is first known as a (r)-3-hydroxyacyl-acyl carrier protein (acp)-coa transferase, actually functions as a 3-hydroxyacyl-acp thioesterase, and the product of pp0763 gene from pseudomonas putida kt2440 has a (r)-3-hydroxyacyl (3 ...	2015	25732207
enzyme fusion for whole-cell biotransformation of long-chain sec-alcohols into esters.	enzyme fusion was investigated as a strategy to improve productivity of a two-step whole-cell biocatalysis. the biotransformation of long-chain sec-alcohols into esters by an alcohol dehydrogenase (adh) and baeyer-villiger monooxygenases (bvmos) was used as the model reaction. the recombinant escherichia coli, expressing the fusion enzymes between the adh of micrococcus luteus nctc2665 and the bvmo of pseudomonas putida kt2440 or rhodococcus jostii rha1, showed significantly greater bioconversio ...	2015	25636834
isolation of oxygenase genes for indigo-forming activity from an artificially polluted soil metagenome by functional screening using pseudomonas putida strains as hosts.	metagenomes contain the dna from many microorganisms, both culturable and non-culturable, and are a potential resource of novel genes. in this study, a 5.2-gb metagenomic dna library was constructed from a soil sample (artificially polluted with four aromatic compounds, i.e., biphenyl, phenanthrene, carbazole, and 3-chlorobenzoate) in escherichia coli by using a broad-host-range cosmid vector. the resultant library was introduced into naphthalene-degrading pseudomonas putida-derived strains havi ...	2015	25573469
expression levels of chaperones influence biotransformation activity of recombinant escherichia coli expressing micrococcus luteus alcohol dehydrogenase and pseudomonas putida baeyer-villiger monooxygenase.	we demonstrated for the first time that the archaeal chaperones (i.e., γ-prefoldin and thermosome) can stabilize enzyme activity in vivo. ricinoleic acid biotransformation activity of recombinant escherichia coli expressing micrococcus luteus alcohol dehydrogenase and the pseudomonas putida kt2440 baeyer-villiger monooxygenase improved significantly with co-expression of γ-prefoldin or recombinant themosome originating from the deep-sea hyperthermophile archaea methanocaldococcus jannaschii. fur ...	2015	25545273
biodegradation of hexachlorobenzene by a constructed microbial consortium.	a consortium comprised of an engineered escherichia coli dh5α and a natural pentachlorophenol (pcp) degrader, sphingobium chlorophenolicum atcc 39723, was assembled for degradation of hexachlorobenzene (hcb), a persistent organic pollutant. the engineered e. coli strain, harbouring a gene cassette (cama (+) camb (+) camc) that encodes the f87w/y96f/l244a/v247l mutant of cytochrome p-450cam (cyp101), oxidised hcb to pcp. the resulting pcp was then further completely degraded by atcc 39723. the re ...	2015	25532745
development of recombinant methioninase to target the general cancer-specific metabolic defect of methionine dependence: a 40-year odyssey.	all tested cancer cell types are methionine dependent in that the cells arrest and eventually die when deprived of methionine, a condition that is generally nontoxic to normal cells. methionine dependence is the only known general metabolic defect in cancer. methionine-deprived cancer cells arrest at the s/g2 phase, an unusual position for cell cycle arrest. in order to exploit the cancer-specific metabolic defect of methionine dependence, methioninases were developed.	2015	25439528
quantitative analysis of chemotaxis towards toluene by pseudomonas putida in a convection-free microfluidic device.	chemotaxis has been shown to be beneficial for the migration of soil-inhabiting bacteria towards industrial chemical pollutants, which they degrade. many studies have demonstrated the importance of this microbial property under various circumstances; however, few quantitative analyses have been undertaken to measure the two essential parameters that characterize the chemotaxis of bioremediation bacteria: the chemotactic sensitivity coefficient χ(0) and the chemotactic receptor constant k(c). the ...	2015	25408100
influence of humic acid on the stability and bacterial toxicity of zinc oxide nanoparticles in water.	the present study investigated the stability of zinc oxide nanoparticles (zno nps) by the adsorption of humic acid (ha) and the mechanism of adsorption. the effect of humic acid on np toxicity was determined by escherichia coli (atcc 13534), e. coli (atcc 25922), and pseudomonas putida (mtcc 4910). the nanoparticles showed low zeta potential and were least stable in the absence of ha. however, the negative surface charge of the particles increased in the presence of ha (0-50mg/l) that reduced th ...	2015	26496792
biomimetic ferrichrome: structural motifs for switching between narrow- and broad-spectrum activities in p. putida and e. coli.	a series of novel ferrichrome (fc) analogs was designed based on the x-ray structure of fc in the fhua transporter of escherichia coli. two strategies were employed: the first strategy optimized the overall size and relative orientation of h-bonding interactions. the second strategy increased h-bonding interactions by introducing external h-donors onto analogs' backbone. tris-amino templates were coupled to succinic or aspartic acid, and the second carboxyl was used for hydroxamate construction. ...	2015	26459799
immobilization of escherichia coli cells expressing 4-oxalocrotonate tautomerase for improved biotransformation of β-nitrostyrene.	the enzyme 4-oxalocrotonate tautomerase (4-ot) encoded by the xylh gene is a part of the degradation pathway of aromatic compounds in pseudomonas putida mt-2. 4-ot was described to catalyze michael-type addition of acetaldehyde to β-nitrostyrene, and the whole cell system based on recombinantly expressed 4-ot has been developed previously. in this study biocatalytic process based on escherichia coli whole cells expressing 4-ot was significantly improved using immobilization and ex situ product r ...	2015	26410191
anthranilate degradation by a cold-adapted pseudomonas sp.	an alpine soil bacterium pseudomonas sp. strain pamc 25931 was characterized as eurypsychrophilic (both psychrophilic and mesotolerant) with a broad temperature range of 5-30 °c both for anthranilate (2-aminobenzoate) degradation and concomitant cell growth. two degradative gene clusters (antabc and catbca) were detected from a fosmid clone in the pamc 25931 genomic library; each cluster was confirmed to be specifically induced by anthranilate. when expressed in escherichia coli, the recombinant ...	2015	23720227
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
isolation and characterisation of rhizosphere bacteria active against meloidogyne incognita, phytophthora nicotianae and the root knot-black shank complex in tobacco.	the use of dually antagonistic bacteria (dab) as alternatives to chemicals for biological control of disease complexes has received little attention. in this study targeting the meloidogyne incognita-phytophthora nicotianae complex, dab from the tobacco rhizosphere were identified and screened against the diseases caused by one or both pathogens in tobacco.	2015	24799254
endophytic bacteria from piper tuberculatum jacq.: isolation, molecular characterization, and in vitro screening for the control of fusarium solani f. sp piperis, the causal agent of root rot disease in black pepper (piper nigrum l.).	endophytic bacteria have been found to colonize internal tissues in many different plants, where they can have several beneficial effects, including defense against pathogens. in this study, we aimed to identify endophytic bacteria associated with roots of the tropical piperaceae piper tuberculatum, which is known for its resistance to infection by fusarium solani f. sp piperis, the causal agent of black pepper (piper nigrum) root rot disease in the amazon region. based on 16s rrna gene sequence ...	2015	26214435
whole-cell-based identification of electrochemically active bacteria in microbial fuel cells by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.	electrochemically active bacteria (eab) that are capable of producing electricity from renewable biomass and organic wastes have been of particular interest in recent years. methods for selective enrichment, accurate identification and easy acquisition of eab fingerprints for phylogenetic characterization would facilitate utilization of these bioenergy-producing species in practical environmental engineering applications.	2015	26522312
a novel d-mandelate dehydrogenase used in three-enzyme cascade reaction for highly efficient synthesis of non-natural chiral amino acids.	a novel nad(+)-dependent d-mandelate dehydrogenase was identified from lactobacillus brevis (lbdmdh). after purified to homogeneity, the optimum ph and temperature for oxidation of d-mandelate were ph 10.0 and 40 °c, and the km and kcat were 1.1 mm and 355 s(-1) respectively. employing the lbdmdh together with a mandelate racemase from pseudomonas putida and a leucine dehydrogenase (esleudh) from exiguobacterium sibiricum, we established a three-step one-pot domino reaction system for preparing ...	2015	25449542
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 preference for carbon source utilization among three strains of aromatic compounds degrading pseudomonas.	soil isolates pseudomonas putida csv86, pseudomonas aeruginosa pp4 and pseudomonas sp. c5pp degrade naphthalene, phthalate isomers and carbaryl, respectively. strain csv86 displayed a diauxic growth pattern on phenylpropanoid compounds (veratraldehyde, ferulic acid, vanillin or vanillic acid) plus glucose with a distinct second lag-phase. the glucose concentration in the medium remained constant with higher cell respiration rates on aromatics and maximum protocatechuate 3,4-dioxygenase activity ...	2015	26316546
genome-scale reconstruction of the metabolic network in pseudomonas stutzeri a1501.	pseudomonas stutzeri a1501 is an endophytic bacterium capable of nitrogen fixation. this strain has been isolated from the rice rhizosphere and provides the plant with fixed nitrogen and phytohormones. these interesting features encouraged us to study the metabolism of this microorganism at the systems-level. in this work, we present the first genome-scale metabolic model (ipb890) for p. stutzeri, involving 890 genes, 1135 reactions, and 813 metabolites. a combination of automatic and manual app ...	2015	26302703
isolation of carbapenem-resistant pseudomonas spp. from food.	pseudomonas spp. are ubiquitous in nature. carbapenem resistance in environmental isolates of members of this genus is thought to be rare but the exact resistance rate is unknown. in this study, carbapenem-resistant pseudomonas spp. were isolated from chicken and pork samples and the mechanisms underlying the carbapenem resistance in these strains were investigated. a total of 16 carbapenem-resistant pseudomonas aeruginosa, pseudomonas putida and pseudomonas otitidis isolates were recovered from ...	2015	27873658
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
diversity of small rnas expressed in pseudomonas species.	rna sequencing (rna-seq) has revealed several hundreds of previously undetected small rnas (srnas) in all bacterial species investigated, including strains of pseudomonas aeruginosa, pseudomonas putida and pseudomonas syringae. nonetheless, only little is known about the extent of conservation of expressed srnas across strains and species. in this study, we have used rna-seq to identify srnas in p. putida dot-t1e and pseudomonas extremaustralis 14-3b. this is the first strain of p. extremaustral ...	2015	25394275
the c-di-gmp phosphodiesterase bifa is involved in the virulence of bacteria from the pseudomonas syringae complex.	in a recent screen for novel virulence factors involved in the interaction between pseudomonas savastanoi pv. savastanoi and the olive tree, a mutant was selected that contained a transposon insertion in a putative cyclic diguanylate (c-di-gmp) phosphodiesterase-encoding gene. this gene displayed high similarity to bifa of pseudomonas aeruginosa and pseudomonas putida. here, we examined the role of bifa in free-living and virulence-related phenotypes of two bacterial plant pathogens in the pseud ...	2015	25385023
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
pseudomonas alkylphenolica sp. nov., a bacterial species able to form special aerial structures when grown on p-cresol.	pseudomonas sp. kl28t is an aerobic, rod-shaped bacterium that was isolated from the soil of changwon, south korea, based on its ability to grow in the presence of linear alkylphenols (c1-c5). despite several studies on strain kl28t, it could not be assigned to any known species in the genus pseudomonas. the name 'pseudomonas alkylphenolia' was proposed for kl28t, but the strain had not until now been characterized taxonomically and the name currently has no standing in the bacterial nomenclatur ...	2015	26276124
photosynthetic aeration in biological wastewater treatment using immobilized microalgae-bacteria symbiosis.	chlorella vulgaris encapsulated in alginate beads were added into a bioreactor treating synthetic wastewater using pseudomonas putida. a symbiotic co2/o2 gas exchange was established between the two microorganisms for photosynthetic aeration of wastewater. during batch operation, glucose removal efficiency in the bioreactor improved from 50% in 12 h without aeration to 100% in 6 h, when the bioreactor was aerated photosynthetically. during continuous operation, the bioreactor was operated at a l ...	2015	26266755
isolation of a diphenylamine-degrading bacterium and characterization of its metabolic capacities, bioremediation and bioaugmentation potential.	the antioxidant diphenylamine (dpa) is used in fruit-packaging plants for the control of the physiological disorder apple scald. its use results in the production of dpa-contaminated wastewater which should be treated before finally discharged. biological treatment systems using tailored-made microbial inocula with specific catabolic activities comprise an appealing and sustainable solution. this study aimed to isolate dpa-degrading bacteria, identify the metabolic pathway of dpa and evaluate th ...	2015	26260839
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
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
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