Publications

cloning and expression of a trehalose synthase from pseudomonas putida kt2440 for the scale-up production of trehalose from maltose.	trehalose synthase (tres) is considered to be a potential biocatalyst for trehalose production. we aimed to scale-up produce the tres protein in escherichia coli and further investigate the bioconversion capacity of tres. the tres gene from pseudomonas putida kt2440 was amplified and expressed in e. coli bl21 (de3). the recombinant tres showed a molecular mass of 67 kda. activity analysis suggested that tres had optimal activity at a temperature of 55 °c, a ph of 7.4, with a substrate concentrat ...	2014	25204684
engineering escherichia coli to overproduce aromatic amino acids and derived compounds.	the production of aromatic amino acids using fermentation processes with recombinant microorganisms can be an advantageous approach to reach their global demands. in addition, a large array of compounds with alimentary and pharmaceutical applications can potentially be synthesized from intermediates of this metabolic pathway. however, contrary to other amino acids and primary metabolites, the artificial channelling of building blocks from central metabolism towards the aromatic amino acid pathwa ...	2014	25200799
the endophytic bacterium, sphingomonas samr12, improves the potential for zinc phytoremediation by its host, sedum alfredii.	the endophytic bacterium, sphingomonas samr12, isolated from sedum alfredii hance, appears to increase plant biomass and zinc-extraction from contaminated soil; however, the mechanism by which this occurs is not clear. here, the ability of samr12 to promote zinc extraction and its effects on root morphology and exudation were examined in hydroponics. zinc treatment increased shoot biomass by 30 to 45%, and by a further 10 to 19% when combined with samr12 inoculation. zinc treatment also increase ...	2014	25198772
proteomic characterization of the outer membrane vesicle of pseudomonas putida kt2440.	outer membrane vesicles (omvs) are produced by various pathogenic gram-negative bacteria such as escherichia coli, pseudomonas aeruginosa, and acinetobacter baumannii. in this study, we isolated omvs from a representative soil bacterium, pseudomonas putida kt2440, which has a biodegradative activity toward various aromatic compounds. proteomic analysis identified the outer membrane proteins (omps) oprc, oprd, opre, oprf, oprh, oprg, and oprw as major components of the omv of p. putida kt2440. th ...	2014	25198519
purification and characterization of melanogenic enzyme tyrosinase from button mushroom.	melanogenesis is a biosynthetic pathway for the formation of the pigment melanin in human skin. a key enzyme, tyrosinase, catalyzes the first and only rate-limiting steps in melanogenesis. since the discovery of its melanogenic properties, tyrosinase has been in prime focus and microbial sources of the enzyme are sought. agaricus bisporus widely known as the common edible mushroom, it's taking place in high amounts of proteins, enzyme, carbohydrates, fibers, and low fat contents are frequently c ...	2014	25197562
complete genome sequence of the radiation-resistant bacterium rubrobacter radiotolerans rsps-4.	rubrobacter radiotolerans strain rsps-4 is a slightly thermophilic member of the phylum "actinobacteria" isolated from a hot spring in são pedro do sul, portugal. this aerobic and halotolerant bacterium is also extremely resistant to gamma and uv radiation, which are the main reasons for the interest in sequencing its genome. here, we present the complete genome sequence of strain rsps-4 as well as its assembly and annotation. we also compare the gene sequence of this organism with that of the t ...	2014	25197483
human oxygen sensing may have origins in prokaryotic elongation factor tu prolyl-hydroxylation.	the roles of 2-oxoglutarate (2og)-dependent prolyl-hydroxylases in eukaryotes include collagen stabilization, hypoxia sensing, and translational regulation. the hypoxia-inducible factor (hif) sensing system is conserved in animals, but not in other organisms. however, bioinformatics imply that 2og-dependent prolyl-hydroxylases (phds) homologous to those acting as sensing components for the hif system in animals occur in prokaryotes. we report cellular, biochemical, and crystallographic analyses ...	2014	25197067
magnetic nanoparticle-mediated isolation of functional bacteria in a complex microbial community.	although uncultured microorganisms have important roles in ecosystems, their ecophysiology in situ remains elusive owing to the difficulty of obtaining live cells from their natural habitats. in this study, we employed a novel magnetic nanoparticle-mediated isolation (mmi) method to recover metabolically active cells of a group of previously uncultured phenol degraders, burkholderiales spp., from coking plant wastewater biosludge; five other culturable phenol degraders-rhodococcus sp., chryseoba ...	2014	25191996
magnetic nanoparticle-mediated isolation of functional bacteria in a complex microbial community.	although uncultured microorganisms have important roles in ecosystems, their ecophysiology in situ remains elusive owing to the difficulty of obtaining live cells from their natural habitats. in this study, we employed a novel magnetic nanoparticle-mediated isolation (mmi) method to recover metabolically active cells of a group of previously uncultured phenol degraders, burkholderiales spp., from coking plant wastewater biosludge; five other culturable phenol degraders-rhodococcus sp., chryseoba ...	2014	25191996
how microorganisms use hydrophobicity and what does this mean for human needs?	cell surface hydrophobicity (csh) plays a crucial role in the attachment to, or detachment from the surfaces. the influence of csh on adhesion of microorganisms to biotic and abiotic surfaces in medicine as well as in bioremediation and fermentation industry has both negative and positive aspects. hydrophobic microorganisms cause the damage of surfaces by biofilm formation; on the other hand, they can readily accumulate on organic pollutants and decompose them. hydrophilic microorganisms also pl ...	2014	25191645
culturable heavy metal-resistant and plant growth promoting bacteria in v-ti magnetite mine tailing soil from panzhihua, china.	to provide a basis for using indigenous bacteria for bioremediation of heavy metal contaminated soil, the heavy metal resistance and plant growth-promoting activity of 136 isolates from v-ti magnetite mine tailing soil were systematically analyzed. among the 13 identified bacterial genera, the most abundant genus was bacillus (79 isolates) out of which 32 represented b. subtilis and 14 b. pumilus, followed by rhizobium sp. (29 isolates) and ochrobactrum intermedium (13 isolates). altogether 93 i ...	2014	25188470
pep2path: automated mass spectrometry-guided genome mining of peptidic natural products.	nonribosomally and ribosomally synthesized bioactive peptides constitute a source of molecules of great biomedical importance, including antibiotics such as penicillin, immunosuppressants such as cyclosporine, and cytostatics such as bleomycin. recently, an innovative mass-spectrometry-based strategy, peptidogenomics, has been pioneered to effectively mine microbial strains for novel peptidic metabolites. even though mass-spectrometric peptide detection can be performed quite fast, true high-thr ...	2014	25188327
identification of glutamate abc-transporter component in clostridium perfringens as a putative drug target.	clostridium perfringens is an anaerobic pathogen known to cause vast number of diseases in mammals and birds. various toxins and hydrolysing enzymes released by the organism are responsible for the necrosis of soft tissues. due to serious safety issues associated with current vaccines against c. perfringens, there is a need for new drug or vaccine targets. c. perfringens is extremely dependent on its host for nutrition which can be targeted for vaccine development or drug design. therefore, it i ...	2014	25187678
surface free energy activated high-throughput cell sorting.	cell sorting is an important screening process in microbiology, biotechnology, and clinical research. existing methods are mainly based on single-cell analysis as in flow cytometric and microfluidic cell sorters. here we report a label-free bulk method for sorting cells by differentiating their characteristic surface free energies (sfes). we demonstrated the feasibility of this method by sorting model binary cell mixtures of various bacterial species, including pseudomonas putida kt2440, enteroc ...	2014	25184988
genome sequencing of a mung bean plant growth promoting strain of p. aeruginosa with biocontrol ability.	pseudomonas aeruginosa pgpr2 is a mung bean rhizosphere strain that produces secondary metabolites and hydrolytic enzymes contributing to excellent antifungal activity against macrophomina phaseolina, one of the prevalent fungal pathogens of mung bean. genome sequencing was performed using the ion torrent personal genome machine generating 1,354,732 reads (6,772,433 sequenced bases) achieving ~25-fold coverage of the genome. reference genome assembly using mira 3.4.0 yielded 198 contigs. the dra ...	2014	25184130
mechanistic insight into the conserved allosteric regulation of periplasmic proteolysis by the signaling molecule cyclic-di-gmp.	stable surface adhesion of cells is one of the early pivotal steps in bacterial biofilm formation, a prevalent adaptation strategy in response to changing environments. in pseudomonas fluorescens, this process is regulated by the lap system and the second messenger cyclic-di-gmp. high cytoplasmic levels of cyclic-di-gmp activate the transmembrane receptor lapd that in turn recruits the periplasmic protease lapg, preventing it from cleaving a cell surface-bound adhesin, thereby promoting cell adh ...	2014	25182848
a blavim-2 plasmid disseminating in extensively drug-resistant clinical pseudomonas aeruginosa and serratia marcescens isolates.		2014	25182641
enzymatic characterization and in vivo function of five terminal oxidases in pseudomonas aeruginosa.	the ubiquitous opportunistic pathogen pseudomonas aeruginosa has five aerobic terminal oxidases: bo(3)-type quinol oxidase (cyo), cyanide-insensitive oxidase (cio), aa3-type cytochrome c oxidase (aa3), and two cbb(3)-type cytochrome c oxidases (cbb(3)-1and cbb(3)-2). these terminal oxidases are differentially regulated under various growth conditions and are thought to contribute to the survival of this microorganism in a wide variety of environmental niches. here, we constructed multiple mutant ...	2014	25182500
the tetr-type mfsr protein of the integrative and conjugative element (ice) iceclc controls both a putative efflux system and initiation of ice transfer.	integrative and conjugating elements (ice) are self-transferable dnas widely present in bacterial genomes, which often carry a variety of auxiliary genes of potential adaptive benefit. one of the model ice is iceclc, an element originally found in pseudomonas knackmussii b13 and known for its propensity to provide its host with the capacity to metabolize chlorocatechols and 2-aminophenol. in this work, we studied the mechanism and target of regulation of mfsr, a tetr-type repressor previously fo ...	2014	25182498
cbb3-type cytochrome c oxidases, aerobic respiratory enzymes, impact the anaerobic life of pseudomonas aeruginosa pao1.	for bacteria, many studies have focused on the role of respiratory enzymes in energy conservation; however, their effect on cell behavior is poorly understood. pseudomonas aeruginosa can perform both aerobic respiration and denitrification. previous studies demonstrated that cbb3-type cytochrome c oxidases that support aerobic respiration are more highly expressed in p. aeruginosa under anoxic conditions than are other aerobic respiratory enzymes. however, little is known about their role under ...	2014	25182494
bicarbonate increases binding affinity of vibrio cholerae toxt to virulence gene promoters.	the major vibrio cholerae virulence gene transcription activator, toxt, is responsible for the production of the diarrhea-inducing cholera toxin (ct) and the major colonization factor, toxin coregulated pilus (tcp). in addition to the two primary virulence factors mentioned, toxt is responsible for the activation of accessory virulence genes, such as alda, taga, acfa, acfd, tcpi, and tarab. toxt activity is negatively modulated by bile and unsaturated fatty acids found in the upper small intesti ...	2014	25182489
identification of multiple soluble fe(iii) reductases in gram-positive thermophilic bacterium thermoanaerobacter indiensis bsb-33.	thermoanaerobacter indiensis bsb-33 has been earlier shown to reduce fe(iii) and cr(vi) anaerobically at 60°c optimally. further, the gram-positive thermophilic bacterium contains cr(vi) reduction activity in both the membrane and cytoplasm. the soluble fraction prepared from t. indiensis cells grown at 60°c was found to contain the majority of fe(iii) reduction activity of the microorganism and produced four distinct bands in nondenaturing fe(iii) reductase activity gel. proteins from each of t ...	2014	25180173
analysis of genes contributing to plant-beneficial functions in plant growth-promoting rhizobacteria and related proteobacteria.	the positive effects of root-colonizing bacteria cooperating with plants lead to improved growth and/or health of their eukaryotic hosts. some of these plant growth-promoting rhizobacteria (pgpr) display several plant-beneficial properties, suggesting that the accumulation of the corresponding genes could have been selected in these bacteria. here, this issue was targeted using 23 genes contributing directly or indirectly to established pgpr effects, based on genome sequence analysis of 304 cont ...	2014	25179219
sulfur source-mediated transcriptional regulation of the rhlabc genes involved in biosurfactants production by pseudomonas sp. strain ak6u.	despite the nutritional significance of sulfur, its influence on biosurfactants production has not been sufficiently studied. we investigated the expression of key biosurfactants production genes, rhlabc, in cultures of pseudomonas sp. ak6u grown with inorganic or organic sulfur sources. ak6u grew with either inorganic sulfate (mgso4), dibenzothiophene (dbt), or dbt-sulfone as a sole sulfur source in the presence of glucose as a carbon source. the ak6u cultures produced variable amounts of biosu ...	2014	25177318
the potential of the ni-resistant tce-degrading pseudomonas putida w619-tce to reduce phytotoxicity and improve phytoremediation efficiency of poplar cuttings on a ni-tce co-contamination.	to examine the potential of pseudomonas putida w619-tce to improve phytoremediation of ni-tce co-contamination, the effects of inoculation of a ni-resistant, tce-degrading root endophyte on ni-tce phytotoxicity, ni uptake and trichloroethylene (tce) degradation of ni-tce-exposed poplar cuttings are evaluated. after inoculation with p. putida w619-tce, root weight of non-exposed poplar cuttings significantly increased. further, inoculation induced a mitigation of the ni-tce phytotoxicity, which w ...	2015	25174423
antibiotic multiresistance analysis of mesophilic and psychrotrophic pseudomonas spp. isolated from goat and lamb slaughterhouse surfaces throughout the meat production process.	the aim of this study was to investigate the phenotypic and genotypic antibiotic resistance profiles of pseudomonads isolated from surfaces of a goat and lamb slaughterhouse, which were representative of areas that are possible sources of meat contamination. mesophilic (85 isolates) and psychrotrophic (37 isolates) pseudomonads identified at the species level generally were resistant to sulfamethoxazole, erythromycin, amoxicillin, ampicillin, chloramphenicol, trimethoprim, rifampin, and ceftazid ...	2014	25172860
heterologous expression and characterization of the manganese-oxidizing protein from erythrobacter sp. strain sd21.	the manganese (mn)-oxidizing protein (mopa) from erythrobacter sp. strain sd21 is part of a unique enzymatic family that is capable of oxidizing soluble mn(ii). this enzyme contains two domains, an animal heme peroxidase domain, which contains the catalytic site, followed by a c-terminal calcium binding domain. different from the bacterial mn-oxidizing multicopper oxidase enzymes, little is known about mopa. to gain a better understanding of mopa and its role in mn(ii) oxidation, the 238-kda ful ...	2014	25172859
mechanism of the 6-hydroxy-3-succinoyl-pyridine 3-monooxygenase flavoprotein from pseudomonas putida s16.	6-hydroxy-3-succinoyl-pyridine (hsp) 3-monooxygenase (hspb), a flavoprotein essential to the pyrrolidine pathway of nicotine degradation, catalyzes pyridine-ring β-hydroxylation, resulting in carbon-carbon cleavage and production of 2,5-dihydroxypyridine. here, we generated his6-tagged hspb in escherichia coli, characterized the properties of the recombinant enzyme, and investigated its mechanism of catalysis. in contrast to conclusions reported previously, the second product of the hspb reactio ...	2014	25172510
crystal structure of the ectoine hydroxylase, a snapshot of the active site.	ectoine and its derivative 5-hydroxyectoine are compatible solutes that are widely synthesized by bacteria to cope physiologically with osmotic stress. they also serve as chemical chaperones and maintain the functionality of macromolecules. 5-hydroxyectoine is produced from ectoine through a stereo-specific hydroxylation, an enzymatic reaction catalyzed by the ectoine hydroxylase (ectd). the ectd protein is a member of the non-heme-containing iron(ii) and 2-oxoglutarate-dependent dioxygenase sup ...	2014	25172507
phytomediated biostimulation of the autochthonous bacterial community for the acceleration of the depletion of polycyclic aromatic hydrocarbons in contaminated sediments.	polycyclic aromatic hydrocarbons (pahs) are a large group of organic contaminants causing hazards to organisms including humans. the objective of the study was to validate the vegetation of dredged sediments with phragmites australis as an exploitable biostimulation approach to accelerate the depletion of pahs in nitrogen spiked sediments. vegetation with phragmites australis resulted in being an efficient biostimulation approach for the depletion of an aged pahs contamination (229.67 ± 15.56 μg ...	2014	25170516
p. aeruginosa sgnh hydrolase-like proteins algj and algx have similar topology but separate and distinct roles in alginate acetylation.	the o-acetylation of polysaccharides is a common modification used by pathogenic organisms to protect against external forces. pseudomonas aeruginosa secretes the anionic, o-acetylated exopolysaccharide alginate during chronic infection in the lungs of cystic fibrosis patients to form the major constituent of a protective biofilm matrix. four proteins have been implicated in the o-acetylation of alginate, algijf and algx. to probe the biological function of algj, we determined its structure to 1 ...	2014	25165982
characterization of the medium- and long-chain n-alkanes degrading pseudomonas aeruginosa strain sjtd-1 and its alkane hydroxylase genes.	a gram-negative aliphatic hydrocarbon-degrading bacterium sjtd-1 isolated from oil-contaminated soil was identified as pseudomonas aeruginosa by comparative analyses of the 16s rrna sequence, phenotype, and physiological features. sjtd-1 could efficiently mineralize medium- and long-chain n-alkanes (c12-c30) as its sole carbon source within seven days, showing the most optimal growth on n-hexadecane, followed by n-octadecane, and n-eicosane. in 36 h, 500 mg/l of tetradecane, hexadecane, and octa ...	2014	25165808
ends of the line for tmrna-smpb.	genes for the rna tmrna and protein smpb, partners in the trans-translation process that rescues stalled ribosomes, have previously been found in all bacteria and some organelles. during a major update of the tmrna website (relocated to http://bioinformatics.sandia.gov/tmrna), including addition of an smpb sequence database, we found some bacteria that lack functionally significant regions of smpb. three groups with reduced genomes have lost the central loop of smpb, which is thought to improve ...	2014	25165464
rna-seq analysis reveals a six-gene soxr regulon in streptomyces coelicolor.	the redox-regulated transcription factor soxr is conserved in diverse bacteria, but emerging studies suggest that this protein plays distinct physiological roles in different bacteria. soxr regulates a global oxidative stress response (involving > 100 genes) against exogenous redox-cycling drugs in escherichia coli and related enterics. in the antibiotic producers streptomyces coelicolor and pseudomonas aeruginosa, however, soxr regulates a smaller number of genes that encode membrane transporte ...	2014	25162599
whole genome sequencing and analysis of plant growth promoting bacteria isolated from the rhizosphere of plantation crops coconut, cocoa and arecanut.	coconut, cocoa and arecanut are commercial plantation crops that play a vital role in the indian economy while sustaining the livelihood of more than 10 million indians. according to 2012 food and agricultural organization's report, india is the third largest producer of coconut and it dominates the production of arecanut worldwide. in this study, three plant growth promoting rhizobacteria (pgpr) from coconut (cpcri-1), cocoa (cpcri-2) and arecanut (cpcri-3) characterized for the pgp activities ...	2014	25162593
foeniculum vulgare mill: a review of its botany, phytochemistry, pharmacology, contemporary application, and toxicology.	foeniculum vulgare mill commonly called fennel has been used in traditional medicine for a wide range of ailments related to digestive, endocrine, reproductive, and respiratory systems. additionally, it is also used as a galactagogue agent for lactating mothers. the review aims to gather the fragmented information available in the literature regarding morphology, ethnomedicinal applications, phytochemistry, pharmacology, and toxicology of foeniculum vulgare. it also compiles available scientific ...	2014	25162032
demethionylation of pro-1 variants of 4-oxalocrotonate tautomerase in escherichia coli by co-expression with an engineered methionine aminopeptidase.	4-oxalocrotonate tautomerase (4-ot) catalyzes the enol-keto tautomerization of 2-hydroxymuconate, utilizing its n-terminal proline (pro-1) as general base catalyst. substituting pro-1 with bulky or charged residues will result in poor or no post-translational removal of the translation-initiating methionine by the methionine aminopeptidase (metap) of the escherichia coli expression host. here, we set out to investigate whether co-expression with previously engineered aminopeptidase metap-∗tg can ...	2014	25161874
ornithine cyclodeaminase/μ-crystallin homolog from the hyperthermophilic archaeon thermococcus litoralis functions as a novel δ(1)-pyrroline-2-carboxylate reductase involved in putative trans-3-hydroxy-l-proline metabolism.	l-ornithine cyclodeaminase (ocd) is involved in l-proline biosynthesis and catalyzes the unique deaminating cyclization of l-ornithine to l-proline via a δ(1)-pyrroline-2-carboxyrate (pyr2c) intermediate. although this pathway functions in only a few bacteria, many archaea possess ocd-like genes (proteins), among which only af1665 protein (gene) from archaeoglobus fulgidus has been characterized as an nad(+)-dependent l-alanine dehydrogenase (afaladh). however, the physiological role of ocd-like ...	2014	25161870
the contribution of escherichia coli from human and animal sources to the integron gene pool in coastal waters.	to understand the contribution of animal- and human-derived fecal pollution sources in shaping integron prevalence and diversity in beach waters, 414 escherichia coli strains were collected from beach waters (bw, n = 166), seagull feces (sf, n = 179), and wastewaters (ww, n = 69), on the world biosphere reserve of the berlenga island, portugal. statistical differences were found between the prevalence of integrons in bw (21%) and ww (10%), but not between bw and sf (19%). the majority of integra ...	2014	25161650
escherichia coli d-malate dehydrogenase, a generalist enzyme active in the leucine biosynthesis pathway.	the enzymes of the β-decarboxylating dehydrogenase superfamily catalyze the oxidative decarboxylation of d-malate-based substrates with various specificities. here, we show that, in addition to its natural function affording bacterial growth on d-malate as a carbon source, the d-malate dehydrogenase of escherichia coli (ecdmla) naturally expressed from its chromosomal gene is capable of complementing leucine auxotrophy in a leub(-) strain lacking the paralogous isopropylmalate dehydrogenase enzy ...	2014	25160617
dna recognition by a σ(54) transcriptional activator from aquifex aeolicus.	transcription initiation by bacterial σ(54)-polymerase requires the action of a transcriptional activator protein. activators bind sequence-specifically upstream of the transcription initiation site via a dna-binding domain (dbd). the structurally characterized dbds from activators all belong to the fis (factor for inversion stimulation) family of helix-turn-helix dna-binding proteins. we report here structures of the free and dna-bound forms of the dbd of ntrc4 (4dbd) from aquifex aeolicus, a m ...	2014	25158097
the role of biotin and oxamate in the carboxyltransferase reaction of pyruvate carboxylase.	pyruvate carboxylase (pc) is a biotin-dependent enzyme that catalyzes the mgatp-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in central metabolism. during catalysis, carboxybiotin is translocated to the carboxyltransferase domain where the carboxyl group is transferred to the acceptor substrate, pyruvate. many studies on the carboxyltransferase domain of pc have demonstrated an enhanced oxaloacetate decarboxylation activity in the presence of oxamate and ...	2014	25157442
unconventionally secreted effectors of two filamentous pathogens target plant salicylate biosynthesis.	plant diseases caused by fungi and oomycetes pose an increasing threat to food security and ecosystem health worldwide. these filamentous pathogens, while taxonomically distinct, modulate host defense responses by secreting effectors, which are typically identified based on the presence of signal peptides. here we show that phytophthora sojae and verticillium dahliae secrete isochorismatases (psisc1 and vdisc1, respectively) that are required for full pathogenesis. psisc1 and vdisc1 can suppress ...	2014	25156390
modulation of biofilm-formation in salmonella enterica serovar typhimurium by the periplasmic dsba/dsbb oxidoreductase system requires the ggdef-eal domain protein stm3615.	in salmonella enterica serovar typhimurium (s. typhimurium), biofilm-formation is controlled by the cytoplasmic intracellular small-molecular second messenger cyclic 3', 5'-di- guanosine monophosphate (c-di-gmp) through the activities of ggdef and eal domain proteins. here we describe that deleting either dsba or dsbb, respectively encoding a periplasmic protein disulfide oxidase and a cytoplasmic membrane disulfide oxidoreductase, resulted in increased biofilm-formation on solid medium. this in ...	2014	25153529
a microbial biomanufacturing platform for natural and semisynthetic opioids.	opiates and related molecules are medically essential, but their production via field cultivation of opium poppy papaver somniferum leads to supply inefficiencies and insecurity. as an alternative production strategy, we developed baker's yeast saccharomyces cerevisiae as a microbial host for the transformation of opiates. yeast strains engineered to express heterologous genes from p. somniferum and bacterium pseudomonas putida m10 convert thebaine to codeine, morphine, hydromorphone, hydrocodon ...	2014	25151135
poly(3-hydroxypropionate): a promising alternative to fossil fuel-based materials.	polyhydroxyalkanoates (phas) are storage compounds synthesized by numerous microorganisms and have attracted the interest of industry since they are biobased and biodegradable alternatives to fossil fuel-derived plastics. among phas, poly(3-hydroxypropionate) [poly(3hp)] has outstanding material characteristics and exhibits a large variety of applications. as it is not brittle like, e.g., the best-studied pha, poly(3-hydroxybutyrate) [poly(3hb)], it can be used as a plasticizer in blends to impr ...	2014	25149521
purification and characterization of plantaricin zj5, a new bacteriocin produced by lactobacillus plantarum zj5.	the aim of this study is to investigate the antimicrobial potential of lactobacillus plantarum zj5, a strain isolated from fermented mustard with a broad range of inhibitory activity against both gram-positive and gram-negative bacteria. here we present the peptide plantaricin zj5 (pzj5), which is an extreme ph and heat-stable. however, it can be digested by pepsin and proteinase k. this peptide has strong activity against staphylococcus aureus. pzj5 has been purified using a multi-step process, ...	2014	25147943
fungal siderophore metabolism with a focus on aspergillus fumigatus.	siderophores are chelators synthesized by microbes to sequester iron. this article summarizes the knowledge on the fungal siderophore metabolism with a focus on aspergillus fumigatus. in recent years, a. fumigatus became a role model for fungal biosynthesis, uptake and degradation of siderophores as well as regulation of siderophore-mediated iron handling and the elucidation of siderophore functions. siderophore functions comprise uptake, intracellular transport and storage of iron. this proved ...	2014	25140791
dissection of the region of pseudomonas aeruginosa para that is important for dimerization and interactions with its partner parb.	pseudomonas aeruginosa para belongs to a large subfamily of walker-type atpases acting as partitioning proteins in bacteria. para has the ability to both self-associate and interact with its partner parb. analysis of the deletion mutants defined the part of the protein involved in dimerization and interactions with parb. here, a set of para alanine substitution mutants in the region between e67 and l85 was created and analysed in vivo and in vitro. all mutants impaired in dimerization (substitut ...	2014	25139949
oligomerization mechanisms of an h-ns family protein, pmr, encoded on the plasmid pcar1 provide a molecular basis for functions of h-ns family members.	enterobacterial h-ns-like proteins and pseudomonas mvat-like proteins share low homology at the amino acid sequence level, but both can function as xenogeneic silencers and are included in the h-ns family of proteins. h-ns family members have dimerization/oligomerization and dna-binding domains connected by a flexible linker and form large nucleoprotein complexes using both domains. pmr, an mvat-like protein encoded on the incp-7 carbazole-degradative plasmid pcar1, is a key regulator of an inte ...	2014	25137042
influence of organic solvents on catalytic behaviors and cell morphology of whole-cell biocatalysts for synthesis of 5'-arabinocytosine laurate.	a whole-cell based method was developed for the regioselective synthesis of arabinocytosine laurate. among the seven kinds of bacteria strains tested in the acylation reaction, pseudomonas fluorescens gave the highest productivity and a higher 5'-regioselectivity than 99%. compared with pure organic solvents, the use of organic solvent mixtures greatly promoted the yield of the whole-cell catalyzed reaction, but showed little influence on the 5'-regioselectivity. of all the tested solvent mixtur ...	2014	25136983
engineering of pseudomonas taiwanensis vlb120 for constitutive solvent tolerance and increased specific styrene epoxidation activity.	the application of whole cells as biocatalysts is often limited by the toxicity of organic solvents, which constitute interesting substrates/products or can be used as a second phase for in situ product removal and as tools to control multistep biocatalysis. solvent-tolerant bacteria, especially pseudomonas strains, are proposed as promising hosts to overcome such limitations due to their inherent solvent tolerance mechanisms. however, potential industrial applications suffer from tedious, unpro ...	2014	25128338
high-level conversion of l-lysine into 5-aminovalerate that can be used for nylon 6,5 synthesis.	l-lysine is a potential feedstock for the production of bio-based precursors for engineering plastics. in this study, we developed a microbial process for high-level conversion of l-lysine into 5-aminovalerate (5ava) that can be used as a monomer in nylon 6,5 synthesis. recombinant escherichia coli wl3110 strain expressing pseudomonas putida delta-aminovaleramidase (dava) and lysine 2-monooxygenase (davb) was grown to high density in fed-batch culture and used as a whole cell catalyst. high-dens ...	2014	25124937
volatilization of arsenic from polluted soil by pseudomonas putida engineered for expression of the arsm arsenic(iii) s-adenosine methyltransferase gene.	even though arsenic is one of the most widespread environmental carcinogens, methods of remediation are still limited. in this report we demonstrate that a strain of pseudomonas putida kt2440 endowed with chromosomal expression of the arsm gene encoding the as(iii) s-adenosylmethionine (sam) methyltransfase from rhodopseudomonas palustris to remove arsenic from contaminated soil. we genetically engineered the p. putida kt2440 with stable expression of an arsm-gfp fusion gene (ge p. putida), whic ...	2014	25122054
mobility and generation of mosaic non-autonomous transposons by tn3-derived inverted-repeat miniature elements (times).	functional transposable elements (tes) of several pseudomonas spp. strains isolated from black shale ore of lubin mine and from post-flotation tailings of zelazny most in poland, were identified using a positive selection trap plasmid strategy. this approach led to the capture and characterization of (i) 13 insertion sequences from 5 is families (is3, is5, isl3, is30 and is1380), (ii) isoforms of two tn3-family transposons--tn5563a and tn4662a (the latter contains a toxin-antitoxin system), as w ...	2014	25121765
biotic interactions in the rhizosphere: a diverse cooperative enterprise for plant productivity.	microbes and plants have evolved biochemical mechanisms to communicate with each other. the molecules responsible for such communication are secreted during beneficial or harmful interactions. hundreds of these molecules secreted into the rhizosphere have been identified, and their functions are being studied in order to understand the mechanisms of interaction and communication among the different members of the rhizosphere community. the importance of root and microbe secretion to the undergro ...	2014	25118253
protein as chemical cue: non-nutritional growth enhancement by exogenous protein in pseudomonas putida kt2440.	research pertaining to microbe-microbe and microbe-plant interactions has been largely limited to small molecules like quorum sensing chemicals. however, a few recent reports have indicated the role of complex molecules like proteins and polysaccharides in microbial communication. here we demonstrate that exogenous proteins present in culture media can considerably accelerate the growth of pseudomonas putida kt2440, even when such proteins are not internalized by the cells. the growth enhancemen ...	2014	25117434
analysis of n-acylhomoserine lactone dynamics in continuous cultures of pseudomonas putida isof by use of elisa and uhplc/qtof-ms-derived measurements and mathematical models.	in this interdisciplinary approach, the dynamics of production and degradation of the quorum sensing signal 3-oxo-decanoylhomoserine lactone were studied for continuous cultures of pseudomonas putida isof. the signal concentrations were quantified over time by use of monoclonal antibodies and elisa. the results were verified by use of ultra-high-performance liquid chromatography. by use of a mathematical model we derived quantitative values for non-induced and induced signal production rate per ...	2014	25116602
biocatalytic coatings for air pollution control: a proof of concept study on voc biodegradation.	although biofilm-based biotechnologies exhibit a large potential as solutions for off-gas treatment, the high water content of biofilms often causes pollutant mass transfer limitations, which ultimately limit their widespread application. the present study reports on the proof of concept of the applicability of bioactive latex coatings for air pollution control. toluene vapors served as a model volatile organic compound (voc). the results showed that pseudomonas putida f1 cells could be successf ...	2015	25115963
structure and function of tatd exonuclease in dna repair.	tatd is an evolutionarily conserved protein with thousands of homologues in all kingdoms of life. it has been suggested that tatd participates in dna fragmentation during apoptosis in eukaryotic cells. however, the cellular functions and biochemical properties of tatd in bacterial and non-apoptotic eukaryotic cells remain elusive. here we show that escherichia coli tatd is a mg(2+)-dependent 3'-5' exonuclease that prefers to digest single-stranded dna and rna. tatd-knockout cells are less resist ...	2014	25114049
purification of chitinase enzymes from bacillus subtilis bacteria tv-125, investigation of kinetic properties and antifungal activity against fusarium culmorum.	chitin is the main structural component of cell walls of fungi, exoskeletons of insects and other arthropods and shells of crustaceans. chitinase enzyme is capable of degrading chitin, and this enzyme can be used as a biological fungicide against phytopathogenic fungi, as well as an insecticide against insect pests.	2014	25112904
characterization of newly isolated lytic bacteriophages active against acinetobacter baumannii.	based on genotyping and host range, two newly isolated lytic bacteriophages, myovirus vb_abam_acibel004 and podovirus vb_abap_acibel007, active against acinetobacter baumannii clinical strains, were selected from a new phage library for further characterization. the complete genomes of the two phages were analyzed. both phages are characterized by broad host range and essential features of potential therapeutic phages, such as short latent period (27 and 21 min, respectively), high burst size (1 ...	2014	25111143
biosurfactant mediated biosynthesis of selected metallic nanoparticles.	developing a reliable experimental protocol for the synthesis of nanomaterials is one of the challenging topics in current nanotechnology particularly in the context of the recent drive to promote green technologies in their synthesis. the increasing need to develop clean, nontoxic and environmentally safe production processes for nanoparticles to reduce environmental impact, minimize waste and increase energy efficiency has become essential in this field. consequently, recent studies on the use ...	2014	25110864
fed-batch strategies using butyrate for high cell density cultivation of pseudomonas putida and its use as a biocatalyst.	a mathematically based fed-batch bioprocess demonstrated the suitability of using a relatively cheap and renewable substrate (butyric acid) for pseudomonas putida ca-3 high cell density cultivation. butyric acid fine-tuned addition is critical to extend the fermentation run and avoid oxygen consumption while maximising the biomass volumetric productivity. a conservative submaximal growth rate (μ of 0.25 h(-1)) achieved 71.3 g l(-1) of biomass after 42 h of fed-batch growth. when a more ambitious ...	2014	25104034
the pseudomonas community in metal-contaminated sediments as revealed by quantitative pcr: a link with metal bioavailability.	pseudomonas bacteria are ubiquitous gram-negative and aerobic microorganisms that are known to harbor metal resistance mechanisms such as efflux pumps and intracellular redox enzymes. specific pseudomonas bacteria have been quantified in some metal-contaminated environments, but the entire pseudomonas population has been poorly investigated under these conditions, and the link with metal bioavailability was not previously examined. in the present study, quantitative pcr and cell cultivation were ...	2014	25102022
variation in plant responsiveness to defense elicitors caused by genotype and environment.		2014	25101103
effect of pseudomonas putida on growth and anthocyanin pigment in two poinsettia (euphorbia pulcherrima) cultivars.	pseudomonas putida is plant growth promoting rhizobacteria (pgpr) that have the capacity to improve growth in plants. the purpose of this study was to determine growth and anthocyanin pigmentation of the bracts in two poinsettia euphorbia pulcherrima cultivars (prestige and sonora marble) using three strains of p. putida, as well as a mixture of the three (mix). comparison with the control group indicated for the most part that prestige grew better than the sonora marble cultivars with the pgpr ...	2014	25097888
pseudomonas soli sp. nov., a novel producer of xantholysin congeners.	a chemoorganotrophic gram-negative bacterium was isolated by means of a diffusion sandwich system from a soil sample from the sierra nevada national park, spain. strain f-279,208(t) was oxidase and catalase positive, strictly aerobic, non-spore-forming and motile by single polar flagellum. phylogenetic analysis of the 16s rrna, gyrb, rpob and rpod genes revealed that strain f-279,208(t) belongs to the pseudomonas putida group with pseudomonas mosselii and pseudomonas entomophila as its closest r ...	2014	25097020
the periplasmic protein tolb as a potential drug target in pseudomonas aeruginosa.	the gram-negative bacterium pseudomonas aeruginosa is one of the most dreaded pathogens in the hospital setting, and represents a prototype of multi-drug resistant "superbug" for which effective therapeutic options are very limited. the identification and characterization of new cellular functions that are essential for p. aeruginosa viability and/or virulence could drive the development of anti-pseudomonas compounds with novel mechanisms of action. in this study we investigated whether tolb, th ...	2014	25093328
production of silver nanoparticles with strong and stable antimicrobial activity against highly pathogenic and multidrug resistant bacteria.	to synthesize, characterize, and analyze antimicrobial activity of agnps of escherichia hermannii (she), citrobacter sedlakii (s11p), and pseudomonas putida (s5).	2014	25093206
structural and functional basis of transcriptional regulation by tetr family protein cprb from s. coelicolor a3(2).	antibiotic production and resistance pathways in streptomyces are dictated by the interplay of transcriptional regulatory proteins that trigger downstream responses via binding to small diffusible molecules. to decipher the mode of dna binding and the associated allosteric mechanism in the sub-class of transcription factors that are induced by γ-butyrolactones, we present the crystal structure of cprb in complex with the consensus dna element to a resolution of 3.25 å. binding of the dna results ...	2014	25092919
lignin valorization through integrated biological funneling and chemical catalysis.	lignin is an energy-dense, heterogeneous polymer comprised of phenylpropanoid monomers used by plants for structure, water transport, and defense, and it is the second most abundant biopolymer on earth after cellulose. in production of fuels and chemicals from biomass, lignin is typically underused as a feedstock and burned for process heat because its inherent heterogeneity and recalcitrance make it difficult to selectively valorize. in nature, however, some organisms have evolved metabolic pat ...	2014	25092344
experimental and kinetic study on the cometabolic biodegradation of phenol and 4-chlorophenol by psychrotrophic pseudomonas putida ly1.	this study investigated the kinetics of phenol and 4-chlorophenol (4-cp) biodegradation by a cold-adapted bacteria, pseudomonas putida ly1, isolated from songhua river sediment. the results showed that p. putida ly1 cannot grow on 4-cp as a sole carbon source. p. putida ly1 had the potential to cometabolic biodegrade phenol and 4-cp in a wide range of temperature (varying from 5 to 35 °c) with the optimal temperature around 25 °c. mixture of phenol and 4-cp were completely removed at two 4-cp co ...	2015	25091164
a proteomic approach to understand the role of the outer membrane porins in the organic solvent-tolerance of pseudomonas aeruginosa psea.	solvent-tolerant microbes have the unique ability to thrive in presence of organic solvents. the present study describes the effect of increasing hydrophobicity (log pow values) of organic solvents on the outer membrane proteome of the solvent-tolerant pseudomonas aeruginosa psea cells. the cells were grown in a medium containing 33% (v/v) alkanes of increasing log pow values. the outer membrane proteins were extracted by alkaline extraction from the late log phase cells and changes in the prote ...	2014	25089526
near-zero growth kinetics of pseudomonas putida deduced from proteomic analysis.	intensive microbial growth typically observed in laboratory rarely occurs in nature. because of severe nutrient deficiency, natural populations exhibit near-zero growth (nzg). there is a long-standing controversy about sustained nzg, specifically whether there is a minimum growth rate below which cells die or whether cells enter a non-growing maintenance state. using chemostat with cell retention (ccr) of pseudomonas putida, we resolve this controversy and show that under nzg conditions, bacteri ...	2015	25088710
pseudomonas aeruginosa mdab and wrba are water-soluble two-electron quinone oxidoreductases with the potential to defend against oxidative stress.	water-soluble quinone oxidoreductases capable of reducing quinone substrates via a concerted two-electron mechanism have been implicated in bacterial antioxidant defence. twoelectron transfer avoids formation of dangerously reactive semi-quinone intermediates, moreover previous work in pseudomonas putida indicated a direct protective effect for the quinols generated by an over-expressed oxidoreductase. here, the pseudomonas aeruginosa orthologs of five quinone oxidoreductases--mdab, chrr, wrba, ...	2014	25085734
the gene cluster for para-nitrophenol catabolism is responsible for 2-chloro-4-nitrophenol degradation in burkholderia sp. strain sj98.	burkholderia sp. strain sj98 (dsm 23195) utilizes 2-chloro-4-nitrophenol (2c4np) or para-nitrophenol (pnp) as a sole source of carbon and energy. here, by genetic and biochemical analyses, a 2c4np catabolic pathway different from those of all other 2c4np utilizers was identified with chloro-1,4-benzoquinone (cbq) as an intermediate. reverse transcription-pcr analysis showed that all of the pnp genes in the pnpaba1cdef cluster were located in a single operon, which is significantly different from ...	2014	25085488
detection of organic compounds with whole-cell bioluminescent bioassays.	natural and manmade organic chemicals are widely deposited across a diverse range of ecosystems including air, surface water, groundwater, wastewater, soil, sediment, and marine environments. some organic compounds, despite their industrial values, are toxic to living organisms and pose significant health risks to humans and wildlife. detection and monitoring of these organic pollutants in environmental matrices therefore is of great interest and need for remediation and health risk assessment. ...	2014	25084996
restoration of a mediterranean forest after a fire: bioremediation and rhizoremediation field-scale trial.	forest fires pose a serious threat to countries in the mediterranean basin, often razing large areas of land each year. after fires, soils are more likely to erode and resilience is inhibited in part by the toxic aromatic hydrocarbons produced during the combustion of cellulose and lignins. in this study, we explored the use of bioremediation and rhizoremediation techniques for soil restoration in a field-scale trial in a protected mediterranean ecosystem after a controlled fire. our bioremediat ...	2014	25079309
restoration of a mediterranean forest after a fire: bioremediation and rhizoremediation field-scale trial.	forest fires pose a serious threat to countries in the mediterranean basin, often razing large areas of land each year. after fires, soils are more likely to erode and resilience is inhibited in part by the toxic aromatic hydrocarbons produced during the combustion of cellulose and lignins. in this study, we explored the use of bioremediation and rhizoremediation techniques for soil restoration in a field-scale trial in a protected mediterranean ecosystem after a controlled fire. our bioremediat ...	2014	25079309
a phasin with many faces: structural insights on phap from azotobacter sp. fa8.	phasins are a group of proteins associated to granules of polyhydroxyalkanoates (phas). apart from their structural role as part of the pha granule cover, different structural and regulatory functions have been found associated to many of them, and several biotechnological applications have been developed using phasin protein fusions. despite their remarkable functional diversity, the structure of these proteins has not been analyzed except in very few studies. phap from azotobacter sp. fa8 (pha ...	2014	25077609
microbial monoterpene transformations-a review.	isoprene and monoterpenes constitute a significant fraction of new plant biomass. emission rates into the atmosphere alone are estimated to be over 500 tg per year. these natural hydrocarbons are mineralized annually in similar quantities. in the atmosphere, abiotic photochemical processes cause lifetimes of minutes to hours. microorganisms encounter isoprene, monoterpenes, and other volatiles of plant origin while living in and on plants, in the soil and in aquatic habitats. below toxic concent ...	2014	25076942
susceptibility to antibiotics in urinary tract infections in a secondary care setting from 2005-2006 and 2010-2011, in são paulo, brazil: data from 11,943 urine cultures.	urinary tract infection (uti) has a high incidence and recurrence, therefore, treatment is empirical in the majority of cases.	2014	25076433
exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics.	symbioses represent a frequent and successful lifestyle on earth and lichens are one of their classic examples. recently, bacterial communities were identified as stable, specific and structurally integrated partners of the lichen symbiosis, but their role has remained largely elusive in comparison to the well-known functions of the fungal and algal partners. we have explored the metabolic potentials of the microbiome using the lung lichen lobaria pulmonaria as the model. metagenomic and proteom ...	2014	25072413
exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics.	symbioses represent a frequent and successful lifestyle on earth and lichens are one of their classic examples. recently, bacterial communities were identified as stable, specific and structurally integrated partners of the lichen symbiosis, but their role has remained largely elusive in comparison to the well-known functions of the fungal and algal partners. we have explored the metabolic potentials of the microbiome using the lung lichen lobaria pulmonaria as the model. metagenomic and proteom ...	2014	25072413
challenges of climate change: omics-based biology of saffron plants and organic agricultural biotechnology for sustainable saffron production.	kashmir valley is a major saffron (crocus sativus kashmirianus) growing area of the world, second only to iran in terms of production. in kashmir, saffron is grown on uplands (termed in the local language as "karewas"), which are lacustrine deposits located at an altitude of 1585 to 1677 m above mean sea level (amsl), under temperate climatic conditions. kashmir, despite being one of the oldest historical saffron-producing areas, faces a rapid decline of saffron industry. among many other factor ...	2014	25072266
single-cell genomics reveals features of a colwellia species that was dominant during the deepwater horizon oil spill.	during the deepwater horizon (dwh) oil spill in the gulf of mexico a deep-sea hydrocarbon plume developed resulting in a rapid succession of bacteria. colwellia eventually supplanted oceanospirillales, which dominated the plume early in the spill. these successional changes may have resulted, in part, from the changing composition and abundance of hydrocarbons over time. colwellia abundance peaked when gaseous and simple aromatic hydrocarbons increased, yet the metabolic pathway used by colwelli ...	2014	25071745
a type vi secretion-related pathway in bacteroidetes mediates interbacterial antagonism.	bacteroidetes are a phylum of gram-negative bacteria abundant in mammalian-associated polymicrobial communities, where they impact digestion, immunity, and resistance to infection. despite the extensive competition at high cell density that occurs in these settings, cell contact-dependent mechanisms of interbacterial antagonism, such as the type vi secretion system (t6ss), have not been defined in this group of organisms. herein we report the bioinformatic and functional characterization of a t6 ...	2014	25070807
self-association is required for occupation of adjacent binding sites in pseudomonas aeruginosa type iii secretion system promoters.	exsa is a member of the arac/xyls family of transcriptional regulators and is required for expression of the pseudomonas aeruginosa type iii secretion system (t3ss). all p. aeruginosa t3ss promoters contain two adjacent binding sites for monomeric exsa. the amino-terminal domain of exsa (ntd) is thought to mediate interactions between the exsa monomers bound to each site. threading the ntd onto the arac backbone revealed an α-helix that likely serves as the primary determinant for dimerization. ...	2014	25070741
identification and use of an alkane transporter plug-in for applications in biocatalysis and whole-cell biosensing of alkanes.	effective application of whole-cell devices in synthetic biology and biocatalysis will always require consideration of the uptake of molecules of interest into the cell. here we demonstrate that the alkl protein from pseudomonas putida gpo1 is an alkane import protein capable of industrially relevant rates of uptake of c7-c16 n-alkanes. without alkl expression, native e.coli n-alkane uptake was the rate-limiting step in both the whole-cell bioconversion of c7-c16 n-alkanes and in the activation ...	2014	25068650
antimicrobial activity of cobalt imidazolate metal-organic frameworks.	two cobalt imidazolate metal-organic frameworks were evaluated as a bactericidal material against the growth of the gram-negative bacteria pseudomonas putida and escherichia coli. under the most unfavourable conditions, within the exponential growth phase and in the culture media for both microorganisms, the growth inhibition reached over 50% for concentrations of biocidal material in the 5-10mgl(-1) range. the release of metal gives excellent durability with the antibacterial effect persisting ...	2014	25065809
flp-frt-based method to obtain unmarked deletions of chu_3237 (poru) and large genomic fragments of cytophaga hutchinsonii.	cytophaga hutchinsonii is a widely distributed cellulolytic bacterium in the phylum bacteroidetes. it can digest crystalline cellulose rapidly without free cellulases or cellulosomes. the mechanism of its cellulose utilization remains a mystery. we developed an efficient method based on a linear dna double-crossover and flp-frt recombination system to obtain unmarked deletions of both single genes and large genomic fragments in c. hutchinsonii. unmarked deletion of chu_3237 (poru), an ortholog o ...	2014	25063660
wound healing potential of antibacterial microneedles loaded with green tea extracts.	this study evaluates the utility of an antibacterial microneedle composed of green tea (gt) extract and hyaluronic acid (ha), for the efficient delivery of gt. these microneedles have the potential to be a patient-friendly method for the conventional sustained release of drugs. in this study, a fabrication method using a mold-based technique to produce gt/ha microneedles with a maximum area of ~50mm(2) with antibacterial properties was used to manufacture transdermal drug delivery systems. fouri ...	2014	25063177
genome sequence of a newly isolated nicotine-degrading bacterium, ochrobactrum sp. sjy1.	ochrobactrum sp. sjy1 uses nicotine as the sources of carbon, nitrogen, and energy. the genome of sjy1 was sequenced in order to provide insights into its mechanism of nicotine degradation. physiological characteristics and genome analysis indicate that strain sjy1 might have a different nicotine degradation pathway from the pyridine or pyrrolidine pathway.	2014	25059869
metagenomic identification of a novel salt tolerance gene from the human gut microbiome which encodes a membrane protein with homology to a brp/blh-family β-carotene 15,15'-monooxygenase.	the human gut microbiome consists of at least 3 million non-redundant genes, 150 times that of the core human genome. herein, we report the identification and characterisation of a novel stress tolerance gene from the human gut metagenome. the locus, assigned brpa, encodes a membrane protein with homology to a brp/blh-family β-carotene monooxygenase. cloning and heterologous expression of brpa in escherichia coli confers a significant salt tolerance phenotype. furthermore, when cultured in the p ...	2014	25058308
response mechanisms of bacterial degraders to environmental contaminants on the level of cell walls and cytoplasmic membrane.	bacterial strains living in the environment must cope with the toxic compounds originating from humans production. surface bacterial structures, cell wall and cytoplasmic membrane, surround each bacterial cell and create selective barriers between the cell interior and the outside world. they are a first site of contact between the cell and toxic compounds. organic pollutants are able to penetrate into cytoplasmic membrane and affect membrane physiological functions. bacteria had to evolve adapt ...	2014	25057269
two structurally different dienelactone hydrolases (tfdei and tfdeii) from cupriavidus necator jmp134 plasmid pjp4 catalyse cis- and trans-dienelactones with similar efficiency.	in this study, dienelactone hydrolases (tfdei and tfdeii) located on plasmid pjp4 of cupriavidus necator jmp134 were cloned, purified, characterized and three dimensional structures were predicted. tfdei and tfdeii genes were cloned into pet21b vector and expressed in e. coli bl21(de3). the enzymes were purified by applying ultra-membrane filtration, anion-exchange qff and gel-filtration columns. the enzyme activity was determined by using cis-dienelactone. the three-dimensional structure of enz ...	2014	25054964
6-hydroxy-3-succinoylpyridine hydroxylase catalyzes a central step of nicotine degradation in agrobacterium tumefaciens s33.	nicotine is a main alkaloid in tobacco and is also the primary toxic compound in tobacco wastes. it can be degraded by bacteria via either pyridine pathway or pyrrolidine pathway. previously, a fused pathway of the pyridine pathway and the pyrrolidine pathway was proposed for nicotine degradation by agrobacterium tumefaciens s33, in which 6-hydroxy-3-succinoylpyridine (hsp) is a key intermediate connecting the two pathways. we report here the purification and properties of an nadh-dependent hsp ...	2014	25054198
metabolic engineering of escherichia coli for poly(3-hydroxypropionate) production from glycerol and glucose.	a new poly(3-hydroxypropionate) (p3hp) biosynthetic pathway employing β-alanine as an intermediate from an inexpensive carbon source was developed in recombinant escherichia coli. after a series of systematic optimization, the genes for l-aspartate decarboxylase and its maturation factor (pand and panm, from e. coli), β-alanine-pyruvate transaminase (pp0596, from pseudomonas putida), 3-hydroxy acid dehydrogenase and 3-hydroxypropionyl-coa synthase (ydfg and prpe respectively, from e. coli), and ...	2014	25048226
programming controlled adhesion of e. coli to target surfaces, cells, and tumors with synthetic adhesins.	in this work we report synthetic adhesins (sas) enabling the rational design of the adhesion properties of e. coli. sas have a modular structure comprising a stable β-domain for outer membrane anchoring and surface-exposed immunoglobulin domains with high affinity and specificity that can be selected from large repertoires. sas are constitutively and stably expressed in an e. coli strain lacking a conserved set of natural adhesins, directing a robust, fast, and specific adhesion of bacteria to t ...	2014	25045780