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rapid metabolic pathway assembly and modification using serine integrase site-specific recombination.synthetic biology requires effective methods to assemble dna parts into devices and to modify these devices once made. here we demonstrate a convenient rapid procedure for dna fragment assembly using site-specific recombination by c31 integrase. using six orthogonal attp/attb recombination site pairs with different overlap sequences, we can assemble up to five dna fragments in a defined order and insert them into a plasmid vector in a single recombination reaction. c31 integrase-mediated assembl ...201324225316
rapid metabolic pathway assembly and modification using serine integrase site-specific recombination.synthetic biology requires effective methods to assemble dna parts into devices and to modify these devices once made. here we demonstrate a convenient rapid procedure for dna fragment assembly using site-specific recombination by c31 integrase. using six orthogonal attp/attb recombination site pairs with different overlap sequences, we can assemble up to five dna fragments in a defined order and insert them into a plasmid vector in a single recombination reaction. c31 integrase-mediated assembl ...201324225316
discovery of pantoea rodasii strain nd03 that produces n-(3-oxo-hexanoyl)-l-homoserine lactone.proteobacteria use quorum sensing to regulate target gene expression in response to population density. quorum sensing (qs) is achieved via so-called signalling molecules and the best-studied qs signalling system uses n-acyl homoserine lactones (ahls). this study aimed to identify and characterize the production of ahls by a bacterium nd03 isolated from a malaysian tropical rainforest waterfall. molecular identification showed that nd03 is a pantoea sp. closely related to pantoea rodasii. we use ...201424859023
characterization of plant carotenoid cyclases as members of the flavoprotein family functioning with no net redox change.the later steps of carotenoid biosynthesis involve the formation of cyclic carotenoids. the reaction is catalyzed by lycopene beta-cyclase (lcy-b), which converts lycopene into beta-carotene, and by capsanthin-capsorubin synthase (ccs), which is mainly dedicated to the synthesis of kappa-cyclic carotenoids (capsanthin and capsorubin) but also has lcy-b activity. although the peptide sequences of plant lcy-bs and ccs contain a putative dinucleotide-binding motif, it is believed that these two car ...201020460582
isolation and screening of bacteria for their diazotrophic potential and their influence on growth promotion of maize seedlings in greenhouses.poor soil fertility is one of the major constraints for crop production. nitrogen is the most limiting nutrient for increasing crop productivity. therefore, there is a need to identify diazotrophic inoculants as an alternative or supplement to n-fertilizers for sustainable agriculture. in the current study, a number of free-living diazotrophic bacteria were isolated from soils collected from maize rhizosphere and from leaves and roots of maize within the kwazulu-natal province, republic of south ...201526779245
isolation and screening of bacteria for their diazotrophic potential and their influence on growth promotion of maize seedlings in greenhouses.poor soil fertility is one of the major constraints for crop production. nitrogen is the most limiting nutrient for increasing crop productivity. therefore, there is a need to identify diazotrophic inoculants as an alternative or supplement to n-fertilizers for sustainable agriculture. in the current study, a number of free-living diazotrophic bacteria were isolated from soils collected from maize rhizosphere and from leaves and roots of maize within the kwazulu-natal province, republic of south ...201526779245
biological role of pigment production for the bacterial phytopathogen pantoea stewartii subsp. stewartii.pantoea stewartii subsp. stewartii, the causal agent of stewart's wilt of sweet corn, produces a yellow carotenoid pigment. a nonpigmented mutant was selected from a bank of mutants generated by random transposon mutagenesis. the transposon insertion site was mapped to the crtb gene, encoding a putative phytoene synthase, an enzyme involved in the early steps of carotenoid biosynthesis. we demonstrate here that the carotenoid pigment imparts protection against uv radiation and also contributes t ...201222820327
identification and elimination of bacterial contamination during in vitro propagation of guadua angustifolia kunth.guadua angustifolia kunth is a very important bamboo species with significant utility in pharmaceutical, paper, charcoal, and construction industries. microbial contamination is a major problem encountered during establishment of in vitro cultures of guadua.201222701279
complete genome sequence of clinical isolate pantoea ananatis lmg 5342.the enterobacterium pantoea ananatis is an ecologically versatile species. it has been found in the environment, as plant epiphyte and endophyte, as an emerging phytopathogen, and as a presumptive, opportunistic human pathogen. here, we report the complete genome sequence of p. ananatis lmg 5342, isolated from a human wound.201222374951
draft genome sequence of the antibiotic-producing epiphytic isolate pantoea ananatis brt175.pantoea is a member of the enterobacteriaceae, whose members have been shown to produce novel antibiotics. here, we report the 4.8-mb genome sequence of pantoea ananatis strain brt175, an epiphytic isolate from strawberries that produces an antibiotic that is effective against the fire blight pathogen, erwinia amylovora.201324201193
characterization of leaf blade- and leaf sheath-associated bacterial communities and assessment of their responses to environmental changes in co₂, temperature, and nitrogen levels under field conditions.rice shoot-associated bacterial communities at the panicle initiation stage were characterized and their responses to elevated surface water-soil temperature (et), low nitrogen (ln), and free-air co2 enrichment (face) were assessed by clone library analyses of the 16s rrna gene. principal coordinate analyses combining all sequence data for leaf blade- and leaf sheath-associated bacteria revealed that each bacterial community had a distinct structure, as supported by pc1 (61.5%), that was mainly ...201525740174
engineering corynebacterium glutamicum for violacein hyper production.corynebacterium glutamicum was used as a metabolic engineering chassis for production of crude violacein (mixture of violacein and deoxyviolacein) due to corynebacterium's gras status and advantages in tryptophan fermentation. the violacein is a commercially potential compound with various applications derived from l-tryptophan.201627557730
gene duplication in the carotenoid biosynthetic pathway preceded evolution of the grasses.despite ongoing research on carotenoid biosynthesis in model organisms, there is a paucity of information on pathway regulation operating in the grasses (poaceae), which include plants of world-wide agronomic importance. as a result, efforts to either breed for or metabolically engineer improvements in carotenoid content or composition in cereal crops have led to unexpected results. in comparison to maize (zea mays), rice (oryza sativa) accumulates no endosperm carotenoids, despite having a func ...200415247400
transformation of the green alga haematococcus pluvialis with a phytoene desaturase for accelerated astaxanthin biosynthesis.astaxanthin is a high-value carotenoid which is used as a pigmentation source in fish aquaculture. additionally, a beneficial role of astaxanthin as a food supplement for humans has been suggested. the unicellular alga haematococcus pluvialis is a suitable biological source for astaxanthin production. in the context of the strong biotechnological relevance of h. pluvialis, we developed a genetic transformation protocol for metabolic engineering of this green alga. first, the gene coding for the ...200617012596
populations of fungi and bacteria associated with samples of stored rice in korea.stored rice was collected from rice processing complexes of national agricultural cooperative federation of 11 regions in korea to evaluate the occurrence of fungi and bacteria and to identify the predominant fungi and bacteria to the genus levels. most rice samples generally produced the higher levels of fungi and bacteria than white rice. the occurrence of fungi and bacteria varied in various locations of korea. among fungi observed, aspergillus spp. and penicillium spp. were dominant in the s ...200724015066
combinatorial genetic transformation generates a library of metabolic phenotypes for the carotenoid pathway in maize.combinatorial nuclear transformation is a novel method for the rapid production of multiplex-transgenic plants, which we have used to dissect and modify a complex metabolic pathway. to demonstrate the principle, we transferred 5 carotenogenic genes controlled by different endosperm-specific promoters into a white maize variety deficient for endosperm carotenoid synthesis. we recovered a diverse population of transgenic plants expressing different enzyme combinations and showing distinct metaboli ...200819011084
the kiwifruit lycopene beta-cyclase plays a significant role in carotenoid accumulation in fruit.the composition of carotenoids, along with anthocyanins and chlorophyll, accounts for the distinctive range of colour found in the actinidia (kiwifruit) species. lutein and beta-carotene are the most abundant carotenoids found during fruit development, with beta-carotene concentration increasing rapidly during fruit maturation and ripening. in addition, the accumulation of beta-carotene and lutein is influenced by the temperature at which harvested fruit are stored. expression analysis of carote ...200919574250
a novel approach for metabolic pathway optimization: oligo-linker mediated assembly (olma) method.imbalances in gene expression of a metabolic pathway can result in less-yield of the desired products. several targets were intensively investigated to balance the gene expression, such as promoter, ribosome binding site (rbs), the order of genes, as well as the species of the enzymes. however, the capability of simultaneous manipulation of multiple targets still needs to be explored.201526702298
modification of targets related to the entner-doudoroff/pentose phosphate pathway route for methyl-d-erythritol 4-phosphate-dependent carotenoid biosynthesis in escherichia coli.in engineered strains of escherichia coli, bioconversion efficiency is determined by not only metabolic flux but also the turnover efficiency of relevant pathways. methyl-d-erythritol 4-phosphate (mep)-dependent carotenoid biosynthesis in e. coli requires efficient turnover of precursors and balanced flux among precursors, cofactors, and cellular energy. however, the imbalanced supply of glyceraldehyde 3-phosphate (g3p) and pyruvate precursors remains the major metabolic bottleneck. to address t ...201526264597
identification and characterization of cronobacter iron acquisition systems.cronobacter spp. are emerging pathogens that cause severe infantile meningitis, septicemia, or necrotizing enterocolitis. contaminated powdered infant formula has been implicated as the source of cronobacter spp. in most cases, but questions still remain regarding the natural habitat and virulence potential for each strain. the iron acquisition systems in 231 cronobacter strains isolated from different sources were identified and characterized. all cronobacter spp. have both the feo and efe syst ...201222706064
the target spectrum of sdsr small rna in salmonella.model enteric bacteria such as escherichia coli and salmonella enterica express hundreds of small non-coding rnas (srnas), targets for most of which are yet unknown. some srnas are remarkably well conserved, indicating that they serve cellular functions that go beyond the necessities of a single species. one of these 'core srnas' of largely unknown function is the abundant ∼100-nucleotide sdsr srna which is transcribed by the general stress σ-factor, σ(s) and accumulates in stationary phase. in ...201627407104
structure and mechanism of an arabidopsis medium/long-chain-length prenyl pyrophosphate synthase.prenyltransferases (ptss) are involved in the biosynthesis of terpenes with diverse functions. here, a novel pts from arabidopsis (arabidopsis thaliana) is identified as a trans-type polyprenyl pyrophosphate synthase (atppps), which forms a trans-double bond during each homoallylic substrate condensation, rather than a homomeric c10-geranyl pyrophosphate synthase as originally proposed. biochemical and genetic complementation analyses indicate that atppps synthesizes c25 to c45 medium/long-chain ...201121220764
symplasmata are a clonal, conditional, and reversible type of bacterial multicellularity.microorganisms are capable of remarkable social behaviours, such as forming transient multicellular assemblages with properties and adaptive abilities exceeding those of individual cells. here, we report on the formation and structure of genets known as symplasmata produced by pantoea eucalypti bacteria. each symplasmatum develops clonally and stochastically from a single bacterium into a membrane-delimited, capsule-embedded cluster of progeny cells and with a frequency that depends on temperatu ...201627534795
investigation of proposed ladderane biosynthetic genes from anammox bacteria by heterologous expression in e. coli.ladderanes are hydrocarbon chains with three or five linearly concatenated cyclobutane rings that are uniquely produced as membrane lipid components by anammox (anaerobic ammonia-oxidizing) bacteria. by virtue of their angle and torsional strain, ladderanes are unusually energetic compounds, and if produced biochemically by engineered microbes, could serve as renewable, high-energy-density jet fuel components. the biochemistry and genetics underlying the ladderane biosynthetic pathway are unknow ...201626975050
identification and characterization of antigens as vaccine candidates against klebsiella pneumoniae.nosocomial infections, also called "hospital acquired infections," occur worldwide and affect both developed and resource-poor countries, thus having a major impact on their health care systems. klebsiella pneumoniae, which is an opportunistic gram-negative pathogen, is responsible for causing pneumonia, urinary tract infections and septicemia in immune compromised hosts such as neonates. unfortunately, there is no vaccine or mab available for prophylactic or therapeutic use against k. pneumonia ...201223250007
draft genome sequence of pantoea sp. strain a4, a rafflesia-associated bacterium that produces n-acylhomoserine lactones as quorum-sensing molecules.pantoea sp. strain a4 is a gram-negative bacterium isolated from the rafflesia flower. we present here, for the first time, the genome sequence of rafflesia-associated pantoea sp. strain a4, which exhibited quorum-sensing activity.201223144374
draft genome sequences of pantoea agglomerans and pantoea vagans isolates associated with termites.the genus pantoea incorporates many economically and clinically important species. the plant-associated species, pantoea agglomerans and pantoea vagans, are closely related and are often isolated from similar environments. plasmids conferring certain metabolic capabilities are also shared amongst these two species. the genomes of two isolates obtained from fungus-growing termites in south africa were sequenced, assembled and annotated. a high number of orthologous genes are conserved within and ...201626937267
generation of structurally novel short carotenoids and study of their biological activity.recent research interest in phytochemicals has consistently driven the efforts in the metabolic engineering field toward microbial production of various carotenoids. in spite of systematic studies, the possibility of using c30 carotenoids as biologically functional compounds has not been explored thus far. here, we generated 13 novel structures of c30 carotenoids and one c35 carotenoid, including acyclic, monocyclic, and bicyclic structures, through directed evolution and combinatorial biosynthe ...201626902326
synergistic interactions between carotene ring hydroxylases drive lutein formation in plant carotenoid biosynthesis.plant carotenoids play essential roles in photosynthesis, photoprotection, and as precursors to apocarotenoids. the plastid-localized carotenoid biosynthetic pathway is mediated by well-defined nucleus-encoded enzymes. however, there is a major gap in understanding the nature of protein interactions and pathway complexes needed to mediate carotenogenesis. in this study, we focused on carotene ring hydroxylation, which is performed by two structurally distinct classes of enzymes, the p450 cyp97a ...201222786888
erwinia teleogrylli sp. nov., a bacterial isolate associated with a chinese cricket.a bacterial isolate (scu-b244t) was obtained in china from crickets (teleogryllus occipitalis) living in cropland deserted for approximately 10 years. the isolated bacteria were gram-negative, facultatively anaerobic, oxidase-negative rods. a preliminary analysis of the 16s rrna gene sequence indicated that the strain belongs to either the genus erwinia or pantoea. analysis of multilocus sequence typing based on concatenated partial atpd, gyrb and infb gene sequences and physiological and bioche ...201626800121
production and assay of cellulolytic enzyme activity of enterobacter cloacae wpl 214 isolated from bovine rumen fluid waste of surabaya abbatoir, indonesia.this study aims to produce and assay cellulolytic enzyme activity (endo-(1,4)-β-d-glucanase, exo-(1,4)-β-d-glucanase, and β-glucosidase, at optimum temperature and optimum ph) of enterobacter cloacae wpl 214 isolated from bovine rumen fluid waste of surabaya abbatoir, indonesia.201527047099
construction of a novel pichia pastoris strain for production of xanthophylls.in this study, we used the yeast carotenogenic producer pichia pastoris pp-ebil strain, which has been metabolically engineered, by heterologously expressing β-carotene-pathway enzymes to produce β-carotene, as a vessel for recombinant astaxanthin expression. for this purpose, we designed new p. pastoris recombinant-strains harboring astaxanthin-encoding genes from carotenogenic microorganism, and thus capable of producing xanthophyllic compounds. we designed and constructed a plasmid (pgapza-wz ...201222534340
draft genome sequence of pantoea ananatis b1-9, a nonpathogenic plant growth-promoting bacterium.pantoea ananatis b1-9 is an endophytic gram-negative rhizobacterium that was isolated for its ability to promote plant growth and improve crop yield in the field. here we report the draft genome sequence of p. ananatis b1-9. comparison of this sequence to the sequenced genome of a plant-pathogenic p. ananatis strain, lmg20103, indicated that the pathogenesis-related genes were absent, but a subset of gene functions that may be related to its plant growth promotion were present.201222247529
biosynthesis of soluble carotenoid holoproteins in escherichia coli.carotenoids are widely distributed natural pigments that are excellent antioxidants acting in photoprotection. they are typically solubilized in membranes or attached to proteins. in cyanobacteria, the photoactive soluble orange carotenoid protein (ocp) is involved in photoprotective mechanisms as a highly active singlet oxygen and excitation energy quencher. here we describe a method for producing large amounts of holo-ocp in e.coli. the six different genes involved in the synthesis of holo-ocp ...201525765842
integrative conjugative elements of the icepan family play a potential role in pantoea ananatis ecological diversification and antibiosis.pantoea ananatis is a highly versatile enterobacterium isolated from diverse environmental sources. the ecological diversity of this species may be attributed, in part, to the acquisition of mobile genetic elements. one such element is an integrative and conjugative element (ice). by means of in silico analyses the ice elements belonging to a novel family, icepan, were identified in the genome sequences of five p. ananatis strains and characterized. pcr screening showed that icepan is prevalent ...201526106378
pantoea ananatis as a cause of corneal infiltrate after rice husk injury.we report a case of an agricultural worker presenting with corneal infiltrate following ocular injury with a rice husk. on examination, a superficial corneal foreign body was removed and sent for culture, which grew pantoea ananatis. this is, to our knowledge, the first clinical case report of pantoea ananatis causing corneal infiltrate.201222461671
characterization of the biosynthetic operon for the antibacterial peptide herbicolin in pantoea vagans biocontrol strain c9-1 and incidence in pantoea species.pantoea vagans c9-1 is a biocontrol strain that produces at least two antibiotics inhibiting the growth of erwinia amylovora, the causal agent of fire blight disease of pear and apple. one antibiotic, herbicolin i, was purified from culture filtrates of p. vagans c9-1 and determined to be 2-amino-3-(oxirane-2,3-dicarboxamido)-propanoyl-valine, also known as n(ß)-epoxysuccinamoyl-dap-valine. a plasposon library was screened for mutants that had lost the ability to produce herbicolin i. it was sho ...201222504810
experimental approaches to identify small rnas and their diverse roles in bacteria--what we have learnt in one decade of mica research.nowadays the identification of small rnas (srnas) and characterization of their role within regulatory networks takes a prominent place in deciphering complex bacterial phenotypes. compared to the study of other components of bacterial cells, this is a relatively new but fast-growing research field. although reports on new srnas appear regularly, some srnas are already subject of research for a longer time. one of such srnas is mica, a srna best described for its role in outer membrane remodelin ...201525974745
characterization of potential drug targets farnesyl diphosphate synthase and geranylgeranyl diphosphate synthase in schistosoma mansoni.schistosomiasis affects over 200 million people worldwide, with over 200,000 deaths annually. currently, praziquantel is the only drug available against schistosomiasis. we report here that schistosoma mansoni farnesyl diphosphate synthase (smfpps) and geranylgeranyl diphosphate synthase (smggpps) are potential drug targets for the treatment of schistosomiasis. we expressed active, recombinant smfpps and smggpps for subsequent kinetic characterization and testing against a variety of bisphosphon ...201324041901
whole-genome comparative analysis of virulence genes unveils similarities and differences between endophytes and other symbiotic bacteria.plant pathogens and endophytes co-exist and often interact with the host plant and within its microbial community. the outcome of these interactions may lead to healthy plants through beneficial interactions, or to disease through the inducible production of molecules known as virulence factors. unravelling the role of virulence in endophytes may crucially improve our understanding of host-associated microbial communities and their correlation with host health. virulence is the outcome of a comp ...201526074885
deep sequencing analyses expands the pseudomonas aeruginosa ampr regulon to include small rna-mediated regulation of iron acquisition, heat shock and oxidative stress response.pathogenicity of pseudomonas aeruginosa, a major cause of many acute and chronic human infections, is determined by tightly regulated expression of multiple virulence factors. quorum sensing (qs) controls expression of many of these pathogenic determinants. previous microarray studies have shown that the ampc β-lactamase regulator ampr, a member of the lysr family of transcription factors, also controls non-β-lactam resistance and multiple virulence mechanisms. using rna-seq and complementary as ...201324157832
deep sequencing analyses expands the pseudomonas aeruginosa ampr regulon to include small rna-mediated regulation of iron acquisition, heat shock and oxidative stress response.pathogenicity of pseudomonas aeruginosa, a major cause of many acute and chronic human infections, is determined by tightly regulated expression of multiple virulence factors. quorum sensing (qs) controls expression of many of these pathogenic determinants. previous microarray studies have shown that the ampc β-lactamase regulator ampr, a member of the lysr family of transcription factors, also controls non-β-lactam resistance and multiple virulence mechanisms. using rna-seq and complementary as ...201324157832
regulation of two carotenoid biosynthesis genes coding for phytoene synthase and carotenoid hydroxylase during stress-induced astaxanthin formation in the green alga haematococcus pluvialis.astaxanthin is a high-value carotenoid used as a pigmentation source in fish aquaculture. in addition, a beneficial role of astaxanthin as a food supplement for humans is becoming evident. the unicellular green alga haematococcus pluvialis seems to be a suitable source for natural astaxanthin. astaxanthin accumulation in h. pluvialis occurs in response to environmental stress such as high light and salt stress. here, the isolation of the h. pluvialis carotenoid biosynthesis gene phytoene synthas ...200111161038
uncovering the lactobacillus plantarum wcfs1 gallate decarboxylase involved in tannin degradation.lactobacillus plantarum is a lactic acid bacterium able to degrade tannins by the subsequent action of tannase and gallate decarboxylase enzymes. the gene encoding tannase had previously been identified, whereas the gene encoding gallate decarboxylase is unknown. sodium dodecyl sulfate-polyacrylamide gel electrophoresis (sds-page) of gallic-acid induced l. plantarum extracts showed a 54-kda protein which was absent in the uninduced cells. this protein was identified as lp_2945, putatively annota ...201323645198
microbial production of isoprenoids enabled by synthetic biology.microorganisms transform inexpensive carbon sources into highly functionalized compounds without toxic by-product generation or significant energy consumption. by redesigning the natural biosynthetic pathways in an industrially suited host, microbial cell factories can produce complex compounds for a variety of industries. isoprenoids include many medically important compounds such as antioxidants and anticancer and antimalarial drugs, all of which have been produced microbially. while a biosynt ...201323577007
new insight into the cleavage reaction of nostoc sp. strain pcc 7120 carotenoid cleavage dioxygenase in natural and nonnatural carotenoids.carotenoid cleavage dioxygenases (ccds) are enzymes that catalyze the oxidative cleavage of carotenoids at a specific double bond to generate apocarotenoids. in this study, we investigated the activity and substrate preferences of nsc3, a ccd of nostoc sp. strain pcc 7120, in vivo and in vitro using natural and nonnatural carotenoid structures. nsc3 cleaved β-apo-8'-carotenal at 3 positions, c-13 c-14, c-15 c-15', and c-13' c-14', revealing a unique cleavage pattern. nsc3 cleaves the natural str ...201323524669
an in-depth analysis of a multilocus phylogeny identifies leus as a reliable phylogenetic marker for the genus pantoea.partial sequences of six core genes (fusa, gyrb, leus, pyrg, rlpb, and rpob) of 37 strains of pantoea species were analyzed in order to obtain a comprehensive view regarding the phylogenetic relationships within the pantoea genus and compare tree topologies to identify gene(s) for reliable species and subspecies differentiation. all genes used in this study were effective at species-level delineation, but the internal nodes represented conflicting common ancestors in fusa- and pyrg-based phyloge ...201425125967
tomato carotenoid cleavage dioxygenases 1a and 1b: relaxed double bond specificity leads to a plenitude of dialdehydes, mono-apocarotenoids and isoprenoid volatiles.the biosynthetic processes leading to many of the isoprenoid volatiles released by tomato fruits are still unknown, though previous reports suggested a clear correlation with the carotenoids contained within the fruit. in this study, we investigated the activity of the tomato (solanum lycopersicum) carotenoid cleavage dioxygenase (slccd1b), which is highly expressed in fruits, and of its homolog slccd1a. using in vitro assays performed with purified recombinant enzymes and by analyzing products ...201425057464
alternative splicing of transcripts from crti and crtyb genes of xanthophyllomyces dendrorhous.xanthophyllomyces dendrorhous is one of the relevant sources of the carotenoid astaxanthin. in this paper, we describe for the first time cloning of unexpected cdnas obtained from the crti and crtyb genes of x. dendrorhous strain ucd 67-385. the cdna of the crti gene conserves 80 bp of the first intron, while the cdna of the crtyb gene conserves 55 bp of the first intron and lacks 111 bp of the second exon. the crti and crtyb rnas could be spliced in alternative splice sites, which produced alte ...200312902257
a high-throughput colorimetric screening assay for terpene synthase activity based on substrate consumption.terpene synthases catalyze the formation of a variety of terpene chemical structures. systematic mutagenesis studies have been effective in providing insights into the characteristic and complex mechanisms of c-c bond formations and in exploring the enzymatic potential for inventing new chemical structures. in addition, there is growing demand to increase terpene synthase activity in heterologous hosts, given the maturation of metabolic engineering and host breeding for terpenoid synthesis. we h ...201424681801
enhancing the health-promoting effects of tomato fruit for biofortified food.consumption of tomato fruits, like those of many other plant species that are part of the human diet, is considered to be associated with several positive effects on health. indeed, tomato fruits are an important source of bioactive compounds with known beneficial effects including vitamins, antioxidants, and anticancer substances. in particular, antioxidant metabolites are a group of vitamins, carotenoids, phenolic compounds, and phenolic acid that can provide effective protection by neutralizi ...201424744504
molecular and functional characterization of a novel chromoplast-specific lycopene beta-cyclase from citrus and its relation to lycopene accumulation.carotenoids are the main pigments responsible of the colouration of citrus fruits. the beta-cyclization of lycopene, catalysed by the lycopene beta-cyclases (beta-lcy), seems to be a key regulatory step of the carotenoid pathway. in the present study, two beta-lcys from orange fruits (citrus sinensis), named csbeta-lcy1 and csbeta-lcy2 have been isolated and the activity of the encoded proteins was demonstrated by functional analysis. csbeta-lcy1 was expressed at low levels and remained relative ...200919325166
the dual role of phytoene synthase genes in carotenogenesis in carrot roots and leaves.carrot (daucus carota l.) is an important food crop and is useful for studying carotenogenesis due to the quantity and diversity of carotenoids in its roots. phytoene synthase catalyzes the first committed step in the carotenoid biosynthesis pathway, and its overexpression is the main driving force in the orange phenotype. at present, we lack fundamental knowledge of the role of these genes and their effects on carotenoid accumulation in leaves. in the present study, three backcross inbred lines ...201426316840
draft genome sequences of the onion center rot pathogen pantoea ananatis pa4 and maize brown stalk rot pathogen p. ananatis bd442.pantoea ananatis is an emerging phytopathogen that infects a broad spectrum of plant hosts. here, we present the genomes of two south african isolates, p. ananatis pa4, which causes center rot of onion, and bd442, isolated from brown stalk rot of maize.201425103759
culturable bacterial endophytes isolated from mangrove tree (rhizophora apiculata blume) enhance seedling growth in rice.endophytic bacteria do have several potential applications in medicine and in other various sectors of biotechnology including agriculture. bacterial endophytes need to be explored for their potential applications in agricultural biotechnology. one of the potential applications of bacterial endophytes in agricultural is to enhance the growth of the agricultural crops. hence, this study was undertaken to explore the plant growth promoting potential application of bacterial endophytes.201425097431
genetic stability developed for β-carotene synthesis in br29 rice line using dihaploid homozygosity.obtaining transgenic crop lines with stable levels of carotenoids is highly desirable. we addressed this issue by employing the anther culture technique to develop dihaploid lines containing genes involved in β-carotene metabolism. first, we used agrobacterium- mediated transformation to develop primary transgenic plants containing the β-carotene biosynthetic genes, phytoene synthase (psy) and phytoene desaturase (crti), which were engineered for expression and accumulation in the endosperm. tra ...201424937154
structure of a heterotetrameric geranyl pyrophosphate synthase from mint (mentha piperita) reveals intersubunit regulation.terpenes (isoprenoids), derived from isoprenyl pyrophosphates, are versatile natural compounds that act as metabolism mediators, plant volatiles, and ecological communicators. divergent evolution of homomeric prenyltransferases (ptss) has allowed ptss to optimize their active-site pockets to achieve catalytic fidelity and diversity. little is known about heteromeric ptss, particularly the mechanisms regulating formation of specific products. here, we report the crystal structure of the (lsu . ss ...201020139160
triterpenoid biosynthesis and engineering in plants.triterpenoid saponins are a diverse group of natural products in plants and are considered defensive compounds against pathogenic microbes and herbivores. because of their various beneficial properties for humans, saponins are used in wide-ranging applications in addition to medicinally. saponin biosynthesis involves three key enzymes: oxidosqualene cyclases, which construct the basic triterpenoid skeletons; cytochrome p450 monooxygenases, which mediate oxidations; and uridine diphosphate-depend ...201122639586
nutritional aspects of phytoene and phytofluene, carotenoid precursors to lycopene.epidemiological studies suggest an inverse relationship between tomato consumption and serum and tissue lycopene (lyc) levels with risk of some chronic diseases, including several cancers and cardiovascular disease. lyc, the red carotenoid found in tomatoes, is often considered to be the primary bioactive carotenoid in tomatoes that mediates health benefits, but other colorless precursor carotenoids, phytoene (pe) and phytofluene (pf), are also present in substantial quantities. pe and pf are re ...201122211189
genome sequence of the aerobic arsenate-reducing bacterium pantoea sp. strain imh.we here report the draft assembly for the genome of pantoea sp. strain imh, isolated from arsenic-contaminated soil in inner mongolia, china, with the ability to aerobically reduce arsenate to arsenite. the genome sequence will allow for the characterization of the molecular mechanisms of arsenate reduction.201424723713
identification and characterization of antigens as vaccine candidates against klebsiella pneumoniae.nosocomial infections, also called "hospital acquired infections," occur worldwide and affect both developed and resource-poor countries, thus having a major impact on their health care systems. klebsiella pneumoniae, which is an opportunistic gram-negative pathogen, is responsible for causing pneumonia, urinary tract infections and septicemia in immune compromised hosts such as neonates. unfortunately, there is no vaccine or mab available for prophylactic or therapeutic use against k. pneumonia ...201223250007
high-level production of the industrial product lycopene by the photosynthetic bacterium rhodospirillum rubrum.the biosynthesis of the major carotenoid spirilloxanthin by the purple nonsulfur bacterium rhodospirillum rubrum is thought to occur via a linear pathway proceeding through phytoene and, later, lycopene as intermediates. this assumption is based solely on early chemical evidence (b. h. davies, biochem. j. 116:93-99, 1970). in most purple bacteria, the desaturation of phytoene, catalyzed by the enzyme phytoene desaturase (crti), leads to neurosporene, involving only three dehydrogenation steps an ...201222865070
carotenoid biosynthesis and overproduction in corynebacterium glutamicum.corynebacterium glutamicum contains the glycosylated c50 carotenoid decaprenoxanthin as yellow pigment. starting from isopentenyl pyrophosphate, which is generated in the non-mevalonate pathway, decaprenoxanthin is synthesized via the intermediates farnesyl pyrophosphate, geranylgeranyl pyrophosphate, lycopene and flavuxanthin.201222963379
polyphyly of gut symbionts in stinkbugs of the family cydnidae.symbiotic bacteria associated with midgut crypts of stinkbugs of the family cydnidae, representing seven species and 13 populations, were investigated. all of the symbionts were species specific, and constituted at least four distinct lineages in the gammaproteobacteria, indicating multiple evolutionary origins of the gut symbionts among the burrower bugs.201222544238
carotenoids play a positive role in the degradation of heterocycles by sphingobium yanoikuyae.microbial oxidative degradation is a potential way of removing pollutants such as heterocycles from the environment. during this process, reactive oxygen species or other oxidants are inevitably produced, and may cause damage to dna, proteins, and membranes, thereby decreasing the degradation rate. carotenoids can serve as membrane-integrated antioxidants, protecting cells from oxidative stress.201222745775
the functional network of the arabidopsis plastoglobule proteome based on quantitative proteomics and genome-wide coexpression analysis.plastoglobules (pgs) in chloroplasts are thylakoid-associated monolayer lipoprotein particles containing prenyl and neutral lipids and several dozen proteins mostly with unknown functions. an integrated view of the role of the pg is lacking. here, we better define the pg proteome and provide a conceptual framework for further studies. the pg proteome from arabidopsis (arabidopsis thaliana) leaf chloroplasts was determined by mass spectrometry of isolated pgs and quantitative comparison with the ...201222274653
identification of a third osmoprotectant transport system, the osmu system, in salmonella enterica.the growth of salmonella enterica serovar typhimurium mutants lacking the prop and prou osmoprotectant transport systems is stimulated by glycine betaine in high-osmolarity media, suggesting that this organism has an additional osmoprotectant transport system. bioinformatic analysis revealed that the genome of this organism contains a hitherto-unidentified operon, designated osmu, consisting of four genes whose products show high similarity to abc-type transport systems for osmoprotectants in ot ...201222609924
genome sequence and description of pantoea septica strain ff5.strain ff5 was isolated from the skin flora of a healthy senegalese 35-year-old woman. this strain was identified as belonging to the species pantoea septica based on rpob sequence identity of 99.7 % with pantoea septica strain lmg 5345(t) and a highest maldi-tof-ms score of 2.3 with pantoea septica. like p. septica, this ff5 strain is a gram-negative, aerobic, motile, and rod-shaped bacterium. currently, 17 genomes have been sequenced within the genus pantoea but none for pantoea septica. herei ...201526568786
quantitative effect of target translation on small rna efficacy reveals a novel mode of interaction.small regulatory rnas (srnas) in bacteria regulate many important cellular activities under normal conditions and in response to stress. many srnas bind to the mrna targets at or near the 5' untranslated region (utr) resulting in translation inhibition and accelerated degradation. often the srna-binding site is adjacent to or overlapping with the ribosomal binding site (rbs), suggesting a possible interplay between srna and ribosome binding. here we combine quantitative experiments with mathemat ...201425294829
genomic resource of rice seed associated bacteria. 201526793183
genomic resource of rice seed associated bacteria. 201526793183
methods for baiting and enriching fungus-feeding (mycophagous) rhizosphere bacteria.mycophagous soil bacteria are able to obtain nutrients from living fungal hyphae. however, with exception of the soil bacterial genus collimonas, occurrence of this feeding strategy has not been well examined. evaluation of the importance of mycophagy in soil bacterial communities requires targeted isolation methods. in this study, we compared two different approaches to obtain mycophagous bacteria from rhizospheric soil. a short-term method based on baiting for bacteria that can rapidly adhere ...201526733962
flux balance analysis inspired bioprocess upgrading for lycopene production by a metabolically engineered strain of yarrowia lipolytica.genome-scale metabolic models embody a significant advantage of systems biology since their applications as metabolic flux simulation models enable predictions for the production of industrially-interesting metabolites. the biotechnological production of lycopene from yarrowia lipolytica is an emerging scope that has not been fully scrutinized, especially for what concerns cultivation conditions of newly generated engineered strains. in this study, by combining flux balance analysis (fba) and pl ...201526703753
improved production of biohydrogen in light-powered escherichia coli by co-expression of proteorhodopsin and heterologous hydrogenase.solar energy is the ultimate energy source on the earth. the conversion of solar energy into fuels and energy sources can be an ideal solution to address energy problems. the recent discovery of proteorhodopsin in uncultured marine γ-proteobacteria has made it possible to construct recombinant escherichia coli with the function of light-driven proton pumps. protons that translocate across membranes by proteorhodopsin generate a proton motive force for atp synthesis by atpase. excess protons can ...201222217184
dna assembler method for construction of zeaxanthin-producing strains of saccharomyces cerevisiae.dna assembler enables design and rapid construction of biochemical pathways in a one-step fashion by exploitation of the in vivo homologous recombination mechanism in saccharomyces cerevisiae. it has many applications in pathway engineering, metabolic engineering, combinatorial biology, and synthetic biology. here we use the zeaxanthin biosynthetic pathway as an example to describe the key steps in the construction of pathways containing multiple genes using the dna assembler approach. methods f ...201222711131
genome sequence of pantoea ananatis strain cfh 7-1, which is associated with a vector-borne cotton fruit disease.pantoea ananatis is a bacterium with versatile niches that vary from pathogenic to beneficial. we present the genome of strain cfh 7-1, which was recovered from a diseased greenhouse cotton boll previously caged with a field-collected cotton fleahopper (pseudatomoscelis seriatus). these data will assist in deciphering the infection process.201526358602
optimized agrobacterium-mediated sorghum transformation protocol and molecular data of transgenic sorghum plants.agrobacterium-mediated sorghum transformation frequency has been enhanced significantly via medium optimization using immature embryos from sorghum variety tx430 as the target tissue. the new transformation protocol includes the addition of elevated copper sulfate and 6-benzylaminopurine in the resting and selection media. using agrobacterium strain lba4404, the transformation frequency reached over 10% using either of two different selection marker genes, mopat or pmi, and any of three differen ...201326316679
optimized agrobacterium-mediated sorghum transformation protocol and molecular data of transgenic sorghum plants.agrobacterium-mediated sorghum transformation frequency has been enhanced significantly via medium optimization using immature embryos from sorghum variety tx430 as the target tissue. the new transformation protocol includes the addition of elevated copper sulfate and 6-benzylaminopurine in the resting and selection media. using agrobacterium strain lba4404, the transformation frequency reached over 10% using either of two different selection marker genes, mopat or pmi, and any of three differen ...201326316679
subchromoplast sequestration of carotenoids affects regulatory mechanisms in tomato lines expressing different carotenoid gene combinations.metabolic engineering of the carotenoid pathway in recent years has successfully enhanced the carotenoid contents of crop plants. it is now clear that only increasing biosynthesis is restrictive, as mechanisms to sequestrate these increased levels in the cell or organelle should be exploited. in this study, biosynthetic pathway genes were overexpressed in tomato (solanum lycopersicum) lines and the effects on carotenoid formation and sequestration revealed. the bacterial crt carotenogenic genes, ...201324249831
comparative genomics reveals that a fish pathogenic bacterium edwardsiella tarda has acquired the locus of enterocyte effacement (lee) through horizontal gene transfer.edwardsiella tarda is an enterobacterium which causes edwardsiellosis, a fatal disease of cultured fishes such as red sea bream, eel, and flounder. preventing the occurrence of e. tarda infection has thus been an important issue in aquaculture. e. tarda has been isolated from other animals and from many environments; however, the relationship between the genotype and evolutionary process of this pathogen is not fully understood. to clarify this relationship, we sequenced and compared the genomes ...201324053667
analysis of l-glutamic acid fermentation by using a dynamic metabolic simulation model of escherichia coli.understanding the process of amino acid fermentation as a comprehensive system is a challenging task. previously, we developed a literature-based dynamic simulation model, which included transcriptional regulation, transcription, translation, and enzymatic reactions related to glycolysis, the pentose phosphate pathway, the tricarboxylic acid (tca) cycle, and the anaplerotic pathway of escherichia coli. during simulation, cell growth was defined such as to reproduce the experimental cell growth p ...201324053676
levels of lycopene β-cyclase 1 modulate carotenoid gene expression and accumulation in daucus carota.plant carotenoids are synthesized and accumulated in plastids through a highly regulated pathway. lycopene β-cyclase (lcyb) is a key enzyme involved directly in the synthesis of α-carotene and β-carotene through the cyclization of lycopene. carotenoids are produced in both carrot (daucus carota) leaves and reserve roots, and high amounts of α-carotene and β-carotene accumulate in the latter. in some plant models, the presence of different isoforms of carotenogenic genes is associated with an org ...201323555569
construction and engineering of large biochemical pathways via dna assembler.dna assembler enables rapid construction and engineering of biochemical pathways in a one-step fashion by exploitation of the in vivo homologous recombination mechanism in saccharomyces cerevisiae. it has many applications in pathway engineering, metabolic engineering, combinatorial biology, and synthetic biology. here we use two examples including the zeaxanthin biosynthetic pathway and the aureothin biosynthetic gene cluster to describe the key steps in the construction of pathways containing ...201323996442
engineered biosynthesis of natural products in heterologous hosts.natural products produced by microorganisms and plants are a major resource of antibacterial and anticancer drugs as well as industrially useful compounds. however, the native producers often suffer from low productivity and titers. here we summarize the recent applications of heterologous biosynthesis for the production of several important classes of natural products such as terpenoids, flavonoids, alkaloids, and polyketides. in addition, we will discuss the new tools and strategies at multi-s ...201525960127
sunlight-induced rapid and efficient biogenic synthesis of silver nanoparticles using aqueous leaf extract of ocimum sanctum linn. with enhanced antibacterial activity.nanotechnology is now regarded as a distinct field of research in modern science and technology with multifaceted areas including biomedical applications. among the various approaches currently available for the generation of metallic nanoparticles, biogenic synthesis is of increasing demand for the purpose of green nanotechnology. among various natural sources, plant materials are the most readily available template-directing matrix offering cost-effectiveness, eco-friendliness, and easy handli ...201425621198
functional analysis of the brassica napus l. phytoene synthase (psy) gene family.phytoene synthase (psy) has been shown to catalyze the first committed and rate-limiting step of carotenogenesis in several crop species, including brassica napus l. due to its pivotal role, psy has been a prime target for breeding and metabolic engineering the carotenoid content of seeds, tubers, fruits and flowers. in arabidopsis thaliana, psy is encoded by a single copy gene but small psy gene families have been described in monocot and dicotyledonous species. we have recently shown that psy ...201425506829
transcription interference and orf nature strongly affect promoter strength in a reconstituted metabolic pathway.fine tuning of individual enzyme expression level is necessary to alleviate metabolic imbalances in synthetic heterologous pathways. a known approach consists of choosing a suitable combination of promoters, based on their characterized strengths in model conditions. we questioned whether each step of a multiple-gene synthetic pathway could be independently tunable at the transcription level. three open reading frames, coding for enzymes involved in a synthetic pathway, were combinatorially asso ...201525767795
transgenic multivitamin corn through biofortification of endosperm with three vitamins representing three distinct metabolic pathways.vitamin deficiency affects up to 50% of the world's population, disproportionately impacting on developing countries where populations endure monotonous, cereal-rich diets. transgenic plants offer an effective way to increase the vitamin content of staple crops, but thus far it has only been possible to enhance individual vitamins. we created elite inbred south african transgenic corn plants in which the levels of 3 vitamins were increased specifically in the endosperm through the simultaneous m ...200919416835
comparative proteomic analysis of labellum and inner lateral petals in cymbidium ensifolium flowers.the labellum in orchids shares homology with the inner lateral petals of the flower. the labellum is a modified petal and often distinguished from other petals and sepals due to its large size and irregular shape. herein, we combined two-dimensional gel electrophoresis (2-de) and matrix assisted laser desorption/ionization time of flight/time of flight (maldi-tof/tof) approaches to identify the differentially expressed proteome between labellum and inner lateral petal in one of orchid species (c ...201425365177
metabolomics of genetically modified crops.metabolomic-based approaches are increasingly applied to analyse genetically modified organisms (gmos) making it possible to obtain broader and deeper information on the composition of gmos compared to that obtained from traditional analytical approaches. the combination in metabolomics of advanced analytical methods and bioinformatics tools provides wide chemical compositional data that contributes to corroborate (or not) the substantial equivalence and occurrence of unintended changes resultin ...201425334064
serotype-converting bacteriophage sfii encodes an acyltransferase protein that mediates 6-o-acetylation of glcnac in shigella flexneri o-antigens, conferring on the host a novel o-antigen epitope.shigella flexneri o-antigen is an important and highly variable cell component presented on the outer leaflet of the outer membrane. most shigella flexneri bacteria share an o-antigen backbone composed of →2)-α-l-rhap(iii)-(1→2)-α-l-rhap(ii)-(1→3)-α-l-rhap(i)-(1→3)-β-d-glcpnac-(1→ repeats, which can be modified by adding various chemical groups to different sugars, giving rise to diverse o-antigen structures and, correspondingly, to various serotypes. the known modifications include glucosylatio ...201425112477
mechanisms of tolerance and high degradation capacity of the herbicide mesotrione by escherichia coli strain dh5-α.the intensive use of agrochemicals has played an important role in increasing agricultural production. one of the impacts of agrochemical use has been changes in population structure of soil microbiota. the aim of this work was to analyze the adaptive strategies that bacteria use to overcome oxidative stress caused by mesotrione, which inhibits 4-hydroxyphenylpyruvate dioxygenase. we also examined antioxidative stress systems, saturation changes of lipid membranes, and the capacity of bacteria t ...201424924203
draft genome sequence of pantoea ananatis strain lmg 2665t, a bacterial pathogen of pineapple fruitlets.we report the draft genome sequence of pantoea ananatis lmg 2665(t), the bacterial causal agent of pineapple fruitlet rot.201424855311
improving industrial yeast strains: exploiting natural and artificial diversity.yeasts have been used for thousands of years to make fermented foods and beverages, such as beer, wine, sake, and bread. however, the choice for a particular yeast strain or species for a specific industrial application is often based on historical, rather than scientific grounds. moreover, new biotechnological yeast applications, such as the production of second-generation biofuels, confront yeast with environments and challenges that differ from those encountered in traditional food fermentati ...201424724938
discovery of function in the enolase superfamily: d-mannonate and d-gluconate dehydratases in the d-mannonate dehydratase subgroup.the continued increase in the size of the protein sequence databases as a result of advances in genome sequencing technology is overwhelming the ability to perform experimental characterization of function. consequently, functions are assigned to the vast majority of proteins via automated, homology-based methods, with the result that as many as 50% are incorrectly annotated or unannotated ( schnoes et al. plos comput. biol. 2009 , 5 ( 12 ), e1000605 ). this manuscript describes a study of the d ...201424697546
enrichment of provitamin a content in wheat (triticum aestivum l.) by introduction of the bacterial carotenoid biosynthetic genes crtb and crti.carotenoid content is a primary determinant of wheat nutritional value and affects its end-use quality. wheat grains contain very low carotenoid levels and trace amounts of provitamin a content. in order to enrich the carotenoid content in wheat grains, the bacterial phytoene synthase gene (crtb) and carotene desaturase gene (crti) were transformed into the common wheat cultivar bobwhite. expression of crtb or crti alone slightly increased the carotenoid content in the grains of transgenic wheat ...201424692648
bacterial communities on classroom surfaces vary with human contact.humans can spend the majority of their time indoors, but little is known about the interactions between the human and built-environment microbiomes or the forces that drive microbial community assembly in the built environment. we sampled 16s rrna genes from four different surface types throughout a university classroom to determine whether bacterial assemblages on each surface were best predicted by routine human interactions or by proximity to other surfaces within the classroom. we then analy ...201424602274
reconstruction of the carotenoid biosynthetic pathway of cronobacter sakazakii baa894 in escherichia coli.cronobacter sakazakii could form yellow-pigmented colonies. however, the chemical structure and the biosynthetic pathway of the yellow pigments have not been identified. in this study, the yellow pigments of c. sakazakii baa894 were purified and analyzed. the major components of the yellow pigments were confirmed as zeaxanthin-monoglycoside and zeaxanthin-diglycoside. a gene cluster containing seven genes responsible for the yellow pigmentation in c. sakazakii baa894 was identified. the seven ge ...201424466219
biotechnological production of carotenoids by yeasts: an overview.nowadays, carotenoids are valuable molecules in different industries such as chemical, pharmaceutical, poultry, food and cosmetics. these pigments not only can act as vitamin a precursors, but also they have coloring and antioxidant properties, which have attracted the attention of the industries and researchers. the carotenoid production through chemical synthesis or extraction from plants is limited by low yields that results in high production costs. this leads to research of microbial produc ...201424443802
h-nst induces lee expression and the formation of attaching and effacing lesions in enterohemorrhagic escherichia coli.enteropathogenic e. coli (epec) and enterohemorrhagic e. coli are important causes of morbidity and mortality worldwide. these enteric pathogens contain a type iii secretion system (t3ss) responsible for the attaching and effacing (a/e) lesion phenotype. the t3ss is encoded by the locus of enterocyte effacement (lee) pathogenicity island. the h-ns-mediated repression of lee expression is counteracted by ler, the major activator of virulence gene expression in a/e pathogens. a regulator present i ...201424466172
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