• The Plant Pathology Journal
• /
• v.29 no.1
• /
• pp.59-66
• /
• 2013

Colonization studies previously performed with a green-fluorescent-protein, GFP, labeled derivative of Bacillus amyloliquefaciens FZB42 revealed that the bacterium behaved different in colonizing surfaces of plant roots of different species (Fan et al., 2012). In order to extend these studies and to elucidate which genes are crucial for root colonization, we applied targeted mutant strains to Arabidopsis seedlings. The fates of root colonization in mutant strains impaired in synthesis of alternative sigma factors, non-ribosomal synthesis of lipopeptides and polyketides, biofilm formation, swarming motility, and plant growth promoting activity were analyzed by confocal laser scanning microscopy. Whilst the wild-type strain heavily colonized surfaces of root tips and lateral roots, the mutant strains were impaired in their ability to colonize root tips and most of them were unable to colonize lateral roots. Ability to colonize plant roots is not only dependent on the ability to form biofilms or swarming motility. Six mutants, deficient in abrB-, sigH-, sigD-, nrfA-, yusV and RBAM017410, but not affected in biofilm formation, displayed significantly reduced root colonization. The nrfA- and yusV-mutant strains colonized border cells and, partly, root surfaces but did not colonize root tips or lateral roots.

• Biomolecules & Therapeutics
• /
• v.15 no.3
• /
• pp.192-198
• /
• 2007

Emodin (1,3,8-trihydroxy-6-methylanthraquinone) is a major constituent of rhubarb. Although it has been claimed to have a wild spectrum of therapeutic value, its side effects, especially in human kidney cells have not been well characterized. In this study, we have carried out in vitro genetic toxicity test of emodin and microarray analysis of differentially expressed genes in response to emodin. The result of Ames test showed mutations with emodin treatment in base substitution strain TA1535 both with and without exogenous metabolic activation. Likewise, emodin showed mutations in frame shift TA98 both with and without exogenous metabolic activation. The result of COMET assay in L5178Y cells with emodin treatment showed DNA damage both with and without exogenous metabolic activation. Emodin did not increase micronuclei in CHO cells both with and without exogenous metabolic activation. 150 Genes were selected as differentially expressed genes in response to emodin by microarray analysis and these genes would be candidate biomarkers of genetic toxic action of emodin.

• Journal of Life Science
• /
• v.11 no.2
• /
• pp.94-98
• /
• 2001

Type I signal peptidase cleaves the signal sequence from the amino terminus of membrane and secreted proteins afters these protein insert across the membrane. This enzyme serves as a potential target for the development of novel antibacterial agents due to its unique physiological and biochemical properties. Despite considerable research, the signal peptidase assay still remains improvement to provide further understanding of the mechanism and high-throughput inhibitor screening of this enzyme. In this paper, three known signal peptidase assays are tested with an E. coli D276A mutant signal peptidase to distinguish the sensitivity of each assays. In vitro assay using the procoat synthesized by in vitro transcription translation shows that the D276A signal peptidase I was inactive while in vivo processing of pro-OmpA expressed in the temperature-sensitive E. coli strain IT41 as well as in vitro assay using pro-OmpA nuclease A substrate show that D276A signal peptidase I has activity like wild-type signal peptidase. These results suggest that in vitro assay using the pro-OmpA nuclease A and in vivo pro-OmpA processing assay are more sensitive monitors than in vitro assay using the pro-coat. In conculsion, caution should be used when interpreting the in vitro results using the procoat.

• Molecules and Cells
• /
• v.39 no.3
• /
• pp.204-210
• /
• 2016

DNA damage responses are important for the maintenance of genome stability and the survival of organisms. Such responses are activated in the presence of DNA damage and lead to cell cycle arrest, apoptosis, and DNA repair. In Caenorhabditis elegans, double-strand breaks induced by DNA damaging agents have been detected indirectly by antibodies against DSB recognizing proteins. In this study we used a comet assay to detect DNA strand breaks and to measure the elimination of DNA strand breaks in mitotic germline nuclei of C. elegans. We found that C. elegans brc-1 mutants were more sensitive to ionizing radiation and camptothecin than the N2 wild-type strain and repaired DNA strand breaks less efficiently than N2. This study is the first demonstration of direct measurement of DNA strand breaks in mitotic germline nuclei of C. elegans. This newly developed assay can be applied to detect DNA strand breaks in different C. elegans mutants that are sensitive to DNA damaging agents.

• Journal of Microbiology and Biotechnology
• /
• v.20 no.5
• /
• pp.875-880
• /
• 2010

Bacterial enoyl-ACP reductase (FabI) has been demonstrated to be a novel antibacterial target. In the course of our screening for FabI inhibitors, we isolated two methyl-branched fatty acids from Streptomyces sp. A251. They were identified as 14-methyl-9(Z)-pentadecenoic acid and 15-methyl-9(Z)-hexadecenoic acid by MS and NMR spectral data. These compounds inhibited Staphylococcus aureus FabI with $IC_{50}$ values of 16.0 and $16.3\;{\mu}M$, respectively, but did not affect FabK, an enoyl-ACP reductase of Streptococcus pneumonia, at $100\;{\mu}M$. Consistent with their selective inhibition for FabI, they blocked intracellular fatty acid synthesis as well as the growth of S. aureus, but did not inhibit the growth of S. pneumonia. Additionally, these compounds showed reduced antibacterial activity against fabI-overexpressing S. aureus, compared with the wild-type strain. These results demonstrate that the methylbranched fatty acids show antibacterial activity by inhibiting FabI in vivo.

• KSBB Journal
• /
• v.8 no.1
• /
• pp.10-16
• /
• 1993

The use of Jerusalem artichoke containing $\beta$-1, 2-fructose oligomer for the production of D-sorbitol and L-sorbose has been studied. The employment of inulinase(0.398%, v/v) for the hydrolysis of 40% (v/w) Jerusalem artichoke juice resulted in 36.7g/1 of glucose and 85.3g/1 of fructose at $50^{\circ}C$. These sugars were utilized as substrates for D-sorbitol and L-sorbose production. Coimmobilization of inulinase and permeabilized cells of Zymomonas mobilis in the mixture of chitin (5%, w/e) and x-carrageenan(4%, w/v) resulted in the production of 30.2g/1 of D-sorbitol by using inulin as a substrate. The process of L-sorbose production from D-sorbitol by Gluconobacter suboxydans was optimized with respect to the substrate concentration, level of dissolved oxygen and glucosic and concentration. Gluconlc acid produced by Zymomonas mobilis from glucose was found to inhibit Gluconobacter suboxtans in conversion of D-sorbitol to L-sorbose. In view of removing such inhibitory effect by gluconic acid, mutants were selected by the NTG (N-methyl-N'-N'-nitro-N-nitrosoguanidlne) treated method. Mutants selected by NTG mutagenesis showed no inhibitory effects of gluconic acrid against L-sorbone production when its concentration increased up to 100g/1. A mutant produced 40.1g/l of L-sorbose in the medium containing 100g/l D-sorbitol and 100g/l-gluconic acid. This result is consider able when compared with L-sorbose concentration (21.7g/1) obtained from the fermentation with wild type strain of Gluconobacter suboxnians.

• Microbiology and Biotechnology Letters
• /
• v.13 no.4
• /
• pp.417-422
• /
• 1985

Streptococcus faecalis var. liquefaciens was examined for the presence of plasmid deoxyribonucleic acid. An analysis by agarose gel electrophoresis revealed the presence of at least four plasmids of approxymately 6.8, 5.2, 2.6, and 2.1 Mdal. Two plasmid cured strains were obtained by novobiocin treatment. SKR2, which lost 5.2 mdal plasmid (pSK2) and 2.1 Mdal plasmid(pSK4) was sensitive to lincomycin and erythromycin. However, all cured strains showed identical response as parental strain in sugar fermentation, temperature sensitivity, proteolytic activity, and liquefaction of gelatin. The results imply that pSK2 or pSK4 is associated with antibiotic resistance of Str. faecalis var. liquefaciens.

• Journal of Microbiology and Biotechnology
• /
• v.17 no.2
• /
• pp.244-252
• /
• 2007

Escherichia coli has a PhoR-PhoB two-component regulatory system to detect and respond to the changes of environmental phosphate concentration. For the E. coli W3110 strain growing under phosphate-limiting condition, the changes of global gene expression levels were investigated by using DNA microarray analysis. The expression levels of some genes that are involved in phosphate metabolism were increased as phosphate became limited, whereas those of the genes involved in ribosomal protein or amino acid metabolism were decreased, owing to the stationary phase response. The upregulated genes could be divided into temporarily and permanently inducible genes by phosphate starvation. At the peak point showing the highest expression levels of the phoB and phoR genes under phosphate-limiting condition, the phoB- and/or phoR-dependent regulatory mechanisms were investigated in detail by comparing the gene expression levels among the wild-type and phoB and/or phoR mutant strains. Overall, the phoB mutation was epistatic over the phoR mutation. It was found that PhoBR and PhoB were responsible for the upregulation of the phosphonate or glycerol phosphate metabolism and high-affinity phosphate transport system, respectively. These results show the complex regulation by the PhoR-PhoB two-component regulatory system in E. coli.

• Journal of Microbiology and Biotechnology
• /
• v.17 no.5
• /
• pp.830-839
• /
• 2007

Pradimicins are potent antifungal antibiotics having an unusual dihydrobenzo[$\alpha$]naphthacenequinone aglycone substituted with D-alanine and sugars. Pradimicins are polyketide antibiotics produced by Actinomadura hibisca P157-2. The gene cluster involved in the biosynthesis of pradimicins was cloned and sequenced. The pradimicin gene cluster was localized to a 39-kb DNA segment and its involvement in the biosynthesis of pradimicin was proven by gene inactivation of prmA and prmB(ketosynthases $\alpha\;and\;\beta$). The pradimicin gene cluster consists of 28 open reading frames(ORFs), encoding a type II polyketide synthase(PKS), the enzymes involved in sugar biosynthesis and tailoring enzymes as well as two resistance proteins. The deduced proteins showed strong similarities to the previously validated gene clusters of angucyclic polyketides such as rubromycin, griseorhodin, and fredericamycin. From the pradimicin gene cluster, prmP3 encoding a component of the acetyl-CoA carboxylase complex was disrupted. The production levels of pradimicins of the resulting mutants decreased to 62% of the level produced by the wild-type strain, which indicate that the acetyl-CoA carboxylase gene would have a significant role in the production of pradimicins through supplying the extender unit precursor, malonyl-CoA.

• Journal of Microbiology
• /
• v.38 no.4
• /
• pp.245-249
• /
• 2000

Catabolic pathways for the degradation of various aromatics by Sphingomonas yanoikuyae Bl are intertwined, joining at the level of substituted benzoates, which are further degraded vita ring cleavage reactions. The mutant strain EK497, which was constructed by deleting a large DNA region containing most of the genes for biphenyl, naphthalene, m-xylene, and m-toluate degradation, was unable to grow on all of the aromatics tested except for benzoate as the sole source of carbon and energy.S. yanoikuyae EK497 was found to possess only catechol ortho-ring cleavage activity due to deletion of the genes for the meta-cleavage pathway. Wild-type S. yanoikuyae Bl grown on benzoate has both catechol orthoand meta-cleavage activity. However, m-xylene and m-toluate, which are metabolized through methylbenzoate, and biphenyl, which is metabolized through benzoate, induce only the meta-cleavage pathway, suggesting the presence of a substrate-dependent induction mechanism.