Rice OsERG3 encodes an unusual small C2-domain protein containing a Ca(2+)-binding module but lacking phospholipid-binding properties.

BACKGROUND: The C2 domain is a Ca(2+)/phospholipid-binding motif found in many proteins involved in signal transduction or membrane trafficking. OsERG3 is a homolog of OsERG1, a gene encoding a small C2-domain protein in rice. METHODS: OsERG3 Ca(2+)-binding and phospholipid-binding assays were carried out using (3)H-labeled phospholipid liposomes and a (45)Ca(2+) overlay assay, respectively. Cytosolic expression of OsERG3 was investigated by Western blot analysis and the OsERG3::smGFP transient expression assay. RESULTS: OsERG3 transcript levels were greatly enhanced by treatment with a fungal elicitor and Ca(2+)-ionophore. OsERG3 protein proved unable to interact with phospholipids regardless of the presence or absence of Ca(2+) ions. Nonetheless, OsERG3 displayed calcium-binding activity in an in vitro(45)Ca(2+)-binding assay, a property not observed with OsERG1. The cytosolic location of OsERG3 was not altered by the presence of fungal elicitor or Ca(2+)-ionophore. CONCLUSIONS: OsERG3 encodes a small C2-domain protein consisting of a single C2 domain. OsERG3 binds Ca(2+) ions but not phospholipids. OsERG3 is a cytosolic soluble protein. The OsERG3 gene may play a role in signaling pathway involving Ca(2+) ions. GENERAL SIGNIFICANCE: The data demonstrate that OsERG3 is an unusual small C2-domain protein containing a Ca(2+)-binding module but lacking phospholipid-binding properties.

Silver-stained fibrin zymography: separation of proteases and activity detection using a single substrate-containing gel.

A new zymogram method, silver-stained fibrin zymography, for separation of protease bands and activity detection using a single substrate gel, was developed. The method takes advantage of the nanoscale sensitivity of both zymography and silver staining. After SDS-PAGE in a gel containing fibrin, the gel was incubated in enzyme reaction buffer and the zymogram was silver-stained. Bands with protease activity were stained with silver in clear areas where the protein substrate had been degraded. The molecular sizes of proteases were accurately determined. Furthermore, proteases of high molecular weight were clearly and sharply resolved.

Activity assay for nisin-like acidic bacteriocins using an optimal pH-conditioned gel matrix.

A new zymography for detecting nisin-like acidic bacteriocins was developed using a tricine-sodium dodecyl sulfate (SDS) gel and an acidic gel matrix (pH 4.0). After electrophoresis, proteins in the tricine gel were electrotransferred to an optimal pH-conditioned gel matrix (OP-CGM). The OP-CGM was overlaid with indicator cells (Bacillus cereus) embedded in nutrient broth soft agar (0.8%, w/v). Antibacterial activity shown as a growth inhibition using B. cereus was detected at approximately 3.8kDa. Because nisin is unstable in buffers at pH values over 6.0, the common electrophoretic systems, SDS-polyacrylamide gel electrophoresis and tricine gel, are not suitable for detection of nisin-like acidic bacteriocins.

Production of pure beta-glucan by Aureobasidium pullulans after pullulan synthetase gene disruption.

By disruption of the pullulan synthetase gene (pul) of Aureobasidium pullulans IMS822 KCTC11179BP, we constructed a mutant strain, A. pullulans NP1221, which produced a pure beta-glucan exopolysaccharide. The mutant NP1221 was white, whereas the wild-type strain produced a black dye. When we compared fermentation kinetics between wide-type and mutant strains, the mutant NP1221 did not produce pullulan. Substrate uptake rate and beta-glucan production were similar in both strains. However, the biomass yield of mutant NP1221 was 2.3-fold (9.2 g l(-1)) greater than that of wild-type.

Diversity and abundance of ammonia-oxidizing bacteria in activated sludge treating different types of wastewater.

The diversity and abundance of ammonia-oxidizing bacteria (AOB) in activated sludge were compared using PCR-DGGE and real-time PCR assays. Activated sludge samples were collected from five different types of wastewater treatment plants (WWTPs) mainly treating textile, paper, food and livestock wastewater or domestic sewage. The composition of total bacteria determined by PCR-DGGE was highly diverse between the samples, whereas the community of AOB was similar across all the investigated activated sludge. Total bacterial numbers and AOB numbers in the aerated mixed liquor were in the range of 1.8x10(10) to 3.8x10(12) and 1.7x10(6) to 2.7x10(10) copies/l, respectively. Activated sludge from livestock, textile, and sewage treating WWTPs contained relatively high amoA gene copies (more than 10(5) copies/l) whereas activated sludge from food and paper WWTPs revealed the low number of amoA gene (less than 10(3) copies/L). The value of the amoA gene copy effectively showed the difference in composition of bacteria in different activated sludge samples and this was better than the measurement with the AOB 16S rRNA or total 16S rRNA gene. These results suggest that the quantification of the amoA gene can help monitor AOB and ammonia oxidation in WWTPs.

Ionizing radiation can induce GSK-3beta phosphorylation and NF-kappaB transcriptional transactivation in ATM-deficient fibroblasts.

DNA damage by ionizing radiation (IR) can induce activations of both NF-kappaB and p53 through the upstream kinase ataxia telangiectasia mutated (ATM). NF-kappaB activation could also be signaled through two distinct or overlapped pathways; IkappaB kinases (IKKs)-IkappaBalpha and Akt-glycogen synthase kinase-3 (GSK-3). In the present study, however, we show that activation of Akt1 and the subsequent phosphorylation and inactivation of GSK-3beta by IR could also occur in ATM-deficient AT5BIVA cells as well as in normal MRC5CV1 fibroblasts. Similarly, lithium chloride (LiCl) was found to increase the phosphorylation of GSK-3beta independently of ATM. Transfection with either wild-type or kinase dead mutant GSK-3beta to the cells further indicated that phosphorylations of Akt1 and GSK-3beta were closely associated with the transcriptional transactivation of NF-kappaB in response to ionizing radiation. On the other hand, LiCl, having no effect on caspase-3 activation, significantly increased p53 phosphorylation and apoptotic death of the normal MRC5CV1 cells while IR, activating both caspase-3 and p53, profoundly affected AT5BIVA cell death. Hence, our data suggest that although ATM-mediated IKK-IkappaBalpha pathway might be a typical pathway for IR-induced NF-kappaB activation, GSK-3beta phosphorylation could also partially contribute to the transcriptional transactivation of NF-kappaB in an ATM-independent manner and that GSK-3beta phosphorylation could induce ATM-mediated cell apoptosis through the activation of p53.

Monitoring bacterial population dynamics using real-time PCR during the bioremediation of crude-oil-contaminated soil.

We evaluated the activity and abundance of the crude oil- degrading bacterium Nocardia sp. H17-1 during bioremediation of oil-contaminated soil, using real-time PCR. The total petroleum hydrocarbon (TPH) degradation rate constants (k) of the soils treated with and without H17-1 were 0.103 d-1 and 0.028 d-1, respectively. The degradation rate constant was 3.6 times higher in the soil with H17-1 than in the soil without H17-1. In order to detect and quantify the Nocardia sp. H17-1 in soil samples, we quantified the genes encoding 16S ribosomal RNA (16S rRNA), alkane monooxygenase (alkB4), and catechol 2,3-dioxygenase (23CAT) with real-time PCR using SYBR green. The amounts of H17-1 16S rRNA and alkB4 detected increased rapidly up to 1,000-folds for the first 10 days, and then continued to increase only slightly or leveled off. However, the abundance of the 23CAT gene detected in H17-1-treated soil, where H17-1 had neither the 23CAT gene for the degradation of aromatic hydrocarbons nor the catechol 2,3-dioxygenase activity, did not differ significantly from that of the untreated soil (alpha=0.05, p>0.22). These results indicated that H17-1 is a potential candidate for the bioaugmentation of alkane-contaminated soil. Overall, we evaluated the abundance and metabolic activity of the bioremediation strain H17-1 using real-time PCR, independent of cultivation.

Monitoring of microbial diversity and activity during bioremediation of crude oil-contaminated soil with different treatments.

The present study compared the microbial diversity and activity during the application of various bioremediation processes to crude oil-contaminated soil. Five different treatments, including natural attenuation (NA), biostimulation (BS), biosurfactant addition (BE), bioaugmentation (BA), and a combined treatment (CT) of biostimulation, biosurfactant addition, and bioaugmentation, were used to analyze the degradation rate and microbial communities. After 120 days, the level of remaining hydrocarbons after all the treatments was similar, however, the highest rate (k) of total petroleum hydrocarbon (TPH) degradatioN was observed with the CT treatment (P < 0.05). The total bacterial counts increased during the first 2 weeks with all the treatments, and then remained stable. The bacterial communities and alkane monooxygenase gene fragment, alkB, were compared by denaturing gradient gel electrophoresis (DGGE). The DGGE analyses of the BA and CT treatments, which included Nocardia sp. H17-1, revealed a simple dominant population structure, compared with the other treatments. The Shannon-Weaver diversity index (H') and Simpson dominance index (D), calculated from the DGGE profiles using 16S rDNA, showed considerable qualitative differences in the community structure before and after the bioremediation treatment as well as between treatment conditions.

BRD-glucan exhibits potent immunochemotherapeutic activity in vitro and in vivo.

We carried out in vitro and in vivo assays to investigate the immunomodulatory and immunochemotherapeutic action mechanism of BRD-glucan, a high molecular weight ( approximately 3,500 kDa) polysaccharide isolated from Aureobasidium sp, and assessed the efficacy of BRD-glucan/adriamycin co-treatment of animal cancer models. RT-PCR and suspension hemolytic, plaque forming, wounding, invasion and cell proliferation assays were utilized to investigate the in vitro immunochemotherapeutic effects of BRD-glucan. In vivo, the effects of BRD-glucan and BRD-glucan/adriamycin co-treatment were tested in a B16 melanoma initiation model and in C57BL/6 mice. In vitro, BRD-glucan did not affect the cellular wounding response or invasion activity; treatment with BRD-glucan led to increase proliferation of B cells, natural killer cells and macrophages, but not T cells. In addition, we found that the BRD-glucan activation of B cells and macrophages was dependent on Toll-like receptor2 (TLR2) and TLR4, which play important roles in innate and adaptive immunity. In vivo, BRD-glucan/adriamycin co-treatment effectively reduced the number and size of metastatic colonies. Based on the results of our in vitro and in vivo toxicity, safety and immunochemotherapy assays, we propose that BRD-glucan is a promising immunochemotherapeutic anti-tumor agent.

Zymosan and PMA activate the immune responses of Mutz3-derived dendritic cells synergistically.

Beta-glucan (ß-glucan) including zymosan has been known as a super food because of its multifunctional activities, such as the enhancement of immune responses. To study the functional mechanism of ß-glucan in immune stimulation, the effect of zymosan on dendritic cell (DC) was investigated by monitoring the production of TNF-α, a pro-inflammatory cytokine. DC was differentiated from Mutz-3, a human acute myeloid leukemia cell line, by cytokine treatment and characterized. DC-specific cell surface markers were increased during the differentiation. Especially, Dectin-1, a ß-glucan receptor, was upregulated during DC differentiation, and mediated zymosan-induced TNF-α production, which was inhibited by silencing of dectin-1. Zymosan exhibited synergistic effect with other immune stimuli such as lipopolysaccharide (LPS) and phorbol 12-myristate 13-acetate (PMA), a well-known PKC activator. Simultaneous treatment of zymosan and PMA enhanced the nuclear translocation of NF-κB subunits, p50 and p65, mediating the increase of TNF-α production. Bay 11-7082, an NF-κB inhibitor, blocked morphological changes and TNF-α production induced by zymosan and/or PMA treatment. Western blot analysis has showed zymosan-Dectin-1 pathway mediated destructive phosphorylation of inhibitor of NF-κB (IκB) kinase α subunit (IKKα) in IKK complexes, while PMA-PKC pathway regulated selective phosphorylation and degradation of IKKß. Simultaneous phosphorylation of separate IKK subunits by co-treatment of zymosan and PMA resulted in cooperative activation of NF-κB and TNF-α production.

Production of pinostilbene compounds by the expression of resveratrol O-methyltransferase genes in Escherichia coli.

Resveratrol (3,4',5-trans-trihydroxystilbene) is a polyphenolic phytoalexin that belongs to a family of naturally occurring stilbenes. It has been reported that the health-promoting activities of certain methylated resveratrol derivatives are more effective than those of unmodified resveratrol. In this study, we isolated two candidate genes with resveratrol O-methyltransferase (ROMT) activity from grape (Vitis riparia) and sorghum (Sorghum bicolor). To assess their ROMT activities in vivo, we synthesized VrROMT and SbROMT3 following codon-optimization and expressed the VrROMTsyn and SbROMT3syn genes using a dual expression vector system. Furthermore, we attempted to produce pterostilbene from resveratrol as a substrate by the expression of two putative ROMT proteins in Escherichia coli. Unexpectedly, expression of the SbROMT3syn gene in E. coli led to the production of mono-methylated stilbene (3,4'-dihydroxy-5-methoxy-trans-stilbene, pinostilbene) from resveratrol compounds. However, a very small amount of di-methylated stilbene (3,5-dimethoxy-4'-hydroxy-trans-stilbene, pterostilbene) was also detected. Consistently, we found that in vitro methylation assays of resveratrol by recombinant SbROMT3syn produced pinostilbene as the major product besides a very small amount of pterostilbene. By contrast, very small amounts of methylated resveratrol derivatives were detected in E. coli expressing the VrROMTsyn protein. This suggests that the SbROMT3syn is more useful in the production of pinostilbene compounds than pterostilbene from resveratrol in E. coli.

Rice small C2-domain proteins are phosphorylated by calcium-dependent protein kinase.

We previously reported that OsERG1 and OsERG3 encode rice small C2-domain proteins with different biochemical properties in Ca(2+)- and phospholipid-binding assays. Os-ERG1 exhibited Ca(2+)-dependent phospholipid binding, which was not observed with OsERG3. In the present study, we show that both OsERG1 and OsERG3 proteins exhibit oligomerization properties as determined by native polyacrylamide gel electrophoresis (PAGE) and glutaraldehyde cross-linking experiments. Furthermore, in vitro phosphorylation assays reveal the phosphorylation of OsERG1 and OsERG3 by a rice calcium-dependent protein kinase, OsCDPK5. Our mutation analysis on putative serine phosphorylation sites shows that the first serine (Ser) at position 41 of OsERG1 may be an essential residue for phosphorylation by OsCDPK5. Mutation of Ser41 to alanine (OsERG1S41A) and aspartate (OsERG1S41D) abolishes the ability of OsERG1 to bind phospholipids regardless of the presence or absence of Ca(2+) ions. In addition, unlike the OsERG1 wild-type form, the mutant OsERG1 (S41A)::smGFP construct lost the ability to translocate from the cytosol to the plasma membrane in response to calcium ions or fungal elicitor. These results indicate that Ser41 may be essential for the function of OsERG1.

beta-Glucan enhanced apoptosis in human colon cancer cells SNU-C4.

The apoptotic effect of bacteria-derived beta-glucan was investigated in human colon cancer cells SNU-C4 using terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick end labeling (TUNEL) assay, reverse transcription-polymerase chain reaction (RT-PCR) expressions of Bcl-2, Bax, and Caspase-3 genes, and assay of caspase-3 enzyme activity. beta-Glucan of 10, 50, and 100 microg/mL decreased cell viability in a dose-dependent manner with typical apoptotic characteristics, such as morphological changes of chromatin condensation and apoptotic body formation from TUNEL assay. In addition, beta-glucan (100 microg/mL) decreased the expression of Bcl-2 by 0.6 times, whereas the expression of Bax and Caspase-3 were increased by 3.1 and 2.3 times, respectively, compared to untreated control group. Furthermore, the caspase-3 activity in the beta-glucan-treated group was significantly increased compared to those in control group (P < 0.05). Bacterial derived beta-glucan could be used as an effective compound inducing apoptosis in human colon cancer.

Cloning of srfA operon from Bacillus subtilis C9 and its expression in E. coli.

The srfA operon is required for the nonribosomal biosynthesis of the cyclic lipopeptide, surfactin. The srfA operon is composed of the four genes, srfAA, srfAB, srfAC, and srfAD, encoding the surfactin synthetase subunits, plus the sfp gene that encodes phosphopantetheinyl transferase. In the present study, 32 kb of the srfA operon was amplified from Bacillus subtilis C9 using a long and accurate PCR (LA-PCR), and ligated into a pIndigoBAC536 vector. The ligated plasmid was then transformed into Escherichia coli DH10B. The transformant ET2 showed positive signals to all the probes for each open reading frame (ORF) region of the srfA operon in southern hybridization, and a reduced surface tension in a culture broth. Even though the surface-active compound extracted from the E. coli transformant exhibited a different R(f) value of 0.52 from B. subtilis C9 or authentic surfactin (R(f) = 0.63) in a thin layer chromatography (TLC) analysis, the transformant exhibited a much higher surface-tension-reducing activity than the wild-type strain E. coli DH10B. Thus, it would appear that an intermediate metabolite of surfactin was expressed in the E. coli transformant harboring the srfA operon.

Extracellular production of a glycolipid biosurfactant, mannosylerythritol lipid, by Candida sp. SY16 using fed-batch fermentation.

Candida sp. strain SY16 produces a glycolipid-type biosurfactant, mannosylerythritol lipid (MEL-SY16), which can reduce the surface tension of a culture broth from 72 to 30 dyne cm(-1) and highly emulsify hydrocarbons when cultured in soybean-oil-containing media. As such, laboratory-scale fermentation for MEL-SY16 production was performed using optimized conditions. In batch fermentation, MEL-SY16 was mainly produced during the stationary phase of growth, and the concentration of MEL-SY16 reached 37 g l(-1) after 200 h. The effect of pH control on the production of MEL-SY16 was also examined in batch fermentation. The highest production yield of MEL-SY16 was when the pH was controlled at 4.0, and the production was significantly improved compared to batch fermentation without pH control. In fed-batch fermentation, glucose and soybean oil (1:1, w/w) were used in combination as the initial carbon sources for cell growth, and soybean oil was used as the feeding carbon source during the MEL production phase. The feeding of soybean oil resulted in the disappearance of any foam and a sharp increase in the MEL production until 200 h, at which point the concentration of MEL-SY16 was 95 g l(-1). Among the investigated culture systems, the highest MEL-SY16 production and volumetric production rate were achieved with fed-batch fermentation.

Chromosomal integration of sfp gene in Bacillus subtilis to enhance bioavailability of hydrophobic liquids.

Bacillus subtilis C9 effectively degrades aliphatic hydrocarbons up to a chain length of C19 and produces a lipopeptide-type biosurfactant, surfactin, yet it has no genetic competency. Therefore, to obtain a transformable surfactin producer, the sfp gene cloned from B. subtilis C9 was integrated into the chromosome of B. subtilis 168, a non-surfactin producer, by homologous recombination. The transformants reduced the surface tension of the culture broth from 70.0 mN/m to 28.0 mN/m, plus the surface-active compound produced by the transformants exhibited the same Rf value as that from B. subtilis C9 and authentic surfactin in a thin-layer chromatographic analysis. The integration of the sfp gene into the chromosome of B. subtilis 168 was confirmed by Southern hybridization. Like B. subtilis C9, the transformants readily degraded n-hexadecane, although the original strain did not. It was also statistically confirmed that the hydrocarbon degradation of the transformants was highly correlated to their surfactin production by the determination of the correlation coefficient (r2 = 0.997, P < 0.01). Therefore, these results indicate that the surfactin produced from B. subtilis enhances the bioavailability of hydrophobic liquids.

Paenibacillus kribbensis sp. nov. and Paenibacillus terrae sp. nov., bioflocculants for efficient harvesting of algal cells.

Two strains of Gram-variable, rod-shaped, endospore-forming, peritrichously flagellated, rod-shaped bacteria were isolated from a soil sample collected in Taejon City, Korea. The two strains (AM49T and AM141T) were found to be members of the genus Paenibacillus, on the basis of the results of phenotypic and phylogenetic analyses. Strains AM49T and AM141T were found to have a cell-wall peptidoglycan based on meso-diaminopimelic acid, MK-7 as their predominant menaquinone and anteiso-C15:0 as their major fatty acid. The DNA G + C contents of strains AM49T and AM141T were 48 and 47 mol%, respectively. The two strains formed distinct phylogenetic lineages within the radiation of the cluster comprising Paenibacillus spp. and a coherent cluster with Paenibacillus jamilae, Paenibacillus polymyxa, Paenibacillus azotofixans and Paenibacillus peoriae. The level of 16S rDNA similarity between strains AM49T and AM141T was 97.6%, and 16S rDNA similarity values between strains AM49T and AM141T and the type strains of other Paenibacillus spp. ranged from 90.3 to 98.7%. Levels of DNA-DNA similarity between the two strains and members of the genus Paenibacillus indicated that strains AM49T and AM141T were distinguishable from each other and from four phylogenetically related Paenibacillus spp. Therefore, on the basis of their phenotypic properties, phylogeny and genomic distinctiveness, it is proposed that strains AM49T and AM141T be placed in the genus Paenibacillus as two distinct novel species, Paenibacillus kribbensis (AM49T =KCTC 0766BPT =JCM 11465T) and Paenibacillus terrae (AM141T =KCCM 41557T =JCM 11466T).

Effects of crude oil, oil components, and bioremediation on plant growth.

The phytotoxic effects of crude oil and oil components on the growth of red beans (Phaseolus nipponesis OWH1) and corn (Zea mays) was investigated. In addition, the beneficial effects of bioremediation with the oil-degrading microorganism, Nocardia sp. H17-1, on corn and red bean growth in oil-contaminated soil was also determined. It was found that crude oil-contaminated soil (10,000mg/kg) was phytotoxic to corn and red beans. In contrast, obvious phytotoxicity was not observed in soils contaminated with 0-1000 mg/kg of aliphatic hydrocarbons such as decane (C10) and eicosane (C20). Phytotoxicity was observed in soils contaminated with 10-1000mg/kg of the poly aromatic hydrocarbons (PAHs) naphthalene, phenanthrene, and pyrene. It was observed that phytotoxicity increased with the number of aromatic rings, and that corn was more sensitive than red beans to PAH-contaminated soil. Bioremediation with Nocardia sp. H17-1 reduced phytotoxicity more in corn than in red bean, suggesting that this microbial species might degrade PAHs to some degree.

Selective control of cyanobacteria by surfactin-containing culture broth of Bacillus subtilis C1.

Of several types of chemical surfactants and biosurfactants, only the culture broth of Bacillus subtilis C1 containing surfactin at 10 mg l(-1) completely inhibited the growth of Microcystis aeruginosa, a bloom-forming cyanobacterium in highly eutrophic lakes. The broth with 10 mg surfactin l(-1) also removed 85% of the maximally grown M. aeruginosa (chlorophyll-a concentration, 1000 microg l(-1)) within 2 d, and the removal efficiency was enhanced by Ca2+ over 1 mM. The growth of Anabaena affinis, another bloom-forming cyanobacterium, was also inhibited about 70% with surfactin at 10 mg l(-1) broth. However, the effect of the broth was delayed over 3 d in the green algae, Chlorella vulgaris and Scenedesmus sp., and was negligible in a diatom, Navicula sp., indicating the potential for the selective control of cyanobacterial blooms.