BackgroundRieske non-heme iron aromatic ring-hydroxylating oxygenases (RHOs) are multi-component enzyme systems that are remarkably diverse in bacteria isolated from diverse habitats. Since the first classification in 1990, there has been a need to devise a new classification scheme for these enzymes because many RHOs have been discovered, which do not belong to any group in the previous classification. Here, we present a scheme for classification of RHOs reflecting new sequence information and interactions between RHO enzyme components.ResultWe have analyzed a total of 130 RHO enzymes in which 25 well-characterized RHO enzymes were used as standards to test our hypothesis for the proposed classification system. From the sequence analysis of electron transport chain (ETC) components of the standard RHOs, we extracted classification keys that reflect not only the phylogenetic affiliation within each component but also relationship among components. Oxygenase components of standard RHOs were phylogenetically classified into 10 groups with the classification keys derived from ETC components. This phylogenetic classification scheme was converted to a new systematic classification consisting of 5 distinct types. The new classification system was statistically examined to justify its stability. Type I represents two-component RHO systems that consist of an oxygenase and an FNRC-type reductase. Type II contains other two-component RHO systems that consist of an oxygenase and an FNRN-type reductase. Type III represents a group of three-component RHO systems that consist of an oxygenase, a [2Fe-2S]-type ferredoxin and an FNRN-type reductase. Type IV represents another three-component systems that consist of oxygenase, [2Fe-2S]-type ferredoxin and GR-type reductase. Type V represents another different three-component systems that consist of an oxygenase, a [3Fe-4S]-type ferredoxin and a GR-type reductase.ConclusionThe new classification system provides the following features. First, the new classification system analyzes RHO enzymes as a whole. RwithSecond, the new classification system is not static but responds dynamically to the growing pool of RHO enzymes. Third, our classification can be applied reliably to the classification of incomplete RHOs. Fourth, the classification has direct applicability to experimental work. Fifth, the system provides new insights into the evolution of RHO systems based on enzyme interaction.

The effective production and usage of ginsenosides, given their distinct pharmacological effects, are receiving increasing amounts of attention. As the ginsenosides content differs in different parts of Panax ginseng, we wanted to assess and compare the ginsenosides content in the ginseng roots, leave, stems, and berries. To extract the ginsenosides, 70% (v/v) methanol was used. The optimal ultra-performance liquid chromatography-quadrupole time of flight mass spectrometry (UPLC-QTOF/MS) method was used to profile various ginsenosides from the different parts of P. ginseng. The datasets were then subjected to multivariate analysis including principal component analysis (PCA) and hierarchical clustering analysis (HCA). A UPLC-QTOF/MS method with an in-house library was constructed to profile 58 ginsenosides. With this method, a total of 39 ginsenosides were successfully identified and quantified in the ginseng roots, leave, stem, and berries. PCA and HCA characterized the different ginsenosides compositions from the different parts. The quantitative ginsenoside contents were also characterized from each plant part. The results of this study indicate that the UPLC-QTOF/MS method can be an effective tool to characterize various ginsenosides from the different parts of P. ginseng.

Transformed root ("hairy root") cultures have been shown to be a good model for the study of many secondary metabolites. However, economically important compounds such as asiaticoside and madecassoside are produced in insignificant amounts in the root of Centella asiatica (L.) Urban. To overcome this problem, C. asiatica was transformed using Agrobacterium rhizogenes strain R1000 that harbors pCAMBIA1302 encoding the hygromycin phosphotransferase (hpt) and green fluorescence protein (mgfp5) genes and the hairy culture was coupled with elicitation technique. Hairy roots were obtained at a frequency of up to 14.1% from a tissue junction between the leaf and petiole. Abundant hairy roots were observed when co-cultivation of the plant with A. rhizogenes was done for 7 days (36.1%). Transformation was confirmed by PCR and Southern blot analyses. Five weeks after inoculation, no asiaticoside was detected in the hairy root samples. However, when 0.1 mM methyl jasmonate (MJ) was applied as an elicitor to the culture medium for 3 weeks, a large quantity of asiaticoside was generated (7.12 mg/g, dry wt). In the case of gene expression, 12 h after MJ treatment the expression of the CabAS (C. asiatica putative beta-amyrin synthase) gene in the hairy roots is significantly different from that of the control and this level of transcripts was maintained for 14 days. Our results showed that production of C. asiatica hairy roots could be optimized and the resulting cultures could be elicited with MJ treatment for enhanced production of asiaticoside.

Background: Rieske non-heme iron aromatic ring-hydroxylating oxygenases (RHOs) are multi-component enzyme systems that are remarkably diverse in bacteria isolated from diverse habitats. Since the first classification in 1990, there has been a need to devise a new classification scheme for these enzymes because many RHOs have been discovered, which do not belong to any group in the previous classification. Here, we present a scheme for classification of RHOs reflecting new sequence information and interactions between RHO enzyme components.

The swelling and pasting properties of non-waxy rice starch-hydrocolloid mixtures were investigated using commercial and laboratory-generated hydrocolloids. The swelling power of the rice starch-hydrocolloid mixtures was generally depressed at low concentration of hydrocolloids (0-0.05%), but increased directly with increasing hydrocolloid concentrations (0.05-0.1%). In gellan gum dispersion, the swelling power at 1007C was higher than that of control. The rice starch-hydrocolloids mixtures showed shear-thinning flow behavior (n = 0.26-0.49). Hydrocolloids except the exopolysaccharide from S. chungbukensis (EPS-CB) increased apparent viscosity and consistency index (K) of rice starch dispersions, but decreased the n value. Hydrocolloids enhanced the trough and final viscosity of rice starch dispersions but EPS-CB reduced the viscosity of rice starch pastes. Hydrocolloids lowered peak viscosity but addition of guar gum resulted in high peak viscosity, apparent viscosity, and consistency index of rice starch dispersions. Total setback viscosity appeared to be not affected by hydrocolloids at low concentration (0.05%). The hot and cold paste of the starch-gellan gum mixture exhibited the highest viscosity values in the Brookfield viscometer.

Panax ginseng C.A. Meyer, commonly known as Korean or Asian ginseng, is a perennial herb native to Korea and China. Its roots are highly prized for several medicinal properties. The present study describes development and characterization of twentytwo polymorphic microsatellite markers for this species. A total of 99 alleles were detected with an average of 4.5 alleles per locus across 20 accessions. Values for observed (H O ) and expected (H E ) heterozygosities ranged from 0.05 to 1.00 and from 0.18 to 0.73, respectively. Eleven loci deviated from Hardy-Weinberg equilibrium (P < 0.001). Significant (P < 0.05) heterozygote deficiency was observed at 13 loci. Exact test for linkage disequilibrium showed significant values (P < 0.05) between 12 pairs of loci. These microsatellite markers provide powerful tools for understanding population and conservation genetics of this species and also for genetic differentiation and authentication of different Panax species being used in commercial ginseng products.

Recently, new ginseng cultivars having superior agricultural traits have been developed in Korea. For newly developed plant cultivars, the identifi cation of distinctiveness is very important factors not only in plant cultivar management but also in breeding programs. Thus, eighty-fi ve inter simple sequence repeat (ISSR) primers were applied to detect polymorphisms among six major Korean ginseng cultivars and two foreign ginsengs. A total of 197 polymorphic bands with an average 5.8 polymorphic bands and 2.9 banding patterns per assay unit across six Korean ginseng cultivars and foreign ginsengs from 236 amplifi ed ISSR loci with an average 6.9 loci per assay unit were generated by 34 out of 85 ISSR primers. Three species of Panax ginseng including the Korean ginseng cultivars, P. quinquefolius, and P. notoginseng, could be readily discriminated using most tested primers. UBC-821, UBC-868, and UBC-878 generated polymorphic bands among the six Korean ginseng cultivars, and could distinguish them from foreign ginsengs. Sequence characterized amplifi ed region (SCAR) marker system was introduced in order to increase the reproducibility of the polymorphism. One SCAR marker, PgI821C650, was successfully converted from the randomly amplifi ed polymorphism by UBC-821. It showed the expected dominant polymorphism among ginseng samples. In addition, the specifi c polymorphism for Sunwon was generated by treating Taq I restriction enzyme to polymerase chain reaction products of PgI821C650. These results will serve as useful DNA markers for identifi cation of Korean ginseng, especially Sunwon cultivar, seed management, and molecular breeding program supplemented with marker-assisted selection.

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