Natural products are a rich source of biologically active small molecules and a fertile area for lead discovery of new drugs [10, 52]. For instance, 5% of the 1,031 new chemical entities approved as drugs by the US Food and Drug Administration (FDA) were natural products between 1981 and 2002, and another 23% were natural product-derived molecules [53]. These molecules have evolved through millions of years of natural selection to interact with biomolecules in the cells or organisms and offer unrivaled chemical and structural diversity [14, 37]. Nonetheless, a large percentage of nature remains unexplored, in particular, in the marine and microbial environments. Therefore, natural products are still major valuable sources of innovative therapeutic agents for human diseases. However, even when a natural product is found to exhibit biological activity, the cellular target and mode of action of the compound are mostly mysterious. This is also true of many natural products that are currently under clinical trials or have already been approved as clinical drugs [11]. The lack of information on a definitive cellular target for a biologically active natural product prevents the rational design and development of more potent therapeutics. Therefore, there is a great need for new techniques to expedite the rapid identification and validation of cellular targets for biologically active natural products. Chemical genomics is a new integrated research engine toward functional studies of genome and drug discovery [40, 69]. The identification and validation of cellular receptors of biologically active small molecules is one of the key goals of the discipline. This eventually facilitates subsequent rational drug design, and provides valuable information on the receptors in cellular processes. Indeed, several biologically crucial proteins have already been identified as targets for natural products using chemical genomics approach (Table 1). Herein, the representative case studies of chemical genomics using natural products derived from microbes, marine sources, and plants will be introduced.

The present study represents the investigation of in vitro immunopotentiating activities of cellular fractions of major lactic acid bacteria found in kimchi (KLAB) and bifidobacteria. The macrophage cells, RAW264.7, were stimulated with heat-killed whole-cell, cell-wall, and cytoplasmic fractions of four strains of KLAB (Leuconostoc mesenteroides, Leuconostoc citreum, Lactobacillus plantarum, and Lactobacillus sake) and two strains of bifidobacteria (Bifidobacterium longum and Bifidobacterium lactis) each, and then the production of nitric oxide (NO) and cytokines including tumor necrosis $factor-\alpha\;(TNF-\alpha)$ and interleukin-6 (IL-6) was measured by Griess and ELISA assays, respectively. Heat-killed wholecell and cell-wall fractions-but not the cytoplasmic fraction-from all strains of KLAB significantly increased the production of NO in RAW264.7 cells, and all fractions from bifidobacteria exerted similar effects. In the production of $TNF-\alpha$, heat-killed whole-cell and cell-wall fractions of L. plantarum showed the strongest effect, followed by L. sake and B. lactis, whereas other KLAB fractions did not exert any effect. In the production of IL-6, only whole-cell and cell-wall fractions of L. plantarum were effective. These results, taken together, indicate that L. plantarum might playa critical role in the immunopotentiating activities of kimchi.

Tyrosinase is an enzyme that catalyzes the biosynthetic pathway of melanin pigments participating in the coloring of skin, hair, and eyes, and is widely distributed in nature. The inhibitory compounds of tyrosinase have been extensively used as a cosmetic agent with a skin-whitening effect. In this paper, several plant extracts were screened using Melan-a cells for the melanin biosynthesis inhibition activity, and Idesia polycarpa was selected. A melanin biosynthesis inhibitor was isolated from I. polycarpa fruits by activity-guided fractionation, and the inhibitor was identified as 6-hydroxy-2-[[[(1-hydroxy-6-oxo-2-cyclohexenl-yl)carbonyl]oxy]methyl]phenyl$\beta$-D-glucopyranoside (idescrapin) by comparing it with reported spectral data. Idescarpin $(IC_{50}=8{\mu}g/ml)$ reduced melanin content compared with the vehicle. In addition, the inhibitory activity of idescarpin for melanin synthesis is mediated by decreasing tyrosinase protein rather than directly inhibiting the tyrosinase activity. These results suggest that idescarpin isolated from I. polycarpa fruits may be used as a skin-whitening agent.

A perfusion culture of transgenic Nicotiana tabacum cell suspensions, transformed to express recombinant glucuronidase (GUS), was successfully performed in a 5-1 stirred tank bioreactor. With 0.1 $day^{-1}$ of perfusion rate, the maximum dry cell weight (DCW) reached to 29.5 g/l in 16 days, which was 2.1-fold higher than the obtained in batch culture (14.3 g/l). In terms of the production of GUS, the volumetric activity could be increased up to 12.8 U/ml by using perfusion, compared with 4.9 U/ml in batch culture. The specific GUS activities in both perfusion and batch cultures were maintained at similar levels, 200-400 U/g DCW. Consequently, a perfusion culture could be a good strategy for the enhanced production of recombinant proteins in a plant cell culture system.

To remove nitrate from wastewater, a novel bioelectrochemical denitrification system is introduced. In this proposed system, biological reactions are coupled with reactions on the electrode, whereby the electrons are transferred to the bacterial enzymes via a mediator as an electron carrier. The denitrification reaction was achieved with permeabilized Ochrobactrum anthropi SY509 containing denitrifying enzymes, such as nitrate reductase, nitrite reductase, and nitrous oxide reductase, and methyl viologen was used as the mediator. The electron transfer from the electrode to the enzymes in the bacterial cells was confirmed using cyclic voltammetry. A high removal efficiency of nitrate was achieved when the bioelectrochemical system was used with the permeabilized cells. Furthermore, when the permeabilized cells were immobilized to a graphite felt electrode using a calcium alginate matrix containing graphite powder, a high removal efficiency was achieved (4.38 nmol/min mg cell) that was comparable to the result when using the free permeabilized cells.

We have developed a program for generating shotgun data sets from known genome sequences. Generation of synthetic data sets by computer program is a useful alternative to real data to which students and researchers have limited access. Uniformly-distributed-sampling clones that were adopted by previous programs cannot account for the real situation where sampled reads tend to come from particular regions of the target genome. To reflect such situation, a probabilistic model for biased sampling distribution was developed by using an experimental data set derived from a microbial genome project. Among the experimental parameters tested (varied fragment or read lengths, chimerism, and sequencing error), the extent of sequencing error was the most critical factor that hampered sequence assembly. We propose that an optimum sequencing strategy employing different insert lengths and redundancy can be established by performing a variety of simulations.

We investigated the potential use of various carbon sources (fructose, glucose, mannose, lactose, and glycerol) for culturing Phaeodactylum tricornutum UTEX-640 in mixotrophic and heterotrophic batch cultures. Concentrations of carbon substrates tested ranged from 0.005 M to 0.2 M. P. tricornutum did not grow heterotrophically on any of the C-sources used, but successive additions of organic carbon in mixotrophic growth mode substantially increased the biomass concentration and productivity relative to photoautotrophic controls. The maximum biomass productivities in mixotrophic cultures for glycerol, fructose, and glucose were 21.30 mg/l h, 15.80 mg/l h, and 10.20 mg/l h, respectively. These values were respectively 10-, 8-, and 5-fold higher than those obtained in the corresponding photoautotrophic control cultures. Mannose and lactose did not significantly affect microalgal growth. The biomass lipids, eicosapentaenoic acid (EPA) and pigments contents were considerably enhanced with glycerol and fructose in relation to photoautotrophic controls. The EPA content was barely affected by the sugars, but were more than 2-fold higher in glycerol-fed cultures than in photoautotrophic controls.

The dissolved oxygen level of any cell culture environment has a critical effect on cellular metabolism. Specifically, hypoxia condition decreases cell viability and recombinant protein productivity. In this work, to develop CHO cells producing recombinant protein with high productivity, mammalian expression vectors containing a human tissue-type plasminogen activator (t-PA) gene with hypoxia response element (HRE) were constructed and stably transfected into CHO cells. CHO/2HRE-t-PA cells produced 2-folds higher recombinant t-PA production than CHO/t-PA cells in a $Ba^{2+}-alginate$ immobilized culture, and 16.8-folds in a repeated batch culture. In a non-aerated batch culture of suspension-adapted cells, t-PA productivity of CHO/2HRE/t-PA cells was 4.2-folds higher than that of CHO/t-PA cells. Our results indicate that HRE is a useful tool for the enhancement of protein productivity in mammalian cell cultures.

Oil spill was found in 1999 from a diesel storage facility located near the top of Baekun Mountain in Uiwang City. Application of bioremediation techniques was very relevant in removing oil spills in this site, because the geological condition was not amenable for other onsite remediation techniques. For efficient bioremediation, bacterial communities of the contaminated site and the uncontaminated control site were compared using both molecular and cultivation techniques. Soil bacterial populations were observed to be stimulated to grow in the soils contaminated with diesel hydrocarbon, whereas fungal and actinomycetes populations were decreased by diesel contamination. Most of the dieseldegrading bacteria isolated from contaminated forest soils were strains of Pseudomonas, Ralstonia, and Rhodococcus species. Denaturing gradient gel electrophoresis (DGGE) analysis revealed that the profiles were different among the three contaminated sites, whereas those of the control sites were identical to each other. Analysis of 16S rDNA sequences of dominant isolates and clones showed that the bacterial community was less diverse in the oil-contaminated site than at the control site. Sequence analysis of the alkane hydroxylase genes cloned from soil microbial DNAs indicated that their diversity and distribution were different between the contaminated site and the control site. The results indicated that diesel contamination exerted a strong selection on the indigenous microbial community in the contaminated site, leading to predominance of well-adapted microorganisms in concurrence with decrease of microbial diversity.

A biosurfactant-producing bacterial strain was selected from oil-contaminated soil because of its ability to degrade crude oil and tributyrin $(C_{4:0})$. The strain was identified as Bacillus subtilis A8-8 based on its morphological, biochemical, and physiological characteristics. When B. subtilis A8-8 was grown with crude oil as the sole carbon source, the biosurfactant from the strain emulsified crude oil, vegetable oil, and hydrocarbons. Soybean oil was the optimum substrate for the emulsifying activity and emulsion stability of the biosurfactant, both of which were superior to those of several commercially available surfactants. The biosurfactant was purified by a procedure including HCl precipitation, methanol treatment, and silica-gel chromatography. The partially purified biosurfactant was analyzed by TLC (thin-layer chromatography), SDS-PAGE, and HPLC and it reduced the surface tension of water from 72 mN/m to 26 mN/m at a concentration of 30 mg/l. Therefore, the purified lipopeptide biosurfactant has strong properties as an emulsifying agent and acts as an emulsion-stabilizing agent.

A sequence characterized amplified region (SCAR) marker, which was tightly linked with the A1 mating type locus in Phytophthora infestans, was developed. During the random amplified polymorphic DNA-based phylogenic studies of 33 isolates of P infestans collected from year 2002 to 2004, we found an A1 mating type-specific DNA fragment. This 573-bp DNA fragment was generated only in the genomic DNA of the A1 mating types, when OPC-5 primer was used. Based on the specific DNA sequence, we designed the primer sets for generating the A1 mating type-specific 569-bp DNA fragment. When 33 genomic DNAs of P. infestans were subjected to PCR amplification using different primer combinations, the A1 mating type-specific DNA was amplified, when LB-1F and LB-2R primers were used. The specific 569-bp DNA fragment was generated only from all 18 A1 strains, but not from 15 A2 mating type strains. These results corresponded to the mating type discriminating bioassay of 33 isolates of P. infestans. Therefore, the primer combination of LB-1F/LB2R was chosen as a SCAR marker. Overall, this study indicates that the SCAR marker could be developed into a useful tool for mating type determination of P. infestans.

A bacterial strain HJ-14 was isolated as a producer of antioxidants from the coast of Jinhae in Korea. The isolate showed 43.4mol% of G+C content, and contained dihydrogenated ubiquinone with Q8 as a major quinone. Chemotaxonomic analysis as well as phylogenetic analysis, based on the 16S rDNA sequence, identified the isolate as a member of Alteromonas macleodii. For antioxidant production, the optimum medium composition was determined to be 3% dextrin, 0.5% ammonium sulfate, and 2-6% sodium chloride. Optimum culture conditions for production of antioxidant materials with strain HJ-14 were at pH 6.0-8.0 and $25-37^{\circ}C$. The chloroform extract of strain HJ-14 broth showed 1.96-17.5-fold higher antioxidant activity than other organic solvents in term of electron donating ability.

Amplification by universal consensus sequences in pathogenic bacterial DNA would allow rapid identification of pathogenic bacteria, and amplification of genus-specific and species-specific sequences of pathogenic bacterial DNA might be used for genotyping at the genus and species levels. For design of probes for molecular diagnostics, several tools are available as stand-alone programs or as Web application. However, since most programs can design only a few probe sets at one time, they are not suitable for large-scale and automatic probes design. Therefore, for high-throughput design of specific probes in diagnostic array development, an automated design tool is necessary. Thus, we developed a Web-based automatic system for design of genus-specific and species-specific probes for pathogen detection. The system is available at http://www.miprobe.com.

We propose a genome-scale clustering approach to identify whole genome relationships using the functional groups given by the Kyoto Encyclopedia of Genes and Genomes Orthology (KO) database. The metabolic capabilities of each organism were defined by the number of genes in each functional category. The archaeal, bacterial, and eukaryotic genomes were compared by simultaneously applying a two-step clustering method, comprised of a self-organizing tree algorithm followed by unsupervised hierarchical clustering. The clustering results were consistent with various phenotypic characteristics of the organisms analyzed and, additionally, showed a different aspect of the relationship between genomes that have previously been established through rRNA-based comparisons. The proposed approach to collect and cluster the metabolic functional capabilities of organisms should make it a useful tool in predicting relationships among organisms.

Angiotensin I-converting enzyme (ACE) inhibitors have generally been very useful to remedy or prevent hypertension. This study describes the extraction and characterization of an ACE inhibitor from the fruiting body of Pholiota adiposa ASI 24012, which can be used as an antihypertensive drug. The maximal ACE inhibitory activity $(IC_{50};0.25mg)$ was obtained when the fruiting body of Pholiota adiposa ASI 24012 was extracted with distilled water at $30^{\circ}C$ for 12 h. After the purification of ACE inhibitor with ultrafiltration, Sephadex G-25 column chromatography, and reverse-phase HPLC, an active fraction with an $IC_{50}$ of 0.044 mg was obtained. The purified ACE inhibitory peptide was a novel pentapeptide, showing very little similarity to other ACE inhibitory peptide sequences. The molecular mass of the purified ACE inhibitor was estimated to be 414 daltons with a sequence of Gly-Glu-Gly-Gly-Pro, and showed a clear antihypertensive effect on spontaneously hypertensive rats (SHR) at a dosage of 1 mg/kg.

Dihydrochalcomycin (GERI-155), produced by Streptomyces sp. KCTC-0041BP isolated from Korean soil, is a 16-membered macrolide antibiotic consisting of two deoxysugar moieties at C-5 and C-20 positions of a branched lactone ring. The cloning and sequencing of a gene cluster for dihydrochalcomycin biosynthesis revealed a 63-kb nucleotide region containing 25 open reading frames (ORFs). The products of all of these 25 ORFs playa role in dihydrochalcomycin biosynthesis and self-resistance against the compounds synthesized. At the core of this cluster lies a 39.6-kb polyketide synthase (PKS) region encoding eight modules in five giant multifunctional protein-coding genes (gerSI-SV). The genes responsible for the biosynthesis of deoxysugar moieties, D-chalcose and D-mycinose, and their modification and attachment were found on either side of this PKS region. The involvement of this gene cluster in dihydrochalcomycin biosynthesis was confirmed by disruption of the dehydratase (DH) domain in module 3 of the PKS gene and by metabolite analysis.

A novel gene (agiA) required for adventurous gliding motility in Myxococcus xanthus has been identified. Null mutations in this gene caused defects in the gliding movement of isolated cells, suggesting that it belongs to one of the A-motility genes. The isolated agiA mutant cells neither glided nor produced slime trails on agar surface. However, agiA was different from other known A-motility genes in that the agiA mutant created in the $S^-$ mutant background glided in the swarm of cells, since other known A-motility mutants created in the $S^-$ mutant background do not move in the swarm of cells. The agiA mutant was also defective in fruiting body development. Sequence analysis predicted that agiA encodes a 787-amino-acid protein with eight tripeptide repeat motifs.

Catechol 1,2-dioxygenase was purified from cells of R. rhodochrous N75 grown at the expense of benzoate and p-toluate as the sole sources of carbon. A single catechol 1,2-dioxygenase was found to be induced with either growth substrate. The enzyme has an estimated $M_r$ of 71,000 consisting of two identical subunits. Catechol 1,2-dioxygenase from R. rhodochrous N75 exhibits some unusual properties including: broad substrate specificity, extradiol cleavage activity with 4-methylcatechol and low $K_m$ values for halocatechols, suggesting that this enzyme is distinct from other known catechol and chlorocatechol 1,2-dioxygenases.

Cellular components of Lactococcus lactis ssp. lactis (heat-killed whole cells, cytoplasm, and cell walls) were tested for their in vivo immunopotentiating activity. Peritoneal macrophages from mice orally administered with heat-killed whole cells exhibited significantly greater phagocytic activity than the groups administered with cell-wall fraction or cytoplasm fraction. The cytotoxicity of natural-killer cells was the highest in the group administered with whole cells, and the production of cytokines ($IFN-\gamma$, IL-2, and IL-12) in spleen cells was significantly higher, when cellular components were injected, and it tended to be higher in the cell-wall and cytoplasm groups than in the whole-cell group. Interestingly, the cytokine production of Peyer's patch cells was high, when cytoplasm fractions were administered. These results demonstrate that whole cells and cytoplasm and cell-wall fractions of L. lactis ssp. lactis have immunopotentiating activities, which are related to the stimulation of Peyer's patches.

Cyclosophoraose (cyclic $\beta-(1,2)-glucan$, Cys) isolated from Rhizobium meliloti, a soil microorganism, was used as a solubility enhancer for flavonoids. The complexes of the cyclic oligosaccharide with flavonoids were confirmed through $^1H$ nuclear magnetic resonance (NMR) spectroscopic analysis. Flavonoids solubilized by Cys were quantitatively analyzed through high-performance liquid chromatography (HPLC). Among the flavonoids tested, the solubility of naringenin was greatly enhanced by Cys, compared with other compounds. The solubility of naringenin was enhanced about 7.1-fold by adding 10 mM Cys, compared with a control. $^1H$ NMR spectroscopic analysis indicated that the H-6 and H-8 protons, which are located on the A ring of naringenin, were greatly shifted upfield upon the complexation with Cys. This result suggested that Cys showed a regioselective interaction with the naringenin molecule upon the complexation, resulting in the solubility enhancement of naringenin.

The phosphoenolpyruvate-dependent carbohydrate phosphotransferase system (PTS) is responsible for the simultaneous transfer and phosphorylation of various carbon sources in Escherichia coli. The ptsG gene encoding the enzyme $IICB^{Glc}$, the membrane component of the glucose-specific PTS, is repressed by Mlc and activated by the CRP cAMP complex; various other factors, such as Fis, FruR, and ArcA, are also known to be involved in ptsG regulation. Thus, in an attempt to discover a novel gene affecting the regulation of ptsG, a mutant with a decreased ptsG transcription in the presence of glucose compared with the wild-type strain was screened using transposon random mutagenesis. The mutant was found to have a transposon insertion in yhjV, a putative gene encoding a transporter protein whose function is yet unknown.

It was reported that an accumulation of Sadenosyl-L-methionine increases production of actinorhodin in Streptomyces lividans and induces antibiotic biosynthetic genes. We also obtained the same result in Streptomyces coelicolor A3(2). Therefore, in order to identify proteins changed by the addition of S-adenosyl-L-methionine in S. coelicolor A3(2), LC/MS/MS analyses were carried out. Thirteen proteins that were not observed in the control were found.

Bacterial serine proteases, especially those from Bacillus, have been extensively studied. Intracellular serine protease 1 (Isp1) is responsible for most of the proteolytic activity in B. subtilis. To identify Isp1 substrates and study its physiological functions, a mutant of Isp1, which has lost the enzymatic activity, was constructed. Through a GST affinity chromatographic method, several Bacillus proteins that specifically interacted with S246A mutant Isp1 protein were isolated and then identified by MALDI-TOF analysis. ClpC and elongation factor Tu (EF-Tu) were among those proteins specifically bound to mutant Isp1. In addition, several proteins involved in stationary phase adaptive response (such as RNA polymerase sigma factor, spoIIIE) were also identified. These findings led us to suggest that the major function of this serine protease, whose expression is greatly increased during the stationary phase, is to mediate transition of the cell into the stationary phase in a proper and timely manner.

A wbpO gene encoding a putative UDP-N-acetylo-galactosamine dehydrogenase was identified and cloned from Vibrio vulnificus. LPS production was altered by disruption of the wbpO gene through allelic exchanges. The function of the wbpO gene in virulence assessed in vitro and in mice revealed that WbpO is important in both the pathogenesis of V. vulnificus and the biosynthesis of LPS.

The potential genotoxicity of methylsulfonylmethane, a crystalline organic sulfur, derived from chemically modified lignin from plants was evaluated using in vitro and in vivo assays. In the bacterial reverse mutation test using Salmonella typhimurium TA98, TA100, TA1535, and TA1538, methylsulfonylmethane did not induce any significant increase of His' revertants. In the in vitro chromosome aberration test using Chinese Hamster Lung (CHL) cells, no aberration effects were seen. In the in vivo evaluation using a micronucleus test, negative results were obtained. Accordingly, the results indicated that methylsulfonylmethane is not genotoxic and its use is unlikely to present a potential hazard.