• Journal of Microbiology and Biotechnology
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• v.28 no.3
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• pp.473-481
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• 2018

Owing to its high protein secretion capacity, simple nutritional requirements, and GRAS (generally regarded as safe) status, Bacillus licheniformis is widely used as a host for the industrial production of enzymes, antibiotics, and peptides. However, as compared with its close relative Bacillus subtilis, little is known about the physiology and stress responses of B. licheniformis. To explore its temperature-stress metabolome, B. licheniformis strains ATCC 14580 and B186, with respective optimal growth temperatures of $42^{\circ}C$ and $50^{\circ}C$, were cultured at $42^{\circ}C$, $50^{\circ}C$, and $60^{\circ}C$ and their corresponding metabolic profiles were determined by gas chromatography/mass spectrometry and multivariate statistical analyses. It was found that with increased growth temperatures, the two B. licheniformis strains displayed elevated cellular levels of proline, glutamate, lysine, pentadecanoic acid, hexadecanoic acid, heptadecanoic acid, and octadecanoic acid, and decreased levels of glutamine and octadecenoic acid. Regulation of amino acid and fatty acid metabolism is likely to be associated with the evolution of protective biochemical mechanisms of B. licheniformis. Our results will help to optimize the industrial use of B. licheniformis and other important Bacillus species.

• Journal of Ginseng Research
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• v.44 no.6
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• pp.757-769
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• 2020

Background: Panax quinquefolius and Panax notoginseng are widely used and well known for their pharmacological effects. As main pharmacological components, saponins have different distribution patterns in the root tissues of Panax plants. Methods: In this study, the representative ginsenosides were detected and quantified by desorption electrospray ionization mass spectrometry and high-performance liquid chromatography analysis to demonstrate saponin distribution in the root tissues of P. quinquefolius and P. notoginseng, and saponin metabolite profiles were analyzed by metabolomes to obtain the biomarkers of different root tissues. Finally, the transcriptome analysis was performed to demonstrate the molecular mechanisms of saponin distribution by gene profiles. Results: There was saponin distribution in the root tissues differed between P. quinquefolius and P. notoginseng. Eight-eight and 24 potential biomarkers were detected by metabolome analysis, and a total of 340 and 122 transcripts involved in saponin synthesis that were positively correlated with the saponin contents (R > 0.6, P < 0.05) in the root tissues of P. quinquefolius and P. notoginseng, respectively. Among them, GDPS1, CYP51, CYP64, and UGT11 were significantly correlated with the contents of Rg1, Re, Rc, Rb2, and Rd in P. quinquefolius. UGT255 was markedly related to the content of R1; CYP74, CYP89, CYP100, CYP103, CYP109, and UGT190 were markedly correlated with the Rd content in P. notoginseng.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.59-59
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• 2017

Rice (Oryza sativa L.) is the most important crop and its yield must be improved to feed the increasing global population. Recently developed high-yielding varieties with extra-large sink capacity often have a problem in unstable grain-filling. Therefore, understanding limiting factors for improving grain-filling and controlling them are essential for further improvement of rice grain yield. However, since grain-filling rate was determined by complex sink-source balance, the ability of grain-filling was very difficult to evaluate. Source ability for 'grain' was not only determined by the ability of carbon assimilation in leaves, but also that of carbon translocation from leaves to panicles. Sink strength was determined by the complex carbon metabolism from sucrose degradation to starch synthesis. Hence, to evaluate the grain-filling ability and determine its regulatory steps, the whole picture of carbon flow from photosynthesis at leaves to starch synthesis at grains must be revealed in a metabolite level. In this study, the yield and grain growth rate of three high-yielding varieties, which show high sink capacity commonly, were compared. Momiroman showed lower grain filling rate and slower grain growth rate than the other varieties, Hokuriku 193 and Tequing. To clarify the limiting point in the carbon flow of Momiroman, $CO_2$ labeled by stable isotope ($^{13}C$) was fed to three varieties during ripening period. The ratio of $^{13}C$ left in the stem was higher in Momiroman 24 hours after feeding, suggesting inefficient carbon translocation of Momiroman. More interestingly, $^{13}C$ translocation from soluble fraction to insoluble one in the grain seemed to be slower in Momiroman. To get the further insight in a metabolite level, we are now trying the $^{13}C$ labeling metabolome analysis in the developing grains.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.104-104
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• 2017

Sorghum (Sorghum bicolor (L.) Moench.) is one of the most important crops for human and animal nutrition. Nonetheless, sorghum has a cyanogenic glucoside compound which can be degraded into hydrogen cyanide, toxic to humans and animals even with tiny amount. In consequence, breeding materials with a low cyanide level has been a top priority in sorghum breeding programs. To fulfill our long-term goal, we are screening sorghum accessions with low cyanide level, which would be an important breeding material for food safety. We collected seeds of various sorghum accessions and analyzed relevant metabolites to find useful breeding materials of sorghum accessions containing low cyanide. Fourteen wild relatives were obtained from the University of Georgia in US, a reference accession BTx623, and three local varieties from National Agrobiodiversity Center of Rural Development Administration in Korea, and one wild species from the Wild Plant Resources Seed Bank of Korea University in Korea. Sorghum plants were grown in plastic greenhouse under natural conditions. After growing, leaf samples were harvested at different developmental stages: seedling phase, vegetative phase (right before flowering), and reproductive phase (ripening). Using collected samples, quantification analysis were performed by an HPLC system for three metabolites (dhurrin, 4-hydroxybenzaldehyde, and 4-hydroxyphenylacetic acid) in sorghum plants. Prior to metabolome analysis, specific experimental condition for HPLC system was set to be able to separate three metabolites simultaneously. Under this condition, these metabolites were quantified in each accession by HPLC system. We observed that the metabolite contents were changed differently by developmental stages and accessions. We clustered these results into five groups as patterns of their contents by developmental stages. Most of accessions showed that 4-hydroxybenzaldehyde content was very high at seedling stage and decreased rapidly at vegetative phase. Interestingly, the patterns of dhurrin content were very different among clusters. However, 4-hydroxyphenylacetic acid content was maintained at low levels by developmental stages in most accessions. The results would demonstrate how dhurrin and alternative degradation pathways are differentiated in each accession.

• Genomics & Informatics
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• v.4 no.1
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• pp.40-44
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• 2006

Toxicogenomics combines transcriptome, proteome and metabolome profiling with conventional toxicology to investigate the interaction between biological molecules and toxicant or environmental stress in disease caution. Toxicogenomics faces the problems of comparison and integration across different sources of data. Cause of unusual characteristics of toxicogenomic data, researcher should be assisted by data analysis and annotation for getting meaningful information. There are already existing repositories which claim to stand for toxicogenomics database. However, those just contain limited abilities for toxicogenomic research. For supporting toxicologist who comes up against toxicogenomic data flood, now we propose novel toxicogenomics knowledgebase system, XPERANTO-TOX. XPERANTO-TOX is an integrated system for toxicogenomic data management and analysis. It is composed of three distinct but closely connected parts. Firstly, Data Storage System is for reposit many kinds of '-omics' data and conventional toxicology data. Secondly, Data Analysis System consists of analytical modules for integrated toxicogenomics data. At last, Data Annotation System is for giving extensive insight of data to researcher.

• Bulletin of the Korean Chemical Society
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• v.31 no.2
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• pp.379-383
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• 2010

Metabolites of colorectal cancer tissues from 12 patients were analyzed and compared with those of the normal tissues by two-dimensional NMR spectroscopy. NMR data were analyzed with the help of the metabolome database and the statistics software. Cancerous tissues showed significantly altered metabolic profiles as compared to the normal tissues. Among such metabolites, the concentrations of taurine, glutamate, choline were notably increased in the cancerous tissues of most patients, and those of glucose, malate, and glycerol were decreased. Changes in individual metabolites varied significantly from patient to patient, but the combination of such changes could be used to distinguish cancerous tissues from normal ones, which could be done by PCA analysis. The traditional chemometric analysis was also performed using AMIX software. By comparing those two results, the analysis via $^1H-^{13}C$ HSQC spectra proved to be more robust and effective in assessing and classifying global metabolic profiles of the colorectal tissues.

• Molecules and Cells
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• v.27 no.1
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• pp.89-97
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• 2009

We investigate the molecular and cellular etiologies that underlie the deletion of the six amino acid residues (${\Delta}F323-Y328$; ${\Delta}FY$) in human torsin A (HtorA). The most common and severe mutation involved with early-onset torsion dystonia is a glutamic acid deletion (${\Delta}E$ 302/303; ${\Delta}E$) in HtorA which induces protein aggregates in neurons and cells. Even though ${\Delta}FY$ HtorA forms no protein clusters, flies expressing ${\Delta}FY$ HtorA in neurons or muscles manifested a similar but delayed onset of adult locomotor disability compared with flies expressing ${\Delta}E$ in HtorA. In addition, flies expressing ${\Delta}FY$ HtorA had fewer aberrant ultrastructures at synapses compared with flies expressing ${\Delta}E$ HtorA. Taken together, the ${\Delta}FY$ mutation in HtorA may be responsible for behavioral and anatomical aberrations in Drosophila.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.245-250
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• 2003

There are currently about 6000 bacterial species with validly published names, but scientists assume that these may be less than 1% of bacterial species present on the earth. Microbial resource is one of the most important bioresources in bioinderstry and provides us with high economic values. To find missing ones, the studies of metagenome, metabolome, and proteome about microbes have started recently in developed countries. We construct the information system that integrates information on microbial genome resources and manages the information to support efficient research of microbial genome application, and name this system 'Bio-Meta Information System (Bio-MIS)'. Bio-MIS consists of integrated microbial genome resources database, microbial genome resources input system, integrated microbial genome resources search engine, microbial resources on-line distribution system, portal service and management via internet. In the future, we will include public database connection and implement useful bioinformatics software for analyzing microbial genome resources. The web-site is accessible at http://biomis.probionic.com

• BMB Reports
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• v.37 no.1
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• pp.93-106
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• 2004

The new complexity arising from the genome sequencing projects requires new comprehensive post-genomic strategies: advanced studies in regulatory mechanisms, application of new high-throughput technologies at a genome-wide scale, at the different levels of cellular complexity (genome, transcriptome, proteome and metabolome), efficient analysis of the results, and application of new bioinformatic methods in an integrative or systems biology perspective. This can be accomplished in studies with model organisms under controlled conditions. In this review a perspective of the favourable characteristics of yeast as a touchstone model in post-genomic research is presented. The state-of-the art, latest advances in the field and bottlenecks, new strategies, new regulatory mechanisms, applications (patents) and high-throughput technologies, most of them being developed and validated in yeast, are presented. The optimal characteristics of yeast as a well-defined system for comprehensive studies under controlled conditions makes it a perfect model to be used in integrative, 'systems biology' studies to get new insights into the mechanisms of regulation (regulatory networks) responsible of specific phenotypes under particular environmental conditions, to be applied to more complex organisms (e.g. plants, human).

• Journal of the Korean Magnetic Resonance Society
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• v.14 no.1
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• pp.28-37
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• 2010

Metabolites of urine samples from 6 colorectal cancer patients were analyzed by two-dimensional NMR spectroscopy, where the samples were collected before and after the surgical treatments per patient. NMR data were analyzed with the help of the metabolome database and the statistics software. Urine samples before and after the treatments showed significantly different metabolic profiles from each other. We were able to compare 10 different metabolites. Most of the assigned metabolites of every patient showed a tendency of increase after the surgery except for a few cases. The amount of changes in individual metabolites varied significantly from patient to patient, but the combination of such changes could be used to distinguish the condition before the surgery from after, which could be done by PCA analysis. The analysis via $^{1}H-^{13}C$ HSQC spectra proved to be applicable in assessing and classifying global metabolic profiles of the urines from colorectal cancer patients.