Sooah Kim

Global Metabolite Profiling of Synovial Fluid for the Specific Diagnosis of Rheumatoid Arthritis from Other Inflammatory Arthritis

Currently, reliable biomarkers that can be used to distinguish rheumatoid arthritis (RA) from other inflammatory diseases are unavailable. To find possible distinctive metabolic patterns and biomarker candidates for RA, we performed global metabolite profiling of synovial fluid samples. Synovial fluid samples from 38 patients with RA, ankylosing spondylitis, Behçets disease, and gout were analyzed by gas chromatography/time-of-flight mass spectrometry (GC/TOF MS). Orthogonal partial least-squares discriminant and hierarchical clustering analyses were performed for the discrimination of RA and non-RA groups. Variable importance for projection values were determined, and the Wilcoxon-Mann-Whitney test and the breakdown and one-way analysis of variance were conducted to identify potential biomarkers for RA. A total of 105 metabolites were identified from synovial fluid samples. The score plot of orthogonal partial least squares discriminant analysis showed significant discrimination between the RA and non-RA groups. The 20 metabolites, including citrulline, succinate, glutamine, octadecanol, isopalmitic acid, and glycerol, were identified as potential biomarkers for RA. These metabolites were found to be associated with the urea and TCA cycles as well as fatty acid and amino acid metabolism. The metabolomic analysis results demonstrated that global metabolite profiling by GC/TOF MS might be a useful tool for the effective diagnosis and further understanding of RA.

The novel catabolic pathway of 3,6‐anhydro‐L‐galactose, the main component of red macroalgae, in a marine bacterium

The catabolic fate of the major monomeric sugar of red macroalgae, 3,6-anhydro-L-galactose (AHG), is completely unknown in any organisms. AHG is not catabolized by ordinary fermentative microorganisms, and it hampers the utilization of red macroalgae as renewable biomass for biofuel and chemical production. In this study, metabolite and transcriptomic analyses of Vibrio sp., a marine bacterium capable of catabolizing AHG as a sole carbon source, revealed two key metabolic intermediates of AHG, 3,6-anhydrogalactonate (AHGA) and 2-keto-3-deoxy-galactonate; the corresponding genes were verified in vitro enzymatic reactions using their recombinant proteins. Oxidation by an NADP(+) -dependent AHG dehydrogenase and isomerization by an AHGA cycloisomerase are the two key AHG metabolic processes. This newly discovered metabolic route was verified in vivo by demonstrating the growth of Escherichia coli harbouring the genes of these two enzymes on AHG as a sole carbon source. Also, the introduction of only these two enzymes into an ethanologenic E. coli strain increased the ethanol production in E. coli by fermenting both AHG and galactose in an agarose hydrolysate. These findings provide not only insights for the evolutionary adaptation of a central metabolic pathway to utilize uncommon substrates in microbes, but also a metabolic design principle for bioconversion of red macroalgal biomass into biofuels or industrial chemicals.

Visceral adipose tissue as a predictor for metabolic risk factors in the Korean population.

Aims  Visceral adipose tissue (VAT) accumulation is closely associated with an increased risk of cardiovascular disease. We have investigated the appropriate VAT cut‐off values for predicting metabolic risk factors in the Korean population.

PHO13 Deletion-Induced Transcriptional Activation Prevents Sedoheptulose Accumulation during Xylose Metabolism in Engineered Saccharomyces cerevisiae

The deletion of PHO13 (pho13Δ) in Saccharomyces cerevisiae, encoding a phosphatase enzyme of unknown specificity, results in the transcriptional activation of genes related to the pentose phosphate pathway (PPP) such as TAL1 encoding transaldolase. It has been also reported that the pho13Δ mutant of S. cerevisiae expressing a heterologous xylose pathway can metabolize xylose efficiently compared to its parental strain. However, the interaction between the pho13Δ-induced transcriptional changes and the phenotypes of xylose fermentation was not understood. Thus we investigated the global metabolic changes in response to pho13Δ when cells were exponentially growing on xylose. Among the 134 intracellular metabolites that we identified, the 98% reduction of sedoheptulose was found to be the most significant change in the pho13Δ mutant as compared to its parental strain. Because sedoheptulose-7-phosphate (S7P), a substrate of transaldolase, reduced significantly in the pho13Δ mutant as well, we hypothesized that limited transaldolase activity in the parental strain might cause dephosphorylation of S7P, leading to carbon loss and inefficient xylose metabolism. Mutants overexpressing TAL1 at different degrees were constructed, and their TAL1 expression levels and xylose consumption rates were positively correlated. Moreover, as TAL1 expression levels increased, intracellular sedoheptulose concentration dropped significantly. Therefore, we concluded that TAL1 upregulation, preventing the accumulation of sedoheptulose, is the most critical mechanism for the improved xylose metabolism by the pho13Δ mutant of engineered S. cerevisiae.

Pretreatment and saccharification of red macroalgae to produce fermentable sugars

Red macroalgae are currently considered as renewable resources owing to their high carbohydrate and low lignin and hemicellulose contents. However, utilization of red macroalgae has been limited owing to the lack of established methods for pretreatment and an effective saccharification system. Furthermore, marine red macroalgae consist of the non-favorable mixed sugars for industrial microorganisms. In this review, we suggest strategies for converting red macroalgae to bio-based products, focusing on the pretreatment and saccharification of red macroalgae to produce fermentable sugars and the microbial fermentation of these sugars by industrial microorganisms. In particular, some recent breakthroughs for the efficient utilization of red macroalgae include the discovery of key enzymes for the complete monomerization of red macroalgal carbohydrate and the catabolic pathway of 3,6-anhydro-l-galactose, the most abundant sugar in red macroalgae. This review provides a comprehensive perspective for the efficient utilization of red macroalgae as sustainable resources to produce bio-based products.

Food metabolomics: from farm to human

Metabolomics, one of the latest components in the suite of systems biology, has been used to understand the metabolism and physiology of living systems, including microorganisms, plants, animals and humans. Food metabolomics can be defined as the application of metabolomics in food systems, including food resources, food processing and diet for humans. The study of food metabolomics has increased gradually in the recent years, because food systems are directly related to nutrition and human health. This review describes the recent trends and applications of metabolomics to food systems, from farm to human, including food resource production, industrial food processing and food intake by humans.

Fatty acid profiling and proteomic analysis of Salmonella enterica serotype Typhimurium inactivated with supercritical carbon dioxide

Non-thermal sterilization and microbial inactivation processes are currently receiving much attention in food and pharmaceutical industries. In particular, since supercritical carbon dioxide (SC-CO2) treatment, which is conducted at relatively low temperatures, is considered to be a promising alternative method to replace thermal sterilization processes that cannot be safely used in foods and bioactive materials. Although SC-CO2 has been applied to many microorganisms, the inactivation of microbial cells by SC-CO2 has only been evaluated by using a conventional viable cell count such as a plating method, by which it is not possible to systematically elucidate the microbial cell inactivation process. Therefore, in this study the physiological status of SC-CO2 treated Salmonella enterica serotype Typhimurium was analyzed by using GC-MS analysis of fatty acids with principal component analysis and two-dimensional electrophoresis for protein profiling. From the results of these systemic analyses, it was revealed that SC-CO2 caused significant alterations to the profiles of fatty acids and proteins of the cells.

Enhanced drought tolerance in Arabidopsis via genetic manipulation aimed at the reduction of glucosamine-induced ROS generation

In animals, high glucose exerts some of its deleterious effects by activation of the hexosamine biosynthesis pathway (HBP), a branch of the glycolytic pathway that produces amino sugars (Daniels et al. in Mol Endocrinol 7:1041–1048, 1993; Du et al. in Proc Natl Acad Sci USA 97:12222–12226, 2000). Glucosamine (GlcN) is a naturally occurring amino sugar produced by amidation of fructose-6-phosphate. Previously, we observed that glucosamine (GlcN) inhibits hypocotyl elongation in Arabidopsis thaliana by a process involving the significant increase of reactive oxygen species. The present study investigated the relationship between GlcN-induced ROS generation and abiotic stress responses in Arabidopsis by generating two types of transgenic plant. Scavenging of endogenous GlcN by ectopic expression of E. coli glucosamine-6-phosphate deaminase (NagB) was observed to confer enhanced tolerance to oxidative, drought, and cold stress. Consistent with this result, overproduction of GlcN by the ectopic expression of E. coli glucosamine-6-phosphate synthase (GlmS) induced cell death at an early stage. Taken together, these data suggest that genetic manipulation of endogenous GlcN level can effectively lead to the generation of abiotic stress-tolerant transgenic crop plants.

Tolerance to acetic acid is improved by mutations of the TATA-binding protein gene.

Screening a library of overexpressing mutant alleles of the TATA-binding gene SPT15 yielded two Saccharomyces cerevisiae strains (MRRC 3252 and 3253) with enhanced tolerance to acetic acid. They were also tolerant to propionic acid and hydrogen peroxide. Transcriptome profile analysis identified 58 upregulated genes and 106 downregulated genes in MRRC 3252. Stress- and protein synthesis-related transcription factors were predominantly enriched in the upregulated and downregulated genes respectively. Eight deletion mutants for some of the highly downregulated genes were acetic acid-tolerant. The level of intracellular reactive oxygen species was considerably lessened in MRRC 3252 and 3253 upon exposure to acetic acid. Metabolome profile analysis revealed that intracellular concentrations of 5 and 102 metabolites were increased and decreased, respectively, in MRRC 3252, featuring a large increase of urea and a significant decrease of amino acids. The dur1/2Δmutant, in which the urea degradation gene DUR1/2 is deleted, displayed enhanced tolerance to acetic acid. Enhanced tolerance to acetic acid was also observed on the medium containing a low concentration of amino acids. Taken together, this study identified two SPT15 alleles, nine gene deletions and low concentration of amino acids in the medium that confer enhanced tolerance to acetic acid.

Systematic biomarker discovery and coordinative validation for different primary nephrotic syndromes using gas chromatography-mass spectrometry.

The goal of this study is to identify systematic biomarker panel for primary nephrotic syndromes from urine samples by applying a non-target metabolite profiling, and to validate their utility in independent sampling and analysis by multiplex statistical approaches. Nephrotic syndrome (NS) is a nonspecific kidney disorder, which is mostly represented by minimal change disease (MCD), focal segmental glomerulosclerosis (FSGS), and membranous glomerulonephritis (MGN). Since urine metabolites may mirror disease-specific functional perturbations in kidney injury, we examined urine samples for distinctive metabolic changes to identify biomarkers for clinical applications. We developed unbiased multi-component covarianced models from a discovery set with 48 samples (12 healthy controls, 12 MCD, 12 FSGS, and 12 MGN). To extensively validate their diagnostic potential, new batch from 54 patients with primary NS were independently examined a year after. In the independent validation set, the model including citric acid, pyruvic acid, fructose, ethanolamine, and cysteine effectively discriminated each NS using receiver operating characteristic (ROC) analysis except MCD-MGN comparison; nonetheless an additional metabolite multi-composite greatly improved the discrimination power between MCD and MGN. Finally, we proposed the re-constructed metabolic network distinctively dysregulated by the different NSs that may deepen comprehensive understanding of the disease mechanistic, and help the enhanced identification of NS and therapeutic plans for future.