• Herbal Formula Science
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• v.26 no.3
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• pp.237-250
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• 2018

Objectives : This study is a pharmacological network approach, aimed to identify the potential active compounds contained in Curcumae Radix, and their associated targets, to predict the various bio-reactions involved, and finally to establish the cornerstone for the deep-depth study of the representative mechanisms. Methods : The active compounds of Curcumae Radix have been identified using Traditional Chinese Medicine System Pharmacology Database and Analysis Platform. The UniProt database was used to collect each of information of all target proteins associated with the active compounds. To find the bio-metabolic processes associated with each target, the DAVID6.8 Gene Functional classifier tool was used. Compound-Target and Target-Pathway networks were analyzed via Cytoscape 3.40. Results : The target information from 32 potential active compounds of Curcumae Radix was collected through TCMSP analysis. The active compounds interact with 133 target genes engaging in total of 885 biological pathways. The most relevant pathway was the lipid-related metabolism, in which 3 representative active compounds were naringenin, oleic acid, and ${\beta}-sitosterol$. The mostly targeted proteins in the lipid pathway were ApoB, AKT1 and PPAR. Conclusions : The pharmacological network analysis is convenient approach to predict the overall metabolic mechanisms in medicinal herb research, which can reduce the processes of various experimental trial and error and provide key clues that can be used to validate and experimentally verify the core compounds.

• Proceedings of the Korean Society of Life Science Conference
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• 2001.11a
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• pp.3-8
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• 2001

Isopentenyl diphosphate (IPP) is the common, five-carbon building block in the biosynthesis of all carotenoids, IPP in Escherichia coli is synthesized through the non-mevalonate pathway. The first reaction of IPP biosynthesis in E. coli is the formation of 1-deoxy-D-xylulose-5-phosphate (DXP), catalyzed by DXP synthase and encoded by dxs. The second reaction in the pathway is the reduction of DXP to 2-C-methyl-D-erythritol-4-phosphate, catalyzed by DXP reductoisomerase and encoded by dxr. To determine if one or more of the reactions in the non-mevalonate pathway controlled flux to IPP, dxs and dxr were placed on several expression vectors under the control of three different promoters and transformed into three E. coli strains (DH5(, XL1-Blue, and JM101) that had been engineered to produce lycopene. Lycopene production was improved significantly in strains transformed with the dxs expression vectors. When the dxs gene was expressed from the arabinose-inducible araBAD promoter (PBAD) on a medium-copy plasmid, lycopene production was 2-fold higher than when dxs was expressed from the IPTG-inducible trc and lac promoters (Ptrc and Plac, respectively) on medium-copy and high-copy plasmids, Given the low final densities of cells expressing dxs from IPTG-inducible promoters, the low lycopene production was probably due to the metabolic burden of plasmid maintenance and an excessive drain of central metabolic intermediates. At arabinose concentrations between 0 and 1.33 mM, cells expressing both dxs and dxr from PBAD on a medium-copy plasmid produced 1.4 - 2.0 times more lycopene than cells expressing dxs only. However, at higher arabinose concentrations lycopene production in cells expressing both dxs and dxr was lower than in cells expressing dxs only. A comparison of the three E. coli strains transformed with the arabinose-inducible dxs on a medium-copy plamid revealed that lycopene production was highest in XL1-Blue.

• Journal of Applied Biological Chemistry
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• v.60 no.4
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• pp.333-338
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• 2017

Cellulosic alcohol fermentation has recently gained more attention in the production of ethanol, butanol, and 2,3-butanediol. However, it was revealed that the process had several hurdles, such as, an expensive cost for biomass decomposition to yield fermentable sugars and a production of byproduct lignin. As an alternative for the process through biomass saccharification, the alcohol production through syngas from biomass has been studied. In this study, we reviewed acetogen and its central metabolic pathway, Wood-Ljungdahl route, capable of utilizing syngas. Furthermore, the metabolic engineering strategies of acetogen for bio-alcohol production from syngas was also reviewed with a brief perspective.

• Korean Journal of Food Science and Technology
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• v.16 no.1
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• pp.90-94
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• 1984

We deduced a possible metabolic pathway of L-malate in a malo-alcoholic yeast, Schizosaccharomyces japonicus var. japonicus St-3. The malic enzyme (EC 1.1.1.40) prepared from the microorganism was about four times as active as that of malate dehydrogenase (EC 1.1.1.37). And Km values of malic enzyme and malate dehydrogenase for malate were found to be 3.125 mM and 4.761 mM, respectively, which referred to the fact that the affinity of malic enzyme for the substrate was greater than that of malate dehydrogenase. We also found that pyruvate was produced with disappearing malate in malo-alcoholic fermentation, and that the addition of $Mn^{2+}$ activated malic enzyme activity. Based on these results obtained we have deduced a main pathway of malate${\rightarrow}$pyruvate${\rightarrow}$acetaldehyde${\rightarrow}$ethanol for the utilization of L-malate by this malo-alcoholic yeast strain.

• Restorative Dentistry and Endodontics
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• v.17 no.1
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• pp.83-94
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• 1992

This study was executed to measure the biosynthesis of arachidonic acid metabolic products in chronic periapical lesions, to compare the products among periapical granuloma, periapical cyst and chronic periapical abscess, and to understand the pathogensis of chronic periapical lesions. Tissues from 33 chronic periapical lesions of human teeth were enucleated during endodontic surgery. large part of each tissue was contained in liquid nitrogen immediately and the other was examined histologically. In histologically diagnosed 8 cases of periapical granuloma, 9 cases of periapical cyst and 8 cases of chronic periapical abscess. the tissues were homogenatecl and incubated with $_{14}C$-arachidonic acid. Lipid solvent extracts were separated by thin layer chromatography to be analyzed by autoradiography and TLC analyzer. 1. $TXB_2$, 6-keto-$PGF_1{\alpha}$ and $PGE_2$, $LTB_4$, HETEs, and unidentified product which are metabolic products of arachidonic acid were measured in the tissues of chronic peripaical lesions. 2. In all of periapical granuloma, cyst and abscess, the conversion rate of HETEs among all products was the highest(P<0.05), and the percentage of HETEs in total converted products was also the highest(P<0.05). 3. The concentration of each arachidonic acid product was higher in chronic periapical absecss than in periapical granuloma and cyst(P<0.05). The concentration of $TXB_2$ and HETEs in periapical cyst were hight than in periapical granuloma. 4. The relative amounts of total products from lipoxygenase pathway to those from cyclo-oxygenase pathway were about 7 fold in chronic periapical lesions. There was no difference among periapical granuloma, cyst and abscess(P<0.05). The total amount of products from each pathway were higher in chronic periapical abscess than in periapical cyst and granuloma.

• Archives of Pharmacal Research
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• v.26 no.8
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• pp.631-637
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• 2003

Chloroquine has been used for many decades in the prophylaxis and treatment of malaria. It is metabolized in humans through the N-dealkylation pathway, to desethylchloroquine (DCQ) and bisdesethylchloroquine (BDCQ), by cytochrome P450 (CYP). However, until recently, no data are available on the metabolic pathway of chloroquine. Therefore, the metabolic pathway of chloroquine was evaluated using human liver microsomes and cDNA-expressed CYPs. Chloroquine is mainly metabolized to DCQ, and its Eadie-Hofstee plots were biphasic, indicating the involvement of multiple enzymes, with apparent $K_m and V_{max}$ values of 0.21 mM and 1.02 nmol/min/mg protein 3.43 mM and 10.47 nmol/min/mg protein for high and low affinity components, respectively. Of the cDNA-expressing CYPs examined, CYP1A2, 2C8, 2C19, 2D6 and 3A4/5 exhibited significant DCQ formation. A study using chemical inhibitors showed only quercetin (a CYP2C8 inhibitor) and ketoconazole (a CYP3A4/5 inhibitor) inhibited the DCQ formation. In addition, the DCQ formation significantly correlated with the CYP3A4/5-catalyzed midazolam 1-hydroxylation (r=0.868) and CYP2C8-catalyzed paclitaxel 6$\alpha$-hydroxylation (r = 0.900). In conclusion, the results of the present study demonstrated that CYP2C8 and CYP3A4/5 are the major enzymes responsible for the chloroquine N-deethylation to DCQ in human liver microsomes.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.2
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• pp.290-296
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• 2019

Objective: Pigs share many physiological, anatomical and genomic similarities with humans, which make them suitable models for biomedical researches. Understanding the genetic status of Yucatan miniature pigs (YMPs) and their association with human diseases will help to assess their potential as biomedical model animals. This study was performed to identify non-synonymous single nucleotide polymorphisms (nsSNPs) in selective sweep regions of the genome of YMPs and present the genetic nsSNP distributions that are potentially associated with disease occurrence in humans. Methods: nsSNPs in whole genome resequencing data from 12 YMPs were identified and annotated to predict their possible effects on protein function. Sorting intolerant from tolerant (SIFT) and polymorphism phenotyping v2 analyses were used, and gene ontology (GO) network and Kyoto encyclopedia of genes and genomes (KEGG) pathway analyses were performed. Results: The results showed that 8,462 genes, encompassing 72,067 nsSNPs were identified, and 118 nsSNPs in 46 genes were predicted as deleterious. GO network analysis classified 13 genes into 5 GO terms (p<0.05) that were associated with kidney development and metabolic processes. Seven genes encompassing nsSNPs were classified into the term associated with Alzheimer's disease by referencing the genetic association database. The KEGG pathway analysis identified only one significantly enriched pathway (p<0.05), hsa04080: Neuroactive ligand-receptor interaction, among the transcripts. Conclusion: The number of deleterious nsSNPs in YMPs was identified and then these variants-containing genes in YMPs data were adopted as the putative human diseases-related genes. The results revealed that many genes encompassing nsSNPs in YMPs were related to the various human genes which are potentially associated with kidney development and metabolic processes as well as human disease occurrence.

• Journal of Animal Science and Technology
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• v.64 no.2
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• pp.312-329
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• 2022

Feed cost is the main factor affecting the economic benefits of pig industry. Improving the feed efficiency (FE) can reduce the feed cost and improve the economic benefits of pig breeding enterprises. Liver is a complex metabolic organ which affects the distribution of nutrients and regulates the efficiency of energy conversion from nutrients to muscle or fat, thereby affecting feed efficiency. MicroRNAs (miRNAs) are small non-coding RNAs that can regulate feed efficiency through the modulation of gene expression at the post-transcriptional level. In this study, we analyzed miRNA profiling of liver tissues in High-FE and Low-FE pigs for the purpose of identifying key miRNAs related to feed efficiency. A total 212~221 annotated porcine miRNAs and 136~281 novel miRNAs were identified in the pig liver. Among them, 188 annotated miRNAs were co-expressed in High-FE and Low-FE pigs. The 14 miRNAs were significantly differentially expressed (DE) in the livers of high-FE pigs and low-FE pigs, of which 5 were downregulated and 9 were upregulated. Kyoto Encyclopedia of Genes and Genomes analysis of liver DE miRNAs in high-FE pigs and low-FE pigs indicated that the target genes of DE miRNAs were significantly enriched in insulin signaling pathway, Gonadotropin-releasing hormone signaling pathway, and mammalian target of rapamycin signaling pathway. To verify the reliability of sequencing results, 5 DE miRNAs were randomly selected for quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The qRT-PCR results of miRNAs were confirmed to be consistent with sequencing data. DE miRNA data indicated that liver-specific miRNAs synergistically acted with mRNAs to improve feed efficiency. The liver miRNAs expression analysis revealed the metabolic pathways by which the liver miRNAs regulate pig feed efficiency.

• Journal of Microbiology and Biotechnology
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• v.26 no.4
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• pp.710-716
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• 2016

Gamma-aminobutyric acid (GABA) is a non-protein amino acid, which is an important inhibitor of neurotransmission in the human brain. GABA is also used as the precursor of biopolymer Nylon-4 production. In this study, the carbon flux from the tricarboxylic acid cycle was directed to the GABA shunt pathway for the production of GABA from glucose. The GABA shunt enzymes succinate-semialdehyde dehydrogenase (GabD) and GABA aminotransferase (GabT) were co-localized along with the GABA transporter (GadC) by using a synthetic scaffold complex. The co-localized enzyme scaffold complex produced 0.71 g/l of GABA from 10 g/l of glucose. Inactivation of competing metabolic pathways in mutant E. coli strains XBM1 and XBM6 increased GABA production 13% to reach 0.80 g/l GABA by the enzymes co-localized and expressed in the mutant strains. The recombinant E. coli system developed in this study demonstrated the possibility of the pathway of the GABA shunt as a novel GABA production pathway.

• Mycobiology
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• v.39 no.4
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• pp.257-265
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• 2011

L-Phenylalanine is one of the essential amino acids that cannot be synthesized in mammals in adequate amounts to meet the requirements for protein synthesis. Fungi and plants are able to synthesize phenylalanine via the shikimic acid pathway. L-Phenylalanine, derived from the shikimic acid pathway, is used directly for protein synthesis in plants or metabolized through the phenylpropanoid pathway. This phenylpropanoid metabolism leads to the biosynthesis of a wide array of phenylpropanoid secondary products. The first step in this metabolic sequence involves the action of phenylalanine ammonialyase (PAL). The discovery of PAL enzyme in fungi and the detection of $^{14}CO_2$ production from $^{14}C$-ring-labeled phenylalanine and cinnamic acid demonstrated that certain fungi can degrade phenylalanine by a pathway involving an initial deamination to cinnamic acid, as happens in plants. In this review, we provide background information on PAL and a recent update on the presence of PAL genes in fungi.