• 제목/요약/키워드: metabolic pathway

검색결과 509건 처리시간 0.03초

Epigenetic regulation of key gene of PCK1 by enhancer and super-enhancer in the pathogenesis of fatty liver hemorrhagic syndrome

  • Yi Wang;Shuwen Chen;Min Xue;Jinhu Ma;Xinrui Yi;Xinyu Li;Xuejin Lu;Meizi Zhu;Jin Peng;Yunshu Tang;Yaling Zhu
    • Animal Bioscience
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    • 제37권8호
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    • pp.1317-1332
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    • 2024
  • Objective: Rare study of the non-coding and regulatory regions of the genome limits our ability to decode the mechanisms of fatty liver hemorrhage syndrome (FLHS) in chickens. Methods: Herein, we constructed the high-fat diet-induced FLHS chicken model to investigate the genome-wide active enhancers and transcriptome by H3K27ac target chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-Seq) profiles of normal and FLHS liver tissues. Concurrently, an integrative analysis combining ChIP-seq with RNA-Seq and a comparative analysis with chicken FLHS, rat non-alcoholic fatty liver disease (NAFLD) and human NAFLD at the transcriptome level revealed the enhancer and super enhancer target genes and conservative genes involved in metabolic processes. Results: In total, 56 and 199 peak-genes were identified in upregulated peak-genes positively regulated by H3K27ac (Cor (peak-gene correlation) ≥0.5 and log2(FoldChange) ≥1) (PP) and downregulated peak-genes positively regulated by H3K27ac (Cor (peak-gene correlation) ≥0.5 and log2(FoldChange)≤-1) (PN), respectively; then we screened key regulatory targets mainly distributing in lipid metabolism (PCK1, APOA4, APOA1, INHBE) and apoptosis (KIT, NTRK2) together with MAPK and PPAR signaling pathway in FLHS. Intriguingly, PCK1 was also significantly covered in up-regulated super-enhancers (SEs), which further implied the vital role of PCK1 during the development of FLHS. Conclusion: Together, our studies have identified potential therapeutic biomarkers of PCK1 and elucidated novel insights into the pathogenesis of FLHS, especially for the epigenetic perspective.

Analysis of soyasaponin content and biosynthesis-related gene expression in young pea (Pisum sativum L.) sprouts

  • Gang Deok Han;HanGyeol Lee;Jae-Hyeok Park;Young Jae Yun;Gee Woo Kim;Sangyun Jeong;So-Yeon Moon;Hye-Young Seo;Young-Cheon, Kim;Woo Duck Seo;Jeong Hwan Lee
    • Journal of Plant Biotechnology
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    • 제50권
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    • pp.70-75
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    • 2023
  • In legumes, soyasaponins, one of triterpenoid saponins, are major components of secondary metabolites with a more diverse array of bioactive chemicals. Although the biosynthetic pathway of soyasaponins has been largely studied in soybean, the study on the soyasaponin contents and biosynthesis-related gene expression in pea (Pisum sativum L.) is poorly understood. Here, we found the accumulation of only soyasaponin Bb component in the sprouts of two Korean domestic pea cultivars (Dachung and Sachul). This pattern was consistent with our observation that increased expression of PsUGT73P2 and PsUGT91H4 genes, but not PsCYP72A69, could be responsible for biosynthesis of only soyasaponin Bb in pea by examining their gene expression. However, gradual accumulation of soyasaponin Bb at developmental stages was not consistent with the expression of PsUGT73P2 and PsUGT91H4, suggesting that the changes of their protein activities may affect the accumulation patterns of soyasaponin Bb. We also revealed that the increased expression levels of PsUGT73P2 and PsUGT91H4 during light to dark transition led to increase of soyasaponin Bb contents. Collectively, our results provided a molecular basis of metabolic engineering for enhancing useful soyasaponin Bb metabolites in Korean domestic pea cultivars.

Insights into Enzyme Reactions with Redox Cofactors in Biological Conversion of CO2

  • Du-Kyeong Kang;Seung-Hwa Kim;Jung-Hoon Sohn;Bong Hyun Sung
    • Journal of Microbiology and Biotechnology
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    • 제33권11호
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    • pp.1403-1411
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    • 2023
  • Carbon dioxide (CO2) is the most abundant component of greenhouse gases (GHGs) and directly creates environmental issues such as global warming and climate change. Carbon capture and storage have been proposed mainly to solve the problem of increasing CO2 concentration in the atmosphere; however, more emphasis has recently been placed on its use. Among the many methods of using CO2, one of the key environmentally friendly technologies involves biologically converting CO2 into other organic substances such as biofuels, chemicals, and biomass via various metabolic pathways. Although an efficient biocatalyst for industrial applications has not yet been developed, biological CO2 conversion is the needed direction. To this end, this review briefly summarizes seven known natural CO2 fixation pathways according to carbon number and describes recent studies in which natural CO2 assimilation systems have been applied to heterogeneous in vivo and in vitro systems. In addition, studies on the production of methanol through the reduction of CO2 are introduced. The importance of redox cofactors, which are often overlooked in the CO2 assimilation reaction by enzymes, is presented; methods for their recycling are proposed. Although more research is needed, biological CO2 conversion will play an important role in reducing GHG emissions and producing useful substances in terms of resource cycling.

The oncometabolite d-2-hydroxyglutarate induces angiogenic activity through the vascular endothelial growth factor receptor 2 signaling pathway

  • JIYOON SEOK;SOO‑HYUN YOON;SUN‑HEE LEE;JONG HWA JUNG;YOU MIE LEE
    • International Journal of Oncology
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    • 제54권2호
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    • pp.753-763
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    • 2019
  • The mutation of isocitrate dehydrogenase (IDH)1 (R132H) and IDH2 (R172K) and the induction of hypoxia in various solid tumors results in alterations in metabolic profiles, including the production of the d- or l-forms of 2-hydroxyglutarate (2HG) from α-ketoglutarate in aerobic metabolism in the tricarboxylic acid (TCA) cycle. However, it is unclear whether the oncometabolite d-2HG increases angiogenesis in endothelial cells. Therefore, in this study, we analyzed the levels of various metabolites, including d-2HG, under hypoxic conditions and in IDH2R172K mutant breast cancer cells by mass spectrometry. We then further evaluated the effects of this metabolite on angiogenesis in breast cancer cells. The results revealed that treatment with d-2HG increased the levels of secreted vascular endothelial growth factor (VEGF) in cancer cells and enhanced endothelial cell proliferation in a concentration-dependent manner. Wound healing and cell migration (examined by Transwell assay) were significantly increased by d-2HG to a level similar to that induced by VEGF. Tube formation was significantly stimulated by d-2HG, and chick chorioallantoic membrane angiogenesis was also enhanced by d-2HG. d-2HG activated VEGF receptor (VEGFR)2 and VEGFR2 downstream signaling, extracellular signal-regulated kinase 1/2, focal adhesion kinase, AKT and matrix metalloproteinase (MMP)2. Taken together, the findings of this study suggested that d-2HG induced angiogenic activity via VEGFR2 signaling and increased MMP2 activity.

난자-난구세포 복합체에서 발현하는 Rpia 유전자의 종 특이적 발현 (Species-specific Expression of Rpia Transcript in Cumulus-oocyte-complex)

  • 김윤선;윤세진;김은영;이경아
    • Clinical and Experimental Reproductive Medicine
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    • 제34권2호
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    • pp.95-106
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    • 2007
  • 목 적: 본 연구진은 선행연구를 통하여 생쥐의 미성숙 난자와 성숙 난자 사이에 차이 나게 발현하는 유전자(DEGs)의 목록을 보유하고 있는데, 그 중에서 pentose phosphate pathway (PPP)에 필수적 효소인 Ribose 5-phosphate isomerase A (Rpia)를 선택하여 본 연구를 수행하였다. 난자 성숙 과정에 관련된 Rpia의 기능을 알아보기 위한 기초연구로서 생쥐와 돼지의 난소에서 Rpia의 발현을 비교분석 하였다. 연구방법: 생쥐의 각 조직에서 11개의 MII-selective DEGs의 발현을 RT-PCR방법으로 확인하여 난소에서 강하게 발현하는 4개의 유전자를 선택하였고, 다시 이들 4개 유전자 중 난자에서 높게 발현하는 Rpia를 선택하여 생쥐 및 돼지의 난자, 난구세포, 과립세포에서의 발현을 비교분석 하였다. 돼지 Rpia 염기서열은 밝혀져 있지 않아 EST clustering 기법을 통해 동정하였다. 결 과: EST clustering 기법으로 찾아낸 돼지 Rpia 염기서열은 GenBank에 등록하였고 (Accession Number EF213106), 이를 근거로 primer를 작성하여 RT-PCR을 수행하였다. Rpia 유전자는 생쥐에서는 난자 특이적으로 발현하는 반면 돼지에서는 난자, 난구세포, 과립세포에서 모두 발현하는 차이점을 발견하였다. 결 론: 본 연구는 생쥐와 돼지의 난소에서 Rpia유전자 동정에 대한 첫 보고로서, 본 연구결과로부터 생쥐와 돼지의 COCs는 서로 다른 경로로 포도당의 대사가 일어나는 것을 알 수 있었다. 따라서 이와 같은 차이점이 두 종의 난자를 체외 배양할 때 나타나는 난자 성숙률의 차이를 가져오는 기전 중의 하나가 아닐까 추측된다. 난자 성숙을 조절하는 기전을 연구함과 동시에 체외에서 난자 성숙이 어려운 종의 최적의 IVM (in vitro maturation)조건을 찾기 위해서는 앞으로 난자와 주변세포의 포도당 대사과정에 미치는 Rpia의 기능에 대한 후속연구가 필요할 것으로 사료된다.

Effects of Dietary Levels of Glycine, Threonine and Protein on Threonine Efficiency and Threonine Dehydrogenase Activity in Hepatic Mitochondria of Chicks

  • Lee, C.W.;Cho, I.J.;Lee, Y.J.;Son, Y.S.;Kwak, I.;Ahn, Y.T.;Kim, S.C.;An, W.G.
    • Asian-Australasian Journal of Animal Sciences
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    • 제27권1호
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    • pp.69-76
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    • 2014
  • This study was carried out to evaluate the relationship between threonine (Thr) efficiency and Thr dehydrogenase (TDG) activity as an indicator of Thr oxidation on chicks fed with levels of diets (CP [17.5% and 21.5%] and Thr [3.8 and 4.7 g/100 g CP]; glycine [Gly][0.64% and 0.98%] and true digestible Thr [dThr] [0.45% and 0.60%]). Calculation of the Thr efficiency was based on N-balance data and an exponential N-utilization model, and TDG activity was determined as accumulation of aminoacetone and Gly during incubation of hepatic mitochondria. This study found that in the liver of chicks who received a diet containing up to 0.79% Thr (4.7 g Thr/100 g of CP) in the 17.5% CP diet, no significant (p>0.05) effect on TDG activity was observed. However, significantly (p = 0.014) increased TDG activity was observed with a diet containing 21.5% CP (4.7 g Thr/100 g of CP) and the efficiency of Thr utilization showed a significant (p = 0.001) decrease, indicating the end of the Thr limiting range. No significant (p>0.05) effect on the total TDG activity and accumulation of Gly was observed with addition of Gly to a diet containing 0.45% dThr. In addition, addition of Gly to a diet containing 0.60% dThr also did not result in a change in accumulation of Gly. Due to an increase in accumulation of aminoacetone, an elevated effect on total TDG activity was also observed. No significant (p>0.05) reduction in the efficiency of Thr utilization was observed after addition of Gly at the level of 0.45% dThr. However, significantly (p<0.001) reduced efficiency of Thr utilization was observed after addition of Gly at the level of 0.60% dThr. Collectively, we found that TDG was stimulated not only by addition of Thr and protein to the diet, but also by addition of Gly, and efficiency of Thr utilization was favorably affected by addition of Gly at the level near to the optimal Thr concentration. In addition, no metabolic requirement of Gly through the TDG pathway was observed with almost the same accumulation of Gly and a slight increase in TDG activity by addition of Gly. Thus, our findings suggest that determination of TDG activity and parameter of efficiency of Thr utilization may be useful for evaluation of dietary Thr level.

인간 간암세포주 HepG2에서 김 분획물의 항산화 활성을 통한 증식 억제 및 유전자 발현 양상 (Anti-proliferating Effects and Gene Expression Profiles through Antioxidant Activity of Porphyra yezoensis Fractions on Human HepG2 Cell Lines)

  • 오윤정;김정민;방인석
    • 생명과학회지
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    • 제28권2호
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    • pp.176-186
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    • 2018
  • 김(Porphyra yezoensis, Laver)의 MeOH 추출에 의한 유기용매 별 분획물에서 폴리페놀 함량과 항산화 활성 및 간암세포주 HepG2의 세포증식 억제효과를 확인하였다. $CHCl_3$ 분획물의 폴리페놀 함량은 $10.34{\mu}g/mg$으로 물 분획물의 $13.08{\mu}g/mg$ 보다는 다소 적게 나타났으나, DPPH 자유라디칼 소거에 의한 전자공여능(EDA)에서 나타난 $ED_{50}$$16.96{\mu}g/ml$로 가장 높게 나타났다. $CHCl_3$과 EtOAc 분획물은 농도의존적으로 HepG2 세포의 증식을 억제하였으며, 특히 $900{\mu}g/ml$$CHCl_3$ 분획물을 24시간 동안 처리하여 90%의 세포증식이 억제되었다. 한편 $CHCl_3$ 분획물이 처리된 HepG2 세포의 유전자 발현 양상을 microarray로 확인하였다. P. yezoensis의 효능과 연관지은 gene ontology 분석으로 비타민 D 합성 과정, 항균작용에 대한 반응 및 영양물질에 대한 반응에 관련된 유의 유전자들을 탐색하였다. 유의 유전자로 IL6R와 CYP1A1를 선정하였고, 이들 유전자의 상위 조절자는 ARNT 유전자가 선정되었다. 또한 50 및 $100{\mu}g/ml$$CHCl_3$ 분획물이 처리된 HepG2 세포에서 IL6R와 CYP1A1 단백질의 발현과 상위 조절자인 ARNT의 활성을 Western blotting으로 확인하였다.

Differentially expressed serum proteins associated with calcium regulation and hypocalcemia in dairy cows

  • Shu, Shi;Bai, Yunlong;Wang, Gang;Xiao, Xinhuan;Fan, Ziling;Zhang, Jiang;Zhao, Chang;Zhao, Yang;Xia, Cheng;Zhang, Hongyou
    • Asian-Australasian Journal of Animal Sciences
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    • 제30권6호
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    • pp.893-901
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    • 2017
  • Objective: Hypocalcemia is an important metabolic disease of dairy cows during the transition period, although the effect of hypocalcemia on biological function in dairy cows remains unknown. Methods: In this study, proteomic, mass spectrum, bioinformatics and western blotting were employed to identify differentially expressed proteins related to serum Ca concentration. Serum samples from dairy cows were collected at three time points: 3rd days before calving (day -3), the day of calving (day 0), and 3rd days after calving (day +3). According to the Ca concentration on day 0, a total of 27 dairy cows were assigned to one of three groups (clinical, subclinical, and healthy). Samples collected on day -3 were used for discovery of differentially expressed proteins, which were separated and identified via proteomic analysis and mass spectrometry. Bioinformatics analysis was performed to determine the function of the identified proteins (gene ontology and pathway analysis). The differentially expressed proteins were verified by western blot analysis. Results: There were 57 differential spots separated and eight different proteins were identified. Vitamin D-binding protein precursor (group-specific component, GC), alpha-2-macroglobulin (A2M) protein, and apolipoprotein A-IV were related to hypocalcemia by bioinformatics analysis. Due to its specific expression (up-regulated in clinical hypocalcemia and down-regulated in subclinical hypocalcemia), A2M was selected for validation. The results were consistent with those of proteomic analysis. Conclusion: A2M was as an early detection index for distinguishing clinical and subclinical hypocalcemia. The possible pathogenesis of clinical hypocalcemia caused by GC and apolipoprotein A-IV was speculated. The down-regulated expression of GC was a probable cause of the decrease in calcium concentration.

2배체와 4배체 도라지의 단백질 발현양상 비교 분석 (Proteomic Responses of Diploid and Tetraploid Roots in Platycodon grandiflorum)

  • 김혜림;권수정;;조성우;김학현;문영자;부희옥;우선희
    • 한국작물학회지
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    • 제60권3호
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    • pp.394-400
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    • 2015
  • 본 연구는 2배체와 4배체 도라지 단백질 발현지도 제작과 도라지의 생리활성에 관여하는 메카니즘을 분자적 수준에서 해석하기 위한 기초자료를 얻고자 실시하였다. 2배체 및 4배체 도라지의 단백질의 발현 양상은 배수성에 따른 특이성은 관찰 할 수 없었으며, 모두 분자량 15~100 kDa 크기, pH 4.0~8.0의 범위에 분포하는 것으로 나타났다. 동정된 39개의 단백질 중 2배체에 비해 4배체에서 2개의 단백질이 up-regulated 되었고, 37개의 단백질이 down-regulated 되었다. 단백질을 기능별로 분류한 결과, 산화환원효소의 활성(oxidoreductase activity)기능을 갖는 단백질이 23.7%의 비율로 가장 많았고 다음은 nucleotide binding 기능의 단백질이 15.8%의 비율로 높았다.

RNA-Sequencing을 이용한 벼 품종간 수발아 차이 분석 (Analysis of Varietal Differences in Pre-harvest Sprouting of Rice using RNA-Sequencing)

  • 최명구;이현석;황운하;양서영;이윤호;이충근;윤성중;정재혁
    • 한국작물학회지
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    • 제65권4호
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    • pp.274-283
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    • 2020
  • 본 연구는 조평과 조운의 벼 출수 후 적산온도와 검정온도에 따른 수발아 발생 정도를 조사하고, RNA-sequencing 방법을 사용하여 수발아 발생 원인을 찾았다. 품종간 수발아성에 관여하는 생리적, 유전학적 요인을 구명하고자 수행하였으며 분석한 결과는 다음과 같다. 1. 출수 후 적산온도가 높아질수록, 검정온도가 높아질수록 수발아 처리시 수발아율이 높았고, 조운벼가 내수발아성이 강하고, 조평벼가 수발아성이 높은것으로 나타났다. 2. 수발아성이 높은 조평벼를 대상으로 한 RNA-sequencing 결과 ABA 생합성에 관여하는 OsNCEDs의 발현이 감소하고, ABA 분해에 관여하는 OsCYP707As의 발현이 증가하였다. 3. 조평과 조운의 OsNCEDs와 OsCYPY707As의 Quantitation Real-Time PCR 결과 조평보다 조운에서 OsNCEDs의 발현이 높게 나타나 수발성과 상관관계를 보였으나, OsCYP707As는 수발아성과 상관관계를 보이지 않았다. 4. 조운벼는 등숙기간중 종실내 ABA함량이 조평보다 높으며 수발아 처리시 남아있는 ABA함량이 높아 내수발아성이 상대적으로 강하게 나타났다.