• BMB Reports
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• 제57권3호
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• pp.135-142
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• 2024

DNA methylation is one of the most extensively studied epigenetic regulatory mechanisms, known to play crucial roles in various organisms. It has been implicated in the regulation of gene expression and chromatin changes, ranging from global alterations during cell state transitions to locus-specific modifications. 5-hydroxymethylcytosine (5hmC) is produced by a major oxidation, from 5-methylcytosine (5mC), catalyzed by the ten-eleven translocation (TET) enzymes, and is gradually being recognized for its significant role in genome regulation. With the development of state-of-the-art experimental techniques, it has become possible to detect and distinguish 5mC and 5hmC at base resolution. Various techniques have evolved, encompassing chemical and enzymatic approaches, as well as third-generation sequencing techniques. These advancements have paved the way for a thorough exploration of the role of 5hmC across a diverse array of cell types, from embryonic stem cells (ESCs) to various differentiated cells. This review aims to comprehensively report on recent techniques and discuss the emerging roles of 5hmC.

• 한국미생물·생명공학회지
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• 제13권4호
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• pp.361-366
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• 1985

여러 가지 속의 세균을 대상으로 5-fluorocytosine deaminase의 생산균과 기질 특이성을 검토한 결과, 5-fluorocytosine deaminase의 생산성은 종, 속에 관계없이 다양하게 나타났으며 기질로서는 cytosine, 5-fluorocytosine, 5-methylcytosine이 모두 이용될 수 있는 것으로 나타났다. 효소 생산균 중에서 비교적 활성이 높다고 인정되는 Xanthomonas campestris IAM 1671의 효소 생산을 위한 배지의 조성은 glycerin 0.5%, peptone 1%, yeast extract 0.5%. NaCl 0.5% (pH 7.0)로 설정하였다. 본 균의 효소 생산은 500$m\ell$용 진탕 flask에 효소생성 최적배지 90$m\ell$를 넣어 3$0^{\circ}C$에서 24시간 배양했을 때 최대로 나타났다.

• 미생물학회지
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• 제26권4호
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• pp.368-374
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• 1988

Bacillus polymyxa YL38-3이 생성하는 세포의 cytosine deaminase의 효소학적 ,성질을 검토하였다. 본 세포외 효소는 열 안정성이 높으며, 인산완충액(pH6.0)과 $30^{\circ}C$에서 효소활성이 최대를 나타냈다. 본 효소는 cytosine 뿐 아니라 5- fluorocytosine-을 기질로 하나, 5-methylcytosine은 촉매하지 않았다. 더우기 본 효소는 $Cd^{2-}$, $Hg^{2+}$의 중금속이온과 ImM p-chloromercuribenzoate에 의하여 완전히 실활되며, o-phenanthroline과 monoiodoacetate에 의하여 75% 저해되었다. 그러나 1mM 2-mercaptoethanol에 의하여 본 효소의 활성을 약 200% 이상 활성화시켰다.

• Asian-Australasian Journal of Animal Sciences
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• 제30권7호
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• pp.944-949
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• 2017

Objective: Investigated the effect and mechanism of ascorbic acid on the development of porcine embryos produced by somatic cell nuclear transfer (SCNT). Methods: Porcine embryos were produced by SCNT and cultured in the presence or absence of ascorbic acid. Ten-eleven translocation 3 (TET3) in oocytes was knocked down by siRNA injection. After ascorbic acid treatment, reprogramming genes were analyzed by realtime reverse transcription-polymerase chain reaction (RT-PCR). Furthermore, relative 5-methylcytosine and 5-hydroxymethylcytosine content in pronucleus were detected by realtime PCR. Results: Ascorbic acid significantly increased the development of porcine embryos produced by SCNT. After SCNT, transcript levels of reprogramming genes, Pou5f1, Sox2, and Klf were significantly increased in blastocysts. Furthermore, ascorbic acid reduced 5-methylcytosine content in pronuclear embryos compared with the control group. Knock down of TET3 in porcine oocytes significantly prevents the demethylation of somatic cell nucleus after SCNT, even if in the presence of ascorbic acid. Conclusion: Ascorbic acid enhanced the development of porcine SCNT embryos via the increased TET3 mediated demethylation of somatic nucleus.

• Journal of Microbiology and Biotechnology
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• 제14권6호
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• pp.1182-1189
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• 2004

Cytosine deaminase (cytosine aminohydrolase, EC 3.5.4.1) stoichiometrically catalyzes the hydrolytic deamination of cytosine and 5-fluorocytosine to uracil and 5-fluorouracil, respectively. The intracellular cytosine deaminase from Chromobacterium violaceum YK 391 was purified to apparent homogeneity with 272.9-fold purification with an overall yield of $13.8\%$. The enzyme consisted of dimeric polypeptides of 63 kDa, and the total molecular mass was calculated to be approximately 126 kDa. Besides cytosine, the enzyme deaminated 5-fluorocytosine, cytidine, 6-azacytosine, and 5-methylcytosine, but not 5-azacytosine. Optimum pH and temperature for the enzyme reaction were 7.5 and $30^{\circ}C$, respectively. The enzyme was stable at pH 6.0 to 8.0, and at 30T for a week. About $70\%$ of the enzyme activity was retained at $60^{\circ}C$ for 5 min. The apparent $K_{m}$ values for cytosine, 5-fluorocytosine, and 5-methylcytosine were calculated to be 0.38 mM, 0.87 mM, and 2.32 mM, respectively. The enzyme activity was strongly inhibited by 1 mM $Hg^{2+},\;Zn^{2+},\;Cu^{2+},\;Pb^{2+},\;and\;Fe^{3+}$, and by o-phenanthroline, $\alpha,\;{\alpha}'$-dipyridyl, p-choromercuribenzoate, N-bromosuccinimide, and cWoramine­T. In addition, the enzyme activity was strongly inhibited by I mM 2-thiouracil, and weakly inhibited by 2-thiocytosine, or 5-azacytosine. Finally, intracellular and extracellular cytosine deaminases from Chromobacterium violaceum YK 391 were found to have a different optimum temperature, apparent $K_{m}$ value, and molecular mass.

• 미생물학회지
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• 제30권4호
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• pp.305-309
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• 1992

Bacillus stearothermophilus 의 cytosine deaminase (EC 3. 5. 4.1 )를 수율 52.7% 로 7.2배 부분정제했다. 부분정제된 cytosine deaminase 는 cytosine 을 유일한 기질로 이용하였으머 5-methylcytosine 과 5-fluorocytosine 은 기질고 이용되지 못햇으며 cytosine 에 대한 Michaelis 정수 Km 값은 5.9 mM 이었다. 본효소는 pH 4.0 에서 7.0 까지의 폭 넓은 pH 영역에서 안정했으며 80.deg.C 에서 10 분간 열처리하여도 75% 이상의 효소활성이 잔존하여 높은 내열성 효소였다. 본 효소의 반응최적 pH 는 7.0-7.5 였으며 반응 최적 온도는 35. 37.deg.C 였다. 그리고 Arrhenium plot 에 의하여 계산된 활성화 에너지 값(Ea value) 은 26 Kcal/mol 이었다. 본 효소는 중금속인 1 mM의 $Cd^{2+}$ , $Hg^{2+}$ 및 $Cu^{2+}$ 에 의하여 완정히 실활되었으며 GMP 와 CMP 에 의해서는 효소활성이 촉진되었다. 특히 본 효소는 p-chloromercuribenzoate 에 의하여 효소 활성이 강하게 저해되어 thiol 효소임을 추정할 수 있었다.

• Journal of Microbiology and Biotechnology
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• 제31권10호
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• pp.1331-1342
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• 2021

In this study, we evaluated the mechanism of long non-coding RNA MIR22 host gene (LncRNA MIR22HG) in osteosarcoma cells. Forty-eight paired osteosarcoma and adjacent tissues samples were collected and the bioinformatic analyses were performed. Target genes and potential binding sites of MIR22HG, microRNA (miR)-629-5p and tet methylcytosine dioxygenase 3 (TET3) were predicted by Starbase and TargetScan V7.2 and confirmed by dual-luciferase reporter assay. Cell Counting Kit-8, colony formation and flow cytometry assays were utilized to determine the viability, proliferation and apoptosis of transfected osteosarcoma cells. Pearson's analysis was introduced for the correlation analysis between MIR22HG and miR-629-5p in osteosarcoma tissue. Relative expressions of MIR22HG, miR-629-5p and TET3 were measured by quantitative real-time polymerase chain reaction or Western blot. MiR-629-5p could competitively bind with and was negatively correlated with MIR22HG, the latter of which was evidenced by the high expression of miR-629-5p and low expression of MIR22HG in osteosarcoma tissues. Overexpressed MIR22HG repressed the viability and proliferation but enhanced apoptosis of osteosarcoma cells, which was reversed by miR-629-5p upregulation. TET3 was the target gene of miR-629-5p, and the promotive effects of upregulated miR-629-5p on the viability and proliferation as well as its repressive effect on apoptosis were abrogated via overexpressed TET3. To sum up, overexpressed MIR22HG inhibits the viability and proliferation of osteosarcoma cells, which was achieved via regulation of the miR-629-5p/TET3 axis.

• Journal of Microbiology and Biotechnology
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• 제9권2호
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• pp.173-178
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• 1999

The extracellular cytosine deaminase (EC 3.5.4.1) from Chromobacterium violaceum YK 391 was purified 264.7-fold with an overall yield of 14.3%. The enzyme was for the first time homogeneous by the criteria of polyacrylamide gel electrophoresis performed in the absence and in the presence of sodium dodecyl sulfate. The molecular weight of the purified enzyme was estimated to be about 156 kDa. The enzyme consisted of two identical subunits of approximate molecular weight 78 kDa. The isoelectric point of the enzyme was pH 5.55. The enzyme had a pH optimum of 7.5 and a temperature optimum of around 40 to $45^{\circ}C$. Besides cytosine, the enzyme deaminated 5-fluorocytosine, cytidine, 5-methylcytosine, and 6-azacytosine, but not 5-azacytosine. The extracellular cytosine deaminase is believed to be unique because it was active not only on cytosine but also on cytidine. The apparent $K_m$ values for cytosine, 5-fluorocytosine, cytidine, and 5-methylcytosine were determined to be 1.55 mM, 5.52 mM, 10.4 mM, and 67.2 mM, respectively. The enzyme activity was strongly inhibited by heavy metal ions such as $Fe^{2+},Pb^{2+},Cd^{2+},Zn^{2+}, Hg^{2+}, and Cu^{2+}$ at 1 mM, and completely by $\alpha,\alpha$'-dipyridyl, and $\rho$-chloromercuribenzoate at 1 mM, and weakly inhibited by 1mM ο-phenanthroline. The enzyme activity was not affected by various nucleosides and nucleotides.

• 한국발생생물학회:학술대회논문집
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• 한국발생생물학회 2003년도 제3회 국제심포지움 및 학술대회
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• pp.26-28
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• 2003

"Epigenetics" means the study of heritable changes in gene-activity without changes in DNA sequences. Methylation of the cytosine residue in a CpG dinucleotide sequence is a characteristic of the vertebrate genome. In vertebrates, methylation of DNA mainly occurs at the 5′-position of cytosine in a CpG dinucleotide forming 5-methylcytosine. Methylation of DNA plays a profound role in transcriptional repression of gene expression through several mechanisms. Generally, DNA of inactive genes is more heavily methylated than that of active ones; conversely demethylation of DNA reactivates gene expression in vivo and in vitro.

• Molecules and Cells
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• 제38권11호
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• pp.925-935
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• 2015

DNA methylation is a well-characterized epigenetic modification that plays central roles in mammalian development, genomic imprinting, X-chromosome inactivation and silencing of retrotransposon elements. Aberrant DNA methylation pattern is a characteristic feature of cancers and associated with abnormal expression of oncogenes, tumor suppressor genes or repair genes. Ten-eleven-translocation (TET) proteins are recently characterized dioxygenases that catalyze progressive oxidation of 5-methylcytosine to produce 5-hydroxymethylcytosine and further oxidized derivatives. These oxidized methylcytosines not only potentiate DNA demethylation but also behave as independent epigenetic modifications per se. The expression or activity of TET proteins and DNA hydroxymethylation are highly dysregulated in a wide range of cancers including hematologic and non-hematologic malignancies, and accumulating evidence points TET proteins as a novel tumor suppressor in cancers. Here we review DNA demethylation-dependent and -independent functions of TET proteins. We also describe diverse TET loss-of-function mutations that are recurrently found in myeloid and lymphoid malignancies and their potential roles in hematopoietic transformation. We discuss consequences of the deficiency of individual Tet genes and potential compensation between different Tet members in mice. Possible mechanisms underlying facilitated oncogenic transformation of TET-deficient hematopoietic cells are also described. Lastly, we address non-mutational mechanisms that lead to suppression or inactivation of TET proteins in cancers. Strategies to restore normal 5mC oxidation status in cancers by targeting TET proteins may provide new avenues to expedite the development of promising anti-cancer agents.