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1.
Sci Rep ; 6: 39675, 2016 12 21.
Article En | MEDLINE | ID: mdl-28000775

Modified pyrimidine monophosphates such as methyl dCMP (mdCMP), hydroxymethyl dUMP (hmdUMP) and hmdCMP in some phages are synthesized by a large group of enzymes termed as thymidylate synthases (TS). Thymidylate is a nucleotide required for DNA synthesis and thus TS is an important drug target. In the biosynthetic pathway of the nucleoside fungicide mildiomycin isolated from Streptomyces rimofaciens ZJU5119, a cytidylate (CMP) hydroxymethylase, MilA, catalyzes the conversion of CMP into 5'-hydroxymethyl CMP (hmCMP) with an efficiency (kcat/KM) of 5-fold faster than for deoxycytidylate (dCMP). MilA is thus the first enzyme of the TS superfamily preferring CMP to dCMP. Here, we determined the crystal structures of MilA and its complexes with various substrates including CMP, dCMP and hmCMP. Comparing these structures to those of dCMP hydroxymethylase (CH) from T4 phage and TS from Escherichia coli revealed that two residues in the active site of CH and TS, a serine and an arginine, are respectively replaced by an alanine and a lysine, Ala176 and Lys133, in MilA. Mutation of A176S/K133R of MilA resulted in a reversal of substrate preference from CMP to dCMP. This is the first study reporting the evolution of the conserved TS in substrate selection from DNA metabolism to secondary nucleoside biosynthesis.


Bacterial Proteins/metabolism , Cytidine Monophosphate/metabolism , Cytosine/analogs & derivatives , Deoxycytidine/chemistry , Streptomyces/chemistry , Thymidylate Synthase/metabolism , Alanine/chemistry , Binding Sites , Catalytic Domain , Chromatography, High Pressure Liquid , Chromatography, Liquid , Crystallography, X-Ray , Cytosine/biosynthesis , Kinetics , Lysine/chemistry , Mass Spectrometry , Mutagenesis, Site-Directed , Mutation , Ribose/chemistry , Substrate Specificity
2.
Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi ; 32(2): 232-5, 2016 Feb.
Article Zh | MEDLINE | ID: mdl-26927384

OBJECTIVE: To investigate the expression of 5-hydroxymethylcytosine (5hmC) in bladder urothelial carcinoma (UC) and its clinical significance. METHODS: The expression of 5hmC in 21 cases of UC tissues and pericarcinous urinary tract epithelium was detected by immunohistochemical staining. Then the expression of 5hmC in the surgical resection of UC tissues in 92 cases was also surveyed. Non parametric U Mann-Whitney test was used to analyze the correlation between 5hmC expression and clinical data. Single factor survival analysis was performed by Kaplan-Meier test. RESULTS: The expression of 5hmC in normal urinary tract epithelium and UC tissues was significantly different, but there was no significant difference in the expression of 5hmC between low and high grades of UC tissues as well as between different TNM grades. Kaplan-Meier single factor survival analysis showed that there was no significant correlation between the 5hmC expression level and the survival rate or the recurrence-free survival of UC patients. CONCLUSION: The expression level of 5hmC in UC tissues is significantly lower than that in pericarcinous urinary tract epithelium. There is no correlation between the 5hmC expression and the progression, prognosis and recurrence of UC.


Biomarkers, Tumor/biosynthesis , Carcinoma, Transitional Cell/metabolism , Cytosine/analogs & derivatives , Urinary Bladder Neoplasms/metabolism , 5-Methylcytosine/analogs & derivatives , Adult , Aged , Aged, 80 and over , Carcinoma, Transitional Cell/pathology , Cytosine/biosynthesis , Female , Humans , Immunohistochemistry , Kaplan-Meier Estimate , Male , Middle Aged , Neoplasm Staging , Prognosis , Urinary Bladder Neoplasms/pathology
3.
Leuk Res ; 39(10): 1103-8, 2015 Oct.
Article En | MEDLINE | ID: mdl-26277372

Myelodysplastic syndromes (MDS) are myeloid malignancies characterized by ineffective hematopoiesis, dysplasia, peripheral cytopenia and increased risk of progression to acute myeloid leukemia. Refractory cytopenia of childhood (RCC) is the most common subtype of pediatric MDS and has overlapping clinical features with viral infections and autoimmune disorders. Mutations in TET2 gene are found in about 20-25% of adult MDS and are associated with a decrease in 5-hydroxymethylcytosine (5-hmC) content. TET2 deregulation and its malignant potential were reported in adult but not in pediatric MDS. We evaluated the gene expression and the presence of mutations in TET2 gene in 19 patients with RCC. TET2 expression level was correlated with 5-hmC amount in DNA and possible regulatory epigenetic mechanisms. One out of 19 pediatric patients with RCC was a carrier of a TET2 mutation. TET2 expression and 5-hmC levels were decreased in patients when compared to a disease-free group. Lower expression was not associated to the presence of mutation or with the status of promoter methylation, but a significant correlation with microRNA-22 expression was found. These findings suggested that TET2 downregulation and low levels of 5-hmC are inversely related to miR-22 expression. The existence of a regulatory loop between microRNA-22 and TET2 may play a role in MDS pathogenesis.


Cytosine/analogs & derivatives , DNA-Binding Proteins/biosynthesis , Gene Expression Regulation/genetics , MicroRNAs/genetics , Myelodysplastic Syndromes/genetics , Myelodysplastic Syndromes/metabolism , Proto-Oncogene Proteins/biosynthesis , 5-Methylcytosine/analogs & derivatives , Adolescent , Case-Control Studies , Child , Child, Preschool , Cytosine/biosynthesis , DNA Mutational Analysis , DNA-Binding Proteins/genetics , Dioxygenases , Female , High-Throughput Nucleotide Sequencing , Humans , Infant , Male , Mutation , Polymerase Chain Reaction , Proto-Oncogene Proteins/genetics , Transcriptome
4.
Cancer Res ; 75(18): 3912-24, 2015 Sep 15.
Article En | MEDLINE | ID: mdl-26294212

Hypoxia is a hallmark of solid tumors that drives malignant progression by altering epigenetic controls. In breast tumors, aberrant DNA methylation is a prevalent epigenetic feature associated with increased risk of metastasis and poor prognosis. However, the mechanism by which hypoxia alters DNA methylation or other epigenetic controls that promote breast malignancy remains poorly understood. We discovered that hypoxia deregulates TET1 and TET3, the enzymes that catalyze conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), thereby leading to breast tumor-initiating cell (BTIC) properties. TET1/3 and 5hmC levels were closely associated with tumor hypoxia, tumor malignancy, and poor prognosis in breast cancer patients. Mechanistic investigations showed that hypoxia leads to genome-wide changes in DNA hydroxymethylation associated with upregulation of TNFα expression and activation of its downstream p38-MAPK effector pathway. Coordinate functions of TET1 and TET3 were also required to activate TNFα-p38-MAPK signaling as a response to hypoxia. Our results reveal how signal transduction through the TET-TNFα-p38-MAPK signaling axis is required for the acquisition of BTIC characteristics and tumorigenicity in vitro and in vivo, with potential implications for how to eradicate BTIC as a therapeutic strategy.


Breast Neoplasms/genetics , Cell Hypoxia/physiology , DNA Methylation , DNA-Binding Proteins/physiology , Dioxygenases/physiology , Neoplasm Proteins/physiology , Proto-Oncogene Proteins/physiology , Tumor Necrosis Factor-alpha/physiology , p38 Mitogen-Activated Protein Kinases/physiology , 5-Methylcytosine/analogs & derivatives , Animals , Breast Neoplasms/metabolism , Breast Neoplasms/pathology , Cell Hypoxia/genetics , Cell Line, Tumor , Chromatin Immunoprecipitation , Cytosine/analogs & derivatives , Cytosine/biosynthesis , DNA-Binding Proteins/biosynthesis , DNA-Binding Proteins/genetics , Dioxygenases/biosynthesis , Dioxygenases/genetics , Female , Gene Expression Regulation, Neoplastic , Heterografts , Humans , Hypoxia-Inducible Factor 1, alpha Subunit/biosynthesis , Hypoxia-Inducible Factor 1, alpha Subunit/genetics , Mice , Mice, Nude , Mixed Function Oxygenases , Molecular Sequence Data , Neoplasm Proteins/biosynthesis , Neoplasm Proteins/genetics , Neoplastic Stem Cells/cytology , Neoplastic Stem Cells/enzymology , Prognosis , Promoter Regions, Genetic/genetics , Proto-Oncogene Proteins/biosynthesis , Proto-Oncogene Proteins/genetics , Recombinant Fusion Proteins/biosynthesis , Retrospective Studies , Signal Transduction/physiology , Tumor Necrosis Factor-alpha/biosynthesis , Tumor Necrosis Factor-alpha/genetics
5.
Chembiochem ; 16(5): 752-5, 2015 Mar 23.
Article En | MEDLINE | ID: mdl-25676849

RNA methylation is emerging as a regulatory RNA modification that could have important roles in the control and coordination of gene transcription and protein translation. Herein, we describe an in vivo isotope-tracing methodology to demonstrate that the ribonucleoside 5-methylcytidine (m(5)C) is subject to oxidative processing in mammals, forming 5-hydroxymethylcytidine (hm(5)C) and 5-formylcytidine (f(5)C). Furthermore, we have identified hm(5)C in total RNA from all three domains of life and in polyA-enriched RNA fractions from mammalian cells. This suggests m(5)C oxidation is a conserved process that could have critical regulatory functions inside cells.


Cytosine/analogs & derivatives , RNA/chemistry , RNA/metabolism , 5-Methylcytosine/analogs & derivatives , Animals , Chromatography, High Pressure Liquid , Cytosine/biosynthesis , Cytosine/chemistry , Cytosine/metabolism , Mice , Mice, Inbred C57BL , Molecular Structure , Oxidation-Reduction , Tandem Mass Spectrometry
6.
Biochim Biophys Acta ; 1855(2): 144-54, 2015 Apr.
Article En | MEDLINE | ID: mdl-25579174

The epigenetic mark 5-hydroxymethylcytosine (5hmC) has gained interest since 2009, when it was discovered that Ten-Eleven-Translocation (TET) proteins catalyze the conversion of 5-methylcytosine (5mC) into 5hmC. This conversion appears to be an intermediate step in the active DNA demethylation pathway. Factors that regulate DNA hydroxymethylation are frequently affected in cancer, leading to deregulated 5hmC levels. In this review, we will discuss the regulation of DNA hydroxymethylation, defects in this pathway in cancer, and novel therapies that may correct deregulated (hydroxy)methylation of DNA.


Biomarkers, Tumor/biosynthesis , Cytosine/analogs & derivatives , DNA Methylation/genetics , Neoplasms/genetics , 5-Methylcytosine/analogs & derivatives , Cytosine/biosynthesis , DNA-Binding Proteins/genetics , Dioxygenases , Epigenesis, Genetic/genetics , Humans , Isocitrate Dehydrogenase/genetics , Mutation , Neoplasms/pathology , Proto-Oncogene Proteins/genetics
7.
Mod Pathol ; 28(2): 218-29, 2015 Feb.
Article En | MEDLINE | ID: mdl-25081754

Sentinel lymph node biopsies are conducted to stage patients with newly diagnosed melanomas that have histopathological attributes conferring defined levels of metastatic potential. Because benign nevic cells may also form 'deposits' in lymph nodes (nodal nevus), the pathological evaluation for metastatic melanoma within sentinel lymph nodes can be challenging. Twenty-eight sentinel lymph node biopsy cases containing either metastatic melanoma (N=18) or nodal nevi (N=10) were retrieved from the archives of the Brigham and Women's Hospital, Department of Pathology (2011-2014). In addition, two sentinel lymph node cases that were favored to represent metastatic disease but whose histopathological features were viewed as equivocal, with melanoma favored, were also included. Dual labeling for the melanocyte lineage marker, MART-1, and the epigenetic marker, 5-hydroxymethylcytosine, a functionally significant indicator that has been shown to distinguish benign nevi from melanoma, was performed on all cases using immunohistochemistry and/or direct immunofluorescence. All (18 of 18) metastatic melanoma cases showed complete loss of 5-hydroxymethylcytosine nuclear staining in MART-1-positive cells, and all (10 of 10) nodal nevus cases demonstrated 5-hydroxymethylcytosine nuclear staining in MART-1-positive cells. In addition, 5-hydroxymethylcytosine staining confirmed the favored diagnoses of metastatic melanoma in the two 'equivocal' cases. Thus, 5-hydroxymethylcytosine may be a useful adjunctive marker to distinguish between benign nodal nevi and metastatic melanoma during the evaluation of sentinel lymph node biopsies for metastatic melanoma.


Cytosine/analogs & derivatives , Lymph Nodes/pathology , Lymphatic Metastasis/diagnosis , Melanoma/diagnosis , Nevus/diagnosis , Skin Neoplasms/diagnosis , 5-Methylcytosine/analogs & derivatives , Adult , Aged , Aged, 80 and over , Biomarkers, Tumor/analysis , Cytosine/analysis , Cytosine/biosynthesis , Female , Fluorescent Antibody Technique , Humans , Immunohistochemistry , Male , Middle Aged , Sentinel Lymph Node Biopsy
8.
Trends Microbiol ; 23(2): 110-9, 2015 Feb.
Article En | MEDLINE | ID: mdl-25468791

The alarming rise in antibiotic-resistant pathogens has coincided with a decline in the supply of new antibiotics. It is therefore of great importance to find and create new antibiotics. Nucleoside antibiotics are a large family of natural products with diverse biological functions. Their biosynthesis is a complex process through multistep enzymatic reactions and is subject to hierarchical regulation. Genetic and biochemical studies of the biosynthetic machinery have provided the basis for pathway engineering and combinatorial biosynthesis to create new or hybrid nucleoside antibiotics. Dissection of regulatory mechanisms is leading to strategies to increase the titer of bioactive nucleoside antibiotics.


Anti-Bacterial Agents/biosynthesis , Antifungal Agents/metabolism , Antiviral Agents/metabolism , Biotechnology , Nucleosides/biosynthesis , Aminoglycosides/biosynthesis , Aminoglycosides/chemistry , Anti-Bacterial Agents/chemistry , Antifungal Agents/chemistry , Antiviral Agents/chemistry , Cytidine/analogs & derivatives , Cytidine/biosynthesis , Cytosine/analogs & derivatives , Cytosine/biosynthesis , Cytosine/chemistry , Genetic Engineering , Nucleosides/chemistry , Nucleosides/metabolism , Pyrimidine Nucleosides/biosynthesis , Pyrimidine Nucleosides/chemistry
9.
J Cutan Pathol ; 41(12): 901-6, 2014 Dec.
Article En | MEDLINE | ID: mdl-25353265

BACKGROUND: The methylation of DNA at position 5 of cytosine, and the subsequent reduction in intracellular 5-hydroxymethylcytosine (5-hmC) levels, is a key epigenetic event in several cancers, including systemic lymphomas. However, no studies have analyzed this epigenetic marker in cutaneous lymphomas. Therefore, we aimed to analyze the expression of 5-hmC in cutaneous CD30-positive lymphoproliferative disorders and compare it with a control group composed of reactive infectious and inflammatory disorders with CD30-positive cells. METHODS: Retrospective case series study with immunohistochemical analysis using anti-CD30 and anti-5-hmC antibodies in control (n = 19), lymphomatoid papulosis (LyP) (n = 27) and primary cutaneous anaplastic large cell lymphoma (ALCL) (n = 14) specimens. RESULTS: Complete loss of 5-hmC nuclear staining by CD30+ cells was observed in 63% of LyP cases, 57% of ALCL cases and 0% of control cases. CONCLUSIONS: The presence of 5-hmC+ and CD30+ lymphocytes was highly suggestive of a benign process. In contrast, loss of 5-hmC nuclear staining was highly suggestive of a lymphoproliferative disorder (ALCL or LyP). Under these circumstances, the use of 5-hmC staining can be a useful adjunctive tool for discriminating between neoplastic CD30+ lymphoproliferations and inflammatory/infectious simulators harboring reactive CD30+ cells.


Cytosine/analogs & derivatives , Ki-1 Antigen/metabolism , Lymphoma, Primary Cutaneous Anaplastic Large Cell/metabolism , Skin Neoplasms/metabolism , 5-Methylcytosine/analogs & derivatives , Adolescent , Adult , Aged , Aged, 80 and over , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , Case-Control Studies , Child , Cytosine/biosynthesis , Cytosine/metabolism , Epigenesis, Genetic , Female , Humans , Immunohistochemistry/methods , Lymphoma, Primary Cutaneous Anaplastic Large Cell/genetics , Lymphoma, Primary Cutaneous Anaplastic Large Cell/pathology , Lymphomatoid Papulosis/metabolism , Lymphomatoid Papulosis/pathology , Male , Middle Aged , Retrospective Studies , Skin Neoplasms/genetics , Skin Neoplasms/pathology , Young Adult
10.
Cell Rep ; 9(1): 48-60, 2014 Oct 09.
Article En | MEDLINE | ID: mdl-25284789

The development of cancer is driven not only by genetic mutations but also by epigenetic alterations. Here, we show that TET1-mediated production of 5-hydroxymethylcytosine (5hmC) is required for the tumorigenicity of glioblastoma cells. Furthermore, we demonstrate that chromatin target of PRMT1 (CHTOP) binds to 5hmC. We found that CHTOP is associated with an arginine methyltransferase complex, termed the methylosome, and that this promotes the PRMT1-mediated methylation of arginine 3 of histone H4 (H4R3) in genes involved in glioblastomagenesis, including EGFR, AKT3, CDK6, CCND2, and BRAF. Moreover, we found that CHTOP and PRMT1 are essential for the expression of these genes and that CHTOP is required for the tumorigenicity of glioblastoma cells. These results suggest that 5hmC plays a critical role in glioblastomagenesis by recruiting the CHTOP-methylosome complex to selective sites on the chromosome, where it methylates H4R3 and activates the transcription of cancer-related genes.


Brain Neoplasms/metabolism , Carcinogenesis/metabolism , Cytosine/analogs & derivatives , Glioblastoma/metabolism , 5-Methylcytosine/analogs & derivatives , Acetylation , Brain Neoplasms/genetics , Carcinogenesis/genetics , Chromatin/genetics , Chromatin/metabolism , Cytosine/biosynthesis , Cytosine/metabolism , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Gene Expression Regulation, Neoplastic , Glioblastoma/genetics , HEK293 Cells , Histones/genetics , Histones/metabolism , Humans , Methylation , Mixed Function Oxygenases , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Protein-Arginine N-Methyltransferases/genetics , Protein-Arginine N-Methyltransferases/metabolism , Proto-Oncogene Proteins/genetics , Proto-Oncogene Proteins/metabolism , Repressor Proteins/genetics , Repressor Proteins/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , Transcription, Genetic
11.
J Am Chem Soc ; 136(33): 11582-5, 2014 Aug 20.
Article En | MEDLINE | ID: mdl-25073028

Oxidation of 5-methylcytosine in DNA by ten-eleven translocation (Tet) family of enzymes has been demonstrated to play a significant role in epigenetic regulation in mammals. We found that Tet enzymes also possess the activity of catalyzing the formation of 5-hydroxymethylcytidine (5-hmrC) in RNA in vitro. In addition, the catalytic domains of all three Tet enzymes as well as full-length Tet3 could induce the formation of 5-hmrC in human cells. Moreover, 5-hmrC was present at appreciable levels (∼1 per 5000 5-methylcytidine) in RNA of mammalian cells and tissues. Our results suggest the involvement of this oxidation in RNA biology.


Cytosine/analogs & derivatives , DNA-Binding Proteins/metabolism , Dioxygenases/metabolism , Proto-Oncogene Proteins/metabolism , RNA/metabolism , 5-Methylcytosine/analogs & derivatives , Animals , Cytosine/biosynthesis , Cytosine/chemistry , Cytosine/metabolism , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/deficiency , Dioxygenases/chemistry , Dioxygenases/deficiency , Embryonic Stem Cells/metabolism , HEK293 Cells , Humans , Mice , Mixed Function Oxygenases , Proto-Oncogene Proteins/chemistry , Proto-Oncogene Proteins/deficiency , RNA/chemistry
12.
Glia ; 62(6): 914-26, 2014 Jun.
Article En | MEDLINE | ID: mdl-24615693

The ten-eleven translocation (TET) family of methylcytosine dioxygenases catalyze oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and promote DNA demethylation. Despite the abundance of 5hmC and TET proteins in the brain, little is known about their role in oligodendrocytes (OLs). Here, we analyzed TET expression during OL development in vivo and in vitro, and found that three TET family members possess unique subcellular and temporal expression patterns. Furthermore, the level of 5hmC exhibits dynamic changes during OL maturation, which implies that 5hmC modification may play a role in the expression of critical genes necessary for OL maturation. siRNA-mediated silencing of the TET family proteins in OLs demonstrated that each of the TET proteins is required for OL differentiation. However, based on their unique domain structures, we speculate that the three TET members may function by different mechanisms. In summary, we have established the temporal expression of TET proteins and the dynamic level of 5hmC during OL development and demonstrate that all three TET members are necessary for OL differentiation.


Cell Differentiation/physiology , Cytosine/analogs & derivatives , DNA-Binding Proteins/biosynthesis , Dioxygenases/biosynthesis , Oligodendroglia/physiology , Proto-Oncogene Proteins/biosynthesis , 5-Methylcytosine/analogs & derivatives , Amino Acid Sequence , Animals , Animals, Newborn , Cytosine/biosynthesis , DNA-Binding Proteins/genetics , Dioxygenases/genetics , Humans , Mice , Mixed Function Oxygenases , Molecular Sequence Data , Proto-Oncogene Proteins/genetics , Rats , Rats, Sprague-Dawley
13.
Biochem Biophys Res Commun ; 439(4): 522-7, 2013 Oct 04.
Article En | MEDLINE | ID: mdl-24021282

Tet (ten-eleven translocation) methylcytosine dioxygenases, which belong to the iron and 2-oxoglutarate (2OG)-dependent dioxygenase superfamily, convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) in DNA. We recently reported that ascorbate (vitamin C) induces Tet-mediated generation of 5hmC. To initially delineate the role of ascorbate on 5hmC generation, we analyzed whether the effect of ascorbate is dependent upon the conditions of other components involved in the hydroxylation of 5mC catalyzed by Tet. We found that removing iron from the culture medium did not affect the induction of 5hmC by ascorbate (10 µM) in mouse embryonic fibroblasts (MEFs). The effect of ascorbate did not involve an increased expression of Tet1-3 or isocitrate dehydrogenases (IDH1-2), the enzymes responsible for producing 2OG. Interestingly, MEFs cultured with different concentrations of glucose, a major precursor of 2OG, exhibited nearly identical responses to ascorbate treatment. Further, blocking the uptake of the reduced form of vitamin C, ascorbic acid, through the sodium-dependent vitamin C transporters (SVCTs) inhibited the effect of ascorbate on 5hmC. However, inhibition of the facilitative glucose transporters (GLUTs), which mediate the incorporation of the oxidized form of vitamin C, dehydroascorbic acid (DHA), did not modify the ability of ascorbate to induce 5hmC generation. These results indicate that the effect of ascorbate on 5hmC is not dependent upon iron uptake, the expression of Tet and IDH, or the production of 2OG, suggesting that ascorbate may directly participate in the generation of 5hmC, most likely as a cofactor of Tet.


Ascorbic Acid/metabolism , Cytosine/analogs & derivatives , Iron/metabolism , Ketoglutaric Acids/metabolism , 5-Methylcytosine/chemistry , 5-Methylcytosine/metabolism , Animals , Ascorbic Acid/pharmacology , Cytosine/biosynthesis , DNA Methylation , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Dioxygenases , Fibroblasts/metabolism , Isocitrate Dehydrogenase/genetics , Isocitrate Dehydrogenase/metabolism , Mice , Mice, Inbred C57BL , Proto-Oncogene Proteins/genetics , Proto-Oncogene Proteins/metabolism , Sodium-Coupled Vitamin C Transporters/genetics , Sodium-Coupled Vitamin C Transporters/metabolism
14.
J Biol Chem ; 288(19): 13669-74, 2013 May 10.
Article En | MEDLINE | ID: mdl-23548903

BACKGROUND: Tet methylcytosine dioxygenase converts 5-mC to 5-hmC in DNA. RESULTS: Ascorbate significantly and specifically enhances Tet-mediated generation of 5-hmC. CONCLUSION: Our findings suggest that ascorbate enhances 5-hmC generation, most likely by acting as a co-factor for Tet methylcytosine dioxygenase to generate 5-hmC. SIGNIFICANCE: The availability of ascorbate could have significant consequences for health and diseases by modulating the epigenetic control of genome activity. Ascorbate (vitamin C) is best known for its role in scurvy, in which the hydroxylation of collagen catalyzed by dioxygenases is incomplete due to ascorbate deficiency. Here, we report a novel function of ascorbate in the hydroxylation of 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC) in DNA catalyzed by Tet (ten-eleven translocation) methylcytosine dioxygenase. The content of 5-hmC is extremely low in mouse embryonic fibroblasts cultured in ascorbate-free medium. Additions of ascorbate dose- and time-dependently enhance the generation of 5-hmC, without any effects on the expression of Tet genes. Treatment with another reducer glutathione (GSH) does not change the level of 5-hmC. Further, blocking ascorbate entry into cells by phloretin and knocking down Tet (Tet1, Tet2, and Tet3) expression by short interference RNAs (siRNA) significantly inhibit the effect of ascorbate on 5-hmC. These results suggest that ascorbate enhances 5-hmC generation, most likely by acting as a co-factor for Tet methylcytosine dioxygenase to hydroxylate 5-mC. Thus, we have uncovered a novel role for ascorbate in modulating the epigenetic control of genome activity.


Ascorbic Acid/physiology , Cytosine/analogs & derivatives , DNA Methylation , DNA-Binding Proteins/metabolism , Proto-Oncogene Proteins/metabolism , 5-Methylcytosine/analogs & derivatives , Animals , Ascorbic Acid/pharmacology , Cells, Cultured , Cytosine/biosynthesis , DNA-Binding Proteins/genetics , Dioxygenases , Epigenesis, Genetic , Gene Knockdown Techniques , Hydroxylation , Mice , Mice, Inbred C57BL , Phloretin/pharmacology , Proto-Oncogene Proteins/genetics , RNA, Small Interfering/genetics
15.
Melanoma Res ; 23(3): 218-20, 2013 Jun.
Article En | MEDLINE | ID: mdl-23458759

Several research groups have recently reported on markedly reduced levels of 5-hydroxymethylcytosine (5hmC) in human breast, liver, lung, pancreatic, colon, prostate, brain, and myeloid cancers. We studied benign compound nevi (BCN, n=17), dysplastic compound nevi (DCN, n=15), superficial spreading melanomas [SSM, stratified in <1 mm (n=19) and >4 mm (n=18) Breslow tumor thickness], and cutaneous metastatic disease (CMD, n=24). Immunohistochemistry included specific antibodies against 5hmC, 5-methylcytosine (5mC), and ten-eleven translocation 2 protein (TET2). Immunohistological scoring showed significantly (P<0.0001) higher median 5hmC levels in BCN and DCN than in thin SSM, thick SSM, and CMD. 5mC immunoreactivity did not differ significantly (P=0.15) between nevi and melanoma. The intensity of TET2 expression was predominantly weak but was found to be significantly (P<0.0001) more often in nevi than in thin SSM, thick SSM, and CMD. We have shown that 5hmC levels and TET2 expression are significantly reduced in advanced melanomas compared with nevi and thin melanomas. It is suggested that 5hmC and TET2 possibly play an important role in the epigenetic regulation of melanoma development and progression.


Cytosine/analogs & derivatives , DNA-Binding Proteins/biosynthesis , DNA-Binding Proteins/deficiency , Melanoma/metabolism , Proto-Oncogene Proteins/biosynthesis , Proto-Oncogene Proteins/deficiency , Skin Neoplasms/metabolism , 5-Methylcytosine/analogs & derivatives , Biomarkers, Tumor/biosynthesis , Biomarkers, Tumor/metabolism , Cytosine/biosynthesis , Cytosine/metabolism , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Dioxygenases , Disease Progression , Epigenomics , Humans , Melanoma/pathology , Paraffin Embedding , Proto-Oncogene Proteins/genetics , Proto-Oncogene Proteins/metabolism , Skin Neoplasms/pathology , Translocation, Genetic
16.
Chembiochem ; 13(11): 1613-21, 2012 Jul 23.
Article En | MEDLINE | ID: mdl-22753012

Mildiomycin (MIL) is a peptidyl-nucleoside antibiotic produced by Streptoverticillum remofaciens ZJU5119 that exhibits strong inhibitory activity against powdery mildew. The entire MIL biosynthesis gene cluster was cloned and expressed in Streptomyces lividans 1326. Systematic gene disruptions narrowed down the cluster to 16 functional ORFs and identified the boundaries of the gene cluster. A putative cytosylglucuronic acid (CGA) synthase gene, milC, was disrupted in Sv. remofaciens and heterologously expressed in E. coli. An in vitro assay revealed that purified MilC could utilize either cytosine or hydroxymethylcytosine as substrate to yield CGA or hydroxymethyl-CGA (HM-CGA), respectively. MilG is believed to be a key enzyme in the MIL biosynthesis pathway and contains the C(XXX)C(XX)C motif characteristic of members of the radical S-adenosyl methionine (SAM) superfamily. Disruption of milG leads to accumulation of HM-CGA. Labeling experiments with (13)C(6)-L-arginine indicated that decarboxylation at C5 of the pyranoside ring was coupled with the attachment of 5-guanidino-2,4-dihydroxyvalerate side chain through C-C bond formation. In contrast, exogenous (13)C(6)-labeled 4-hydroxy-L-arginine was not incorporated into the MIL structure. Comparative analysis of the 16 MIL ORFs with counterparts involved in the biosynthesis of the structurally similar compound blasticidin S, along with the results above, provide insight into the complete MIL biosynthetic pathway.


Actinomycetales/enzymology , Actinomycetales/genetics , Glucuronosyltransferase/metabolism , Actinomycetales/metabolism , Cytosine/analogs & derivatives , Cytosine/analysis , Cytosine/biosynthesis , Cytosine/metabolism , Glucuronosyltransferase/analysis , Glucuronosyltransferase/genetics , Molecular Sequence Data
17.
Blood ; 118(9): 2551-5, 2011 Sep 01.
Article En | MEDLINE | ID: mdl-21734233

TET2 converts 5-methylcytosine to 5-hydroxymethylcytosine (5-hmC) in DNA and is frequently mutated in myeloid malignancies, including myeloproliferative neoplasms. Here we show that the level of 5-hmC is decreased in granulocyte DNA from myeloproliferative neoplasm patients with TET2 mutations compared with granulocyte DNA from healthy patients. Inhibition of TET2 by RNA interference decreases 5-hmC levels in both human leukemia cell lines and cord blood CD34(+) cells. These results confirm the enzymatic function of TET2 in human hematopoietic cells. Knockdown of TET2 in cord blood CD34(+) cells skews progenitor differentiation toward the granulomonocytic lineage at the expense of lymphoid and erythroid lineages. In addition, by monitoring in vitro granulomonocytic development we found a decreased granulocytic differentiation and an increase in monocytic cells. Our results indicate that TET2 disruption affects 5-hmC levels in human myeloid cells and participates in the pathogenesis of myeloid malignancies through the disturbance of myeloid differentiation.


5-Methylcytosine/metabolism , Cytosine/analogs & derivatives , DNA Methylation/genetics , DNA-Binding Proteins/physiology , Erythropoiesis/genetics , Hematopoietic Stem Cells/cytology , Myelopoiesis/genetics , Proto-Oncogene Proteins/physiology , RNA Interference , RNA, Small Interfering/genetics , Cell Line, Tumor , Cell Lineage , Colony-Forming Units Assay , Cytosine/biosynthesis , DNA-Binding Proteins/antagonists & inhibitors , DNA-Binding Proteins/genetics , Dioxygenases , Erythropoiesis/physiology , Fetal Blood/cytology , Genetic Vectors/genetics , Granulocytes/metabolism , Granulocytes/pathology , Humans , Lentivirus/genetics , Monocytes/metabolism , Monocytes/pathology , Mutation , Myelopoiesis/physiology , Proto-Oncogene Proteins/antagonists & inhibitors , Proto-Oncogene Proteins/genetics , RNA, Small Interfering/administration & dosage
18.
Chembiochem ; 9(8): 1286-94, 2008 May 23.
Article En | MEDLINE | ID: mdl-18412191

Mildiomycin (MIL) is a peptidyl nucleoside antibiotic with strong activity against powdery mildew disease of plants. We have cloned the MIL biosynthetic gene cluster in Streptoverticillum rimofaciens ZJU5119 and shown that this organism also produces the related antifungal compound, deshydroxymethyl mildiomycin (dHM-MIL). A cosmid genomic library was screened for a putative nucleotide hydrolase gene that is related to blsM from the blasticidin S cluster. Six cosmids were identified that contained a 3.5 kb DNA fragment that harbors a homologue of blsM. The sequence of the fragment revealed two open-reading frames that are likely to function in MIL formation: milA is a CMP hydroxymethylase gene and milB is the homologue of the CMP hydrolase gene blsM. Insertional disruption of milA abolished the production of MIL but not dHM-MIL, whereas a milB knockout strain did not produce either of the peptidyl nucleosides. Recombinant MilA was produced in E. coli and shown to specifically introduce a C-5 hydroxymethyl group on CMP, but it did not accept cytosine or dCMP as a substrate. MilB was also expressed and purified from E. coli and shown to efficiently hydrolyze both hydroxymethyl-CMP (HMCMP) and could accept CMP as an alternative substrate. The ratio of free HMC and cytosine released by MilB was ca. 9:1 in in vitro assays, and is consistent with the higher levels of MIL compared to dHM-MIL that are produced by Streptoverticillum rimofaciens.


Cytidine Monophosphate/analogs & derivatives , Cytosine/analogs & derivatives , Streptomycetaceae/chemistry , Streptomycetaceae/metabolism , 5-Methylcytosine/analogs & derivatives , Amino Acid Sequence , Chromatography, High Pressure Liquid , Cloning, Molecular , Cytidine Monophosphate/biosynthesis , Cytidine Monophosphate/chemistry , Cytosine/biosynthesis , Cytosine/chemistry , Mass Spectrometry , Molecular Sequence Data , Molecular Structure , Multigene Family , Sequence Alignment , Streptomycetaceae/genetics , Substrate Specificity
19.
J Zhejiang Univ Sci B ; 9(1): 77-84, 2008 Jan.
Article En | MEDLINE | ID: mdl-18196616

Cytosine-substituted mildiomycin analogue (MIL-C) was produced effectively by supplementing cytosine into the culture of Streptoverticillium rimofaciens. In order to improve the yield of MIL-C, statistically-based experimental designs were applied to optimize the fermentation medium for S. rimofaciens ZJU 5119. Fifteen culture conditions were examined for their significances on MIL-C production using Plackett-Burman design. The Plackett-Burman design and one-variable-at-a-time design indicated that glucose and rice meal as the complex carbon sources, and peanut cake meal and NH4NO3 as the complex nitrogen sources were beneficial for MIL-C production in S. rimofaciens ZJU 5119. The results of further central composition design (CCD) showed that the optimal concentration of glucose, rice meal and peanut cake meal were 18.7 g/L, 64.8 g/L and 65.1 g/L, respectively. By using this optimal fermentation medium, the MIL-C concentration was increased up to 1336.5 mg/L, an approximate 3.8-fold improvement over the previous concentration (350.0 mg/L) with un-optimized medium. This work will be very helpful to the large-scale production of MIL-C in the future.


Anti-Bacterial Agents/biosynthesis , Streptomycetaceae/metabolism , Culture Media , Cytosine/analogs & derivatives , Cytosine/biosynthesis , Fermentation
20.
Enferm. infecc. microbiol. clín. (Ed. impr.) ; 25(2): 143-154, feb. 2007. ilus, tab
Article Es | IBECS | ID: ibc-053522

El reconocimiento de lo extraño es una característica inherente a los seres vivos y garantiza su supervivencia. Burlar este mecanismo de defensa es uno de los objetivos más difíciles para garantizar el éxito de un trasplante pero conlleva una serie de consecuencias, fundamentalmente de causa infecciosa. Los linfocitos T constituyen la piedra angular en la respuesta halogénica. Éstos reconocen los antígenos intracelulares o extracelulares en las células presentadoras sobre las moléculas HLA. Como resultado se produce una expansión linfocitaria que ocurre a varios niveles y que tiene como resultado final una respuesta de tipo humoral o celular. Los regímenes de inmunosupresión utilizados en el trasplante son utilizados en la inducción, en el mantenimiento o como rescate. Las terapias de inducción actúan fundamentalmente disminuyendo la proporción de precursores de células T y disminuyendo la eficacia de presentación de antígenos. En relación a las terapias de mantenimiento, ciclosporina y tacrolimus inhiben la transcripción de citocinas, azatioprina y mofetil micofenolato inhiben la síntesis de nucleótidos y sirolimus y everolimus inhiben la transducción de la señal de factores de crecimiento. Como consecuencia de la inmunosupresión los microorganismos oportunistas aparecen como reactivación endógena de infecciones latentes o desde un origen exógeno. Su prevención, mediante el adecuado conocimiento de factores de riesgo, su rápido diagnóstico y su correcto manejo son fundamentales para garantizar la supervivencia del paciente (AU)


Recognizing a foreign element is an inherent characteristic of living beings and guarantees their survival. Evading this defense mechanism is one of the most difficult requirements for transplant success, but it leads to a series of consequences, mainly related to infection. T lymphocytes are the cornerstone of the allogenic response. These cells recognize intracellular and extracellular antigens over HLA molecules in host cells. As a consequence, lymphocytic expansion occurring on several levels is produced, and a humoral or cellular response is the final result. The immunosuppression regimens used in transplantation include induction, maintenance and rescue therapy. Induction therapy serves primarily to decrease the proportion of T-cell precursors and to lower the efficacy of antigen presentation. With respect to maintenance therapy, cyclosporine and tacrolimus inhibit cytokine transcription, azathioprine, and mycophenolate mofetil inhibit nucleotide synthesis, and sirolimus and everolimus inhibit transduction of growth factor signals. As a consequence of immunosuppression, opportunistic microorganisms may appear with endogenic reactivation of latent infection or from an exogenous origin. Prevention of these infections by proper knowledge of the risk factors, rapid diagnosis, and adequate management are fundamental to guarantee the survival of the patient (AU)


Animals , Humans , Immunosuppressive Agents/adverse effects , Immunosuppressive Agents/classification , Infections/etiology , Postoperative Complications/etiology , Organ Transplantation , Bacterial Infections/drug therapy , Bacterial Infections/etiology , Bacterial Infections/prevention & control , Calcineurin/antagonists & inhibitors , Cytosine/biosynthesis , Gene Expression Regulation , Immunocompromised Host , Immunosuppressive Agents/pharmacology , Intercellular Signaling Peptides and Proteins/biosynthesis , Intercellular Signaling Peptides and Proteins/genetics , Mycoses/drug therapy , Mycoses/etiology , Parasitic Diseases/etiology
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