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Zixin Deng - One of the best experts on this subject based on the ideXlab platform.
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a novel DNA Modification by sulfur dnda is a nifs like cysteine desulfurase capable of assembling dndc as an iron sulfur cluster protein in streptomyces lividans
Biochemistry, 2007Co-Authors: Delin You, Xiufen Zhou, Lianrong Wang, Fen Yao, Zixin DengAbstract:A novel DNA Modification system by sulfur (S) in Streptomyces lividans 66 was reported to be encoded by a cluster of five genes designated dndA-E [Zhou, X., He, X., Liang, J., Li, A., Xu, T., Kieser, T., Helmann, J. D., and Deng, Z. (2005) Mol. Microbiol. 57, 1428-1438]. The dndA gene was cloned and the protein product expressed in Escherichia coli, purified to homogeneity, and characterized as a homodimeric protein of ca. 91 kDa. Purified DndA has a yellow color and UV-visible spectra characteristic of a pyridoxal phosphate-containing enzyme and was proven to be a cysteine desulfurase able to catalyze removal of elemental S atoms from l-cysteine to produce l-alanine with substrate specificity similar to that of E. coli IscS. DndC was also purified to homogeneity and found to contain a 4Fe-4S cluster by spectral analysis and have obvious ATP pyrophosphatase activity. DndA could catalyze iron-sulfur cluster assembly by activation of apo-Fe DndC protein prepared by removal of its iron-sulfur cluster using alpha,alpha'-dipyridyl. A mutated DndA, with serine substituted for cysteine at position 327, which was confirmed to have lost its corresponding cysteine desulfurase activity, also lost its ability to reactivate the apo-Fe DndC. The likely involvement of an interaction between DndA and DndC in the biochemical pathway for the unusual site-specific DNA Modification in S. lividans 66 is discussed.
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DNA Modification by sulfur analysis of the sequence recognition specificity surrounding the Modification sites
Nucleic Acids Research, 2007Co-Authors: Jingdan Liang, Xiufen Zhou, Zhijun Wang, Zixin DengAbstract:The Dnd (DNA degradation) phenotype, reflecting a novel DNA Modification by sulfur in Streptomyces lividans 1326, was strongly aggravated when one (dndB) of the five genes (dndABCDE) controlling it was mutated. Electrophoretic banding patterns of a plasmid (pHZ209), reflecting DNA degradation, displayed a clear change from a preferential Modification site in strain 1326 to more random Modifications in the mutant. Fourteen randomly modifiable sites on pHZ209 were localized, and each seemed to be able to be modified only once. Residues in a region (5'-c-cGGCCgccg-3') including a highly conserved 4-bp central core (5'-GGCC-3') in a well-documented preferential Modification site were assessed for their necessity by site-directed mutagenesis. While the central core (GGCC) was found to be stringently required in 1326 and in the mutant, 'gccg' flanking its right could either abolish or reduce the Modification frequency only in the mutant, and two separate nucleotides to the left had no dramatic effect. The lack of essentiality of DndB for S-Modification suggests that it might only be required for enhancing or stabilizing the activity of a protein complex at the required preferential Modification site, or resolving secondary structures flanking the modifiable site(s), known to constitute an obstacle for efficient Modification.
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a novel DNA Modification by sulfur dnda is a nifs like cysteine desulfurase capable of assembling dndc as an iron sulfur cluster protein in streptomyces lividans
Biochemistry, 2007Co-Authors: Delin You, Xiufen Zhou, Lianrong Wang, Fen Yao, Zixin DengAbstract:A novel DNA Modification system by sulfur (S) in Streptomyces lividans 66 was reported to be encoded by a cluster of five genes designated dndA−E [Zhou, X., He, X., Liang, J., Li, A., Xu, T., Kieser, T., Helmann, J. D., and Deng, Z. (2005) Mol. Microbiol. 57, 1428−1438]. The dndA gene was cloned and the protein product expressed in Escherichia coli, purified to homogeneity, and characterized as a homodimeric protein of ca. 91 kDa. Purified DndA has a yellow color and UV−visible spectra characteristic of a pyridoxal phosphate-containing enzyme and was proven to be a cysteine desulfurase able to catalyze removal of elemental S atoms from l-cysteine to produce l-alanine with substrate specificity similar to that of E. coli IscS. DndC was also purified to homogeneity and found to contain a 4Fe-4S cluster by spectral analysis and have obvious ATP pyrophosphatase activity. DndA could catalyze iron−sulfur cluster assembly by activation of apo-Fe DndC protein prepared by removal of its iron−sulfur cluster using α...
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a novel DNA Modification by sulphur
Molecular Microbiology, 2005Co-Authors: Xiufen Zhou, Jingdan Liang, Tobias Kieser, John D Helmann, Zixin DengAbstract:Streptomyces lividans has a novel DNA Modification, which sensitises its DNA to degradation during electrophoresis (the Dnd phenotype). The entire gene cluster (dnd) involved in this Modification was localized on an 8 kb DNA fragment and was expressed in a S. lividans deletion mutant (dnd) and in several heterologous hosts. Disruption of the dnd locus abolishes the Dnd phenotype, and gain of the dnd locus conferred the Dnd phenotype respectively. Extensive analysis of the dnd gene cluster revealed five open reading frames, whose hypothetic functions suggested an incorporation of sulphur or a sulphur-containing substance into S. lividans genome, yet in an unknown manner. The Dnd phenotype was also discovered to exist in DNA of widespread bacterial species of variable origin and diverse habitat. Similarly organized gene clusters were found in several bacterial genomes representing different genera and in eDNA of marine organisms, suggesting such Modification as a widespread phenomenon. A coincidence between the Dnd phenotype and DNA Modification by sulphur was demonstrated to occur in several representative bacterial genomes by the in vivo(35)S-labelling experiments.
Chuanle Xiao - One of the best experts on this subject based on the ideXlab platform.
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n6 methyladenine DNA Modification in the human genome
Molecular Cell, 2018Co-Authors: Chuanle Xiao, Song Zhu, De Chen, Qian Zhang, Ying Chen, Jinbao Liu, Shangqian Xie, Feng LuoAbstract:DNA N6-methyladenine (6mA) Modification is the most prevalent DNA Modification in prokaryotes, but whether it exists in human cells and whether it plays a role in human diseases remain enigmatic. Here, we showed that 6mA is extensively present in the human genome, and we cataloged 881,240 6mA sites accounting for ∼0.051% of the total adenines. [G/C]AGG[C/T] was the most significantly associated motif with 6mA Modification. 6mA sites were enriched in the coding regions and mark actively transcribed genes in human cells. DNA 6mA and N6-demethyladenine Modification in the human genome were mediated by methyltransferase N6AMT1 and demethylase ALKBH1, respectively. The abundance of 6mA was significantly lower in cancers, accompanied by decreased N6AMT1 and increased ALKBH1 levels, and downregulation of 6mA Modification levels promoted tumorigenesis. Collectively, our results demonstrate that DNA 6mA Modification is extensively present in human cells and the decrease of genomic DNA 6mA promotes human tumorigenesis.
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N6-Methyladenine DNA Modification in Xanthomonas oryzae pv. oryzicola genome
Nature Publishing Group, 2018Co-Authors: Chuanle Xiao, Shangqian Xie, Qing-biao Xie, Zhao-yu Liu, Jian-feng Xing, Jun Tao, Liang-ying Dai, Feng LuoAbstract:Abstract DNA N6-methyladenine (6mA) Modifications expand the information capacity of DNA and have long been known to exist in bacterial genomes. Xanthomonas oryzae pv. Oryzicola (Xoc) is the causative agent of bacterial leaf streak, an emerging and destructive disease in rice worldwide. However, the genome-wide distribution patterns and potential functions of 6mA in Xoc are largely unknown. In this study, we analyzed the levels and global distribution patterns of 6mA Modification in genomic DNA of seven Xoc strains (BLS256, BLS279, CFBP2286, CFBP7331, CFBP7341, L8 and RS105). The 6mA Modification was found to be widely distributed across the seven Xoc genomes, accounting for percent of 3.80, 3.10, 3.70, 4.20, 3.40, 2.10, and 3.10 of the total adenines in BLS256, BLS279, CFBP2286, CFBP7331, CFBP7341, L8, and RS105, respectively. Notably, more than 82% of 6mA sites were located within gene bodies in all seven strains. Two specific motifs for 6 mA Modification, ARGT and AVCG, were prevalent in all seven strains. Comparison of putative DNA methylation motifs from the seven strains reveals that Xoc have a specific DNA methylation system. Furthermore, the 6 mA Modification of rpfC dramatically decreased during Xoc infection indicates the important role for Xoc adaption to environment
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n6 methyladenine DNA Modification in human genome
bioRxiv, 2017Co-Authors: Chuanle Xiao, Song Zhu, De Chen, Ying Chen, Shangqian Xie, Feng Luo, Zhe Liang, Kai Wang, Guangrong YanAbstract:In human cells, DNA 5-methylcytosine (5mC) Modification plays an important role as an epigenetic mark. However, DNA N6-methyladenine Modification (6mA), which is predominantly present in prokaryotes and a limited number of eukaryotes, is considered to be absent in human genomic DNA. Here, we show that 6mA is present in human genome, and we identified 881,240 6mA sites whose density is about 0.051% of the total adenines in the human genome DNA, but more than 0.18% in the mitochondrion genome. [G/C]AGG[C/T] was the most significant motif associated with 6mA Modification. 6mA sites are enriched in the exon coding regions (P=0.02) and associated with transcriptional activation (P<0.001). We further identify that DNA N6-methyladenine and N6-demethyladenine Modification is mediated by 6mA methytransferase N6AMT1 and 6mA demethytransferase ALKBH1, respectively. The 6mA abundance is significantly lower in cancer tissues compared to adjacent normal tissues, always accompanying with lower N6AMT1 and higher ALKBH1 level. Collectively, we uncover a DNA Modification in human and describe a potential role of the N6AMT1/ALKBH1-6mA regulatory axis in the progression of human disease, such as cancer.
Jianping Ding - One of the best experts on this subject based on the ideXlab platform.
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molecular mechanism for vitamin c derived c5 glyceryl methylcytosine DNA Modification catalyzed by algal tet homologue cmd1
Nature Communications, 2021Co-Authors: Tianlong Zhang, Mingliang Sun, Yu Shi, Xiaojie Zhang, Jianping DingAbstract:C5-glyceryl-methylcytosine (5gmC) is a novel DNA Modification catalyzed by algal TET homologue CMD1 using vitamin C (VC) as co-substrate. Here, we report the structures of CMD1 in apo form and in complexes with VC or/and dsDNA. CMD1 exhibits comparable binding affinities for DNAs of different lengths, structures, and 5mC levels, and displays a moderate substrate preference for 5mCpG-containing DNA. CMD1 adopts the typical DSBH fold of Fe2+/2-OG-dependent dioxygenases. The lactone form of VC binds to the active site and mono-coordinates the Fe2+ in a manner different from 2-OG. The dsDNA binds to a positively charged cleft of CMD1 and the 5mC/C is inserted into the active site and recognized by CMD1 in a similar manner as the TET proteins. The functions of key residues are validated by mutagenesis and activity assay. Our structural and biochemical data together reveal the molecular mechanism for the VC-derived 5gmC DNA Modification by CMD1.
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molecular mechanism for vitamin c derived c 5 glyceryl methylcytosine DNA Modification catalyzed by algal tet homologue cmd1
Nature Communications, 2021Co-Authors: Tianlong Zhang, Mingliang Sun, Yu Shi, Xiaojie Zhang, Jianping DingAbstract:C5-glyceryl-methylcytosine (5gmC) is a novel DNA Modification catalyzed by algal TET homologue CMD1 using vitamin C (VC) as co-substrate. Here, we report the structures of CMD1 in apo form and in complexes with VC or/and dsDNA. CMD1 exhibits comparable binding affinities for DNAs of different lengths, structures, and 5mC levels, and displays a moderate substrate preference for 5mCpG-containing DNA. CMD1 adopts the typical DSBH fold of Fe2+/2-OG-dependent dioxygenases. The lactone form of VC binds to the active site and mono-coordinates the Fe2+ in a manner different from 2-OG. The dsDNA binds to a positively charged cleft of CMD1 and the 5mC/C is inserted into the active site and recognized by CMD1 in a similar manner as the TET proteins. The functions of key residues are validated by mutagenesis and activity assay. Our structural and biochemical data together reveal the molecular mechanism for the VC-derived 5gmC DNA Modification by CMD1.
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tet mediated formation of 5 carboxylcytosine and its excision by tdg in mammalian DNA
Science, 2011Co-Authors: Yufei He, Zheng Li, Jianping Ding, Binzhong Li, Yang Wang, Qingyu Tang, Zhangcheng Chen, Lin Li, Xiuxue Li, Chunxiao SongAbstract:The prevalent DNA Modification in higher organisms is the methylation of cytosine to 5-methylcytosine (5mC), which is partially converted to 5-hydroxymethylcytosine (5hmC) by the Tet (ten eleven translocation) family of dioxygenases. Despite their importance in epigenetic regulation, it is unclear how these cytosine Modifications are reversed. Here, we demonstrate that 5mC and 5hmC in DNA are oxidized to 5-carboxylcytosine (5caC) by Tet dioxygenases in vitro and in cultured cells. 5caC is specifically recognized and excised by thymine-DNA glycosylase (TDG). Depletion of TDG in mouse embyronic stem cells leads to accumulation of 5caC to a readily detectable level. These data suggest that oxidation of 5mC by Tet proteins followed by TDG-mediated base excision of 5caC constitutes a pathway for active DNA demethylation.
Xiufen Zhou - One of the best experts on this subject based on the ideXlab platform.
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a novel DNA Modification by sulfur dnda is a nifs like cysteine desulfurase capable of assembling dndc as an iron sulfur cluster protein in streptomyces lividans
Biochemistry, 2007Co-Authors: Delin You, Xiufen Zhou, Lianrong Wang, Fen Yao, Zixin DengAbstract:A novel DNA Modification system by sulfur (S) in Streptomyces lividans 66 was reported to be encoded by a cluster of five genes designated dndA-E [Zhou, X., He, X., Liang, J., Li, A., Xu, T., Kieser, T., Helmann, J. D., and Deng, Z. (2005) Mol. Microbiol. 57, 1428-1438]. The dndA gene was cloned and the protein product expressed in Escherichia coli, purified to homogeneity, and characterized as a homodimeric protein of ca. 91 kDa. Purified DndA has a yellow color and UV-visible spectra characteristic of a pyridoxal phosphate-containing enzyme and was proven to be a cysteine desulfurase able to catalyze removal of elemental S atoms from l-cysteine to produce l-alanine with substrate specificity similar to that of E. coli IscS. DndC was also purified to homogeneity and found to contain a 4Fe-4S cluster by spectral analysis and have obvious ATP pyrophosphatase activity. DndA could catalyze iron-sulfur cluster assembly by activation of apo-Fe DndC protein prepared by removal of its iron-sulfur cluster using alpha,alpha'-dipyridyl. A mutated DndA, with serine substituted for cysteine at position 327, which was confirmed to have lost its corresponding cysteine desulfurase activity, also lost its ability to reactivate the apo-Fe DndC. The likely involvement of an interaction between DndA and DndC in the biochemical pathway for the unusual site-specific DNA Modification in S. lividans 66 is discussed.
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DNA Modification by sulfur analysis of the sequence recognition specificity surrounding the Modification sites
Nucleic Acids Research, 2007Co-Authors: Jingdan Liang, Xiufen Zhou, Zhijun Wang, Zixin DengAbstract:The Dnd (DNA degradation) phenotype, reflecting a novel DNA Modification by sulfur in Streptomyces lividans 1326, was strongly aggravated when one (dndB) of the five genes (dndABCDE) controlling it was mutated. Electrophoretic banding patterns of a plasmid (pHZ209), reflecting DNA degradation, displayed a clear change from a preferential Modification site in strain 1326 to more random Modifications in the mutant. Fourteen randomly modifiable sites on pHZ209 were localized, and each seemed to be able to be modified only once. Residues in a region (5'-c-cGGCCgccg-3') including a highly conserved 4-bp central core (5'-GGCC-3') in a well-documented preferential Modification site were assessed for their necessity by site-directed mutagenesis. While the central core (GGCC) was found to be stringently required in 1326 and in the mutant, 'gccg' flanking its right could either abolish or reduce the Modification frequency only in the mutant, and two separate nucleotides to the left had no dramatic effect. The lack of essentiality of DndB for S-Modification suggests that it might only be required for enhancing or stabilizing the activity of a protein complex at the required preferential Modification site, or resolving secondary structures flanking the modifiable site(s), known to constitute an obstacle for efficient Modification.
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a novel DNA Modification by sulfur dnda is a nifs like cysteine desulfurase capable of assembling dndc as an iron sulfur cluster protein in streptomyces lividans
Biochemistry, 2007Co-Authors: Delin You, Xiufen Zhou, Lianrong Wang, Fen Yao, Zixin DengAbstract:A novel DNA Modification system by sulfur (S) in Streptomyces lividans 66 was reported to be encoded by a cluster of five genes designated dndA−E [Zhou, X., He, X., Liang, J., Li, A., Xu, T., Kieser, T., Helmann, J. D., and Deng, Z. (2005) Mol. Microbiol. 57, 1428−1438]. The dndA gene was cloned and the protein product expressed in Escherichia coli, purified to homogeneity, and characterized as a homodimeric protein of ca. 91 kDa. Purified DndA has a yellow color and UV−visible spectra characteristic of a pyridoxal phosphate-containing enzyme and was proven to be a cysteine desulfurase able to catalyze removal of elemental S atoms from l-cysteine to produce l-alanine with substrate specificity similar to that of E. coli IscS. DndC was also purified to homogeneity and found to contain a 4Fe-4S cluster by spectral analysis and have obvious ATP pyrophosphatase activity. DndA could catalyze iron−sulfur cluster assembly by activation of apo-Fe DndC protein prepared by removal of its iron−sulfur cluster using α...
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a novel DNA Modification by sulphur
Molecular Microbiology, 2005Co-Authors: Xiufen Zhou, Jingdan Liang, Tobias Kieser, John D Helmann, Zixin DengAbstract:Streptomyces lividans has a novel DNA Modification, which sensitises its DNA to degradation during electrophoresis (the Dnd phenotype). The entire gene cluster (dnd) involved in this Modification was localized on an 8 kb DNA fragment and was expressed in a S. lividans deletion mutant (dnd) and in several heterologous hosts. Disruption of the dnd locus abolishes the Dnd phenotype, and gain of the dnd locus conferred the Dnd phenotype respectively. Extensive analysis of the dnd gene cluster revealed five open reading frames, whose hypothetic functions suggested an incorporation of sulphur or a sulphur-containing substance into S. lividans genome, yet in an unknown manner. The Dnd phenotype was also discovered to exist in DNA of widespread bacterial species of variable origin and diverse habitat. Similarly organized gene clusters were found in several bacterial genomes representing different genera and in eDNA of marine organisms, suggesting such Modification as a widespread phenomenon. A coincidence between the Dnd phenotype and DNA Modification by sulphur was demonstrated to occur in several representative bacterial genomes by the in vivo(35)S-labelling experiments.
Shankar Balasubramanian - One of the best experts on this subject based on the ideXlab platform.
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5 formylcytosine can be a stable DNA Modification in mammals
Nature Chemical Biology, 2015Co-Authors: Martin Bachman, Xiaoping Yang, Adele Murrell, Santiago Uribelewis, Heather E Burgess, Mario Iurlaro, Wolf Reik, Shankar BalasubramanianAbstract:5-Formylcytosine (5fC) is a rare base found in mammalian DNA and thought to be involved in active DNA demethylation. Here, we show that developmental dynamics of 5fC levels in mouse DNA differ from those of 5-hydroxymethylcytosine (5hmC), and using stable isotope labeling in vivo, we show that 5fC can be a stable DNA Modification. These results suggest that 5fC has functional roles in DNA that go beyond being a demethylation intermediate.
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5-Hydroxymethylcytosine is a predominantly stable DNA Modification
Nature chemistry, 2014Co-Authors: Martin Bachman, Santiago Uribe-lewis, Xiaoping Yang, Michael Williams, Adele Murrell, Shankar BalasubramanianAbstract:5-Hydroxymethylcytosine (hmC) is an oxidation product of 5-methylcytosine which is present in the deoxyribonucleic acid (DNA) of most mammalian cells. Reduction of hmC levels in DNA is a hallmark of cancers. Elucidating the dynamics of this oxidation reaction and the lifetime of hmC in DNA is fundamental to understanding hmC function. Using stable isotope labelling of cytosine derivatives in the DNA of mammalian cells and ultrasensitive tandem liquid-chromatography mass spectrometry, we show that the majority of hmC is a stable Modification, as opposed to a transient intermediate. In contrast with DNA methylation, which occurs immediately during replication, hmC forms slowly during the first 30 hours following DNA synthesis. Isotopic labelling of DNA in mouse tissues confirmed the stability of hmC in vivo and demonstrated a relationship between global levels of hmC and cell proliferation. These insights have important implications for understanding the states of chemically modified DNA bases in health and disease.