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  • 1
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    Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-04-25
    Description: Escherichia coli AlkB and its human homologues ABH2 and ABH3 repair DNA/RNA base lesions by using a direct oxidative dealkylation mechanism. ABH2 has the primary role of guarding mammalian genomes against 1-meA damage by repairing this lesion in double-stranded DNA (dsDNA), whereas AlkB and ABH3 preferentially repair single-stranded DNA (ssDNA) lesions and can repair damaged bases in RNA. Here we show the first crystal structures of AlkB-dsDNA and ABH2-dsDNA complexes, stabilized by a chemical cross-linking strategy. This study reveals that AlkB uses an unprecedented base-flipping mechanism to access the damaged base: it squeezes together the two bases flanking the flipped-out one to maintain the base stack, explaining the preference of AlkB for repairing ssDNA lesions over dsDNA ones. In addition, the first crystal structure of ABH2, presented here, provides a structural basis for designing inhibitors of this human DNA repair protein.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2587245/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2587245/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Cai-Guang -- Yi, Chengqi -- Duguid, Erica M -- Sullivan, Christopher T -- Jian, Xing -- Rice, Phoebe A -- He, Chuan -- GM071440/GM/NIGMS NIH HHS/ -- R01 GM071440/GM/NIGMS NIH HHS/ -- R01 GM071440-03/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Apr 24;452(7190):961-5. doi: 10.1038/nature06889.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18432238" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/analogs & derivatives/metabolism ; Binding Sites ; Cross-Linking Reagents/chemistry ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA Damage ; DNA Repair ; DNA Repair Enzymes/*chemistry/metabolism ; DNA-Binding Proteins/chemistry/metabolism ; Dioxygenases/*chemistry/*metabolism ; Escherichia coli Proteins/*chemistry/*metabolism ; Humans ; Mixed Function Oxygenases/*chemistry/*metabolism ; Models, Molecular ; Protein Binding ; RNA/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Detection of functional haematopoietic stem cell niche using real-time imaging (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-12-05
    Description: Haematopoietic stem cell (HSC) niches, although proposed decades ago, have only recently been identified as separate osteoblastic and vascular microenvironments. Their interrelationships and interactions with HSCs in vivo remain largely unknown. Here we report the use of a newly developed ex vivo real-time imaging technology and immunoassaying to trace the homing of purified green-fluorescent-protein-expressing (GFP(+)) HSCs. We found that transplanted HSCs tended to home to the endosteum (an inner bone surface) in irradiated mice, but were randomly distributed and unstable in non-irradiated mice. Moreover, GFP(+) HSCs were more frequently detected in the trabecular bone area compared with compact bone area, and this was validated by live imaging bioluminescence driven by the stem-cell-leukaemia (Scl) promoter-enhancer. HSCs home to bone marrow through the vascular system. We found that the endosteum is well vascularized and that vasculature is frequently localized near N-cadherin(+) pre-osteoblastic cells, a known niche component. By monitoring individual HSC behaviour using real-time imaging, we found that a portion of the homed HSCs underwent active division in the irradiated mice, coinciding with their expansion as measured by flow assay. Thus, in contrast to central marrow, the endosteum formed a special zone, which normally maintains HSCs but promotes their expansion in response to bone marrow damage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xie, Yucai -- Yin, Tong -- Wiegraebe, Winfried -- He, Xi C -- Miller, Diana -- Stark, Danny -- Perko, Katherine -- Alexander, Richard -- Schwartz, Joel -- Grindley, Justin C -- Park, Jungeun -- Haug, Jeff S -- Wunderlich, Joshua P -- Li, Hua -- Zhang, Simon -- Johnson, Teri -- Feldman, Ricardo A -- Li, Linheng -- England -- Nature. 2009 Jan 1;457(7225):97-101. doi: 10.1038/nature07639. Epub 2008 Dec 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, Missouri 64110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19052548" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, CD31/analysis ; Blood Vessels/cytology ; Bone Marrow/pathology ; Cadherins/analysis ; Cell Division ; *Cell Movement ; Cell Separation ; Femur/cytology ; Hematopoietic Stem Cells/*cytology ; Immunoassay/*methods ; Immunohistochemistry ; Mice ; Models, Animal ; Osteoblasts/cytology ; Stem Cell Niche/*cytology ; Tibia/cytology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
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    A Xanthomonas uridine 5'-monophosphate transferase inhibits plant immune kinases (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-04-17
    Description: Plant innate immunity is activated on the detection of pathogen-associated molecular patterns (PAMPs) at the cell surface, or of pathogen effector proteins inside the plant cell. Together, PAMP-triggered immunity and effector-triggered immunity constitute powerful defences against various phytopathogens. Pathogenic bacteria inject a variety of effector proteins into the host cell to assist infection or propagation. A number of effector proteins have been shown to inhibit plant immunity, but the biochemical basis remains unknown for the vast majority of these effectors. Here we show that the Xanthomonas campestris pathovar campestris type III effector AvrAC enhances virulence and inhibits plant immunity by specifically targeting Arabidopsis BIK1 and RIPK, two receptor-like cytoplasmic kinases known to mediate immune signalling. AvrAC is a uridylyl transferase that adds uridine 5'-monophosphate to and conceals conserved phosphorylation sites in the activation loop of BIK1 and RIPK, reducing their kinase activity and consequently inhibiting downstream signalling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Feng, Feng -- Yang, Fan -- Rong, Wei -- Wu, Xiaogang -- Zhang, Jie -- Chen, She -- He, Chaozu -- Zhou, Jian-Min -- England -- Nature. 2012 Apr 15;485(7396):114-8. doi: 10.1038/nature10962.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Life Sciences, Tsinghua University, Beijing 100084, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22504181" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/*enzymology/*immunology/microbiology ; Arabidopsis Proteins/*antagonists & inhibitors/chemistry/immunology/metabolism ; Bacterial Proteins/*metabolism ; Brassica/immunology/microbiology ; Molecular Sequence Data ; Phosphorylation ; Plant Diseases/immunology/microbiology ; *Plant Immunity/immunology ; Plants, Genetically Modified ; Protein Kinases/chemistry/immunology/metabolism ; Protein-Serine-Threonine Kinases/*antagonists & ; inhibitors/chemistry/immunology/metabolism ; Signal Transduction ; Virulence ; Xanthomonas campestris/*enzymology/immunology/pathogenicity
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Maternal imprinting at the H19-Igf2 locus maintains adult haematopoietic stem cell quiescence (2013)
    Nature Publishing Group (NPG)
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    Publication Date: 2013-07-19
    Description: The epigenetic regulation of imprinted genes by monoallelic DNA methylation of either maternal or paternal alleles is critical for embryonic growth and development. Imprinted genes were recently shown to be expressed in mammalian adult stem cells to support self-renewal of neural and lung stem cells; however, a role for imprinting per se in adult stem cells remains elusive. Here we show upregulation of growth-restricting imprinted genes, including in the H19-Igf2 locus, in long-term haematopoietic stem cells and their downregulation upon haematopoietic stem cell activation and proliferation. A differentially methylated region upstream of H19 (H19-DMR), serving as the imprinting control region, determines the reciprocal expression of H19 from the maternal allele and Igf2 from the paternal allele. In addition, H19 serves as a source of miR-675, which restricts Igf1r expression. We demonstrate that conditional deletion of the maternal but not the paternal H19-DMR reduces adult haematopoietic stem cell quiescence, a state required for long-term maintenance of haematopoietic stem cells, and compromises haematopoietic stem cell function. Maternal-specific H19-DMR deletion results in activation of the Igf2-Igfr1 pathway, as shown by the translocation of phosphorylated FoxO3 (an inactive form) from nucleus to cytoplasm and the release of FoxO3-mediated cell cycle arrest, thus leading to increased activation, proliferation and eventual exhaustion of haematopoietic stem cells. Mechanistically, maternal-specific H19-DMR deletion leads to Igf2 upregulation and increased translation of Igf1r, which is normally suppressed by H19-derived miR-675. Similarly, genetic inactivation of Igf1r partly rescues the H19-DMR deletion phenotype. Our work establishes a new role for this unique form of epigenetic control at the H19-Igf2 locus in maintaining adult stem cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3896866/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3896866/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Venkatraman, Aparna -- He, Xi C -- Thorvaldsen, Joanne L -- Sugimura, Ryohichi -- Perry, John M -- Tao, Fang -- Zhao, Meng -- Christenson, Matthew K -- Sanchez, Rebeca -- Yu, Jaclyn Y -- Peng, Lai -- Haug, Jeffrey S -- Paulson, Ariel -- Li, Hua -- Zhong, Xiao-bo -- Clemens, Thomas L -- Bartolomei, Marisa S -- Li, Linheng -- GM51279/GM/NIGMS NIH HHS/ -- R01 GM087376/GM/NIGMS NIH HHS/ -- R37 GM051279/GM/NIGMS NIH HHS/ -- England -- Nature. 2013 Aug 15;500(7462):345-9. doi: 10.1038/nature12303. Epub 2013 Jul 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23863936" target="_blank"〉PubMed〈/a〉
    Keywords: Adult Stem Cells/*cytology/*physiology ; Animals ; Epigenesis, Genetic/genetics ; Gene Expression Regulation, Developmental ; *Genomic Imprinting ; Insulin-Like Growth Factor II/*genetics/*metabolism ; Mice ; RNA, Long Noncoding/*genetics/*metabolism ; Receptor, IGF Type 1/genetics ; Signal Transduction ; Transcriptional Activation
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
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    Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex (2015)
    Nature Publishing Group (NPG)
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    Publication Date: 2015-07-01
    Description: DNA methylation at selective cytosine residues (5-methylcytosine (5mC)) and their removal by TET-mediated DNA demethylation are critical for setting up pluripotent states in early embryonic development. TET enzymes successively convert 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), with 5fC and 5caC subject to removal by thymine DNA glycosylase (TDG) in conjunction with base excision repair. Early reports indicate that 5fC and 5caC could be stably detected on enhancers, promoters and gene bodies, with distinct effects on gene expression, but the mechanisms have remained elusive. Here we determined the X-ray crystal structure of yeast elongating RNA polymerase II (Pol II) in complex with a DNA template containing oxidized 5mCs, revealing specific hydrogen bonds between the 5-carboxyl group of 5caC and the conserved epi-DNA recognition loop in the polymerase. This causes a positional shift for incoming nucleoside 5'-triphosphate (NTP), thus compromising nucleotide addition. To test the implication of this structural insight in vivo, we determined the global effect of increased 5fC/5caC levels on transcription, finding that such DNA modifications indeed retarded Pol II elongation on gene bodies. These results demonstrate the functional impact of oxidized 5mCs on gene expression and suggest a novel role for Pol II as a specific and direct epigenetic sensor during transcription elongation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4521995/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4521995/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Lanfeng -- Zhou, Yu -- Xu, Liang -- Xiao, Rui -- Lu, Xingyu -- Chen, Liang -- Chong, Jenny -- Li, Hairi -- He, Chuan -- Fu, Xiang-Dong -- Wang, Dong -- GM052872/GM/NIGMS NIH HHS/ -- GM102362/GM/NIGMS NIH HHS/ -- HG004659/HG/NHGRI NIH HHS/ -- HG006827/HG/NHGRI NIH HHS/ -- R01 GM052872/GM/NIGMS NIH HHS/ -- R01 GM102362/GM/NIGMS NIH HHS/ -- R01 HG004659/HG/NHGRI NIH HHS/ -- R01 HG006827/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Jul 30;523(7562):621-5. doi: 10.1038/nature14482. Epub 2015 Jun 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. ; Department of Cellular and Molecular Medicine, School of Medicine, The University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. ; Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26123024" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Cytosine/*analogs & derivatives/chemistry/metabolism ; DNA Methylation ; DNA Repair ; Epigenesis, Genetic ; Hydrogen Bonding ; Kinetics ; RNA Polymerase II/*chemistry/*metabolism ; Saccharomyces cerevisiae/*enzymology/genetics/metabolism ; Substrate Specificity ; Templates, Genetic ; Thymine DNA Glycosylase/metabolism ; *Transcription Elongation, Genetic
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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