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  • 1
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    Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-12-19
    Description: Here we report on a 3.0 A crystal structure of a ternary complex of wild-type Thermus thermophilus argonaute bound to a 5'-phosphorylated 21-nucleotide guide DNA and a 20-nucleotide target RNA containing cleavage-preventing mismatches at the 10-11 step. The seed segment (positions 2 to 8) adopts an A-helical-like Watson-Crick paired duplex, with both ends of the guide strand anchored in the complex. An arginine, inserted between guide-strand bases 10 and 11 in the binary complex, locking it in an inactive conformation, is released on ternary complex formation. The nucleic-acid-binding channel between the PAZ- and PIWI-containing lobes of argonaute widens on formation of a more open ternary complex. The relationship of structure to function was established by determining cleavage activity of ternary complexes containing position-dependent base mismatch, bulge and 2'-O-methyl modifications. Consistent with the geometry of the ternary complex, bulges residing in the seed segments of the target, but not the guide strand, were better accommodated and their complexes were catalytically active.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2765400/" 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/PMC2765400/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Yanli -- Juranek, Stefan -- Li, Haitao -- Sheng, Gang -- Tuschl, Thomas -- Patel, Dinshaw J -- R01 AI068776/AI/NIAID NIH HHS/ -- R01 AI068776-02/AI/NIAID NIH HHS/ -- England -- Nature. 2008 Dec 18;456(7224):921-6. doi: 10.1038/nature07666.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Program, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19092929" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/genetics/*metabolism ; Base Pair Mismatch ; Base Pairing ; Base Sequence ; Crystallography, X-Ray ; DNA/chemistry/genetics/*metabolism ; Methylation ; Models, Molecular ; Phosphorylation ; Protein Conformation ; RNA/chemistry/genetics/*metabolism ; RNA Interference ; RNA-Induced Silencing Complex/*chemistry/genetics/*metabolism ; Substrate Specificity ; Thermus thermophilus/*chemistry
    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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    Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-10-09
    Description: The slicer activity of the RNA-induced silencing complex resides within its Argonaute (Ago) component, in which the PIWI domain provides the catalytic residues governing guide-strand mediated site-specific cleavage of target RNA. Here we report on structures of ternary complexes of Thermus thermophilus Ago catalytic mutants with 5'-phosphorylated 21-nucleotide guide DNA and complementary target RNAs of 12, 15 and 19 nucleotides in length, which define the molecular basis for Mg(2+)-facilitated site-specific cleavage of the target. We observe pivot-like domain movements within the Ago scaffold on proceeding from nucleation to propagation steps of guide-target duplex formation, with duplex zippering beyond one turn of the helix requiring the release of the 3'-end of the guide from the PAZ pocket. Cleavage assays on targets of various lengths supported this model, and sugar-phosphate-backbone-modified target strands showed the importance of structural and catalytic divalent metal ions observed in the crystal structures.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880917/" 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/PMC2880917/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Yanli -- Juranek, Stefan -- Li, Haitao -- Sheng, Gang -- Wardle, Greg S -- Tuschl, Thomas -- Patel, Dinshaw J -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 AI068776/AI/NIAID NIH HHS/ -- R01 AI068776-04/AI/NIAID NIH HHS/ -- R01 AI068776-05/AI/NIAID NIH HHS/ -- R01 GM068476/GM/NIGMS NIH HHS/ -- R01 GM068476-05/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Oct 8;461(7265):754-61. doi: 10.1038/nature08434.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Program, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19812667" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Biocatalysis ; Catalytic Domain/genetics ; Cations, Divalent/metabolism ; Crystallography, X-Ray ; DNA/chemistry/genetics/metabolism ; *Gene Silencing ; Magnesium/metabolism ; Models, Molecular ; Phosphorylation ; RNA/chemistry/genetics/*metabolism ; RNA-Induced Silencing Complex/*chemistry/genetics/*metabolism ; Structure-Activity Relationship ; Substrate Specificity ; Thermus thermophilus/*enzymology/genetics
    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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    WSTF regulates the H2A.X DNA damage response via a novel tyrosine kinase activity (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-12-19
    Description: DNA double-stranded breaks present a serious challenge for eukaryotic cells. The inability to repair breaks leads to genomic instability, carcinogenesis and cell death. During the double-strand break response, mammalian chromatin undergoes reorganization demarcated by H2A.X Ser 139 phosphorylation (gamma-H2A.X). However, the regulation of gamma-H2A.X phosphorylation and its precise role in chromatin remodelling during the repair process remain unclear. Here we report a new regulatory mechanism mediated by WSTF (Williams-Beuren syndrome transcription factor, also known as BAZ1B)-a component of the WICH complex (WSTF-ISWI ATP-dependent chromatin-remodelling complex). We show that WSTF has intrinsic tyrosine kinase activity by means of a domain that shares no sequence homology to any known kinase fold. We show that WSTF phosphorylates Tyr 142 of H2A.X, and that WSTF activity has an important role in regulating several events that are critical for the DNA damage response. Our work demonstrates a new mechanism that regulates the DNA damage response and expands our knowledge of domains that contain intrinsic tyrosine kinase activity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2854499/" 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/PMC2854499/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xiao, Andrew -- Li, Haitao -- Shechter, David -- Ahn, Sung Hee -- Fabrizio, Laura A -- Erdjument-Bromage, Hediye -- Ishibe-Murakami, Satoko -- Wang, Bin -- Tempst, Paul -- Hofmann, Kay -- Patel, Dinshaw J -- Elledge, Stephen J -- Allis, C David -- F32 GM075486/GM/NIGMS NIH HHS/ -- P30 CA08748/CA/NCI NIH HHS/ -- R01 GM040922/GM/NIGMS NIH HHS/ -- R01 GM040922-24/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Jan 1;457(7225):57-62. doi: 10.1038/nature07668. Epub 2008 Dec 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19092802" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/metabolism ; Animals ; Chromatin Assembly and Disassembly ; Chromosomal Proteins, Non-Histone/metabolism ; *DNA Damage ; Histones/genetics/*metabolism ; Humans ; Mice ; NIH 3T3 Cells ; Nucleosomes/metabolism ; Phosphorylation ; Phosphotyrosine/metabolism ; Protein Structure, Tertiary ; Protein-Tyrosine Kinases/*metabolism ; Transcription Factors/chemistry/deficiency/genetics/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
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    Dicer recognizes the 5' end of RNA for efficient and accurate processing (2011)
    Nature Publishing Group (NPG)
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    Publication Date: 2011-07-15
    Description: A hallmark of RNA silencing is a class of approximately 22-nucleotide RNAs that are processed from double-stranded RNA precursors by Dicer. Accurate processing by Dicer is crucial for the functionality of microRNAs (miRNAs). The current model posits that Dicer selects cleavage sites by measuring a set distance from the 3' overhang of the double-stranded RNA terminus. Here we report that human Dicer anchors not only the 3' end but also the 5' end, with the cleavage site determined mainly by the distance ( approximately 22 nucleotides) from the 5' end (5' counting rule). This cleavage requires a 5'-terminal phosphate group. Further, we identify a novel basic motif (5' pocket) in human Dicer that recognizes the 5'-phosphorylated end. The 5' counting rule and the 5' anchoring residues are conserved in Drosophila Dicer-1, but not in Giardia Dicer. Mutations in the 5' pocket reduce processing efficiency and alter cleavage sites in vitro. Consistently, miRNA biogenesis is perturbed in vivo when Dicer-null embryonic stem cells are replenished with the 5'-pocket mutant. Thus, 5'-end recognition by Dicer is important for precise and effective biogenesis of miRNAs. Insights from this study should also afford practical benefits to the design of small hairpin RNAs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4693635/" 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/PMC4693635/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Park, Jong-Eun -- Heo, Inha -- Tian, Yuan -- Simanshu, Dhirendra K -- Chang, Hyeshik -- Jee, David -- Patel, Dinshaw J -- Kim, V Narry -- P30 CA008748/CA/NCI NIH HHS/ -- R01 AI068776/AI/NIAID NIH HHS/ -- England -- Nature. 2011 Jul 13;475(7355):201-5. doi: 10.1038/nature10198.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, Seoul National University, Seoul 151-742, Korea.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21753850" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites/genetics ; DEAD-box RNA Helicases/deficiency/genetics/*metabolism ; Drosophila Proteins/metabolism ; Embryonic Stem Cells/metabolism ; Evolution, Molecular ; Giardia/enzymology ; HEK293 Cells ; Humans ; MicroRNAs/biosynthesis/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Mutant Proteins/chemistry/genetics/metabolism ; Mutation/genetics ; Phosphates/metabolism ; Phosphorylation ; RNA Helicases/metabolism ; Ribonuclease III/deficiency/genetics/*metabolism ; Substrate Specificity/genetics
    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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    EGFR modulates microRNA maturation in response to hypoxia through phosphorylation of AGO2 (2013)
    Nature Publishing Group (NPG)
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    Publication Date: 2013-05-03
    Description: MicroRNAs (miRNAs) are generated by two-step processing to yield small RNAs that negatively regulate target gene expression at the post-transcriptional level. Deregulation of miRNAs has been linked to diverse pathological processes, including cancer. Recent studies have also implicated miRNAs in the regulation of cellular response to a spectrum of stresses, such as hypoxia, which is frequently encountered in the poorly angiogenic core of a solid tumour. However, the upstream regulators of miRNA biogenesis machineries remain obscure, raising the question of how tumour cells efficiently coordinate and impose specificity on miRNA expression and function in response to stresses. Here we show that epidermal growth factor receptor (EGFR), which is the product of a well-characterized oncogene in human cancers, suppresses the maturation of specific tumour-suppressor-like miRNAs in response to hypoxic stress through phosphorylation of argonaute 2 (AGO2) at Tyr 393. The association between EGFR and AGO2 is enhanced by hypoxia, leading to elevated AGO2-Y393 phosphorylation, which in turn reduces the binding of Dicer to AGO2 and inhibits miRNA processing from precursor miRNAs to mature miRNAs. We also identify a long-loop structure in precursor miRNAs as a critical regulatory element in phospho-Y393-AGO2-mediated miRNA maturation. Furthermore, AGO2-Y393 phosphorylation mediates EGFR-enhanced cell survival and invasiveness under hypoxia, and correlates with poorer overall survival in breast cancer patients. Our study reveals a previously unrecognized function of EGFR in miRNA maturation and demonstrates how EGFR is likely to function as a regulator of AGO2 through novel post-translational modification. These findings suggest that modulation of miRNA biogenesis is important for stress response in tumour cells and has potential clinical implications.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3717558/" 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/PMC3717558/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shen, Jia -- Xia, Weiya -- Khotskaya, Yekaterina B -- Huo, Longfei -- Nakanishi, Kotaro -- Lim, Seung-Oe -- Du, Yi -- Wang, Yan -- Chang, Wei-Chao -- Chen, Chung-Hsuan -- Hsu, Jennifer L -- Wu, Yun -- Lam, Yung Carmen -- James, Brian P -- Liu, Xiuping -- Liu, Chang-Gong -- Patel, Dinshaw J -- Hung, Mien-Chie -- CA099031/CA/NCI NIH HHS/ -- CA109311/CA/NCI NIH HHS/ -- CA16672/CA/NCI NIH HHS/ -- P01 CA099031/CA/NCI NIH HHS/ -- P30 CA016672/CA/NCI NIH HHS/ -- R01 CA109311/CA/NCI NIH HHS/ -- England -- Nature. 2013 May 16;497(7449):383-7. doi: 10.1038/nature12080. Epub 2013 May 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23636329" target="_blank"〉PubMed〈/a〉
    Keywords: Argonaute Proteins/*chemistry/*metabolism ; Breast Neoplasms/genetics/metabolism/mortality/pathology ; Cell Hypoxia/genetics/*physiology ; Cell Line, Tumor ; Cell Survival ; Female ; Gene Expression Regulation, Neoplastic ; Humans ; MicroRNAs/biosynthesis/chemistry/genetics/*metabolism ; Neoplasm Invasiveness ; Nucleic Acid Conformation ; Phosphorylation ; Phosphotyrosine/metabolism ; Prognosis ; Protein Binding ; RNA Precursors/chemistry/genetics/metabolism ; Receptor, Epidermal Growth Factor/*metabolism ; Ribonuclease III/metabolism ; Survival Analysis
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
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    DNA-guided DNA interference by a prokaryotic Argonaute (2014)
    Nature Publishing Group (NPG)
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    Publication Date: 2014-02-18
    Description: RNA interference is widely distributed in eukaryotes and has a variety of functions, including antiviral defence and gene regulation. All RNA interference pathways use small single-stranded RNA (ssRNA) molecules that guide proteins of the Argonaute (Ago) family to complementary ssRNA targets: RNA-guided RNA interference. The role of prokaryotic Ago variants has remained elusive, although bioinformatics analysis has suggested their involvement in host defence. Here we demonstrate that Ago of the bacterium Thermus thermophilus (TtAgo) acts as a barrier for the uptake and propagation of foreign DNA. In vivo, TtAgo is loaded with 5'-phosphorylated DNA guides, 13-25 nucleotides in length, that are mostly plasmid derived and have a strong bias for a 5'-end deoxycytidine. These small interfering DNAs guide TtAgo to cleave complementary DNA strands. Hence, despite structural homology to its eukaryotic counterparts, TtAgo functions in host defence by DNA-guided DNA interference.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697943/" 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/PMC4697943/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Swarts, Daan C -- Jore, Matthijs M -- Westra, Edze R -- Zhu, Yifan -- Janssen, Jorijn H -- Snijders, Ambrosius P -- Wang, Yanli -- Patel, Dinshaw J -- Berenguer, Jose -- Brouns, Stan J J -- van der Oost, John -- P30 CA008748/CA/NCI NIH HHS/ -- R01 GM104962/GM/NIGMS NIH HHS/ -- England -- Nature. 2014 Mar 13;507(7491):258-61. doi: 10.1038/nature12971. Epub 2014 Feb 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands [2]. ; Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands. ; Clare Hall Laboratories, Cancer Research UK, London Research Institute, South Mimms EN6 3LD, UK. ; Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. ; Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA. ; Centro de Biologia Molecular Severo Ochoa, UAM-CSIC, Campus de Cantoblanco, 28049 Madrid, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24531762" target="_blank"〉PubMed〈/a〉
    Keywords: Argonaute Proteins/*metabolism ; Base Pairing/genetics ; Base Sequence ; DNA/genetics/*metabolism ; *DNA Cleavage ; Deoxycytidine/genetics/metabolism ; *Gene Silencing ; Phosphorylation ; Plasmids/genetics ; Prokaryotic Cells/*metabolism ; Thermus thermophilus/*genetics/*metabolism
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    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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