Mechanism of Hepatitis B Virus Cccdna Formation
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LIG1 Antibody Cat
LIG1 Antibody Cat. No.: 26-847 LIG1 Antibody Specifications HOST SPECIES: Rabbit SPECIES REACTIVITY: Human, Mouse Antibody produced in rabbits immunized with a synthetic peptide corresponding a region IMMUNOGEN: of human LIG1. TESTED APPLICATIONS: ELISA, WB LIG1 antibody can be used for detection of LIG1 by ELISA at 1:62500. LIG1 antibody can be APPLICATIONS: used for detection of LIG1 by western blot at 1 μg/mL, and HRP conjugated secondary antibody should be diluted 1:50,000 - 100,000. POSITIVE CONTROL: 1) 721_B Cell Lysate PREDICTED MOLECULAR 102 kDa WEIGHT: Properties PURIFICATION: Antibody is purified by peptide affinity chromatography method. CLONALITY: Polyclonal CONJUGATE: Unconjugated PHYSICAL STATE: Liquid September 29, 2021 1 https://www.prosci-inc.com/lig1-antibody-26-847.html Purified antibody supplied in 1x PBS buffer with 0.09% (w/v) sodium azide and 2% BUFFER: sucrose. CONCENTRATION: batch dependent For short periods of storage (days) store at 4˚C. For longer periods of storage, store LIG1 STORAGE CONDITIONS: antibody at -20˚C. As with any antibody avoid repeat freeze-thaw cycles. Additional Info OFFICIAL SYMBOL: LIG1 ALTERNATE NAMES: LIG1, MGC117397, MGC130025, ACCESSION NO.: NP_000225 PROTEIN GI NO.: 4557719 GENE ID: 3978 USER NOTE: Optimal dilutions for each application to be determined by the researcher. Background and References LIG1is DNA ligase I, with functions in DNA replication and the base excision repair process. Mutations in LIG1 that lead to DNA ligase I deficiency result in immunodeficiency and increased sensitivity to DNA-damaging agents.LIG1 encodes DNA ligase I, with functions in DNA replication and the base excision repair process. -
Intracellular Trafficking of HBV Particles
cells Review Intracellular Trafficking of HBV Particles Bingfu Jiang 1 and Eberhard Hildt 1,2,* 1 Department of Virology, Paul-Ehrlich-Institut, D-63225 Langen, Germany; [email protected] 2 German Center for Infection Research (DZIF), TTU Hepatitis, Marburg-Gießen-Langen, D63225 Langen, Germany * Correspondence: [email protected]; Tel.: +49-61-0377-2140 Received: 12 August 2020; Accepted: 2 September 2020; Published: 2 September 2020 Abstract: The human hepatitis B virus (HBV), that is causative for more than 240 million cases of chronic liver inflammation (hepatitis), is an enveloped virus with a partially double-stranded DNA genome. After virion uptake by receptor-mediated endocytosis, the viral nucleocapsid is transported towards the nuclear pore complex. In the nuclear basket, the nucleocapsid disassembles. The viral genome that is covalently linked to the viral polymerase, which harbors a bipartite NLS, is imported into the nucleus. Here, the partially double-stranded DNA genome is converted in a minichromosome-like structure, the covalently closed circular DNA (cccDNA). The DNA virus HBV replicates via a pregenomic RNA (pgRNA)-intermediate that is reverse transcribed into DNA. HBV-infected cells release apart from the infectious viral parrticle two forms of non-infectious subviral particles (spheres and filaments), which are assembled by the surface proteins but lack any capsid and nucleic acid. In addition, naked capsids are released by HBV replicating cells. Infectious viral particles and filaments are released via multivesicular bodies; spheres are secreted by the classic constitutive secretory pathway. The release of naked capsids is still not fully understood, autophagosomal processes are discussed. This review describes intracellular trafficking pathways involved in virus entry, morphogenesis and release of (sub)viral particles. -
Inhibition of Hepadnaviral Replication by Polyethylenimine-Based Intravenous Delivery of Antisense Phosphodiester Oligodeoxynucleotides to the Liver
Gene Therapy (2001) 8, 874–881 2001 Nature Publishing Group All rights reserved 0969-7128/01 $15.00 www.nature.com/gt RESEARCH ARTICLE Inhibition of hepadnaviral replication by polyethylenimine-based intravenous delivery of antisense phosphodiester oligodeoxynucleotides to the liver M Robaczewska1,2, S Guerret3, J-S Remy4, I Chemin1, W-B Offensperger5, M Chevallier6, J-P Behr4, AJ Podhajska2, HE Blum5, C Trepo1 and L Cova1 1INSERM U271, Lyon, France; 2Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland; 3Biomaterials Laboratory, Faculty of Pharmacy, Lyon; 4Faculty of Pharmacy, Illkirch, France; 5Department of Medicine, University of Freiburg, Germany; and 6Laboratoires Marcel Me´rieux, Lyon, France Antisense oligodeoxynucleotides (ODNs) appear as attract- fold as compared with the O-ODN-AS2. Following 9-day ive anti-hepatitis B virus (HBV) agents. We investigated in therapy the intrahepatic levels of both DHBV DNA and RNA vivo, in the duck HBV (DHBV) infection model, whether lin- were significantly decreased in the lPEI/O-ODN-AS2-treated ear polyethylenimine (lPEI)-based intravenous delivery of group as compared with the O-ODN-AS2-treated, control the natural antisense phosphodiester ODNs (O-ODNs) can lPEI/O-ODN-treated, and untreated controls. In addition, prevent their degradation and allow viral replication inhibition inhibition of intrahepatic viral replication by lPEI/O-ODN-AS2 in the liver. DHBV-infected Pekin ducklings were injected was not associated with toxicity and was comparable with with antisense O-ODNs covering the initiation codon of the that induced by the phosphorothioate S-ODN-AS2 at a five- DHBV large envelope protein, either in free form (O-ODN- fold higher dose. -
Discovery of a Highly Divergent Hepadnavirus in Shrews from China
Virology 531 (2019) 162–170 Contents lists available at ScienceDirect Virology journal homepage: www.elsevier.com/locate/virology Discovery of a highly divergent hepadnavirus in shrews from China T Fang-Yuan Niea,b,1, Jun-Hua Tianc,1, Xian-Dan Lind,1, Bin Yuc, Jian-Guang Xinge, Jian-Hai Caof, ⁎ ⁎⁎ Edward C. Holmesg,h, Runlin Z. Maa, , Yong-Zhen Zhangb,h, a State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China b State Key Laboratory for Infectious Disease Prevention and Control; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases; Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China c Wuhan Center for Disease Control and Prevention, Wuhan, China d Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang Province, China e Wencheng Center for Disease Control and Prevention, Wencheng, Zhejiang Province, China f Longwan Center for Disease Control and Prevention, Longwan District, Wenzhou, Zhejiang Province, China g Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia h Shanghai Public Health Clinical Center & Institute of Biomedical Sciences, Fudan University, Shanghai, China ARTICLE INFO ABSTRACT Keywords: Limited sampling means that relatively little is known about the diversity and evolutionary history of mam- Hepadnaviruses malian members of the Hepadnaviridae (genus Orthohepadnavirus). An important case in point are shrews, the Shrews fourth largest group of mammals, but for which there is limited knowledge on the role they play in viral evo- Phylogeny lution and emergence. -
Kinetic Analysis of Human DNA Ligase III by Justin R. Mcnally A
Kinetic Analysis of Human DNA Ligase III by Justin R. McNally A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Biological Chemistry) in the University of Michigan 2019 Doctoral Committee: Associate Professor Patrick J. O’Brien, Chair Associate Professor Bruce A. Palfey Associate Professor JoAnn M. Sekiguchi Associate Professor Raymond C. Trievel Professor Thomas E. Wilson Justin R. McNally [email protected] ORCID iD: 0000-0003-2694-2410 © Justin R. McNally 2019 Table of Contents List of Tables iii List of Figures iv Abstract vii Chapter 1 Introduction to the human DNA ligases 1 Chapter 2 Kinetic Analyses of Single-Strand Break Repair by Human DNA Ligase III Isoforms Reveal Biochemical Differences from DNA Ligase I 20 Chapter 3 The LIG3 N-terminus, in its entirety, contributes to single-strand DNA break ligation 56 Chapter 4 Comparative end-joining by human DNA ligases I and III 82 Chapter 5 A real-time DNA ligase assay suitable for high throughput screening 113 Chapter 6 Conclusions and Future Directions 137 ii List of Tables Table 2.1: Comparison of kinetic parameters for multiple turnover ligation by human DNA ligases 31 Table 2.2: Comparison of single-turnover parameters of LIG3β and LIG1 34 Table 3.1: Comparison of LIG3β N-terminal mutant kinetic parameters 67 Table 4.1: Rate constants for sequential ligation by LIG3β 95 Table 5.1: Comparison of multiple turnover kinetic parameters determined by real-time fluorescence assay and reported values 129 iii List of Figures Figure -
Tricarboxylic Acid Cycle Metabolites As Mediators of DNA Methylation Reprogramming in Bovine Preimplantation Embryos
Supplementary Materials Tricarboxylic Acid Cycle Metabolites as Mediators of DNA Methylation Reprogramming in Bovine Preimplantation Embryos Figure S1. (A) Total number of cells in fast (FBL) and slow (SBL) blastocysts; (B) Fluorescence intensity for 5-methylcytosine and 5-hydroxymethylcytosine of fast and slow blastocysts of cells from Trophoectoderm (TE) or inner cell mass (ICM). Fluorescence intensity for 5-methylcytosine of cells from the ICM or TE in blastocysts cultured with (C) dimethyl-succinate or (D) dimethyl-α- ketoglutarate. Statistical significance is identified by different letters. Figure S2. Experimental design. Table S1. Selected genes related to metabolism and epigenetic mechanisms from RNA-Seq analysis of bovine blastocysts (slow vs. fast). Genes in blue represent upregulation in slow blastocysts, genes in red represent upregulation in fast blastocysts. log2FoldCh Gene p-value p-Adj ange PDHB −1.425 0.000 0.000 MDH1 −1.206 0.000 0.000 APEX1 −1.193 0.000 0.000 OGDHL −3.417 0.000 0.002 PGK1 −0.942 0.000 0.002 GLS2 1.493 0.000 0.002 AICDA 1.171 0.001 0.005 ACO2 0.693 0.002 0.011 CS −0.660 0.002 0.011 SLC25A1 1.181 0.007 0.032 IDH3A −0.728 0.008 0.035 GSS 1.039 0.013 0.053 TET3 0.662 0.026 0.093 GLUD1 −0.450 0.032 0.108 SDHD −0.619 0.049 0.143 FH −0.547 0.054 0.149 OGDH 0.316 0.133 0.287 ACO1 −0.364 0.141 0.297 SDHC −0.335 0.149 0.311 LIG3 0.338 0.165 0.334 SUCLG −0.332 0.174 0.349 SDHA 0.297 0.210 0.396 SUCLA2 −0.324 0.248 0.439 DNMT1 0.266 0.279 0.486 IDH3B1 −0.269 0.296 0.503 SDHB −0.213 0.339 0.544 DNMT3B 0.181 0.386 0.598 APOBEC1 0.629 0.386 0.598 TDG 0.427 0.398 0.611 IDH3G 0.237 0.468 0.675 NEIL2 0.509 0.572 0.720 IDH2 0.298 0.571 0.720 DNMT3L 1.306 0.590 0.722 GLS 0.120 0.706 0.821 XRCC1 0.108 0.793 0.887 TET1 −0.028 0.879 0.919 DNMT3A 0.029 0.893 0.920 MBD4 −0.056 0.885 0.920 PDHX 0.033 0.890 0.920 SMUG1 0.053 0.936 0.954 TET2 −0.002 0.991 0.991 Table S2. -
Herpes Simplex Virus Type 1 Oril Is Not Required for Virus Infection In
JOURNAL OF VIROLOGY, Nov. 1987, p. 3528-3535 Vol. 61, No. 11 0022-538X/87/113528-08$02.00/0 Copyright C 1987, American Society for Microbiology Herpes Simplex Virus Type 1 oriL Is Not Required for Virus Replication or for the Establishment and Reactivation of Latent Infection in Mice MARYELLEN POLVINO-BODNAR, PAULO K. ORBERG, AND PRISCILLA A. SCHAFFER* Laboratory of Tumor Virus Genetics, Dana-Farber Cancer Institute, and Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115 Received 11 May 1987/Accepted 31 July 1987 During the course of experiments designed to isolate deletion mutants of herpes simplex virus type 1 in the gene encoding the major DNA-binding protein, ICP8, a mutant, d61, that grew efficiently in ICP8-expressing Vero cells but not in normal Vero cells was isolated (P. K. Orberg and P. A. Schaffer, J. Virol. 61:1136-1146, 1987). d61 was derived by cotransfection of ICP8-expressing Vero cells with infectious wild-type viral DNA and a plasmid, pDX, that contains an engineered 780-base-pair (bp) deletion in the ICP8 gene, as well as a spontaneous -55-bp deletion in OriL. Gel electrophoresis and Southern blot analysis indicated that d61 DNA carried both deletions present in pDX. The ability of d61 to replicate despite the deletion in OriL suggested that a functional OriL is not essential for virus replication in vitro. Because d61 harbored two mutations, a second mutant, ts+7, with a deletion in oriL-associated sequences and an intact ICP8 gene was constructed. Both d61 and ts+7 replicated efficiently in their respective permissive host cells, although their yields were slightly lower than those of control viruses with intact oriL sequences. -
Foamy Virus Assembly with Emphasis on Pol Encapsidation
Viruses 2013, 5, 886-900; doi:10.3390/v5030886 OPEN ACCESS viruses ISSN 1999-4915 www.mdpi.com/journal/viruses Review Foamy Virus Assembly with Emphasis on Pol Encapsidation Eun-Gyung Lee 1, Carolyn R. Stenbak 2 and Maxine L. Linial 1,* 1 Fred Hutchinson Cancer Research Center, Basic Sciences Division; 1100 Fairview Avenue North, Seattle, WA 98109, USA; E-Mails: [email protected] (EGL); [email protected] (MLL) 2 Seattle University, Biology Department; 901 12th Avenue, Seattle, WA 98122, USA; E-Mail: [email protected] * Authors to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-206- 667-4442; Fax: +1-206-667-5939 Received: 31 January 2013; in revised form: 11 March 2013 / Accepted: 14 March 2013 / Published: 20 March 2013 Abstract: Foamy viruses (FVs) differ from all other genera of retroviruses (orthoretroviruses) in many aspects of viral replication. In this review, we discuss FV assembly, with special emphasis on Pol incorporation. FV assembly takes place intracellularly, near the pericentriolar region, at a site similar to that used by betaretroviruses. The regions of Gag, Pol and genomic RNA required for viral assembly are described. In contrast to orthoretroviral Pol, which is synthesized as a Gag-Pol fusion protein and packaged through Gag-Gag interactions, FV Pol is synthesized from a spliced mRNA lacking all Gag sequences. Thus, encapsidation of FV Pol requires a different mechanism. We detail how WT Pol lacking Gag sequences is incorporated into virus particles. In addition, a mutant in which Pol is expressed as an orthoretroviral-like Gag-Pol fusion protein is discussed. -
Topological Analysis of the Gp41 MPER on Lipid Bilayers Relevant to the Metastable HIV-1 Envelope Prefusion State
Topological analysis of the gp41 MPER on lipid bilayers relevant to the metastable HIV-1 envelope prefusion state Yi Wanga,b, Pavanjeet Kaurc,d, Zhen-Yu J. Sune,1, Mostafa A. Elbahnasawya,b,2, Zahra Hayatic,d, Zhi-Song Qiaoa,b,3, Nhat N. Buic, Camila Chilea,b,4, Mahmoud L. Nasre,5, Gerhard Wagnere, Jia-Huai Wanga,f, Likai Songc, Ellis L. Reinherza,b,6, and Mikyung Kima,g,6 aLaboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115; bDepartment of Medicine, Harvard Medical School, Boston, MA 02115; cNational High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32306; dDepartment of Physics, Florida State University, Tallahassee, FL 32306; eDepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115; fDepartment of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215; and gDepartment of Dermatology, Harvard Medical School, Boston, MA 02215 Edited by Peter Palese, Icahn School of Medicine at Mount Sinai, New York, NY, and approved September 23, 2019 (received for review July 18, 2019) The membrane proximal external region (MPER) of HIV-1 envelope immunologically vulnerable epitopes targeted by several of the most glycoprotein (gp) 41 is an attractive vaccine target for elicitation of broadly neutralizing antibodies (bNAbs) developed during the broadly neutralizing antibodies (bNAbs) by vaccination. However, course of natural HIV-1 infection (10–13). Insertion, deletion, current details regarding the quaternary structural organization of and mutations of residues in the MPER defined the functional the MPER within the native prefusion trimer [(gp120/41)3] are elu- importance of the MPER in Env incorporation, viral fusion, and sive and even contradictory, hindering rational MPER immunogen infectivity (14–16). -
HBV Cccdna: Viral Persistence Reservoir and Key Obstacle for a Cure of Chronic Hepatitis B Michael Nassal
Downloaded from http://gut.bmj.com/ on June 8, 2015 - Published by group.bmj.com Gut Online First, published on June 5, 2015 as 10.1136/gutjnl-2015-309809 Recent advances in basic science HBV cccDNA: viral persistence reservoir and key obstacle for a cure of chronic hepatitis B Michael Nassal Correspondence to ABSTRACT frequent viral rebound upon therapy withdrawal Dr Michael Nassal, Department At least 250 million people worldwide are chronically indicates a need for lifelong treatment.6 of Internal Medicine II/ Molecular Biology, University infected with HBV, a small hepatotropic DNA virus that Reactivation can even occur, upon immunosuppres- Hospital Freiburg, Hugstetter replicates through reverse transcription. Chronic infection sion, in patients who resolved an acute HBV infec- Str. 55, Freiburg D-79106, greatly increases the risk for terminal liver disease. tion decades ago,7 indicating that the virus can be Germany; Current therapies rarely achieve a cure due to the immunologically controlled but is not eliminated. [email protected] refractory nature of an intracellular viral replication The virological key to this persistence is an intra- Received 17 April 2015 intermediate termed covalently closed circular (ccc) DNA. cellular HBV replication intermediate, called cova- Revised 12 May 2015 Upon infection, cccDNA is generated as a plasmid-like lently closed circular (ccc) DNA, which resides in Accepted 13 May 2015 episome in the host cell nucleus from the protein-linked the nucleus of infected cells as an episomal (ie, relaxed circular (RC) DNA genome in incoming virions. non-integrated) plasmid-like molecule that gives Its fundamental role is that as template for all viral rise to progeny virus. -
Evidence Supporting Dissimilatory And
University of Massachusetts Amherst ScholarWorks@UMass Amherst Microbiology Department Faculty Publication Microbiology Series 2013 Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1 Kristen DeAngelis University of Massachusetts Amherst, [email protected] Deepak Sharma University of Massachusetts Amherst Rebecca Varney University of Massachusetts Amherst Blake Simmons Joint BioEnergy Institute Nancy G. Isern Environmental Molecular Sciences Laboratory See next page for additional authors Follow this and additional works at: https://scholarworks.umass.edu/micro_faculty_pubs Part of the Microbiology Commons Recommended Citation DeAngelis, Kristen; Sharma, Deepak; Varney, Rebecca; Simmons, Blake; Isern, Nancy G.; Markillie, Lye Meng; Nicora, Carrie; Norbeck, Angela D.; Taylor, Ronald C.; Aldrich, Joshua T.; and Robinson, Errol W., "Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1" (2013). Frontiers in Microbiology. 303. 10.3389/fmicb.2013.00280 This Article is brought to you for free and open access by the Microbiology at ScholarWorks@UMass Amherst. It has been accepted for inclusion in Microbiology Department Faculty Publication Series by an authorized administrator of ScholarWorks@UMass Amherst. For more information, please contact [email protected]. Authors Kristen DeAngelis, Deepak Sharma, Rebecca Varney, Blake Simmons, Nancy G. Isern, Lye Meng Markillie, Carrie Nicora, Angela D. Norbeck, Ronald C. Taylor, Joshua T. Aldrich, and Errol W. Robinson This article is available at ScholarWorks@UMass Amherst: https://scholarworks.umass.edu/micro_faculty_pubs/303 ORIGINAL RESEARCH ARTICLE published: 19 September 2013 doi: 10.3389/fmicb.2013.00280 Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1 Kristen M. DeAngelis 1*, Deepak Sharma 1, Rebecca Varney 1, Blake Simmons 2,3, Nancy G. -
Methylation Profile of Hepatitis B Virus Is Not Influenced by Interferon Α in Human Liver Cancer Cells
MOLECULAR MEDICINE REPORTS 24: 715, 2021 Methylation profile of hepatitis B virus is not influenced by interferon α in human liver cancer cells IN YOUNG MOON1 and JIN‑WOOK KIM1,2 1Department of Medicine, Seoul National University Bundang Hospital, Seongnam, Gyeonggi 13620; 2Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea Received December 20, 2020; Accepted July 12, 2021 DOI: 10.3892/mmr.2021.12354 Abstract. Interferon (IFN) α is used for the treatment of Introduction chronic hepatitis B virus (HBV) infection, but the molecular mechanisms underlying its antiviral effect have not been fully Hepatitis B virus (HBV) is one of the commonest causes elucidated. Epigenetic modifications regulate the transcrip‑ of chronic hepatitis worldwide (1). The chronicity of HBV tional activity of covalently closed circular DNA (cccDNA) in infection is related to the fact that HBV produces very cells with chronic HBV infection. IFN‑α has been shown to stable viral genome in the host cells (1). The HBV genome modify cccDNA‑bound histones, but it is not known whether is partially double‑stranded relaxed circular DNA (rcDNA), the anti‑HBV effect of IFN‑α involves methylation of cccDNA. which is converted to complete double‑stranded covalently The present study aimed to determine whether IFN‑α induced closed circular DNA (cccDNA) in the nucleus of infected methylation of HBV cccDNA in a cell‑based model in which hepatocytes (2). HBV cccDNA remains the main hurdle in the HepG2 cells were directly infected with wild‑type HBV eradication of infected HBV as current antiviral agents cannot virions.