title: In Vitro Assays for RNA Binding and Protein Priming of Hepatitis B Virus Polymerase.
abstract: The hepatitis B virus (HBV) polymerase synthesizes the viral DNA genome from the pre-genomic RNA (pgRNA) template through reverse transcription. Initiation of viral DNA synthesis is accomplished via a novel protein priming mechanism, so named because the polymerase itself acts as a primer, whereby the initiating nucleotide becomes covalently linked to a tyrosine residue on the viral polymerase. Protein priming, in turn, depends on specific recognition of the packaging signal on pgRNA called epsilon. These early events in viral DNA synthesis can now be dissected in vitro as described here.The polymerase is expressed in mammalian cells and purified by immunoprecipitation. The purified protein is associated with host cell factors, is enzymatically active, and its priming activity is epsilon dependent. A minimal epsilon RNA construct from pgRNA is co-expressed with the polymerase in cells. This RNA binds to and co-immunoprecipitates with the polymerase. Modifications can be made to either the epsilon RNA or the polymerase protein by manipulating the expression plasmids. Also, the priming reaction itself can be modified to assay for the initiation or subsequent DNA synthesis during protein priming, the susceptibility of the polymerase to chemical inhibitors, and the precise identification of the DNA products upon their release from the polymerase. The identity of associated host factors can also be evaluated. This protocol closely mirrors our current understanding of the RNA binding and protein priming steps of the HBV replication cycle, and it is amenable to modification. It should therefore facilitate both basic research and drug discovery.
authors.affiliation: Department of Microbiology and Immunology-H107, The Pennsylvania State University College of Medicine, 500 University Dr., Hershey, PA, 17033, USA. dnc142@psu.edu.
authors.forename: Daniel N
authors.initials: DN
authors.lastname: Clark
authors.affiliation: Department of Microbiology and Immunology-H107, The Pennsylvania State University College of Medicine, 500 University Dr., Hershey, PA, 17033, USA.|Nevada Division of Public and Behavioral Health, Primary Care Office, 4150 Technology Way, Suite 104, Carson City, NV, 89706, USA.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jones
authors.affiliation: Department of Microbiology and Immunology-H107, The Pennsylvania State University College of Medicine, 500 University Dr., Hershey, PA, 17033, USA.
authors.forename: Jianming
authors.initials: J
authors.lastname: Hu
mesh_terms: D002460:Cell Line; D053837:DNA Cleavage; D004268:DNA-Binding Proteins; D004789:Enzyme Activation; D015870:Gene Expression; D015684:Gene Products, pol / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D006515:Hepatitis B virus / Q000201:enzymology / Q000502:physiology*; D006801:Humans; D066298:In Vitro Techniques; D046912:Multiprotein Complexes; D009687:Nuclear Proteins / Q000378:metabolism; D010727:Phosphoric Diester Hydrolases; D010957:Plasmids / Q000235:genetics; D011485:Protein Binding; D012367:RNA, Viral / Q000235:genetics*; D011994:Recombinant Proteins / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D048348:Reverse Transcription; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic; D014162:Transfection; D014779:Virus Replication
chemical_list: D004268:DNA-Binding Proteins; D015684:Gene Products, pol; D046912:Multiprotein Complexes; D009687:Nuclear Proteins; C066027:P protein, Hepatitis B virus; D012367:RNA, Viral; D011994:Recombinant Proteins; D014157:Transcription Factors; D010727:Phosphoric Diester Hydrolases; C474866:TDP2 protein, human
keywords: Hepatitis B virus; Polymerase; Protein priming; RNA binding; Reverse transcriptase