HIV and hepatitis delta virus: evolution takes different paths to relieve blocks in transcriptional elongation

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RNA-dependent RNA replication is a special process reserved exclusively for RNA viruses but not cellular RNAs. Almost all RNA viruses (except retroviruses) undergo RNAdependent RNA replication by a virus-encoded RNA-dependent RNA polymerase (RdRP), which specifically replicates the viral RNA genome. Satellite viral RNAs do not encode their own polymerase but rely on the RdRP from the coexisting helper virus for their replication. Hepatitis delta virus (HDV) and plant viroids present an exception which still confounds the conventional thinking. None of them encode an RdRP, and yet they can undergo robust RNA replication autonomously once inside the cells. It is intuitive that they have to replicate their RNA genome using a cellular enzyme. However, unlike plants and lower animal species, which encode RdRPs that are putatively involved in gene silencing (11,13,57,58), no mammalian cells have been shown to encode any RdRP or its equivalent. Nevertheless, the RNA interference phenomena suggest the possibility that RNA-templated RNA amplification may also take place in the mammalian cells (61). Thus, viroids and HDV present both a challenge and an opportunity for understanding a potentially physiological flow of genetic information from RNA to RNA in the mammalian cells. Viroids and HDV differ in that viroids do not encode any protein, whereas HDV encodes a protein (hepatitis delta antigen [HDAg]) which is intimately involved in RNA replication. In addition, HDV RNA not only has to replicate itself but also needs to transcribe a subgenomic mRNA species that encodes HDAg. The transcription of the HDAg-encoding mRNA has all of the hallmarks of the conventional mRNA transcription in the cells except for the nature of the template (DNA versus RNA). Therefore, HDV represents a hybrid of the conventional DNA-dependent transcription and the unique RNAdependent RNA synthesis in the absence of an RdRP.HDV causes chronic, and occasionally fulminant, hepatitis (20). It is always associated with hepatitis B virus (HBV) infection because HDV cannot form virus particles on its own (54). It was prevalent worldwide, with a particularly high prevalence rate in the Mediterranean countries. In recent years, the incidence of new HDV infection has precipitously declined, partially due to HBV vaccination. Nevertheless, the scientific mystery surrounding HDV replication thickens. STRUCTURE OF HDV RNA AND HDAgHDV contains a circular RNA genome of 1.7 kilobases which can replicate on its own but requires HBV as the helper virus to supply HBV surface antigen for the production of virus particles. The genome sequence is nearly self-complementary such that the viral RNA forms a rodlike double-stranded RNA structure under the native conditions (29, 70). As such, HDV RNA is very similar to viroid RNAs; indeed, part of the HDV RNA sequence is evolutionarily related to viroids (15). However, HDV RNA is 3 to 4 times longer than the typical viroid, with the additional sequences being attributed to a coding sequence for HDAg on the complementary (anti...

Section: The Role Of Hdag In Hdv Rna Replicationmentioning

confidence: 99%

RNA Replication without RNA-Dependent RNA Polymerase: Surprises from Hepatitis Delta Virus

Lai

2005

130

119

“…HDAg has been shown to transport HDV RNA to the nucleus, where replication occurs (12). In addition, HDAg interacts with RNA polymerase II (Pol II) (13,14); this interaction may recruit the polymerase to bound HDV RNA and has been proposed to effect changes in the polymerase that permit RNA-directed transcription (14)(15)(16)(17). RNPs formed by HDAg and HDV RNA are also packaged into virions (18,19); these complexes include a modified form of HDAg that interferes with RNA synthesis (20)(21)(22)(23)(24).…”

mentioning

confidence: 99%

Arginine-Rich Motifs Are Not Required for Hepatitis Delta Virus RNA Binding Activity of the Hepatitis Delta Antigen

Daigh

Griffin

Soroush

et al. 2013

Hepatitis delta virus (HDV) is a unique human pathogen that increases the severity of liver disease in those infected with its helper virus, hepatitis B virus (HBV). The ϳ1,680-nucleotide (nt) single-stranded circular RNA genome assumes a characteristic unbranched rodlike structure in which ϳ70% of the nucleotides form Watson-Crick base pairs (1, 2). Genome replication occurs via a double-rolling-circle mechanism in which host RNA polymerase is redirected to synthesize genomic and antigenomic HDV RNAs, as well as the mRNA for hepatitis delta antigen (HDAg), the sole viral protein (reviewed in references 3 and 4). HDAg forms RNA-protein complexes (RNPs) with both genomic and antigenomic HDV RNAs, and these complexes play essential roles in this unique replication process (5-11). HDAg has been shown to transport HDV RNA to the nucleus, where replication occurs (12). In addition, HDAg interacts with RNA polymerase II (Pol II) (13,14); this interaction may recruit the polymerase to bound HDV RNA and has been proposed to effect changes in the polymerase that permit RNA-directed transcription (14-17). RNPs formed by HDAg and HDV RNA are also packaged into virions (18, 19); these complexes include a modified form of HDAg that interferes with RNA synthesis (20-24). Understanding how HDV RNPs function depends on knowing their structural features, which remains a critical goal.Several studies have attempted to identify regions of HDAg that directly contribute to binding HDV RNA and forming HDV RNPs, but a consistent picture has not yet emerged. In a widely cited model, two arginine-rich motifs (ARM I and ARM II) in the middle region of the protein are thought to form a bipartite RNA binding domain (8). This model is based largely on two in vitro binding studies using bacterially expressed HDAg fusion proteins. One of these studies showed that only fusion proteins containing the middle region of the protein, which includes the ARMs, could bind HDV RNA (25); no RNA binding activity was associated with the N-terminal 78 amino acids (aa). The other study showed loss of in vitro RNA binding activity when either of the ARMs, particularly ARM I, was disrupted by replacement of two basic residues with other amino acids (8). Both reports relied heavily on RNAprotein blots (Northwestern blots), which depend on the ability to remove bound detergent and properly refold proteins following electrophoresis and blotting. In contrast, other in vitro studies implicated the amino-terminal domain of HDAg in binding HDV . However, these analyses were limited by the use of small segments of the protein; Poisson et al. used small peptide fragments (28), and Huang and Wu and Wang et al. employed an N-terminal 88-aa region that bound equally well to HDV and non-HDV RNAs (26,27).Analyses of HDAg-HDV RNA interactions in cells have also yielded conflicting interpretations. Wang et al. (11) found that mutation of ARM I severely diminished the ability of HDAg to package the RNA into secreted particles, a result that could suggest a role for ARM I in ...

“…The CTD is phosphorylated differentially during the transcription cycle and interacts with a number of factors involved in all steps of mRNA maturation (26). Pol II transcription and RNA processing are influenced not only by cellular factors such as CTD kinases and phosphatases but also by viral proteins (30).…”

mentioning

confidence: 99%

Association of the Influenza A Virus RNA-Dependent RNA Polymerase with Cellular RNA Polymerase II

Engelhardt

Smith

Fodor

2005

212

220

Transcription by the influenza virus RNA-dependent RNA polymerase is dependent on cellular RNA processing activities that are known to be associated with cellular RNA polymerase II (Pol II) transcription, namely, capping and splicing. Therefore, it had been hypothesized that transcription by the viral RNA polymerase and Pol II might be functionally linked. Here, we demonstrate for the first time that the influenza virus RNA polymerase complex interacts with the large subunit of Pol II via its C-terminal domain. The viral polymerase binds hyperphosphorylated forms of Pol II, indicating that it targets actively transcribing Pol II. In addition, immunofluorescence analysis is consistent with a new model showing that influenza virus polymerase accumulates at Pol II transcription sites. The present findings provide a framework for further studies to elucidate the mechanistic principles of transcription by a viral RNA polymerase and have implications for the regulation of Pol II activities in infected cells.