Characterization of RNA-binding domains of hepatitis delta antigen

Poisson, Francis; Roingeard, Philippe; Baillou, Armelle; Dubois, Frédéric; Bonelli, Fabrizio; Calogero, Raffaele; Goudeau, Alain

doi:10.1099/0022-1317-74-11-2473

Cited by 36 publications

(26 citation statements)

References 33 publications

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“…The observation (Fig. 5) that the N-terminal region of HDAg is in close contact with RNA bound in a discrete complex goes beyond previous observations that N-terminal fragments of HDAg can bind RNA (26)(27)(28). Our analysis of HDAg fragments from both the N-terminal and middle regions of the protein indicated that the nature of the complexes formed by these fragments was considerably different from RNPs formed by HDAg-160, particularly regarding the lack of specificity for unbranched rodlike HDV RNAs (Fig.…”

Section: Discussionmentioning

confidence: 47%

“…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 RNA (26)(27)(28). 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).…”

mentioning

confidence: 97%

“…6). Alanines were substituted for basic amino acids in 5 clusters of 2 or 3 basic amino acids that are more than 95% conserved among HDV genotype 1 isolates and for the 4 highly conserved arginines near the N terminus of the protein (28). We also substituted alanines for K25 and K26, which, according to a crystal structure, could be positioned to interact with bound RNA (35).…”

Section: Mutation Of Arm I or Arm Ii Does Not Decrease Rna Binding Bymentioning

confidence: 99%

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

Daigh

Griffin

Soroush

et al. 2013

J Virol

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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 ...

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Section: Discussionmentioning

confidence: 47%

mentioning

confidence: 97%

Section: Mutation Of Arm I or Arm Ii Does Not Decrease Rna Binding Bymentioning

confidence: 99%

See 1 more Smart Citation

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

Daigh

Griffin

Soroush

et al. 2013

J Virol

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“…Others have shown that regions within the first 39 amino acids of HDAg possess RNA binding activity (5,19). Furthermore, a coiled-coil domain resides in this region, and its deletion is expected to preclude stable multimeric assembly on RNA (33).…”

Section: Resultsmentioning

confidence: 99%

Hepatitis Delta Virus Minimal Substrates Competent for Editing by ADAR1 and ADAR2

Sato

Wong

Lazinski

2001

J Virol

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A host-mediated RNA-editing event allows hepatitis delta virus (HDV) to express two essential proteins, the small delta antigen (HDAg-S) and the large delta antigen (HDAg-L), from a single open reading frame. One or several members of the ADAR (adenosine deaminases that act on RNA) family are thought to convert the adenosine to an inosine (I) within the HDAg-S amber codon in antigenomic RNA. As a consequence of replication, the UIG codon is converted to a UGG (tryptophan [W]) codon in the resulting HDAg-L message. Here, we used a novel reporter system to monitor the editing of the HDV amber/W site in the absence of replication. In cultured cells, we observed that both human ADAR1 (hADAR1) and hADAR2 were capable of editing the amber/W site with comparable efficiencies. We also defined the minimal HDV substrate required for hADAR1-and hADAR2-mediated editing. Only 24 nucleotides from the amber/W site were sufficient to enable efficient editing by hADAR1. Hence, the HDV amber/W site represents the smallest ADAR substrate yet identified. In contrast, the minimal substrate competent for hADAR2-mediated editing contained 66 nucleotides.

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“…Arginine residues have been shown to mediate RNA recognition (Calnan et al, 1991) and synthetic peptides rich in arginine residues derived from viral proteins can bind RNA (Lazinski et al, 1989;Poisson et al, 1993;Weeks et al, 1990). Interestingly, the TuMV protein has a very basic domain, RSSRAMKQKRARERRRAQQ, spanning residues 150 to 168 which has the potential of interacting with nucleic acids; basic residues (K, R) could form ionic bonds with negatively charged phosphate groups whereas amide (Q), acid (E) or hydroxylated (S) amino acids could interact via hydrogen bonds with nucleic acid bases.…”

Section: Discussionmentioning

confidence: 99%

Nucleic acid-binding properties of the P1 protein of turnip mosaic potyvirus produced in Escherichia coli

Soumounou

Laliberté

1994

Journal of General Virology

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The N-terminal P1 protein of tumip mosaic potyvirus (TuMV) polyprotein was overexpressed in Escherichia coli, purified by metal chelation chromatography under denaturing conditions and renatured. U.v. cross-linking experiments indicated that the recombinant protein interacted with RNA, and gel retardation electrophoresis demonstrated that more than one molecule of P1 bound one molecule of RNA. Formation of the protein-RNA complexes was dependent on the conformational state of P1 and was stable at relatively high concentrations of NaCI. P1 had the ability to bind ssRNA and ssDNA, with similar affinity, but was not able to bind to dsDNA. The TuMV protein had the additional characteristic of binding dsRNA with affinity similar to that observed with single-stranded nucleic acids.

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Characterization of RNA-binding domains of hepatitis delta antigen

Cited by 36 publications

References 33 publications

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

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

Hepatitis Delta Virus Minimal Substrates Competent for Editing by ADAR1 and ADAR2

Nucleic acid-binding properties of the P1 protein of turnip mosaic potyvirus produced in Escherichia coli

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