The role of a metastable RNA secondary structure in hepatitis delta virus genotype III RNA editing

ABSTRACT Hepatitis delta virus (HDV) produces two essential forms of the sole viral protein from the same open reading frame by using host RNA editing activity at the amber/W site in the antigenomic RNA. The roles of these two forms, HDAg-S and HDAg-L, are opposed. HDAg-S is required for viral RNA replication, whereas HDAg-L, which is produced as a result of editing, inhibits viral RNA replication and is required for virion packaging. Both the rate and amount of editing are important because excessive editing will inhibit viral RNA replication, whereas insufficient editing will reduce virus secretion. Here we show that for HDV genotype III, which is associated with severe HDV disease, HDAg-L strongly inhibits editing of a nonreplicating genotype III reporter RNA, while HDAg-S inhibits only when expressed at much higher levels. The different inhibitory efficiencies are due to RNA structural elements located ca. 25 bp 3′ of the editing site in the double-hairpin RNA structure required for editing at the amber/W site in HDV genotype III RNA. These results are consistent with regulation of amber/W editing in HDV genotype III by a negative-feedback mechanism due to differential interactions between structural elements in the HDV genotype III RNA and the two forms of HDAg.

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Effects of Conserved RNA Secondary Structures on Hepatitis Delta Virus Genotype I RNA Editing, Replication, and Virus Production

Journal of Virology ◽

10.1128/jvi.79.17.11187-11193.2005 ◽

2005 ◽

Vol 79 (17) ◽

pp. 11187-11193 ◽

Cited By ~ 13

Author(s):

Geetha C. Jayan ◽

John L. Casey

Keyword(s):

Secondary Structure ◽

Rna Editing ◽

Hepatitis Delta Virus ◽

Virus Production ◽

Rna Replication ◽

Base Pairing ◽

Genotype I ◽

Hepatitis Delta ◽

Hdv Genotype ◽

Delta Virus

ABSTRACT RNA editing of the hepatitis delta virus (HDV) antigenome at the amber/W site by the host RNA adenosine deaminase ADAR1 is a critical step in the HDV replication cycle. Editing is required for production of the viral protein hepatitis delta antigen long form (HDAg-L), which is necessary for viral particle production but can inhibit HDV RNA replication. The RNA secondary structural features in ADAR1 substrates are not completely defined, but base pairing in the 20-nucleotide (nt) region 3′ of editing sites is thought to be important. The 25-nt region 3′ of the HDV amber/W site in HDV genotype I RNA consists of a conserved secondary structure that is mostly base paired but also has asymmetric internal loops and single-base bulges. To understand the effect of this 3′ region on the HDV replication cycle, mutations that either increase or decrease base pairing in this region were created and the effects of these changes on amber/W site editing, RNA replication, and virus production were studied. Increased base pairing, particularly in the region 15 to 25 nt 3′ of the editing site, significantly increased editing; disruption of base pairing in this region had little effect. Increased editing resulted in a dramatic inhibition of HDV RNA synthesis, mostly due to excess HDAg-L production. Although virus production at early times was unaffected by this reduced RNA replication, at later times it was significantly reduced. Therefore, it appears that the conserved RNA secondary structure around the HDV genotype I amber/W site has been selected not for the highest editing efficiency but for optimal viral replication and secretion.

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The fraction of RNA that folds into the correct branched secondary structure determines hepatitis delta virus type 3 RNA editing levels

RNA ◽

10.1261/rna.1504009 ◽

2009 ◽

Vol 15 (6) ◽

pp. 1177-1187 ◽

Cited By ~ 16

Author(s):

S. D. Linnstaedt ◽

W. K. Kasprzak ◽

B. A. Shapiro ◽

J. L. Casey

Keyword(s):

Secondary Structure ◽

Rna Editing ◽

Virus Type ◽

Hepatitis Delta Virus ◽

Hepatitis Delta ◽

Type 3 ◽

Delta Virus

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RNA Editing in Hepatitis Delta Virus Genotype III Requires a Branched Double-Hairpin RNA Structure

Journal of Virology ◽

10.1128/jvi.76.15.7385-7397.2002 ◽

2002 ◽

Vol 76 (15) ◽

pp. 7385-7397 ◽

Cited By ~ 29

Author(s):

John L. Casey

Keyword(s):

Rna Editing ◽

Hepatitis Delta Virus ◽

Severe Disease ◽

Hairpin Structure ◽

Structural Motif ◽

Structure Characteristic ◽

Hepatitis Delta ◽

Genotype Iii ◽

Hdv Genotype ◽

Delta Virus

ABSTRACT RNA editing at the amber/W site plays a central role in the replication scheme of hepatitis delta virus (HDV), allowing the virus to produce two functionally distinct forms of the sole viral protein, hepatitis delta antigen (HDAg), from the same open reading frame. Editing is carried out by a cellular activity known as ADAR (adenosine deaminase), which acts on RNA substrates that are at least partially double stranded. In HDV genotype I, editing requires a highly conserved base-paired structure that occurs within the context of the unbranched rod structure characteristic of HDV RNA. This base-paired structure is disrupted in the unbranched rod of HDV genotype III, which is the most distantly related of the three known HDV genotypes and is associated with the most severe disease. Here I show that RNA editing in HDV genotype III requires a branched double-hairpin structure that deviates substantially from the unbranched rod structure, involving the rearrangement of nearly 80 bp. The structure includes a UNCG RNA tetraloop, a highly stable structural motif frequently involved in the folding of large RNAs such as rRNA. The double-hairpin structure is required for editing, and hence for virion formation, but not for HDV RNA replication, which requires the unbranched rod structure. HDV genotype III thus relies on a dynamic conformational switch between the two different RNA structures: the unbranched rod characteristic of HDV RNA and a branched double-hairpin structure that is required for RNA editing. The different mechanisms of editing in genotypes I and III underscore their functional differences and may be related to pathogenic differences as well.

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Role of hepatitis B, hepatitis C and hepatitis delta virus in dual and triple chronic hepatitis coinfection

Journal of Hepatology ◽

10.1016/s0168-8278(01)80441-4 ◽

2001 ◽

Vol 34 (0) ◽

pp. 122

Author(s):

X Costa

Keyword(s):

Chronic Hepatitis ◽

Hepatitis C ◽

Hepatitis B ◽

Hepatitis Delta Virus ◽

Hepatitis Delta ◽

Delta Virus

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Phylodynamic and Phylogeographic Analysis of Hepatitis Delta Virus Genotype 3 Isolated in South America

Viruses ◽

10.3390/v11110995 ◽

2019 ◽

Vol 11 (11) ◽

pp. 995 ◽

Cited By ~ 1

Author(s):

Felipe Souza Nogueira-Lima ◽

Luan Felipo Botelho-Souza ◽

Tárcio Peixoto Roca ◽

Alcione Oliveira dos Santos ◽

Suyane da Costa Oliveira ◽

...

Keyword(s):

South America ◽

Hepatitis Delta Virus ◽

Recent Common Ancestor ◽

Screening Methods ◽

Genotype 3 ◽

Virus Genotype ◽

Serological Screening ◽

Hepatitis Delta ◽

Most Recent Common Ancestor ◽

Delta Virus

The hepatitis delta virus (HDV) is a globally distributed agent, and its genetic variability allows for it to be organized into eight genotypes with different geographic distributions. In South America, genotype 3 (HDV-3) is frequently isolated and responsible for the most severe form of infection. The objective of this study was to evaluate the evolutionary and epidemiological dynamics of HDV-3 over the years and to describe its distribution throughout this continent in an evolutionary perspective. While using Bayesian analysis, with strains being deposited in the Nucleotide database, the most recent common ancestor was dated back to 1964 and phylogenetic analysis indicated that the dispersion may have started in Brazil, spreading to Venezuela and then to Colombia, respectively. Exponential growth in the effective number of infections was observed between the 1950s and 1970s, years after the first report of the presence of HDV on the continent, during the Labrea Black Fever outbreak, which showed that the virus continued to spread, increasing the number of cases decades after the first reports. Subsequently, the analysis showed a decrease in the epidemiological levels of HDV, which was probably due to the implantation of the vaccine against its helper virus, hepatitis B virus, and serological screening methods implemented in the blood banks.

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RNA Editing and its Control in Hepatitis Delta Virus Replication

Viruses ◽

10.3390/v2010131 ◽

2010 ◽

Vol 2 (1) ◽

pp. 131-146 ◽

Cited By ~ 6

Author(s):

Renxiang Chen ◽

Sarah Linnstaedt ◽

John Casey

Keyword(s):

Rna Editing ◽

Virus Replication ◽

Hepatitis Delta Virus ◽

Hepatitis Delta ◽

Delta Virus

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RNA editing of hepatitis delta virus antigenome by dsRNA-adenosine deaminase

Nature ◽

10.1038/380454a0 ◽

1996 ◽

Vol 380 (6573) ◽

pp. 454-456 ◽

Cited By ~ 211

Author(s):

Andrew G. Poison ◽

Brenda L. Bass ◽

John L. Casey

Keyword(s):

Adenosine Deaminase ◽

Rna Editing ◽

Hepatitis Delta Virus ◽

Hepatitis Delta ◽

Delta Virus

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Increased RNA Editing and Inhibition of Hepatitis Delta Virus Replication by High-Level Expression of ADAR1 and ADAR2

Journal of Virology ◽

10.1128/jvi.76.8.3819-3827.2002 ◽

2002 ◽

Vol 76 (8) ◽

pp. 3819-3827 ◽

Cited By ~ 50

Author(s):

Geetha C. Jayan ◽

John L. Casey

Keyword(s):

Rna Editing ◽

Hepatitis Delta Virus ◽

Rna Replication ◽

Rna Packaging ◽

High Level Expression ◽

Hepatitis Delta ◽

Huh7 Cells ◽

Hepatitis Delta Antigen ◽

High Level ◽

Delta Virus

ABSTRACT Hepatitis delta virus (HDV) is a subviral human pathogen that uses specific RNA editing activity of the host to produce two essential forms of the sole viral protein, hepatitis delta antigen (HDAg). Editing at the amber/W site of HDV antigenomic RNA leads to the production of the longer form (HDAg-L), which is required for RNA packaging but which is a potent trans-dominant inhibitor of HDV RNA replication. Editing in infected cells is thought to be catalyzed by one or more of the cellular enzymes known as adenosine deaminases that act on RNA (ADARs). We examined the effects of increased ADAR1 and ADAR2 expression on HDV RNA editing and replication in transfected Huh7 cells. We found that both ADARs dramatically increased RNA editing, which was correlated with strong inhibition of HDV RNA replication. While increased HDAg-L production was the primary mechanism of inhibition, we observed at least two additional means by which ADARs can suppress HDV replication. High-level expression of both ADAR1 and ADAR2 led to extensive hyperediting at non-amber/W sites and subsequent production of HDAg variants that acted as trans-dominant inhibitors of HDV RNA replication. Moreover, we also observed weak inhibition of HDV RNA replication by mutated forms of ADARs defective for deaminase activity. Our results indicate that HDV requires highly regulated and selective editing and that the level of ADAR expression can play an important role: overexpression of ADARs inhibits HDV RNA replication and compromises virus viability.

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