Adenosine Deamination at the AmberW Site in the HDV Antigenome

One difficulty encountered in establishing the mechanism of editing at the amber/W site was identifying the RNA substrate: assays performed on repli cating RNAs could not definitively determine whether the substrate for editing was the genome or the antigenome, or even whether editing was the result of co-transcriptional misincorporation. Although initial attempts led to the erroneous suggestion that the genomic RNA might be the substrate, in which case editing would occur as a U to C transition (Casey et al. 1992; Zheng et al. 1992), the use of nonreplicating RNA expression constructs that could exclusively produce either genomic or antigenomic RNA in transfected cells led to the unambiguous conclusion that editing occurs on the antigenome RNA (Casey and Gerin 1995). This result was further supported by analysis of editing on in vitro transcribed RNAs mixed with nuclear extracts: only antigenomic RNA was edited at the amber/W site (Casey and Gerin 1995). This observation indicated that HDV editing occurs post-transcriptionally, and is not the result of transcriptional misincorporation. Subsequently, it was shown that RNA adenosine deaminase (ADAR) from Xenopus laevis can edit the amber/W site in the HDV antigenome with considerable specificity in vitro (Polson et al. 1996).

Accordingly, the type of RNA editing used by HDV is adenosine deamina-tion. In this process, the amino group of adenosine is removed and replaced with a keto oxygen. Because this position of the base is changed from a hydrogen bond donor to an acceptor, the Watson-Crick base-pairing preference of this nucleotide is changed from pairing with U to pairing with C. Therefore, in any subsequent functions that involve base pairing (such as translation, RNA-templated transcription, and splice site identification) the edited position will behave as G rather than the original A. Adenosine deamination has the potential to produce as many as 15 different recodings of an RNA transcript, including the creation of a methionine start codon and the abolition of stop codons. Thus, for example, when the adenosine at the amber/W site in the HDV RNA is edited, a UAG amber stop codon is changed to UIG, which behaves like UGG, and encodes tryptophan. As indicated by this example, sites in RNAs that undergo adenosine deamination have been named according to the coding change brought about by editing.

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