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the action of an adenosine deaminase converts the adenosine in theUAG stop
codon of the small delta antigen to an inosine. Inosine is read as a guanosine,
resulting in a UGG tryptophan codon in lieu of the stop codon, which
extends the C-terminus by 19 amino acids, producing the large form of
the delta antigen. 24 As no other proteins are produced from the viroid,
HDV is completely dependent on the host and helper virus-encoded
machinery for replication and packaging into active viral particles. 18,25,26
In the second pathway, rolling-circle replication produces antigenomic
transcripts that are greater than unit-length genomic RNA. Processing of
these antigenomic concatemers into unit-length antisense genomes is
achieved without the aid of any host, helper virus, or viroid proteins. To
process these RNAs, HDV instead employs a catalytic RNA in the form
of the antigenomic HDV ribozyme. The ribozyme promotes scission of
the phosphate backbone between the nucleotide 5 0 to the structure (the
leader sequence) and the first nucleotide of the ribozyme. 27,28 Ligation into
a circular RNA is achieved with the aid of a host RNA ligase. 29 The viroid
also contains a second, genomic version of the ribozyme with a similar sec-
ondary structure to the antigenomic form that is responsible for processing of
the concatemeric genomic RNA that arises from rolling-circle replication of
the antigenomic RNA ( Fig. 4.1 ).
As the products of the self-scission reaction are a 2 0 -3 0 cyclic phosphate,
and a 5 0 hydroxyl group, the host ligase must utilize these two functional
groups to circularize the genomic and antigenomic RNAs. Although host
machinery necessary for this step has not been identified, an enzyme with
similar activity has been identified in plants and the chordate Branchiostoma
floridae , and the bacteriophage T4 kinase/ligase system serves as the classical
example of such a reaction. 30-32
An interesting aspect to the rolling-circle replication scheme employed
by HDV is how the virus stops the self-cleavage activity of the ribozyme
during times when the viral RNA is acting as the template for RNA syn-
thesis. The mechanism that prevents subsequent scission of the HDV
ribozymes once they have been ligated with their 3 0 termini is not known,
but a recent study of a bacterial RNA editing system provides a potential
mechanism in which a 2 0 -3 0 cyclic phosphate is a substrate for an enzyme
complex that hydrolyzes the phosphate and methylates the 2 0 hydroxyl
group before ligating the cleaved strands together. 33 Methylation of the
2 0 hydroxyl prevents formation of the oxyanion that initiates the attack
on the scissile phosphate during self-scission, thus preventing subsequent
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