Many plant viruses and animal pathogens undergo rolling circle replicationfrom a small circular genome.
When DNA or RNA is copied from these templates, the polymerase generates a continuous, repetitive strand
that must be cut into pieces that encode single copies of an entire genome (e.g., herpesvirus DNA) or into
individual genes (e.g., certain plant viroids and hepatitis delta virus). In the case of viroidssuch as avocado
sunblotch virus or tobacco ringspot virus, RNA is transcribed as a continuous strand and the regions between
genes then fold into catalytic tertiary structures. These are known as the hammerhead and hairpin ribozyme
motifs, respectively. These motifs undergo self-cleavage reactionswhere the RNA is cleaved into small
pieces that encode individual proteins (Figure 7.38).^68 Such ribozymes have been developed as tools for
biotechnology.
286 Chapter 7
Figure 7.37 Three different types of ribozymes derived viroids and viruses. The secondary structures of (a) ham-
merhead (b) hairpin and (c) hepatitis delta ribozymes are shown, with arrows indicating the sites of
cleavage. The catalytic core of the hammerhead ribozyme is shown in red
Figure 7.38 Mechanisms of rolling circle replication. (a) The positive stranded genome of certain viroids (bold
circle around “”) is copied continuously into a long minus-strand RNA (red line) that is cleaved into
antigenomic units with a ribozyme (grey arrows). The minus strand RNA circularizes (red circle), is copied
into plus strand RNA (black line), which is cleaved into genomic units with another ribozyme (grey
arrows, left).^68 In pathogens such as the avocado sunblotch virus, the hammerhead ribozyme motif
cleaves both () and () strands, while other viroids/viruses utilize hammerhead or other ribozyme
motifs (such as the hairpin). (b) Sometimes the circular () strand is copied into a minus strand that
does not circularize, but which is copied into a new plus strand that is self-cleaved by ribozyme motifs