HDV Family of Self-Cleaving Ribozymes - Progress in Molecular Biology and Translational Science - page 149

5.10. Additional RT-associated ribozymes
Structure-based searches for HDV-like ribozymes within the EST database,
known RT-containing mRNAs, and genomic repeat regions as defined by
RepeatMasker revealed many more ribozymes that map to various non-
LTR retrotransposons. 126 In addition to the R2 ribozymes in Drosophila ,
the R2 elements of the termites Kalotermes flavicollis and Reticulitermes
lucifugus , 129 the sea squirt Ciona intestinalis , 130 the black-legged tick Ixodes
scapularis (GenBank ™ accession ABJB010506112), the horseshoe shrimp
Triops cancriformis (GenBank ™ accession EU854578), and the Zebra finch
Taeniopygia guttata 131 were all found to harbor HDV-like ribozymes in their
5 0 terminal region. Other rDNA-associated retrotransposons with
ribozymes include the R4 element 132 in the human intestinal roundworm
Ascaris lumbricoides , the horse intestinal roundworm Parascaris equorum , and
the R6Ag1 and R6Ag3 elements in A . gambiae . 133 With the exception of
the A . gambiae elements, all of these ribozymes possess the extended J1/2
region observed in the Drosophila isolates. Since this region can adopt
numerous conformations without abolishing self-cleavage, conservation
of the extended J1/2 region is likely attributable to each ribozyme's function
as an IRES. The JAM1 RTE 134 from the yellow fever mosquito Aedes
aegypti , the SARTPx2 133,135 element from the Asian swallowtail butterfly
Papilio xuthus , and the Baggins retrotransposons from Drosophila are also
under the influence of HDV-like ribozymes. Both the JAM1 and SARTPx2
associated ribozymes, like the R6Ag1 and Ag3 ribozymes from A . gambiae ,
lack the extended J1/2 region that is a hallmark of other rDNA-associated
retrotransposon ribozymes. These ribozymes do, however, contain P4 heli-
ces that are longer than those seen in the Drosophila R2 sequences, perhaps in
part to compensate for the loss of stability associated with a shorter J1/
2 motif.
Several ribozymes have been identified upstream of regions that display
high similarity to RT-coding motifs in a number of organisms, including
A . aegypti , the butterfly Heliconius numata , the flatworm Schistosoma mansoni ,
the sea slug Aplysia californica , the common sea urchin Paracentrotus lividus ,
the Indonesian coelacanth Latimeria menadoesnsis , the sea lamprey
Petromyzon marinus , the little skate Leucoraja erinacea , and the painted turtle
Chrysemys picta .
5.11. HDV-like ribozyme cores similar to drz-Agam-1
In addition to drz-Agam-like ribozymes found in retrotransposons, a num-
ber of other sequences have been identified in genomes and ESTs from