HDV Family of Self-Cleaving Ribozymes - Progress in Molecular Biology and Translational Science - page 154

deletions to the L3 core and P3 helices in conjunction with mutations to the
cleavage-site guanosine likely render all but a few of these sequences inac-
tive. Nevertheless, ESTs are detected for many drz-Bflo-2 copies, indicating
that they are transcribed in vivo (e.g., EST BW882616).

5.14. Petromyzon marinus ribozymes
The genome of the lamprey eel P . marinus contains an HDV-like ribozyme,
drz-Pmar-1, that was identified using structure-based searches. Drz-Pmar-1,
like the drz-Spur-1 and -2, drz-Bflo-2, and CPEB3 sequences, contains only
a single G-C base pair in the P1.1 helix. Several copies of the ribozyme are
present in the genome, although the exact numbers are unknown due to
incomplete genome assembly for the organism. One of these copies resides
in a zinc finger gene, and it is expressed in vivo (EST FD713707). Several of
the copies are likely inactive due to a poorly paired P1 helix or active-site
C56Umutations. Interestingly, ribozymes sharing the drz-Pmar-1 sequence
are readily detected in the genomes of the spiny dogfish shark Squalus
acanthias , where the sequence is expressed (EST ES605876), and the coela-
canth Latimeria menadoensis , where drz-Lmen-1 cleaves in vitro and shows
strong temperature dependence. 7

5.15. Nematode ribozymes
Nematodes represent one of the most diverse phylums of eukaryotic organ-
isms on the planet, with estimates of species diversity ranging from 100,000
to 1,000,000. 136 It is, therefore, not surprising that HDV-like ribozymes are
readily detected in this vast sequence space. Two nematodes, C . japonica and
P . pacificus , possess ribozymes with confirmed in vitro activity ( Fig. 4.10 ). 3
In both organisms, only a single family of HDV-like self-cleaving molecules
is found, but each family is present many times throughout the genome.
In P . pacificus , the copy number rivals that of the most abundant R2
ribozymes, and the copy number in the C . japonica genome is greater still.
There are approximately 120 copies of the drz-Cjap-1 family of
ribozymes in the C . japonica genome. Because the C . japonica genome is
not completely assembled, it is likely that some of these are overlapping reads
from the sequencing of the organism. However, alignment of the copies
reveals many to have differentiated upstream regions but conserved
sequences downstream of the ribozymes ( Fig. 4.10 ). Furthermore, none
of the ribozymes appears in regions that map to known C . japonica genes,
but an RTE-like RT-coding region does appear downstream of

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