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various organisms using sequence-based search methods. Although
sequence-based searching is generally challenging for folded, functional
RNA molecules, additional HDV-like motifs were found based on their
highly similar P3 and L3 regions relative to the drz-Agam-1 family of
sequences.
3
In insects, ribozymes were found in the pea aphid
Acyrothosiphon
pisum
, a second mosquito,
Anopheles funestus
(EST CD578134), and in sev-
eral ESTs from the central nervous system of the insect
Rhodinus prolixus
,a
vector for Chagas disease parasite
Trypanosoma cruzi
(e.g., EST FG545964).
HDV-like ribozymes with identical P3 and L3 regions were also found in
several fungi and plants.
In the fungus kingdom, the antifungal biocontrol fungus
Trichoderma atro-
viride
possesses a confirmed HDV-like ribozyme (
k
obs
1.8 h
1
in 10 mM
Mg
2
þ
at 37
C), as does the mycosporadic fungus
Trichoderma virens
.
7
The
red bread mold
Neurospora crassa
contains a ribozyme active
in vitro
and which
appears self-cleaved at the 5
0
end of an EST in the organism (EST
GE968064).
7
Putative ribozymes are also found in the RNase H gene of
the fungus
Ajellomyces capsultans
(EST XM_001543659), the filamentous
fungi
Podospora anserine
, the invasive fungus
Neosartorya fischeri
, and the plant
pathogenic fungi
Magnaportha grisae
,
Phaeosphaeria nodurm SN15
, and
Alternaria brassicicolla
.
7
Plant HDV-like ribozymes with identical cores are
detected in ESTs from the artichoke
Cynara scolymus
(EST GE606767)
and the sunflower
Helianthus annus
(EST DY925396).
3
Ribozymes sharing the drz-Agam-1 core are also found in ESTs from the
tapeworm
Moniezia expansa
(EST FE942699).
3
However, these ribozymes
are likely inactive or under tight regulation
in vivo
, as the EST extends
beyond the presumed cleavage site for the motif. An active HDV-like ribo-
zyme is present in the free-living marine protist
Diplonema papillatum
(
k
obs
¼
approximately 100 h
1
in 10 mM Mg
2
þ
at 37
C), and resides bet-
ween the splice leader for the 5S rRNA and 5S rRNA itself. Since the
sequence exhibits robust
in vitro
activity, it is likely involved in the
processing of noncoding RNAs in the organism. The pacific abalone
Haliotis
discus
also contains an HDV-like ribozyme that is one of the smallest
HDV-like sequences identified to date at just 58 nt.
7
¼
5.12. Stronglyocentrotus purpuratus ribozymes
Structure-based searching revealed multiple HDV-like ribozymes in the
genome of the purple sea urchin
S
.
purpuratus
(
Fig. 4.9
). Based on the sec-
ondary structure, the ribozymes can be divided into four families of
sequences, drz-Spur-1 to -4. This distinction is made largely based on the
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