Worm Breeder's Gazette 11(5): 58

These abstracts should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with the consent of the author.

The Spliced Leader RNA Genes from a Brazilian Free-Living Soil Nematode

Carlos E. Winter and Tom Blumenthal

We have isolated from a soil sample, in Sao Paulo - Brazil, a 
rhabditid nematode which we are characterizing at the morphological, 
biological and molecular levels.  The isolate we are studying is 
temporarily being called B6/D6 until species and genus designations 
can be confirmed.  C.  elegans and B6/D6 probably belong to two 
different subfamilies of the Rhabditidae.  Our object in these studies 
is to characterize a species sufficiently far from C.  elegans such 
that only highly selected sequences have been maintained, but 
sufficiently close that unequivocal sequence alignments can be made.  
We chose B6/D6 because it is morphologically very similar to C.  
elegans, but so distant that the C.  elegans vit genes fail to cross-
hybridize with B6/D6 DNA at low stringency.
The first genes we have studied are those coding for the SL RNA, the 
donor in trans-splicing.  By Southern blot we have shown that the SL1 
RNA genes of B6/D6 are dispersed throughout the genome and that they 
are not physically linked to the 5S rRNA genes.  This is in contrast 
to what has been shown in C.  elegans where the SL1 RNA genes are 
physically linked to the 5S rRNA in a single cluster in the genome (1).
The organization of B6/D6 SL1 RNA genes is more like what has been 
found in Onchocerca volvulus, a parasitic nematode of man (2).
We have isolated and sequenced two B6/D6 SL1 RNA genes from a 
genomic library.  At the primary sequence level there are differences 
at 17 out of 99 positions within the transcribed portion of the genes, 
whereas the 5' flanking regions appear unrelated to one another.  The 
predicted SL RNA products are only distantly related to the C.  
elegans SL1 RNA, but they can adopt the characteristic SL RNA 
secondary structure, and the SL sequence itself is identical to the 
SL1 sequence found in all nematodes examined to date.  Besides the 
primary sequence divergence between C.  elegans and B6/D6 SL1 RNAs, 
there are two other findings which suggest these two species are quite 
distant from one another.  First, neither B6/D6 SL1 RNA gene contains 
a sequence in its upstream region related to the highly conserved 
proximal sequence element of the C.  elegans snRNA genes (3).  Second, 
we have failed to detect any signal when an SL2 oligonucleotide was 
used to probe both the B6/D6 genomic Southern blot and library.  This 
result suggests that SL2 may be restricted to the Caenorhabditis genus 
or at least to the Peloderinae subfamily.
We hope that B6/D6 may be of use to researchers performing sequence 
comparisons to help identify important regions.  We have also cloned 
the B6/D6 vit-6 homolog.  So far we have sequenced a third of this 
gene.  The B6/D6 protein is 43% identical to the C.  elegans 
vitellogenin, and intriguingly, there are some different asymmetries 
in codon usage.
Supported by FAPESP, CNPQ & USP-BID