Worm Breeder's Gazette 10(2): 104

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.

Update on the deb-1 Gene

Robert Barstead and Robert Waterston

The deb-1 gene encodes a 107,000 dalton peptide found at the base of 
the muscle dense-bodies.  Some time ago we obtained a clone for this 
gene from an expression library.  We have almost completed the 
sequencing of 12 kb around the original cloned fragment.  The sequence 
data reveals some features which are atypical compared to other C.  
elegans genes.  First, its codon usage is not sufficiently biased to 
allow us to use measures of codon bias as a reliable means to identify 
the smaller exons.  This may be a reflection of the fact that the gene 
encodes a relatively low abundance product and may not have the same 
pattern of codon usage as an abundantly expressed gene.  In order to 
identify the exons we have constructed a cDNA library in the vector 
lambdaZAP and obtained a 2.3 kb cDNA for the deb-1 gene.  This 
accounts for about 60% of the mRNA size.  About 80% of this cDNA has 
been sequenced.  With the direct identification of the intron-exon 
boundaries through the cDNA we were somewhat surprised to find that 
many of the potential coding regions in the middle of the gene are not 
in the cDNA; rather, there is a large 1.6 kb intron.  This points to 
another unusual feature of the gene; it has large and frequent introns.
With these introns the gene spans 8-9 kb, whereas the length of its 
mRNA is only 3.8 kb.  Finally, in regard to the identification of 
splice junctions, in every case except one the splice junction 
sequences are as similar or more similar to the general eukaryotic 
consensus sequence than to the nematode splice junction consensus 
sequence.  This exceptional case was significant, however, because it 
was not identified at all using the general consensus, but was 
identified when compared to the nematode consensus.
Aside from the analysis of the deb-1 cDNA, the cDNA library 
mentioned above is largely uncharacterized.  The initial unexpanded 
library contained 2x10+E6 phage.  Approximately 85% of these were 
white on X-GAL plates.  The median insert size is about 1.1 kb.  The 
maximum detected insert is 4.5 kb and the minimum is 0.5 kb.  The 
library can be screened with both DNA and antibody probes.  The 
lambdaZAP system allows for excision of the cDNA as a plasmid clone by 
coinfecting with an m13 helper phage, thus eliminating the sometimes 
tedious step of subcloning.  Finally, using a probe obtained from Don 
Moerman for the unc-52 gene we have also recovered unc-52 hybridizing