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.
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 cDNAs.