Worm Breeder's Gazette 11(4): 35

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.

Sequence of mec-3 from the Caenorhabditis strain WS9-6

Jeff Way

From Chris Link's lambda library of DNAs from WS9-6, a male-female 
Caenorhabditis strain, I isolated an apparent mec-3 homologue.  A 4kb 
EcoRI fragment contains exons corresponding to all the exons of mec-3 
in C.  elegans, as well as four long conserved regions upstream of the 
start codons.
The regions of sequence similarity between the C.  elegans and WS9-6 
mec-3 genes are very much like the regions of similarity between C.  
elegans and C.  briggsae described by Ding Xue and Marty Chalfie in 
the last newsletter (including their revision of the coding sequence), 
except that the overall level of similarity between the C.  elegans 
and WS9-6 genes seems higher.  There are four long upstream regions of 
conservation of 71,30,30 and 24 bp, and a few shorter ones.  In the 
entire coding sequence, there are 29 amino acid substitutions, 19 of 
which are between the LIM and homeodomains.  There are no amino acid 
changes in the homeodomain.
In introns, there is no apparent similarity between the sequences.  
Also, the WS9-6 introns are generally shorter: the first intron, 395 
bp in C.  elegans, is only 73 bp in WS9-6.  The fact that the intron 
sequences have completely drifted suggests that the conserved upstream 
regions have been preserved by selection.
The four conserved upstream regions (hereafter termed regions I, II, 
III and IV) have distinctive features that may relate to how mec-3 is 
regulated.  Regions I and II each have sequences very similar to the 
POU consensus binding site, and region III contains a close relative 
to the ISL-1 binding site (ISL-1 is a transcription factor for the 
insulin gene and is closely related to mec-3.)  Region IV contains no 
obvious sequence features, but can be deleted to cause expression of a 
mec-3-lacZ fusion in extra cells (Way, WBG 11,2).  A provisional 
organization scheme for this region would thus be that regions I and 
II mediate unc-86 binding and establishment expression, region III 
mediates mec-3 binding and maintenance expression, and region IV 
mediates negative regulation by unidentified proteins.
With unc-86 protein from Mike Finney, I have shown that a 
restriction fragment containing regions I, II and III can be 'band-
shifted'.  I have not yet done a footprint to identify the actual unc-
86 binding sites.
(Since C.  elegans and C.  briggsae are both hermaphrodite species 
while WS9-6 is male/female, it would appear that the male/female sex 
pattern is derived from the male/hermaphrodite pattern.  It would be 
interesting to see which of the sex-determination genes of C.  elegans 
have been altered in WS9-6 to account for this change.)