I'm not sure how many molecular/genetic ciliatologists read these
messages, but if you're one I'd appreciate your response to the following.
Internal eliminated sequences (IESs) vary among ciliates, but those I'm
aware of are all flanked by short direct repeats, one copy of which is
retained in the macronucleus. This goes for the longer IESs (some of
which are apparently transposons) as well as the short ones. In Euplotes
and Paramecium all of the IESs are flanked by 5'-TA-3' dinucleotide direct
repeats (am I right?). In Tetrahymena and Oxytricha the direct repeats are
variable, but...
don't they all include either 5'-TA-3'(most of them) or 5'-CA-3' (the rest of
them)? I'm wondering if this might be due to the instability of 5'-TA-3'
and 5'-CA-3' dinucleotides compared to the other dinucleotides.
A.A. Travers and J.W.R. Schwabe (1993, Current Biology, Vol. 3, No. 12, pp.
898-900) pointed out that the TBP protein appears to exploit this
instability when it unwinds DNA in the TATA box of Pol II promoters.
They noted that cis-acting sites for recombination or initiation of
DNA replication, like sites for initiation of transcription, also usually
include 5'-TA-3'. Many 5'-TA-3' and 5'-CA-3' sequencess are known to be
functionally unwound by DNA-binding proteins.
Travers and Schwabe cited papers reporting 5'-TA-3' to be the least
stable dinucleotide due to relatively weak stacking interactions. I'm
suspecting that this may explain the target
site specificity of the IS630-Tc1 family of transposons, presumably
because it's easier to unwind and transpose into 5'-TA-3' targets. In
ciliates, the ability for IESs of all types to be precisely excised during
macronuclear developmnent would also be critical.
Please let me know if:
- you're aware of contradictory evidence, such as IESs not flanked by
repeats including 5'-TA-3' or 5'-CA-3', or
- you're aware of other people thinking along the same lines as I am
(maybe it's in the literature already and I missed it)
Thanks!
