simple polymeric repeats

[S. A. Modena]

In article <1993Feb9.215414.26044 at magnus.acs.ohio-state.edu> cbreiten at magnus.acs.ohio-state.edu (Caroline A Breitenberger) writes:
>
>in mitochondrial gene expression, and which has 20 glutamines
>interrupted by one glutamic acid.  
........
>                   Our gene uses both gln codons in the
>gln repeat, *suggesting* that it is the amino acid sequence that
>matters, rather than the nucleotide sequence, and consistent with
>the possibility that it is some sort of hydrophilic, hydrogen-bond-
>forming linker or structural element.  We have not looked (yet) for
>instability of the gln repeat in our gene.
>
>In response to Steve Modena's gracious post [  ;^)  ], these are not Q-
>linkers as described in Wootton and Drummond, Prot. Eng. 2, 535
>(1989).  For one thing, we're not talking about "relatively rich in
>glutamine, etc.", we're talking *exclusively* gln (or very nearly
>so).  In addition, these authors point out regularly spaced
>hydrophobic residues (4-5 amino acid periodicity) near the C-
>terminus of the so-called Q-linker, which is clearly not the case
>here.

That's correct: "we" are not talking about.........on the other hand,
what rang a bell with me was that the *same* amino acids were
predominantly involved.  And that Wootton has a concept under development
for classifying regions of proteins...following along after the 'Q-linker'
algorithm expressed in the paper cited....

>............  In the case of SBMA, the polymorphic repeat is in
>the androgen receptor mentioned in Cassandra's post and involves
>amplification of a stretch of glutamines.  In both MD and fragile
>X, the repeats are close to, but not in protein coding sequences. 
>[See Caskey et al., Science 256, 784 (1992).]  So what does it all
>mean?

My peripheral interest stems from the idea that polymerases (senu lato)
might have problems with poly-homo-anything.....and sometimes the loss of
register tracking is beneficial and sometimes not-so-beneficial, but that
interesting genomic adaptive strategies may arise to prevent genetic death.

>Caroline Breitenberger, Assistant Professor
>email: caroline+ at osu.edu

Steve
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