The Serine Shift

R M Bernstein ralph at ccit.arizona.edu
Fri Sep 15 22:19:27 EST 1995

In Article <349 at reservoir.win-uk.net>, shane at reservoir.win-uk.net (Shane
McKee) wrote:

>In article <437ce6$6to at hecate.umd.edu>,
> Ram Samudrala (ram at mbisgi.umd.edu) writes:
> (I wrote)
>>>Sorry if it seems like a bizarre question, but my own feeling is
>>>that the codons ought to be conserved even between widely


>itch) are common, then it might have implications for
>our understanding of mutagenesis.
>I agree that as long as the protein is OK, the organism is
>unlikely to care which codon is there.

Hmmm, I dont know about that.   There is some recent evidence (9th Intl
Congress Immunol, July 95, SF, USA) that this isn't true-at least in some
cases.  In the recombination of antibody genes there are certain specific
and ubiquitous enzymes that do the recombination (no kidding).  The regions
recombined are flanked by RSS's and 12mer 23 mer spacers, all non coding
(still no surprise).  In the coding sequence for antibodies there are
regions that are reffered to as frameworks and cdrs.  (frameworks form the
v-region "framework" or "pretty-much-immutable sites", the cdrs are the
complimentary determining regions or hypervariable regions)  In frame work
1, and (i think) frame work 3, there are nucleotide sequences conserved thru
phylogeny that arent always codon conserved.  It has been hypothesized,
however briefly, that these are _conserved recombination machinery sites_. 
Not for the recombination event, per se, but perhaps for the additional
enzymes that a) add terminal nucleotides, eg TDT, or b) cut away
nucleotides, eg endonucleases, etc.

Hope you all think that's nifty.
Regards, Ralph

>Shane McKee (SHO, RVH, Belfast)  | /      Art becomes science when
>Shane at reservoir.win-uk.net     --O--    you start trying to figure
>                               / |  out what the heck you're doing
Ralph M. Bernstein
Dept of Micro/Immuno
University of Arizona
Ph: 602 626 2585
Fx: 602 626 2100
url: http://lamprey.medmicro.arizona.edu

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