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exons & protein domains

R M Bernstein ralph at ccit.arizona.edu
Wed Jul 17 10:54:57 EST 1996

In Article <4shs8v$94q at agate.berkeley.edu>, Amie Franklin <amief> wrote:
>Your thesis of using exons to compare protein domains touches on a somewhat
>topic of introns old versus introns new (and conversely exons old versus exons
new).  Several
>years ago the theory was put forth (I don't remember the author) that new
proteins arise from
>exon shuffling and consequently both exons and introns are ancient. 

hi bob,
these are theories perhaps suggested by crick himself (prediction of rna
world and all that it implies), and since championed by gilbert and more
recently wf doolittle-and others.  as amie suggested, it seems that the
intron-late school have "won"-if there is winning to be done.  the question
of introns early and introns late, however, may have little to do with your
goal.  functional domains- as defined not only by exons that encode a
"functional" area of a protein, but that are separated by introns from other
exons, and not themselves interrupted- do indeed exist, even though the TPI
genes from dipterins seem to have introns inserted within the domains
gilbert implied would not.  your study, could provide quite an insight into
how protein domains evolve, and as to whether they evolved before or after
the insertion of those introns-early-theory-defying introns.

i would perhaps suggest domains that seem to be at the core or start of
replication, etc.  perhaps the family a,b, and X polymerases, as well as the
elongation factors, and maybe RAD 51 genes, which are fairly highly
conserved from yeast to humans. (do you have netscape & freehand plugin? see
vertebrate rad51s:  http://lamprey.medmicro.arizona.edu/rad51.fhc).

all errors in the story above are open to correction/clarification


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