Path: utzoo!utgpu!water!watmath!clyde!rutgers!ames!hc!beta!dd
From: dd@beta.UUCP (Dan Davison)
Newsgroups: sci.bio
Subject: Re: Determining whether repetitive sequences are trash
Summary: do they move under their own power?
Keywords: E. coli REP, gene conversion, evolutionary vestiges
Message-ID: <14293@beta.UUCP>
Date: 14 Jan 88 00:25:18 GMT
References: <1552@aecom.YU.EDU>
Organization: Los Alamos Natl Lab, Los Alamos, N.M.
Lines: 38

In article <1552@aecom.YU.EDU>, diaz@aecom.YU.EDU (Dan D) writes:
> Not long ago, it was discovered that ~25% of E. coli transcripts contain
> the repetitive extragenic palindromic sequences (REP) dicovered by
> Higgins, et.al. (Cell 37,1015).  This figure extrapolates to about 1% of
> the E. coli and Salmonella genomes.
> [ deleted two paragraphs]
> The question is, how would you determine whether these sequences are
> selfish DNA in prokaryotes?  Could they be involved in recombination? Or
> as organizers for prokaryotic histone-like proteins?  
> How can we approach such speculative evolutionary questions
> experimentally?
> -- 

First, the deleted stuff was an excellent summary.  To answer the first que-
stion, I sort of regard it as partly metaphysical; selfishness is in the eye
of the beholder.  However, a less flip answer is that if the DNA can replicate
and move around in the genome under its own power, that is, does not require 
errors of host replication to reproduce itself, it's selfish DNA.  As an
aside, there is a Shigella dysenteriae strain in which IS1 has gone wild; there
is one copy on the average every 20KB, or about 4% of the genome.  It works
out to about 350 copies of the element in the genome, instead of the usual 10 or
so.  Now that's selfish.

The second question, are they involved in recombination/histone-like processes,
good suspicion.  Only time and experiment will tell though.

One approaches speculative evolutionary questions with extreme caution.  For
instance, Lin Chao's work on the evolutionary fitness of IS(2?) insertions
(Molecular Biology and Evolution, vol. 1 or 2) is an excellent example.


dan davison/theoretical biology/t-10 ms k710/los alamos national laboratory
los alamos, nm 875545/dd@lanl.gov (arpa)/dd@lanl.uucp(new)/..cmcl2!lanl!dd
-- 
dan davison/theoretical biology/t-10 ms k710/los alamos national laboratory
los alamos, nm 875545/dd@lanl.gov (arpa)/dd@lanl.uucp(new)/..cmcl2!lanl!dd
"I refuse to be intimidated by reality any more"  "What is reality anyway?
Nuthin' but a collective hunch!" --Jane Wagner,via Lily Tomlin