Path: utzoo!utgpu!water!watmath!clyde!rutgers!princeton!udel!rochester!cornell!uw-beaver!mit-eddie!husc6!linus!philabs!aecom!diaz
From: diaz@aecom.YU.EDU (Dan D)
Newsgroups: sci.bio
Subject: Determining whether repetitive sequences are trash
Keywords: E. coli REP, gene conversion, evolutionary vestiges
Message-ID: <1552@aecom.YU.EDU>
Date: 11 Jan 88 03:31:53 GMT
Organization: Graduate School of Hard Knocks
Lines: 29

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.

REPs are always found within transcription units, always outside the
coding regions.  In multicistronic messages, REPs often separate
differentially expressed cistrons, suggesting that REPs are involved in
mRNA stabilization.  Recent evidence (Cell 48,297) suggests that REPs
may help stabilize message upstream.  This may be a fortuitous
side-effect and not necessarily something selected for by evolution.

This is all fine, but there are differentially expressed genes in
operons that aren't separated by REPs.  And if the formation of
secondary structures were the only requirement for the protection of
upstream message from nucleases, why is the REP sequence conserved as it
is?  REPs can exist in tandem.  Whenever they do, adjacent REPs are
always in an inverted orientation with respect to one another.

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?  Perhaps the reason
we see them only in extragenic positions is that when they were
introduced elsewhere by whatever mechanism, it caused a lethal mutation.
How can we approach such speculative evolutionary questions
experimentally?
-- 
       dn/dx  Dan D diaz@aecom.yu.edu  Dept. Molecular Biology & Plumbing
       Ein Stein Call Age of Meddy Sin of Your Shiva You Nee Verse Itty