diaz@aecom.YU.EDU (Dan D) (01/11/88)
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
dd@beta.UUCP (Dan Davison) (01/14/88)
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