Talmudic Question #39
Except for viroids, can you think of any place where there are "naked," (capsidless) viruses outside of hosts?
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I remember reading measurements of DNA in certain marine environments, outside of cells. Much higher than expected. I can't find the reference at present, for which I apologize. There may be DNA elements of the type you hypothesize floating around. And just like IS elements, how would we know unless they caused phenotypic changes in organisms that we study? I think that some of the phage-a-holics (and I love their work) are looking for phage-specific genes in the environment. From lysed phage heads? Or naked DNA? If there are many mechanisms by which naked DNA is taken up by prokaryotic cells, why not some DNA elements that "parasitize" that process?
I WAS going to say "F plasmids", but I guess conjugational plasmids don't really count since they're not normally really 'extracellular" at any point in the process.
I suppose one might count genes aquired by "natural competence" (like the shiny new Desulforudis audvaxiator mentioned in the current issue of "Science"), but since those don't normally continue to spread that way I doubt that would count either.
(Or would they? Surely by now there's a chance that at least one community somewhere has ended up with a chunk of genetic material that promotes cell lysis AND easy uptake via natural competence among its host population at some point in history...)
I like Epicanis' response of natural competence...
Otherwise, another food for thought, there is a lot of DNA found in Pseudomonas biofilms which is suppose to support attachment and thus facilitate biofilm growth. However, the presence of DNA may also have an alternative role besides it's "stickyness"...who knows??
Rhea and Top Dog (that's what Epicanis stand for, right?),
You make great points but maybe that's not what the question asked for. I realize that a capsidless virus ends up looking like free nucleic acids, but we were wondering about something more virus-related. However, I'm glad you went there. As for Rhea's point of DNA being something other than the queen of the molecules, we made that point in an old post . See what else DNA is good for at http://schaechter.asmblog.org/schaechter/2006/12/gifts_from_abov.html
Thanks for your comments.
Elio
When you are talking about naked nucleic acids existing outside the cell, the term virus loses meaning. Certainly there must be transposons floating around in the environment, we just don't observe this because they can't have an effect exogenously. Perhaps if there were some super competent bacterial cell that could pick up sequences from its environment we would see this.