Field of Science

Blogging on (30-year-old) peer-reviewed literature

I'm reading a 1979 paper about GTA (Yen, Hu and Marrs, Journal of Molecular Biology 131:157-168).  The authors devised a way to select for mutants that overproduced GTA, and used these to find out more about how the particles are produced and the DNA they contain.

The mutant they focused on produces enough GTA that culture supernatants transfers any one chromosomal marker to about 0.0001 to 0.001  of the cells in a recipient culture.  As each particle contains about 0.001 of the donor chromosome, and recombination of such short fragments is relatively inefficient, this means that the supernatant probably contains about as many particles as there are cells in the recipient culture.  That was probably about 10^9 per ml.

The mutant grew poorly, and the authors interpreted this as a consequence of increased cell lysis associated with the increased GTA production.  They maintained the strain by growing it in medium they had found to inhibit GTA production (PYE medium), and transfered it to a GTA-inducing medium (RCV) when they wanted GTA.  After this transfer they observed that after several cell divisions about 10-20% of the cells died at the same time that high levels of GTA became detectable in the medium.  

This is a very provocative result (too bad they don't show any data), because it implies that GTA production is very deleterious . I'd never heard of either medium; I wanted to find out what's in them but one of the disadvantages of reading old papers is that they and their references are often not available online.  But simply Googling "PYE RCV" led me to the recipes - apparently they're quite widely used.  PYE is just 0.3% peptone and 0.3% yeast extract, which makes it a slightly more dilute version of our old favourite rich medium LB.  RCV is a defined medium used for R. capsulatus photosynthetic growth; it contains 0.4% malic acid as the only carbon source, 0.1% ammonium sulfate, thiamine, and other salts specified in papers that Springer will show me for $32.

So cells make lots of GTA in rich medium but not in the very poor medium used for photosynthetic growth.  Hmmm...

But searching for the paper with the recipes for these media led me to an even older paper that I need to first read.  This is Marrs 1974, PNAS 71:971-973, and PNAS is on line all the way back to the beginning.  So I'll take a break to read this paper, and post on it before continuing.


  1. I think it's important to clarify a couple of points about GTA. It's a very provocative phenomenon, and the evolutionary angle demands some critical thinking.

    GTA looks like it was inherited once in an alpha-proteo progenitor, then passed along vertically; the GTA phylogeny essentially recapitulates the bacterial phylogeny. And the thing has been around a *long* time, so long that it would be riddled with non-sense mutations (or deleted) if it weren't under active selection. Further, it only transfers ~4.5 kb of apparently non-specific DNA, whereas the "prophage" is ~15 kb. All this implies it's not a selfish, mobile element or a dead remnant thereof, making its persistence a fascinating puzzle.

    The only scenario that makes sense to me is some sort of selection at the level of the cell for maintenance of the GTA. But what? I'm no fan of the blind assumption that recombination is beneficial, but GTA is so fascinating precisely because there's no evidence it does anything else. Some folks have suggested to me it's a suicide mechanism, but that would require some pretty contrived selective conditions. The only reasonable alternative I can think of would involve some bacteriocidal activity for eliminating competitors. But to my knowledge there's no evidence for such activity, and until/unless there is, GTA stands out as a bacterial recombination mechanism seemingly evolved for just that function.

    --Dave Kysela

  2. Hi Dave,

    (I don't know when you wrote your comment, so this may be a very delayed response.)

    The things you say are certainly in the literature. But much of the experimental data looks pretty bad, and I think that conclusions about GA's function have to wait until we know more about what it really does and how it does it (e.g. does it kill the producer cells).


  3. Hi Rosie,

    It would be quite a mechanical marvel if it didn't kill the producer. I don't know of any tailed phage that can get out without lysing the cell, and since they're tens of nm across, that's no wonder.

    This should be relatively easy to test. The overproducer strain of R. capsulatus already exists. Though I don't think measuring cell density or reproductive rate would be very useful (the mutant isn't mapped to my knowledge, and may very well involve pleiotropic regulatory effects), it may be possible to catch cells in the act by EM.

    Notably, according to the Beatty lab, the over-producer mutation appears to be unstable, suggesting a cost of production. A directed GTA knockout in the over-producer would provide an interesting competitor against a knockout in the wild-type background. Again, pleiotropic mutations introduce a difficult wrinkle, but if a GTA knockout derived from the over-producer competes like a GTA knockout derived from the wild-type, that would provide a compelling case that phenotypes observed in the over-producer are specific to GTA rather than global regulatory mutations and the like.



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