Our vindication is on hold...

The result I was raving about a couple of weeks ago turns out to not be as solid as I had thought. This was the comparison of hypercompetent cells with and without the purine-binding repressor PurR. The result appeared to show that getting rid of the repressor let the cells become much more competent, solidifying our hypothesis that cells turn on competence genes because they run out of purines.

There were two problems with the results. First, the PurR+ and PurR- cells were tested on different days, not in a single experiment. This means that uncontrollable variables could have been responsible for the difference. Second and worse, an important controllable variable was changed in the second experiment; the PurR- cells were treated with a lower concentration of purines than was used for the Pur+ cells.

The obvious correction is to repeat the experiment, with both cell types treated with the same concentration. This has now been done, and the exciting difference largely disappeared.

We still think that the purine repressor does repress one of the competence genes, as the gene's promoter has what appears to be a very good binding site for the repressor. But the analysis is confounded by the complexities of purine interconversion in the cytoplasm, and by the toxicity of high purine concentrations for the cells. This means we probably won't get a clean answer until we've done a lot more experiments.