A visiting colleague participated in Monday's lab meeting, and his ideas got me thinking seriously about doing an experiment that I've long claimed wouldn't really prove anything.
The question is whether DNA uptake can provide bacteria with enough nutrients to make a difference to their growth rates. I've always argued that getting some nutrients from the DNA is inevitable, so so demonstrating that this increases growth in a lab culture would not be good evidence that selection for these nutrients is why cells take up DNA. But maybe I was wrong.
In the past we have tried to show that H. influenzae can use nucleotides from DNA for growth, but the experiments have had lots of problems, I think in part because H. influenzae is quite fastidious in its nutrient requirements, and in part because we didn't devote a full-press of our time and brain-power to it.
Our colleague Steve Finkel has shown that E. coli can use nutrients probably acquired by DNA uptake for growth, but the effects are modest. This is probably because the cells are only taking up very small amounts of DNA because their competence genes are not induced under normal culture conditions.
Rather than now trying again with H. influenzae, I'm considering trying to demonstrate nutritional benefits of DNA uptake using Bacillus subtilis. B. subtilis is a soil bacterium, very easy to grow and not at all fastidious. I've worked with it before and one of the post-docs did her PhD work on it. B. subtilis takes up lots of DNA under lab conditions, though not during exponential growth. Competence is induced under conditions referred to as 'post-exponential growth', meaning after cell growth has stalled because nutrients are depleted.
Keeping cells competent over a long period might be complicated, because B. subtilis competence and sporulation are induced simultaneously (though apparently in different sub-populations of the culture). I'd first have to read up on the latest work on the regulation of DNA uptake, and try to find the best conditions for observing a growth effect. But if I can show that B. subtilis cultures grow better when they can take up DNA, I think many other biologists would find the result much more compelling than I do. This would be good, because they are not at all convinced by the results that I think are compelling.
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