Outline for Why do bacteria take up DNA

As I said in the previous post, this will be a review article emphasizing how we can decide why bacteria take up DNA, rather than claiming we have enough evidence to decide.

It will begin with an overview about why this question is so important. To make the writing easier I can probably modify text from my grant proposals and from Do bacteria have sex, but this new introduction should be a lot shorter than the coverage of this issue in that article. The basic things to say are:

1. Recombination between bacteria has been enormously important in their evolution, so we really should try to understand why it happens.
2. It's usually been assumed that the processes that cause recombination exist because the recombination they cause is selectively advantageous. (This might be viewed as meta-selection - selection acting on how genetic variation arises.) But studies of the evolution of sex in eukaryotes have shown that the costs and benefits of recombination are very complex.
3. What are these processes? Consider gene transfer separately from physical recombination. The major gene transfer processes are conjugation, transduction and transformation. Some 'minor' processes also contribute to bacterial recombination: gene transfer agent is the only one that comes to mind right now. In other cases, genetic parasites (transposable elements, and probably integrons) hitchhike on processes that transfer genes. I won't discuss these, though I may say that I won't discuss them. Physical recombination acts on DNA that has entered the cytoplasm ("foreign DNA").
   
4. The proximate causes of most bacterial recombination are reasonably well understood, at least at the molecular level (what happens inside cells, and when cells encounter other cells, phages or DNA. We know much less about the processes that determine when such encounters happen, but that's probably not a topic for this review.
5. Some of the ultimate (evolutionary) causes are also understood. We understand the 'primary' evolutionary forces acting on cells, phages and conjugative elements. By 'primary' I guess I mean forces that directly impact survival and reproduction.
6. These forces appear to provide sufficient explanation for the existence of many of the processes that contribute to bacterial recombination. Specifically, strong selection for replication by infectious transfer to new hosts explains why phages and conjugative elements exist, and strong selection for DNA maintenance and repair explains why the cytoplasmic proteins that cause physical breaking, pairing and joining of DNA exist. This logic needs to be spelled out very clearly.
   
7. The need for nucleotides and other 'nutrients' obtained from DNA breakdowncould also explain why cells take up DNA, but this question is more complicated than the others.
8. Describe the other potential advantages of DNA uptake: templates for DNA repair, and genetic variation by recombination.

To be continued...