So maybe the DprA and ComM proteins don't directly protect DNA from nucleases, at least not in Haemophilus. Maybe instead they do something (or two different somethings) that promote homologous recombination, and the recombination is just the normal consequence of not recombining.
But in S. pneumoniae, I think there's good evidence that DNA that can't recombine with the chromosome degrades faster in a dprA-knockout strain. Better check... OK, an excellent 2003 paper by Berge et al. showed that incoming plasmid DNA with no homology to the chromosome is rapidly degraded in both recA and dprA mutants. The degradation is faster than the normal kinetics of recombination in wildtype cells, so it isn't just a consequence of the lack of recombination.
Back to the roles of specific nucleases. Something certainly degrades the DNA, and the control transformations of our nuclease experiments confirm that it isn't ExoV or ExoI or RecJ, because each nuclease mutation reduces the transformation frequency. (We can't even claim originality on this conclusion, because the researchers who made the nuclease mutants also showed this.)
Why do I care what these two proteins do? Both have been interpreted as evidence that the selected function of DNA uptake is to generate recombinants. I think this is incorrect because of the larger picture view of selection for recombination, not because of any flaw in the experiments. The big question is, what do these proteins do for cells in the absence of DNA uptake.
To a first approximation, the dprA and comM mutants show normal viability and growth and sensitivity to UV. The E. coli DprA paper showed that E. coli DprA can partially complement the transformation defect of an H. influenzae knockout, which the authors interpreted as meaning that DprA's function in non-competent cells also contributes to transformation in cells that take up DNA.
Subrahmanyan Chandrasekhar: A study in fortitude and rigor
19 hours ago in The Curious Wavefunction