The grad student's research

I met with the grad student this morning and we went over his data.  His experiments aren't clean (he's still learning to slow down and think carefully about what he's going to do, and to keep careful thorough notes), but they provide a strong indication that the ComM protein's function is not to protect DNA from the RecJ and ExoI nucleases.  The undergrad who worked on this before him showed the same thing for DprA, and the undergrad before that showed it for ComM and ExoV and I showed it before that for DprA and ExoV.

So here's a plan:  First we write out an outline of the paper we hope to publish about these results.  What will this paper say?  First, it will summarize the evidence that DprA and ComM protect DNA from degradation.  For DprA this has been done thoroughly for Streptococcus pneumoniae; in other bacteria the dprA knockout phenotype is consistent with this but I don't know if DNA degradation has been directly measured.  But the comM gene isn't present in other competent bacteria, so I think we might first need to show that it does indeed protect incoming DNA against nuclease attack.

Hmmm, I just looked at the 1998 paper describing the discovery of comM and characterization of the mutant phenotype (Gwinn et al. 1998. J. Bacteriol. 180:746-748).  They did translocation assays (figure below) where cells were given linearized end-labeled  DNA - one fragment cloned from the chromosome*, one vector fragment.  The fragments were degraded, and the radioactivity from both fragments wound up in the chromosome, but not any faster in the comM mutant than in wildtype cells.  This doesn't provide any support for my assumption that ComM protects DNA from degradation!  The rec2 and comF mutants are controls, blocking translocation of DNA into the cytoplasm, and the rec1 mutation blocks homologous recombination. 

So, if ComM (maybe) doesn't protect DNA from degradation, what else might it be doing that promotes recombination?  And maybe DprA too - the party line is that it 'conveys DNA to RecA for recombination'.  I doubt the 'for recombination' part, but lgiven DprA's presence in all the noncompetent species it must be doing something useful fro replication or repair.  But DprA mutants and ComM mutants are not repair-defective (at least not especially sensitive to UV).

Maybe it's time for me to let go of my idea that both these proteins protect DNA from nucleases, and to instead start thinking more clearly about what the experimental evidence says they do.  It's certainly time to reread that E. coli DprA paper (Smeets et al. 2006).

*I suspect the larger fragment is the chromosomal insert, taken up faster because it has USS.