When H. influenzae cells take up DNA into their cytoplasm, the DNA may be degraded to nucleotides or, if a chromosomal sequence has enough similarity, may recombine with it. Three H. influenzae proteins are known to be be needed for the recombination but not the uptake. If H. influenzae and other bacteria take up DNA only for the nucleotides, why would they encode proteins to help it recombine? Does the existence of these proteins mean that the recombination has been selected for?
We understand why one of the proteins exists. RecA's real job is DNA repair, and its action on incoming DNA is just a side effect of this. RecA has evolved to both detect DNA damage and use recombination to repair gaps arising from replication of damaged DNA. RecA is not induced in competent cells, and everything it does that promotes recombination with foreign DNA is most parsimoniously explained as side effects of its selected action on damaged DNA.
The other two proteins, ComM and DprA, are harder to explain. Both have been shown in other competent bacteria to limit the degradation of the DNA that has been taken up by competent cells, and this has been interpreted as an adaptation to promote recombination. The H. influenzae homologs of both have good CRP-S sites in their promoters and are strongly induced in competent cells. This means that they must be beneficial under the conditions that induce DNA uptake. In a previous post I put forward the idea that these conditions induce two kinds of processes, DNA uptake and stabilization of stalled replication forks, and that DprA and ComM have evolved because of roles in this latter function.
While trying to clean up my desk I came across a table from a 2004 paper on the AAA+ class of ATP-binding proteins, showing alignments of ComM with related proteins. This reminded me that both ComM and DprA are widely distributed in bacteria, including many species not known to take up DNA. This distribution suggests that these proteins may indeed have an important cellular function that's independent of their affect on recombination.
So I just did BLAST searches with both protein sequences. Their homologs are indeed widespread, and very highly conserved, with E-values throughout the gamma-proteobacteria of better than 10^-120 for ComM homologs, and better than 10^-60 for for DprA homologs.
So what do they do? Nobody knows!
ComM: AAA+ proteins whose functions have been studied have very diverse roles. They share "a structurally conserved ATP-binding module that oligomerizes into active arrays" (Erzberger and Berger 2006). I'll need to carefully read this big review to understand the 'arrays' part, but some of these proteins form hexamer rings around DNA at replication forks, and some form spiral filaments involved in the initiation of DNA replication (e.g. DnaA). ComM is in subgroup of members with diverse or unknown functions; some use ATP hydrolysis to generate forces (e.g. dynein), and some push Mg++ into chlorophyll (!). None of the orthologs of ComM in bacteria appear to have examined for roles outside of competence.
DprA: DprA is known to limit degradation of incoming DNA in many different competent bacteria (H. influenzae, Bacillus subtilis, Streptococcus pneumoniae, Campylobacter jejuni), but nothing is known about a more fundamental role in almost all bacteria (only some obligate intracellular pathogens lack it). Last year a Dutch group reported an attempt to find out what DprA does for E. coli. They found that knocking out the gene had no significant effect on growth rate or various repair-dependent or recombination-dependent processes, even in cells lacking other genes involved in repair and/or recombination. They found that the E. coli gene could partially restore transformability to a H. influenzae dprA knockout. It had been previously shown that the H. influenzae dprA gene can restore transformation to a C. jejuni dprA knockout, so we can be pretty sure that whatever this gene does for non-competent species allows it to also prevent DNA degradation during transformation in competent species.
Conclusions? These are two ubiquitous and very strongly conserved genes. Their effects on transformation in naturally competent cells are likely to be only side effects of more important functions in all cells, but we remain quite ignorant of what these functions might be.
Geologists in the land of the Kangaroo
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