One of the postdocs just raised an issue I've never seriously considered. Many surface structures on bacterial cells undergo what's called "phase variation". That is, a key gene controlling the structure has evolved to have a high rate of mutations that switch it from an active allele to an inactive allele, and from the inactive allele to an active one.
By "high frequency" here I mean more often than one switch per million cell divisions. Switching is thus still a very rare event, but is much higher than the background mutation rate for normal DNA sequences. Such elevated frequencies are usually caused either by short sequence repeats that cause DNA polymerase to add or miss bases in critical positions, or by specific DNA-altering enzymes that recognize the gene.
That's the proximate cause of the variation. The ultimate cause (the evolutionary cause) is thought to be natural selection created by predators or host immune systems that recognize the surface structure and attack cells expressing it. Under such pressure, a cell that has turned the structure off will have an advantage, so cells with elevated mutation rates affecting the structure are favoured. Because the structure is strongly advantageous in the absence of external attack, selection favours cells that also have a high rate of reversion mutations that switch the structure back on. Such genes are often called "contingency loci".
Competence for DNA uptake requires expressing DNA uptake proteins on the cell surface, so it's a logical target for attack by the host immune system, and thus perhaps for phase variation. But how would we detect it? In Neisseria competence is known to be phase variable, but only because it depends on the phase-variable expression of type 4 pili, a phenotype that is easily assayed in the lab. Screening H. influenzae cells for phase variation of competence is likely to be very difficult, as our only assays are uptake of radioactive DNA and transformation to antibiotic resistance.
Rather than screening for variation, a more efficient approach is to examine the H. influenzae genome for sequences that could promote such variation, and check each for its ability to affect competence. These have been thoroughly investigated by Richard Moxon and his colleagues. They found no enzymatic switches but many short sequence repeats affecting production of complex carbohydrates on the cell surface. Now we need to carefully check whether any of these could also affect genes needed for DNA uptake.
Weird news - a real stopcock
6 hours ago in The Phytophactor