I've turned my focus on trying to figure out how/why the various competence mutants we have alter regular competence. To do this, I'm comparing expression of competence genes between strains.
A quick message about normalization:
DESeq2 (the R package I used to normalize the count data) normalizes data to allow, for instance, a comparison between gene A in condition X and gene A in condition Y. It does not normalize in a way that makes comparisons between gene A and gene B possible because it does not take into account differences in gene length (longer genes are expected to have more reads).
To make comparisons between genes possible, instead of asking "how much expression of gene A is there?" I ask "how much expression of gene A is there compared to gene A expression in KW20 M0?" I did this by dividing normalized count values by the normalized count in KW20 M0. In essence, KW20 M0 is treated as a baseline and measurements are deviations from that baseline.
Here is some data (error bars are standard error):
The first set of plots shows KW20 competence gene expression. As you can see, most competence genes are ~10-100x induced in M2 relative to M0. Compare this to the sxy or crp knockout where very little induction is seen. Interestingly, HI0365 seems to be particularly down in these knockouts.
The toxin and double toxin/antitoxin knockout strains behave similarly to KW20 (except for the toxin/antitoxin genes, of course) and peak at pretty much the same levels in M2 as KW20. Competence expression in the double knockout (taxx) seems to be a bit lower than KW20 in M3 though. Overall, nothing unexpected.
it has a motif that suggests that). Interesting to note though, the 3-enzyme restriction modification system hsdR, hsdM, and hsdS is hugely upregulated in the toxin/antoxin double knockout. This is odd because you'd think removing both the toxin and antitoxin should have no effect whatsoever on the transcriptome (or that you would see the same thing if you just removed the toxin...?)