I haven't yet tested whether different growth/non-growth conditions alter the expression of the ppdA fusion (though I did get the sxy manuscript resubmitted today), but a paper I came across reminded me of another issue I need to consider.
The paper is an opinion piece titled "Laboratory strains of Escherichia coli: model citizens or deceitful delinquents growing old disgracefully?"; it just came out in the journal Molecular Microbiology (Mol. Micb. 64:881-885). The authors argue that the standard K-12-derived strains of E. coli that microbiologists and molecular biologists typically use are not at all representative of the strains out in the natural environment. For one thing, lab strains have lost about 20% of their genomes. These are (by definition) non-essential genes, but their loss no doubt affects cellular metabolism, so that the metabolic interactions we see in K-12 strains may be quite different than those in natural strains. Furthermore, the culture conditions we use (rich broth, lots of oxygen, no competitors) are unlikely to ever occur in nature. Their long maintenance under these and other unnatural conditions means that the lab strains will have evolved by accumulating cryptic mutations that are beneficial under lab culture conditions but that may have very different and perhaps harmful effects in the natural environment.
I already knew this. It has important implications for my search for conditions that induce expression of competence genes in E. coli. Right now I'm working with standard lab strains, but it's all too possible that one of their ancestors lost the ability to express the genes encoding homologs of H. influenzae's competence genes, or to assemble the proteins into functional DNA uptake machinery.
So I should perform my tests on a less lab-adapted, more 'natural' strain as well as on the K-12 strain the ppdA::lacZ fusion is in. But this raises two problems. First, which strain should I use? I do have a fairly-ancestral K-12 strain, but really I should use a 'wild' strain recently isolated from the environment. The NCBI Microbial Genomes page lists 8 completely sequenced E. coli genomes; their sizes range from 4.6 million bp (K-12) to 5.6 million bp (O157:H7). And the various wild strains have genomes that are quite different from each other - does this mean I would need to test many strains before giving up? I'm also not meticulous enough to be trusted with a strain that's seriously pathogenic to humans, so the two O157:H7 strains are out, as is the uropathogenic strain*.
Second, I'll need to transfer the necessary genes into this strain; first a lacZ mutation making it Lac-, then the ppdA::lacZ fusion so I can assay induction by Sxy. This might mean that I need to get my P1 transductions working after all (I had been thinking I could let them slide now that I've found that the ppdA::lacZ fusion can be used as an indicator of CRP-S induction by Sxy). I don't need P1 to move in the ppdA fusion because it's on a plasmid, but transduction would certainly be the easiest way to move a lac- mutation in. If I'm lucky, maybe some of the wild strains are naturally Lac-. (Probably not; most screens for wild E. coli start by treating anything that's Lac- as not E. coli.)
* NCBI also lists 6 sequenced 'Shigella' genomes - we now know that the bacterial strains assigned to the genus Shigella are really variants of E. coli. But I have absolutely no intention of working with these very pathogenic bacteria.
Modular drug design software?
2 hours ago in The Curious Wavefunction