Aarrghhh! So long since I've posted any science here (or for that matter any teaching on RRTeaching). This short post is just to get me going again...
The Research Associate recently gave me a new version of her manuscript on how purine nucleotides regulate the development of natural competence, and we just finished discussing how the various pieces of information should be organized. She starts with the evidence that disproves my once-favourite hypothesis that competence genes are repressed by the purine repressor PurR. She then presents new evidence that providing cells with a purine nucleotide (AMP or GMP) reduces competence by reducing the translation (but not transcription) of the sxy gene.
Sxy activates competence genes by working in concert with the activator protein CRP. Its translation is known to be limited by a base-paired stem in sxy mRNA, and the RA has now shown that mutations that weaken this stem also make cells immune to the effects of added AMP or GMP.
How might this work? She's able to rule out two hypotheses - that the sxy mRNA stem functions as a purine-sensitive riboswitch, and that the AMP/GMP effect involves an Hfq-dependent small RNA. She also shows that induction of competence is influenced by intracellular purine pools, because it is reduced when the purine biosynthesis pathway is constitutively activated by a purR knockout. The effect of constitutive purine synthesis must be due to purine nucleotides and not biosynthetic intermediates, because normal competence is restored when the last step in nucleotide biosynthesis is knocked out by a purH mutation.
(Hmmm, this makes more sense now than it did in our discussion. More evidence that writing blog posts helps me think clearly.)
Kurt Gödel's Open World
6 hours ago in The Curious Wavefunction