The post-docs have finished the first-pass analysis of how E. coli gene expression is affected by both the E. coli Sxy and the H. influenzae Sxy proteins. I suppose I shouldn't be surprised that it's more complicated than I had hoped. For example, unlike the situation in H. influenzae, in E. coli there are also groups of genes whose expression goes down when Sxy is present.
One complication is that these cells are probably seriously OVER-producing Sxy. Unlike H. influenzae, where we've only done arrays of cells expressing a single-copy sxy gene under its natural promoter, these E. coli studies used a sxy gene on a high-copy plasmid and under a highly inducible promoter. We know that prolonged expression of Sxy from this plasmid produces large quantities of denatured Sxy (in inclusion bodies) and we don't know the extent to which even the 30-minute expression used for the array studies might create a situation unlike that of natural sxy expression.
Idiosyncratic Thinking: a computer heuristics lecture
18 hours ago in Doc Madhattan