None of the unanswered questions can be answered by simple experiments, and if we were to follow this trail we would want to work in Haemophilus influenzae, the species our research focuses on. In particular, the two analyses recommended by the reviewer would both be a waste of time. One, knocking out the sxy gene in a strain that transforms very poorly, wouldn't tell us anything about why the strain doesn't transform better. Neither would the other, sequencing all the competence genes in a strain that transforms well and comparing them to the already-sequenced genes of this strain, because we have no functional framework for interpreting any differences we might find (i.e. we don't know anything about how the encoded proteins do their jobs).
So the post-doc and I spent much of yesterday rewriting the manuscript to address the reviewers' concerns and misunderstandings, and composing a tactful cover letter to the Editor explaining why we aren't going to do the experiments. The paper is much better now - while rewriting we realized that we had been underplaying an important implication of one of the experiments - the demonstration that the A. pleuropneumoniae sxy gene works perfectly in H. influenzae. These genes are quite divergent (only 24% amino acid identity) and because the two species are in the two different Pasteurellaceae subclades, this result lets us conclude that Sxy functions identically in all of the Pasteurellaceae.
We've now sent the revisions off to our London coauthors (without the point-by-point response to the reviews, which we need to compose today). They've been a bit more cautions than us on this manuscript, arguing even before we submitted it that more experiments probably should have been done, even though they don't have the resources to do them. Hopefully our arguments will convince them that we should just send the revised manuscript back to the Editor and hope for the best. Our cover letter to the Editor does say that, if he still thinks it necessary, we will make and test the sxy knockout, but by 'we' we mean them.