Sunday, March 28, 2010

Planning a review article (or two)

I think it's high time we wrote a review article.  The preliminary title is 'Regulation of Competence by Nutritional Signals'.  I think it should be aimed at molecular biologists/microbiologists rather than evolutionary biologists.  No, I think there should be two versions of this article, one aimed at each audience, but both calling on the same body of data.

How would these versions differ?  The one for the molecular biologists/microbiologists (call it review-MB) would be longer, and would go into the regulatory details for each species.  The evolutionary issues would be mentioned but not emphasized in the introductory paragraphs, and given a bit more emphasis at the end.  The version for evolutionary biologists (review-E) would be shorter.  It would  lay out the evolutionary issues in some detail in the introduction, make the main points of the regulatory analysis laid out by review-MB (citing that as a reference), and then reemphasize the evolutionary conclusions at the end.

Outline for Review-MB:
  • Introduction:  What competence and transformation are, and what their consequences are (genetic and otherwise). Mechanisms are quite conserved (or convergent) but regulation is complex and very variable.  Studies of regulation have generally been interpreted in a genetic-consequence framework.  We will try to take a broader view.
  • Organism-by-organism analysis (including relatives that have similar regulation)
  • Bacillus subtilis.  Here also discuss quorum sensing/diffusion sensing.
  • Streptococcus pneumoniae
  • Acinetobacter
  • Thermus
  • Other Gram positive bacteria
  • Haemophilus influenzae
  • Vibrio cholerae
  • Escherichia coli
  • Pseudomonas
  • Neisseria
  • Summary/Conclusions
Outline for Review-E:
  • Introduce competence and transformation; what happens and what the consequences are.  More detail for this audience.
  • Importance of knowing how natural selection has acted.  Implications for understanding the evolution of meiotic sex.
  • How we should decide.  Why analysis of 'functional design' s the most useful.
  • Applying functional analysis to other parasexual processes and to the 'recombination machinery'.  Conclude that E. coli and other non-competent bacteria don't have sex.  (This is why we now focus on natural competence.)
  • Why focus on regulation.  How preconceptions about function sometimes have compromised interpretations of the molecular biology.
  • Evidence about regulation.  Maybe a page for H. influenzae, a couple of paragraphs for each of the other well-studied species, and a single paragraph for each of the others.
  • Remaining issues:  Uptake sequences, active DNA release, cannibalism, DNA protection in the cytoplasm, induction of 'recombination' machinery.
  • Conclusions
Time to get to work!