Saturday, April 3, 2010

Next step for Review-MB

Outline for Review-MB (from previous post):

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


In the introduction to regulation, distinguish between genes for DNA uptake (call these 'competence genes'?), genes affecting what happens to DNA in the cytoplasm (degradation, protection, recombination), and genes with no apparent connection to DNA uptake.  Also genes that are in competence regulons and/or consistently associated with competence but also common or ubiquitous in bacteria not known to take up DNA.  Also distinguish between what happens in lab culture and under more natural conditions.

What are the points to consider, for each organism?
  • Under what culture conditions is competence observed?
  • Is there a regulon that unites most or all of the genes needed for DNA uptake?  
  • If there is no regulon, are individual DNA uptake genes known to be regulated?
  • If not, is there any evidence implicating regulation?
  • If there is a regulon, are some known DNA uptake genes outside of this regulon ?  If so, are they known to be regulated?
  • What other genes belong to this regulon?  Have microarrays been used to characterize the regulon?  

Maybe I should discuss the Gram negative bacteria first, because what we know of their regulation is much simpler.  For H. influenzae, it's one regulon with few genes not involved in DNA uptake.

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