Thursday, April 8, 2010

Next steps

I think the next step for our big review of the regulation of competence is to clarify the basic points we want to consider for each organism (some points will apply to all organisms, some only to one or a few of the organisms or groups), and then divide up the data-gathering between us.  Here's a revised version of the organism list I made last week:
  • Haemophilus influenzae
  • Vibrio cholerae
  • Escherichia coli
  • Pseudomonas
  • Neisseria
  • Other Gram negative bacteria
  • Bacillus subtilis.  Here also discuss quorum sensing/diffusion sensing, which also regulates competence in S. pneumoniae.
  • Streptococcus pneumoniae
  • Acinetobacter
  • Thermus
  • Other Gram positive bacteria
What are the main 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?  
  • What external or metabolic signals are implicated in controlling expression of competence genes?
  • ???What else???


  1. To consider:
    - why is there a need for a review? and who would care / read it?
    - what is common to conditions under which competence is observed?
    - what hasn't been tested (e.g. starvation may work for most bacteria but may not have been tested)?
    - what about conditions we know under which competence is NOT observed (e.g. E. coli)?

  2. I'm happy to take the first 5:
    # Haemophilus influenzae
    # Vibrio cholerae
    # Escherichia coli
    # Pseudomonas
    # Neisseria

    or we could do H. influenzae together...