Monday, October 11, 2010

Survey of competence regulation

Need a Table of the homologs.

Perhaps we should also propose a uniform generalized nomenclature.

What are the main points to consider for each organism? (some points will apply to all organisms, some only to one or a few of the organisms or groups):
  • 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 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?
The organisms (survey):

The species/taxa we'll consider, grouped phylogenetically according to the Wu and Eisen 2008 tree:


A critical issue here is distinguishing between the regulation of type IV pili and of competence.

  • Haemophilus influenzae
  • Vibrio cholerae
  • Escherichia coli
  • Pseudomonas
  • Moraxella
  • Acinetobacter 
  • Legionella (Stone 1999)
  •  Neisseria
  • Burkholderia  (and Ralstonia)

  • Helicobacter
  • Campylobacter
  Other proteobacteria?

  • Aquifex
  • Bacteroides
  • Kingella?
  • Deinococcus/Thermus

Here also discuss quorum sensing/diffusion sensing, which also regulates competence.
  • Bacillus subtilis.  
  • Streptococcus pneumoniae
  • Acinetobacter
Mitochondria! (Weber-Lofti et al 2009)

Synechocystis Yoshihara 2001

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