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:

Proteobacteria:

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

  Gamma:

• Haemophilus influenzae
• Vibrio cholerae
• Escherichia coli
• Pseudomonas
• Moraxella
• Acinetobacter 
• Legionella (Stone 1999)

  Beta

•  Neisseria
• Burkholderia  (and Ralstonia)

  Epsilonproteobacteria

• Helicobacter
• Campylobacter

  Other proteobacteria?

Aquificae

• Aquifex

Bacteroides  

• Bacteroides
• Kingella?

Deinococcus/Thermus

• Deinococcus/Thermus

Fermicutes

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