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 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
- Legionella (Stone 1999)
- Burkholderia (and Ralstonia)
Here also discuss quorum sensing/diffusion sensing, which also regulates competence.
- Bacillus subtilis.
- Streptococcus pneumoniae
Synechocystis Yoshihara 2001