Friday, April 9, 2010

Ideas for the Introduction and the Discussion

Some of these ideas come from comments on the previous post (from the RA) and from a short discussion with both co-authors.

For the Introduction:  We need to clearly explain why we think this review is needed.

We also need to be clear in our own minds about who will care enough to read it, and how to ensure that they see it.

We might also want to spell out the implications of different kinds of regulation for different ideas about function.  For example, if uptake is selected because incoming DNA provides templates for DNA repair, competence should be regulated by the same damage signals that induce recA, or that induce the RecA-regulated SOS response.  If uptake is selected because incoming DNA provides nucleotides and other nutrients, competence should be regulated by nucleotide pools and/or by processes that sense availability of sources of C, N and P.  If uptake is selected because incoming DNA sometimes carries beneficial new alleles that replace 'inferior' alleles in the chromosome by recombination, then competence should be regulated by ... what? ... I've suggested that competence should be a 'when all else fails' response, induced when the cell's other stress responses have mobilized the relevant genes and expression of these genes has failed to solve the problem.  How strictly this test is applied would probably depend on how costly DNA uptake and recombination were, considering both the physiological costs/risks of DNA uptake and the genetic costs of recombining in alleles that reduce fitness.

For the Discussion: 

We're pretty sure that we won't find one regulatory factor common to all competence-regulating systems, if only because many factors haven't been tested in many species.  But maybe regulatory factors that are often seen?

One important limitation is that we know that individual strains of a species may have very different degrees of competence when exposed to the same competence-inducing treatment.  I don't think there's any direct evidence that the mode of regulation necessarily differs between strains, but there is very little evidence to the contrary either.

What is known not to regulate competence?  It is not known to be regulated by the presence of external DNA (how often has this been directly tested?).

Is important information missing for some species?  Have some forms of regulation or methods of induction not been tested in some bacteria.

Relate back to the significance raised in the Introduction.  Summarize breadth of evidence of regulation by DNA damage?  By nucleotide availability?  By energy supply?  By other stress responses?

Conclude that inferring function from mode of regulation isn't ideal, but given our inability to directly investigate the benefits of competence in the natural environments of bacteria, it may be the best indicator we have.

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