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.

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???

Introduction to Review-MB

From an earlier post:

Introduction: What competence and transformation are, and what their consequences are (genetic and otherwise). Mechanisms are quite conserved (or convergent) but regulation is complex and very variable. Studies of regulation have generally been interpreted in a genetic-consequence framework. We will try to take a broader view.

In the introduction, distinguish between genes for DNA uptake (call these 'competence genes'?), genes affecting what happens to DNA in the cytoplasm (degradation, protection, recombination), and genes with no apparent connection to DNA uptake.  Also genes that are in competence regulons and/or consistently associated with competence but also common or ubiquitous in bacteria not known to take up DNA.  Also distinguish between what happens in lab culture and under more natural conditions.

Detailed outline:

• Attention-capturing first sentence.
• Competence is the ability to take up DNA.  Here we're concerned with 'natural competence'; due to expression of genetically encoded machinery for DNA uptake (distinguish from artificial permeabilization methods).
• Transformation refers to genetic changes that result from recombination of this DNA with the chromosome.  This is how competence (and the role of DNA) was discovered, and remains the easiest way to detect DNA uptake.  Whether or not transformation results from DNA uptake depends on whether the incoming DNA carries homologous sequences similar enough for recombination, whether it carries different alleles, the extent to which it is degraded during uptake and in the cytoplasm, and the activity of the cellular DNA replication and repair proteins that carry out recombination.
• Competence is widespread but the distribution is locally sporadic.  Detecting competence is most easily done by assays of transformation, and transformable bacteria have been found in many families of both gram positive and gram negative bacteria,  However, within these families, many species are reported to be not transformable, and the 'transformable' species that have been investigated usually are found to include nontransformable isolates.
• The mechanisms of DNA uptake used by different groups are very similar, with all bacteria transport a single strand of DNA into the cytoplasm with the same inner-membrane channel.  Except for Helicobacter and Campylobacter (use family name?), (use ???), all bacteria also use force-generating proteins of the type 4 pili/type II secretion system complex to pull double-stranded DNA to the cytoplasmic/inner membrane.  
• Regulation of competence is much more diverse.  Different bacteria reported to regulate competence in many different ways (here list some of the extremes).  In some cases the regulation appears to be competence-specific, but in others the 'competence' regulons include not only genes that act after DNA has been taken up (affecting its degradation and recombination, but many other genes whose functions appear unrelated to DNA uptake.  Another complication is that many bacteria not known to be naturally competent have homologs of genes that are competence-regulated in other bacteria.
• The function of natural competence is controversial, which is one reason for paying close attention to its regulation.  Transformation is its most widely known consequence, but DNA from the environment also provides cells with deoxynucleotides that can be recycled for DNA replication or as sources of other nutrients (C, N, P) and with DNA strands that can be used as templates for DNA repair.  The genes responsible for the regulation of competence may have evolved to optimize the benefits of DNA uptake (depending on the extent to which the regulation is specific to DNA uptake).
• In this review we will examine the diversity of competence regulation, looking for unifying features, particularly those related to the various benefits DNA uptake can bring.  We will also consider how the regulation observed in lab cultures is likely to affect expression of competence in the natural environment.

Next step for Review-MB

Outline for Review-MB (from previous post):

Introduction:  What competence and transformation are, and what their consequences are (genetic and otherwise). Mechanisms are quite conserved (or convergent) but regulation is complex and very variable.  Studies of regulation have generally been interpreted in a genetic-consequence framework.  We will try to take a broader view.

Organism-by-organism analysis (including relatives that have similar regulation)

• Bacillus subtilis.  Here also discuss quorum sensing/diffusion sensing.
• Streptococcus pneumoniae
• Acinetobacter
• Thermus
• Other Gram positive bacteria
• Haemophilus influenzae
• Vibrio cholerae
• Escherichia coli
• Pseudomonas
• Neisseria

Summary/Conclusions

Plans:

In the introduction to regulation, distinguish between genes for DNA uptake (call these 'competence genes'?), genes affecting what happens to DNA in the cytoplasm (degradation, protection, recombination), and genes with no apparent connection to DNA uptake.  Also genes that are in competence regulons and/or consistently associated with competence but also common or ubiquitous in bacteria not known to take up DNA.  Also distinguish between what happens in lab culture and under more natural conditions.

What are the 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?  
• 
  

Maybe I should discuss the Gram negative bacteria first, because what we know of their regulation is much simpler.  For H. influenzae, it's one regulon with few genes not involved in DNA uptake.