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.