Competence variation: causes and consequences

A potential postdoc is interested in the role of gene exchange in natural populations, and I think this might be a very nice way to build on other work we've done and will be doing. It would also fit well into the NIH proposal we're preparing.

Work we've done: We know that DNA uptake and transformability are very variable in natural populations, but we don't know why (neither the molecular nor the evolutionary/ecological 'why'). The best study was by a recent postdoc, who analyzed 30+ natural isolates of H. influenzae for both DNA uptake and transformation. She found that very few took up as much DNA or transformed as well as the lab strain KW20. Some of these strains had sequenced genomes, but in most cases the genotype did not explain the phenotype.

Work we will be doing: A new postdoc is investigating the molecular constraints on transformation, to fully characterize the sequence biases that affect each stage of DNA uptake and recombination. This should give us a good picture of what transformational recombination looks like, at the genome-wide level.

The nice extension has two parts:

Part 1: Before we can hope to understand the evolutionary cause of the variation in competence and transformability, we need to find out its molecular causes - what are the genetic changes underlying the differences in DNA uptake and transformation? This is probably best done by a combination of genetics and genome sequencing. Genome sequencing has gotten so cheap that we can afford to do a lot of strains, not probably to the assembly stage (too much person-work), but enough to get the sequences of all the homologs of genes known from KW20 and other strains with assembled genomes. We could certainly do all the strains the postdoc characterized, but we might be able to do a much more comprehensive survey. (Maybe someone else is already doing this... I've just emailed the likely suspect so we can coordinate our efforts.)

With lots of genome sequences of strains of known phenotype, we can look for the individual causes of the different competence phenotypes and also look for patterns in these causes. Identifying the causes for individual strains will entail benchwork, using natural transformation to confirm that specific alleles are responsible for specific phenotypes. I would think that some of this could be a project for an undergraduate or M.Sc. student, but the new post-doc is bursting with ideas of how to do this efficiently for many strains - I’ll let him post these on his blog. Then we can ask whether the causes appear to be a random subset of the possible mutations, or whether there are consistent causes in the different strains. We can also ask how recent the changes are (have multiple mutations accumulated in the competence genes?), and maybe even ask whether the most recent ancestors were indeed competent (but this may not be possible - see our recent PLoS One paper).

Part 2: Once we have genome sequences and the results of the other post-doc’s genome-wide recombination analysis, we can not only examine the genomes for evidence of recombination, but also ask whether the recombination fits the pattern expected for transformation, and whether the differences in recombination correlate in any way with the differences in transformability. For example, do nontransformable strains have a history of reduced recombination? If yes, can we tell how recent this is? And is only the transformational component of recombination reduced? Is there evidence that transformation by other causes (conjugation, transduction) is increased in strains that don't transform? Can we tell whether the changes causing reduced competence and transformability are themselves due to recombination?

This is a great project because it can go in lots of directions and because all of the possible answers are interesting.