Here is the Abstract of our old NIH grant proposal (funded Jan. 1 2000).

The entire proposal is available as a pdf file. Don't forget to get the figures too.

Genetic exchange is a major driving force in bacterial evolution, and is often assumed to have evolved for that purpose. This research will test this assumption by determining the function of the sequence-specific DNA uptake systems of the important human pathogens Haemophilus influenzae, Actinobacillus actinomycetemcomitans, Neisseria meningitidis and N. gonorrhoeae. Many bacteria can take up DNA and thus acquire genes affecting virulence, host range and antibiotic resistance. Haemophilus and Neisseria preferentially take up homologous DNA, by recognising a short highly-repeated sequence, the USS. The H. influenzae genome has 1465 copies of a 9bp USS, a substantial fraction of its otherwise streamlined genome. USS-dependent DNA uptake appears to be the best evidence that selection promotes genetic exchange. However we know of no selective processes that could have produced this system, and it is just as likely to have arisen from forces unconnected to genetic exchange. Once we understand their function, USS may provide targets for intervention in infections by competent bacteria - either as a drug-delivery mechanism or as a process to be inhibited by new drugs.

The problem of USS evolution is wide open; we know of no other laboratory working on it. We propose to address the following questions:

Modeling:

I. Nucleotide acquisition is an inevitable benefit of DNA uptake. Is it consistently much larger than the other potential benefits?

II. A biased DNA-uptake receptor can increase the frequency of its preferred sequence in the genome. Will receptor bias inevitably do so if cells take up homologous DNA?

III. USS are not randomly distributed around the genome. Can the spacing be explained by bias-driven accumulation?

Genomics:

IV. Is non-random spacing seen in other genomes with USS?

V. Most H. influenzae USSs are in coding sequences. How do they constrain protein function?

VI. Related species may share a common USS. Has this led to substantial genetic exchange?

Experiments:

VII. Uptake of heterologous DNA can kill the Rd strain of H. influenzae. Does this lethality occur in other strains?

VIII. Respiratory tract mucus contains high concentrations of DNA. Can DNA be taken up by H. influenzae growing in or under mucus?

IX. The strength of the H. influenzae uptake bias is poorly defined. How strongly does DNA uptake depend on the USS?

X. The USS-binding structure on competent H. influenzae cells has not been identified. Can the USS be cross-linked to a specific protein on the cell surface?

XI. The USS may have an intracellular function. Is there a cytoplasmic or inner membrane protein that specifically binds the H. influenzae USS?