Field of Science

Should we be searching for cryptic uptake specificity?

I was just reading the draft Discussion section of the post-doc's uptake-specificity manuscript, and realized that something we've only been casually mentioning may actually be a critical test of the hypothesis that uptake specificity is an adaptation to promote recombination.  This test should certainly be included in our revised grant proposal.

In bacteria of the family Pasteurellaceae and the genus Neisseria, the sequence bias of the DNA uptake machinery was discovered because the genomes of these bacteria contain many occurrences of the preferred motif, which causes these cells to preferentially take up DNA from their own and closely related species ('self' DNA).  We think that the genomic uptake sequences have accumulated as an indirect consequence of the uptake bias, due to molecular drive arising from recombinational replacement of poor uptake sequences with better ones.

Our computer simulation model shows that the strength of this drive depends on the strength of the bias, on the frequencies of DNA uptake and of recombination, and on the mutation rate.  If the mutation rate is high, the bias must be strong and DNA uptake must be both frequent and frequently followed by recombination.

A preference for self DNA has not been detected in most other bacterial species that can take up DNA*, and their genomes are not conspicuously enriched for anything that looks like an uptake sequence motif.  However, although these species are usually considered to have unbiased uptake, this has not been explicitly tested.

We are in an excellent position to test the Gram-negative species for uptake bias.  The experiment would use a degenerate uptake fragment like that used for the post-doc's H. influenzae analysis, but the central sequence would be fully random.  The cells would need to carry a rec2 mutation to prevent DNA degradation, but I think the presence of Illumina sequencing tags in the fragment means that we would not need to optimize (or even use?) the DNA recovery procedure.  We'd just give the test fragment to competent cells, wash the cells thoroughly, and isolate and sequence the input and recovered DNA.

Finding any uptake bias in a species whose genome is not enriched for the preferred motif would be strong evidence that the bias is mechanistic and has not been selected to promote recombination.  This would be a very important result.

*  The exception are Campylobacter and Helicobacter; their genomes don't have recognizable uptake sequence motifs, and the uptake bias is hypothesized to depend on a DNA modification.

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