Genome-wide analysis of DNA uptake across the outer membrane of naturally competent Haemophilus influenzae

The genomes of naturally competent Pasteurellaceae and Neisseriaceae have many short uptake sequences (USS), which allow them to distinguish self-DNA from foreign DNA. To fully characterize this preference we developed genome-wide maps of DNA uptake using both a sequence-based computational model and genomic DNA that had been sequenced after uptake by and recovery from competent Haemophilus influenzae cells. When DNA fragments were shorter than the average USS spacing of ∼1,000 bp, sharp peaks of uptake were centered at USS and separated by valleys with 1000-fold lower uptake. Long DNA fragments (1.5–17 kb) gave much less variation, with 90% of positions having uptake within 2-fold of the mean. All detectable uptake biases arose from sequences that fit the USS uptake motif. Simulated competition predicted that, in its respiratory tract environment, H. influenzae will efficiently take up its own DNA even when human DNA is present in 100-fold excess. [Display omitted] •For short DNA fragments, an uptake sequence (USS) improves DNA uptake 1000-fold•Most longer H. influenzae fragments have USS, giving even uptake across the genome•Preferred USS are stiff, so strand melting may facilitate kinking for uptake•H. influenzae will take up its own DNA 100-fold better than human DNA Molecular Biology; Microbiology