Defining the DNA uptake specificity of naturally competent Haemophilus influenzae cells

Some naturally competent bacteria exhibit both a strong preference for DNA fragments containing specific ‘uptake sequences’ and dramatic overrepresentation of these sequences in their genomes. Uptake sequences are often assumed to directly reflect the specificity of the DNA uptake machinery, but the actual specificity has not been well characterized for any bacterium. We produced a detailed analysis of Haemophilus influenzae’s uptake specificity, using Illumina sequencing of degenerate uptake sequences in fragments recovered from competent cells. This identified an uptake motif with the same consensus as the motif overrepresented in the genome, with a 9 bp core (AAGTGCGGT) and two short flanking T-rich tracts. Only four core bases (GCGG) were critical for uptake, suggesting that these make strong specific contacts with the uptake machinery. Other core bases had weaker roles when considered individually, as did the T-tracts, but interaction effects between these were also determinants of uptake. The properties of genomic uptake sequences are also constrained by mutational biases and selective forces acting on USSs with coding and termination functions. Our findings define constraints on gene transfer by natural transformation and suggest how the DNA uptake machinery overcomes the physical constraints imposed by stiff highly charged DNA molecules.