Sequence and uptake specificity of cloned sonicated fragments of Haemophilus influenzae DNA

Our data support the conclusion that all tight binding of DNA by competent cells of Haemophilus influenzae is due to 9 base pairs (bp) of the 11-bp motif 5'-AAGTGCGGTCA or its inverse complement, TGACCGCACTT. Sonicated chromosomal DNA of H. influenzae was absorbed and extracted from competent cells to prepare a subpopulation of uptake fragments enriched for single uptake (binding) sequences. This DNA was inserted into the plasmid pUC18 and cloned into Escherichia coli. Whole sonicated chromosomal DNA was also cloned in pUC18 as a population of control fragments. Seventy-one plasmids were labeled with 3H and tested for DNA binding, and the inserts of 28 of them were sequenced. The control plasmid pUC18 was absorbed to competent H. influenzae cells at low levels of 5 to 10% of DNA added. The plasmids containing uptake inserts were mostly absorbed at levels of 70 to 80%, but a significant number contained inserts with an intermediate level of binding, 20 to 30%. The inserts of 15 plasmids were excised and tested for DNA uptake to demonstrate good agreement between uptake of these plasmids and their insert fragments. Sequencing of inserts revealed that the presence of 9 bp of the 11-bp motif was associated with tight binding. Some inserts with intermediate levels of binding had no significant similarities to the 9-bp sequence. The 9-bp sequence appeared to account for most of the binding to competent cells, but appreciable binding occurred with fragments without 9-bp homology. About one-third of the 9-bp uptake sequences were found as inverted repeats that could form strong stem-loop structures. It has been suggested by Goodman and Scocca (Proc. Nal. Acad. Sci. USA 85:6982-6986, 1988) that in Neisseria gonorrhoeae, uptake sequences occur as palindromes and act as transcription terminators. Although consistent, the data are insufficient to make this conclusion for uptake sequence palindromes in H. influenzae.