Evolutionary stability of DNA uptake signal sequences in the Pasteurellaceae

Abstract

The DNA-uptake signal sequence (USS) of the bacterium Haemophilus influenzae is highly over-represented in its genome (1,471 copies of the core sequence AAGTGCGGT), and DNA fragments containing USS are preferentially taken up by competent cells. Because this bias favors uptake of conspecific DNA, USSs are often considered a kind of mate recognition system in bacteria, acting as species-specific barriers against uptake of unrelated DNA. However, the H. influenzae USS is highly over-represented in the genomes of three otherwise-divergent Pasteurellaceae species (Pasteurella multocida, Haemophilus somnus, and Actinobacillus actinomycetemcomitans, 927, 1,205, and 1,760 copies, respectively), suggesting that USSs do not always limit exchange. USSs in all these genomes are mainly in coding regions and show no orientation bias around the chromosome, weakening proposed USS functions in transcription termination and chromosome replication. Alignment of homologous genes was used to determine evolutionary relationships between individual USSs. Most H. influenzae USSs were found to have perfect or imperfect homologs (USS at the same location) in at least one other species, and most USSs in the other species had perfect or imperfect homologs in H. influenzae. These homologies suggest that the use of a common USS is due to inheritance of the USS-based uptake system from a common ancestor of the Pasteurellaceae, and it indicates that individual USSs can be evolutionarily stable elements of their genomes. The pattern is consistent with a molecular drive model of USS evolution, with new USSs arising by mutation and preferentially spread to new genomes by the biased DNA-uptake system.

Fig. 1.

Comparison of USSs in all H. influenzae and P. multocida genes (dark bars) with those in genes with named homologs (light bars).

Fig. 2.

Schematic analysis of the H. influenzae and P. multocida homologs of a hypothetical gene a. H. influenzae gene a contains three USSs, with position scores s =–0.2, s = 0.6, and s = 0.85. P. multocida gene a contains two USSs, with scores s = 0.6 and s =–0.8 (position 0.8 in the negative orientation). Plotting all these scores against each other gives the six spots shown in the graph. One comparison falls on the diagonal and is thus between putative homologs (comparison Ha-2:Pa-1), and the remaining five comparisons fall off the diagonal and are likely between nonhomologous USSs.

Fig. 3.

Relationship between positions and orientations of H. influenzae and P. multocida USSs within homologous genes (see text and Fig. 2 for detailed explanation of the analysis). Each point represents a single intragenic USS comparison. Positive and negative values reflect USSs orientation with respect to the direction of transcription.