Bacterial DNA uptake sequences can accumulate by molecular drive alone

Area of Science:

• Microbiology
• Genomics
• Evolutionary Biology

Background:

• Competent bacteria, including Pasteurellaceae and Neisseria, utilize specific DNA motifs called uptake signal sequences (USS) to facilitate DNA import.
• Genomes of these bacteria exhibit significant overrepresentation of USS, suggesting a bias in DNA uptake machinery favoring related DNA.
• The evolutionary mechanisms driving the high frequency of USS remain poorly understood and are not adequately explained by existing models of bacterial competence evolution.

Purpose of the Study:

• To investigate the molecular and evolutionary forces responsible for the abundance of uptake signal sequences in bacterial genomes.
• To evaluate the hypothesis that biased DNA uptake coupled with neutral recombination can drive USS accumulation.
• To refine understanding of DNA uptake specificity in *Haemophilus influenzae*.

Main Methods:

• Development and application of a computer simulation model to test the molecular drive hypothesis for USS accumulation.
• Utilizing an unbiased search algorithm to identify and characterize USS within bacterial genomes.
• Conducting DNA uptake assays to determine the precise uptake specificity of *Haemophilus influenzae*.

Main Results:

• Computer simulations demonstrated that biased DNA uptake and neutral recombination are sufficient to drive USS to high densities in genomes.
• The simulated USS exhibited characteristics mirroring those found in natural genomes, including specific spacings, stabilities, and strong consensus.
• Experimental data refined the understanding of *Haemophilus influenzae*'s DNA uptake specificity.

Conclusions:

• The accumulation of uptake signal sequences in bacterial genomes can be explained by a passive process of molecular drive, driven by biased uptake and neutral recombination.
• This finding simplifies the investigation of the functional benefits of DNA uptake, as it provides a mechanism for the non-selected accumulation of cognate sequences.
• The study offers a parsimonious explanation for the widespread presence and overrepresentation of USS in competent bacterial species.