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Hunter, K. E.

Publications and source records attributed to Hunter, K. E..

2 recordsLinked to original sources

Using a simplified Rough Mount Fuji model to disentangle how multi-peaked fitness landscapes can be highly navigable

Evolving populations, especially in the strong-selection-weak-mutation limit, can be modelled as adaptive walks on fitness landscapes, moving in fitness-increasing mutational steps until reaching a fitness peak--a local optimum. Simulations of such adaptive walks--on a multi-peaked empirical landscape of the folA gene and on landscapes generated by the Rough Mount Fuji (RMF) model-- have shown that some landscapes are highly navigable, meaning that the highest x% of peaks are reached by >> x% of adaptive walks. This prompts the question of how adaptive walks can be so successful despite the local, myopic rules behind each adaptive step. Here, we investigate this question using simulations and mathematical approximations of random adaptive walks on a simplified RMF landscape. The landscape has a low-to-intermediate fitness region, whose size reconciles a low peak density with a high peak number. Despite the high number of peaks, walkers are likely to exit this region without terminating at a peak because the probability of a peak transition at each step is low and a fitness gradient guides walkers to the high-fitness region in few steps. Thus, three features are sufficient to explain why adaptive walks in the simplified RMF landscape are likely to reach a small fraction of top-ranking peaks: a low-to-intermediate fitness region with a high number of peaks, a low peak-transition probability, and which is crossed in few steps. We find that these three features are also present in the empirical folA landscape, suggesting that similar principles may apply.

evolutionary biology↗

The Helicobacter pylori Methylome is Acid-Responsive due to Regulation by the Two-Component System ArsRS and the Type I DNA Methyltransferase HsdM1 (HP0463)

In addition to its role in genome protection, DNA methylation can regulate gene expression. In this study, we characterized the impact of acidity, phase variation, and the ArsRS TCS on the expression of the Type I m6A DNA methyltransferase HsdM1 (HP0463) of Helicobacter pylori 26695 and their subsequent effects on the methylome. Transcription of hsdM1 increases at least 4-fold in the absence of the sensory histidine kinase ArsS, the major acid-sensing protein of H. pylori. hsdM1 exists in the phase-variable operon hsdR1-hsdM1. Phase-locking hsdR1 (HP0464), the restriction endonuclease gene, has significant impacts on the transcription of hsdM1. To determine the impacts of methyltransferase transcription patterns on the methylome, we conducted methylome sequencing on samples cultured at pH 7 or pH 5. We found differentially methylated motifs between these growth conditions, and that deletions of arsS and/or hsdM1 interfere with the epigenetic acid response. Deletion of arsS leads to altered activity of HsdM1 and multiple other methyltransferases under both pH conditions indicating that the ArsRS TCS, in addition to direct effects on regulon transcription during acid acclimation, may also indirectly impact gene expression via regulation of the methylome. We determined the target motif of HsdM1 (HP0463) to be the complementary bipartite sequence pair 5-(HH)TCAm6AVN6TGY-3 and 3-AGTN6GAm6ACA-5. The Type II m5C DNA methyltransferase M.HpyAVIII (HP1121) is regulated by ArsS and HsdM1. This complex regulation of DNA methyltransferases, and thus differential methylation patterns, may have implications for the decades-long persistent infection by H. pylori. ImportanceThis study expands the possibilities for complex, epigenomic regulation in Helicobacter pylori. We demonstrate that the H. pylori methylome is plastic and acid-sensitive via the two-component system ArsRS and the DNA methyltransferase HsdM1. The control of a methyltransferase by ArsRS may allow for a layered response to changing acidity. Likely, an early response whereby ArsR[~]P affects regulon expression, including the methyltransferase hsdM1. Then, a somewhat later effect as the altered methylome, due to altered HsdM1 expression, subsequently alters the expression of other genes involved in acclimation. The intermediate methylation of certain motifs supports the hypothesis that methyltransferases play a regulatory role. Untangling this additional web of regulation could play a key role in understanding H. pylori colonization and persistence.

microbiology↗