Date of Completion

Spring 6-6-2023

Thesis Advisor(s)

Johann Peter Gogarten

Honors Major

Biological Sciences

Abstract

This research studies a methylase family in Actinobacteriophages that has been invaded by three different elements: an intein, an additional homing endonuclease and a domain of unknown function. Selfish genomic elements such as inteins and Homing Endonucleases are often found inserted into the exteins of Actinobacteriophages. These elements can spread through different bacteriophage lineages over time through the mechanisms of homing. The ShiLan domain, a found insertion that was found inserted in the ShiLan phage, an intein, and a Homing Endonuclease domain have been found inserted into a DNA methylase. The evolutionary history of these insertions within the DNA methylase Phams of 105558 and 106461 were analyzed and showed that two of the three inserts were scattered throughout these two Phams. Both the inteins and the ShiLan domain sequences appeared to be more related among themselves than the exteins of the phages they inserted into were. In contrast, the Homing Endonuclease domain that was not a part of the intein was only found in a group of related exteins. Trees for the methylase family were created that were constrained to group the methylases for each of the phage Clusters within the Phams together, as well as trees that were constrained to group either the intein, ShiLan, or Homing Endonuclease domain containing phages into a single group. The AU-test was used to evaluate the constrained trees finding that the intein, ShiLan domain, and Cluster F were rejected (significance level below the 95% confidence level) to form clades, but the clades of methylases containing the Homing Endonuclease domain, and methylases from Clusters E, A, AR, AS, I, P, and J were not rejected. Overall, the results suggested that the intein and ShiLan domain recently invaded divergent DNA methylase as they had invaded divergent methylases from multiple clusters while remaining highly related.

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