Yagmur Bingul

Date of Award

2024

Document Type

Thesis

Degree Name

Bachelor of Science

Department

Biochemistry & Molecular Biol.

First Advisor

Dr. Eugene Wu

Abstract

The transition from the RNA to the DNA world stands as an important event, demanding the emergence of enzymatic activities for DNA precursor synthesis, retro-transcription of RNA templates, and replication of single and double-stranded DNA molecules. The distribution of protein families associated with these activities across the three domains of life—Archaea, Eukarya, and Bacteria—adds layers of complexity to the narrative. While Archaea and Eukarya often share similar protein structures, structural biology shows homologous, but distinct, structures in Bacteria. On the other hand, viral polymerases emerge as a crucial part of genome replication and transcription. Their versatility, including RNA-dependent RNA polymerase, RNA-dependent DNA polymerase, DNA-dependent RNA polymerase, and DNA-dependent RNA polymerases, is tailored to diverse genome types and specific viral requirements. These single-protein entities employ various mechanisms for recognizing binding sites, ensuring processive elongation, terminating replication, and coordinating nucleic acid synthesis with other enzymatic activities. This variation of the viral proteins places them as the possible answer for the origin and evolution of the DNA replication proteins and explains the reason for the structural difference between different types of proteins that function in a similar process. In this paper, in order to test this hypothesis, we used structural phylogenetics techniques, as it often reveals deep evolutionary relationships for proteins that are not apparent in protein sequences. The results suggest an ancient relationship between the viral and eukaryotic A Family DNA polymerases, compared to bacterial A Family DNA polymerases, shedding light to the questions about the evolution of viral proteins.

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