Date of Award
December 2017
Document Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
Department
Genetics and Biochemistry
Committee Member
Weiguo Cao
Committee Member
Alex Feltus
Committee Member
Cheryl Ingram-Smith
Committee Member
Jeremy Tzeng
Abstract
Uracil DNA glycosylase (UDG) is a crucial member in the base excision (BER) pathway that is able to specially recognize and cleave the deaminated DNA bases, including uracil (U), hypoxanthine (inosine, I), xanthine (X) and oxanine (O). Currently, based on the sequence similarity of 3 functional motifs, the UDG superfamily is divided into 6 families. Each family has evolved distinct substrate specificity and properties. In this thesis, I broadened the UDG superfamily by characterization of three new groups of enzymes. In chapter 2, we identified a new subgroup of enzyme in family 3 SMUG1 from Listeria Innocua. This newly found SMUG1-like enzyme has distinct catalytic residues and exhibits strong preference on single-stranded DNA substrates. In chapter 3, we extensively investigated an untraditional family 1 UNG enzyme from Nitratifractor salsuginis (Nsa UNG). This enzyme is able to form a unique salt bridge network with uracil-containing DNA. In addition, this untraditional family 1 UNG can’t be inhibited by uracil DNA glycosylase inhibitor (Ugi). In chapter 4, a potential evolutionary immediate between family 1 UNG and family 4 UDGa was isolated from Janthinobacterium agaricidamnosum (Jag UNG). In the functional motifs, Jag UNG has evolved family 1 UNG unique features, but still keeps some features of family 4 UDGa. Through site-directed mutagenesis, molecular modeling and biophysical analysis, we estimated that QD in family 1 UNG might be coevolved from EG in family 4 UDGa. In addition, we found another two important sites (A82E and L245H) that may have special meaning in the evolutionary history. All these work reveal the evolutionary diversity of UDG superfamily.
Recommended Citation
Li, Jing, "The Evolutionary Diversity of Uracil DNA Glycosylase Superfamily" (2017). All Dissertations. 2546.
https://open.clemson.edu/all_dissertations/2546