Doctor of Philosophy (PhD)


Biological Sciences

Document Type



Dps (DNA protection during starvation) proteins play an important role in the protection of prokaryotic macromolecules from damage by reactive oxygen species. The Dps homolog, Dps-1, from the radiation-resistant bacterium Deinococcus radiodurans has an extended N-terminal tail. In the crystal structure of Dps-1, the first ~30 N-terminal residues are invisible and the remaining 25 residues form a loop that harbors a novel metal binding site. The data presented here show that retention of this N-terminal metal site is necessary for formation of the dodecameric protein assembly. Previous studies have suggested that the lysine-rich N-terminus of Dps proteins participates in DNA binding. Accordingly, deletion of the N-terminal tail of Dps-1 obliterates DNA/Dps-1 interaction. Electrophoretic mobility shift assays using DNA modified with specific major/minor groove reagents show that Dps-1 interacts through the DNA major groove. Dodecameric Dps-1 can bind ≥ 22bp DNA duplexes with very high affinity (Kd ~0.4 nM); considering interactions in the DNA major grooves, the requirement for two complete helical turns implies optimal interactions involving two consecutive major grooves. The data further suggests that high-affinity DNA binding depends on occupancy of the N-terminal metal site. Stoichiometric titration of dodecameric Dps-1 with 22 bp DNA revealed the presence of 6 DNA binding sites in each dodecamer. DNA cyclization assays show that dodecameric Dps-1 inhibits DNA bending. Taken together, the mode of DNA interaction by Dps-1 is consistent with the previously proposed layered assembly of protein and DNA that leads to DNA compaction. Using Dps-1-promoter-lacZ fusion constructs, it is shown that Dps-1 expression in D. radiodurans is relatively constant throughout both exponential and stationary phase growth. As E. coli cells expressing Dps-1 feature significant nucleoid condensation, as shown by transmission electron microscopy and nucleoid staining, a role for Dps-1 in chromosomal DNA packaging is suggested. The presence of a novel iron exit channel is most likely responsible for the inability of Dps-1 to protect DNA from hydroxyl radical-mediated DNA degradation. The release of iron from the core upon DNA binding suggests that Dps-1 may be involved in the process of DNA degradation that contributes the first response to DNA damage.



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Committee Chair

Anne Grove