Physiological roles and regulation of the cryptic prophage-encoded small protein DicB and small RNA DicF in Escherichia coli

Bacterial adaptation to stress conditions is vital for their survival in different environments. In the past decade, the important roles that small RNAs (sRNAs) and small proteins perform in regulating the stress response in bacteria has become evident. While the roles of numerous sRNAs and small proteins encoded on the bacterial core genome have been characterized, very few that are phage or prophage-encoded have been studied. This dissertation describes the roles and regulation of the sRNA DicF and small protein DicB encoded on the Qin cryptic prophage of Escherichia coli K12. Bacterial genomes harbor cryptic prophages that have lost genes required for induction, excision from host chromosomes, or production of phage progeny. DicB and DicF are encoded on the dicBF operon, which is located in the immunity region of the cryptic prophage Qin. DicB and DicF have previously been implicated in inhibiting cell division of the host bacterium. In this study, we show that the small protein DicB protects the host cells from phage infection. DicB specifically inhibits infection by λ and other phages that use ManYZ inner membrane proteins to inject their DNA into the host cell. DicB also inhibits the canonical function of ManYZ, which is mannose sugar transport. We demonstrated that the previously known interaction between DicB and MinC, a host protein involved in proper positioning of the Z ring during cell division, is necessary for the DicB-dependent phenotypes involving ManYZ identified in this study. The sRNA DicF is widely conserved is many E. coli strains and inhibits ftsZ mRNA translation in E. coli. In this study, we establish the mechanism of this regulation by characterizing the base pairing interaction between DicF and ftsZ, and delineate the roles of other host factors involved in this regulation. Additionally, we identify new mRNA targets of the sRNA DicF, that are primarily involved in host cell metabolism. The final part of this thesis work describes the genetic mechanisms defining the regulation of the dicBF operon. The dicBF operon is constantly repressed under laboratory conditions by the repressor DicA. In this work, we identified that the protein Rem impairs DicA repression of the dicBF operon and is the antirepressor of DicA. We show that Rem induces expression of dicB and dicF, which leads to the concomitant cell filamentation phenotype as DicB and DicF are cell division inhibitors. In the absence of the dicBF gene products, the promoter of the dicBF operon was found to undergo spontaneous induction in a subset of cells, reminiscent of the λ phage bistable genetic switch. Lastly, urea and high temperature were identified as strong inducers of the dicBF promoter in strains deleted for the dicBF operon. Our results suggest that expression of the dicBF operon is regulated in multiple ways in E. coli K12, indicative of the complex relationship that exists between the host cell and cryptic prophages.U of I OnlyAuthor requested U of Illinois access only (OA after 2yrs) in Vireo ETD syste