The work presented in this thesis was initiated with the isolation of an E. coli mutant, sensitive to various DNA damaging agents, in the previously uncharacterized yjiD gene. Based on the work presented in chapter 2 and 3, we renamed yjiD as iraD, which stands for Inhibitor of RssB Activity after DNA Damage. Our data suggest that the function of IraD is to promote the accumulation of the alternative transcription sigma factor, RpoS, by binding to the adaptor RssB protein that targets RpoS for degradation. Our results for the first time demonstrate the physiological importance of this mode of regulation, and underscore the importance of the RpoS regulon in a DNA damage response in actively growing cells.;In agreement with its role in the regulation of RpoS proteolysis, we show that iraD is growth phase regulated, such that it is induced in late-logarithmic phase of growth and into stationary phase, and repressed during exponential growth. We present evidence that the two key players involved in signaling of the stringent response in E.coli , ppGpp and DksA, act upstream of iraD as a positive and a negative regulator respectively. These data suggest that iraD is important for regulation of RpoS not only in response to DNA damage, but also perhaps in response to other stressful conditions such as starvation.;The IraD/RpoS and SOS regulatory pathways appear to act synergistically to ensure survival of cells faced with oxidative or DNA damaging stress during cellular growth. We show that iraD transcription is induced by DNA damage via a novel mechanism independent of the SOS response. In chapter 5, we hypothesize that this novel DNA damage sensing mechanism upstream of iraD is through DnaA, a key replication initiation protein and a transcription factor in E.coli. Our model proposes a new mechanism for sensing the presence of stalled replication forks through the action of DnaA and the beta clamp.
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