Mechanism of gene regulation by the NF-kappaB p52 homodimer and Bcl3

The mammalian Rel/NF-[kappa]B family of transcription factors plays a central role in the immune system by regulating various processes involving in both innate and adaptive immunity, inflammation, lymphocyte differentiation, and lymphoid malignancies. A wide variety of signals activate NF-[kappa]B driven gene expression through different NF-[kappa]B signaling pathways in a stimulus- and cell type-dependent manner. Due to the diverse regulatory mechanism acting on NF-[kappa]B signaling, the signal dependent activation of NF-[kappa]B remains a challenging area of research. This thesis describes the mechanism of gene regulation by the NF- [kappa]B p52 homodimer with its specific transcriptional co-regulator Bcl3. Chapter I introduces the NF-κB family transcription factors together with its regulation through the I[kappa]B family, NF-[kappa]B signaling pathways, and its DNA recognition in gene transcription initiation. Chapter II describes the promoter specificity by NF-[kappa]B p52 homodimers. Our results show that a single nucleotide change in the central base pair of [kappa]B DNA discriminates between classical RelA containing NF-[kappa]B dimers versus the p52:Bcl3 complex. Chapter III studies the degradation, re-synthesis, and processing of NF-[kappa]B2/p100 and the generation of p52 in non-canonical NF-[kappa]B signaling pathway as well as inhibitory function of NF-[kappa]2/p100 referred as I[kappa]B[delta]. Our results showed that LT[beta]- mediated non-canonical signaling is a NIK-dependent biphasic event, which induces both the activation and suppression of NF-[kappa]B activity. Chapter IV studies the phosphorylation state of Bcl3 and its function in terms of p52:Bcl3 gene activation. Two new Bcl3 phosphorylation sites were identified and biochemical analysis showed that these two phosphorylations enhance the protein-protein interaction between p52 and Bcl3, which in turn enhance their specific gene activation. Chapter V employed a combination of X-ray crystallography and biochemical technique to investigate the molecular basis of p52:Bcl3 complex formation. Stable p52:Bcl3 core complex was identified and crystallize