Investigating the mechanism of DNA binding enhancement by the RelA transcription activation domain.

Abstract

The p50/RelA heterodimer of the NF-κB family of transcription factors activates genes involved in inflammation and immunity in response to cellular stressors. Both p50 and RelA (p65) contain a Rel homology domain which, when dimerized, binds to DNA. In addition, RelA contains a 230-residue intrinsically disordered transcription activation domain (TAD). The RelA TAD interacts with co-activator proteins and was previously believed to function independently from the DNA-binding Rel homology domain. However, we found that the presence of the RelA TAD enhances the DNA binding affinity of the p50/RelA heterodimer: full length p50/RelA binds to DNA with higher affinity than the truncated Rel homology domain. The strongest binding enhancement was observed for DNA sequences that do not match the κB consensus motif, leading to an overall decrease in sequence specificity when the RelA TAD is intact. We found that a proline-rich region consisting of the first 100 residues of the TAD is sufficient for this binding enhancement. We investigated the sequence features necessary for this phenomenon and the effects of the RelA TAD on the structure and dynamics of the p50/RelA heterodimer.