An intrinsically disordered transcription activation domain alters the DNA binding affinity and specificity of NFκB p50/RelA

Baughman, H. E. R.; Narang, D.; Chen, W.; Suarez, A. C. V.; Lee, J.; Bachochin, M. J.; Gunther, T. R.; Wolynes, P. G.; Komives, E. A.

doi:10.1101/2022.04.11.487922

bioRxiv · 10.1101/2022.04.11.487922

An intrinsically disordered transcription activation domain alters the DNA binding affinity and specificity of NFκB p50/RelA

Baughman, H. E. R.·Narang, D.·Chen, W.·Suarez, A. C. V.·Lee, J.·Bachochin, M. J.·Gunther, T. R.·Wolynes, P. G.·Komives, E. A.

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Abstract

Many transcription factors contain intrinsically disordered transcription activation domains (TADs), which mediate interactions with co-activators to activate transcription. Historically, DNA-binding domains and TADs have been considered as modular units, but recent studies have shown that TADs can influence DNA binding. We biophysically characterized the NF{kappa}B p50/RelA heterodimer including the RelA TAD and investigated the TADs influence on NF{kappa}B-DNA interactions. In solution the RelA TAD is disordered but compact, with helical tendency in two regions that interact with co-activators. The presence of the TAD increased the stoichiometry of NF{kappa}B-DNA complexes containing promoter DNA sequences with tandem {kappa}B recognition motifs by promoting the binding of NF{kappa}B dimers in excess of the number of {kappa}B sites. We measured the binding affinity of p50/RelA for DNA containing tandem {kappa}B sites and single {kappa}B sites. While the presence of the TAD enhanced the binding affinity of p50/RelA for all {kappa}B sequences tested, it increased the affinity for non-specific DNA sequences by over 10-fold, leading to an overall decrease in specificity for {kappa}B DNA sequences. Our results reveal a novel function of the RelA TAD in promoting binding to non-consensus DNA previously observed by in vivo studies of NF{kappa}B-DNA binding in response to strong inflammatory signals.

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Baughman, H. E. R., Narang, D., Chen, W., Suarez, A. C. V., Lee, J., Bachochin, M. J., Gunther, T. R., Wolynes, P. G., Komives, E. A.. 2022-04-11. An intrinsically disordered transcription activation domain alters the DNA binding affinity and specificity of NFκB p50/RelA. https://doi.org/10.1101/2022.04.11.487922

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