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Cited by 27NF-κB Signaling PathwaysProtein Structure and DynamicsGenomics and Chromatin Dynamics

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

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Baughman, Hannah E.R., Narang, Dominic, Chen, Wei, Villagrán Suárez, Amalia C., Lee, Joan, Bachochin, Maxwell J., Gunther, Tristan R., Wolynes, Peter G., Komives, Elizabeth A.·2022·Journal of Biological Chemistry
DOI 10.1016/j.jbc.2022.102349PMC PMC9440430

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Abstract

Many transcription factors contain intrinsically disordered transcription activation domains (TADs), which mediate interactions with coactivators 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. Whether these results can be generalized to more TADs is not clear. Here, we biophysically characterized the NFκB p50/RelA heterodimer including the RelA TAD and investigated the TAD's influence on NFκB-DNA interactions. In solution, we show the RelA TAD is disordered but compact, with helical tendency in two regions that interact with coactivators. We determined that the presence of the TAD increased the stoichiometry of NFκB-DNA complexes containing promoter DNA sequences with tandem κB recognition motifs by promoting the binding of NFκB dimers in excess of the number of κB sites. In addition, we measured the binding affinity of p50/RelA for DNA containing tandem κB sites and single κB sites. While the presence of the TAD enhanced the binding affinity of p50/RelA for all κB sequences tested, it also increased the affinity for nonspecific DNA sequences by over 10-fold, leading to an overall decrease in specificity for κB DNA sequences. In contrast, previous studies have generally reported that TADs decrease DNA-binding affinity and increase sequence specificity. Our results reveal a novel function of the RelA TAD in promoting binding to nonconsensus DNA, which sheds light on previous observations of extensive nonconsensus DNA binding by NFκB in vivo in response to strong inflammatory signals.

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Metadata

Authors
Baughman, H. E. R., Narang, D., Chen, W., Villagrán Suárez, A. C., Lee, J., Bachochin, M. J., Gunther, T. R., Wolynes, P. G., & Komives, E. A.
Affiliations
  • University of California San Diego (US)
  • Center for Theoretical Biological Physics (US)
Corresponding author
Komives, Elizabeth A.
ORCID
Venue
Journal of Biological Chemistry
Publisher
Elsevier BV
Published
2022-09
Volume
298
Issue
9
Pages
102349
ISSN
0021-9258 (ISSN-L)
DOI
10.1016/j.jbc.2022.102349
PMC
PMC9440430
OpenAlex
W4289994798
Cited by
27
References
5
Citations by year
2026: 3 · 2025: 6 · 2024: 9 · 2023: 8 · 2022: 1
FWCI
2.53
Type
journal article
Language
en
Open access
Licence
Locations
  • Journal of Biological Chemistry (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • eScholarship (California Digital Library) (submittedVersion, cc-by)
  • Rice Research Repository (Rice University) (submittedVersion, cc-by)
Funders
  • Rice University (C-0016)
  • G Harold and Leila Y Mathers Foundation (MF-2012–01149)
  • National Institutes of Health (PO1 GM071862)
  • American Cancer Society (PF-22-073-01-DMC)
  • G. Harold and Leila Y. Mathers Charitable Foundation (K12 GM068524)
  • National Institute of General Medical Sciences (P30 GM124169)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › NF-κB Signaling Pathways
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
intrinsically disordered proteins, transcription activation domain, DNA binding affinity, sequence specificity, coactivator binding, transcriptional activation
MeSH terms
Protein Domains, Base Sequence, DNA, Protein Binding, Transcriptional Activation, Transcription Factor RelA, NF-kappa B p50 Subunit, Protein Multimerization

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