CoChat
Sign Up
Cited by 23

The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.

The disordered p53 transactivation domain is the target of FOXO4 and the senolytic compound FOXO4-DRI

Bourgeois, Benjamin, Spreitzer, Emil, Platero-Rochart, Daniel, Paar, Margret, Zhou, Qishun, Usluer, Sinem, de Keizer, Peter L. J., Burgering, Boudewijn M. T., Sánchez-Murcia, Pedro A., Madl, Tobias·2025·Nature Communications
DOI 10.1038/s41467-025-60844-9
Open this paper in CoChat — free account

Abstract

A central process contributing to the phenotype of aging is cellular senescence. We recently identified the FOXO4 – p53 axis as pivotal in maintaining the viability of senescent cells, and that senescent cells can be targeted selectively with the senolytic peptide FOXO4-DRI. Here, we solve the solution NMR structural models of the p53 transactivation domain in complex with the FOXO4 forkhead domain and in complex with FOXO4-DRI. Strikingly, we find that the disordered FOXO4-DRI binds to the disordered p53 TAD2 and forms a transiently folded complex. In this complex, both, the FOXO4-derived region and the cationic cell permeability peptide contribute to the interaction. Furthermore, we show that p53 phosphorylation enhances the affinity for both FOXO4 and FOXO4-DRI. Summarizing we provide a detailed characterization of the interaction of p53 with FOXO4 and FOXO4-DRI which is the basis for development of p53 inhibitors to treat diseases linked to cellular senescence such as cancers.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41467-025-60844-9

Cites

8 of 8 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Show all 8 references

Research works printed but not linked: 58

  1. Soto-Gamez, A. & Demaria, M. Therapeutic interventions for aging: the case of cellular senescence. Drug Discov. Today 22, 786–795 (2017). · DOI · Paper page
  2. Zhang, C. et al. FOXO4-DRI alleviates age-related testosterone secretion insufficiency by targeting senescent Leydig cells in aged mice. Aging12, 1272–1284 (2020). · DOI
  3. Huang, Y., He, Y., Makarcyzk, M. J. & Lin, H. Senolytic peptide FOXO4-DRI selectively removes senescent cells from. Front. Bioeng. Biotechnol. 9, 677576 (2021). · DOI · Paper page
  4. Han, X. et al. FOXO4 peptide targets myofibroblast ameliorates bleomycin-induced pulmonary fibrosis in mice through ECM-receptor interaction pathway. J. Cell Mol. Med. 26, 3269–3280 (2022). · DOI
  5. Levine, A. J. p53: 800 million years of evolution and 40 years of discovery. Nat. Rev. Cancer 20, 471–480 (2020). · DOI
  6. Hassin, O. & Oren, M. Drugging p53 in cancer: one protein, many targets. Nat. Rev. Drug Discov. 22, 127–144 (2023). · DOI
  7. Muller, P. A. & Vousden, K. H. p53 mutations in cancer. Nat. Cell Biol. 15, 2–8 (2013). · DOI · Paper page
  8. Boutelle, A. M. & Attardi, L. D. p53 and tumor suppression: it takes a network. Trends Cell Biol. 31, 298–310 (2021). · DOI
  9. Sun X., Dyson H. J. & Wright P. E. A phosphorylation-dependent switch in the disordered p53 transactivation domain regulates DNA binding. Proc. Natl. Acad. Sci. USA 118, e2021456118 (2021). · DOI
  10. He, F. et al. Interaction between p53 N terminus and core domain regulates specific and nonspecific DNA binding. Proc. Natl. Acad. Sci. USA 116, 8859–8868 (2019). · DOI
  11. Van Orden, K., Giebler, H. A., Lemasson, I., Gonzales, M. & Nyborg, J. K. Binding of p53 to the KIX domain of CREB binding protein. A potential link to human T-cell leukemia virus, type I-associated leukemogenesis. J. Biol. Chem. 274, 26321–26328 (1999). · DOI
  12. Rowell, J. P., Simpson, K. L., Stott, K., Watson, M. & Thomas, J. O. HMGB1-facilitated p53 DNA binding occurs via HMG-Box/p53 transactivation domain interaction, regulated by the acidic tail. Structure 20, 2014–2024 (2012). · DOI
  13. Rajagopalan, S., Andreeva, A., Teufel, D. P., Freund, S. M. & Fersht, A. R. Interaction between the transactivation domain of p53 and PC4 exemplifies acidic activation domains as single-stranded DNA mimics. J. Biol. Chem. 284, 21728–21737 (2009). · DOI
  14. Rajagopalan, S., Andreeva, A., Rutherford, T. J. & Fersht, A. R. Mapping the physical and functional interactions between the tumor suppressors p53 and BRCA2. Proc. Natl. Acad. Sci. USA 107, 8587–8592 (2010). · DOI
  15. Kussie, P. H. et al. Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science 274, 948–953 (1996). · DOI · Paper page
  16. Usluer, S. et al. Disordered regions mediate the interaction of p53 and MRE11. Biochim. Biophys. Acta Mol. Cell Res. 1871, 119654 (2024). · DOI · Paper page
  17. Usluer S., Spreitzer E., Bourgeois B. & Madl T. p53 transactivation domain mediates binding and phase separation with poly-PR/GR. Int. J. Mol. Sci. 22, 11431 (2021). · DOI
  18. Mandal, R. et al. FOXO4 interacts with p53 TAD and CRD and inhibits its binding to DNA. Protein Sci. 31, e4287 (2022). · DOI
  19. Kim, J., Ahn, D. & Park, C. J. Biophysical investigation of the dual binding surfaces of human transcription factors FOXO4 and p53. FEBS J. 289, 3163–3182 (2022). · DOI
  20. Hannenhalli, S. & Kaestner, K. H. The evolution of Fox genes and their role in development and disease. Nat. Rev. Genet. 10, 233–240 (2009). · DOI
  21. Eijkelenboom, A. & Burgering, B. M. FOXOs: signalling integrators for homeostasis maintenance. Nat. Rev. Mol. Cell Biol. 14, 83–97 (2013). · DOI
  22. Hu, W. et al. Roles of forkhead box O (FoxO) transcription factors in neurodegenerative diseases: a panoramic view. Prog. Neurobiol. 181, 101645 (2019). · DOI
  23. Ludikhuize, M. C. & Rodriguez Colman, M. J. Metabolic regulation of stem cells and differentiation: a forkhead box O transcription factor perspective. Antioxid. Redox Signal. 34, 1004–1024 (2021). · DOI
  24. Calissi, G., Lam, E. W. & Link, W. Therapeutic strategies targeting FOXO transcription factors. Nat. Rev. Drug Discov. 20, 21–38 (2021). · DOI
  25. Gui, T. & Burgering, B. M. T. FOXOs: masters of the equilibrium. FEBS J. 289, 7918–7939 (2022). · DOI
  26. Rodriguez-Colman, M. J., Dansen, T. B. & Burgering, B. M. T. FOXO transcription factors as mediators of stress adaptation. Nat. Rev. Mol. Cell Biol. 25, 46–64 (2024). · DOI
  27. Bourgeois, B. & Madl, T. Regulation of cellular senescence via the FOXO4-p53 axis. FEBS Lett. 592, 2083–2097 (2018). · DOI
  28. Spreitzer, E. et al. FOXO transcription factors differ in their dynamics and intra/intermolecular interactions. Curr. Res. Struct. Biol. 4, 118–133 (2022). · DOI
  29. Psenakova K. et al. Forkhead domains of FOXO transcription factors differ in both overall conformation and dynamics. Cells 8, 966 (2019). · DOI
  30. Wang, F. et al. Biochemical and structural characterization of an intramolecular interaction in FOXO3a and its binding with p53. J. Mol. Biol. 384, 590–603 (2008). · DOI
  31. Chen, Y., Dey, R. & Chen, L. Crystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer. Structure 18, 246–256 (2010). · DOI
  32. Hartlmüller, C., Spreitzer, E., Göbl, C., Falsone, F. & Madl, T. NMR characterization of solvent accessibility and transient structure in intrinsically disordered proteins. J. Biomol. NMR 73, 305–317 (2019). · DOI
  33. Jenkins, L. M., Durell, S. R., Mazur, S. J. & Appella, E. p53 N-terminal phosphorylation: a defining layer of complex regulation. Carcinogenesis 33, 1441–1449 (2012). · DOI
  34. Shan, B., Li, D. W., Bruschweiler-Li, L. & Bruschweiler, R. Competitive binding between dynamic p53 transactivation subdomains to human MDM2 protein: implications for regulating the p53.MDM2/MDMX interaction. J. Biol. Chem. 287, 30376–30384 (2012). · DOI
  35. Boura, E., Rezabkova, L., Brynda, J., Obsilova, V. & Obsil, T. Structure of the human FOXO4-DBD-DNA complex at 1.9Å resolution reveals new details of FOXO binding to the DNA. Acta Crystallogr. D. Biol. Crystallogr. 66, 1351–1357 (2010). · DOI
  36. Bourgeois, B. et al. Multiple regulatory intrinsically disordered motifs control FOXO4 transcription factor binding and function. Cell Rep. 36, 109446 (2021). · DOI
  37. Choi, Y. et al. FOXL2 and FOXA1 cooperatively assemble on the TP53 promoter in alternative dimer configurations. Nucleic Acids Res. 50, 8929–8946 (2022). · DOI
  38. Renault, V. M. et al. The pro-longevity gene FoxO3 is a direct target of the p53 tumor suppressor. Oncogene 30, 3207–3221 (2011). · DOI
  39. Kamagata, K. et al. Rational design using sequence information only produces a peptide that binds to the intrinsically disordered region of p53. Sci. Rep. 9, 8584 (2019). · DOI
  40. Smeenk, L. et al. Role of p53 serine 46 in p53 target gene regulation. PLoS ONE 6, e17574 (2011). · DOI
  41. Li, H. H., Li, A. G., Sheppard, H. M. & Liu, X. Phosphorylation on Thr-55 by TAF1 mediates degradation of p53: a role for TAF1 in cell G1 progression. Mol. Cell 13, 867–878 (2004). · DOI
  42. Schrempf, A. et al. POLtheta processes ssDNA gaps and promotes replication fork progression in BRCA1-deficient cells. Cell Rep. 41, 111716 (2022). · DOI
  43. Skinner, S. P. et al. CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis. J. Biomol. NMR 66, 111–124 (2016). · DOI
  44. Massi, F., Grey, M. J. & Palmer, A. G. 3rd Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR R1rho relaxation experiments. Protein Sci. 14, 735–742 (2005). · DOI
  45. Baldwin, A. J. & Kay, L. E. An R(1rho) expression for a spin in chemical exchange between two sites with unequal transverse relaxation rates. J. Biomol. NMR 55, 211–218 (2013). · DOI
  46. Battiste, J. L. & Wagner, G. Utilization of site-directed spin labeling and high-resolution heteronuclear nuclear magnetic resonance for global fold determination of large proteins with limited nuclear overhauser effect data. Biochemistry 39, 5355–5365 (2000). · DOI
  47. Simon, B., Madl, T., Mackereth, C. D., Nilges, M. & Sattler, M. An efficient protocol for NMR-spectroscopy-based structure determination of protein complexes in solution. Angew. Chem. Int. Ed. Engl. 49, 1967–1970 (2010). · DOI
  48. Linge, J. P., Habeck, M., Rieping, W. & Nilges, M. ARIA: automated NOE assignment and NMR structure calculation. Bioinformatics 19, 315–316 (2003). · DOI
  49. Weigelt, J., Climent, I., Dahlman-Wright, K. & Wikström, M. Solution structure of the DNA binding domain of the human forkhead transcription factor AFX (FOXO4). Biochemistry 40, 5861–5869 (2001). · DOI
  50. Shen, Y. & Bax, A. Protein structural information derived from NMR chemical shift with the neural network program TALOS-N. Methods Mol. Biol. 1260, 17–32 (2015). · DOI
  51. Tian, C. et al. ff19SB: amino-acid-specific protein backbone parameters trained against quantum mechanics energy surfaces in solution. J. Chem. Theory Comput. 16, 528–552 (2020). · DOI
  52. Izadi, S., Anandakrishnan, R. & Onufriev, A. V. Building water models: a different approach. J. Phys. Chem. Lett. 5, 3863–3871 (2014). · DOI
  53. Homeyer, N., Horn, A. H., Lanig, H. & Sticht, H. AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine. J. Mol. Model. 12, 281–289 (2006). · DOI
  54. Case, D. A. et al. AmberTools. J. Chem. Inf. Model. 63, 6183–6191 (2023). · DOI
  55. Gonzalez-Aleman, R. et al. BitQT: a graph-based approach to the quality threshold clustering of molecular dynamics. Bioinformatics 38, 73–79 (2021). · DOI
  56. Husic, B. E. & Pande, V. S. Markov state models: from an art to a science. J. Am. Chem. Soc. 140, 2386–2396 (2018). · DOI
  57. Noe, F. & Clementi, C. Kinetic distance and kinetic maps from molecular dynamics simulation. J. Chem. Theory Comput. 11, 5002–5011 (2015). · DOI
  58. Scherer, M. K. et al. PyEMMA 2: a software package for estimation, validation, and analysis of Markov models. J. Chem. Theory Comput. 11, 5525–5542 (2015). · DOI

Cited by

Sorted by citations

See all 23

Metadata

Authors
Bourgeois, B., Spreitzer, E., Platero-Rochart, D., Paar, M., Zhou, Q., Usluer, S., de Keizer, P. L. J., Burgering, B. M. T., Sánchez-Murcia, P. A., & Madl, T.
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2025-07-01
Volume
16
Issue
1
ISSN
2041-1723
DOI
10.1038/s41467-025-60844-9
Cited by
23
References
8
Language
en
Licence
Funders
  • Austrian Science Fund (10.55776/COE14, 10.55776/P28854, 10.55776/I3792, 10.55776/DOC130, 10.55776/W1226)
  • Österreichische Forschungsförderungsgesellschaft (864690, 870454, 912192)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review