CoChat
Sign Up
Cited by 3Plant Molecular Biology ResearchLight effects on plantsPlant Parasitism and Resistance

The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.

Diversification of functional requirements for proteolysis of auxin response factors

Open access
de Roij, Martijn, Heijdra, Esmée, Lamers, Jasper, Nishihama, Ryuichi, Borst, Jan Willem, Weijers, Dolf·2026·Nature Communications
DOI 10.1038/s41467-026-70440-0PMC PMC13128892

Published version of a preprint

Open this paper in CoChat — free accountOpen PDF

Abstract

Abstract Auxin signaling through the Nuclear Auxin Pathway is essential for plant development and is mediated by competing A-class and B-class Auxin Response Factor (ARF) transcription factors. Recently, proteasomal ARF degradation through a degradation signal embedded within the DNA-Binding Domain, was identified as a key component of auxin response. Here, we investigate the structural requirements and biological relevance of ARF degradation in the bryophyte Marchantia polymorpha . We identify a critical residue for proteolysis of the repressive, B-class MpARF2, and find it to be functionally conserved in degradation of the activating, A-class MpARF1. Unlike MpARF2, however, impaired MpARF1 degradation had little effect on auxin response and development, suggesting differential integration in biological function. We find that MpARF2 degradation occurs across all developmental stages of the life cycle, and is required for MpARF2 function during development. Our findings reveal a degradation mechanism targeting A- and B-class ARFs which shares the same origin, but has evolved along unique evolutionary trajectories.

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/s41467-026-70440-0

Cites

2 of 2 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

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

Research works printed but not linked: 36

  1. Vanneste, S., Pei, Y. & Friml, J. Mechanisms of auxin action in plant growth and development. Nat. Rev. Mol. Cell Biol. https://doi.org/10.1038/s41580-025-00851-2 (2025). · DOI
  2. Lavy, M. & Estelle, M. Mechanisms of auxin signaling. Development 143, 3226–3229 (2016). · DOI
  3. Chapman, E. J. & Estelle, M. Mechanism of auxin-regulated gene expression in plants. Annu Rev. Genet 43, 265–285 (2009). · DOI
  4. Gray, W. M., Kepinski, S., Rouse, D., Leyser, O. & Estelle, M. Auxin regulates SCF(TIR1)-dependent degradation of AUX/IAA proteins. Nature 414, 271–276 (2001). · DOI
  5. Dharmasiri, N., Dharmasiri, S. & Estelle, M. The F-box protein TIR1 is an auxin receptor. Nature 435, 441–445 (2005). · DOI · Paper page
  6. Kepinski, S. & Leyser, O. The Arabidopsis F-box protein TIR1 is an auxin receptor. Nature 435, 446–451 (2005). · DOI
  7. Ulmasov, T., Murfett, J., Hagen, G. & Guilfoyle, T. J. Aux/IAA proteins repress expression of reporter genes containing natural and highly active synthetic auxin response elements. Plant Cell 9, 1963–1971 (1997).
  8. Vernoux, T. et al. The auxin signalling network translates dynamic input into robust patterning at the shoot apex. Mol. Syst. Biol. 7, 508 (2011). · DOI · Paper page
  9. Roosjen, M., Paque, S. & Weijers, D. Auxin Response Factors: output control in auxin biology. J. Exp. Bot. 69, 179–188 (2018). · DOI
  10. Boer, D. R. et al. Structural basis for DNA binding specificity by the auxin-dependent ARF transcription factors. Cell 156, 577–589 (2014). · DOI
  11. Rienstra, J., Carrillo-Carrasco, V. P., de Roij, M., Hernandez-Garcia, J. & Weijers, D. A conserved ARF-DNA interface underlies auxin-triggered transcriptional response. Proc. Natl. Acad. Sci. USA 122, e2501915122 (2025). · DOI
  12. Kato, H. et al. Design principles of a minimal auxin response system. Nat. Plants 6, 473–482 (2020). · DOI
  13. Lavy, M. et al. Constitutive auxin response in Physcomitrella reveals complex interactions between Aux/IAA and ARF proteins. Elife 5 https://doi.org/10.7554/eLife.13325 (2016). · DOI
  14. de Roij, M., Borst, J. W. & Weijers, D. Protein degradation in the auxin response. Plant Cell https://doi.org/10.1093/plcell/koae125 (2024). · DOI
  15. Liu, L., Yahaya, B. S., Li, J. & Wu, F. Enigmatic role of auxin response factors in plant growth and stress tolerance. Front Plant Sci. 15, 1398818 (2024). · DOI
  16. Lakehal, A. et al. A Molecular Framework for the Control of Adventitious Rooting by TIR1/AFB2-Aux/IAA-Dependent Auxin Signaling in Arabidopsis. Mol. Plant 12, 1499–1514 (2019). · DOI
  17. Das, S. et al. Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination. Plant Commun, 101039 https://doi.org/10.1016/j.xplc.2024.101039 (2024). · DOI
  18. Jing, H. et al. Regulation of AUXIN RESPONSE FACTOR condensation and nucleo-cytoplasmic partitioning. Nat. Commun. 13, 4015 (2022). · DOI
  19. Prigge, M. J. et al. Comparative mutant analyses reveal a novel mechanism of ARF regulation in land plants. Nat. Plants 11, 821–835 (2025). · DOI
  20. de Roij, M., Hernandez Garcia, J., Das, S., Borst, J. W. & Weijers, D. ARF degradation defines a deeply conserved step in auxin response. Nat. Plants 11, 717–724 (2025). · DOI · Paper page
  21. Mutte, S. K. et al. Origin and evolution of the nuclear auxin response system. Elife 7 https://doi.org/10.7554/eLife.33399 (2018). · DOI
  22. Hernandez-Garcia, J. et al. Evolutionary origins and functional diversification of Auxin Response Factors. Nat. Commun. 15, 10909 (2024). · DOI · Paper page
  23. Romani, F. et al. The landscape of transcription factor promoter activity during vegetative development in Marchantia. Plant Cell 36, 2140–2159 (2024). · DOI
  24. Kato, H. et al. The Roles of the Sole Activator-Type Auxin Response Factor in Pattern Formation of Marchantia polymorpha. Plant Cell Physiol. 58, 1642–1651 (2017). · DOI
  25. Kato, H., Yasui, Y. & Ishizaki, K. Gemma cup and gemma development in Marchantia polymorpha. N. Phytol. 228, 459–465 (2020). · DOI
  26. Flores-Sandoval, E. et al. The B-class auxin response factor MpARF2 is essential for meristem organization in free-living plant gametophytes. Curr. Biol. https://doi.org/10.1016/j.cub.2025.11.015 (2025). · DOI
  27. Nishimura, T. et al. Yucasin is a potent inhibitor of YUCCA, a key enzyme in auxin biosynthesis. Plant J. 77, 352–366 (2014). · DOI
  28. Harris, B. J. et al. Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants. Nat. Ecol. Evol. 6, 1634–1643 (2022). · DOI · Paper page
  29. Zhao, S., Zhang, M. L., Ma, T. L. & Wang, Y. Phosphorylation of ARF2 Relieves Its Repression of Transcription of the K+ Transporter Gene HAK5 in Response to Low Potassium Stress. Plant Cell 28, 3005–3019 (2016). · DOI
  30. Salmon, J., Ramos, J. & Callis, J. Degradation of the auxin response factor ARF1. Plant J. 54, 118–128 (2008). · DOI
  31. Cavalleri, A. et al. Auxin-dependent post-translational regulation of MONOPTEROS in the Arabidopsis root. Cell Rep. 43, 115083 (2024). · DOI
  32. McFadden, W. M. & Yanowitz, J. L. idpr: A package for profiling and analyzing Intrinsically Disordered Proteins in R. PLoS One 17, e0266929 (2022). · DOI
  33. Sauret-Gueto, S. et al. Systematic Tools for Reprogramming Plant Gene Expression in a Simple Model, Marchantia polymorpha. ACS Synth. Biol. 9, 864–882 (2020). · DOI
  34. Ishizaki, K. et al. Development of gateway binary vector series with four different selection markers for the liverwort marchantia polymorpha. PLoS One 10, e0138876 (2015). · DOI
  35. Nishihama, R., Ishida, S., Urawa, H., Kamei, Y. & Kohchi, T. Conditional gene expression/deletion systems for marchantia polymorpha using its own heat-shock promoter and Cre/loxP-mediated site-specific recombination. Plant Cell Physiol. 57, 271–280 (2016). · DOI
  36. Kubota, A., Ishizaki, K., Hosaka, M. & Kohchi, T. Efficient agrobacterium-mediated transformation of the liverwort Marchantia polymorpha using regenerating thalli. Biosci. Biotechnol. Biochem. 77, 167–172 (2013). · DOI

Metadata

Authors
de Roij, M., Heijdra, E., Lamers, J., Nishihama, R., Borst, J. W., & Weijers, D.
Affiliations
  • Wageningen University & Research (NL)
  • Tokyo University of Science (JP)
Corresponding author
Weijers, Dolf
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2026-03-13
Volume
17
Issue
1
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-026-70440-0
PMC
PMC13128892
OpenAlex
W7135178000
Cited by
3
References
2
Citations by year
2026: 3
FWCI
11.10
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Socio-Environmental Systems Modeling (submittedVersion, cc-by-nc-nd)
Funders
  • Nederlandse Organisatie voor Wetenschappelijk Onderzoek
  • Japan Society for the Promotion of Science (JP20H04884, JP22H04733, JP18H04836)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Light effects on plants
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Parasitism and Resistance
Keywords
auxin response factor, proteasomal degradation, auxin signaling, Marchantia polymorpha, liverworts, bryophytes, DNA-binding domain, plant development, transcriptional repression
MeSH terms
Amino Acid Sequence, Indoleacetic Acids, Plant Proteins, Transcription Factors, Signal Transduction, Gene Expression Regulation, Plant, Marchantia, Proteolysis

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