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Cited by 46Plant Molecular Biology ResearchLight effects on plantsChromosomal and Genetic Variations

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Evolutionary origins and functional diversification of Auxin Response Factors

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Hernández-García, Jorge, Carrillo-Carrasco, Vanessa Polet, Rienstra, Juriaan, Tanaka, Keita, de Roij, Martijn, Dipp-Álvarez, Melissa, Freire-Ríos, Alejandra, Crespo, Isidro, Boer, Roeland, van den Berg, Willy A. M., Lindhoud, Simon, Weijers, Dolf·2024·Nature Communications
DOI 10.1038/s41467-024-55278-8PMC PMC11685440

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Abstract

The Auxin Response Factors (ARFs) family of transcription factors are the central mediators of auxin-triggered transcriptional regulation. Functionally different classes of extant ARFs operate as antagonistic auxin-dependent and -independent regulators. While part of the evolutionary trajectory to the present auxin response functions has been reconstructed, it is unclear how ARFs emerged, and how early diversification led to functionally different proteins. Here, we use in silico and in vivo analyses to revisit the molecular events that led to the origin and subsequent evolution of the ARFs. We reveal the shared origin of ARFs from preexisting domains, uncovering a protein fold homologous to the ARF DNA-binding fold in a conserved eukaryotic chromatin regulator. Building on this, we reconstruct the complete evolutionary history of ARFs, including the divergence events leading to the appearance of the ARF classes and defining the main molecular targets for their functional diversification. We derive a complete evolutionary trajectory that led to the emergence of the nuclear auxin signalling pathway.

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Metadata

Authors
Hernández-García, J., Carrillo-Carrasco, V. P., Rienstra, J., Tanaka, K., de Roij, M., Dipp-Álvarez, M., Freire-Ríos, A., Crespo, I., Boer, R., van den Berg, W. A. M., Lindhoud, S., & Weijers, D.
Affiliations
  • Wageningen University & Research (NL)
  • Chinese Academy of Sciences (CN)
  • ALBA Synchrotron (Spain) (ES)
Corresponding author
Weijers, Dolf
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2024-12-30
Volume
15
Issue
1
Pages
10909-10909
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-024-55278-8
PMC
PMC11685440
OpenAlex
W4405894752
Cited by
46
References
1
Citations by year
2026: 22 · 2025: 23 · 2024: 1
FWCI
11.23
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Socio-Environmental Systems Modeling (submittedVersion, cc-by)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • EC | Horizon 2020 Framework Programme (H2020-MSCA-IF-2020)
  • Nederlandse Organisatie voor Wetenschappelijk Onderzoek (GSGT.GSGT.2018.013, OCENW.KLEIN.027)
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 › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
Keywords
auxin response factor, auxin signaling, transcription factor evolution, functional diversification, protein fold evolution, chromatin regulation, phylogenetic inference
MeSH terms
Indoleacetic Acids, Phylogeny, Transcription Factors, Signal Transduction, Arabidopsis, Gene Expression Regulation, Plant, Evolution, Molecular, Arabidopsis Proteins

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