@article{19601,
  abstract     = {In land plants, the signalling molecule auxin profoundly controls growth and development, chiefly through a transcriptional response system. The auxin response is mediated by modulating the activity of DNA-binding auxin response factor (ARF) proteins. The concentrations and stoichiometry of the competing A- and B-class ARFs define cells’ capacity for auxin response. In the minimal auxin response system of the liverwort Marchantia polymorpha, both A- and B-ARFs are unstable, but the underlying mechanisms, developmental relevance and evolutionary history of this instability are unknown. Here we identify a minimal motif that is necessary for MpARF2 (B-class) degradation and show that it is critical for development and the auxin response. Through comparative analysis and motif swaps among all ARF classes in extant algae and land plants, we infer that the emergence of ARF instability probably occurred in the ancestor of the A- and B-ARF clades and, therefore, preceded or coincided with the origin of the auxin response system.},
  author       = {De Roij, Martijn and Hernández García, Jorge and Das, Shubhajit and Borst, Jan Willem and Weijers, Dolf},
  issn         = {2055-0278},
  journal      = {Nature Plants},
  pages        = {717--724},
  publisher    = {Springer Nature},
  title        = {{ARF degradation defines a deeply conserved step in auxin response}},
  doi          = {10.1038/s41477-025-01975-1},
  volume       = {11},
  year         = {2025},
}

@article{17436,
  abstract     = {The auxin signaling molecule controls a variety of growth and developmental processes in land plants. Auxin regulates gene expression through a nuclear auxin signaling pathway (NAP) consisting of the ubiquitin ligase auxin receptor TIR1/AFB, its Aux/IAA degradation substrate, and DNA-binding ARF transcription factors. Although extensive qualitative understanding of the pathway and its interactions has been obtained, mostly by studying the flowering plant Arabidopsis thaliana, it remains unknown how these translate to quantitative system behavior in vivo, a problem that is confounded by the large NAP gene families in most species. Here, we used the minimal NAP of the liverwort Marchantia polymorpha to quantitatively map NAP protein accumulation and dynamics in vivo through the use of knockin fluorescent fusion proteins. Beyond revealing the dynamic native accumulation profile of the entire NAP protein network, we discovered that the two central ARFs, MpARF1 and MpARF2, are proteasomally degraded. This auxin-independent degradation tunes ARF protein stoichiometry to favor gene activation, thereby reprogramming auxin response during the developmental progression. Thus, quantitative analysis of the entire NAP has enabled us to identify ARF degradation and the stoichiometries of activator and repressor ARFs as a potential mechanism for controlling gemma germination.},
  author       = {Das, Shubhajit and De Roij, Martijn and Bellows, Simon and Alvarez, Melissa Dipp and Mutte, Sumanth and Kohlen, Wouter and Farcot, Etienne and Weijers, Dolf and Borst, Jan Willem},
  issn         = {2590-3462},
  journal      = {Plant Communications},
  number       = {11},
  publisher    = {Elsevier},
  title        = {{Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination}},
  doi          = {10.1016/j.xplc.2024.101039},
  volume       = {5},
  year         = {2024},
}