Biology subjects

de Roij, M.

Publications and source records attributed to de Roij, M..

4 recordsLinked to original sources

bioRxiv2025

Diversification of functional requirements for proteolysis of Auxin Response Factors

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.

plant biology↗

bioRxiv2024

ARF degradation defines a deeply conserved step in auxin response

Auxin response critically depends on the concentrations and stoichiometry of competing A- and B-class AUXIN RESPONSE FACTOR (ARF) proteins. In Marchantia polymorpha, both A- and B-ARFs are unstable, and here we identify a minimal necessary and sufficient region for ARF degradation that is critical for development, and auxin response. Through comparative analysis, we find that ARF instability likely preceded the emergence of the auxin response system.

plant biology↗

bioRxiv2024

Evolutionary Origins and Functional Diversification of Auxin Response Factors

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.

plant biology↗

bioRxiv2022

Selective degradation of ARF monomers controls auxin response in Marchantia

The plant signaling molecule auxin controls a variety of growth and developmental processes in land plants. Auxin regulates gene expression through a nuclear auxin signaling pathway (NAP) consisting of a ubiquitin ligase auxin receptor TIR1/AFB, its Aux/IAA degradation substrate, and the DNA-binding ARF transcription factors. While extensive qualitative understanding of the pathway and its interactions has been obtained by studying the flowering plant Arabidopsis thaliana, it is so far unknown how these translate to quantitative system behaviour in vivo, a problem that is confounded by large NAP gene families in this 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 knock-in fluorescent fusion proteins. Beyond revealing the native accumulation profile of the entire NAP protein network, we discovered that the two central ARFs MpARF1 and MpARF2 are proteasomally degraded. This degradation serves two functions: it tunes the stoichiometry of auxin-responsive, positively acting MpARF1 and auxin-independent, negatively acting MpARF2, thereby permitting auxin response. Secondly, through mapping a minimal degradation motif, we found that degradation is likely selective for MpARF2 monomers and favours accumulation of dimers. Interfering with MpARF1:MpARF2 stoichiometry or preventing degradation of MpARF2 monomers caused strong growth defects associated with auxin response defects. Thus, quantitative analysis of the entire Marchantia NAP, allowed to identify a novel regulatory mechanism in auxin response, built on regulated ARF degradation.

plant biology↗