Abstract
In Arabidopsis thaliana the root stem cell niche (SCN) is maintained by a complex regulatory network crucial for growth and developmental plasticity. However, many aspects of this network, particularly concerning stem cell quiescence and replenishment, remain unclear. Here, we investigate the interactions of key transcription factors (TFs) BRASSINOSTEROID AT VASCULAR AND ORGANIZING CENTRE (BRAVO), PLETHORA 3 (PLT3), and WUSCHEL-RELATED HOMEOBOX 5 (WOX5) in SCN maintenance. Analysis of mutants reveals their combinatorial regulation of cell fates and divisions in the SCN. In addition, studies using Fluorescence Resonance Energy Transfer Fluorescence Lifetime Imaging Microscopy (FRET-FLIM) in combination with novel analysis methods enable us to quantify protein–protein interaction (PPI) affinities and higher-order complex formation among these TFs. Our findings were integrated into a computational model, indicating that cell-type specific protein complex profiles and formations, influenced by prion-like domains in PLT3, play an important role in regulating the SCN. We propose that these unique protein complex signatures may serve as indicators of cell specificity, enriching the regulatory network that governs stem cell maintenance and replenishment in the Arabidopsis root.
| Original language | English |
|---|---|
| Pages (from-to) | 2323-2346 |
| Number of pages | 24 |
| Journal | EMBO Reports |
| Volume | 26 |
| Issue number | 9 |
| Early online date | 19 Mar 2025 |
| DOIs | |
| Publication status | Published - May 2025 |
Bibliographical note
Publisher Copyright:© The Author(s) 2025.
Funding
Large parts of the work and the manuscript are based on the published PhD thesis of VIS (Heinrich-Heine University, Duesseldorf). We would like to acknowledge funding of VIS by the Deutsche Forschungsgemeinschaft (DFG) through grant 432468382 to YS. MLGG is supported by the long-term program PlantXR: A new generation of breeding tools for extra-resilient crops (KICH3.LTP.20.005) which is financed by the Dutch Research Council (NWO), the Foundation for Food & Agriculture Research (FFAR), companies in the plant breeding and processing industry, and Dutch universities. These parties collaborate in the CropXR Institute (www.cropxr.org) that is funded through the National Growth Fund (NGF) of the Netherlands. We thank Rebecca C. Burkart for sharing PLT3, PLT3 Delta PrD, and WOX5 constructs and stable Arabidopsis lines. The authors thank Ana Cano-Delgado for sharing seeds of bravo-2 single and bravo-2 wox5-1 double mutants. The authors thank Kirsten ten Tusscher for insightful discussions on the modeling and Jan Kees van Amerongen for the management of computational facilities of the Theoretical Biology group (Utrecht University). The authors thank Cornelia Gieseler, Carin Theres and Silke Winters for technical assistance. The authors thank Meik H. Thiele for help with statistical analyses and data visualization with R. The authors also thank Jan E Maika for help with fitting FRET-FLIM data. The authors would like to acknowledge the Center for Advanced Imaging (CAi) at Heinrich-Heine-University Duesseldorf for providing access to the Zeiss LSM 780 and LSM 880 and especially Dr. Sebastian Haensch and Prof. Dr. Stefanie Weidtkamp-Peters for general support during imaging and analysis. Funding for instrumentation: Zeiss LSM 780: DFG- INST 208/551-1 FUGG and Zeiss LSM880: DFG- INST 208/746-1 FUGG. Furthermore, the authors thank Ksenia Kroo ss (NFDI4BIOIMAGE, DFG project ID 501864659) for help with metadata annotation and upload to the BioImage Archive repository.
| Funders | Funder number |
|---|---|
| Deutsche Forschungsgemeinschaft (DFG) | INST 208/746-1 FUGG, 501864659 |
| Dutch Research Council (NWO) | KICH3.LTP.20.005 |
| Foundation for Food & Agriculture Research (FFAR) | |
| National Growth Fund (NGF) of the Netherlands | |
| Not added | 432468382 |
| Not added | INST 208/551-1 FUGG |
Keywords
- FRET-FLIM
- Mathematical Modeling
- Root Stem Cell Niche
- Transcription Factor Complexes