Chloe Zubieta Tel. : 04 38 78 06 54 Laboratoire Physiologie Cellulaire & Végétale CEA-Grenoble 17 avenue des Martyrs 38 054 Grenoble cedex 9 France

The StrucDev team is dedicated to uncovering the molecular mechanisms that drive plant development and environmental response. Over the past decade, we have integrated structural biology and biophysics approaches to reveal how protein structure of transcription factors and coregulators dictates gene regulation. Our research focuses on key transcriptional complexes involved in flowering, reproductive development, and temperature sensing.

The team has produced seminal studies on the role of the MADS transcription factors in flower development. Our pioneering work on MADS transcription factors provided critical insights into floral organ development and evolution. In addition to continuing these studies on the molecular mechanisms of plant reproduction, we have recently started work of the field of temperature sensing and liquid-liquid phase separation using an integrated structural, biophysical and transgenic approach. These projects are the main ongoing studies in the lab.

 ​© C. Morel / CNRS

Structural determinants of MADS function and evo-devo 

Flower morphology is orchestrated by master regulators of organ identity—MADS transcription factors (TFs), a key focus of Dr. Hugouvieux's research. MADS TFs are highly conserved across all eukaryotes. A fundamental question our team has been investigating for over a decade is how these complexes achieve their highly specific and diverse gene regulatory functions despite sharing a remarkably conserved domain structure - particularly in their DNA-binding domain. ​

 ​© C. Morel / CNRS

While MADS TF complexes exhibit differential DNA binding, the underlying mechanisms driving this specificity remain a mystery. To address this, we have taken an integrated structure-function approach. Our research has shown that in Arabidopsis, the functional identity of MADS tetrameric complexes is dictated by a small domain that governs protein-protein interaction specificity at the level of the dimer and a plant-specific coiled-coil domain that allows the formation of higher order tetrameric complexes. These interactions influence the selection of DNA binding sites and the intersite spacing between binding sites, ultimately determining the function of the MADS transcriptional complex. 

Our work has elucidated the atomic and molecular determinants of function, revealing how the selection of protein partners and the formation of higher-order transcriptional complexes are crucial for their physiological role.

By combining structural biology with transgenic approaches, we have provided unique insights into the molecular mechanisms underlying TF complex formation in plant reproductive development. This integrative strategy has positioned StrucDev as a leader in the study of MADS transcription factor function in triggering organ development in plants. ​

 ​© C. Morel / CNRS

Building on this work, we are now investigating tetramerization in seed plants and exploring whether male and female organ identity complexes from evolutionarily distant species are functionally equivalent. this research, we aim to uncover the fundamental principles that drive transcriptional specificity in plant reproductive development.

Liquid-liquid phase separation as a mechanism for thermosensing​

The past decade has seen an unprecedented streak of record-breaking temperatures, with each of the last ten years ranking among the hottest on record. In 2024, global temperatures surpassed the 1.5°C threshold above pre-industrial levels. As sessile organisms, plants continuously sense and respond to even small temperature fluctuations, adjusting key developmental processes such as flowering time, seed production, and biomass accumulation. The effects of global warming have profound consequences, yet the underlying molecular mechanisms plants use to sense temperature remain poorly understood.

 ​© C. Morel / CNRS

Dr. Hutin leads our research on plant thermosensing mechanisms, focusing on the molecular organization and function of EARLY FLOWERING 3 (ELF3), a key thermosensory protein in Arabidopsis thaliana. ELF3 is largely an intrinsically disordered protein that functions as a scaffold in forming the Evening Complex (EC)—a transcriptional repressor composed of ELF3, the DNA-binding protein LUX ARRHYTHMO, and the adapter protein ELF4. Remarkably, ELF3 undergoes phase separation (PS) as a function of temperature in vitro and in vivo. PS leads to the derepression of EC target genes that regulate elongation growth and flowering. This work represents one of the first direct demonstrations of thermosensing via protein condensation in plants and constitutes a foundational study in the field of PS.

Building on this discovery, Dr. Hutin and soon-to-be-recruited thesis students and postdocs are now investigating the molecular and structural dynamics of other proteins, mainly transcription factors and regulators, that undergo PS. By integrating structural biology, biophysics, and biochemical approaches, we aim to trace the effects of phase separation from the molecular to the organismal level, including phenotypic consequences in plant mutants. This research will provide crucial insights into temperature-dependent gene regulation and plant adaptation to a warming climate.

Contributions to Methods and Protocols for the Scientific Community

Methods development is a central focus of our team, driving innovation in structural biology, biophysics, and computational approaches. Over the past five years, we have published more than ten methodological advancements, including refined small-angle X-ray scattering (SAXS) techniques (collaboration with Dr. Mark Tully, European Synchrotron Radiation Facility, ESRF), optimized DNA-affinity purification and sequencing protocols in collaboration with the Floral Regulators Team, and new band shift assays to study how temperature affects transcriptional complex-DNA interactions in vitro.         

​   ​   ​© C. Morel / CNRS​

Additionally, we have developed improved fluorescence recovery after photobleaching (FRAP) protocols, allowing for precise analysis of liquid droplets and phase separation dynamics. 

Recently, in collaboration with Dr. Max Nanao at the ESRF, we have applied AI-based structure prediction using AlphaFold to model multimeric protein complexes. By integrating experimental yeast two-hybrid and mass spectrometry data, we have enhanced the accuracy of complex formation predictions, opening new avenues for understanding protein-protein interactions.

These methodological advancements not only strengthen our own research but also provide valuable tools for the broader scientific community, pushing the boundaries of molecular plant biology.​​