Biology subjects

Dumas, R.

Publications and source records attributed to Dumas, R..

9 recordsLinked to original sources

bioRxiv2026

Structural Evolution of LEAFY Reveals DNA-Mediated Cooperativity and Dimerization Shifts at the Water-to-Land Transition

The evolution of transcription factor (TF) DNA-binding specificity is a major driver of gene regulatory innovation. Unlike most TFs, which diversify through gene duplication and neofunctionalization, the plant-specific LEAFY (LFY) TF evolved novel binding specificities without extensive duplication. Here, we combine experimental structural determination and biochemical assays to reveal how LFYs dimerization and DNA-binding preferences shifted during the water-to-land transition. We present crystal structures of the LFY DNA-binding domain (DBD) from the hornwort Nothoceros aenigmaticus and the alga Interfilum paradoxum bound to DNA, demonstrating two distinct dimerization mechanisms: one mediated by direct protein-protein interactions and another driven by DNA-mediated cooperativity. In the ancestral state, LFY likely bound DNA as a dimer through DNA-mediated cooperativity, with protein-protein dimerization emerging later, enforcing new DNA-binding preferences. Our findings support a revised evolutionary scenario for LFY, highlighting the dynamic interplay between protein-DNA and protein-protein interactions as key drivers of TF binding specificity. This work deepens our understanding of how structural adaptations in TFs underpin evolutionary transitions in gene regulation.

plant biology↗

bioRxiv2024

RF Channel-Based Adaptive Beamforming for 3D Ultrasound Localization Microscopy

Ultrasound Localization Microscopy (ULM) has been applied in various preclinical settings and in the clinic to reveal the microvasculature in deep organs. However, most ULM images employ standard Delay-and-Sum (DAS) beamforming. In standard ULM conditions, lengthy acquisition times are required to fully reconstruct small vessels due to the need for spatially isolated microbubbles, resulting in low temporal resolution. When microbubbles are densely packed, localizing a point spread function with significant main and side lobes becomes challenging due to matrix arrays low signal-to-noise ratio and spatial resolution. In this work, we applied adaptive beamforming such as high order DAS known as (pDAS), Coherence Factor (CF), Coherence Factor with Gaussian Filtering (CFGF), and statistical interpretation of beamforming (iMAP) to provide a more complete 3D ULM maps in vitro and in vivo (rat kidney). Specifically, the CF and 1MAP adaptive beamformers achieved higher resolution (32.9 microns and 27.2 microns respectively), as measured by the Fourier Shell Correlation (FSC), compared to the standard DAS beamformer, which had an FSC value of 38.6 microns.

physiology↗

bioRxiv2023

The ALOG domain defines a new family of plant-specific transcription factors acting during Arabidopsis flower development

The ALOGs (Arabidopsis LIGHT-DEPENDENT SHORT HYPOCOTYLS 1 and Oryza G1) are Transcription Factors (TFs) from an evolutionarily conserved plant-specific family shown to play critical roles in meristem identity, inflorescence architecture and organ boundaries in diverse species from mosses to higher flowering plants. However, the DNA binding-specificity and molecular determinants of protein-DNA interactions of this family were uncharacterized. Using in vitro genome-wide studies, we identified the conserved DNA motif bound by ALOG proteins from the liverwort Marchantia polymorpha and the flowering plants Arabidopsis, tomato and rice. In order to determine the amino acids responsible for DNA-binding specificity, we solved the 2.1[A] structure of the ALOG DNA binding domain in complex with its cognate DNA. The ALOG DBD is an all-alpha helical domain with a structural zinc ribbon insertion and an N-terminal disordered NLS. The NLS sequence forms an integral part of the DNA binding domain and contributes to direct base read-out. To define the function of a group of redundant ALOG proteins in the model plant Arabidopsis thaliana, we generated a series of alog mutants and uncovered their participation in a gene regulatory network involving the other floral regulators LEAFY, BLADE-ON-PETIOLE and PUCHI, all active in defining boundary regions between reproductive meristems and repressing bracts development. Taken together, this work provides the biochemical and structural basis for DNA-binding specificity of an evolutionarily conserved TF family and reveals its role as a key player in defining organ boundaries in Arabidopsis. Significance StatementTranscription Factors (TFs) are key proteins that bind specific regions in the genome and regulate the expression of associated genes. Not all organisms possess the same set of TFs and some, like the ALOGs, are specific to the plant kingdom. These TFs have been shown to play important roles from mosses to flowering plants. However, it was not known what DNA motif they recognize and how they bind DNA. Here we identify this motif, we show it is widely conserved in evolution and we understand how this new type of DNA binding domain works at the structural level. In addition, we also show that several ALOG genes from Arabidopsis share a redundant function within the genetic network underlying correct floral meristem development.

plant biology↗

bioRxiv2022

Plant-TFClass: a structural classification for plant transcription factors

Transcription factors (TFs) bind DNA at specific sequences to regulate gene expression. This universal process is achieved thanks to the DNA-binding domain (DBD) present in each TF. DBDs show a vast diversity of protein folds within and across organisms, ranging from simple long basic alpha helices to complex structural combinations of alpha, beta and loop folds. In mammals, the structural conformation of the DBDs and the way it establishes contact with DNA has been used to organize TFs in a hierarchical classification named TFClass. However, such classification is missing from plants that possess many DBD types absent from mammals. Here, we reviewed the numerous TF DBD 3D-structures and models available for plants to organize all plant TFs types following the TFClass hierarchy (Superclass/Class/Family/Subfamily). We classified most of the 55 recognized plant TF types within the existing TFClass framework. This extended classification led us to add six new classes and 34 new families corresponding to TF DBD structures absent in mammals. Plant-TFClass provides a unique resource for TF and TF binding sites comparison across TF families and across organisms.

plant biology↗

bioRxiv2022

Accuracy of a markerless motion capture system for balance related quantities

BackgroundBalance studies usually focus on quantities describing the global body motion, such as the position of the whole-body centre of mass (CoM), its associated extrapolated centre of mass (XCoM) and the whole-body angular momentum (WBAM). Assessing such quantities using classical marker-based approach can be tedious and modify the participants behaviour. The recent development of markerless motion capture methods could bypass the issues related to the use of markers. Research questionCan we use markerless motion capture systems to study quantities that are relevant for balance studies? MethodsSixteen young healthy participants performed four different motor tasks: walking at self-selected speed, balance loss, walking on a narrow beam and countermovement jumps. Their movements were recorded simultaneously by marker-based and markerless motion capture systems. Videos were processed using a commercial markerless pose estimation software, Theia3D. The position of their CoM was computed, and the associated XCoM and WBAM were derived. Bland-Altman analysis was performed and root mean square error and coefficient of determination were computed to compare the results obtained with marker-based and markerless methods across all participants and tasks. ResultsBias remained of the magnitude of a few mm for CoM and XCoM position, and RMSE of CoM and XCoM was around 1 cm. Confidence interval for CoM and XCoM was under 2 cm except for one task in one direction. RMSE of the WBAM was less than 8% of the total amplitude in any direction, and bias was less than 1%. SignificanceResults suggest that the markerless motion capture system can be used in balance studies as the measured errors are in the range of the differences found between different models or populations in the literature. Nevertheless, one should be careful when assessing dynamic movements such as jumping, as they displayed the biggest errors. HighlightsO_LIMarkerless motion capture could bypass issues from classical marker-based approaches C_LIO_LIWe compared balance related quantities computed from both approaches C_LIO_LIMean differences were about 1cm on the position of the whole-body center of mass C_LIO_LIObtained differences are acceptable for most applications C_LI

bioengineering↗

bioRxiv2022

Description, Development and Dissemination of Two Consistent Marker-based and Markerless Multibody Models

In human movement analysis, multibody models are an indispensable part of the process both for marker-based and video-based markerless approaches. Constituents (segments, joint constraints, body segment inertial parameters etc.) of such models and modelers choice play an important role in the accuracy of estimated results (segmental and joint kinematics, segmental and whole-body center of mass positions etc.). For marker-based method, although standard models exist, particularly for the lower extremity (e.g., Conventional Gait Model or models embedded in OpenSim), there seems to be a lack of consolidated explanation on the constituents of the whole-body model. For the markerless approach, multibody kinematic models (e.g., the Theia3D model) have been in use lately. However, there is no clear explanation on the estimated quantities (e.g., joint centers, body surface landmarks etc.) and their relation to the underlying anatomy. This also motivates the need for a description of the markerless multibody model. Moreover, comparing markerless results to those of classical marker-based method is currently the most commonly used approach for evaluation of markerless approaches. This study first aims to develop and describe a whole-body marker-based model ready to be used for human movement analysis. Second, the markerless multibody model embedded in Theia3D is described and inertial parameters are redefined. We also report assessment of the markerless approach compared to marker-based method for a static T-pose performed by 15 subjects. Finally, we disseminate the marker-based and markerless multibody models for their use in Visual3D.

bioengineering↗

bioRxiv2021

The LEAFY floral regulator displays pioneer transcription factor properties

Pioneer transcription factors (TFs) are a special category of TFs with the capacity to bind to closed chromatin regions in which DNA is wrapped around histones and often highly methylated. Subsequently, they are able to modify the chromatin state to initiate gene expression. In plants, LEAFY (LFY) is a master floral regulator and has been suggested to act as a pioneer TF in Arabidopsis. Here, we demonstrate that LFY is able to bind both methylated and non-methylated DNA using a combination of in vitro genome-wide binding experiments and structural modeling. Comparisons between regions bound by LFY in vivo and chromatin accessibility data suggest that LFY binds a subset of regions occupied by nucleosomes. We confirm that LFY is able to bind nucleosomal DNA in vitro using reconstituted nucleosomes. Finally, we show that constitutive LFY expression in seedling tissues is sufficient to induce chromatin accessibility in the LFY direct target genes, APETALA1 and AGAMOUS. Taken together, our study suggests that LFY possesses key pioneer TF features that contribute to launch the floral gene expression program.

plant biology↗

bioRxiv2018

Origin of gibberellin-dependent transcriptional regulation by molecular exploitation of a transactivation domain in DELLA proteins

DELLA proteins are land-plant specific transcriptional regulators known to interact through their C-terminal GRAS domain with over 150 transcription factors in Arabidopsis thaliana. Besides, DELLAs from vascular plants can interact through the N-terminal domain with the gibberellin receptor encoded by GID1, through which gibberellins promote DELLA degradation. However, this regulation is absent in non-vascular land plants, which lack active gibberellins or a proper GID1 receptor. Current knowledge indicates that DELLAs are important pieces of the signalling machinery of vascular plants, especially angiosperms, but nothing is known about DELLA function during early land plant evolution or if they exist at all in charophytan algae. We have now elucidated the evolutionary origin of DELLA proteins, showing that algal GRAS proteins are monophyletic and evolved independently from those of land plants, which explains why there are no DELLAs outside land plants. DELLA genes have been maintained throughout land plant evolution with only two major duplication events kept among plants. Furthermore, we show that the features needed for DELLA interaction with the receptor were already present in the ancestor of all land plants, and propose that these DELLA N-terminal motifs have been tightly conserved in non-vascular land plants for their function in transcriptional co-activation, which allowed subsequent exaptation for the interaction with the GID1 receptor when vascular plants developed gibberellin synthesis and the corresponding perception module.

evolutionary biology↗

bioRxiv2018

Capturing auxin response factors syntax using DNA binding models

Auxin is a key hormone performing a wealth of functions throughout the plant life cycle. It acts largely by regulating genes at the transcriptional level through a family of transcription factors (TF) called auxin response factors (ARF). Even if all ARF monomers analysed so far bind a similar DNA sequence, there is evidence that ARFs differ in their target genomic regions and regulated genes. Here we use position weight matrices (PWM) to model ARF DNA binding specificity based on published DNA affinity purification sequencing (DAP-seq) data. We find that the genome binding of two ARFs (ARF2 and ARF5/Monopteros/MP) differ largely because these two factors have different preferred ARF binding site (ARFbs) arrangements (orientation and spacing). We illustrate why PWMs are more versatile to reliably identify ARFbs than the widely used consensus sequences and demonstrate their power with biochemical experiments on the regulatory regions of the IAA19 model gene. Finally, we combined gene regulation by auxin with ARF-bound regions and identified specific ARFbs configurations that are over-represented in auxin up-regulated genes, thus deciphering the ARFbs syntax functional for regulation. This provides a general method to exploit the potential of genome-wide DNA binding assays and decode gene regulation.

plant biology↗