Biology subjects

Boudaoud, A.

Publications and source records attributed to Boudaoud, A..

At least 19 recordsLinked to original sources

bioRxiv2025

Dual role of the receptor kinase FERONIA in regulating tissue mechanics and growth

During morphogenesis, growing organisms adapt to internal and external mechanical stress. In plants, the receptor kinase FERONIA is involved in a broad range of responses to perturbations of the cell wall, but it is unclear which cues are sensed and how this sensing controls growth. Here, we addressed these questions in Marchantia vegetative propagules. We combined culture in microfluidic chips to quantify growth and mechanical properties of propagules, perturbations with osmotic treatments, characterisation of cell wall polysaccharides, and a mathematical model of cell wall expansion that incorporates sensing. We found that FERONIA independently regulates tissue mechanical properties and growth rates. We propose that the regulation of growth by the FERONIA pathway relies on both a positive feedback from elastic deformation of the wall and a negative feedback from wall expansion. Altogether, we expect our quantitative framework to be broadly relevant to the investigation of how mechanical cues guide development.

plant biology↗

bioRxiv2025

Inferring diffusion, reaction, and exchange parameters from imperfect FRAP

Fluorescence recovery after photobleaching (FRAP) is broadly used to investigate the dynamics of molecules in cells and tissues, notably to quantify diffusion coefficients. FRAP is based on the spatiotemporal imaging of fluorescent molecules following an initial bleaching of fluorescence in a region of the sample. Although a large number of methods have been developed to infer kinetic parameters from experiments, it is still a challenge to fully characterize molecular dynamics from noisy experiments in which diffusion is coupled to other molecular processes or in which the initial bleaching profile is not perfectly controlled. To address this challenge, we have developed HiFRAP to quantify the reaction-(or exchange-)diffusion kinetic parameters from FRAP under imperfect experimental conditions. HiFRAP is based on a low-rank approximation of a kernel related to the model Greens function and is implemented as an ImageJ/Python macro for (potentially curved) one-dimensional systems and for two-dimensional systems. To the best of our knowledge, HiFRAP offers features that have not been combined together: making no assumption on the initial bleaching profile, which does not need to be known; accounting for the limitation of the optical setup by diffraction; inferring several kinetic parameters from a single experiment; providing errors on parameter estimation; and testing model goodness. In the future, our approach could be applied to other dynamical processes described by linear partial differential equations, which could be useful beyond FRAP, in experiments where the concentration fields are monitored over space and time. SIGNIFICANCEFluorescence recovery after photobleaching (FRAP) is a microscopy approach that is widely used to investigate the diffusion and transport of molecules in life sciences and in material sciences. Numerous methods have been developed to derive kinetic parameters such as diffusion and binding coefficients. However, these methods suffer from limitations associated with experimental constraints, such as technical noise or an imperfectly known initial condition. To circumvent these limitations, we developed a comprehensive approach to estimate several kinetic parameters from a single experiment, to assess the precision of estimation, and to test whether the underlying model is well-suited. We implemented this approach in HiFRAP, an ImageJ/Python macro of broad applicability to one- and two-dimensional systems.

biophysics↗

bioRxiv2024

Mechanical regulation of tissue flatness in Marchantia

The production of flat organs involves a tight regulation of tissue expansion. During growth, the cell wall is under mechanical tension and continuous remodelling, requiring mechanisms to sense and maintain cell wall integrity (CWI). Here we studied the link between CWI sensing and flatness of Marchantia polymorpha thalli. We considered FERONIA (FER), a CWI sensor, and assessed its role in the maintenance of thallus shape. We developed a pipeline to quantify flatness at multiple scales. We found that both abolishing and increasing FER expression leads to loss of flatness. Based on experiments that reduce cell wall tension and partially restore wild-type cell size and thallus morphology, we ascribe loss of flatness to under- or to over-reaction of plants to mechanical stress. Altogether, our results support the concept that responses to mechanical stress contribute to the robustness of morphogenesis

plant biology↗

bioRxiv2023

Growth couples temporal and spatial fluctuations of tissue properties during morphogenesis

Living tissues display fluctuations - random spatial and temporal variations of tissue properties around their reference values - at multiple scales. It is believed that such fluctuations may enable tissues to sense their state or their size. Recent theoretical studies developed specific models of fluctuations in growing tissues and predicted that fluctuations of growth show long-range correlations. Here we elaborated upon these predictions and we tested them using experimental data. We first introduced a minimal model for the fluctuations of any quantity that has some level of temporal persistence or memory, such as concentration of a molecule, local growth rate, or mechanical property. We found that long-range correlations are generic, applying to any such quantity, and that growth couples temporal and spatial fluctuations, through a mechanism that we call fluctuation stretching -- growth enlarges the lengthscale of variation of this quantity. We then analysed growth data from sepals of the model plant Arabidopsis and we quantified spatial and temporal fluctuations of cell growth using the previously developed Cellular Fourier Transform. Growth appears to have long-range correlations. We compared different genotypes and growth conditions: mutants with lower or higher response to mechanical stress have lower temporal correlations and longer-range spatial correlations than wild-type plants. Finally, we used theoretical predictions to merge experimental data from all conditions and developmental stages into an unifying curve, validating the notion that temporal and spatial fluctuations are coupled by growth. Altogether, our work reveals kinematic constraints on spatiotemporal fluctuations that have an impact on the robustness of morphogenesis. Significance StatementHow do organs and organisms grow and achieve robust shapes in the face of subcellular and cellular variability? In order to address this outstanding mystery, we investigated the variability of growth at multiple scales and we analysed experimental data from growing plant tissues. Our results support the prediction that tissue expansion couples temporal memory of growth with spatial variability of growth. Our work reveals a constraint on the spatial and temporal variability of growth that may impact the robustness of morphogenesis.

biophysics↗

bioRxiv2023

Puzzle cell shape emerges from the interaction of growth with mechanical constraints

Puzzle-shaped epidermal cells not only reduce mechanical stress during organ growth but also record the expansion history of the tissue in their outlines. By combining mechanical simulations with time-lapse imaging, we show that transitions from directional to isotropic expansion induce new lobes to form along the previous growth axis, and that switching the order of anisotropic and isotropic phases yields hybrid shapes that reliably preserve those transitions. In maize, model predictions and live imaging coincide precisely, and in Ara-bidopsis, final lobe patterns correlate more with growth history than with cell size alone. Ge-netic or pharmacological disruption of lobe formation constrains leaf expansion or drives compensatory elongation, which underscores a mechanical function. A broad survey of living and fossil vascular plants reveals that the mechanism to make puzzle-shaped cells is both widespread and developmentally plastic, suggesting that single snapshots of leaves can give insight into their growth history. Together, these findings demonstrate that puzzle cells trans-form cell geometry into a living record of how tissues grow.

plant biology↗

bioRxiv2023

Assessing the link between tissue elasticity and plant growth

Multicellular organisms grow and acquire their shapes through the differential expansion and deformation of their cells. Recent research has addressed the role of cell and tissue mechanical properties in these processes. In plants, it is believed that growth rate is a function of the mechanical stress exerted on the cell wall, the thin polymeric layer surrounding cells, involving an effective viscosity. Nevertheless, recent studies have questioned this view, suggesting that cell wall elasticity sets growth rate or that uptake of water is limiting for plant growth. To assess these issues, we developed a microfluidic device to quantify growth rates, elastic properties, and hydraulic conductivity of individual Marchantia polymorpha plants in a controlled environment with a high throughput. We characterized the effect of osmotic treatment and of abscisic acid on growth and hydromechanical properties. Overall, the instantaneous growth rate of individuals is correlated to both bulk elastic modulus and hydraulic conductivity. Our results are consistent with a framework in which growth rate is determined primarily by elasticity of the wall and its remodelling, and secondarily by hydraulic conductivity. Accordingly, the coupling between chemistry of the cell wall and hydromechanics of the cell appears as key to set growth patterns during morphogenesis.

biophysics↗

bioRxiv2023

Chimeric identities and reduced stiffness characterise the shoot apex of Arabidopsis stem cell mutants

Stem cell homeostasis in the shoot apical meristem involves a core regulatory feedback loop between the signalling peptide CLAVATA3, produced in stem cells, and the transcription factor WUSCHEL, expressed in the underlying organising centre. clavata mutants display massive meristem overgrowth, which is thought to be caused by stem cell overproliferation, although it is unknown how uncontrolled stem cell divisions lead to this altered morphology. Here we first reveal local buckling defects in mutant meristems, and use analytical models to show how mechanical properties and growth rates may contribute to the phenotype. Indeed, clavata meristems are mechanically more heterogeneous than the wild type, and also display regional growth heterogeneities. Furthermore, stereotypical wild-type meristem organisation is lost in mutants, in which cells simultaneously express distinct fate markers. Finally, cells in mutant meristems are auxin responsive, suggesting that they are functionally different from wild-type stem cells. Thus all benchmarks show that clavata meristem cells are different from wild-type stem cells, suggesting that fasciation is caused by the disruption of a more complex regulatory framework that maintains distinct genetic and functional domains at the shoot apex. Summary statementHeterogeneities in cell mechanics, growth, function and identity contribute to buckling in clavata mutant shoot apices.

plant biology↗

bioRxiv2023

Growth directions and stiffness across cell layers determine whether tissues stay smooth or buckle

From smooth shapes to buckles, nature exhibits organs of various shapes and forms. How cells grow to produce smooth shaped leaves and sepals remain unclear. Here, we show that growth along the longitudinal axis during early developmental stages and comparable stiffness across both epidermal layers of Arabidopsis sepals are essential for smoothness, as seen in the wild type. We identified a mutant (as2-7D) with ectopic expression of ASYMMETRIC LEAVES 2 (AS2) on the outer epidermis. Our analysis reveals that ectopic AS2 expression causes the outer epidermis of as2-7D sepals to buckle during early stages of sepal development. We show that buckling of the outer epidermis occurs due to conflicting cell growth directions and unequal tissue stiffness across the epidermal layers. Overexpression of cyclin-dependent kinase (CDK) inhibitor Kip-related protein 1 (KRP1) in as2-7D restores sepal smoothness by aligning the growth directions of the outer epidermal cells along the longitudinal axis, while also increasing the overall stiffness of the outer epidermis. Furthermore, buckling is associated with the convergence of auxin efflux transporter protein PIN-FORMED 1 (PIN1) to generate outgrowth in the sepals at later stages, suggesting that buckling can initiate outgrowths. Our findings suggest that in addition to molecular cues influencing tissue mechanics, tissue mechanics can also modulate molecular signals, giving rise to well-defined shapes. One-Sentence SummaryThe asymmetric leaves 2-7D mutant sepals buckle due to discoordination of growth between the two epidermal layers.

developmental biology↗

bioRxiv2023

A mechanohydraulic model supports a role for plasmodesmata in cotton fiber elongation

Plant cell growth depends on turgor pressure, the cell hydrodynamic pressure, which drives expansion of the extracellular matrix (the cell wall). Turgor pressure regulation depends on several physical, chemical and biological factors, including: vacuolar invertases, which modulate osmotic pressure of the cell, aquaporins, which determine the permeability of the plasma membrane to water, cell wall remodeling factors, which determine cell wall extensibility (inverse of effective viscosity), and plasmodesmata, which are membrane-lined channels that allow free movement of water and solutes between cytoplasms of neighbouring cells, like gap junctions in animals. Plasmodesmata permeability varies during plant development and experimental studies have correlated changes in the permeability of plasmodesmal channels to turgor pressure variations. Here we study the role of plasmodesmal permeability in cotton fiber growth, a type of cell that increases in length by at least 3 orders of magnitude in a few weeks. We incorporated plasmodesma-dependent movement of water and solutes into a classical model of plant cell expansion. We performed a sensitivity analysis to changes in values of model parameters and found that plasmodesmal permeability is among the most important factors for building up turgor pressure and expanding cotton fibers. Moreover, we found that non-monotonic behaviors of turgor pressure that have been reported previously in cotton fibers cannot be recovered without accounting for dynamic changes of the parameters used in the model. Altogether, our results suggest an important role for plasmodesmal permeability in the regulation of turgor pressure. Significance StatementThe cotton fiber is among the plant cells with the highest growth rates. In cultivars, a single fiber cell generally reaches a few centimeters in length. How such size is achieved is still poorly understood. In order to tackle this question, we built a comprehensive mathematical model of fiber elongation, considering cell mechanics and water entry into the cell. Model predictions agree with experimental observations, provided that we take into account active opening and closure of plasmodesmata, the nano-channels that connect the fiber with neighboring cells. Because cotton fiber length is a key factor for yarn quality, our work may help understanding the mechanisms behind an important agronomic trait.

developmental biology↗

bioRxiv2022

Spatial consistency of cell growth direction during organ morphogenesis requires CELLULOSE-SYNTHASE INTERACTIVE1

Extracellular matrices generally contain fibril-like polymers that may be organized in parallel arrays. Although their role in morphogenesis has been long recognized, it is still unclear how the subcellular control of fibril synthesis translates into well-defined organ shape. Here, we addressed this question using the Arabidopsis sepal as a model organ. In plants, cell growth is driven by turgor pressure and restrained by the extracellular matrix known as the cell wall. Cellulose is the main load-bearing component of the plant cell wall and cellulose microfibrils are thought to channel growth perpendicularly to their main orientation. Given the key function of CELLULOSE SYNTHASE INTERACTIVE 1 (CSI1) in guidance of cellulose synthesis, we investigated the role of CSI1 in sepal morphogenesis. We observed that sepals from csi1 mutants are shorter, although their newest cellulose microfibrils are more aligned compared to wild type. Surprisingly, cell growth anisotropy was similar in csi1 and wild-type plants. We resolved this apparent paradox using polarized Raman microspectroscopy, live imaging of growing sepals, and bespoke mechanical assays. We found that CSI1 is required for spatial consistency of growth direction across the sepal and for the maintenance of overall organ elongation. Our work illustrates how the subcellular regulation of the extracellular matrix may control morphogenesis at multiple scales.

developmental biology↗

bioRxiv2022

Cell Wall Dynamics in a Filamentous Fungus

Hyphal tip growth allows filamentous fungi to colonize space, reproduce or infect. It features remarkable morphogenetic plasticity including unusually fast elongation rates, tip turning, branching or bulging. These shape changes are all driven from the expansion of a protective cell wall (CW) secreted from apical pools of exocytic vesicles. How CW secretion, remodeling and deformation are modulated in concert to support rapid tip growth and morphogenesis while ensuring surface integrity remains poorly understood. We implemented sub-resolution imaging to map the dynamics of CW thickness and secretory vesicles in Aspergillus nidulans. We found that tip growth is associated with balanced rates of CW secretion and expansion, which limit temporal fluctuations in CW thickness, elongation speed and vesicle amount, to less than 10-15%. Affecting this balance through modulations of growth or trafficking yield to near-immediate changes in CW thickness, mechanics and shape. We developed a model with mechanical feedback which accounts for steady states of hyphal growth as well as rapid adaptation of CW mechanics and vesicle recruitment to different perturbations. These data provide unprecedented details on how CW dynamics emerges from material secretion and expansion, to stabilize fungal tip growth as well as promote its morphogenetic plasticity.

cell biology↗

bioRxiv2022

Robustness of organ morphology is associated with modules of co-expressed genes related to plant cell wall

Control of organ morphology is a fundamental feature of living organisms. There is, however, observable variation in organ size and shape within a given genotype. Taking the sepal of Arabidopsis as a model, we investigated whether we can use variability of gene expression alongside variability of organ morphology to identify gene regulatory networks potentially involved in organ size and shape determination. We produced a dataset composed of morphological parameters and genome-wide transcriptome obtained from 27 individual sepals from wild-type plants with nearly identical genetic backgrounds, environment, and developmental stage. Sepals exhibited appreciable variability in both morphology and transcriptome, with response to stimulus genes and cell-wall related genes displaying high variability in expression. We additionally identified five modules of co-expressed genes which correlated significantly with morphology, revealing biologically relevant gene regulatory networks. Interestingly, cell-wall related genes were overrepresented in two of the top three modules. Overall, our work highlights the benefit of using coupled variation in gene expression and phenotype in wild-type plants to shed light on the mechanisms underlying organ size and shape determination. Although causality between gene expression and sepal morphology has not been established, our approach opens the way to informed analysis for mutant characterization and functional studies.

plant biology↗

bioRxiv2021

INTEGUMENT-SPECIFIC TRANSCRIPTIONAL REGULATION IN THE MID- STAGE OF FLAX SEED DEVELOPMENT INFLUENCES THE RELEASE OF MUCILAGE AND THE SEED OIL CONTENT

Flax (Linum usitatissimum L.) seed oil, which accumulates in the embryo, and mucilage, which is synthesized in the seed coat, are of great economic importance for food, pharmaceutical as well as chemical industries. Theories on the link between oil and mucilage production in seeds consist in the spatio-temporal competition of both compounds for photosynthates during the very early stages of seed development. In this study, we demonstrate a positive relationship between seed oil production and seed coat mucilage extrusion in the agronomic model, flax. Three recombinant inbred lines were selected for low, medium and high mucilage and seed oil contents. Metabolite and transcript profiling (1H NMR and DNA oligo-microarrays) was performed on the seeds during seed development. These analyses showed main changes in the seed coat transcriptome during the mid-phase of seed development (25 Days Post-Anthesis), once the mucilage biosynthesis and modification processes are thought to be finished. These transcriptome changes comprised genes that are putatively involved in mucilage chemical modification and oil synthesis, as well as gibberellic acid (GA) metabolism. The results of these integrative biology approach, suggest that transcriptional regulations of seed oil and fatty acid (FA) metabolism could occur in the seed coat during the mid-stage of seed development, once the seed coat carbon supplies have been used for mucilage biosynthesis and mechanochemical properties of the mucilage secretory cells.

plant biology↗

bioRxiv2021

Dandelion pappus morphing is actuated by radially patterned material swelling

Plants can generate motion by absorbing and releasing water. Such motion often facilitates reproductive success through the dispersal of seeds and fruits or their self-burial into the soil. Asteraceae plants, such as the dandelion, often have a hairy pappus attached to their fruits to allow them to fly and in many cases, these can open and close depending on moisture levels to modify dispersal. Here we demonstrate the relationship between structure, composition and function of the underlying hygroscopic actuator. By investigating the structure and properties of the actuator cell walls we have identified the mechanism by which the dandelion pappus closes and developed a structural computational model that can capture observed pappus closing. This model was used to explore the contribution of differential material domains in the actuator function and the critical design features. We find that the actuator relies on the radial arrangement of vascular bundles and surrounding tissues including cortex and the floral podium around a central cavity. This allows heterogeneous swelling in a radially symmetric manner to co-ordinate precise movements of the pappus hairs attached at the upper flank. This actuator is a derivative of bilayer structures, but is radial and can synchronise the movement of a planar or lateral attachment. The simple, material-based mechanism presents a promising biomimetic potential in robotics and functional materials.

bioengineering↗

bioRxiv2021

The pH-dependent processivity of Arabidopsis AtPME2 can control cell wall mechanical properties

Pectin methylesterases (PMEs) modify homogalacturonans (HG) chemistry and play a key role in regulating primary cell wall mechanical properties. How PME activity can fine-tune pectin structure in the growing plant has remained elusive. Here we report on the Arabidopsis AtPME2, which we found to be highly expressed during lateral root emergence and dark-grown hypocotyl elongation. We produced the mature active enzyme using heterologous expression in Pichia pastoris and characterized it through the use of a generic plant PME antiserum suitable for detecting recombinant and native enzyme independent of species source. At neutral pH AtPME2 is preferentially active on pectins with a degree of 55-70% methylesterification and can be inhibited by PME inhibitor protein (PMEI). We show that the mode of action for AtPME2 can switch from full processivity (at pH 8), creating large blocks of unmethylated galacturonic acid, to low processivity (at pH 5) and relate these observations to the differences in electrostatic potential of the protein at acidic and alkaline pH. To assess the role of AtPME2 in development, we characterized two knock-out lines. We show that in the context of acidified apoplast, low-processive demethylesterification by AtPME2 can loosen the cell wall, with consequent increase in cell elongation and etiolated hypocotyl length. Our study brings insights into how the pH-dependent regulation by PME activity could affect pectin structure and associated cell wall mechanical properties in expansion. One sentence summaryThe processivity of AtPME2, a pectin methylesterase that fine-tunes cell wall pectins is modulated by pH in vitro and impacts the mechanical properties of the wall, affecting development in planta.

plant biology↗

bioRxiv2020

Developmental constraints modulate reproductive fate and plasticity within the Arabidopsis ovule primordium

In multicellular organisms, sexual reproduction requires the separation of the germline from the soma. In flowering plants, the first cells of the germline, so-called spore mother cells (SMCs), differentiate as the reproductive organs form. Here, we explored how organ growth influences and contributes to SMC differentiation. We generated a collection of 92 annotated 3D images capturing ovule primordium ontogeny at cellular resolution in Arabidopsis. We identified a spatio-temporal pattern of cell divisions that acts in a domain-specific manner as the primordium forms, which is coupled with the emergence of a single SMC. Using tissue growth models, we uncovered plausible morphogenetic principles involving a spatially confined growth signal, differential mechanical properties, and cell growth anisotropy. Our analysis also reveals that SMC characteristics first arise in more than one cell but SMC fate becomes progressively restricted to a single cell during organ growth. Altered primordium geometry coincided with a delay in this fate restriction process in katanin mutants. Altogether, our study suggests that tissue geometry canalizes and modulates reproductive cell fate in the Arabidopsis ovule primordium.

plant biology↗

bioRxiv2020

Timing of organ initiation is crucial for robust organ size

AbstractOrgans precisely regulate their size and shape to ensure proper function1-6. The contribution of organ initiation timing to final organ size and shape is often masked by compensatory adjustments to growth later in development7-9. Here we show that DEVELOPMENT RELATED MYB-LIKE1 (DRMY1) is required for both proper organ initiation timing and growth leading to robust sepal size in Arabidopsis. Within each drmy1 flower, the initiation of some sepals is variably delayed. Late-initiating sepals in drmy1 mutants remain smaller throughout development resulting in variability in sepal size. DRMY1 focuses the spatiotemporal signaling patterns of the plant hormones auxin and cytokinin, which jointly control the timing of sepal initiation. Contrary to expectation, our findings demonstrate that timing of organ initiation contributes to robust organ size throughout development.

plant biology↗

bioRxiv2019

Strain- or Stress-sensing in mechanochemical patterning by the phytohormone auxin

Both chemical and mechanical fields are known to play a major role in morphogenesis. In plants, the phytohormone auxin and its directional transport are essential for the formation of robust patterns of organs, such as flowers or leaves, known as phyllotactic patterns. The transport of auxin was recently shown to be affected by mechanical signals, and conversely, auxin accumulation in incipient organs affects the mechanical properties of the cells. The precise interaction between mechanical fields and auxin transport, however, is poorly understood. In particular, it is unknown whether transport is sensitive to the strain or to the stress exerted on a given cell. Here, we investigate the nature of this coupling with the help of theoretical models. Namely, we introduce the effects of either mechanical stress or mechanical strain in a model of auxin transport, and compare the patterns predicted with available experimental results, in which the tissue is perturbed by ablations, chemical treatments, or genetic manipulations. We also study the robustness of the patterning mechanism to noise and investigate the effect of a shock that changes abruptly its parameters. Although the model predictions with the two different feedbacks are often indistinguishable, the strain-feedback seems to better agree with some of the experiments. The computational modeling approach used here, which enables us to distinguish between several possible mechanical feedbacks, offers promising perspectives to elucidate the role of mechanics in tissue development, and may help providing insight into the underlying molecular mechanisms.

plant biology↗