Quantifying cell shape and gene expression in the shoot apical meristem using MorphoGraphX

Pectin methylesterification state and cell wall mechanical properties contribute to neighbor proximity-induced hypocotyl growth in Arabidopsis

Plants growing with neighbors compete for light and consequently increase the growth of their vegetative organs to enhance access to sunlight. This response, called shade avoidance syndrome (SAS), involves photoreceptors such as phytochromes as well as phytochrome interacting factors (PIFs), which regulate the expression of growth-mediating genes. Numerous cell wall-related genes belong to the putative targets of PIFs, and the importance of cell wall modifications for enabling growth was extensively shown in developmental models such as dark-grown hypocotyl. However, the contribution of the cell wall in the growth of de-etiolated seedlings regulated by shade cues remains poorly established. Through analyses of mechanical and biochemical properties of the cell wall coupled with transcriptomic analysis of cell wall-related genes from previously published data, we provide evidence suggesting that cell wall modifications are important for neighbor proximity-induced elongation. Further analysis using loss-of-function mutants impaired in the synthesis and remodeling of the main cell wall polymers corroborated this. We focused on the cgr2cgr3 double mutant that is defective in methylesterification of homogalacturonan (HG)-type pectins. By following hypocotyl growth kinetically and spatially and analyzing the mechanical and biochemical properties of cell walls, we found that methylesterification of HG-type pectins was required to enable global cell wall modifications underlying neighbor proximity-induced hypocotyl growth. Collectively, our work suggests that plant competition for light induces changes in the expression of numerous cell wall genes to enable modifications in biochemical and mechanical properties of cell walls that contribute to neighbor proximity-induced growth.

Quantitative Live Confocal Imaging in AquilegiaFloral Meristems

In this study, we present a detailed protocol for live imaging and quantitative analysis of floral meristem development in Aquilegia coerulea, a member of the buttercup family (Ranunculaceae). Using confocal microscopy and the image analysis software MorphoGraphX, we were able to examine the cellular growth dynamics during floral organ primordia initiation, and the transition from floral meristem proliferation to termination. This protocol provides a powerful tool to study the development of the meristem and floral organ primordia, and should be easily adaptable to many plant lineages, including other emerging model systems. It will allow researchers to explore questions outside the scope of common model systems.

Multi-Angle In Vivo Imaging of the Arabidopsis thaliana Shoot Apical Meristem (SAM)

Fluorescent imaging, especially in living tissue, has become a key method in modern life sciences, with the development of new tools for sample preparation, imaging, and data analysis continuously advancing our understanding of biological principles. Here, we present our strategy for in vivo imaging of the Arabidopsis shoot apical meristem (SAM), a central structure in plant development. We implement simplifications to previously published workflows and present a novel approach to subsequentially image the meristem from multiple angles at high resolution. This tool may represent a valuable resource for shoot meristem-centered research in general, but also for studies on plasmodesmata or intercellular connectivity within the SAM: via the analysis of fluorescently labeled plasmodesmata-localized proteins, via the tracing of fluorescent dyes, via analyzing the cell-to-cell mobility of fluorescently labeled proteins, but also via the analysis of morphological features of meristematic cells in mutants or upon perturbation of symplastic connectivity.

Cell fate coordinates mechano-osmotic forces in intestinal crypt formation

Intestinal organoids derived from single cells undergo complex crypt-villus patterning and morphogenesis. However, the nature and coordination of the underlying forces remains poorly characterized. Here, using light-sheet microscopy and large-scale imaging quantification, we demonstrate that crypt formation coincides with a stark reduction in lumen volume. We develop a 3D biophysical model to computationally screen different mechanical scenarios of crypt morphogenesis. Combining this with live-imaging data and multiple mechanical perturbations, we show that actomyosin-driven crypt apical contraction and villus basal tension work synergistically with lumen volume reduction to drive crypt morphogenesis, and demonstrate the existence of a critical point in differential tensions above which crypt morphology becomes robust to volume changes. Finally, we identified a sodium/glucose cotransporter that is specific to differentiated enterocytes that modulates lumen volume reduction through cell swelling in the villus region. Together, our study uncovers the cellular basis of how cell fate modulates osmotic and actomyosin forces to coordinate robust morphogenesis.

Imaging flowers: a guide to current microscopy and tomography techniques to study flower development

Developmental biology relies heavily on our ability to generate three-dimensional images of live biological specimens through time, and to map gene expression and hormone response in these specimens as they undergo development. The last two decades have seen an explosion of new bioimaging technologies that have pushed the limits of spatial and temporal resolution and provided biologists with invaluable new tools. However, plant tissues are difficult to image, and no single technology fits all purposes; choosing between many bioimaging techniques is not trivial. Here, we review modern light microscopy and computed projection tomography methods, their capabilities and limitations, and we discuss their current and potential applications to the study of flower development and fertilization.

Methods to Visualize Auxin and Cytokinin Signaling Activity in the Shoot Apical Meristem

Visualizing the distribution of hormone signaling activity such as auxin and cytokinins is of key importance for understanding regulation of plant development and physiology. Live imaging and genetically encoded hormone biosensors and reporters allow monitoring the spatial and temporal distribution of these phytohormones. Here, we describe how to cultivate live shoot apical meristems after dissection for observation under the confocal microscope for up to 4 days. The shoot apical meristems are maintained on an appropriate medium allowing them to grow and initiate new organs at a frequency similar to plants grown on soil. Meristems expressing hormone biosensors and reporters allows following hormone signaling activity distribution at high spatiotemporal resolution without chemical fixation, an approach that that can also be applied to follow the dynamics of expression in vivo of any fluorescent marker.

WUSCHEL acts as an auxin response rheostat to maintain apical stem cells in Arabidopsis

To maintain the balance between long-term stem cell self-renewal and differentiation, dynamic signals need to be translated into spatially precise and temporally stable gene expression states. In the apical plant stem cell system, local accumulation of the small, highly mobile phytohormone auxin triggers differentiation while at the same time, pluripotent stem cells are maintained throughout the entire life-cycle. We find that stem cells are resistant to auxin mediated differentiation, but require low levels of signaling for their maintenance. We demonstrate that the WUSCHEL transcription factor confers this behavior by rheostatically controlling the auxin signaling and response pathway. Finally, we show that WUSCHEL acts via regulation of histone acetylation at target loci, including those with functions in the auxin pathway. Our results reveal an important mechanism that allows cells to differentially translate a potent and highly dynamic developmental signal into stable cell behavior with high spatial precision and temporal robustness.

Spatial control of auxin signaling maintains a balance between stem-cell self-renewal and differentiation at the plant shoot apex. Here Ma et al. show that rheostatic control of auxin response by the WUSCHEL transcription factor maintains stem cells by conferring resistance to auxin mediated differentiation.

Quantifying Plant Growth and Cell Proliferation with MorphoGraphX

Confocal microscopy is widely used to live-image plant tissue. Cell outlines can be visualized using fluorescent probes that mark the cell wall or plasma membrane, enabling the confocal microscope to be used as a 3D scanner with submicron precision. After imaging, the data needs to be analyzed by specialized software to quantify the features of interest, such as cell size and shape, growth rates and anisotropy, and gene expression. Here we present a protocol for the 3D image processing software MorphoGraphX ( www.MorphoGraphX.org ) using time-lapse images of an Arabidopsis thaliana sepal and the shoot apex of tomato.

Morphogenesis and Compartmentalization of the Intestinal Crypt

The adult mammalian intestine is composed of two connected structures, the absorptive villi and the crypts, which house progenitor cells. Mouse crypts develop postnatally and are the architectural unit of the stem cell niche, yet the pathways that drive their formation are not known. Here, we combine transcriptomic, quantitative morphometric, and genetic analyses to identify mechanisms of crypt development. We uncover the upregulation of a contractility gene network at the earliest stage of crypt formation, which drives myosin II-dependent apical constriction and invagination of the crypt progenitor cells. Subsequently, hinges form, compartmentalizing crypts from villi. Hinges contain basally constricted cells, and this cell shape change was inhibited by increased hemidesmosomal adhesion in Rac1 null mice. Loss of hinges resulted in reduced villar spacing, revealing an unexpected role for crypts in tissue architecture and physiology. These studies provide a framework for studying crypt morphogenesis and identify essential regulators of niche formation.

In Situ Proximity Ligation Assay to Detect the Interaction Between Plant Transcription Factors and Other Regulatory Proteins

In plants, a lot of transcription factors fulfill their roles in gene regulation through the interaction with other regulatory proteins and co-factors. Thus, confirmation of protein-protein interaction is key to understand the precise function of transcription factors. Many methods have been developed to investigate the protein-protein interaction in vivo and in vitro. In situ Proximity Ligation Assay (PLA) is an innovative method to test protein-protein interaction in your tissues or cells of interest in vivo. Furthermore, this method allows us to detect transient interaction and low-abundance protein interaction with single molecule resolution. In this chapter, we describe a detailed protocol for the study of interaction between plant transcription factors and other regulatory proteins, in the scale of single nuclei of plant organ, tissues and cells.

Live Confocal Imaging of Developing Arabidopsis Flowers

The study of plant growth and development has long relied on experimental techniques using dead, fixed tissues and lacking proper cellular resolution. Recent advances in confocal microscopy, combined with the development of numerous fluorophores, have overcome these issues and opened the possibility to study the expression of several genes simultaneously, with a good cellular resolution, in live samples. Live confocal imaging provides plant biologists with a powerful tool to study development, and has been extensively used to study root growth and the formation of lateral organs on the flanks of the shoot apical meristem. However, it has not been widely applied to the study of flower development, in part due to challenges that are specific to imaging flowers, such as the sepals that grow over the flower meristem, and filter out the fluorescence from underlying tissues. Here, we present a detailed protocol to perform live confocal imaging on live, developing Arabidopsis flower buds, using either an upright or an inverted microscope.

DRACO-STEM: An Automatic Tool to Generate High-Quality 3D Meshes of Shoot Apical Meristem Tissue at Cell Resolution

Context: The shoot apical meristem (SAM), origin of all aerial organs of the plant, is a restricted niche of stem cells whose growth is regulated by a complex network of genetic, hormonal and mechanical interactions. Studying the development of this area at cell level using 3D microscopy time-lapse imaging is a newly emerging key to understand the processes controlling plant morphogenesis. Computational models have been proposed to simulate those mechanisms, however their validation on real-life data is an essential step that requires an adequate representation of the growing tissue to be carried out. Achievements: The tool we introduce is a two-stage computational pipeline that generates a complete 3D triangular mesh of the tissue volume based on a segmented tissue image stack. DRACO (Dual Reconstruction by Adjacency Complex Optimization) is designed to retrieve the underlying 3D topological structure of the tissue and compute its dual geometry, while STEM (SAM Tissue Enhanced Mesh) returns a faithful triangular mesh optimized along several quality criteria (intrinsic quality, tissue reconstruction, visual adequacy). Quantitative evaluation tools measuring the performance of the method along those different dimensions are also provided. The resulting meshes can be used as input and validation for biomechanical simulations. Availability: DRACO-STEM is supplied as a package of the open-source multi-platform plant modeling library OpenAlea (http://openalea.github.io/) implemented in Python, and is freely distributed on GitHub (https://github.com/VirtualPlants/draco-stem) along with guidelines for installation and use.

The Specification of Geometric Edges by a Plant Rab GTPase Is an Essential Cell-Patterning Principle During Organogenesis in Arabidopsis

Plant organogenesis requires control over division planes and anisotropic cell wall growth, which each require spatial patterning of cells. Polyhedral plant cells can display complex patterning in which individual faces are established as biochemically distinct domains by endomembrane trafficking. We now show that, during organogenesis, the Arabidopsis endomembrane system specifies an important additional cellular spatial domain: the geometric edges. Previously unidentified membrane vesicles lying immediately beneath the plasma membrane at cell edges were revealed through localization of RAB-A5c, a plant GTPase of the Rab family of membrane-trafficking regulators. Specific inhibition of RAB-A5c activity grossly perturbed cell geometry in developing lateral organs by interfering independently with growth anisotropy and cytokinesis without disrupting default membrane trafficking. The initial loss of normal cell geometry can be explained by a failure to maintain wall stiffness specifically at geometric edges. RAB-A5c thus meets a requirement to specify this cellular spatial domain during organogenesis.

Breaking the mold: understanding the evolution and development of lateral organs in diverse plant models

The formation of complex three-dimensional shape differs significantly between plants and animals due to the presence of the cell wall in the former, which prevents all cell migration. Instead, in lateral plant organs such as leaves or petals, shape is controlled by a series of developmental phases in which the organ acquires polarity, cells undergo proliferation, and, lastly, cells expand to their final shape and size. Although these processes were first described based on mutagenesis approaches in major model systems like Arabidopsis thaliana, further insight into their complexity is best provided by studies of natural variation in organ shape in alternative model systems that sample a broader range of plant form. Weaving together work from both forward and evolutionary genetics, this review focuses on how modification in polarity establishment, cell proliferation and cell expansion drives modifications in the fundamental lateral organ developmental program to create diversity in shape.

Regulation of Meristem Morphogenesis by Cell Wall Synthases in Arabidopsis

The cell walls of the shoot apical meristem (SAM), containing the stem cell niche that gives rise to the above-ground tissues, are crucially involved in regulating differentiation. It is currently unknown how these walls are built and refined or their role, if any, in influencing meristem developmental dynamics. We have combined polysaccharide linkage analysis, immuno-labeling, and transcriptome profiling of the SAM to provide a spatiotemporal plan of the walls of this dynamic structure. We find that meristematic cells express only a core subset of 152 genes encoding cell wall glycosyltransferases (GTs). Systemic localization of all these GT mRNAs by in situ hybridization reveals members with either enrichment in or specificity to apical subdomains such as emerging flower primordia, and a large class with high expression in dividing cells. The highly localized and coordinated expression of GTs in the SAM suggests distinct wall properties of meristematic cells and specific differences between newly forming walls and their mature descendants. Functional analysis demonstrates that a subset of CSLD genes is essential for proper meristem maintenance, confirming the key role of walls in developmental pathways.

Live confocal imaging of Arabidopsis flower buds

Recent advances in confocal microscopy, coupled with the development of numerous fluorescent reporters, provide us with a powerful tool to study the development of plants. Live confocal imaging has been used extensively to further our understanding of the mechanisms underlying the formation of roots, shoots and leaves. However, it has not been widely applied to flowers, partly because of specific challenges associated with the imaging of flower buds. Here, we describe how to prepare and grow shoot apices of Arabidopsis in vitro, to perform both single-point and time-lapse imaging of live, developing flower buds with either an upright or an inverted confocal microscope.

A computational framework for 3D mechanical modeling of plant morphogenesis with cellular resolution

The link between genetic regulation and the definition of form and size during morphogenesis remains largely an open question in both plant and animal biology. This is partially due to the complexity of the process, involving extensive molecular networks, multiple feedbacks between different scales of organization and physical forces operating at multiple levels. Here we present a conceptual and modeling framework aimed at generating an integrated understanding of morphogenesis in plants. This framework is based on the biophysical properties of plant cells, which are under high internal turgor pressure, and are prevented from bursting because of the presence of a rigid cell wall. To control cell growth, the underlying molecular networks must interfere locally with the elastic and/or plastic extensibility of this cell wall. We present a model in the form of a three dimensional (3D) virtual tissue, where growth depends on the local modulation of wall mechanical properties and turgor pressure. The model shows how forces generated by turgor-pressure can act both cell autonomously and non-cell autonomously to drive growth in different directions. We use simulations to explore lateral organ formation at the shoot apical meristem. Although different scenarios lead to similar shape changes, they are not equivalent and lead to different, testable predictions regarding the mechanical and geometrical properties of the growing lateral organs. Using flower development as an example, we further show how a limited number of gene activities can explain the complex shape changes that accompany organ outgrowth.