Biology subjects

Meyerowitz, E. M.

Publications and source records attributed to Meyerowitz, E. M..

17 recordsLinked to original sources

bioRxiv2025

Plasticity and invariance of Arabidopsis inflorescence and floral shoot apical meristems in response to mineral nutrients

In many species, floral organ production is invariant while flower production rate can be plastic. This allows plants to adapt flower number to their environment whilst maintaining a constant flower structure. The CLAVATA/WUSCHEL feedback loop underpins both inflorescence (IM) and floral meristem (FM) activity, respectively responsible for flower and floral organ production. We explore how plasticity and invariance can differ between IM and FM in response to nutrient availability. FM size is less sensitive to changes in nutrients than IM size, and floral organ production is insensitive to these small size changes. However, clavata3 mutants display larger changes in FM size, approaching those observed in WT IM under nutrient change, with increased floral organ number. This suggests that invariant floral organ production requires that FM size undergoes limited changes in response to nutrients. Compared to the IM, in the FM, levels of cytokinin (CK) signaling are lower and CK signaling and WUSCHEL expression are less impacted by nutrient level. Through genetic perturbations, we show a reduced response of FMs to varying cytokinin levels. Our work shows one way that the balance between plasticity and invariance can be set differently in different contexts.

plant biology↗

bioRxiv2024

Comprehensive annotations of alternative splicing, lncRNAs, and circRNAs in seven species of flowering plants

The successful occupation of terrestrial habitats by early plants was catalyzed by the adaptive evolution of new organs able to supply water and compensate for the gravitational impact under changing land conditions. Because plants are sessile, it has been proposed that the capacity of plants to innovate specialized organs is driven by a complex interplay between developmental gene expression and regulatory RNAs such as lncRNAs and circRNAs, evolving through sequence polymorphisms, genomic rearrangements, and expression divergence. Despite the importance of alternative and noncoding transcripts for enabling plant life, their accurate quantification causes major challenges as many of them are expressed at low levels and tissue-specific. Here, we describe the re-annotation of seven land plant genomes based on deep, organ-specific, ribo-depleted developmental RNA-Seq data. Using this comparative resource, we uncover 5,000 new lncRNAs and 2,000 new circular RNAs that are promising candidates for further functional investigation. Our annotation will become a reference catalog for studies on plant organ evolution and for uncovering tissue-specific patterns of transcript emergence.

plant biology↗

bioRxiv2024

Single-nucleus transcriptomics resolves differentiation dynamics between shoot stem cells and primary stem.

The shoot apical meristem (SAM), located at the plant apex, is accountable for the formation of above-ground organs such as leaves, stem and flowers. Although transcriptional profiling has elucidated some cell-types observed within stems or flowers, the differentiation transcriptional dynamics from shoot stem cells to multiple cell identities remain unknown. We employed a single-nucleus RNA-sequencing approach to assess the transcriptional heterogeneity and cell differentiation processes within the SAM. By collecting dissected inflorescence meristems, we constructed an inflorescence single-nucleus SAM atlas from Arabidopsis thaliana. Our analysis unveiled regulatory elements for most previously known cell types such as the boundary domain, vasculature, early primordia, epidermis and internal stem cells. We also identified previously unobserved transcriptional profiles, revealing that the stem cortex is defined early within forming primordia. Moreover, trajectory inference analysis allowed us to capture spatial control of S-phase machinery by floral homeotic genes and differentiation gene expression dynamics from internal shoot stem cells toward internal layers such as cortex, cambium, xylem and phloem. The results advance our understanding of the cellular and transcriptional heterogeneity underlying the cell-fate transcriptional dynamics shaping shoot organs and architecture.

developmental biology↗

bioRxiv2024

Rapid evolution of gene expression patterns in flowering plants

Phenotypic differences between species are largely driven by changes in both protein-coding sequence and gene expression 1. The evolutionary history of angiosperms (flowering plants) is characterised by a highly accelerated rate of diversification, which Darwin referred to as an "abominable mystery" 2. Here we show, by analysing the transcriptomes from eight organs across seven species, that angiosperm protein-coding gene expression patterns evolve rapidly: within 45 million years, expression levels of orthologous genes diverged so strongly that they are more similar between different organs within a species than between what are considered homologous organs from different species. This finding differs from previous observations in mammals, which demonstrated that organ-dependent gene expression levels are largely conserved 3, 4, 5. Among the angiosperm organs, meristems and leaves show the highest degree of expression conservation, whereas stamen and pollen transcriptomes diverge rapidly. Examining changes in the expression level of functionally related genes, we found low rates for those involved in key cellular, metabolic and developmental processes. In contrast, particularly high rates were observed for genes that are involved in the response to endogenous and external stimuli, presumably reflecting an adaptive response of flowering plants to ever-changing environments. Our work reveals that the evolution of gene expression progresses at different rates in angiosperms and mammals, and provides a comprehensive resource to perform cross-kingdom comparative studies of transcriptome evolution.

plant biology↗

bioRxiv2023

Dynamical states of self-organized waves in a giant single-celled organism feeding on light

A hallmark of self-organisation in living systems is their capacity to stabilise their own dynamics, often appearing to anticipate and act upon potential outcomes. Caulerpa brachypus is a marine green alga consisting of differentiated organs resembling leaves, stems and roots. While an individual can exceed a metre in size, it is a single multinucleated giant cell. Thus Caulerpa presents the mystery of morphogenesis on macroscopic scales in the absence of cellularization. The experiments reported here reveal self-organised waves of greenness -- chloroplasts -- that propagate throughout the alga in anticipation of the day-night light cycle. Using dynamical systems analysis we show that these waves are coupled to a self-sustained oscillator, and demonstrate their entrainment to light. Under constant conditions light intensity affects the natural period and drives transition to temporal disorder. Moreover, we find distinct morphologies depending on light temporal patterns, suggesting waves of chlorophyll could link biological oscillators to metabolism and morphogenesis in this giant single-celled organism.

developmental biology↗

bioRxiv2023

Cytokinins regulate spatially-specific ethylene production to control root growth in Arabidopsis

The two principal growth regulators cytokinins and ethylene are known to interact in the regulation of plant growth. However, information about underlying molecular mechanism and positional specificity of the cytokinin/ethylene crosstalk in root growth control is scarce. We have identified spatial specificity of cytokinin-regulated root elongation and root apical meristem (RAM) size, both of which we demonstrate to be ethylene biosynthesis-dependent. Upregulation of the cytokinin biosynthetic gene ISOPENTENYLTRANSFERASE (IPT) in proximal and peripheral tissues leads to both root and RAM shortening. In contrast, IPT activation in distal and inner tissues reduces RAM size while leaving the root length comparable to mock-treated controls. We show that cytokinins regulate two steps specific to ethylene biosynthesis, the production of ACC by ACC SYNTHASEs (ACSs), and its conversion to ethylene by ACC OXIDASEs (ACOs). We describe cytokinin- and ethylene-specific regulation controlling the activity of ACSs and ACOs that are spatially discrete along both proximo/distal and radial root axes. Using direct ethylene measurements, we identify ACO2, ACO3 and ACO4 as being responsible for ethylene biosynthesis and the ethylene-regulated root and RAM shortening in cytokinin-treated Arabidopsis. Finally, we describe the tight cooperation between cytokinin and ethylene signaling in cytokinin-induced, ethylene-regulated control of ACO4 due to the direct interaction between ARABIDOPSIS RESPONSE REGULATOR 2 (ARR2), a member of the multistep phosphorelay cascade and the C-terminal portion of ETHYLENE INSENSITIVE 2 (EIN2-C), a key regulator of canonical ethylene signaling.

plant biology↗

bioRxiv2022

Bimodally oriented cellulose fibers and reticulated homogalacturonan networks - A direct visualization of Allium cepa primary cell walls

One hallmark of plant cells is their pecto-cellulosic cell walls. They protect cells against the environment and high turgor and mediate morphogenesis through the dynamics of their mechanical and chemical properties. The walls are a complex polysaccharidic structure. Although their biochemical composition is well known, how the different components organize in the volume of the cell wall and interact with each other is not well understood and yet is key to the walls mechanical properties. To investigate the ultrastructure of the plant cell wall, we imaged the walls of onion (Allium cepa) bulbs in a near-native state via cryo-Focused Ion Beam milling (cryo-FIB-milling) and cryo-Electron Tomography (cryo-ET). This allowed the high-resolution visualization of cellulose fibers in situ (in muro). We reveal the coexistence of dense fiber fields bathed in a reticulated matrix we termed "meshing," which is more abundant at the inner surface of the cell wall. The fibers adopted a regular bimodal angular distribution at all depths in the cell wall and bundled according to their orientation, creating layers within the cell wall. Concomitantly, employing homogalacturonan (HG)-specific enzymatic digestion, we observed changes in the meshing, suggesting that it is at least in part composed of HG pectins. We propose the following model for the construction of the abaxial epidermal primary cell wall: The cell deposits successive layers of cellulose fibers at -45{degrees} and +45{degrees} relative to the cells long axis and secretes the surrounding HG-rich meshing proximal to the plasma membrane, which then migrates to more distal regions of the cell wall.

plant biology↗

bioRxiv2020

A multiscale analysis of early flower development in Arabidopsis provides an integrated view of molecular regulation and growth control

The link between gene regulation and morphogenesis of multicellular organisms is a fundamental problem in biology. We address this question in the floral meristem of Arabidopsis, which generates new tissues and organs through complex changes in growth patterns. Starting from high-resolution time-lapse images, we generated a comprehensive 4-D atlas of early flower development including cell lineage, cellular growth rates and the expression patterns of 28 regulatory genes. This information was introduced in MorphoNet, a web-based open-access platform. The application of mechanistic computational models indicated that the molecular network based on the literature only explained a minority of the expression patterns. This was substantially improved by adding single regulatory hypotheses for individual genes. We next used the integrated information to correlate growth with the combinatorial expression of multiple genes. This led us to propose a set of hypotheses for the action of individual genes in morphogenesis, not visible by simply correlating gene expression and growth. This identified the central transcription factor LEAFY as a potential regulator of heterogeneous growth, which was supported by quantifying growth patterns in a leafy mutant. By providing an integrated, multiscale view of flower development, this atlas should represent a fundamental step towards mechanistic multiscale-scale models of flower development.

developmental biology↗

bioRxiv2020

Structure of the bacterial cellulose ribbon and its assembly-guiding cytoskeleton by electron cryotomography

Cellulose is a widespread component of bacterial biofilms, where its properties of exceptional water retention, high tensile strength and stiffness prevents dehydration and mechanical disruption of the biofilm. Bacteria in the Gluconacetobacter genus secrete crystalline cellulose, with a structure very similar to that found in plant cell walls. How this higher-order structure is produced is poorly understood. We used cryo-electron tomography and focused ion beam milling of native bacterial biofilms to image cellulose-synthesizing G. hansenii and G. xylinus bacteria in a frozen-hydrated, near-native state. We confirm previous results suggesting that cellulose crystallization occurs serially following its secretion along one side of the cell, leading to a cellulose ribbon that can reach several microns in length and combine with ribbons from other cells to form a robust biofilm matrix. We were able to take direct measurements in a near-native state of the cellulose sheets. Our results also reveal a novel cytoskeletal structure, that we name the cortical belt, adjacent to the inner membrane and underlying the sites where cellulose is seen emerging from the cell. We find that this structure is not present in other cellulose-synthesizing bacterial species, Agrobacterium tumefaciens and Escherichia coli 1094, which do not produce organized cellulose ribbons. We therefore propose that the cortical belt holds the cellulose synthase complexes in a line, to form higher-order cellulose structures such as sheets and ribbons.

microbiology↗

bioRxiv2019

Live imaging-assisted domain-specific CRISPR genome editing at single cell resolution in plants

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technology has been widely used for genome engineering in a wide range of organisms1, but much of the development of CRISPR-based genome editing has been aimed toward improving its efficiency and accuracy, so as to obtain genetic materials carrying known and stably heritable genome modifications. Precise spatiotemporal control over genome editing technology at cell type resolution is a key challenge for gene function studies. Some tissue-specific CRISPR genome editing methods relying on phenotypic characterization and fluorescent immune-staining techniques have been developed for biomedical research and gene therapy, they function by spatially controlling expression of Cas9 2. Recent work establishes the presence and location of mutational events at a single cell level in Arabidopsis roots and stomata3,4. Here we present an efficient domain-specific CRISPR-Cas9 system combined with a high resolution live-imaging based screening strategy, applied in the shoot apical meristem of Arabidopsis thaliana. Using the system we investigate PIN-FORMED1 (PIN1) protein functions in tissue morphogenesis and PIN1 mechanical stress response in a cell layer-specific fashion. We find that reported failure to generate new primordia in epidermal PIN1 knockout SAMs is due to a reduction in mechanical stress differences in the sub-epidermal layer. The methods described are applicable to spatial-temporal gene manipulation in plants.

plant biology↗

bioRxiv2019

Cytoskeletal organization in isolated plant cells under geometry control.

Specific cell and tissue form is essential to support many biological functions of living organisms. During development, the creation of different shapes at the cellular and tissue level fundamentally requires the integration of genetic, biochemical and physical inputs.\n\nIt is well established that the cortical microtubule network plays a key role in the morphogenesis of the plant cell wall by guiding the organisation of new cell wall material. Moreover, it has been suggested that light or mechanical stresses can orient the microtubules thereby controlling wall architecture and plant cell shape. The cytoskeleton is thus a major determinant of plant cell shape. What is less clear is how cell shape in turn influences cytoskeletal organization.\n\nRecent in vitro experiments and numerical simulations predicted that a geometry-based rule is sufficient to explain some of the microtubule organization observed in cells. Due to their high flexural rigidity and persistence length of the order of a few millimeters, MTs are rigid over cellular dimensions and are thus expected to align along their long axis if constrained in specific geometries. This hypothesis remains to be tested in cellulo.\n\nHere we present an experimental approach to explore the relative contribution of geometry to the final organization of actin and microtubule cytoskeletons in single plant cells. We show that, in cells constrained in rectangular shapes, the cytoskeleton align along the long axis of the cells. By studying actin and microtubules in cells with the same system we show that while actin organisation requires microtubules to be present to align the converse is not the case. A model of self organizing microtubules in 3D predicts that severing of microtubules is an important parameter controlling the anisotropy of the microtubule network. We experimentally confirmed the model predictions by analysing the response to shape change in plant cells with altered microtubule severing dynamics. This work is a first step towards assessing quantitatively how cell geometry contributes to the control of cytoskeletal organization in living plant cells.

biophysics↗

bioRxiv2018

Observing the Cell in Its Native State: Imaging Subcellular Dynamics in Multicellular Organisms

True physiological imaging of subcellular dynamics requires studying cells within their parent organisms, where all the environmental cues that drive gene expression, and hence the phenotypes we actually observe, are present. A complete understanding also requires volumetric imaging of the cell and its surroundings at high spatiotemporal resolution without inducing undue stress on either. We combined lattice light sheet microscopy with two-channel adaptive optics to achieve, across large multicellular volumes, noninvasive aberration-free imaging of subcellular processes, including endocytosis, organelle remodeling during mitosis, and the migration of axons, immune cells, and metastatic cancer cells in vivo. The technology reveals the phenotypic diversity within cells across different organisms and developmental stages, and may offer insights into how cells harness their intrinsic variability to adapt to different physiological environments.\n\nOne Sentence SummaryCombining lattice light sheet microscopy with adaptive optics enables high speed, high resolution in vivo 3D imaging of dynamic processes inside cells under physiological conditions within their parent organisms.

cell biology↗

bioRxiv2017

Nitrate modulates stem cell dynamics by regulating WUSCHEL expression through cytokinins

The shoot apical meristem (SAM) is responsible for the generation of all of the aerial parts of plants1. Given its critical role, dynamical changes in SAM activity should play a central role in the adaptation of plant architecture to the environment2. Using quantitative microscopy, grafting experiments and genetic perturbations, we connect the plant environment to the SAM, by describing the molecular mechanism by which cytokinins signal the level of nutrient availability to the SAM. We show that a systemic signal of cytokinin precursors3 mediates the adaptation of SAM size and organogenesis rate to the availability of mineral nutrients by modulating the expression of WUSCHEL, a key regulator of stem cell homeostasis4. In time-lapse experiments, we further show that this mechanism allows meristems to adapt to rapid changes in nitrate concentration, and thereby modulate their rate of organ production to the availability of mineral nutrients within a few days. Our work sheds new light on the role of the stem cell regulatory network, by showing that it does not only maintain meristem homeostasis but also allows plants to adapt to rapid changes in the environment.

plant biology↗

bioRxiv2017

Gene expression dynamics and inter-tissue recognition mechanisms during tissue fusion at the Arabidopsis graft junction

The ability for cut tissues to join together and form a chimeric organism is a remarkable property of many plants, however, grafting is poorly characterized at the molecular level. To better understand this process we monitored genome-wide temporal and spatial gene expression changes in grafted Arabidopsis thaliana hypocotyls. Tissues above and below the graft rapidly developed an asymmetry such that many genes were more highly expressed on one side than the other. This asymmetry correlated with sugar responsive genes and we observed an accumulation of starch above the graft that decreased along with asymmetry once the sugar-transporting vascular tissues reconnected. Despite the initial starvation response below the graft, many genes associated with vascular formation were rapidly activated in grafted tissues but not in cut and separated tissues indicating that a recognition mechanism activated that was independent of functional vascular connections. Auxin which is transported cell-to-cell, had a rapidly elevated response that was symmetric, suggesting that auxin was perceived by the root within hours of tissue attachment to activate the vascular regeneration process. A subset of genes were expressed only in grafted tissues, indicating that wound healing proceeded via different mechanisms depending on the presence or absence of adjoining tissues. Such a recognition process could have broader relevance for tissue regeneration, inter-tissue communication and tissue fusion events.

plant biology↗

bioRxiv2017

Cell Cycle Control by Nuclear Sequestration of CDC20 and CDH1 mRNA in Plant Stem Cells

In eukaryotic cells, most RNA molecules are exported into the cytoplasm after being transcribed in the nucleus. Long noncoding RNAs (lncRNAs) have been found to reside and function primarily inside the nucleus, but nuclear localization of protein-coding messenger RNAs (mRNAs) has been considered rare in both animals and plants. Here we show that two mRNAs, transcribed from the CDC20 and CCS52B (plant orthologue of CDH1) genes, are specifically sequestered inside the nucleus during the cell cycle. CDC20 and CDH1 both function as coactivators of the anaphase-promoting complex or cyclosome (APC/C) E3 ligase to trigger cyclin B (C YCB) destruction. In the Arabidopsis thaliana shoot apical meristem (SAM), we find CDC20 and CCS52B are co-expressed with CYCBs in mitotic cells. CYCB transcripts can be exported and translated, whereas CDC20 and CCS52B mRNAs are strictly confined to the nucleus at prophase and the cognate proteins are not translated until the redistribution of the mRNAs to the cytoplasm after nuclear envelope breakdown (NEBD) at prometaphase. The 5 untranslated region (UTR) is necessary and sufficient for CDC20 mRNA nuclear localization as well as protein translation. Mitotic enrichment of CDC20 and CCS52B transcripts enables the timely and rapid activation of APC/C, while their nuclear sequestration at prophase appears to protect cyclins from precocious degradation.

cell biology↗

bioRxiv2017

Cell type boundaries organize plant development

In plants the dorsoventral boundary of leaves defines an axis of symmetry through the centre of the organ separating the top (dorsal) and bottom (ventral) tissues. Although the positioning of this boundary is critical for leaf morphogenesis, how the boundary is established and how it influences development remains unclear. Using live-imaging and perturbation experiments we show that leaf orientation, morphology and position are pre-patterned by HD-ZIPIII and KAN gene expression in the shoot, leading to a model in which dorsoventral genes coordinate to regulate plant development by localizing auxin response between their expression domains. However we also find that auxin levels feedback on dorsoventral patterning by spatially organizing HD-ZIPIII and KAN expression in the shoot periphery. By demonstrating that the regulation of these genes by auxin also governs their response to wounds, our results also provide a parsimonious explanation for the influence of wounds on leaf dorsoventrality.\n\nOnce sentence summaryCell type boundaries regulate plant development

developmental biology↗

bioRxiv2017

SUPERMAN prevents stamen formation and promotes stem cell termination in the fourth whorl of the Arabidopsis flower

The molecular and genetic networks underlying the determination of floral organ identity are well studied, but much less is known about how the flower is partitioned into four developmentally distinct whorls. The SUPERMAN gene is required for proper specification of the boundary between stamens in whorl 3 and carpels in whorl 4, as superman mutants exhibit supernumerary stamens but usually lack carpels. However, it has remained unclear whether extra stamens in superman mutants originate from an organ identity change in whorl 4 or the overproliferation of whorl 3. Using live confocal imaging, we show that the extra stamens in superman mutants arise from cells in whorl 4, which change their fate from female to male, while floral stem cells proliferate longer, allowing for the production of additional stamens.

developmental biology↗