Publications by authors named "Elliot Meyerowitz"

107 Publications

Visualization of Protein Coding, Long Noncoding, and Nuclear RNAs by Fluorescence in Situ Hybridization in Sections of Shoot Apical Meristems and Developing Flowers1[OPEN].

Plant Physiol 2020 Jan;182(1):147-158

Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom.

In addition to transcriptional regulation, gene expression is further modulated through mRNA spatiotemporal distribution, by RNA movement between cells, and by RNA localization within cells. Here, we have adapted RNA fluorescence in situ hybridization (FISH) to explore RNA localization in Arabidopsis (Arabidopsis thaliana). We show that RNA FISH on sectioned material can be applied to investigate the tissue and subcellular localization of meristem and flower development genes, cell cycle transcripts, and plant long noncoding RNAs. We also developed double RNA FISH to dissect the coexpression of different mRNAs at the shoot apex and nuclear-cytoplasmic separation of cell cycle gene transcripts in dividing cells. By coupling RNA FISH with fluorescence immunocytochemistry, we further demonstrate that a gene's mRNA and protein may be simultaneously detected, for example revealing uniform distribution of PIN-FORMED1 (PIN1) mRNA and polar localization of PIN1 protein in the same cells. Therefore, our method enables the visualization of gene expression at both transcriptional and translational levels with subcellular spatial resolution, opening up the possibility of systematically tracking the dynamics of RNA molecules and their cognate proteins in plant cells.
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http://dx.doi.org/10.1104/pp.19.00980DOI Listing
January 2020

Molecular mechanism of cytokinin-activated cell division in .

Science 2021 03 25;371(6536):1350-1355. Epub 2021 Feb 25.

Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK.

Mitogens trigger cell division in animals. In plants, cytokinins, a group of phytohormones derived from adenine, stimulate cell proliferation. Cytokinin signaling is initiated by membrane-associated histidine kinase receptors and transduced through a phosphorelay system. We show that in the shoot apical meristem (SAM), cytokinin regulates cell division by promoting nuclear shuttling of Myb-domain protein 3R4 (MYB3R4), a transcription factor that activates mitotic gene expression. Newly synthesized MYB3R4 protein resides predominantly in the cytoplasm. At the G2-to-M transition, rapid nuclear accumulation of MYB3R4-consistent with an associated transient peak in cytokinin concentration-feeds a positive feedback loop involving importins and initiates a transcriptional cascade that drives mitosis and cytokinesis. An engineered nuclear-restricted MYB3R4 mimics the cytokinin effects of enhanced cell proliferation and meristem growth.
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http://dx.doi.org/10.1126/science.abe2305DOI Listing
March 2021

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

Dev Cell 2021 Feb;56(4):540-556.e8

Laboratoire RDP, Université de Lyon 1, ENS-Lyon, INRAE, CNRS, UCBL, 69364 Lyon, France. Electronic address:

We have analyzed the link between the gene regulation and growth during the early stages of flower development in Arabidopsis. Starting from time-lapse images, we generated a 4D atlas of early flower development, including cell lineage, cellular growth rates, and the expression patterns of regulatory genes. This information was introduced in MorphoNet, a web-based platform. Using computational models, we found that the literature-based molecular network only explained a minority of the gene expression patterns. This was substantially improved by adding regulatory hypotheses for individual genes. Correlating growth with the combinatorial expression of multiple regulators led to a set of hypotheses for the action of individual genes in morphogenesis. This identified the central factor LEAFY as a potential regulator of heterogeneous growth, which was supported by quantifying growth patterns in a leafy mutant. By providing an integrated view, this atlas should represent a fundamental step toward mechanistic models of flower development.
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http://dx.doi.org/10.1016/j.devcel.2021.01.019DOI Listing
February 2021

Structure of the Bacterial Cellulose Ribbon and Its Assembly-Guiding Cytoskeleton by Electron Cryotomography.

J Bacteriol 2021 Jan 11;203(3). Epub 2021 Jan 11.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA

Cellulose is a widespread component of bacterial biofilms, where its properties of exceptional water retention, high tensile strength, and stiffness prevent dehydration and mechanical disruption of the biofilm. Bacteria in the 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 and 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 micrometers 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, which we have named the cortical belt, adjacent to the inner membrane and underlying the sites where cellulose is seen emerging from the cell. We found that this structure is not present in other cellulose-synthesizing bacterial species, and 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. This work's relevance for the microbiology community is twofold. It delivers for the first time high-resolution near-native snapshots of spp. (previously spp.) in the process of cellulose ribbon synthesis, in their native biofilm environment. It puts forward a noncharacterized cytoskeleton element associated with the side of the cell where the cellulose synthesis occurs. This represents a step forward in the understanding of the cell-guided process of crystalline cellulose synthesis, studied specifically in the genus and still not fully understood. Additionally, our successful attempt to use cryo-focused-ion-beam milling through biofilms to image the cells in their native environment will drive the community to use this tool for the morphological characterization of other studied biofilms.
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http://dx.doi.org/10.1128/JB.00371-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7811197PMC
January 2021

The Overlapping and Distinct Roles of HAM Family Genes in Shoot Meristems.

Front Plant Sci 2020 4;11:541968. Epub 2020 Sep 4.

Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States.

In shoot apical meristems (SAMs), a well-characterized regulatory loop between WUSCHEL (WUS) and CLAVATA3 (CLV3) maintains stem cell homeostasis by regulating the balance between cell proliferation and cell differentiation. WUS proteins, translated in deep cell layers, move into the overlaying stem cells to activate . The secreted peptide CLV3 then regulates levels through a ligand-receptor mediated signaling cascade. is specifically expressed in the stem cells and repressed in the deep cell layers despite presence of the WUS activator, forming an apical-basal polarity along the axis of the SAM. Previously, we proposed and validated a hypothesis that the HAIRY MERISTEM (HAM) family genes regulate this polarity, keeping the expression of off in interior cells of the SAM. However, the specific role of each individual member of the HAM family in this process remains to be elucidated. Combining live imaging and molecular genetics, we have dissected the conserved and distinct functions of different HAM family members in control of patterning in the SAMs and in the shoot stem cell niches as well.
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http://dx.doi.org/10.3389/fpls.2020.541968DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7498855PMC
September 2020

Cytoskeletal organization in isolated plant cells under geometry control.

Proc Natl Acad Sci U S A 2020 07 8;117(29):17399-17408. Epub 2020 Jul 8.

The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom;

The cytoskeleton plays a key role in establishing robust cell shape. In animals, it is well established that cell shape can also influence cytoskeletal organization. Cytoskeletal proteins are well conserved between animal and plant kingdoms; nevertheless, because plant cells exhibit major structural differences to animal cells, the question arises whether the plant cytoskeleton also responds to geometrical cues. Recent numerical simulations predicted that a geometry-based rule is sufficient to explain the microtubule (MT) 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 Here, we explore the relative contribution of geometry to the final organization of actin and MT cytoskeletons in single plant cells of We show that the cytoskeleton aligns with the long axis of the cells. We find that actin organization relies on MTs but not the opposite. We develop a model of self-organizing MTs in three dimensions, which predicts the importance of MT severing, which we confirm experimentally. This work is a first step toward assessing quantitatively how cellular geometry contributes to the control of cytoskeletal organization in living plant cells.
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http://dx.doi.org/10.1073/pnas.2003184117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7382239PMC
July 2020

Pectin homogalacturonan nanofilament expansion drives morphogenesis in plant epidermal cells.

Science 2020 02;367(6481):1003-1007

Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France.

The process by which plant cells expand and gain shape has presented a challenge for researchers. Current models propose that these processes are driven by turgor pressure acting on the cell wall. Using nanoimaging, we show that the cell wall contains pectin nanofilaments that possess an intrinsic expansion capacity. Additionally, we use growth models containing such structures to show that a complex plant cell shape can derive from chemically induced local and polarized expansion of the pectin nanofilaments without turgor-driven growth. Thus, the plant cell wall, outside of the cell itself, is an active participant in shaping plant cells. Extracellular matrix function may similarly guide cell shape in other kingdoms, including Animalia.
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http://dx.doi.org/10.1126/science.aaz5103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7932746PMC
February 2020

Visualization of Protein Coding, Long Noncoding, and Nuclear RNAs by Fluorescence in Situ Hybridization in Sections of Shoot Apical Meristems and Developing Flowers.

Plant Physiol 2020 01 13;182(1):147-158. Epub 2019 Nov 13.

Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom

In addition to transcriptional regulation, gene expression is further modulated through mRNA spatiotemporal distribution, by RNA movement between cells, and by RNA localization within cells. Here, we have adapted RNA fluorescence in situ hybridization (FISH) to explore RNA localization in Arabidopsis (). We show that RNA FISH on sectioned material can be applied to investigate the tissue and subcellular localization of meristem and flower development genes, cell cycle transcripts, and plant long noncoding RNAs. We also developed double RNA FISH to dissect the coexpression of different mRNAs at the shoot apex and nuclear-cytoplasmic separation of cell cycle gene transcripts in dividing cells. By coupling RNA FISH with fluorescence immunocytochemistry, we further demonstrate that a gene's mRNA and protein may be simultaneously detected, for example revealing uniform distribution of () mRNA and polar localization of PIN1 protein in the same cells. Therefore, our method enables the visualization of gene expression at both transcriptional and translational levels with subcellular spatial resolution, opening up the possibility of systematically tracking the dynamics of RNA molecules and their cognate proteins in plant cells.
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http://dx.doi.org/10.1104/pp.19.00980DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6945838PMC
January 2020

ETR1 Integrates Response to Ethylene and Cytokinins into a Single Multistep Phosphorelay Pathway to Control Root Growth.

Mol Plant 2019 10 7;12(10):1338-1352. Epub 2019 Jun 7.

Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CETEC-MU, Kamenice 5/A2, 625 00 Brno, Czech Republic. Electronic address:

Cytokinins and ethylene control plant development via sensors from the histidine kinase (HK) family. However, downstream signaling pathways for the key phytohormones are distinct. Here we report that not only cytokinin but also ethylene is able to control root apical meristem (RAM) size through activation of the multistep phosphorelay (MSP) pathway. We found that both cytokinin and ethylene-dependent RAM shortening requires ethylene binding to ETR1 and the HK activity of ETR1. The receiver domain of ETR1 interacts with MSP signaling intermediates acting downstream of cytokinin receptors, further substantiating the role of ETR1 in MSP signaling. We revealed that both cytokinin and ethylene induce the MSP in similar and distinct cell types with ETR1-mediated ethylene signaling controlling MSP output specifically in the root transition zone. We identified members of the MSP pathway specific and common to both hormones and showed that ETR1-regulated ARR3 controls RAM size. ETR1-mediated MSP spatially differs from canonical CTR1/EIN2/EIN3 ethylene signaling and is independent of EIN2, indicating that both pathways can be spatially and functionally separated. Furthermore, we demonstrated that canonical ethylene signaling controls MSP responsiveness to cytokinin specifically in the root transition zone, presumably via regulation of ARR10, one of the positive regulators of MSP signaling in Arabidopsis.
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http://dx.doi.org/10.1016/j.molp.2019.05.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8040967PMC
October 2019

Primary wall cellulose synthase regulates shoot apical meristem mechanics and growth.

Development 2019 05 24;146(10). Epub 2019 May 24.

Howard Hughes Medical Institute and Division of Biology and Biological Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA.

How organisms attain their specific shapes and modify their growth patterns in response to environmental and chemical signals has been the subject of many investigations. Plant cells are at high turgor pressure and are surrounded by a rigid yet flexible cell wall, which is the primary determinant of plant growth and morphogenesis. Cellulose microfibrils, synthesized by plasma membrane-localized cellulose synthase complexes, are major tension-bearing components of the cell wall that mediate directional growth. Despite advances in understanding the genetic and biophysical regulation of morphogenesis, direct studies of cellulose biosynthesis and its impact on morphogenesis of different cell and tissue types are largely lacking. In this study, we took advantage of mutants of three primary cellulose synthase () genes that are involved in primary wall cellulose synthesis. Using field emission scanning electron microscopy, live cell imaging and biophysical measurements, we aimed to understand how the primary wall CESA complex acts during shoot apical meristem development. Our results indicate that cellulose biosynthesis impacts the mechanics and growth of the shoot apical meristem.
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http://dx.doi.org/10.1242/dev.179036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6550022PMC
May 2019

Primed histone demethylation regulates shoot regenerative competency.

Nat Commun 2019 04 16;10(1):1786. Epub 2019 Apr 16.

Faculty of Science and Technology, Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.

Acquisition of pluripotency by somatic cells is a striking process that enables multicellular organisms to regenerate organs. This process includes silencing of genes to erase original tissue memory and priming of additional cell type specification genes, which are then poised for activation by external signal inputs. Here, through analysis of genome-wide histone modifications and gene expression profiles, we show that a gene priming mechanism involving LYSINE-SPECIFIC DEMETHYLASE 1-LIKE 3 (LDL3) specifically eliminates H3K4me2 during formation of the intermediate pluripotent cell mass known as callus derived from Arabidopsis root cells. While LDL3-mediated H3K4me2 removal does not immediately affect gene expression, it does facilitate the later activation of genes that act to form shoot progenitors when external cues lead to shoot induction. These results give insights into the role of H3K4 methylation in plants, and into the primed state that provides plant cells with high regenerative competency.
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http://dx.doi.org/10.1038/s41467-019-09386-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6467990PMC
April 2019

Calcium signals are necessary to establish auxin transporter polarity in a plant stem cell niche.

Nat Commun 2019 02 13;10(1):726. Epub 2019 Feb 13.

Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA.

In plants mechanical signals pattern morphogenesis through the polar transport of the hormone auxin and through regulation of interphase microtubule (MT) orientation. To date, the mechanisms by which such signals induce changes in cell polarity remain unknown. Through a combination of time-lapse imaging, and chemical and mechanical perturbations, we show that mechanical stimulation of the SAM causes transient changes in cytoplasmic calcium ion concentration (Ca) and that transient Ca response is required for downstream changes in PIN-FORMED 1 (PIN1) polarity. We also find that dynamic changes in Ca occur during development of the SAM and this Ca response is required for changes in PIN1 polarity, though not sufficient. In contrast, we find that Ca is not necessary for the response of MTs to mechanical perturbations revealing that Ca specifically acts downstream of mechanics to regulate PIN1 polarity response.
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http://dx.doi.org/10.1038/s41467-019-08575-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6374474PMC
February 2019

A gene expression map of shoot domains reveals regulatory mechanisms.

Nat Commun 2019 01 11;10(1):141. Epub 2019 Jan 11.

State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.

Gene regulatory networks control development via domain-specific gene expression. In seed plants, self-renewing stem cells located in the shoot apical meristem (SAM) produce leaves from the SAM peripheral zone. After initiation, leaves develop polarity patterns to form a planar shape. Here we compare translating RNAs among SAM and leaf domains. Using translating ribosome affinity purification and RNA sequencing to quantify gene expression in target domains, we generate a domain-specific translatome map covering representative vegetative stage SAM and leaf domains. We discuss the predicted cellular functions of these domains and provide evidence that dome seemingly unrelated domains, utilize common regulatory modules. Experimental follow up shows that the RABBIT EARS and HANABA TARANU transcription factors have roles in axillary meristem initiation. This dataset provides a community resource for further study of shoot development and response to internal and environmental signals.
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http://dx.doi.org/10.1038/s41467-018-08083-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6329838PMC
January 2019

HAIRY MERISTEM with WUSCHEL confines CLAVATA3 expression to the outer apical meristem layers.

Science 2018 08;361(6401):502-506

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.

The control of the location and activity of stem cells depends on spatial regulation of gene activities in the stem cell niche. Using computational and experimental approaches, we have tested and found support for a hypothesis for gene interactions that specify the apical stem cell population. The hypothesis explains how the WUSCHEL gene product, synthesized basally in the meristem, induces -expressing stem cells in the meristem apex but, paradoxically, not in the basal domain where itself is expressed. The answer involves the activity of the small family of genes, which prevent the activation of and which are expressed basally in the shoot meristem.
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http://dx.doi.org/10.1126/science.aar8638DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6095697PMC
August 2018

SUPERMAN regulates floral whorl boundaries through control of auxin biosynthesis.

EMBO J 2018 06 15;37(11). Epub 2018 May 15.

Temasek Life Sciences Laboratory (TLL), National University of Singapore, Singapore, Singapore

Proper floral patterning, including the number and position of floral organs in most plant species, is tightly controlled by the precise regulation of the persistence and size of floral meristems (FMs). In , two known feedback pathways, one composed of WUSCHEL (WUS) and CLAVATA3 (CLV3) and the other composed of AGAMOUS (AG) and WUS, spatially and temporally control floral stem cells, respectively. However, mounting evidence suggests that other factors, including phytohormones, are also involved in floral meristem regulation. Here, we show that the boundary gene () bridges floral organogenesis and floral meristem determinacy in another pathway that involves auxin signaling. SUP interacts with components of polycomb repressive complex 2 (PRC2) and fine-tunes local auxin signaling by negatively regulating the expression of the auxin biosynthesis genes (). In mutants, derepressed local activity elevates auxin levels at the boundary between whorls 3 and 4, which leads to an increase in the number and the prolonged maintenance of floral stem cells, and consequently an increase in the number of reproductive organs. Our work presents a new floral meristem regulatory mechanism, in which , a boundary gene, coordinates floral organogenesis and floral meristem size through fine-tuning auxin biosynthesis.
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http://dx.doi.org/10.15252/embj.201797499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5983216PMC
June 2018

Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms.

Science 2018 04;360(6386)

Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.

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 that 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 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.
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http://dx.doi.org/10.1126/science.aaq1392DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6040645PMC
April 2018

The self-organization of plant microtubules inside the cell volume yields their cortical localization, stable alignment, and sensitivity to external cues.

PLoS Comput Biol 2018 02 20;14(2):e1006011. Epub 2018 Feb 20.

Reproduction et Développement des Plantes, Univ. Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69364 Lyon, France.

Many cell functions rely on the ability of microtubules to self-organize as complex networks. In plants, cortical microtubules are essential to determine cell shape as they guide the deposition of cellulose microfibrils, and thus control mechanical anisotropy of the cell wall. Here we analyze how, in turn, cell shape may influence microtubule behavior. Building upon previous models that confined microtubules to the cell surface, we introduce an agent model of microtubules enclosed in a three-dimensional volume. We show that the microtubule network has spontaneous aligned configurations that could explain many experimental observations without resorting to specific regulation. In particular, we find that the preferred cortical localization of microtubules emerges from directional persistence of the microtubules, and their interactions with each other and with the stiff wall. We also identify microtubule parameters that seem relatively insensitive to cell shape, such as length or number. In contrast, microtubule array anisotropy depends on local curvature of the cell surface and global orientation follows robustly the longest axis of the cell. Lastly, we find that geometric cues may be overcome, as the network is capable of reorienting toward weak external directional cues. Altogether our simulations show that the microtubule network is a good transducer of weak external polarity, while at the same time, easily reaching stable global configurations.
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http://dx.doi.org/10.1371/journal.pcbi.1006011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5834207PMC
February 2018

Transcriptome dynamics at graft junctions reveal an intertissue recognition mechanism that activates vascular regeneration.

Proc Natl Acad Sci U S A 2018 03 13;115(10):E2447-E2456. Epub 2018 Feb 13.

Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom.

The ability for cut tissues to join 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 gene expression changes in grafted hypocotyls. We observed a sequential activation of genes associated with cambium, phloem, and xylem formation. Tissues above and below the graft rapidly developed an asymmetry such that many genes were more highly expressed on one side than on the other. This asymmetry correlated with sugar-responsive genes, and we observed an accumulation of starch above the graft junction. This accumulation 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 was activated independently 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 was 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, intertissue communication, and tissue fusion events.
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http://dx.doi.org/10.1073/pnas.1718263115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5878008PMC
March 2018

Nitrate modulates stem cell dynamics in shoot meristems through cytokinins.

Proc Natl Acad Sci U S A 2018 02 23;115(6):1382-1387. Epub 2018 Jan 23.

Sainsbury Laboratory, University of Cambridge, CB2 1LR Cambridge, United Kingdom;

The shoot apical meristem (SAM) is responsible for the generation of all the aerial parts of plants. Given its critical role, dynamical changes in SAM activity should play a central role in the adaptation of plant architecture to the environment. 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 precursors mediates the adaptation of SAM size and organogenesis rate to the availability of mineral nutrients by modulating the expression of , a key regulator of stem cell homeostasis. 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 light on the role of the stem cell regulatory network by showing that it not only maintains meristem homeostasis but also allows plants to adapt to rapid changes in the environment.
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http://dx.doi.org/10.1073/pnas.1718670115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5819446PMC
February 2018

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

Mol Cell 2017 12 7;68(6):1108-1119.e3. Epub 2017 Dec 7.

Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK; Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA. Electronic address:

In eukaryotes, most RNA molecules are exported into the cytoplasm after transcription. Long noncoding RNAs (lncRNAs) reside and function primarily inside the nucleus, but nuclear localization of mRNAs has been considered rare in both animals and plants. Here we show that Arabidopsis anaphase-promoting complex/cyclosome (APC/C) coactivator genes CDC20 and CCS52B (CDH1 ortholog) are co-expressed with their target cyclin B genes (CYCBs) during mitosis. CYCB transcripts can be exported and translated; however, CDC20 and CCS52B mRNAs are 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) plays dual roles in CDC20 mRNA nuclear localization and translation. Mitotic accumulation of CDC20 and CCS52B transcripts enables the timely and rapid activation of APC/C, while the nuclear sequestration of these transcripts at prophase appears to protect cyclins from precocious degradation.
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http://dx.doi.org/10.1016/j.molcel.2017.11.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6013263PMC
December 2017

Cell type boundaries organize plant development.

Elife 2017 09 12;6. Epub 2017 Sep 12.

European Molecular Biology Laboratory, Heidelberg, Germany.

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.
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http://dx.doi.org/10.7554/eLife.27421DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617630PMC
September 2017

prevents class B gene expression and promotes stem cell termination in the fourth whorl of flowers.

Proc Natl Acad Sci U S A 2017 07 20;114(27):7166-7171. Epub 2017 Jun 20.

Department of Biological Sciences, Dartmouth College, Hanover, NH 03755.

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 gene is required for proper specification of the boundary between stamens in whorl 3 and carpels in whorl 4, as mutants exhibit supernumerary stamens but usually lack carpels. However, it has remained unclear whether extra stamens in 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 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.
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http://dx.doi.org/10.1073/pnas.1705977114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502645PMC
July 2017

Cell size and growth regulation in the Arabidopsis thaliana apical stem cell niche.

Proc Natl Acad Sci U S A 2016 12 5;113(51):E8238-E8246. Epub 2016 Dec 5.

The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom;

Cell size and growth kinetics are fundamental cellular properties with important physiological implications. Classical studies on yeast, and recently on bacteria, have identified rules for cell size regulation in single cells, but in the more complex environment of multicellular tissues, data have been lacking. In this study, to characterize cell size and growth regulation in a multicellular context, we developed a 4D imaging pipeline and applied it to track and quantify epidermal cells over 3-4 d in Arabidopsis thaliana shoot apical meristems. We found that a cell size checkpoint is not the trigger for G2/M or cytokinesis, refuting the unexamined assumption that meristematic cells trigger cell cycle phases upon reaching a critical size. Our data also rule out models in which cells undergo G2/M at a fixed time after birth, or by adding a critical size increment between G2/M transitions. Rather, cell size regulation was intermediate between the critical size and critical increment paradigms, meaning that cell size fluctuations decay by ∼75% in one generation compared with 100% (critical size) and 50% (critical increment). Notably, this behavior was independent of local cell-cell contact topologies and of position within the tissue. Cells grew exponentially throughout the first >80% of the cell cycle, but following an asymmetrical division, the small daughter grew at a faster exponential rate than the large daughter, an observation that potentially challenges present models of growth regulation. These growth and division behaviors place strong constraints on quantitative mechanistic descriptions of the cell cycle and growth control.
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http://dx.doi.org/10.1073/pnas.1616768113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5187701PMC
December 2016

Field Guide to Plant Model Systems.

Cell 2016 Oct;167(2):325-339

Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA. Electronic address:

For the past several decades, advances in plant development, physiology, cell biology, and genetics have relied heavily on the model (or reference) plant Arabidopsis thaliana. Arabidopsis resembles other plants, including crop plants, in many but by no means all respects. Study of Arabidopsis alone provides little information on the evolutionary history of plants, evolutionary differences between species, plants that survive in different environments, or plants that access nutrients and photosynthesize differently. Empowered by the availability of large-scale sequencing and new technologies for investigating gene function, many new plant models are being proposed and studied.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5068971PMC
http://dx.doi.org/10.1016/j.cell.2016.08.031DOI Listing
October 2016

Genetics and plant development.

C R Biol 2016 Jul-Aug;339(7-8):240-6. Epub 2016 May 26.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA. Electronic address:

There are only three grand theories in biology: the theory of the cell, the theory of the gene, and the theory of evolution. Two of these, the cell and gene theories, originated in the study of plants, with the third resulting in part from botanical considerations as well. Mendel's elucidation of the rules of inheritance was a result of his experiments on peas. The rediscovery of Mendel's work in 1900 was by the botanists de Vries, Correns, and Tschermak. It was only in subsequent years that animals were also shown to have segregation of genetic elements in the exact same manner as had been shown in plants. The story of developmental biology is different - while the development of plants has long been studied, the experimental and genetic approaches to developmental mechanism were developed via experiments on animals, and the importance of genes in development (e.g., Waddington, 1940) and their use for understanding developmental mechanisms came to botanical science much later - as late as the 1980s.
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http://dx.doi.org/10.1016/j.crvi.2016.05.003DOI Listing
February 2017

Regulation of Meristem Morphogenesis by Cell Wall Synthases in Arabidopsis.

Curr Biol 2016 06 19;26(11):1404-15. Epub 2016 May 19.

Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK; Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA. Electronic address:

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.
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http://dx.doi.org/10.1016/j.cub.2016.04.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5024349PMC
June 2016

An epidermis-driven mechanism positions and scales stem cell niches in plants.

Sci Adv 2016 Jan 29;2(1):e1500989. Epub 2016 Jan 29.

Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK.; Computational Biology and Biological Physics Group, Department of Astronomy and Theoretical Physics, Lund University, S-221 00 Lund, Sweden.

How molecular patterning scales to organ size is highly debated in developmental biology. We explore this question for the characteristic gene expression domains of the plant stem cell niche residing in the shoot apical meristem. We show that a combination of signals originating from the epidermal cell layer can correctly pattern the key gene expression domains and notably leads to adaptive scaling of these domains to the size of the tissue. Using live imaging, we experimentally confirm this prediction. The identified mechanism is also sufficient to explain de novo stem cell niches in emerging flowers. Our findings suggest that the deformation of the tissue transposes meristem geometry into an instructive scaling and positional input for the apical plant stem cell niche.
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http://dx.doi.org/10.1126/sciadv.1500989DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4846443PMC
January 2016

Live confocal imaging of Arabidopsis flower buds.

Dev Biol 2016 11 15;419(1):114-120. Epub 2016 Mar 15.

Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA.

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.
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http://dx.doi.org/10.1016/j.ydbio.2016.03.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5025338PMC
November 2016

Real-Time Lineage Analysis to Study Cell Division Orientation in the Arabidopsis Shoot Meristem.

Methods Mol Biol 2016 ;1370:147-67

Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA.

Cells in the Arabidopsis shoot apical meristem are small and divide frequently throughout the life-time of the organism making them good candidates for studying the mechanisms of cell division in plants. But tracking these cell divisions requires multiple images to be taken of the same specimen over time which means the specimen must stay alive throughout the process. This chapter provides details on how to prepare plants for live imaging, keep them alive and growing through multiple time points, and how to process the data to extract cell boundary coordinates from three-dimensional images.
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http://dx.doi.org/10.1007/978-1-4939-3142-2_12DOI Listing
October 2016

50 years of Arabidopsis research: highlights and future directions.

New Phytol 2016 Feb 14;209(3):921-44. Epub 2015 Oct 14.

Department of Cell & Systems Biology/CAGEF, University of Toronto, Toronto, ON, M5S 3B2, Canada.

922 I. 922 II. 922 III. 925 IV. 925 V. 926 VI. 927 VII. 928 VIII. 929 IX. 930 X. 931 XI. 932 XII. 933 XIII. Natural variation and genome-wide association studies 934 XIV. 934 XV. 935 XVI. 936 XVII. 937 937 References 937 SUMMARY: The year 2014 marked the 25(th) International Conference on Arabidopsis Research. In the 50 yr since the first International Conference on Arabidopsis Research, held in 1965 in Göttingen, Germany, > 54 000 papers that mention Arabidopsis thaliana in the title, abstract or keywords have been published. We present herein a citational network analysis of these papers, and touch on some of the important discoveries in plant biology that have been made in this powerful model system, and highlight how these discoveries have then had an impact in crop species. We also look to the future, highlighting some outstanding questions that can be readily addressed in Arabidopsis. Topics that are discussed include Arabidopsis reverse genetic resources, stock centers, databases and online tools, cell biology, development, hormones, plant immunity, signaling in response to abiotic stress, transporters, biosynthesis of cells walls and macromolecules such as starch and lipids, epigenetics and epigenomics, genome-wide association studies and natural variation, gene regulatory networks, modeling and systems biology, and synthetic biology.
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http://dx.doi.org/10.1111/nph.13687DOI Listing
February 2016