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Mody TA, Rolle A, Stucki N, Roll F, Bauer U, Schneitz K. Topological analysis of 3D digital ovules identifies cellular patterns associated with ovule shape diversity. Development 2024; 151:dev202590. [PMID: 38738635 PMCID: PMC11168579 DOI: 10.1242/dev.202590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/25/2024] [Indexed: 05/14/2024]
Abstract
Tissue morphogenesis remains poorly understood. In plants, a central problem is how the 3D cellular architecture of a developing organ contributes to its final shape. We address this question through a comparative analysis of ovule morphogenesis, taking advantage of the diversity in ovule shape across angiosperms. Here, we provide a 3D digital atlas of Cardamine hirsuta ovule development at single cell resolution and compare it with an equivalent atlas of Arabidopsis thaliana. We introduce nerve-based topological analysis as a tool for unbiased detection of differences in cellular architectures and corroborate identified topological differences between two homologous tissues by comparative morphometrics and visual inspection. We find that differences in topology, cell volume variation and tissue growth patterns in the sheet-like integuments and the bulbous chalaza are associated with differences in ovule curvature. In contrast, the radialized conical ovule primordia and nucelli exhibit similar shapes, despite differences in internal cellular topology and tissue growth patterns. Our results support the notion that the structural organization of a tissue is associated with its susceptibility to shape changes during evolutionary shifts in 3D cellular architecture.
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Affiliation(s)
- Tejasvinee Atul Mody
- Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Strasse 4, 85354 Freising, Germany
| | - Alexander Rolle
- Applied and Computational Topology, TUM School of Computation, Information and Technology, Technical University of Munich, Boltzmannstrasse 3, 85747 Garching, Germany
| | - Nico Stucki
- Applied and Computational Topology, TUM School of Computation, Information and Technology, Technical University of Munich, Boltzmannstrasse 3, 85747 Garching, Germany
- Munich Data Science Institute, Technical University of Munich, Walther-von-Dyck Strasse 10, 85747 Garching, Germany
| | - Fabian Roll
- Applied and Computational Topology, TUM School of Computation, Information and Technology, Technical University of Munich, Boltzmannstrasse 3, 85747 Garching, Germany
| | - Ulrich Bauer
- Applied and Computational Topology, TUM School of Computation, Information and Technology, Technical University of Munich, Boltzmannstrasse 3, 85747 Garching, Germany
- Munich Data Science Institute, Technical University of Munich, Walther-von-Dyck Strasse 10, 85747 Garching, Germany
| | - Kay Schneitz
- Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Strasse 4, 85354 Freising, Germany
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2
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Chen Y, Burian A, Johannes F. Somatic epigenetic drift during shoot branching: a cell lineage-based model. Genetics 2024; 227:iyae091. [PMID: 38809088 DOI: 10.1093/genetics/iyae091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/14/2024] [Accepted: 05/20/2024] [Indexed: 05/30/2024] Open
Abstract
Plant architecture is shaped by the production of new organs, most of which emerge postembryonically. This process includes the formation of new lateral branches along existing shoots. Current evidence supports a detached-meristem model as the cellular basis of lateral shoot initiation. In this model, a small number of undifferentiated cells are sampled from the periphery of the shoot apical meristem (SAM) to act as precursors for axillary buds, which eventually develop into new shoots. Repeated branching thus creates cellular bottlenecks (i.e. somatic drift) that affect how de novo (epi)genetic mutations propagate through the plant body during development. Somatic drift could be particularly relevant for stochastic DNA methylation gains and losses (i.e. spontaneous epimutations), as they have been shown to arise rapidly with each cell division. Here, we formalize a special case of the detached-meristem model, where precursor cells are randomly sampled from the SAM periphery in a way that maximizes cell lineage independence. We show that somatic drift during repeated branching gives rise to a mixture of cellular phylogenies within the SAM over time. This process is dependent on the number of branch points, the strength of drift as well as the epimutation rate. Our model predicts that cell-to-cell DNA methylation heterogeneity in the SAM converges to nonzero states during development, suggesting that epigenetic variation is an inherent property of the SAM cell population. Our insights have direct implications for empirical studies of somatic (epi)genomic diversity in long-lived perennial and clonal species using bulk or single-cell sequencing approaches.
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Affiliation(s)
- Yifan Chen
- Department of Mathematics, Technical University of Munich, Garching 85748, Germany
- Department of Molecular Life Sciences, Plant Epigenomics, Technical University of Munich, Freising 85354, Germany
| | - Agata Burian
- Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice 40-032, Poland
| | - Frank Johannes
- Department of Molecular Life Sciences, Plant Epigenomics, Technical University of Munich, Freising 85354, Germany
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3
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Yu L, Renton J, Burian A, Khachaturyan M, Bayer T, Kotta J, Stachowicz JJ, DuBois K, Baums IB, Werner B, Reusch TBH. A somatic genetic clock for clonal species. Nat Ecol Evol 2024; 8:1327-1336. [PMID: 38858515 PMCID: PMC11239492 DOI: 10.1038/s41559-024-02439-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 05/07/2024] [Indexed: 06/12/2024]
Abstract
Age and longevity are key parameters for demography and life-history evolution of organisms. In clonal species, a widespread life history among animals, plants, macroalgae and fungi, the sexually produced offspring (genet) grows indeterminately by producing iterative modules, or ramets, and so obscure their age. Here we present a novel molecular clock based on the accumulation of fixed somatic genetic variation that segregates among ramets. Using a stochastic model, we demonstrate that the accumulation of fixed somatic genetic variation will approach linearity after a lag phase, and is determined by the mitotic mutation rate, without direct dependence on asexual generation time. The lag phase decreased with lower stem cell population size, number of founder cells for the formation of new modules, and the ratio of symmetric versus asymmetric cell divisions. We calibrated the somatic genetic clock on cultivated eelgrass Zostera marina genets (4 and 17 years respectively). In a global data set of 20 eelgrass populations, genet ages were up to 1,403 years. The somatic genetic clock is applicable to any multicellular clonal species where the number of founder cells is small, opening novel research avenues to study longevity and, hence, demography and population dynamics of clonal species.
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Affiliation(s)
- Lei Yu
- GEOMAR Helmholtz-Center for Ocean Research Kiel, Marine Evolutionary Ecology, Kiel, Germany
| | - Jessie Renton
- Evolutionary Dynamics Group, Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Agata Burian
- Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Marina Khachaturyan
- GEOMAR Helmholtz-Center for Ocean Research Kiel, Marine Evolutionary Ecology, Kiel, Germany
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Till Bayer
- GEOMAR Helmholtz-Center for Ocean Research Kiel, Marine Evolutionary Ecology, Kiel, Germany
| | - Jonne Kotta
- Estonian Marine Institute, University of Tartu, Tallinn, Estonia
| | - John J Stachowicz
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Katherine DuBois
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Iliana B Baums
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Oldenburg, Germany
- Alfred Wegener Institute, Helmholtz-Centre for Polar and Marine Research (AWI), Bremerhaven, Germany
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Benjamin Werner
- Evolutionary Dynamics Group, Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
| | - Thorsten B H Reusch
- GEOMAR Helmholtz-Center for Ocean Research Kiel, Marine Evolutionary Ecology, Kiel, Germany.
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4
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Duran-Nebreda S, Jackson MDB, Bassel GW. A quantitative morphospace of multicellular organ design in the plant Arabidopsis. Curr Biol 2023; 33:4798-4806.e3. [PMID: 37827150 DOI: 10.1016/j.cub.2023.09.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/23/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023]
Abstract
Organ function emerges from the interactions between their constituent cells. The investigation of cellular organization can provide insight into organ function following structure-function relationships. Here, we investigate the extent to which properties in cellular organization can arise "for free" as an emergent property of embedding cells in space versus those that are actively generated by patterning processes. Default cellular configurations were established using three-dimensional (3D) digital tissue models. Network-based analysis of these synthetic cellular assemblies established a quantitative topological baseline of cellular organization, granted by virtue of passive spatial packing and the minimal amount of order that emerges for free in tessellated tissues. A 3D cellular-resolution digital tissue atlas for the model plant species Arabidopsis was generated, and the extent to which the organs in this organism conform to the default configurations was established through statistical comparisons with digital tissue models. Cells in different tissues of Arabidopsis do not conform to random packing arrangements to varying degrees. Most closely matching the random models was the undifferentiated shoot apical meristem (SAM) from which aerial organs emanate. By contrast, leaf and sepal tissue showed the greatest deviation from this baseline, suggesting these to be the most "complex" tissues in Arabidopsis. Investigation of the patterning principles responsible for the gap between these tissues and default patterns revealed cell elongation and the introduction of air spaces to contribute toward additional organ patterning complexity. This work establishes a quantitative morphospace to understand the principles of organ construction and its diversity within a single organism.
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Affiliation(s)
| | | | - George W Bassel
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
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5
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Fischer SC, Bassel GW, Kollmannsberger P. Tissues as networks of cells: towards generative rules of complex organ development. J R Soc Interface 2023; 20:20230115. [PMID: 37491909 PMCID: PMC10369035 DOI: 10.1098/rsif.2023.0115] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/05/2023] [Indexed: 07/27/2023] Open
Abstract
Network analysis is a well-known and powerful tool in molecular biology. More recently, it has been introduced in developmental biology. Tissues can be readily translated into spatial networks such that cells are represented by nodes and intercellular connections by edges. This discretization of cellular organization enables mathematical approaches rooted in network science to be applied towards the understanding of tissue structure and function. Here, we describe how such tissue abstractions can enable the principles that underpin tissue formation and function to be uncovered. We provide an introduction into biologically relevant network measures, then present an overview of different areas of developmental biology where these approaches have been applied. We then summarize the general developmental rules underpinning tissue topology generation. Finally, we discuss how generative models can help to link the developmental rule back to the tissue topologies. Our collection of results points at general mechanisms as to how local developmental rules can give rise to observed topological properties in multicellular systems.
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Affiliation(s)
- Sabine C. Fischer
- Center for Computational and Theoretical Biology, Faculty of Biology, University of Würzburg, Würzburg, Germany
| | - George W. Bassel
- School of Life Sciences, The University of Warwick, Coventry, UK
| | - Philip Kollmannsberger
- Biomedical Physics, Department of Physics, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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6
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Zhao L, Fonseca A, Meschichi A, Sicard A, Rosa S. Whole-mount smFISH allows combining RNA and protein quantification at cellular and subcellular resolution. NATURE PLANTS 2023; 9:1094-1102. [PMID: 37322128 PMCID: PMC10356603 DOI: 10.1038/s41477-023-01442-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/12/2023] [Indexed: 06/17/2023]
Abstract
Multicellular organisms result from complex developmental processes largely orchestrated through the quantitative spatiotemporal regulation of gene expression. Yet, obtaining absolute counts of messenger RNAs at a three-dimensional resolution remains challenging, especially in plants, owing to high levels of tissue autofluorescence that prevent the detection of diffraction-limited fluorescent spots. In situ hybridization methods based on amplification cycles have recently emerged, but they are laborious and often lead to quantification biases. In this article, we present a simple method based on single-molecule RNA fluorescence in situ hybridization to visualize and count the number of mRNA molecules in several intact plant tissues. In addition, with the use of fluorescent protein reporters, our method also enables simultaneous detection of mRNA and protein quantity, as well as subcellular distribution, in single cells. With this method, research in plants can now fully explore the benefits of the quantitative analysis of transcription and protein levels at cellular and subcellular resolution in plant tissues.
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Affiliation(s)
- Lihua Zhao
- Department of Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Alejandro Fonseca
- Department of Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Anis Meschichi
- Department of Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Adrien Sicard
- Department of Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
| | - Stefanie Rosa
- Department of Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
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7
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Composition, structure and robustness of Lichen guilds. Sci Rep 2023; 13:3295. [PMID: 36841885 PMCID: PMC9968342 DOI: 10.1038/s41598-023-30357-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023] Open
Abstract
Symbiosis is a major engine of evolutionary innovation underlying many extant complex organisms. Lichens are a paradigmatic example that offers a unique perspective on the role of symbiosis in ecological success and evolutionary diversification. Lichen studies have produced a wealth of information regarding the importance of symbiosis, but they frequently focus on a few species, limiting our understanding of large-scale phenomena such as guilds. Guilds are groupings of lichens that assist each other's proliferation and are intimately linked by a shared set of photobionts, constituting an extensive network of relationships. To characterize the network of lichen symbionts, we used a large data set ([Formula: see text] publications) of natural photobiont-mycobiont associations. The entire lichen network was found to be modular, but this organization does not directly match taxonomic information in the data set, prompting a reconsideration of lichen guild structure and composition. The multiscale nature of this network reveals that the major lichen guilds are better represented as clusters with several substructures rather than as monolithic communities. Heterogeneous guild structure fosters robustness, with keystone species functioning as bridges between guilds and whose extinction would endanger global stability.
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8
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Lintilhac PM. Stochasticity and the limits of molecular signaling in plant development. FRONTIERS IN PLANT SCIENCE 2022; 13:999304. [PMID: 36340340 PMCID: PMC9627605 DOI: 10.3389/fpls.2022.999304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Understanding plant development is in part a theoretical endeavor that can only succeed if it is based upon a correctly contrived axiomatic framework. Here I revisit some of the basic assumptions that frame our understanding of plant development and suggest that we consider an alternative informational ecosystem that more faithfully reflects the physical and architectural realities of plant tissue and organ growth. I discuss molecular signaling as a stochastic process and propose that the iterative and architectural nature of plant growth is more usefully represented by deterministic models based upon structural, surficial, and stress-mechanical information networks that come into play at the trans-cellular level.
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9
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Matz TW, Wang Y, Kulshreshtha R, Sampathkumar A, Nikoloski Z. Topological properties accurately predict cell division events and organization of shoot apical meristem in Arabidopsis thaliana. Development 2022; 149:276347. [DOI: 10.1242/dev.201024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/15/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Cell division and the resulting changes to the cell organization affect the shape and functionality of all tissues. Thus, understanding the determinants of the tissue-wide changes imposed by cell division is a key question in developmental biology. Here, we use a network representation of live cell imaging data from shoot apical meristems (SAMs) in Arabidopsis thaliana to predict cell division events and their consequences at the tissue level. We show that a support vector machine classifier based on the SAM network properties is predictive of cell division events, with test accuracy of 76%, which matches that based on cell size alone. Furthermore, we demonstrate that the combination of topological and biological properties, including cell size, perimeter, distance and shared cell wall between cells, can further boost the prediction accuracy of resulting changes in topology triggered by cell division. Using our classifiers, we demonstrate the importance of microtubule-mediated cell-to-cell growth coordination in influencing tissue-level topology. Together, the results from our network-based analysis demonstrate a feedback mechanism between tissue topology and cell division in A. thaliana SAMs.
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Affiliation(s)
- Timon W. Matz
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam 1 , 14476 Potsdam , Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology 2 , 14476 Potsdam , Germany
| | - Yang Wang
- Plant Cell Biology and Microscopy, Max Planck Institute of Molecular Plant Physiology 3 , 14476 Potsdam , Germany
| | - Ritika Kulshreshtha
- Plant Cell Biology and Microscopy, Max Planck Institute of Molecular Plant Physiology 3 , 14476 Potsdam , Germany
| | - Arun Sampathkumar
- Plant Cell Biology and Microscopy, Max Planck Institute of Molecular Plant Physiology 3 , 14476 Potsdam , Germany
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam 1 , 14476 Potsdam , Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology 2 , 14476 Potsdam , Germany
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10
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Poulin V, Amesefe D, Gonzalez E, Alexandre H, Joly S. Testing candidate genes linked to corolla shape variation of a pollinator shift in Rhytidophyllum (Gesneriaceae). PLoS One 2022; 17:e0267540. [PMID: 35853078 PMCID: PMC9295946 DOI: 10.1371/journal.pone.0267540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/12/2022] [Indexed: 11/18/2022] Open
Abstract
Floral adaptations to specific pollinators like corolla shape variation often result in reproductive isolation and thus speciation. But despite their ecological importance, the genetic bases of corolla shape transitions are still poorly understood, especially outside model species. Hence, our goal was to identify candidate genes potentially involved in corolla shape variation between two closely related species of the Rhytidophyllum genus (Gesneriaceae family) from the Antilles with contrasting pollination strategies. Rhytidophyllum rupincola has a tubular corolla and is strictly pollinated by hummingbirds, whereas R. auriculatum has more open flowers and is pollinated by hummingbirds, bats, and insects. We surveyed the literature and used a comparative transcriptome sequence analysis of synonymous and non-synonymous nucleotide substitutions to obtain a list of genes that could explain floral variation between R. auriculatum and R. rupincola. We then tested their association with corolla shape variation using QTL mapping in a F2 hybrid population. Out of 28 genes tested, three were found to be good candidates because of a strong association with corolla shape: RADIALIS, GLOBOSA, and JAGGED. Although the role of these genes in Rhytidophyllum corolla shape variation remains to be confirmed, these findings are a first step towards identifying the genes that have been under selection by pollinators and thus involved in reproductive isolation and speciation in this genus.
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Affiliation(s)
- Valérie Poulin
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
| | - Delase Amesefe
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
| | - Emmanuel Gonzalez
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
- Department of Human Genetics, Canadian Centre for Computational Genomics (C3G), McGill University, Montréal, QC, Canada
- Microbiome Research Platform, McGill Interdisciplinary Initiative in Infection and Immunity (MI4), Genome Centre, McGill University, Montréal, QC, Canada
| | - Hermine Alexandre
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
| | - Simon Joly
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
- Montreal Botanical Garden, Montréal, Canada
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11
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Vijayan A, Strauss S, Tofanelli R, Mody TA, Lee K, Tsiantis M, Smith RS, Schneitz K. The annotation and analysis of complex 3D plant organs using 3DCoordX. PLANT PHYSIOLOGY 2022; 189:1278-1295. [PMID: 35348744 PMCID: PMC9237718 DOI: 10.1093/plphys/kiac145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/05/2022] [Indexed: 06/14/2023]
Abstract
A fundamental question in biology concerns how molecular and cellular processes become integrated during morphogenesis. In plants, characterization of 3D digital representations of organs at single-cell resolution represents a promising approach to addressing this problem. A major challenge is to provide organ-centric spatial context to cells of an organ. We developed several general rules for the annotation of cell position and embodied them in 3DCoordX, a user-interactive computer toolbox implemented in the open-source software MorphoGraphX. 3DCoordX enables rapid spatial annotation of cells even in highly curved biological shapes. Using 3DCoordX, we analyzed cellular growth patterns in organs of several species. For example, the data indicated the presence of a basal cell proliferation zone in the ovule primordium of Arabidopsis (Arabidopsis thaliana). Proof-of-concept analyses suggested a preferential increase in cell length associated with neck elongation in the archegonium of Marchantia (Marchantia polymorpha) and variations in cell volume linked to central morphogenetic features of a trap of the carnivorous plant Utricularia (Utricularia gibba). Our work demonstrates the broad applicability of the developed strategies as they provide organ-centric spatial context to cellular features in plant organs of diverse shape complexity.
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Affiliation(s)
| | | | - Rachele Tofanelli
- Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Tejasvinee Atul Mody
- Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | | | - Miltos Tsiantis
- Department of Comparative Developmental and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Richard S Smith
- Department of Comparative Developmental and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- The John Innes Centre, Norwich, UK
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12
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Banwarth-Kuhn M, Rodriguez K, Michael C, Ta CK, Plong A, Bourgain-Chang E, Nematbakhsh A, Chen W, Roy-Chowdhury A, Reddy GV, Alber M. Combined computational modeling and experimental analysis integrating chemical and mechanical signals suggests possible mechanism of shoot meristem maintenance. PLoS Comput Biol 2022; 18:e1010199. [PMID: 35727850 PMCID: PMC9249181 DOI: 10.1371/journal.pcbi.1010199] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 07/01/2022] [Accepted: 05/12/2022] [Indexed: 11/19/2022] Open
Abstract
Stem cell maintenance in multilayered shoot apical meristems (SAMs) of plants requires strict regulation of cell growth and division. Exactly how the complex milieu of chemical and mechanical signals interact in the central region of the SAM to regulate cell division plane orientation is not well understood. In this paper, simulations using a newly developed multiscale computational model are combined with experimental studies to suggest and test three hypothesized mechanisms for the regulation of cell division plane orientation and the direction of anisotropic cell expansion in the corpus. Simulations predict that in the Apical corpus, WUSCHEL and cytokinin regulate the direction of anisotropic cell expansion, and cells divide according to tensile stress on the cell wall. In the Basal corpus, model simulations suggest dual roles for WUSCHEL and cytokinin in regulating both the direction of anisotropic cell expansion and cell division plane orientation. Simulation results are followed by a detailed analysis of changes in cell characteristics upon manipulation of WUSCHEL and cytokinin in experiments that support model predictions. Moreover, simulations predict that this layer-specific mechanism maintains both the experimentally observed shape and structure of the SAM as well as the distribution of WUSCHEL in the tissue. This provides an additional link between the roles of WUSCHEL, cytokinin, and mechanical stress in regulating SAM growth and proper stem cell maintenance in the SAM.
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Affiliation(s)
- Mikahl Banwarth-Kuhn
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Applied Mathematics, University of California, Merced, California, United States of America
- Department of Mathematics, University of California, Riverside, California, United States of America
| | - Kevin Rodriguez
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
- Center for Plant Cell Biology, University of California, Riverside, California, United States of America
- Institute for Integrative Genome Biology, University of California, Riverside, California, United States of America
| | - Christian Michael
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Mathematics, University of California, Riverside, California, United States of America
| | - Calvin-Khang Ta
- Computer Science and Engineering Department, University of California, Riverside, California, United States of America
| | - Alexander Plong
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
- Center for Plant Cell Biology, University of California, Riverside, California, United States of America
- Institute for Integrative Genome Biology, University of California, Riverside, California, United States of America
| | - Eric Bourgain-Chang
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Mathematics, University of California, Riverside, California, United States of America
| | - Ali Nematbakhsh
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Mathematics, University of California, Riverside, California, United States of America
| | - Weitao Chen
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Mathematics, University of California, Riverside, California, United States of America
| | - Amit Roy-Chowdhury
- Computer Science and Engineering Department, University of California, Riverside, California, United States of America
- Department of Electrical and Computer Engineering, University of California, Riverside, California, United States of America
| | - G. Venugopala Reddy
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
- Center for Plant Cell Biology, University of California, Riverside, California, United States of America
- Institute for Integrative Genome Biology, University of California, Riverside, California, United States of America
| | - Mark Alber
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Mathematics, University of California, Riverside, California, United States of America
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13
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Strauss S, Runions A, Lane B, Eschweiler D, Bajpai N, Trozzi N, Routier-Kierzkowska AL, Yoshida S, Rodrigues da Silveira S, Vijayan A, Tofanelli R, Majda M, Echevin E, Le Gloanec C, Bertrand-Rakusova H, Adibi M, Schneitz K, Bassel G, Kierzkowski D, Stegmaier J, Tsiantis M, Smith RS. Using positional information to provide context for biological image analysis with MorphoGraphX 2.0. eLife 2022; 11:72601. [PMID: 35510843 PMCID: PMC9159754 DOI: 10.7554/elife.72601] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
Positional information is a central concept in developmental biology. In developing organs, positional information can be idealized as a local coordinate system that arises from morphogen gradients controlled by organizers at key locations. This offers a plausible mechanism for the integration of the molecular networks operating in individual cells into the spatially coordinated multicellular responses necessary for the organization of emergent forms. Understanding how positional cues guide morphogenesis requires the quantification of gene expression and growth dynamics in the context of their underlying coordinate systems. Here, we present recent advances in the MorphoGraphX software (Barbier de Reuille et al., 2015) that implement a generalized framework to annotate developing organs with local coordinate systems. These coordinate systems introduce an organ-centric spatial context to microscopy data, allowing gene expression and growth to be quantified and compared in the context of the positional information thought to control them.
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Affiliation(s)
- Sören Strauss
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Adam Runions
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Dennis Eschweiler
- Institute of Imaging and Computer Vision, RWTH Aachen University, Aachen, Germany
| | - Namrata Bajpai
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | | | - Saiko Yoshida
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Athul Vijayan
- School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Rachele Tofanelli
- School of Life Sciences, Technical University of Munich, Freising, Germany
| | | | - Emillie Echevin
- Department of Biological Sciences, University of Montreal, Montreal, Canada
| | | | | | - Milad Adibi
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kay Schneitz
- School of Life Sciences, Technical University of Munich, Freising, Germany
| | - George Bassel
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Daniel Kierzkowski
- Department of Biological Sciences, University of Montreal, Montreal, Canada
| | - Johannes Stegmaier
- Institute of Imaging and Computer Vision, RWTH Aachen University, Aachen, Germany
| | - Miltos Tsiantis
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
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14
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Stöckle D, Reyes-Hernández BJ, Barro AV, Nenadić M, Winter Z, Marc-Martin S, Bald L, Ursache R, Fujita S, Maizel A, Vermeer JEM. Microtubule-based perception of mechanical conflicts controls plant organ morphogenesis. SCIENCE ADVANCES 2022; 8:eabm4974. [PMID: 35138892 PMCID: PMC8827652 DOI: 10.1126/sciadv.abm4974] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/22/2021] [Indexed: 05/30/2023]
Abstract
Precise coordination between cells and tissues is essential for differential growth in plants. During lateral root formation in Arabidopsis thaliana, the endodermis is actively remodeled to allow outgrowth of the new organ. Here, we show that microtubule arrays facing lateral root founder cells display a higher order compared to arrays on the opposite side of the same cell, and this asymmetry is required for endodermal remodeling and lateral root initiation. We identify that MICROTUBULE ASSOCIATED PROTEIN 70-5 (MAP70-5) is necessary for the establishment of this spatially defined microtubule organization and endodermis remodeling and thus contributes to lateral root morphogenesis. We propose that MAP70-5 and cortical microtubule arrays in the endodermis integrate the mechanical signals generated by lateral root outgrowth, facilitating the channeling of organogenesis.
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Affiliation(s)
- Dorothee Stöckle
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
- Laboratory of Cell and Molecular Biology, Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, CH-2000 Neuchâtel, Switzerland
| | | | - Amaya Vilches Barro
- Center for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Milica Nenadić
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Zsofiá Winter
- Laboratory of Cell and Molecular Biology, Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Sophie Marc-Martin
- Laboratory of Cell and Molecular Biology, Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Lotte Bald
- Center for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Robertas Ursache
- Department of Molecular Plant Biology, University of Lausanne, UNIL-Sorge, 1015 Lausanne, Switzerland
| | - Satoshi Fujita
- Department of Molecular Plant Biology, University of Lausanne, UNIL-Sorge, 1015 Lausanne, Switzerland
| | - Alexis Maizel
- Laboratory of Cell and Molecular Biology, Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Joop EM Vermeer
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
- Laboratory of Cell and Molecular Biology, Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, CH-2000 Neuchâtel, Switzerland
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15
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Duncan KE, Czymmek KJ, Jiang N, Thies AC, Topp CN. X-ray microscopy enables multiscale high-resolution 3D imaging of plant cells, tissues, and organs. PLANT PHYSIOLOGY 2022; 188:831-845. [PMID: 34618094 PMCID: PMC8825331 DOI: 10.1093/plphys/kiab405] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/29/2021] [Indexed: 05/12/2023]
Abstract
Capturing complete internal anatomies of plant organs and tissues within their relevant morphological context remains a key challenge in plant science. While plant growth and development are inherently multiscale, conventional light, fluorescence, and electron microscopy platforms are typically limited to imaging of plant microstructure from small flat samples that lack a direct spatial context to, and represent only a small portion of, the relevant plant macrostructures. We demonstrate technical advances with a lab-based X-ray microscope (XRM) that bridge the imaging gap by providing multiscale high-resolution three-dimensional (3D) volumes of intact plant samples from the cell to the whole plant level. Serial imaging of a single sample is shown to provide sub-micron 3D volumes co-registered with lower magnification scans for explicit contextual reference. High-quality 3D volume data from our enhanced methods facilitate sophisticated and effective computational segmentation. Advances in sample preparation make multimodal correlative imaging workflows possible, where a single resin-embedded plant sample is scanned via XRM to generate a 3D cell-level map, and then used to identify and zoom in on sub-cellular regions of interest for high-resolution scanning electron microscopy. In total, we present the methodologies for use of XRM in the multiscale and multimodal analysis of 3D plant features using numerous economically and scientifically important plant systems.
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Affiliation(s)
- Keith E Duncan
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
| | - Kirk J Czymmek
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
| | - Ni Jiang
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
| | | | - Christopher N Topp
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
- Author for communication:
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16
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van Schijndel L, Snoek BL, ten Tusscher K. Embodiment in distributed information processing: "Solid" plants versus "liquid" ant colonies. QUANTITATIVE PLANT BIOLOGY 2022; 3:e27. [PMID: 37077985 PMCID: PMC10095861 DOI: 10.1017/qpb.2022.22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 05/02/2023]
Abstract
Information processing is an essential part of biology, enabling coordination of intra-organismal processes such as development, environmental adaptation and inter-organismal communication. Whilst in animals with specialised brain tissue a substantial amount of information processing occurs in a centralised manner, most biological computing is distributed across multiple entities, such as cells in a tissue, roots in a root system or ants in a colony. Physical context, called embodiment, also affects the nature of biological computing. While plants and ant colonies both perform distributed computing, in plants the units occupy fixed positions while individual ants move around. This distinction, solid versus liquid brain computing, shapes the nature of computations. Here we compare information processing in plants and ant colonies, highlighting how similarities and differences originate in, as well as make use of, the differences in embodiment. We end with a discussion on how this embodiment perspective may inform the debate on plant cognition.
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Affiliation(s)
- Laura van Schijndel
- Laboratory of Genetics, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | - Basten L. Snoek
- Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Kirsten ten Tusscher
- Computational Developmental Biology Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
- Author for correspondence: K. ten Tusscher, E-mail:
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17
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Refahi Y, Zardilis A, Michelin G, Wightman R, Leggio B, Legrand J, Faure E, Vachez L, Armezzani A, Risson AE, Zhao F, Das P, Prunet N, Meyerowitz EM, Godin C, Malandain G, Jönsson H, Traas J. A multiscale analysis of early flower development in Arabidopsis provides an integrated view of molecular regulation and growth control. Dev Cell 2021; 56:540-556.e8. [PMID: 33621494 PMCID: PMC8519405 DOI: 10.1016/j.devcel.2021.01.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/17/2020] [Accepted: 01/25/2021] [Indexed: 12/31/2022]
Abstract
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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Affiliation(s)
- Yassin Refahi
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK; Laboratoire RDP, Université de Lyon 1, ENS-Lyon, INRAE, CNRS, UCBL, 69364 Lyon, France; Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, 51097 Reims, France.
| | - Argyris Zardilis
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - Gaël Michelin
- Université Côte d'Azur, Inria, Sophia Antipolis, CNRS, I3S, France
| | - Raymond Wightman
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - Bruno Leggio
- Laboratoire RDP, Université de Lyon 1, ENS-Lyon, INRAE, CNRS, UCBL, 69364 Lyon, France
| | - Jonathan Legrand
- Laboratoire RDP, Université de Lyon 1, ENS-Lyon, INRAE, CNRS, UCBL, 69364 Lyon, France
| | | | - Laetitia Vachez
- Laboratoire RDP, Université de Lyon 1, ENS-Lyon, INRAE, CNRS, UCBL, 69364 Lyon, France
| | - Alessia Armezzani
- Laboratoire RDP, Université de Lyon 1, ENS-Lyon, INRAE, CNRS, UCBL, 69364 Lyon, France
| | - Anne-Evodie Risson
- Laboratoire RDP, Université de Lyon 1, ENS-Lyon, INRAE, CNRS, UCBL, 69364 Lyon, France
| | - Feng Zhao
- Laboratoire RDP, Université de Lyon 1, ENS-Lyon, INRAE, CNRS, UCBL, 69364 Lyon, France
| | - Pradeep Das
- Laboratoire RDP, Université de Lyon 1, ENS-Lyon, INRAE, CNRS, UCBL, 69364 Lyon, France
| | - Nathanaël Prunet
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
| | - Elliot M Meyerowitz
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK; Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute and Division of Biology and Biological Engineering 156-29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Christophe Godin
- Laboratoire RDP, Université de Lyon 1, ENS-Lyon, INRAE, CNRS, UCBL, 69364 Lyon, France
| | | | - Henrik Jönsson
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK; Computational Biology and Biological Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden; Department of Applied Mathematics and Theoretical Physics (DAMTP), University of Cambridge, Cambridge, UK.
| | - Jan Traas
- Laboratoire RDP, Université de Lyon 1, ENS-Lyon, INRAE, CNRS, UCBL, 69364 Lyon, France.
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18
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Genetic Architecture and Genome-Wide Adaptive Signatures Underlying Stem Lenticel Traits in Populus tomentosa. Int J Mol Sci 2021; 22:ijms22179249. [PMID: 34502156 PMCID: PMC8431110 DOI: 10.3390/ijms22179249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/21/2021] [Accepted: 08/25/2021] [Indexed: 11/17/2022] Open
Abstract
The stem lenticel is a highly specialized tissue of woody plants that has evolved to balance stem water retention and gas exchange as an adaptation to local environments. In this study, we applied genome-wide association studies and selective sweeping analysis to characterize the genetic architecture and genome-wide adaptive signatures underlying stem lenticel traits among 303 unrelated accessions of P. tomentosa, which has significant phenotypic and genetic variations according to climate region across its natural distribution. In total, we detected 108 significant single-nucleotide polymorphisms, annotated to 88 candidate genes for lenticel, of which 9 causative genes showed significantly different selection signatures among climate regions. Furthermore, PtoNAC083 and PtoMYB46 showed significant association signals and abiotic stress response, so we overexpressed these two genes in Arabidopsis thaliana and found that the number of stem cells in all three overexpression lines was significantly reduced by PtoNAC083 overexpression but slightly increased by PtoMYB46 overexpression, suggesting that both genes are involved in cell division and expansion during lenticel formation. The findings of this study demonstrate the successful application of an integrated strategy for dissecting the genetic basis and landscape genetics of complex adaptive traits, which will facilitate the molecular design of tree ideotypes that may adapt to future climate and environmental changes.
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19
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Robinson S. Mechanobiology of cell division in plant growth. THE NEW PHYTOLOGIST 2021; 231:559-564. [PMID: 33774836 DOI: 10.1111/nph.17369] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
Cell division in plants is particularly important as cells cannot rearrange. It therefore determines the arrangement of cells (topology) and their size and shape (geometry). Cell division reduces mechanical stress locally by producing smaller cells and alters mechanical properties by reinforcing the mechanical wall network, both of which can alter overall tissue morphology. Division orientation is often regarded as following geometric rules, however recent work has suggested that divisions align with the direction of maximal tensile stress. Mechanical stress has already been shown to feed into many processes of development including those that alter mechanical properties. Such an alignment may enable cell division to selectively reinforce the cell wall network in the direction of maximal tensile stress. Therefore there exists potential feedback between cell division, mechanical stress and growth. Improving our understanding of this topic will help to shed light on the debated role of cell division in organ scale growth.
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Affiliation(s)
- Sarah Robinson
- Sainsbury Laboratory, Cambridge University, Bateman St., Cambridge, CB2 1LR, UK
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20
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Vernoux T, Besnard F, Godin C. What shoots can teach about theories of plant form. NATURE PLANTS 2021; 7:716-724. [PMID: 34099903 DOI: 10.1038/s41477-021-00930-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
Plants generate a large variety of shoot forms with regular geometries. These forms emerge primarily from the activity of a stem cell niche at the shoot tip. Recent efforts have established a theoretical framework of form emergence at the shoot tip, which has empowered the use of modelling in conjunction with biological approaches to begin to disentangle the biochemical and physical mechanisms controlling form development at the shoot tip. Here, we discuss how these advances get us closer to identifying the construction principles of plant shoot tips. Considering the current limits of our knowledge, we propose a roadmap for developing a general theory of form development at the shoot tip.
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Affiliation(s)
- Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA, Lyon, France.
| | - Fabrice Besnard
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA, Lyon, France
| | - Christophe Godin
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA, Lyon, France
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21
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Yin X. Phyllotaxis: from classical knowledge to molecular genetics. JOURNAL OF PLANT RESEARCH 2021; 134:373-401. [PMID: 33550488 DOI: 10.1007/s10265-020-01247-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Plant organs are repetitively generated at the shoot apical meristem (SAM) in recognizable patterns. This phenomenon, known as phyllotaxis, has long fascinated scientists from different disciplines. While we have an enriched body of knowledge on phyllotactic patterns, parameters, and transitions, only in the past 20 years, however, have we started to identify genes and elucidate genetic pathways that involved in phyllotaxis. In this review, I first summarize the classical knowledge of phyllotaxis from a morphological perspective. I then discuss recent advances in the regulation of phyllotaxis, from a molecular genetics perspective. I show that the morphological beauty of phyllotaxis we appreciate is the manifestation of many regulators, in addition to the critical role of auxin as a patterning signal, exerting their respective effects in a coordinated fashion either directly or indirectly in the SAM.
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Affiliation(s)
- Xiaofeng Yin
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Japan Society for the Promotion of Science, Tokyo, Japan.
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22
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Zhang X, Man Y, Zhuang X, Shen J, Zhang Y, Cui Y, Yu M, Xing J, Wang G, Lian N, Hu Z, Ma L, Shen W, Yang S, Xu H, Bian J, Jing Y, Li X, Li R, Mao T, Jiao Y, Sodmergen, Ren H, Lin J. Plant multiscale networks: charting plant connectivity by multi-level analysis and imaging techniques. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1392-1422. [PMID: 33974222 DOI: 10.1007/s11427-020-1910-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/04/2021] [Indexed: 12/21/2022]
Abstract
In multicellular and even single-celled organisms, individual components are interconnected at multiscale levels to produce enormously complex biological networks that help these systems maintain homeostasis for development and environmental adaptation. Systems biology studies initially adopted network analysis to explore how relationships between individual components give rise to complex biological processes. Network analysis has been applied to dissect the complex connectivity of mammalian brains across different scales in time and space in The Human Brain Project. In plant science, network analysis has similarly been applied to study the connectivity of plant components at the molecular, subcellular, cellular, organic, and organism levels. Analysis of these multiscale networks contributes to our understanding of how genotype determines phenotype. In this review, we summarized the theoretical framework of plant multiscale networks and introduced studies investigating plant networks by various experimental and computational modalities. We next discussed the currently available analytic methodologies and multi-level imaging techniques used to map multiscale networks in plants. Finally, we highlighted some of the technical challenges and key questions remaining to be addressed in this emerging field.
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Affiliation(s)
- Xi Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yi Man
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaohong Zhuang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Jinbo Shen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Yi Zhang
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Science, Beijing Normal University, Beijing, 100875, China
| | - Yaning Cui
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Meng Yu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Jingjing Xing
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 457004, China
| | - Guangchao Wang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Na Lian
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Zijian Hu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Lingyu Ma
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Weiwei Shen
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Shunyao Yang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Huimin Xu
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jiahui Bian
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yanping Jing
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaojuan Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Ruili Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Tonglin Mao
- State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing, 100101, China
| | - Sodmergen
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Haiyun Ren
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Science, Beijing Normal University, Beijing, 100875, China
| | - Jinxing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China. .,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
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23
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Vijayan A, Tofanelli R, Strauss S, Cerrone L, Wolny A, Strohmeier J, Kreshuk A, Hamprecht FA, Smith RS, Schneitz K. A digital 3D reference atlas reveals cellular growth patterns shaping the Arabidopsis ovule. eLife 2021; 10:e63262. [PMID: 33404501 PMCID: PMC7787667 DOI: 10.7554/elife.63262] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 12/19/2020] [Indexed: 12/23/2022] Open
Abstract
A fundamental question in biology is how morphogenesis integrates the multitude of processes that act at different scales, ranging from the molecular control of gene expression to cellular coordination in a tissue. Using machine-learning-based digital image analysis, we generated a three-dimensional atlas of ovule development in Arabidopsis thaliana, enabling the quantitative spatio-temporal analysis of cellular and gene expression patterns with cell and tissue resolution. We discovered novel morphological manifestations of ovule polarity, a new mode of cell layer formation, and previously unrecognized subepidermal cell populations that initiate ovule curvature. The data suggest an irregular cellular build-up of WUSCHEL expression in the primordium and new functions for INNER NO OUTER in restricting nucellar cell proliferation and the organization of the interior chalaza. Our work demonstrates the analytical power of a three-dimensional digital representation when studying the morphogenesis of an organ of complex architecture that eventually consists of 1900 cells.
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Affiliation(s)
- Athul Vijayan
- Plant Developmental Biology, School of Life Sciences, Technical University of MunichFreisingGermany
| | - Rachele Tofanelli
- Plant Developmental Biology, School of Life Sciences, Technical University of MunichFreisingGermany
| | - Sören Strauss
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding ResearchCologneGermany
| | - Lorenzo Cerrone
- Heidelberg Collaboratory for Image Processing, Dept. of Physics and Astronomy, Heidelberg UniversityHeidelbergGermany
| | - Adrian Wolny
- Heidelberg Collaboratory for Image Processing, Dept. of Physics and Astronomy, Heidelberg UniversityHeidelbergGermany
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Joanna Strohmeier
- Plant Developmental Biology, School of Life Sciences, Technical University of MunichFreisingGermany
| | - Anna Kreshuk
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Fred A Hamprecht
- Heidelberg Collaboratory for Image Processing, Dept. of Physics and Astronomy, Heidelberg UniversityHeidelbergGermany
| | - Richard S Smith
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding ResearchCologneGermany
| | - Kay Schneitz
- Plant Developmental Biology, School of Life Sciences, Technical University of MunichFreisingGermany
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24
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Autran D, Bassel GW, Chae E, Ezer D, Ferjani A, Fleck C, Hamant O, Hartmann FP, Jiao Y, Johnston IG, Kwiatkowska D, Lim BL, Mahönen AP, Morris RJ, Mulder BM, Nakayama N, Sozzani R, Strader LC, ten Tusscher K, Ueda M, Wolf S. What is quantitative plant biology? QUANTITATIVE PLANT BIOLOGY 2021; 2:e10. [PMID: 37077212 PMCID: PMC10095877 DOI: 10.1017/qpb.2021.8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 05/03/2023]
Abstract
Quantitative plant biology is an interdisciplinary field that builds on a long history of biomathematics and biophysics. Today, thanks to high spatiotemporal resolution tools and computational modelling, it sets a new standard in plant science. Acquired data, whether molecular, geometric or mechanical, are quantified, statistically assessed and integrated at multiple scales and across fields. They feed testable predictions that, in turn, guide further experimental tests. Quantitative features such as variability, noise, robustness, delays or feedback loops are included to account for the inner dynamics of plants and their interactions with the environment. Here, we present the main features of this ongoing revolution, through new questions around signalling networks, tissue topology, shape plasticity, biomechanics, bioenergetics, ecology and engineering. In the end, quantitative plant biology allows us to question and better understand our interactions with plants. In turn, this field opens the door to transdisciplinary projects with the society, notably through citizen science.
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Affiliation(s)
- Daphné Autran
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - George W. Bassel
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Eunyoung Chae
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Daphne Ezer
- The Alan Turing Institute, London, United Kingdom
- Department of Statistics, University of Warwick, Coventry, United Kingdom
- Department of Biology, University of York, York, United Kingdom
| | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, Tokyo, Japan
| | - Christian Fleck
- Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Breisgau, Germany
| | - Olivier Hamant
- Laboratoire de Reproduction et Développement des Plantes, École normale supérieure (ENS) de Lyon, Université Claude Bernard Lyon (UCBL), Lyon, France
- Institut national de recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), CNRS, Université de Lyon, Lyon, France
- Author for correspondence: O. Hamant and A. P. Mahönen, E-mail: ,
| | | | - Yuling Jiao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Dorota Kwiatkowska
- Institute of Biology, Biotechnology and Environment Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Boon L. Lim
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Ari Pekka Mahönen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Richard J. Morris
- Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Bela M. Mulder
- Department of Living Matter, Institute AMOLF, Amsterdam, The Netherlands
| | - Naomi Nakayama
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Ross Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North CarolinaUSA
| | - Lucia C. Strader
- Department of Biology, Duke University, Durham, North Carolina, USA
- NSF Science and Technology Center for Engineering Mechanobiology, Department of Biology, Washington University in St. Louis, St. Louis, MissouriUSA
| | - Kirsten ten Tusscher
- Theoretical Biology, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Minako Ueda
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Sebastian Wolf
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
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25
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Serra L, Robinson S. Plant cell divisions: variations from the shortest symmetric path. Biochem Soc Trans 2020; 48:2743-2752. [PMID: 33336690 PMCID: PMC7752081 DOI: 10.1042/bst20200529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 02/08/2023]
Abstract
In plants, the spatial arrangement of cells within tissues and organs is a direct consequence of the positioning of the new cell walls during cell division. Since the nineteenth century, scientists have proposed rules to explain the orientation of plant cell divisions. Most of these rules predict the new wall will follow the shortest path passing through the cell centroid halving the cell into two equal volumes. However, in some developmental contexts, divisions deviate significantly from this rule. In these situations, mechanical stress, hormonal signalling, or cell polarity have been described to influence the division path. Here we discuss the mechanism and subcellular structure required to define the cell division placement then we provide an overview of the situations where division deviates from the shortest symmetric path.
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Affiliation(s)
- Léo Serra
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, U.K
| | - Sarah Robinson
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, U.K
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Abstract
A transition from qualitative to quantitative descriptors of morphology has been facilitated through the growing field of morphometrics, representing the conversion of shapes and patterns into numbers. The analysis of plant form at the macromorphological scale using morphometric approaches quantifies what is commonly referred to as a phenotype. Quantitative phenotypic analysis of individuals with contrasting genotypes in turn provides a means to establish links between genes and shapes. The path from a gene to a morphological phenotype is, however, not direct, with instructive information progressing both across multiple scales of biological complexity and through nonintuitive feedback, such as mechanical signals. In this review, we explore morphometric approaches used to perform whole-plant phenotyping and quantitative approaches in capture processes in the mesoscales, which bridge the gaps between genes and shapes in plants. Quantitative frameworks involving both the computational simulation and the discretization of data into networks provide a putative path to predicting emergent shape from underlying genetic programs.
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Affiliation(s)
- Hao Xu
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom;
| | - George W Bassel
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom;
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27
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Unraveling spatial cellular pattern by computational tissue shuffling. Commun Biol 2020; 3:605. [PMID: 33097821 PMCID: PMC7584651 DOI: 10.1038/s42003-020-01323-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 09/23/2020] [Indexed: 11/08/2022] Open
Abstract
Cell biology relies largely on reproducible visual observations. Unlike cell culture, tissues are heterogeneous, making difficult the collection of biological replicates that would spotlight a precise location. In consequence, there is no standard approach for estimating the statistical significance of an observed pattern in a tissue sample. Here, we introduce SET (for Synthesis of Epithelial Tissue), a method that can accurately reconstruct the cell tessellation formed by an epithelium in a microscopy image as well as thousands of alternative synthetic tessellations made of the exact same cells. SET can build an accurate null distribution to statistically test if any local pattern is necessarily the result of a process, or if it could be explained by chance in the given context. We provide examples in various tissues where visible, and invisible, cell and subcellular patterns are unraveled in a statistically significant manner using a single image and without any parameter settings.
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28
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Zhang X, Hu Z, Guo Y, Shan X, Li X, Lin J. High-efficiency procedure to characterize, segment, and quantify complex multicellularity in raw micrographs in plants. PLANT METHODS 2020; 16:100. [PMID: 32742298 PMCID: PMC7390866 DOI: 10.1186/s13007-020-00642-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/20/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND The increasing number of novel approaches for large-scale, multi-dimensional imaging of cells has created an unprecedented opportunity to analyze plant morphogenesis. However, complex image processing, including identifying specific cells and quantitating parameters, and high running cost of some image analysis softwares remains challenging. Therefore, it is essential to develop an efficient method for identifying plant complex multicellularity in raw micrographs in plants. RESULTS Here, we developed a high-efficiency procedure to characterize, segment, and quantify plant multicellularity in various raw images using the open-source software packages ImageJ and SR-Tesseler. This procedure allows for the rapid, accurate, automatic quantification of cell patterns and organization at different scales, from large tissues down to the cellular level. We validated our method using different images captured from Arabidopsis thaliana roots and seeds and Populus tremula stems, including fluorescently labeled images, Micro-CT scans, and dyed sections. Finally, we determined the area, centroid coordinate, perimeter, and Feret's diameter of the cells and harvested the cell distribution patterns from Voronoï diagrams by setting the threshold at localization density, mean distance, or area. CONCLUSIONS This procedure can be used to determine the character and organization of multicellular plant tissues at high efficiency, including precise parameter identification and polygon-based segmentation of plant cells.
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Affiliation(s)
- Xi Zhang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 10083 China
| | - Zijian Hu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 10083 China
| | - Yayu Guo
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 10083 China
| | - Xiaoyi Shan
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 10083 China
| | - Xiaojuan Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 10083 China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 10083 China
| | - Jinxing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 10083 China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 10083 China
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29
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Duran-Nebreda S, Johnston IG, Bassel GW. Efficient vasculature investment in tissues can be determined without global information. J R Soc Interface 2020; 17:20200137. [PMID: 32316879 PMCID: PMC7211487 DOI: 10.1098/rsif.2020.0137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/24/2020] [Indexed: 12/28/2022] Open
Abstract
Cells are the fundamental building blocks of organs and tissues. Information and mass flow through cellular contacts in these structures is vital for the orchestration of organ function. Constraints imposed by packing and cell immobility limit intercellular communication, particularly as organs and organisms scale up to greater sizes. In order to transcend transport limitations, delivery systems including vascular and respiratory systems evolved to facilitate the movement of matter and information. The construction of these delivery systems has an associated cost, as vascular elements do not perform the metabolic functions of the organs they are part of. This study investigates a fundamental trade-off in vascularization in multicellular tissues: the reduction of path lengths for communication versus the cost associated with producing vasculature. Biologically realistic generative models, using multicellular templates of different dimensionalities, revealed a limited advantage to the vascularization of two-dimensional tissues. Strikingly, scale-free improvements in transport efficiency can be achieved even in the absence of global knowledge of tissue organization. A point of diminishing returns in the investment of additional vascular tissue to the increased reduction of path length in 2.5- and three-dimensional tissues was identified. Applying this theory to experimentally determined biological tissue structures, we show the possibility of a co-dependency between the method used to limit path length and the organization of cells it acts upon. These results provide insight as to why tissues are or are not vascularized in nature, the robustness of developmental generative mechanisms and the extent to which vasculature is advantageous in the support of organ function.
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Affiliation(s)
| | - Iain G Johnston
- Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen, Norway
| | - George W Bassel
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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30
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31
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A system-level mechanistic explanation for asymmetric stem cell fates: Arabidopsis thaliana root niche as a study system. Sci Rep 2020; 10:3525. [PMID: 32103059 PMCID: PMC7044435 DOI: 10.1038/s41598-020-60251-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/23/2019] [Indexed: 11/09/2022] Open
Abstract
Asymmetric divisions maintain long-term stem cell populations while producing new cells that proliferate and then differentiate. Recent reports in animal systems show that divisions of stem cells can be uncoupled from their progeny differentiation, and the outcome of a division could be influenced by microenvironmental signals. But the underlying system-level mechanisms, and whether this dynamics also occur in plant stem cell niches (SCN), remain elusive. This article presents a cell fate regulatory network model that contributes to understanding such mechanism and identify critical cues for cell fate transitions in the root SCN. Novel computational and experimental results show that the transcriptional regulator SHR is critical for the most frequent asymmetric division previously described for quiescent centre stem cells. A multi-scale model of the root tip that simulated each cell's intracellular regulatory network, and the dynamics of SHR intercellular transport as a cell-cell coupling mechanism, was developed. It revealed that quiescent centre cell divisions produce two identical cells, that may acquire different fates depending on the feedback between SHR's availability and the state of the regulatory network. Novel experimental data presented here validates our model, which in turn, constitutes the first proposed systemic mechanism for uncoupled SCN cell division and differentiation.
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32
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Ovečka M, Luptovčiak I, Komis G, Šamajová O, Samakovli D, Šamaj J. Spatiotemporal Pattern of Ectopic Cell Divisions Contribute to Mis-Shaped Phenotype of Primary and Lateral Roots of katanin1 Mutant. FRONTIERS IN PLANT SCIENCE 2020; 11:734. [PMID: 32582258 PMCID: PMC7296145 DOI: 10.3389/fpls.2020.00734] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/07/2020] [Indexed: 05/04/2023]
Abstract
Pattern formation, cell proliferation, and directional cell growth, are driving factors of plant organ shape, size, and overall vegetative development. The establishment of vegetative morphogenesis strongly depends on spatiotemporal control and synchronization of formative and proliferative cell division patterns. In this context, the progression of cell division and the regulation of cell division plane orientation are defined by molecular mechanisms converging to the proper positioning and temporal reorganization of microtubule arrays such as the preprophase microtubule band, the mitotic spindle and the cytokinetic phragmoplast. By focusing on the tractable example of primary root development and lateral root emergence in Arabidopsis thaliana, genetic studies have highlighted the importance of mechanisms underlying microtubule reorganization in the establishment of the root system. In this regard, severe alterations of root growth, and development found in extensively studied katanin1 mutants of A. thaliana (fra2, lue1, and ktn1-2), were previously attributed to defective rearrangements of cortical microtubules and aberrant cell division plane reorientation. How KATANIN1-mediated microtubule severing contributes to tissue patterning and organ morphogenesis, ultimately leading to anisotropy in microtubule organization is a trending topic under vigorous investigation. Here we addressed this issue during root development, using advanced light-sheet fluorescence microscopy (LSFM) and long-term imaging of ktn1-2 mutant expressing the GFP-TUA6 microtubule marker. This method allowed spatial and temporal monitoring of cell division patterns in growing roots. Analysis of acquired multidimensional data sets revealed the occurrence of ectopic cell divisions in various tissues including the calyptrogen and the protoxylem of the main root, as well as in lateral root primordia. Notably the ktn1-2 mutant exhibited excessive longitudinal cell divisions (parallel to the root axis) at ectopic positions. This suggested that changes in the cell division pattern and the occurrence of ectopic cell divisions contributed significantly to pleiotropic root phenotypes of ktn1-2 mutant. LSFM provided evidence that KATANIN1 is required for the spatiotemporal control of cell divisions and establishment of tissue patterns in living A. thaliana roots.
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33
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Jones AR, Band LR, Murray JAH. Double or Nothing? Cell Division and Cell Size Control. TRENDS IN PLANT SCIENCE 2019; 24:1083-1093. [PMID: 31630972 DOI: 10.1016/j.tplants.2019.09.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 08/08/2019] [Accepted: 09/06/2019] [Indexed: 06/10/2023]
Abstract
Size is a fundamental property that must be tightly regulated to ensure that cells and tissues function efficiently. Dynamic size control allows unicellular organisms to adapt to environmental changes, but cell size is also integral to multicellular development, affecting tissue size and structure. Despite clear evidence for homeostatic cell size maintenance, we are only now beginning to understand cell size regulation in the actively dividing meristematic tissues of higher plants. We discuss here how coupled advances in live cell imaging and modelling are uncovering dynamic mechanisms for size control mediated at the cellular level. We argue that integrated models of cell growth and division will be necessary to predict cell size and fully understand multicellular growth and development.
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Affiliation(s)
- Angharad R Jones
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK.
| | - Leah R Band
- Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK; Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - James A H Murray
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK
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34
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Echevin E, Le Gloanec C, Skowrońska N, Routier-Kierzkowska AL, Burian A, Kierzkowski D. Growth and biomechanics of shoot organs. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3573-3585. [PMID: 31037307 DOI: 10.1093/jxb/erz205] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 04/17/2019] [Indexed: 06/09/2023]
Abstract
Plant organs arise through complex interactions between biological and physical factors that control morphogenesis. While there has been tremendous progress in the understanding of the genetics behind development, we know much less about how mechanical forces control growth in plants. In recent years, new multidisciplinary research combining genetics, live-imaging, physics, and computational modeling has begun to fill this gap by revealing the crucial role of biomechanics in the establishment of plant organs. In this review, we provide an overview of our current understanding of growth during initiation, patterning, and expansion of shoot lateral organs. We discuss how growth is controlled by physical forces, and how mechanical stresses generated during growth can control morphogenesis at the level of both cells and tissues. Understanding the mechanical basis of growth and morphogenesis in plants is in its early days, and many puzzling facts are yet to be deciphered.
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Affiliation(s)
- Emilie Echevin
- Institut de Recherche en Biologie Végétale, Department of Biological Sciences, University of Montreal, Montréal, QC, Canada
| | - Constance Le Gloanec
- Institut de Recherche en Biologie Végétale, Department of Biological Sciences, University of Montreal, Montréal, QC, Canada
| | - Nikolina Skowrońska
- Department of Biophysics and Morphogenesis of Plants, University of Silesia, Jagiellońska, Katowice, Poland
| | - Anne-Lise Routier-Kierzkowska
- Institut de Recherche en Biologie Végétale, Department of Biological Sciences, University of Montreal, Montréal, QC, Canada
| | - Agata Burian
- Department of Biophysics and Morphogenesis of Plants, University of Silesia, Jagiellońska, Katowice, Poland
| | - Daniel Kierzkowski
- Institut de Recherche en Biologie Végétale, Department of Biological Sciences, University of Montreal, Montréal, QC, Canada
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35
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Bassel GW. Multicellular Systems Biology: Quantifying Cellular Patterning and Function in Plant Organs Using Network Science. MOLECULAR PLANT 2019; 12:731-742. [PMID: 30794885 DOI: 10.1016/j.molp.2019.02.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 02/14/2019] [Accepted: 02/14/2019] [Indexed: 06/09/2023]
Abstract
Organ function is at least partially shaped and constrained by the organization of their constituent cells. Extensive investigation has revealed mechanisms explaining how these patterns are generated, with less being known about their functional relevance. In this paper, a methodology to discretize and quantitatively analyze cellular patterning is described. By performing global organ-scale cellular interaction mapping, the organization of cells can be extracted and analyzed using network science. This provides a means to take the developmental analysis of cellular organization in complex organisms beyond qualitative descriptions and provides data-driven approaches to inferring cellular function. The bridging of a structure-function relationship in hypocotyl epidermal cell patterning through global topological analysis provides support for this approach. The analysis of cellular topologies from patterning mutants further enables the contribution of gene activity toward the organizational properties of tissues to be linked, bridging molecular and tissue scales. This systems-based approach to investigate multicellular complexity paves the way to uncovering the principles of complex organ design and achieving predictive genotype-phenotype mapping.
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Affiliation(s)
- George W Bassel
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK.
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36
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Beemster GTS. Cellular Dynamics, a Systems Biology Bottleneck. TRENDS IN PLANT SCIENCE 2019; 24:386-388. [PMID: 30905523 DOI: 10.1016/j.tplants.2019.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 06/09/2023]
Abstract
Developing a mechanistic understanding of plant growth regulation requires studying cell division and cell expansion in addition to molecular studies. A recent time-lapse confocal microscopy study (Fox, S. et al. PLoS Biol. 2018:16;e2005952) quantifying these processes in individual cells in growing organs in combination with multiscale modeling provides profound new insights into the regulatory mechanisms involved.
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Affiliation(s)
- Gerrit T S Beemster
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp 2020, Belgium.
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37
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Tofanelli R, Vijayan A, Scholz S, Schneitz K. Protocol for rapid clearing and staining of fixed Arabidopsis ovules for improved imaging by confocal laser scanning microscopy. PLANT METHODS 2019; 15:120. [PMID: 31673277 PMCID: PMC6814113 DOI: 10.1186/s13007-019-0505-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/17/2019] [Indexed: 05/15/2023]
Abstract
BACKGROUND A salient topic in developmental biology relates to the molecular and genetic mechanisms that underlie tissue morphogenesis. Modern quantitative approaches to this central question frequently involve digital cellular models of the organ or tissue under study. The ovules of the model species Arabidopsis thaliana have long been established as a model system for the study of organogenesis in plants. While ovule development in Arabidopsis can be followed by a variety of different imaging techniques, no experimental strategy presently exists that enables an easy and straightforward investigation of the morphology of internal tissues of the ovule with cellular resolution. RESULTS We developed a protocol for rapid and robust confocal microscopy of fixed Arabidopsis ovules of all stages. The method combines clearing of fixed ovules in ClearSee solution with marking the cell outline using the cell wall stain SCRI Renaissance 2200 and the nuclei with the stain TO-PRO-3 iodide. We further improved the microscopy by employing a homogenous immersion system aimed at minimizing refractive index differences. The method allows complete inspection of the cellular architecture even deep within the ovule. Using the new protocol we were able to generate digital three-dimensional models of ovules of various stages. CONCLUSIONS The protocol enables the quick and reproducible imaging of fixed Arabidopsis ovules of all developmental stages. From the imaging data three-dimensional digital ovule models with cellular resolution can be rapidly generated using image analysis software, for example MorphographX. Such digital models will provide the foundation for a future quantitative analysis of ovule morphogenesis in a model species.
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Affiliation(s)
- Rachele Tofanelli
- Entwicklungsbiologie der Pflanzen, Wissenschaftszentrum Weihenstephan, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Athul Vijayan
- Entwicklungsbiologie der Pflanzen, Wissenschaftszentrum Weihenstephan, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Sebastian Scholz
- Entwicklungsbiologie der Pflanzen, Wissenschaftszentrum Weihenstephan, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising, Germany
- Present Address: EU Research Lab, Technische Hochschule Wildau, 15745 Wildau, Germany
| | - Kay Schneitz
- Entwicklungsbiologie der Pflanzen, Wissenschaftszentrum Weihenstephan, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising, Germany
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38
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Montenegro-Johnson T, Strauss S, Jackson MDB, Walker L, Smith RS, Bassel GW. 3DCellAtlas Meristem: a tool for the global cellular annotation of shoot apical meristems. PLANT METHODS 2019; 15:33. [PMID: 30988692 PMCID: PMC6448224 DOI: 10.1186/s13007-019-0413-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 03/13/2019] [Indexed: 05/05/2023]
Abstract
Modern imaging approaches enable the acquisition of 3D and 4D datasets capturing plant organ development at cellular resolution. Computational analyses of these data enable the digitization and analysis of individual cells. In order to fully harness the information encoded within these datasets, annotation of the cell types within organs may be performed. This enables data points to be placed within the context of their position and identity, and for equivalent cell types to be compared between samples. The shoot apical meristem (SAM) in plants is the apical stem cell niche from which all above ground organs are derived. We developed 3DCellAtlas Meristem which enables the complete cellular annotation of all cells within the SAM with up to 96% accuracy across all cell types in Arabidopsis and 99% accuracy in tomato SAMs. Successive layers of cells are identified along with the central stem cells, boundary regions, and layers within developing primordia. Geometric analyses provide insight into the morphogenetic process that occurs during these developmental processes. Coupling these digital analyses with reporter expression will enable multidimensional analyses to be performed at single cell resolution. This provides a rapid and robust means to perform comprehensive cellular annotation of plant SAMs and digital single cell analyses, including cell geometry and gene expression. This fills a key gap in our ability to analyse and understand complex multicellular biology in the apical plant stem cell niche and paves the way for digital cellular atlases and analyses.
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Affiliation(s)
| | - Soeren Strauss
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Matthew D. B. Jackson
- School of Biosciences, College of Life and Environmental and Life Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Liam Walker
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL UK
| | - Richard S. Smith
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - George W. Bassel
- School of Biosciences, College of Life and Environmental and Life Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
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