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Chen M, Dai Y, Liao J, Wu H, Lv Q, Huang Y, Liu L, Feng Y, Lv H, Zhou B, Peng D. TARGET OF MONOPTEROS: key transcription factors orchestrating plant development and environmental response. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2214-2234. [PMID: 38195092 DOI: 10.1093/jxb/erae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/04/2024] [Indexed: 01/11/2024]
Abstract
Plants have an incredible ability to sustain root and vascular growth after initiation of the embryonic root and the specification of vascular tissue in early embryos. Microarray assays have revealed that a group of transcription factors, TARGET OF MONOPTEROS (TMO), are important for embryonic root initiation in Arabidopsis. Despite the discovery of their auxin responsiveness early on, their function and mode of action remained unknown for many years. The advent of genome editing has accelerated the study of TMO transcription factors, revealing novel functions for biological processes such as vascular development, root system architecture, and response to environmental cues. This review covers recent achievements in understanding the developmental function and the genetic mode of action of TMO transcription factors in Arabidopsis and other plant species. We highlight the transcriptional and post-transcriptional regulation of TMO transcription factors in relation to their function, mainly in Arabidopsis. Finally, we provide suggestions for further research and potential applications in plant genetic engineering.
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Affiliation(s)
- Min Chen
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Yani Dai
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Jiamin Liao
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Huan Wu
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Qiang Lv
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Yu Huang
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Lichang Liu
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Yu Feng
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Hongxuan Lv
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Bo Zhou
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
- Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province, 438107, Huaihua, Hunan, China
- National Engineering Laboratory of Applied Technology for Forestry and Ecology in Southern China, 410004, Changsha, Hunan, China
- Forestry Biotechnology Hunan Key Laboratories, Hunan, China
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
- Yuelushan Laboratory Carbon Sinks Forests Variety Innovation Center, 410004, Changsha, Hunan, China
| | - Dan Peng
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
- Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province, 438107, Huaihua, Hunan, China
- Forestry Biotechnology Hunan Key Laboratories, Hunan, China
- Yuelushan Laboratory Carbon Sinks Forests Variety Innovation Center, 410004, Changsha, Hunan, China
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2
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Do Plasmodesmata Play a Prominent Role in Regulation of Auxin-Dependent Genes at Early Stages of Embryogenesis? Cells 2021; 10:cells10040733. [PMID: 33810252 PMCID: PMC8066550 DOI: 10.3390/cells10040733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 01/24/2023] Open
Abstract
Plasmodesmata form intercellular channels which ensure the transport of various molecules during embryogenesis and postembryonic growth. However, high permeability of plasmodesmata may interfere with the establishment of auxin maxima, which are required for cellular patterning and the development of distinct tissues. Therefore, diffusion through plasmodesmata is not always desirable and the symplastic continuum must be broken up to induce or accomplish some developmental processes. Many data show the role of auxin maxima in the regulation of auxin-responsive genes and the establishment of various cellular patterns. However, still little is known whether and how these maxima are formed in the embryo proper before 16-cell stage, that is, when there is still a nonpolar distribution of auxin efflux carriers. In this work, we focused on auxin-dependent regulation of plasmodesmata function, which may provide rapid and transient changes of their permeability, and thus take part in the regulation of gene expression.
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3
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Smit ME, Llavata-Peris CI, Roosjen M, van Beijnum H, Novikova D, Levitsky V, Sevilem I, Roszak P, Slane D, Jürgens G, Mironova V, Brady SM, Weijers D. Specification and regulation of vascular tissue identity in the Arabidopsis embryo. Development 2020; 147:dev186130. [PMID: 32198154 DOI: 10.1242/dev.186130] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/05/2020] [Indexed: 12/30/2022]
Abstract
Development of plant vascular tissues involves tissue identity specification, growth, pattern formation and cell-type differentiation. Although later developmental steps are understood in some detail, it is still largely unknown how the tissue is initially specified. We used the early Arabidopsis embryo as a simple model to study this process. Using a large collection of marker genes, we found that vascular identity was specified in the 16-cell embryo. After a transient precursor state, however, there was no persistent uniform tissue identity. Auxin is intimately connected to vascular tissue development. We found that, although an AUXIN RESPONSE FACTOR5/MONOPTEROS (ARF5/MP)-dependent auxin response was required, it was not sufficient for tissue specification. We therefore used a large-scale enhanced yeast one-hybrid assay to identify potential regulators of vascular identity. Network and functional analysis of candidate regulators suggest that vascular identity is under robust, complex control. We found that one candidate regulator, the G-class bZIP transcription factor GBF2, can modulate vascular gene expression by tuning MP output through direct interaction. Our work uncovers components of a gene regulatory network that controls the initial specification of vascular tissue identity.
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Affiliation(s)
- Margot E Smit
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Cristina I Llavata-Peris
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Mark Roosjen
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Henriette van Beijnum
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Daria Novikova
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, 6708WE, The Netherlands
- Novosibirsk State University, LCT&EB, Novosibirsk, 630090, Russia
- Institute of Cytology and Genetics, Novosibirsk, 630090, Russia
| | - Victor Levitsky
- Novosibirsk State University, LCT&EB, Novosibirsk, 630090, Russia
- Institute of Cytology and Genetics, Novosibirsk, 630090, Russia
| | - Iris Sevilem
- Institute of Biotechnology, HiLIFE/Organismal and Evolurionary Biology Research Programma, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
| | - Pawel Roszak
- Institute of Biotechnology, HiLIFE/Organismal and Evolurionary Biology Research Programma, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | - Daniel Slane
- Max Planck Institute for Developmental Biology, Cell Biology, Tübingen, 72076, Germany
| | - Gerd Jürgens
- Max Planck Institute for Developmental Biology, Cell Biology, Tübingen, 72076, Germany
| | - Victoria Mironova
- Novosibirsk State University, LCT&EB, Novosibirsk, 630090, Russia
- Institute of Cytology and Genetics, Novosibirsk, 630090, Russia
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 95616, USA
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, 6708WE, The Netherlands
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Liao CY, Weijers D. Analyzing Subcellular Reorganization During Early Arabidopsis Embryogenesis Using Fluorescent Markers. Methods Mol Biol 2020; 2122:49-61. [PMID: 31975295 DOI: 10.1007/978-1-0716-0342-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Virtually all growth, developmental, physiological, and defense responses in plants are accompanied by reorganization of subcellular structures to enable altered cellular growth, differentiation or function. Visualizing cellular reorganization is therefore critical to understand plant biology at the cellular scale. Fluorescently labeled markers for organelles, or for cellular components are widely used in combination with confocal microscopy to visualize cellular reorganization. Early during plant embryogenesis, the precursors for all major tissues of the seedling are established, and in Arabidopsis, this entails a set of nearly invariant switches in cell division orientation and directional cell expansion. Given that these cellular reorganization events are genetically regulated and coupled to formative events in plant development, they offer a good model to understand the genetic control of cellular reorganization in plant development. Until recently, it has been challenging to visualize subcellular structures in the early Arabidopsis embryo for two reasons: embryos are deeply embedded in seed coat and fruit, and in addition, no dedicated fluorescent markers, expressed in the embryo, were available. We recently established both an imaging approach and a set of markers for the early Arabidopsis embryo. Here, we describe a detailed protocol to use these new tools in imaging cellular reorganization.
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Affiliation(s)
- Che-Yang Liao
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands.
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Radoeva T, Albrecht C, Piepers M, de Vries S, Weijers D. Suspensor-derived somatic embryogenesis in Arabidopsis. Development 2020; 147:dev.188912. [DOI: 10.1242/dev.188912] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 06/08/2020] [Indexed: 01/16/2023]
Abstract
In many flowering plants, asymmetric division of the zygote generates apical and basal cells with different fates. In Arabidopsis thaliana, the apical cell generates the embryo while the basal cell divides anticlinally, leading to a suspensor of 6-9 cells that remain extra-embryonic and eventually senesce. In some genetic backgrounds, or upon ablation of the embryo, suspensor cells can undergo periclinal cell divisions and eventually form a second, twin embryo. Likewise, embryogenesis can be induced from somatic cells by various genes, but the relation to suspensor-derived embryos is unclear. Here, we addressed the nature of the suspensor to embryo fate transformation, and its genetic triggers. We expressed most known embryogenesis-inducing genes specifically in suspensor cells. We next analyzed morphology and fate marker expression in embryos in which suspensor division were activated by different triggers to address the developmental paths towards reprogramming. Our results show that reprogramming of Arabidopsis suspensor cells towards embryonic identity is a specific cellular response that is triggered by defined regulators, follows a conserved developmental trajectory and shares similarity to the process of somatic embryogenesis from post-embryonic tissues.
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Affiliation(s)
- Tatyana Radoeva
- Wageningen University, Laboratory of Biochemistry, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Catherine Albrecht
- Wageningen University, Laboratory of Biochemistry, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Marcel Piepers
- Wageningen University, Laboratory of Biochemistry, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Sacco de Vries
- Wageningen University, Laboratory of Biochemistry, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dolf Weijers
- Wageningen University, Laboratory of Biochemistry, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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Yoshida S, van der Schuren A, van Dop M, van Galen L, Saiga S, Adibi M, Möller B, Ten Hove CA, Marhavy P, Smith R, Friml J, Weijers D. A SOSEKI-based coordinate system interprets global polarity cues in Arabidopsis. NATURE PLANTS 2019; 5:160-166. [PMID: 30737509 PMCID: PMC6420093 DOI: 10.1038/s41477-019-0363-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 01/08/2019] [Indexed: 05/05/2023]
Abstract
Multicellular development requires coordinated cell polarization relative to body axes, and translation to oriented cell division1-3. In plants, it is unknown how cell polarities are connected to organismal axes and translated to division. Here, we identify Arabidopsis SOSEKI proteins that integrate apical-basal and radial organismal axes to localize to polar cell edges. Localization does not depend on tissue context, requires cell wall integrity and is defined by a transferrable, protein-specific motif. A Domain of Unknown Function in SOSEKI proteins resembles the DIX oligomerization domain in the animal Dishevelled polarity regulator. The DIX-like domain self-interacts and is required for edge localization and for influencing division orientation, together with a second domain that defines the polar membrane domain. Our work shows that SOSEKI proteins locally interpret global polarity cues and can influence cell division orientation. Furthermore, this work reveals that, despite fundamental differences, cell polarity mechanisms in plants and animals converge on a similar protein domain.
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Affiliation(s)
- Saiko Yoshida
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands.
- Institute of Science and Technology, Klosterneuburg, Austria.
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
| | - Alja van der Schuren
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Maritza van Dop
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Luc van Galen
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Shunsuke Saiga
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Milad Adibi
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Barbara Möller
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Colette A Ten Hove
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Peter Marhavy
- Institute of Science and Technology, Klosterneuburg, Austria
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Richard Smith
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jiri Friml
- Institute of Science and Technology, Klosterneuburg, Austria
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands.
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7
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DOF2.1 Controls Cytokinin-Dependent Vascular Cell Proliferation Downstream of TMO5/LHW. Curr Biol 2019; 29:520-529.e6. [PMID: 30686737 PMCID: PMC6370950 DOI: 10.1016/j.cub.2018.12.041] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/12/2018] [Accepted: 12/21/2018] [Indexed: 01/04/2023]
Abstract
To create a three-dimensional structure, plants rely on oriented cell divisions and cell elongation. Oriented cell divisions are specifically important in procambium cells of the root to establish the different vascular cell types [1, 2]. These divisions are in part controlled by the auxin-controlled TARGET OF MONOPTEROS5 (TMO5) and LONESOME HIGHWAY (LHW) transcription factor complex [3, 4, 5, 6, 7]. Loss-of-function of tmo5 or lhw clade members results in strongly reduced vascular cell file numbers, whereas ectopic expression of both TMO5 and LHW can ubiquitously induce periclinal and radial cell divisions in all cell types of the root meristem. TMO5 and LHW interact only in young xylem cells, where they promote expression of two direct target genes involved in the final step of cytokinin (CK) biosynthesis, LONELY GUY3 (LOG3) and LOG4 [8, 9] Therefore, CK was hypothesized to act as a mobile signal from the xylem to trigger divisions in the neighboring procambium cells [3, 6]. To unravel how TMO5/LHW-dependent cytokinin regulates cell proliferation, we analyzed the transcriptional responses upon simultaneous induction of both transcription factors. Using inferred network analysis, we identified AT2G28510/DOF2.1 as a cytokinin-dependent downstream target gene. We further showed that DOF2.1 controls specific procambium cell divisions without inducing other cytokinin-dependent effects such as the inhibition of vascular differentiation. In summary, our results suggest that DOF2.1 and its closest homologs control vascular cell proliferation, thus leading to radial expansion of the root. DOF2.1 acts as a major transcriptional hub downstream of TMO5/LHW The CK-inducible DOF2.1 is sufficient to trigger periclinal and radial cell divisions DOF transcription factors redundantly regulate specific procambium divisions
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8
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Liao C, Weijers D. A toolkit for studying cellular reorganization during early embryogenesis in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:963-976. [PMID: 29383853 PMCID: PMC5887935 DOI: 10.1111/tpj.13841] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/21/2017] [Accepted: 01/09/2018] [Indexed: 05/02/2023]
Abstract
Considerable progress has been made in understanding the influence of physical and genetic factors on the patterns of cell division in various model systems. However, how each of these factors directs changes in subcellular structures has remained unclear. Generic machineries for the execution of cell expansion and division have been characterized, but how these are influenced by genetic regulators and physical cell properties remains an open question. To a large degree, the complexity of growing post-embryonic tissues and a lack of precise predictability have prevented the extraction of rigid correlations between subcellular structures and future orientation of cell division. The Arabidopsis embryo offers an exquisitely predictable and simple model for studying such correlations, but so far the tools and methodology for studying subcellular structures in the early embryo have been lacking. Here, we describe a set of markers to visualize a range of subcellular structures in the early Arabidopsis embryo. We have designed a series of fluorescent cellular reporters optimized for embryos, and demonstrate the effectiveness of using these 'ACE' reporters with simple three-dimensional imaging procedures that preserve delicate cellular structures. We describe the ontogeny of subcellular structures in the early embryo and find that central/peripheral cell polarity is established much earlier than suspected. In addition, we show that the actin and microtubule cytoskeleton has distinct topologies in the embryo. These tools and methods will allow detailed analysis of the events of cellular reorganization that underlie morphogenesis in the Arabidopsis embryo.
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Affiliation(s)
- Che‐Yang Liao
- Laboratory of BiochemistryWageningen UniversityStippeneng 46708WE Wageningenthe Netherlands
| | - Dolf Weijers
- Laboratory of BiochemistryWageningen UniversityStippeneng 46708WE Wageningenthe Netherlands
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9
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Palovaara J, Saiga S, Wendrich JR, van 't Wout Hofland N, van Schayck JP, Hater F, Mutte S, Sjollema J, Boekschoten M, Hooiveld GJ, Weijers D. Transcriptome dynamics revealed by a gene expression atlas of the early Arabidopsis embryo. NATURE PLANTS 2017; 3:894-904. [PMID: 29116234 PMCID: PMC5687563 DOI: 10.1038/s41477-017-0035-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 09/19/2017] [Indexed: 05/02/2023]
Abstract
During early plant embryogenesis, precursors for all major tissues and stem cells are formed. While several components of the regulatory framework are known, how cell fates are instructed by genome-wide transcriptional activity remains unanswered-in part because of difficulties in capturing transcriptome changes at cellular resolution. Here, we have adapted a two-component transgenic labelling system to purify cell-type-specific nuclear RNA and generate a transcriptome atlas of early Arabidopsis embryo development, with a focus on root stem cell niche formation. We validated the dataset through gene expression analysis, and show that gene activity shifts in a spatio-temporal manner, probably signifying transcriptional reprogramming, to induce developmental processes reflecting cell states and state transitions. This atlas provides the most comprehensive tissue- and cell-specific description of genome-wide gene activity in the early plant embryo, and serves as a valuable resource for understanding the genetic control of early plant development.
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Affiliation(s)
- Joakim Palovaara
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Shunsuke Saiga
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Jos R Wendrich
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
- Department of Plant Biotechnology and Bioinformatics and VIB Center for Plant Systems Biology, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | | | - J Paul van Schayck
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Friederike Hater
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Sumanth Mutte
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Jouke Sjollema
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Mark Boekschoten
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Guido J Hooiveld
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands.
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10
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Wendrich JR, Möller BK, Uddin B, Radoeva T, Lokerse AS, De Rybel B, Weijers D. A set of domain-specific markers in the Arabidopsis embryo. PLANT REPRODUCTION 2015. [PMID: 26216537 PMCID: PMC4623083 DOI: 10.1007/s00497-015-0266-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We describe a novel set of domain-specific markers that can be used in genetic studies, and we used two examples to show loss of stem cells in a monopteros background. Multicellular organisms can be defined by their ability to establish distinct cell identities, and it is therefore of critical importance to distinguish cell types. One step that leads to cell identity specification is activation of unique sets of transcripts. This property is often exploited in order to infer cell identity; the availability of good domain-specific marker lines is, however, poor in the Arabidopsis embryo. Here we describe a novel set of domain-specific marker lines that can be used in Arabidopsis (embryo) research. Based on transcriptomic data, we selected 12 genes for expression analysis, and according to the observed expression domain during embryogenesis, we divided them into four categories (1-ground tissue; 2-root stem cell; 3-shoot apical meristem; 4-post-embryonic). We additionally show the use of two markers from the "stem cell" category in a genetic study, where we use the absence of the markers to infer developmental defects in the monopteros mutant background. Finally, in order to judge whether the established marker lines also play a role in normal development, we generated loss-of-function resources. None of the analyzed T-DNA insertion, artificial microRNA, or misexpression lines showed any apparent phenotypic difference from wild type, indicating that these genes are not nonredundantly required for development, but also suggesting that marker activation can be considered an output of the patterning process. This set of domain-specific marker lines is therefore a valuable addition to the currently available markers and will help to move toward a generic set of tissue identity markers.
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Affiliation(s)
- Jos R Wendrich
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA, Wageningen, The Netherlands
| | - Barbara K Möller
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA, Wageningen, The Netherlands
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - Borhan Uddin
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA, Wageningen, The Netherlands
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Dhaka, Savar, Bangladesh
- Zentrum für Molekulare Biologie der Universität Heidelberg, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
| | - Tatyana Radoeva
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA, Wageningen, The Netherlands
| | - Annemarie S Lokerse
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA, Wageningen, The Netherlands
| | - Bert De Rybel
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA, Wageningen, The Netherlands
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA, Wageningen, The Netherlands.
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11
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Vera-Sirera F, De Rybel B, Úrbez C, Kouklas E, Pesquera M, Álvarez-Mahecha J, Minguet E, Tuominen H, Carbonell J, Borst J, Weijers D, Blázquez M. A bHLH-Based Feedback Loop Restricts Vascular Cell Proliferation in Plants. Dev Cell 2015; 35:432-43. [DOI: 10.1016/j.devcel.2015.10.022] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 10/05/2015] [Accepted: 10/23/2015] [Indexed: 01/04/2023]
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12
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Reporters for sensitive and quantitative measurement of auxin response. Nat Methods 2015; 12:207-10, 2 p following 210. [PMID: 25643149 PMCID: PMC4344836 DOI: 10.1038/nmeth.3279] [Citation(s) in RCA: 268] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 12/23/2014] [Indexed: 01/25/2023]
Abstract
Visualization of hormonal signaling input and output is of key importance for understanding regulation of multicellular development. The plant signaling molecule auxin triggers many growth and developmental responses, but current tools lack sensitivity or precision to visualize these. We developed a set of novel fluorescent reporters that allow sensitive and semi-quantitative readout of auxin responses at cellular resolution in Arabidopsis. These generic tools are suitable for any transformable plant species.
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De Rybel B, Adibi M, Breda AS, Wendrich JR, Smit ME, Novák O, Yamaguchi N, Yoshida S, Van Isterdael G, Palovaara J, Nijsse B, Boekschoten MV, Hooiveld G, Beeckman T, Wagner D, Ljung K, Fleck C, Weijers D. Plant development. Integration of growth and patterning during vascular tissue formation in Arabidopsis. Science 2014; 345:1255215. [PMID: 25104393 DOI: 10.1126/science.1255215] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Coordination of cell division and pattern formation is central to tissue and organ development, particularly in plants where walls prevent cell migration. Auxin and cytokinin are both critical for division and patterning, but it is unknown how these hormones converge upon tissue development. We identify a genetic network that reinforces an early embryonic bias in auxin distribution to create a local, nonresponding cytokinin source within the root vascular tissue. Experimental and theoretical evidence shows that these cells act as a tissue organizer by positioning the domain of oriented cell divisions. We further demonstrate that the auxin-cytokinin interaction acts as a spatial incoherent feed-forward loop, which is essential to generate distinct hormonal response zones, thus establishing a stable pattern within a growing vascular tissue.
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Affiliation(s)
- Bert De Rybel
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703HA Wageningen, the Netherlands
| | - Milad Adibi
- LifeGlimmer GmbH, Markelstrasse 38, 12163 Berlin, Germany. Albert-Ludwigs-University Freiburg, Faculty of Biology, Plant Biotechnology, Schaenzlestrasse 1, D-79104 Freiburg, Germany. Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenlaan 3, 6703HA Wageningen, the Netherlands
| | - Alice S Breda
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703HA Wageningen, the Netherlands
| | - Jos R Wendrich
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703HA Wageningen, the Netherlands
| | - Margot E Smit
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703HA Wageningen, the Netherlands
| | - Ondřej Novák
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, SLU, SE-901 83 Umeå, Sweden. Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University and Institute of Experimental Botany AS CR, Šlechtitelů 11, CZ-78371 Olomouc, Czech Republic
| | - Nobutoshi Yamaguchi
- Department of Biology, University of Pennsylvania, Philadelphia, PA 190104-6084, USA
| | - Saiko Yoshida
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703HA Wageningen, the Netherlands
| | - Gert Van Isterdael
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium. Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
| | - Joakim Palovaara
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703HA Wageningen, the Netherlands
| | - Bart Nijsse
- Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenlaan 3, 6703HA Wageningen, the Netherlands
| | - Mark V Boekschoten
- Division of Human Nutrition, Wageningen University, Dreijenlaan 2, 6703HA Wageningen, the Netherlands. TI Food and Nutrition, 6703HA Wageningen, the Netherlands
| | - Guido Hooiveld
- Division of Human Nutrition, Wageningen University, Dreijenlaan 2, 6703HA Wageningen, the Netherlands
| | - Tom Beeckman
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium. Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA 190104-6084, USA
| | - Karin Ljung
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, SLU, SE-901 83 Umeå, Sweden
| | - Christian Fleck
- Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenlaan 3, 6703HA Wageningen, the Netherlands.
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703HA Wageningen, the Netherlands.
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Abstract
The astonishingly long lives of plants and their regeneration capacity depend on the activity of plant stem cells. As in animals, stem cells reside in stem cell niches, which produce signals that regulate the balance between self-renewal and the generation of daughter cells that differentiate into new tissues. Plant stem cell niches are located within the meristems, which are organized structures that are responsible for most post-embryonic development. The continuous organ production that is characteristic of plant growth requires a robust regulatory network to keep the balance between pluripotent stem cells and differentiating progeny. Components of this network have now been elucidated and provide a unique opportunity for comparing strategies that were developed in the animal and plant kingdoms, which underlie the logic of stem cell behaviour.
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