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Wang H, Santuari L, Wijsman T, Wachsman G, Haase H, Nodine M, Scheres B, Heidstra R. Arabidopsis ribosomal RNA processing meerling mutants exhibit suspensor-derived polyembryony due to direct reprogramming of the suspensor. THE PLANT CELL 2024; 36:2550-2569. [PMID: 38513608 PMCID: PMC11218825 DOI: 10.1093/plcell/koae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/06/2024] [Accepted: 02/27/2024] [Indexed: 03/23/2024]
Abstract
Embryo development in Arabidopsis (Arabidopsis thaliana) starts off with an asymmetric division of the zygote to generate the precursors of the embryo proper and the supporting extraembryonic suspensor. The suspensor degenerates as the development of the embryo proper proceeds beyond the heart stage. Until the globular stage, the suspensor maintains embryonic potential and can form embryos in the absence of the developing embryo proper. We report a mutant called meerling-1 (mrl-1), which shows a high penetrance of suspensor-derived polyembryony due to delayed development of the embryo proper. Eventually, embryos from both apical and suspensor lineages successfully develop into normal plants and complete their life cycle. We identified the causal mutation as a genomic rearrangement altering the promoter of the Arabidopsis U3 SMALL NUCLEOLAR RNA-ASSOCIATED PROTEIN 18 (UTP18) homolog that encodes a nucleolar-localized WD40-repeat protein involved in processing 18S preribosomal RNA. Accordingly, root-specific knockout of UTP18 caused growth arrest and accumulation of unprocessed 18S pre-rRNA. We generated the mrl-2 loss-of-function mutant and observed asynchronous megagametophyte development causing embryo sac abortion. Together, our results indicate that promoter rearrangement decreased UTP18 protein abundance during early stage embryo proper development, triggering suspensor-derived embryogenesis. Our data support the existence of noncell autonomous signaling from the embryo proper to prevent direct reprogramming of the suspensor toward embryonic fate.
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Affiliation(s)
- Honglei Wang
- Cluster of Plant Developmental Biology, Laboratory of Cell and Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Luca Santuari
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Tristan Wijsman
- Cluster of Plant Developmental Biology, Laboratory of Cell and Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Guy Wachsman
- Molecular Genetics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Hannah Haase
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Michael Nodine
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Ben Scheres
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Renze Heidstra
- Cluster of Plant Developmental Biology, Laboratory of Cell and Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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2
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Kim JY, Symeonidi E, Pang TY, Denyer T, Weidauer D, Bezrutczyk M, Miras M, Zöllner N, Hartwig T, Wudick MM, Lercher M, Chen LQ, Timmermans MCP, Frommer WB. Distinct identities of leaf phloem cells revealed by single cell transcriptomics. THE PLANT CELL 2021; 33:511-530. [PMID: 33955487 PMCID: PMC8136902 DOI: 10.1093/plcell/koaa060] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/18/2020] [Indexed: 05/20/2023]
Abstract
The leaf vasculature plays a key role in solute translocation. Veins consist of at least seven distinct cell types, with specific roles in transport, metabolism, and signaling. Little is known about leaf vascular cells, in particular the phloem parenchyma (PP). PP effluxes sucrose into the apoplasm as a basis for phloem loading, yet PP has been characterized only microscopically. Here, we enriched vascular cells from Arabidopsis leaves to generate a single-cell transcriptome atlas of leaf vasculature. We identified at least 19 cell clusters, encompassing epidermis, guard cells, hydathodes, mesophyll, and all vascular cell types, and used metabolic pathway analysis to define their roles. Clusters comprising PP cells were enriched for transporters, including SWEET11 and SWEET12 sucrose and UmamiT amino acid efflux carriers. We provide evidence that PP development occurs independently from ALTERED PHLOEM DEVELOPMENT, a transcription factor required for phloem differentiation. PP cells have a unique pattern of amino acid metabolism activity distinct from companion cells (CCs), explaining differential distribution/metabolism of amino acids in veins. The kinship relation of the vascular clusters is strikingly similar to the vein morphology, except for a clear separation of CC from the other vascular cells including PP. In summary, our single-cell RNA-sequencing analysis provides a wide range of information into the leaf vasculature and the role and relationship of the leaf cell types.
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Affiliation(s)
- Ji-Yun Kim
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Author for correspondence: (W.B.F.), (J.-Y.K.)
| | - Efthymia Symeonidi
- Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
| | - Tin Yau Pang
- Institute for Computer Science and Department of Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Tom Denyer
- Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
| | - Diana Weidauer
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Margaret Bezrutczyk
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Manuel Miras
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Nora Zöllner
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Thomas Hartwig
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Michael M Wudick
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Martin Lercher
- Institute for Computer Science and Department of Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Li-Qing Chen
- Department of Plant Biology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Marja C P Timmermans
- Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
| | - Wolf B Frommer
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan
- Author for correspondence: (W.B.F.), (J.-Y.K.)
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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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4
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Román Á, Golz JF, Webb AAR, Graham IA, Haydon MJ. Combining GAL4 GFP enhancer trap with split luciferase to measure spatiotemporal promoter activity in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:187-198. [PMID: 31692146 PMCID: PMC7217008 DOI: 10.1111/tpj.14603] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 10/31/2019] [Indexed: 05/28/2023]
Abstract
In multicellular organisms different types of tissues have distinct gene expression profiles associated with specific function or structure of the cell. Quantification of gene expression in whole organs or whole organisms can give misleading information about levels or dynamics of expression in specific cell types. Tissue- or cell-specific analysis of gene expression has potential to enhance our understanding of gene regulation and interactions of cell signalling networks. The Arabidopsis circadian oscillator is a gene network which orchestrates rhythmic expression across the day/night cycle. There is heterogeneity between cell and tissue types of the composition and behaviour of the oscillator. In order to better understand the spatial and temporal patterns of gene expression, flexible tools are required. By combining a Gateway®-compatible split luciferase construct with a GAL4 GFP enhancer trap system, we describe a tissue-specific split luciferase assay for non-invasive detection of spatiotemporal gene expression in Arabidopsis. We demonstrate the utility of this enhancer trap-compatible split luciferase assay (ETSLA) system to investigate tissue-specific dynamics of circadian gene expression. We confirm spatial heterogeneity of circadian gene expression in Arabidopsis leaves and describe the resources available to investigate any gene of interest.
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Affiliation(s)
- Ángela Román
- School of BioSciencesUniversity of MelbourneMelbourneAustralia
- Department of BiologyUniversity of YorkYorkUnited Kingdom
| | - John F. Golz
- School of BioSciencesUniversity of MelbourneMelbourneAustralia
| | - Alex A. R. Webb
- Department of Plant SciencesUniversity of CambridgeCambridgeUnited Kingdom
| | - Ian A. Graham
- Department of BiologyUniversity of YorkYorkUnited Kingdom
| | - Michael J. Haydon
- School of BioSciencesUniversity of MelbourneMelbourneAustralia
- Department of BiologyUniversity of YorkYorkUnited Kingdom
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5
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Genetic Screens to Target Embryo and Endosperm Pathways in Arabidopsis and Maize. Methods Mol Biol 2020. [PMID: 31975291 DOI: 10.1007/978-1-0716-0342-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The major tissue types and stem-cell niches of plants are established during embryogenesis, and thus knowledge of embryo development is essential for a full understanding of plant development. Studies of seed development are also important for human health, because the nutrients stored in both the embryo and endosperm of plant seeds provide an essential part of our diet. Arabidopsis and maize have evolved different types of seeds, opening a range of experimental opportunities. Development of the Arabidopsis embryo follows an almost invariant pattern, while cell division patterns of maize embryos are variable. Embryo-endosperm interactions are also different between the two species: in Arabidopsis, the endosperm is consumed during seed development, while mature maize seeds contain an enormous endosperm. Genetic screens have provided important insights into seed development in both species. In the genomic era, genetic analysis will continue to provide important tools for understanding embryo and endosperm biology in plants, because single gene functional studies can now be integrated with genome-wide information. Here, we lay out important factors to consider when designing genetic screens to identify new genes or to probe known pathways in seed development. We then highlight the technical details of two previous genetic screens that may serve as useful examples for future experiments.
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6
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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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7
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Li N, Yuan D, Huang LJ. Development of a Gateway-compatible two-component expression vector system for plants. Transgenic Res 2019; 28:561-572. [PMID: 31435821 DOI: 10.1007/s11248-019-00167-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 08/17/2019] [Indexed: 10/26/2022]
Abstract
Genetic transformation of plants offers the possibility of functional characterization of individual genes and the improvement of plant traits. Development of novel transformation vectors is essential to improve plant genetic transformation technologies for various applications. Here, we present the development of a Gateway-compatible two-component expression vector system for Agrobacterium-mediated plant transformation. The expression system contains two independent plasmid vector sets, the activator vector and the reporter vector, based on the concept of the GAL4/UAS trans-activation system. The activator vector expresses a modified GAL4 protein (GAL4-VP16) under the control of specific promoter. The GAL4-VP16 protein targets the UAS in the reporter vector and subsequently activates reporter gene expression. Both the activator and reporter vectors contain the Gateway recombination cassette, which can be rapidly and efficiently replaced by any specific promoter and reporter gene of interest, to facilitate gene cloning procedures. The efficiency of the activator-reporter expression system has been assessed using agroinfiltration mediated transient expression assay in Nicotiana benthamiana and stable transgenic expression in Arabidopsis thaliana. The reporter genes were highly expressed with precise tissue-specific and subcellular localization. This Gateway-compatible two-component expression vector system will be a useful tool for advancing plant gene engineering.
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Affiliation(s)
- Ning Li
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Changsha, 410004, Hunan, China
| | - Deyi Yuan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Changsha, 410004, Hunan, China
| | - Li-Jun Huang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Changsha, 410004, Hunan, China.
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8
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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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9
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Zhang L, Qin LN, Zeng ZR, Wu CZ, Gong YY, Liu LH, Cao FQ. Molecular identification of a root apical cell-specific and stress-responsive enhancer from an Arabidopsis enhancer trap line. PLANT METHODS 2019; 15:8. [PMID: 30733820 PMCID: PMC6354418 DOI: 10.1186/s13007-019-0393-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/21/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Plant root apex is the major part to direct the root growth and development by responding to various signals/cues from internal and soil environments. To study and understand root system biology particularly at a molecular and cellular level, an Arabidopsis T-DNA insertional enhancer trap line J3411 expressing reporters (GFP) only in the root tip was adopted in this study to isolate a DNA fragment. RESULTS Using nested PCR, DNA sequencing and sequence homology search, the T-DNA insertion site(s) and its flanking genes were characterised in J3411 line. Subsequently, a 2000 bp plant DNA-fragment (Ertip1) upstream of the insert position of the coding T-DNA was in silico analysed, revealing certain putative promoter/enhancer cis-regulatory elements. Cloning and transformation of this DNA fragment and its truncated segments tagged with or without 35S minimal promoter (35Smini), all of which were fused with a GFP or GUS reporter, allowed to detect GFP and GUS expression mediated only by Ertip1 + 35mini (PErtip1+35Smini) specifically in the Arabidopsis root tip region. The PErtip1+35Smini activity was further tested to be strong and stable under many different growth conditions but suppressed by cold, salt, alkaline pH and higher ammonium and phosphorus. CONCLUSION This work describes a promising strategy to isolate a tissue-/cell-specific enhancer sequence from the enhancer trap lines, which are publically available. The reported synthetic promoter i.e. PErtip1+35Smini may provide a valuable and potent molecular-tool for comprehensive investigation of a gene function related to root growth and development as well as molecular engineering of root-architectural formation aiming to improve plant growth.
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Affiliation(s)
- Lei Zhang
- 1Key Laboratory of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193 China
| | - Li-Na Qin
- 1Key Laboratory of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193 China
- Zhaoyuan Agricultural Technology Extension Centre, Zhaoyuan, 265400 Shandong China
| | - Zi-Rui Zeng
- 1Key Laboratory of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193 China
| | - Chang-Zheng Wu
- 1Key Laboratory of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193 China
| | - Yuan-Yong Gong
- 1Key Laboratory of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193 China
- 3Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China
| | - Lai-Hua Liu
- 1Key Laboratory of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193 China
| | - Feng-Qiu Cao
- 4Shanghai Centre for Plant Stress Biology of Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201602 China
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10
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Radoeva T, Lokerse AS, Llavata-Peris CI, Wendrich JR, Xiang D, Liao CY, Vlaar L, Boekschoten M, Hooiveld G, Datla R, Weijers D. A Robust Auxin Response Network Controls Embryo and Suspensor Development through a Basic Helix Loop Helix Transcriptional Module. THE PLANT CELL 2019; 31:52-67. [PMID: 30573473 PMCID: PMC6391696 DOI: 10.1105/tpc.18.00518] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/27/2018] [Accepted: 12/19/2018] [Indexed: 05/07/2023]
Abstract
Land plants reproduce sexually by developing an embryo from a fertilized egg cell. However, embryos can also be formed from other cell types in many plant species. Thus, a key question is how embryo identity in plants is controlled, and how this process is modified during nonzygotic embryogenesis. The Arabidopsis (Arabidopsis thaliana) zygote divides to produce an embryonic lineage and an extra-embryonic suspensor. Yet, normally quiescent suspensor cells can develop a second embryo when the initial embryo is damaged, or when response to the signaling molecule auxin is locally blocked. Here we used auxin-dependent suspensor embryogenesis as a model to determine transcriptome changes during embryonic reprogramming. We found that reprogramming is complex and accompanied by large transcriptomic changes before anatomical changes. This analysis revealed a strong enrichment for genes encoding components of auxin homeostasis and response among misregulated genes. Strikingly, deregulation among multiple auxin-related gene families converged upon the re-establishment of cellular auxin levels or response. This finding points to a remarkable degree of feedback regulation to create resilience in the auxin response during embryo development. Starting from the transcriptome of auxin-deregulated embryos, we identified an auxin-dependent basic Helix Loop Helix transcription factor network that mediates the activity of this hormone in suppressing embryo development from the suspensor.
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Affiliation(s)
- Tatyana Radoeva
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708WE Wageningen, the Netherlands
| | - Annemarie S. Lokerse
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708WE Wageningen, the Netherlands
| | - Cristina I. Llavata-Peris
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708WE Wageningen, the Netherlands
| | - Jos R. Wendrich
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708WE Wageningen, the Netherlands
| | - Daoquan Xiang
- Plant Biotechnology Institute, National Research Council, 110 Gymnasium Place, Saskatoon, Saskatchewan, Canada S7N 0W9
| | - Che-Yang Liao
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708WE Wageningen, the Netherlands
| | - Lieke Vlaar
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708WE Wageningen, the Netherlands
| | - Mark Boekschoten
- Division of Human Nutrition, Wageningen University & Research, Stippeneng 4, 6708WE Wageningen, the Netherlands
- Top Institute Food & Nutrition, Nieuwe Kanaal 9A, 6709 PA Wageningen, the Netherlands
| | - Guido Hooiveld
- Division of Human Nutrition, Wageningen University & Research, Stippeneng 4, 6708WE Wageningen, the Netherlands
| | - Raju Datla
- Plant Biotechnology Institute, National Research Council, 110 Gymnasium Place, Saskatoon, Saskatchewan, Canada S7N 0W9
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708WE Wageningen, the Netherlands
- Address correspondence to
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Development of a GAL4-VP16/UAS trans-activation system for tissue specific expression in Medicago truncatula. PLoS One 2017; 12:e0188923. [PMID: 29186192 PMCID: PMC5706680 DOI: 10.1371/journal.pone.0188923] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 11/15/2017] [Indexed: 11/19/2022] Open
Abstract
Promoters with tissue-specific activity are very useful to address cell-autonomous and non cell autonomous functions of candidate genes. Although this strategy is widely used in Arabidopsis thaliana, its use to study tissue-specific regulation of root symbiotic interactions in legumes has only started recently. Moreover, using tissue specific promoter activity to drive a GAL4-VP16 chimeric transcription factor that can bind short upstream activation sequences (UAS) is an efficient way to target and enhance the expression of any gene of interest. Here, we developed a collection of promoters with different root cell layers specific activities in Medicago truncatula and tested their abilities to drive the expression of a chimeric GAL4-VP16 transcription factor in a trans-activation UAS: β-Glucuronidase (GUS) reporter gene system. By developing a binary vector devoted to modular Golden Gate cloning together with a collection of adapted tissue specific promoters and coding sequences we could test the activity of four of these promoters in trans-activation GAL4/UAS systems and compare them to “classical” promoter GUS fusions. Roots showing high levels of tissue specific expression of the GUS activity could be obtained with this trans-activation system. We therefore provide the legume community with new tools for efficient modular Golden Gate cloning, tissue specific expression and a trans-activation system. This study provides the ground work for future development of stable transgenic lines in Medicago truncatula.
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12
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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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13
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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 DOI: 10.1038/s41477-017-0035-33] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 09/19/2017] [Indexed: 05/22/2023]
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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