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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. Plant Cell 2024:koae087. [PMID: 38513608 DOI: 10.1093/plcell/koae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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 pre-ribosomal 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 non-cell autonomous signaling from the embryo proper to prevent direct reprogramming of the suspensor towards 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
| | | | - 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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Zaragoza JZ, Klap K, Heidstra R, Zhou W, Scheres B. The dual role of the RETINOBLASTOMA-RELATED protein in the DNA damage response is coordinated by the interaction with LXCXE-containing proteins. Plant J 2024. [PMID: 38321589 DOI: 10.1111/tpj.16665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 01/10/2024] [Accepted: 01/18/2024] [Indexed: 02/08/2024]
Abstract
Living organisms possess mechanisms to safeguard genome integrity. To avoid spreading mutations, DNA lesions are detected and cell division is temporarily arrested to allow repair mechanisms. Afterward, cells either resume division or respond to unsuccessful repair by undergoing programmed cell death (PCD). How the success rate of DNA repair connects to later cell fate decisions remains incompletely known, particularly in plants. The Arabidopsis thaliana RETINOBLASTOMA-RELATED1 (RBR) protein and its partner E2FA, play both structural and transcriptional functions in the DNA damage response (DDR). Here we provide evidence that distinct RBR protein interactions with LXCXE motif-containing proteins guide these processes. Using the N849F substitution in the RBR B-pocket domain, which specifically disrupts binding to the LXCXE motif, we show that these interactions are dispensable in unchallenging conditions. However, N849F substitution abolishes RBR nuclear foci and promotes PCD and growth arrest upon genotoxic stress. NAC044, which promotes growth arrest and PCD, accumulates after the initial recruitment of RBR to foci and can bind non-focalized RBR through the LXCXE motif in a phosphorylation-independent manner, allowing interaction at different cell cycle phases. Disrupting NAC044-RBR interaction impairs PCD, but their genetic interaction points to opposite independent roles in the regulation of PCD. The LXCXE-binding dependency of the roles of RBR in the DDR suggests a coordinating mechanism to translate DNA repair success to cell survival. We propose that RBR and NAC044 act in two distinct DDR pathways, but interact to integrate input from both DDR pathways to decide upon an irreversible cell fate decision.
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Affiliation(s)
- Jorge Zamora Zaragoza
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Department of Biotechnology, Rijk Zwaan Breeding B.V., Eerste Kruisweg 9, 4793 RS, Fijnaart, The Netherlands
| | - Katinka Klap
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Renze Heidstra
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Wenkun Zhou
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Ben Scheres
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Department of Biotechnology, Rijk Zwaan Breeding B.V., Eerste Kruisweg 9, 4793 RS, Fijnaart, The Netherlands
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3
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Pardal R, Scheres B, Heidstra R. SCHIZORIZA domain-function analysis identifies requirements for its specific role in cell fate segregation. Plant Physiol 2023; 193:1866-1879. [PMID: 37584278 PMCID: PMC10602604 DOI: 10.1093/plphys/kiad456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 08/17/2023]
Abstract
Plant development continues postembryonically with a lifelong ability to form new tissues and organs. Asymmetric cell division, coupled with fate segregation, is essential to create cellular diversity during tissue and organ formation. Arabidopsis (Arabidopsis thaliana) plants harboring mutations in the SCHIZORIZA (SCZ) gene display fate segregation defects in their roots, resulting in the presence of an additional layer of endodermis, production of root hairs from subepidermal tissue, and misexpression of several tissue identity markers. Some of these defects are observed in tissues where SCZ is not expressed, indicating that part of the SCZ function is nonautonomous. As a class B HEAT-SHOCK TRANSCRIPTION FACTOR (HSFB), the SCZ protein contains several conserved domains and motifs. However, which domain(s) discriminates SCZ from its family members to obtain a role in development remains unknown. Here, we investigate how each domain contributes to SCZ function in Arabidopsis root patterning by generating altered versions of SCZ by domain swapping and mutation. We show that the SCZ DNA-binding domain is the main factor for its developmental function, and that SCZ likely acts as a nonmotile transcriptional repressor. Our results demonstrate how members of the HSF family can evolve toward functions beyond stress response.
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Affiliation(s)
- Renan Pardal
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB, Wageningen, The Netherlands
| | - Ben Scheres
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB, Wageningen, The Netherlands
| | - Renze Heidstra
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB, Wageningen, The Netherlands
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Hao R, Zhou W, Li J, Luo M, Scheres B, Guo Y. On salt stress, PLETHORA signaling maintains root meristems. Dev Cell 2023; 58:1657-1669.e5. [PMID: 37480843 DOI: 10.1016/j.devcel.2023.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 04/02/2023] [Accepted: 06/30/2023] [Indexed: 07/24/2023]
Abstract
Salt stress is one of the unfavorable environmental factors to affect plants. Salinity represses root growth, resulting in reduced biomass of agricultural plants. Little is known about how plants maintain root growth to counteract salt stress. The AP2-domain transcription factors PLETHORA1/2 (PLT1/2) act as master regulators in root meristem maintenance in Arabidopsis. In this study, we report that the salt overly sensitive (SOS) pathway component SOS2 regulates PLT1/2 at the post-transcriptional level. Salt-activated SOS2 interacts and phosphorylates PLT1/2 through their conserved C-terminal motifs to stabilize PLT1/2, critical for root apical meristem maintenance under salt stress. The phospho-mimetic version of PLT1/2 restored meristem and primary root length reduction of sos2-2 and plt1-4 plt2-2 mutants on salt treatment. Moreover, SOS2-mediated PLT1/2 phosphorylation improves root growth recovery after salt stress alleviation. We identify a SOS2-PLT1/2 core protein module that is required for protecting primary root growth and meristem maintenance from salt stress.
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Affiliation(s)
- Rong Hao
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wenkun Zhou
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Jingrui Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Manqing Luo
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Ben Scheres
- Laboratory of Plant Developmental Biology, Wageningen University and Research, 6708 PB Wageningen, the Netherlands; Rijk Zwaan R&D, 4793 RS Fijnaart, the Netherlands
| | - Yan Guo
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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Hesen V, Boele Y, Bakx-Schotman T, van Beersum F, Raaijmakers C, Scheres B, Willemsen V, van der Putten WH. Pioneer Arabidopsis thaliana spans the succession gradient revealing a diverse root-associated microbiome. Environ Microbiome 2023; 18:62. [PMID: 37468998 DOI: 10.1186/s40793-023-00511-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/22/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Soil microbiomes are increasingly acknowledged to affect plant functioning. Research in molecular model species Arabidopsis thaliana has given detailed insights of such plant-microbiome interactions. However, the circumstances under which natural A. thaliana plants have been studied so far might represent only a subset of A. thaliana's full ecological context and potential biotic diversity of its root-associated microbiome. RESULTS We collected A. thaliana root-associated soils from a secondary succession gradient covering 40 years of land abandonment. All field sites were situated on the same parent soil material and in the same climatic region. By sequencing the bacterial and fungal communities and soil abiotic analysis we discovered differences in both the biotic and abiotic composition of the root-associated soil of A. thaliana and these differences are in accordance with the successional class of the field sites. As the studied sites all have been under (former) agricultural use, and a climatic cline is absent, we were able to reveal a more complete variety of ecological contexts A. thaliana can appear and sustain in. CONCLUSIONS Our findings lead to the conclusion that although A. thaliana is considered a pioneer plant species and previously almost exclusively studied in early succession and disturbed sites, plants can successfully establish in soils which have experienced years of ecological development. Thereby, A. thaliana can be exposed to a much wider variation in soil ecological context than is currently presumed. This knowledge opens up new opportunities to enhance our understanding of causal plant-microbiome interactions as A. thaliana cannot only grow in contrasting soil biotic and abiotic conditions along a latitudinal gradient, but also when those conditions vary along a secondary succession gradient. Future research could give insights in important plant factors to grow in more ecologically complex later-secondary succession soils, which is an impending direction of our current agricultural systems.
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Affiliation(s)
- Vera Hesen
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands.
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6700 AB, the Netherlands.
| | - Yvet Boele
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands
| | - Tanja Bakx-Schotman
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6700 AB, the Netherlands
| | - Femke van Beersum
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6700 AB, the Netherlands
- Plant Ecology and Nature Conservation Group, Wageningen University, Droevendaalsesteeg 3a, Wageningen, 6708 PB, the Netherlands
| | - Ciska Raaijmakers
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6700 AB, the Netherlands
| | - Ben Scheres
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands
- Department of Biotechnology, Rijk Zwaan Breeding B.V., Eerste Kruisweg 9, Fijnaart, 4793 RS, the Netherlands
| | - Viola Willemsen
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands.
| | - Wim H van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6700 AB, the Netherlands.
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands.
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León-Ruiz J, Espinal-Centeno A, Blilou I, Scheres B, Arteaga-Vázquez M, Cruz-Ramírez A. RETINOBLASTOMA-RELATED interactions with key factors of the RNA-directed DNA methylation (RdDM) pathway and its influence on root development. Planta 2023; 257:105. [PMID: 37120771 DOI: 10.1007/s00425-023-04135-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/11/2023] [Indexed: 05/03/2023]
Abstract
MAIN CONCLUSION Our study presents evidence for a novel mechanism for RBR function in transcriptional gene silencing by interacting with key players of the RdDM pathway in Arabidopsis and several plant clades. Transposable elements and other repetitive elements are silenced by the RNA-directed DNA methylation pathway (RdDM). In RdDM, POLIV-derived transcripts are converted into double-stranded RNA (dsRNA) by the activity of RDR2 and subsequently processed into 24 nucleotide short interfering RNAs (24-nt siRNAs) by DCL3. 24-nt siRNAs serve as guides to direct AGO4-siRNA complexes to chromatin-bound POLV-derived transcripts generated from the template/target DNA. The interaction between POLV, AGO4, DMS3, DRD1, RDM1 and DRM2 promotes DRM2-mediated de novo DNA methylation. The Arabidopsis Retinoblastoma protein homolog (RBR) is a master regulator of the cell cycle, stem cell maintenance, and development. We in silico predicted and explored experimentally the protein-protein interactions (PPIs) between RBR and members of the RdDM pathway. We found that the largest subunits of POLIV and POLV (NRPD1 and NRPE1), the shared second largest subunit of POLIV and POLV (NRPD/E2), RDR1, RDR2, DCL3, DRM2, and SUVR2 contain canonical and non-canonical RBR binding motifs and several of them are conserved since algae and bryophytes. We validated experimentally PPIs between Arabidopsis RBR and several of the RdDM pathway proteins. Moreover, seedlings from loss-of-function mutants in RdDM and RBR show similar phenotypes in the root apical meristem. We show that RdDM and SUVR2 targets are up-regulated in the 35S:AmiGO-RBR background.
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Affiliation(s)
- Jesús León-Ruiz
- Laboratory of Molecular and Developmental Complexity at Laboratorio Nacional de Genómica Para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, del Instituto Politécnico Nacional, (CINVESTAV-IPN), 36590, Irapuato, México
| | - Annie Espinal-Centeno
- Laboratory of Molecular and Developmental Complexity at Laboratorio Nacional de Genómica Para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, del Instituto Politécnico Nacional, (CINVESTAV-IPN), 36590, Irapuato, México
| | - Ikram Blilou
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Ben Scheres
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | - Mario Arteaga-Vázquez
- Group of Epigenetics and Developmental Biology, Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, 91090, Xalapa, México.
| | - Alfredo Cruz-Ramírez
- Laboratory of Molecular and Developmental Complexity at Laboratorio Nacional de Genómica Para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, del Instituto Politécnico Nacional, (CINVESTAV-IPN), 36590, Irapuato, México.
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7
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Roszak P, Heo JO, Blob B, Toyokura K, Sugiyama Y, de Luis Balaguer MA, Lau WWY, Hamey F, Cirrone J, Madej E, Bouatta AM, Wang X, Guichard M, Ursache R, Tavares H, Verstaen K, Wendrich J, Melnyk CW, Oda Y, Shasha D, Ahnert SE, Saeys Y, De Rybel B, Heidstra R, Scheres B, Grossmann G, Mähönen AP, Denninger P, Göttgens B, Sozzani R, Birnbaum KD, Helariutta Y. Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization. Science 2021; 374:eaba5531. [PMID: 34941412 PMCID: PMC8730638 DOI: 10.1126/science.aba5531] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In the plant meristem, tissue-wide maturation gradients are coordinated with specialized cell networks to establish various developmental phases required for indeterminate growth. Here, we used single-cell transcriptomics to reconstruct the protophloem developmental trajectory from the birth of cell progenitors to terminal differentiation in the Arabidopsis thaliana root. PHLOEM EARLY DNA-BINDING-WITH-ONE-FINGER (PEAR) transcription factors mediate lineage bifurcation by activating guanosine triphosphatase signaling and prime a transcriptional differentiation program. This program is initially repressed by a meristem-wide gradient of PLETHORA transcription factors. Only the dissipation of PLETHORA gradient permits activation of the differentiation program that involves mutual inhibition of early versus late meristem regulators. Thus, for phloem development, broad maturation gradients interface with cell-type-specific transcriptional regulators to stage cellular differentiation.
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Affiliation(s)
- Pawel Roszak
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Jung-Ok Heo
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Institute of Biotechnology, HiLIFE/Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Bernhard Blob
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Koichi Toyokura
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
- Faculty of Science and Engineering, Konan University, Kobe, Japan
- GRA&GREEN Inc., Incubation Facility, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Yuki Sugiyama
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
| | | | - Winnie W Y Lau
- Wellcome Trust and MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK
| | - Fiona Hamey
- Wellcome Trust and MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK
| | - Jacopo Cirrone
- Computer Science Department, Courant Institute for Mathematical Sciences, New York University, New York, NY, USA
| | - Ewelina Madej
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Alida M Bouatta
- Plant Systems Biology, Technical University of Munich, Freising, Germany
| | - Xin Wang
- Institute of Biotechnology, HiLIFE/Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Marjorie Guichard
- Institute of Cell and Interaction Biology, CEPLAS, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Robertas Ursache
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Hugo Tavares
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Bioinformatics Training Facility, Department of Genetics, University of Cambridge, Cambridge, UK
| | - Kevin Verstaen
- Data Mining and Modelling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Jos Wendrich
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Charles W Melnyk
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Yoshihisa Oda
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
- Department of Genetics, the Graduate University for Advanced Studies, SOKENDAI, Mishima, Japan
| | - Dennis Shasha
- Computer Science Department, Courant Institute for Mathematical Sciences, New York University, New York, NY, USA
| | - Sebastian E Ahnert
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- The Alan Turing Institute, British Library, London, UK
| | - Yvan Saeys
- Data Mining and Modelling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Renze Heidstra
- Department of Plant Sciences, Wageningen University and Research, Wageningen, Netherlands
| | - Ben Scheres
- Department of Plant Sciences, Wageningen University and Research, Wageningen, Netherlands
- Rijk Zwaan R&D, 4793 Fijnaart, Netherlands
| | - Guido Grossmann
- Institute of Cell and Interaction Biology, CEPLAS, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Ari Pekka Mähönen
- Institute of Biotechnology, HiLIFE/Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Philipp Denninger
- Plant Systems Biology, Technical University of Munich, Freising, Germany
| | - Berthold Göttgens
- Wellcome Trust and MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK
| | - Rosangela Sozzani
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, USA
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Yrjö Helariutta
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Institute of Biotechnology, HiLIFE/Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
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8
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van den Berg T, Yalamanchili K, de Gernier H, Santos Teixeira J, Beeckman T, Scheres B, Willemsen V, Ten Tusscher K. A reflux-and-growth mechanism explains oscillatory patterning of lateral root branching sites. Dev Cell 2021; 56:2176-2191.e10. [PMID: 34343477 DOI: 10.1016/j.devcel.2021.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/19/2021] [Accepted: 07/09/2021] [Indexed: 10/20/2022]
Abstract
Modular, repetitive structures are a key component of complex multicellular body plans across the tree of life. Typically, these structures are prepatterned by temporal oscillations in gene expression or signaling. Although a clock-and-wavefront mechanism was identified and plant leaf phyllotaxis arises from a Turing-type patterning for vertebrate somitogenesis and arthropod segmentation, the mechanism underlying lateral root patterning has remained elusive. To resolve this enigma, we combined computational modeling with in planta experiments. Intriguingly, auxin oscillations automatically emerge in our model from the interplay between a reflux-loop-generated auxin loading zone and stem-cell-driven growth dynamics generating periodic cell-size variations. In contrast to the clock-and-wavefront mechanism and Turing patterning, the uncovered mechanism predicts both frequency and spacing of lateral-root-forming sites to positively correlate with root meristem growth. We validate this prediction experimentally. Combined, our model and experimental results support that a reflux-and-growth patterning mechanism underlies lateral root priming.
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Affiliation(s)
- Thea van den Berg
- Computational Developmental Biology, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Kavya Yalamanchili
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, Wageningen, the Netherlands
| | - Hugues de Gernier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Joana Santos Teixeira
- Computational Developmental Biology, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ben Scheres
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, Wageningen, the Netherlands; Rijk Zwaan Breeding B.V., Department of Biotechnology, Eerste Kruisweg 9, 4793 RS Fijnaart, the Netherlands
| | - Viola Willemsen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, Wageningen, the Netherlands
| | - Kirsten Ten Tusscher
- Computational Developmental Biology, Department of Biology, Utrecht University, Utrecht, the Netherlands.
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9
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Benjamins R, Barbez E, Ortbauer M, Terpstra I, Lucyshyn D, Moulinier-Anzola J, Khan MA, Leitner J, Malenica N, Butt H, Korbei B, Scheres B, Kleine-Vehn J, Luschnig C. Retraction Note: PPP1, a plant-specific regulator of transcription controls Arabidopsis development and PIN expression. Sci Rep 2021; 11:8131. [PMID: 33833351 PMCID: PMC8032828 DOI: 10.1038/s41598-021-87406-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Editor's Note: this Article has been retracted; the Retraction Note is available at https://doi.org/10.1038/s41598-021-87406-5.
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Affiliation(s)
- René Benjamins
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Wien, Austria. .,Plant Developmental Biology, Wageningen University Research, 6708 PB, Wageningen, The Netherlands. .,Syngenta Seeds B.V., Westeinde 62, 1601 BK, Enkhuizen, The Netherlands.
| | - Elke Barbez
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Wien, Austria.,Gregor Mendel Institute of Molecular Plant Biology, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Martina Ortbauer
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Wien, Austria
| | - Inez Terpstra
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, 1090 GE, Amsterdam, The Netherlands
| | - Doris Lucyshyn
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Wien, Austria
| | - Jeanette Moulinier-Anzola
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Wien, Austria
| | - Muhammad Asaf Khan
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Wien, Austria.,Department of Bioinformatics and Biotechnology (BNB), Government College University, Faisalabad (GCUF), Allama Iqbal Road, Faisalabad, 38000, Pakistan
| | - Johannes Leitner
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Wien, Austria
| | - Nenad Malenica
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Wien, Austria.,Faculty of Science, Department of Molecular Biology, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - Haroon Butt
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Wien, Austria
| | - Barbara Korbei
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Wien, Austria
| | - Ben Scheres
- Plant Developmental Biology, Wageningen University Research, 6708 PB, Wageningen, The Netherlands
| | - Jürgen Kleine-Vehn
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Wien, Austria
| | - Christian Luschnig
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Wien, Austria.
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10
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Durgaprasad K, Roy MV, Venugopal M A, Kareem A, Raj K, Willemsen V, Mähönen AP, Scheres B, Prasad K. Gradient Expression of Transcription Factor Imposes a Boundary on Organ Regeneration Potential in Plants. Cell Rep 2020; 29:453-463.e3. [PMID: 31597103 DOI: 10.1016/j.celrep.2019.08.099] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 07/11/2019] [Accepted: 08/29/2019] [Indexed: 11/19/2022] Open
Abstract
A wide variety of multicellular organisms across the kingdoms display remarkable ability to restore their tissues or organs when they suffer damage. However, the ability to repair damage is not uniformly distributed throughout body parts. Here, we unravel the elusive mechanistic basis of boundaries on organ regeneration potential using root tip resection as a model and show that the dosage of gradient-expressed PLT2 transcription factor is the underlying cause. While transient downregulation of PLT2 in distinct set of plt mutant backgrounds renders meristematic cells incapable of regeneration, forced expression of PLT2 acts through auto-activation to confer regeneration potential to the cells undergoing differentiation. Surprisingly, sustained exposure to nuclear PLT2, beyond a threshold, leads to reduction of regeneration potential despite giving rise to longer meristem. Our studies reveal dosage-dependent role of gradient-expressed PLT2 in root tip regeneration and uncouple the size of an organ from its regeneration potential.
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Affiliation(s)
- Kavya Durgaprasad
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India
| | - Merin V Roy
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India
| | - Anjali Venugopal M
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India
| | - Abdul Kareem
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India
| | - Kiran Raj
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India
| | - Viola Willemsen
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen 6708PB, the Netherlands
| | - Ari Pekka Mähönen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00014, Finland; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki 00014, Finland
| | - Ben Scheres
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen 6708PB, the Netherlands; Rijk Zwaan R&D, Fijnaart 4793 RS, the Netherlands
| | - Kalika Prasad
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India.
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11
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Radhakrishnan D, Shanmukhan AP, Kareem A, Aiyaz M, Varapparambathu V, Toms A, Kerstens M, Valsakumar D, Landge AN, Shaji A, Mathew MK, Sawchuk MG, Scarpella E, Krizek BA, Efroni I, Mähönen AP, Willemsen V, Scheres B, Prasad K. A coherent feed-forward loop drives vascular regeneration in damaged aerial organs of plants growing in a normal developmental context. Development 2020; 147:dev185710. [PMID: 32108025 DOI: 10.1242/dev.185710] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 02/17/2020] [Indexed: 03/01/2024]
Abstract
Aerial organs of plants, being highly prone to local injuries, require tissue restoration to ensure their survival. However, knowledge of the underlying mechanism is sparse. In this study, we mimicked natural injuries in growing leaves and stems to study the reunion between mechanically disconnected tissues. We show that PLETHORA (PLT) and AINTEGUMENTA (ANT) genes, which encode stem cell-promoting factors, are activated and contribute to vascular regeneration in response to these injuries. PLT proteins bind to and activate the CUC2 promoter. PLT proteins and CUC2 regulate the transcription of the local auxin biosynthesis gene YUC4 in a coherent feed-forward loop, and this process is necessary to drive vascular regeneration. In the absence of this PLT-mediated regeneration response, leaf ground tissue cells can neither acquire the early vascular identity marker ATHB8, nor properly polarise auxin transporters to specify new venation paths. The PLT-CUC2 module is required for vascular regeneration, but is dispensable for midvein formation in leaves. We reveal the mechanisms of vascular regeneration in plants and distinguish between the wound-repair ability of the tissue and its formation during normal development.
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Affiliation(s)
- Dhanya Radhakrishnan
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India
| | | | - Abdul Kareem
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India
| | - Mohammed Aiyaz
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India
| | - Vijina Varapparambathu
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India
| | - Ashna Toms
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India
| | - Merijn Kerstens
- Plant Developmental Biology, Wageningen University Research, Wageningen 6708 PB, The Netherlands
| | - Devisree Valsakumar
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India
| | - Amit N Landge
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India
| | - Anil Shaji
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India
| | - Mathew K Mathew
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, 15, Bengaluru, 560065, India
| | - Megan G Sawchuk
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Enrico Scarpella
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Beth A Krizek
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Idan Efroni
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University, Rehovot 76100, Israel
| | - Ari Pekka Mähönen
- Institute of Biotechnology HiLIFE, University of Helsinki, 00014 Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Viola Willemsen
- Plant Developmental Biology, Wageningen University Research, Wageningen 6708 PB, The Netherlands
| | - Ben Scheres
- Plant Developmental Biology, Wageningen University Research, Wageningen 6708 PB, The Netherlands
| | - Kalika Prasad
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India
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12
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Tang H, Duijts K, Bezanilla M, Scheres B, Vermeer JEM, Willemsen V. Geometric cues forecast the switch from two- to three-dimensional growth in Physcomitrella patens. New Phytol 2020; 225:1945-1955. [PMID: 31639220 PMCID: PMC7027797 DOI: 10.1111/nph.16276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/12/2019] [Indexed: 05/02/2023]
Abstract
During land colonization, plants acquired a range of body plan adaptations, of which the innovation of three-dimensional (3D) tissues increased organismal complexity and reproductivity. In the moss, Physcomitrella patens, a 3D leafy gametophore originates from filamentous cells that grow in a two-dimensional (2D) plane through a series of asymmetric cell divisions. Asymmetric cell divisions that coincide with different cell division planes and growth directions enable the developmental switch from 2D to 3D, but insights into the underlying mechanisms coordinating this switch are still incomplete. Using 2D and 3D imaging and image segmentation, we characterized two geometric cues, the width of the initial cell and the angle of the transition division plane, which sufficiently distinguished a gametophore initial cell from a branch initial cell. These identified cues were further confirmed in gametophore formation mutants. The identification of a fluorescent marker allowed us to successfully predict the gametophore initial cell with > 90% accuracy before morphological changes, supporting our hypothesis that, before the transition division, parental cells of the gametophore initials possess different properties from those of the branch initials. Our results suggest that the cell fate decision of the initial cell is determined in the parental cell, before the transition division.
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Affiliation(s)
- Han Tang
- Laboratory of Plant Developmental BiologyWageningen University & Research6708 PBWageningenthe Netherlands
- Laboratory of Cell BiologyWageningen University & Research6708 PEWageningenthe Netherlands
| | - Kilian Duijts
- Laboratory of Cell BiologyWageningen University & Research6708 PEWageningenthe Netherlands
| | | | - Ben Scheres
- Laboratory of Plant Developmental BiologyWageningen University & Research6708 PBWageningenthe Netherlands
| | - Joop E. M. Vermeer
- Laboratory of Cell and Molecular BiologyInstitute of BiologyUniversity of Neuchâtel2000NeuchâtelSwitzerland
| | - Viola Willemsen
- Laboratory of Plant Developmental BiologyWageningen University & Research6708 PBWageningenthe Netherlands
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13
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Lokdarshi A, Papdi C, Pettkó-Szandtner A, Dorokhov S, Scheres B, Magyar Z, von Arnim AG, Bögre L, Horváth BM. ErbB-3 BINDING PROTEIN 1 Regulates Translation and Counteracts RETINOBLASTOMA RELATED to Maintain the Root Meristem. Plant Physiol 2020; 182:919-932. [PMID: 31818906 PMCID: PMC6997692 DOI: 10.1104/pp.19.00805] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/22/2019] [Indexed: 05/09/2023]
Abstract
The ErbB-3 BINDING PROTEIN 1 (EBP1) drives growth, but the mechanism of how it acts in plants is little understood. Here, we show that EBP1 expression and protein abundance in Arabidopsis (Arabidopsis thaliana) are predominantly confined to meristematic cells and are induced by sucrose and partially dependent on TARGET OF RAPAMYCIN (TOR) kinase activity. Consistent with being downstream of TOR, silencing of EBP1 restrains, while overexpression promotes, root growth, mostly under sucrose-limiting conditions. Inducible overexpression of RETINOBLASTOMA RELATED (RBR), a sugar-dependent transcriptional repressor of cell proliferation, depletes meristematic activity and causes precocious differentiation, which is attenuated by EBP1. To understand the molecular mechanism, we searched for EBP1- and RBR-interacting proteins by affinity purification and mass spectrometry. In line with the double-stranded RNA-binding activity of EBP1 in human (Homo sapiens) cells, the overwhelming majority of EBP1 interactors are part of ribonucleoprotein complexes regulating many aspects of protein synthesis, including ribosome biogenesis and mRNA translation. We confirmed that EBP1 associates with ribosomes and that EBP1 silencing hinders ribosomal RNA processing. We revealed that RBR also interacts with a set of EBP1-associated nucleolar proteins as well as factors that function in protein translation. This suggests EBP1 and RBR act antagonistically on common processes that determine the capacity for translation to tune meristematic activity in relation to available resources.
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Affiliation(s)
- Ansul Lokdarshi
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Csaba Papdi
- Department of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham Hill, Egham TW20 0EX, United Kingdom
| | - Aladár Pettkó-Szandtner
- Laboratory of Proteomics Research, Biological Research Centre, POB 521, H-6701 Szeged, Hungary
| | - Stefan Dorokhov
- Department of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham Hill, Egham TW20 0EX, United Kingdom
| | - Ben Scheres
- Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Zoltán Magyar
- Institute of Plant Biology, Biological Research Centre, POB 521, H-6701 Szeged, Hungary
| | - Albrecht G von Arnim
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
- UT-ORNL Graduate School of Genome Science and Technology, Knoxville, Tennessee 37996
| | - László Bögre
- Department of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham Hill, Egham TW20 0EX, United Kingdom
| | - Beatrix M Horváth
- Department of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham Hill, Egham TW20 0EX, United Kingdom
- Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
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14
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Shimotohno A, Scheres B. Topology of regulatory networks that guide plant meristem activity: similarities and differences. Curr Opin Plant Biol 2019; 51:74-80. [PMID: 31102928 DOI: 10.1016/j.pbi.2019.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/07/2019] [Accepted: 04/12/2019] [Indexed: 06/09/2023]
Abstract
Plants adapt their morphology in response to variable environmental conditions such as nitrate availability, drought, and temperature shifts. Three crucial aspects to this developmental plasticity are the control of initiation, identity and activity of meristems. At the cellular level, the activity of meristems is controlled by balancing self-renewal in stem cells, amplifying divisions in their daughter cells, and cell differentiation. Recent studies in plants have uncovered transcription factors regulating meristem activity at cellular resolution, and regulatory networks that couple these factors with phytohormone signalling for global plant growth regulation. Here, we highlight selected recent advances in our understanding of the multidimensional transcriptional networks that regulate meristem activity and discuss emerging insights on how a selection of environmental cues impinges on these networks.
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Affiliation(s)
- Akie Shimotohno
- Department of Biological Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Ben Scheres
- Department of Plant Sciences, Wageningen University and Research, Wageningen 6708PB, The Netherlands; Rijk Zwaan Research and Development, Fijnaart 4793 RS, The Netherlands.
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15
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Zhou W, Lozano-Torres JL, Blilou I, Zhang X, Zhai Q, Smant G, Li C, Scheres B. A Jasmonate Signaling Network Activates Root Stem Cells and Promotes Regeneration. Cell 2019; 177:942-956.e14. [PMID: 30955889 DOI: 10.1016/j.cell.2019.03.006] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 01/08/2019] [Accepted: 03/04/2019] [Indexed: 12/22/2022]
Abstract
Plants are sessile and have to cope with environmentally induced damage through modification of growth and defense pathways. How tissue regeneration is triggered in such responses and whether this involves stem cell activation is an open question. The stress hormone jasmonate (JA) plays well-established roles in wounding and defense responses. JA also affects growth, which is hitherto interpreted as a trade-off between growth and defense. Here, we describe a molecular network triggered by wound-induced JA that promotes stem cell activation and regeneration. JA regulates organizer cell activity in the root stem cell niche through the RBR-SCR network and stress response protein ERF115. Moreover, JA-induced ERF109 transcription stimulates CYCD6;1 expression, functions upstream of ERF115, and promotes regeneration. Soil penetration and response to nematode herbivory induce and require this JA-mediated regeneration response. Therefore, the JA tissue damage response pathway induces stem cell activation and regeneration and activates growth after environmental stress.
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Affiliation(s)
- Wenkun Zhou
- Laboratory of Plant Developmental Biology, Wageningen University and Research, 6708 PB Wageningen, the Netherlands; State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jose L Lozano-Torres
- Laboratory of Nematology, Wageningen University and Research, 6708 PB Wageningen, the Netherlands
| | - Ikram Blilou
- Laboratory of Plant Developmental Biology, Wageningen University and Research, 6708 PB Wageningen, the Netherlands; KAUST, Thuwall 23955, Saudi Arabia
| | - Xiaoyue Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qingzhe Zhai
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Geert Smant
- Laboratory of Nematology, Wageningen University and Research, 6708 PB Wageningen, the Netherlands
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Ben Scheres
- Laboratory of Plant Developmental Biology, Wageningen University and Research, 6708 PB Wageningen, the Netherlands; Rijk Zwaan R&D, 4793 RS Fijnaart, the Netherlands.
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16
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Shimotohno A, Heidstra R, Blilou I, Scheres B. Root stem cell niche organizer specification by molecular convergence of PLETHORA and SCARECROW transcription factor modules. Genes Dev 2018; 32:1085-1100. [PMID: 30018102 PMCID: PMC6075145 DOI: 10.1101/gad.314096.118] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/31/2018] [Indexed: 12/17/2022]
Abstract
Here, Shimotohno et al. investigated how upstream factors that regulate WUS and WOX genes converge to position organizer cells during embryogenesis, initiation of new lateral organs, and regeneration after tissue damage in Arabodopsis. Here, they show that PLT and SCR genes genetically and physically interact with plant-specific teosinte-branched cycloidea PCNA (TCP) transcription factors to specify the stem cell niche during embryogenesis and maintain organizer cells post-embryonically. Continuous formation of somatic tissues in plants requires functional stem cell niches where undifferentiated cells are maintained. In Arabidopsis thaliana, PLETHORA (PLT) and SCARECROW (SCR) genes are outputs of apical–basal and radial patterning systems, and both are required for root stem cell specification and maintenance. The WUSCHEL-RELATED HOMEOBOX 5 (WOX5) gene is specifically expressed in and required for functions of a small group of root stem cell organizer cells, also called the quiescent center (QC). PLT and SCR are required for QC function, and their expression overlaps in the QC; however, how they specify the organizer has remained unknown. We show that PLT and SCR genetically and physically interact with plant-specific teosinte-branched cycloidea PCNA (TCP) transcription factors to specify the stem cell niche during embryogenesis and maintain organizer cells post-embryonically. PLT–TCP–SCR complexes converge on PLT-binding sites in the WOX5 promoter to induce expression.
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Affiliation(s)
- Akie Shimotohno
- Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands.,Department of Biological Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Renze Heidstra
- Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands.,Department of Plant Sciences, Wageningen University and Research, Wageningen 6708PB, The Netherlands
| | - Ikram Blilou
- Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands.,Department of Plant Sciences, Wageningen University and Research, Wageningen 6708PB, The Netherlands
| | - Ben Scheres
- Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands.,Department of Plant Sciences, Wageningen University and Research, Wageningen 6708PB, The Netherlands
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17
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Abstract
Precise coordination of cell differentiation and division within a tissue context is critical for plant development. In this issue of Developmental Cell, Han et al. (2018) report a transcriptional switch that ensures proper patterning, the final cell division, and terminal differentiation of stomata.
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Affiliation(s)
| | - Ben Scheres
- Wageningen University and Research, Wageningen, the Netherlands; Rijk Zwaan Department of Biotechnology, Fijnaart, the Netherlands.
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18
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Scheres B, Krizek BA. Coordination of growth in root and shoot apices by AIL/PLT transcription factors. Curr Opin Plant Biol 2018; 41:95-101. [PMID: 29121612 DOI: 10.1016/j.pbi.2017.10.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/11/2017] [Accepted: 10/17/2017] [Indexed: 05/27/2023]
Abstract
Growth at the root tip and organ generation at the shoot tip depend on the proper functioning of apical meristems and the transitioning of meristematic cell descendants from a proliferating state to cell elongation and differentiation. Members of the AINTEGUMENTA-LIKE/PLETHORA (AIL/PLT) transcription factor family, a clade of two-AP2 domain proteins, specify both stem cell fate and control cellular progression of stem cell daughter cells toward differentiation. Here we highlight the importance of an AIL/PLT protein gradient in controlling distinct cellular behaviors in the root through the regulation of distinct targets in different parts of the root tip. Within the shoot, AIL/PLT proteins also promote organ growth and inhibit differentiation pointing to conserved roles in meristem function. However, they exhibit unequal genetic redundancy in these functions and do not always act in a purely additive manner. Differences in AIL/PLT regulation and perhaps transcriptional targets in roots and shoots suggest that these growth regulators have adapted to mediate growth control in distinct ways in these organ systems.
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Affiliation(s)
- Ben Scheres
- Department of Plant Biology, Wageningen University Research, The Netherlands.
| | - Beth A Krizek
- Department of Biological Sciences, University of South Carolina, USA
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19
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Chakrabortty B, Blilou I, Scheres B, Mulder BM. A computational framework for cortical microtubule dynamics in realistically shaped plant cells. PLoS Comput Biol 2018; 14:e1005959. [PMID: 29394250 PMCID: PMC5812663 DOI: 10.1371/journal.pcbi.1005959] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 02/14/2018] [Accepted: 01/05/2018] [Indexed: 01/07/2023] Open
Abstract
Plant morphogenesis is strongly dependent on the directional growth and the subsequent oriented division of individual cells. It has been shown that the plant cortical microtubule array plays a key role in controlling both these processes. This ordered structure emerges as the collective result of stochastic interactions between large numbers of dynamic microtubules. To elucidate this complex self-organization process a number of analytical and computational approaches to study the dynamics of cortical microtubules have been proposed. To date, however, these models have been restricted to two dimensional planes or geometrically simple surfaces in three dimensions, which strongly limits their applicability as plant cells display a wide variety of shapes. This limitation is even more acute, as both local as well as global geometrical features of cells are expected to influence the overall organization of the array. Here we describe a framework for efficiently simulating microtubule dynamics on triangulated approximations of arbitrary three dimensional surfaces. This allows the study of microtubule array organization on realistic cell surfaces obtained by segmentation of microscopic images. We validate the framework against expected or known results for the spherical and cubical geometry. We then use it to systematically study the individual contributions of global geometry, cell-edge induced catastrophes and cell-face induced stability to array organization in a cuboidal geometry. Finally, we apply our framework to analyze the highly non-trivial geometry of leaf pavement cells of Arabidopsis thaliana, Nicotiana benthamiana and Hedera helix. We show that our simulations can predict multiple features of the microtubule array structure in these cells, revealing, among others, strong constraints on the orientation of division planes.
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Affiliation(s)
- Bandan Chakrabortty
- Plant Developmental Biology, Wageningen University, Wageningen, The Netherlands
- Department of Living Matter, Institute AMOLF, Amsterdam, The Netherlands
| | - Ikram Blilou
- Laboratory of plant cell and developmental biology, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Ben Scheres
- Plant Developmental Biology, Wageningen University, Wageningen, The Netherlands
| | - Bela M. Mulder
- Department of Living Matter, Institute AMOLF, Amsterdam, The Netherlands
- Cell Biology, Wageningen University, Wageningen, The Netherlands
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20
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Abstract
Root systems can display variable architectures that contribute to survival strategies of plants. The model plant Arabidopsis thaliana possesses a tap root system, in which the primary root and lateral roots (LRs) are major architectural determinants. The phytohormone auxin fulfils multiple roles throughout LR development. In this review, we summarize recent advances in our understanding of four aspects of LR formation: (i) LR positioning, which determines the spatial distribution of lateral root primordia (LRP) and LRs along primary roots; (ii) LR initiation, encompassing the activation of nuclear migration in specified lateral root founder cells (LRFCs) up to the first asymmetric cell division; (iii) LR outgrowth, the 'primordium-intrinsic' patterning of de novo organ tissues and a meristem; and (iv) LR emergence, an interaction between LRP and overlaying tissues to allow passage through cell layers. We discuss how auxin signaling, embedded in a changing developmental context, plays important roles in all four phases. In addition, we discuss how rapid progress in gene network identification and analysis, modeling, and four-dimensional imaging techniques have led to an increasingly detailed understanding of the dynamic regulatory networks that control LR development.
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Affiliation(s)
- Yujuan Du
- Plant Developmental Biology Group, Wageningen University Research, the Netherlands
| | - Ben Scheres
- Plant Developmental Biology Group, Wageningen University Research, the Netherlands
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21
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Long Y, Stahl Y, Weidtkamp-Peters S, Smet W, Du Y, Gadella TWJ, Goedhart J, Scheres B, Blilou I. Optimizing FRET-FLIM Labeling Conditions to Detect Nuclear Protein Interactions at Native Expression Levels in Living Arabidopsis Roots. Front Plant Sci 2018; 9:639. [PMID: 29868092 PMCID: PMC5962846 DOI: 10.3389/fpls.2018.00639] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 04/25/2018] [Indexed: 05/21/2023]
Abstract
Protein complex formation has been extensively studied using Förster resonance energy transfer (FRET) measured by Fluorescence Lifetime Imaging Microscopy (FLIM). However, implementing this technology to detect protein interactions in living multicellular organism at single-cell resolution and under native condition is still difficult to achieve. Here we describe the optimization of the labeling conditions to detect FRET-FLIM in living plants. This study exemplifies optimization procedure involving the identification of the optimal position for the labels either at the N or C terminal region and the selection of the bright and suitable, fluorescent proteins as donor and acceptor labels for the FRET study. With an effective optimization strategy, we were able to detect the interaction between the stem cell regulators SHORT-ROOT and SCARECROW at endogenous expression levels in the root pole of living Arabidopsis embryos and developing lateral roots by FRET-FLIM. Using this approach we show that the spatial profile of interaction between two transcription factors can be highly modulated in reoccurring and structurally resembling organs, thus providing new information on the dynamic redistribution of nuclear protein complex configurations in different developmental stages. In principle, our optimization procedure for transcription factor complexes is applicable to any biological system.
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Affiliation(s)
- Yuchen Long
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen, Netherlands
| | - Yvonne Stahl
- Institute for Developmental Genetics, Heinrich Heine University, Düsseldorf, Germany
| | | | - Wouter Smet
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen, Netherlands
| | - Yujuan Du
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen, Netherlands
| | - Theodorus W. J. Gadella
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Joachim Goedhart
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Ben Scheres
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen, Netherlands
| | - Ikram Blilou
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen, Netherlands
- Plant Cell and Developmental Biology, King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering (BESE), Thuwal, Saudi Arabia
- *Correspondence: Ikram Blilou
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22
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Zhao C, Lasses T, Bako L, Kong D, Zhao B, Chanda B, Bombarely A, Cruz-Ramírez A, Scheres B, Brunner AM, Beers EP. XYLEM NAC DOMAIN1, an angiosperm NAC transcription factor, inhibits xylem differentiation through conserved motifs that interact with RETINOBLASTOMA-RELATED. New Phytol 2017; 216:76-89. [PMID: 28742236 DOI: 10.1111/nph.14704] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 06/13/2017] [Indexed: 05/19/2023]
Abstract
The Arabidopsis thaliana gene XYLEM NAC DOMAIN1 (XND1) is upregulated in xylem tracheary elements. Yet overexpression of XND1 blocks differentiation of tracheary elements. The molecular mechanism of XND1 action was investigated. Phylogenetic and motif analyses indicated that XND1 and its homologs are present only in angiosperms and possess a highly conserved C-terminal region containing linear motifs (CKII-acidic, LXCXE, E2FTD -like and LXCXE-mimic) predicted to interact with the cell cycle and differentiation regulator RETINOBLASTOMA-RELATED (RBR). Protein-protein interaction and functional analyses of XND1 deletion mutants were used to test the importance of RBR-interaction motifs. Deletion of either the LXCXE or the LXCXE-mimic motif reduced both the XND1-RBR interaction and XND1 efficacy as a repressor of differentiation, with loss of the LXCXE motif having the strongest negative impacts. The function of the XND1 C-terminal domain could be partially replaced by RBR fused to the N-terminal domain of XND1. XND1 also transactivated gene expression in yeast and plants. The properties of XND1, a transactivator that depends on multiple linear RBR-interaction motifs to inhibit differentiation, have not previously been described for a plant protein. XND1 harbors an apparently angiosperm-specific combination of interaction motifs potentially linking the general differentiation regulator RBR with a xylem-specific pathway for inhibition of differentiation.
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Affiliation(s)
- Chengsong Zhao
- Department of Horticulture, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Theres Lasses
- Department of Plant Physiology, Umeå Plant Science Center, Umeå University, S-901 87, Umeå, Sweden
| | - Laszlo Bako
- Department of Plant Physiology, Umeå Plant Science Center, Umeå University, S-901 87, Umeå, Sweden
| | - Danyu Kong
- Department of Horticulture, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Bingyu Zhao
- Department of Horticulture, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Bidisha Chanda
- Department of Horticulture, Virginia Tech, Blacksburg, VA, 24061, USA
| | | | - Alfredo Cruz-Ramírez
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, CINVESTAV, Irapuato, Guanajuato, 36821, México
| | - Ben Scheres
- Plant Developmental Biology, Wageningen University & Research, 6708PB, Wageningen, the Netherlands
| | - Amy M Brunner
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Eric P Beers
- Department of Horticulture, Virginia Tech, Blacksburg, VA, 24061, USA
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23
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Sheng L, Hu X, Du Y, Zhang G, Huang H, Scheres B, Xu L. Non-canonical WOX11-mediated root branching contributes to plasticity in Arabidopsis root system architecture. Development 2017; 144:3126-3133. [PMID: 28743799 PMCID: PMC5611959 DOI: 10.1242/dev.152132] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/19/2017] [Indexed: 12/30/2022]
Abstract
Lateral roots (LRs), which originate from the growing root, and adventitious roots (ARs), which are formed from non-root organs, are the main contributors to the post-embryonic root system in Arabidopsis. However, our knowledge of how formation of the root system is altered in response to diverse inductive cues is limited. Here, we show that WOX11 contributes to root system plasticity. When seedlings are grown vertically on medium, WOX11 is not expressed in LR founder cells. During AR initiation, WOX11 is expressed in AR founder cells and activates LBD16. LBD16 also functions in LR formation and is activated in that context by ARF7/19 and not by WOX11. This indicates that divergent initial processes that lead to ARs and LRs may converge on a similar mechanism for primordium development. Furthermore, we demonstrated that when plants are grown in soil or upon wounding on medium, the primary root is able to produce both WOX11-mediated and non-WOX11-mediated roots. The discovery of WOX11-mediated root-derived roots reveals a previously uncharacterized pathway that confers plasticity during the generation of root system architecture in response to different inductive cues. Summary: Root system development can respond flexibly to developmental and environmental cues by utilizing WOX11-mediated and non-WOX11-mediated pathways, which converge on a common mechanism for primordium development involving LBD16.
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Affiliation(s)
- Lihong Sheng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xiaomei Hu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Yujuan Du
- Plant Developmental Biology Group, Wageningen University Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Guifang Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Hai Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Ben Scheres
- Plant Developmental Biology Group, Wageningen University Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China .,University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
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24
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Horvath BM, Kourova H, Nagy S, Nemeth E, Magyar Z, Papdi C, Ahmad Z, Sanchez-Perez GF, Perilli S, Blilou I, Pettkó-Szandtner A, Darula Z, Meszaros T, Binarova P, Bogre L, Scheres B. Arabidopsis RETINOBLASTOMA RELATED directly regulates DNA damage responses through functions beyond cell cycle control. EMBO J 2017; 36:1261-1278. [PMID: 28320736 PMCID: PMC5412863 DOI: 10.15252/embj.201694561] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 02/20/2017] [Accepted: 02/23/2017] [Indexed: 12/26/2022] Open
Abstract
The rapidly proliferating cells in plant meristems must be protected from genome damage. Here, we show that the regulatory role of the Arabidopsis RETINOBLASTOMA RELATED (RBR) in cell proliferation can be separated from a novel function in safeguarding genome integrity. Upon DNA damage, RBR and its binding partner E2FA are recruited to heterochromatic γH2AX‐labelled DNA damage foci in an ATM‐ and ATR‐dependent manner. These γH2AX‐labelled DNA lesions are more dispersedly occupied by the conserved repair protein, AtBRCA1, which can also co‐localise with RBR foci. RBR and AtBRCA1 physically interact in vitro and in planta. Genetic interaction between the RBR‐silenced amiRBR and Atbrca1 mutants suggests that RBR and AtBRCA1 may function together in maintaining genome integrity. Together with E2FA, RBR is directly involved in the transcriptional DNA damage response as well as in the cell death pathway that is independent of SOG1, the plant functional analogue of p53. Thus, plant homologs and analogues of major mammalian tumour suppressor proteins form a regulatory network that coordinates cell proliferation with cell and genome integrity.
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Affiliation(s)
- Beatrix M Horvath
- School of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK .,Department of Molecular Genetics, Utrecht University, Utrecht, The Netherlands
| | - Hana Kourova
- Institute of Microbiology CAS, v.v.i., Laboratory of Cell Reproduction, Prague 4, Czech Republic
| | - Szilvia Nagy
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Edit Nemeth
- School of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK
| | - Zoltan Magyar
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Csaba Papdi
- School of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK
| | - Zaki Ahmad
- School of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK
| | - Gabino F Sanchez-Perez
- Department of Plant Sciences, Wageningen University Research Centre, Wageningen, The Netherlands
| | - Serena Perilli
- Department of Plant Sciences, Wageningen University Research Centre, Wageningen, The Netherlands
| | - Ikram Blilou
- Department of Plant Sciences, Wageningen University Research Centre, Wageningen, The Netherlands
| | | | - Zsuzsanna Darula
- Laboratory of Proteomic Research, Biological Research Centre, Szeged, Hungary
| | - Tamas Meszaros
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary.,Technical Analytical Research Group of HAS, Budapest, Hungary
| | - Pavla Binarova
- Institute of Microbiology CAS, v.v.i., Laboratory of Cell Reproduction, Prague 4, Czech Republic
| | - Laszlo Bogre
- School of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK
| | - Ben Scheres
- Department of Molecular Genetics, Utrecht University, Utrecht, The Netherlands .,Department of Plant Sciences, Wageningen University Research Centre, Wageningen, The Netherlands
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25
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Scheres B, van der Putten WH. The plant perceptron connects environment to development. Nature 2017; 543:337-345. [DOI: 10.1038/nature22010] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 01/10/2017] [Indexed: 12/23/2022]
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26
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Santuari L, Sanchez-Perez GF, Luijten M, Rutjens B, Terpstra I, Berke L, Gorte M, Prasad K, Bao D, Timmermans-Hereijgers JLPM, Maeo K, Nakamura K, Shimotohno A, Pencik A, Novak O, Ljung K, van Heesch S, de Bruijn E, Cuppen E, Willemsen V, Mähönen AP, Lukowitz W, Snel B, de Ridder D, Scheres B, Heidstra R. The PLETHORA Gene Regulatory Network Guides Growth and Cell Differentiation in Arabidopsis Roots. Plant Cell 2016; 28:2937-2951. [PMID: 27920338 PMCID: PMC5240741 DOI: 10.1105/tpc.16.00656] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/16/2016] [Accepted: 11/30/2016] [Indexed: 05/18/2023]
Abstract
Organ formation in animals and plants relies on precise control of cell state transitions to turn stem cell daughters into fully differentiated cells. In plants, cells cannot rearrange due to shared cell walls. Thus, differentiation progression and the accompanying cell expansion must be tightly coordinated across tissues. PLETHORA (PLT) transcription factor gradients are unique in their ability to guide the progression of cell differentiation at different positions in the growing Arabidopsis thaliana root, which contrasts with well-described transcription factor gradients in animals specifying distinct cell fates within an essentially static context. To understand the output of the PLT gradient, we studied the gene set transcriptionally controlled by PLTs. Our work reveals how the PLT gradient can regulate cell state by region-specific induction of cell proliferation genes and repression of differentiation. Moreover, PLT targets include major patterning genes and autoregulatory feedback components, enforcing their role as master regulators of organ development.
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Affiliation(s)
- Luca Santuari
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen 6708PB, The Netherlands
- Bioinformatics Group, Wageningen University and Research Centre, Wageningen 6708PB, The Netherlands
| | - Gabino F Sanchez-Perez
- Bioinformatics Group, Wageningen University and Research Centre, Wageningen 6708PB, The Netherlands
- Applied Bioinformatics, Bioscience, Plant Research International, Wageningen University and Research Centre, Wageningen 6708PB, The Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Marijn Luijten
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Bas Rutjens
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen 6708PB, The Netherlands
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Inez Terpstra
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Lidija Berke
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht 3584 CH, The Netherlands
- Biosystematics Group, Wageningen University and Research Centre, 6708PB Wageningen, The Netherlands
| | - Maartje Gorte
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Kalika Prasad
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Dongping Bao
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands
| | | | - Kenichiro Maeo
- Laboratory of Biochemistry, Graduate School of Bioagricultural Science, Nagoya University, Nagoya 464-8601, Japan
| | - Kenzo Nakamura
- Laboratory of Biochemistry, Graduate School of Bioagricultural Science, Nagoya University, Nagoya 464-8601, Japan
| | - Akie Shimotohno
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Ales Pencik
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå SE-901 83, Sweden
| | - Ondrej Novak
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå SE-901 83, Sweden
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå SE-901 83, Sweden
| | - Sebastiaan van Heesch
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht 3584 CT, The Netherlands
| | - Ewart de Bruijn
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht 3584 CT, The Netherlands
- Hartwig Medical Foundation, 1098 XH Amsterdam, The Netherlands
| | - Edwin Cuppen
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht 3584 CT, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
| | - Viola Willemsen
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen 6708PB, The Netherlands
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Ari Pekka Mähönen
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Wolfgang Lukowitz
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602-7271
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University and Research Centre, Wageningen 6708PB, The Netherlands
| | - Ben Scheres
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen 6708PB, The Netherlands
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Renze Heidstra
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen 6708PB, The Netherlands
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands
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27
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Porco S, Larrieu A, Du Y, Gaudinier A, Goh T, Swarup K, Swarup R, Kuempers B, Bishopp A, Lavenus J, Casimiro I, Hill K, Benkova E, Fukaki H, Brady SM, Scheres B, Péret B, Bennett MJ. Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development 2016; 143:3340-9. [PMID: 27578783 DOI: 10.1242/dev.136283] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 08/04/2016] [Indexed: 10/21/2022]
Abstract
Lateral root primordia (LRP) originate from pericycle stem cells located deep within parental root tissues. LRP emerge through overlying root tissues by inducing auxin-dependent cell separation and hydraulic changes in adjacent cells. The auxin-inducible auxin influx carrier LAX3 plays a key role concentrating this signal in cells overlying LRP. Delimiting LAX3 expression to two adjacent cell files overlying new LRP is crucial to ensure that auxin-regulated cell separation occurs solely along their shared walls. Multiscale modeling has predicted that this highly focused pattern of expression requires auxin to sequentially induce auxin efflux and influx carriers PIN3 and LAX3, respectively. Consistent with model predictions, we report that auxin-inducible LAX3 expression is regulated indirectly by AUXIN RESPONSE FACTOR 7 (ARF7). Yeast one-hybrid screens revealed that the LAX3 promoter is bound by the transcription factor LBD29, which is a direct target for regulation by ARF7. Disrupting auxin-inducible LBD29 expression or expressing an LBD29-SRDX transcriptional repressor phenocopied the lax3 mutant, resulting in delayed lateral root emergence. We conclude that sequential LBD29 and LAX3 induction by auxin is required to coordinate cell separation and organ emergence.
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Affiliation(s)
- Silvana Porco
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Antoine Larrieu
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK Laboratoire Reproduction et Développement des Plantes, Univ. Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
| | - Yujuan Du
- Molecular Genetics, Department of Biology, Faculty of Science, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Allison Gaudinier
- Department of Plant Biology and Genome Center, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Tatsuaki Goh
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Kamal Swarup
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Ranjan Swarup
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Britta Kuempers
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Anthony Bishopp
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Julien Lavenus
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK Institute of Plant Sciences, 21 Altenbergrain, Bern 3006, Switzerland
| | - Ilda Casimiro
- Departamento Anatomia, Biologia Celular Y Zoologia, Facultad de Ciencias, Universidad de Extremadura, Badajoz 06006, Spain
| | - Kristine Hill
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Eva Benkova
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Hidehiro Fukaki
- Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Ben Scheres
- Molecular Genetics, Department of Biology, Faculty of Science, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Benjamin Péret
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK Centre National de la Recherche Scientifique, Biochimie et Physiologie Moléculaire des Plantes, Montpellier SupAgro, 2 Place Pierre Viala, Montpellier 34060, France
| | - Malcolm J Bennett
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
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28
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Moreno-Risueno MA, Sozzani R, Yardımcı GG, Petricka JJ, Vernoux T, Blilou I, Alonso J, Winter CM, Ohler U, Scheres B, Benfey PN. Transcriptional control of tissue formation throughout root development. Science 2016; 350:426-30. [PMID: 26494755 DOI: 10.1126/science.aad1171] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Tissue patterns are dynamically maintained. Continuous formation of plant tissues during postembryonic growth requires asymmetric divisions and the specification of cell lineages. We show that the BIRDs and SCARECROW regulate lineage identity, positional signals, patterning, and formative divisions throughout Arabidopsis root growth. These transcription factors are postembryonic determinants of the ground tissue stem cells and their lineage. Upon further activation by the positional signal SHORT-ROOT (a mobile transcription factor), they direct asymmetric cell divisions and patterning of cell types. The BIRDs and SCARECROW with SHORT-ROOT organize tissue patterns at all formative steps during growth, ensuring developmental plasticity.
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Affiliation(s)
- Miguel A Moreno-Risueno
- Department of Biotechnology, Center for Plant Genomics and Biotechnology, Universidad Politecnica de Madrid, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Rosangela Sozzani
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Galip Gürkan Yardımcı
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Jalean J Petricka
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Teva Vernoux
- Laboratoire de Reproduction et Développement des Plantes, CNRS, INRA, ENS Lyon, UCBL, Université de Lyon, 69364 Lyon, France
| | - Ikram Blilou
- Department of Plant Biology, Wageningen University Research, Wageningen, Netherlands
| | - Jose Alonso
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Cara M Winter
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Uwe Ohler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Ben Scheres
- Department of Plant Biology, Wageningen University Research, Wageningen, Netherlands
| | - Philip N Benfey
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA.
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Affiliation(s)
- Ben Scheres
- Plant Developmental Biology, Wageningen University Research, Building 107 (Radix), Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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30
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Siligato R, Wang X, Yadav SR, Lehesranta S, Ma G, Ursache R, Sevilem I, Zhang J, Gorte M, Prasad K, Wrzaczek M, Heidstra R, Murphy A, Scheres B, Mähönen AP. MultiSite Gateway-Compatible Cell Type-Specific Gene-Inducible System for Plants. Plant Physiol 2016; 170:627-41. [PMID: 26644504 PMCID: PMC4734558 DOI: 10.1104/pp.15.01246] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/07/2015] [Indexed: 05/02/2023]
Abstract
A powerful method to study gene function is expression or overexpression in an inducible, cell type-specific system followed by observation of consequent phenotypic changes and visualization of linked reporters in the target tissue. Multiple inducible gene overexpression systems have been developed for plants, but very few of these combine plant selection markers, control of expression domains, access to multiple promoters and protein fusion reporters, chemical induction, and high-throughput cloning capabilities. Here, we introduce a MultiSite Gateway-compatible inducible system for Arabidopsis (Arabidopsis thaliana) plants that provides the capability to generate such constructs in a single cloning step. The system is based on the tightly controlled, estrogen-inducible XVE system. We demonstrate that the transformants generated with this system exhibit the expected cell type-specific expression, similar to what is observed with constitutively expressed native promoters. With this new system, cloning of inducible constructs is no longer limited to a few special cases but can be used as a standard approach when gene function is studied. In addition, we present a set of entry clones consisting of histochemical and fluorescent reporter variants designed for gene and promoter expression studies.
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Affiliation(s)
- Riccardo Siligato
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Xin Wang
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Shri Ram Yadav
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Satu Lehesranta
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Guojie Ma
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Robertas Ursache
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Iris Sevilem
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Jing Zhang
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Maartje Gorte
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Kalika Prasad
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Michael Wrzaczek
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Renze Heidstra
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Angus Murphy
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Ben Scheres
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Ari Pekka Mähönen
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
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Long Y, Goedhart J, Schneijderberg M, Terpstra I, Shimotohno A, Bouchet BP, Akhmanova A, Gadella TWJ, Heidstra R, Scheres B, Blilou I. SCARECROW-LIKE23 and SCARECROW jointly specify endodermal cell fate but distinctly control SHORT-ROOT movement. Plant J 2015; 84:773-84. [PMID: 26415082 DOI: 10.1111/tpj.13038] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 09/15/2015] [Accepted: 09/18/2015] [Indexed: 05/27/2023]
Abstract
Intercellular signaling through trafficking of regulatory proteins is a widespread phenomenon in plants and can deliver positional information for the determination of cell fate. In the Arabidopsis root meristem, the cell fate determinant SHORT-ROOT (SHR), a GRAS domain transcription factor, acts as a signaling molecule from the stele to the adjacent layer to specify endodermal cell fate. Upon exiting the stele, SHR activates another GRAS domain transcription factor, SCARCROW (SCR), which, together with several BIRD/INDETERMINATE DOMAIN proteins, restricts movement of SHR to define a single cell layer of endodermis. Here we report that endodermal cell fate also requires the joint activity of both SCR and its closest homologue SCARECROW-LIKE23 (SCL23). We show that SCL23 protein moves with zonation-dependent directionality. Within the meristem, SCL23 exhibits short-ranged movement from ground tissue to vasculature. Away from the meristem, SCL23 displays long-range rootward movement into meristematic vasculature and a bidirectional radial spread, respectively. As a known target of SHR and SCR, SCL23 also interacts with SCR and SHR and can restrict intercellular outspread of SHR without relying on nuclear retention as SCR does. Collectively, our data show that SCL23 is a mobile protein that controls movement of SHR and acts redundantly with SCR to specify endodermal fate in the root meristem.
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Affiliation(s)
- Yuchen Long
- Plant Developmental Biology, Plant Sciences, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen, 6708PB, the Netherlands
- Molecular Genetics, Department Biology, Padualaan 8, Utrecht, 3581CH, the Netherlands
| | - Joachim Goedhart
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, the Netherlands
| | | | - Inez Terpstra
- Molecular Genetics, Department Biology, Padualaan 8, Utrecht, 3581CH, the Netherlands
| | - Akie Shimotohno
- Molecular Genetics, Department Biology, Padualaan 8, Utrecht, 3581CH, the Netherlands
| | - Benjamin P Bouchet
- Cell Biology, Department Biology, Utrecht University, Padualaan 8, Utrecht, 3581CH, the Netherlands
| | - Anna Akhmanova
- Cell Biology, Department Biology, Utrecht University, Padualaan 8, Utrecht, 3581CH, the Netherlands
| | - Theodorus W J Gadella
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, the Netherlands
| | - Renze Heidstra
- Plant Developmental Biology, Plant Sciences, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen, 6708PB, the Netherlands
- Molecular Genetics, Department Biology, Padualaan 8, Utrecht, 3581CH, the Netherlands
| | - Ben Scheres
- Plant Developmental Biology, Plant Sciences, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen, 6708PB, the Netherlands
- Molecular Genetics, Department Biology, Padualaan 8, Utrecht, 3581CH, the Netherlands
| | - Ikram Blilou
- Plant Developmental Biology, Plant Sciences, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen, 6708PB, the Netherlands
- Molecular Genetics, Department Biology, Padualaan 8, Utrecht, 3581CH, the Netherlands
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Dhonukshe P, Huang F, Galvan-Ampudia CS, Mähönen AP, Kleine-Vehn J, Xu J, Quint A, Prasad K, Friml J, Scheres B, Offringa R. Plasma membrane-bound AGC3 kinases phosphorylate PIN auxin carriers at TPRXS(N/S) motifs to direct apical PIN recycling. Development 2015; 142:2386-7. [DOI: 10.1242/dev.127415] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Pankaj Dhonukshe
- Section of Molecular Genetics, Department of Biology, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Fang Huang
- Molecular and Developmental Genetics, Institute Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333BE Leiden, The Netherlands
| | - Carlos S. Galvan-Ampudia
- Molecular and Developmental Genetics, Institute Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333BE Leiden, The Netherlands
| | - Ari Pekka Mähönen
- Section of Molecular Genetics, Department of Biology, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Jürgen Kleine-Vehn
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, Technologiepark 927, 9052 Ghent, Belgium
| | - Jian Xu
- Section of Molecular Genetics, Department of Biology, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Ab Quint
- Molecular and Developmental Genetics, Institute Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333BE Leiden, The Netherlands
| | - Kalika Prasad
- Section of Molecular Genetics, Department of Biology, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Jiří Friml
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, Technologiepark 927, 9052 Ghent, Belgium
| | - Ben Scheres
- Section of Molecular Genetics, Department of Biology, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Remko Offringa
- Molecular and Developmental Genetics, Institute Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333BE Leiden, The Netherlands
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33
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Long Y, Smet W, Cruz-Ramírez A, Castelijns B, de Jonge W, Mähönen AP, Bouchet BP, Perez GS, Akhmanova A, Scheres B, Blilou I. Arabidopsis BIRD Zinc Finger Proteins Jointly Stabilize Tissue Boundaries by Confining the Cell Fate Regulator SHORT-ROOT and Contributing to Fate Specification. Plant Cell 2015; 27:1185-99. [PMID: 25829440 PMCID: PMC4558684 DOI: 10.1105/tpc.114.132407] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Revised: 02/10/2015] [Accepted: 03/10/2015] [Indexed: 05/18/2023]
Abstract
Plant cells cannot rearrange their positions; therefore, sharp tissue boundaries must be accurately programmed. Movement of the cell fate regulator SHORT-ROOT from the stele to the ground tissue has been associated with transferring positional information across tissue boundaries. The zinc finger BIRD protein JACKDAW has been shown to constrain SHORT-ROOT movement to a single layer, and other BIRD family proteins were postulated to counteract JACKDAW's role in restricting SHORT-ROOT action range. Here, we report that regulation of SHORT-ROOT movement requires additional BIRD proteins whose action is critical for the establishment and maintenance of the boundary between stele and ground tissue. We show that BIRD proteins act in concert and not in opposition. The exploitation of asymmetric redundancies allows the separation of two BIRD functions: constraining SHORT-ROOT spread through nuclear retention and transcriptional regulation of key downstream SHORT-ROOT targets, including SCARECROW and CYCLIND6. Our data indicate that BIRD proteins promote formative divisions and tissue specification in the Arabidopsis thaliana root meristem ground tissue by tethering and regulating transcriptional competence of SHORT-ROOT complexes. As a result, a tissue boundary is not "locked in" after initial patterning like in many animal systems, but possesses considerable developmental plasticity due to continuous reliance on mobile transcription factors.
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Affiliation(s)
- Yuchen Long
- Plant Developmental Biology, Wageningen University, Wageningen 6708PB, The Netherlands Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3581CH, The Netherlands
| | - Wouter Smet
- Plant Developmental Biology, Wageningen University, Wageningen 6708PB, The Netherlands Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3581CH, The Netherlands
| | - Alfredo Cruz-Ramírez
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3581CH, The Netherlands
| | - Bas Castelijns
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3581CH, The Netherlands
| | - Wim de Jonge
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3581CH, The Netherlands
| | - Ari Pekka Mähönen
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Helsinki 00014, Finland
| | - Benjamin P Bouchet
- Cell Biology, Faculty of Science, Utrecht University, Utrecht 3581CH, The Netherlands
| | - Gabino Sanchez Perez
- Bioinformatics, Plant Sciences, Wageningen University, Wageningen 6708PB, The Netherlands
| | - Anna Akhmanova
- Cell Biology, Faculty of Science, Utrecht University, Utrecht 3581CH, The Netherlands
| | - Ben Scheres
- Plant Developmental Biology, Wageningen University, Wageningen 6708PB, The Netherlands Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3581CH, The Netherlands
| | - Ikram Blilou
- Plant Developmental Biology, Wageningen University, Wageningen 6708PB, The Netherlands Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3581CH, The Netherlands
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34
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Kareem A, Durgaprasad K, Sugimoto K, Du Y, Pulianmackal AJ, Trivedi ZB, Abhayadev PV, Pinon V, Meyerowitz EM, Scheres B, Prasad K. PLETHORA Genes Control Regeneration by a Two-Step Mechanism. Curr Biol 2015; 25:1017-30. [PMID: 25819565 PMCID: PMC4829346 DOI: 10.1016/j.cub.2015.02.022] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/14/2015] [Accepted: 02/04/2015] [Indexed: 10/23/2022]
Abstract
Regeneration, a remarkable example of developmental plasticity displayed by both plants and animals, involves successive developmental events driven in response to environmental cues. Despite decades of study on the ability of the plant tissues to regenerate a complete fertile shoot system after inductive cues, the mechanisms by which cells acquire pluripotency and subsequently regenerate complete organs remain unknown. Here, we show that three PLETHORA (PLT) genes, PLT3, PLT5, and PLT7, regulate de novo shoot regeneration in Arabidopsis by controlling two distinct developmental events. Cumulative loss of function of these three genes causes the intermediate cell mass, callus, to be incompetent to form shoot progenitors, whereas induction of PLT5 or PLT7 can render shoot regeneration hormone-independent. We further show that PLT3, PLT5, and PLT7 establish pluripotency by activating root stem cell regulators PLT1 and PLT2, as reconstitution of either PLT1 or PLT2 in the plt3; plt5-2; plt7 mutant re-established the competence to regenerate shoot progenitor cells but did not lead to the completion of shoot regeneration. PLT3, PLT5, and PLT7 additionally regulate and require the shoot-promoting factor CUP-SHAPED COTYLEDON2 (CUC2) to complete the shoot-formation program. Our findings uncouple the acquisition of competence to regenerate shoot progenitor cells from completion of shoot formation, indicating a two-step mechanism of de novo shoot regeneration that operates in all tested plant tissues irrespective of their origin. Our studies reveal intermediate developmental phases of regeneration and provide a deeper understanding into the mechanistic basis of regeneration.
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Affiliation(s)
- Abdul Kareem
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695016, India
| | - Kavya Durgaprasad
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695016, India
| | - Kaoru Sugimoto
- Division of Biology and Biological Engineering and Howard Hughes Medical Institute, 156-29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yujuan Du
- Plant Developmental Biology, Wageningen University Research, Wageningen 6708 PB, the Netherlands
| | - Ajai J Pulianmackal
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695016, India
| | - Zankhana B Trivedi
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695016, India
| | - Pazhoor V Abhayadev
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695016, India
| | - Violaine Pinon
- Plant Developmental Biology, Wageningen University Research, Wageningen 6708 PB, the Netherlands
| | - Elliot M Meyerowitz
- Division of Biology and Biological Engineering and Howard Hughes Medical Institute, 156-29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ben Scheres
- Plant Developmental Biology, Wageningen University Research, Wageningen 6708 PB, the Netherlands
| | - Kalika Prasad
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695016, India.
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Kinoshita A, ten Hove CA, Tabata R, Yamada M, Shimizu N, Ishida T, Yamaguchi K, Shigenobu S, Takebayashi Y, Iuchi S, Kobayashi M, Kurata T, Wada T, Seo M, Hasebe M, Blilou I, Fukuda H, Scheres B, Heidstra R, Kamiya Y, Sawa S. A plant U-box protein, PUB4, regulates asymmetric cell division and cell proliferation in the root meristem. Development 2015; 142:444-53. [PMID: 25605779 DOI: 10.1242/dev.113167] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The root meristem (RM) is a fundamental structure that is responsible for postembryonic root growth. The RM contains the quiescent center (QC), stem cells and frequently dividing meristematic cells, in which the timing and the frequency of cell division are tightly regulated. In Arabidopsis thaliana, several gain-of-function analyses have demonstrated that peptide ligands of the Clavata3 (CLV3)/embryo surrounding region-related (CLE) family are important for maintaining RM size. Here, we demonstrate that a plant U-box E3 ubiquitin ligase, PUB4, is a novel downstream component of CLV3/CLE signaling in the RM. Mutations in PUB4 reduced the inhibitory effect of exogenous CLV3/CLE peptide on root cell proliferation and columella stem cell maintenance. Moreover, pub4 mutants grown without exogenous CLV3/CLE peptide exhibited characteristic phenotypes in the RM, such as enhanced root growth, increased number of cortex/endodermis stem cells and decreased number of columella layers. Our phenotypic and gene expression analyses indicated that PUB4 promotes expression of a cell cycle regulatory gene, CYCD6;1, and regulates formative periclinal asymmetric cell divisions in endodermis and cortex/endodermis initial daughters. These data suggest that PUB4 functions as a global regulator of cell proliferation and the timing of asymmetric cell division that are important for final root architecture.
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Affiliation(s)
- Atsuko Kinoshita
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Colette A ten Hove
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, Wageningen 6703HA, The Netherlands
| | - Ryo Tabata
- Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Masashi Yamada
- Department of Biology and Institute for Genome Science and Policy Center for Systems Biology, Duke University, Durham, NC 27708, USA
| | - Noriko Shimizu
- Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Takashi Ishida
- Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Katsushi Yamaguchi
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Shuji Shigenobu
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki 444-8585, Japan School of Life Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan
| | - Yumiko Takebayashi
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Satoshi Iuchi
- RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Masatomo Kobayashi
- RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Tetsuya Kurata
- Graduate School of Biological Sciences, NAIST, Ikoma 630-0192, Japan
| | - Takuji Wada
- Graduate School of Biosphere Sciences, Hiroshima University, Higashi-Hiroshima 739-8528, Japan
| | - Mitsunori Seo
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Mitsuyasu Hasebe
- School of Life Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Ikram Blilou
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands Plant Developmental Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen 6700AP, The Netherlands
| | - Hiroo Fukuda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ben Scheres
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands Plant Developmental Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen 6700AP, The Netherlands
| | - Renze Heidstra
- Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands Plant Developmental Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen 6700AP, The Netherlands
| | - Yuji Kamiya
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Shinichiro Sawa
- Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
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Abstract
Mobile transcription factors play many roles in plant development. Here, we compare the use of mobile transcription factors as signals with some canonical signal transduction processes in prokaryotes and eukaryotes. After an initial survey, we focus on the SHORT-ROOT pathway in Arabidopsis roots to show that, despite the simplicity of the concept of mobile transcription factor signalling, many lines of evidence reveal a surprising complexity in control mechanisms linked to this process. We argue that these controls bestow precision, robustness, and versatility on mobile transcription factor signalling.
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Affiliation(s)
- Yuchen Long
- Plant Developmental Biology, Plant Sciences, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Ben Scheres
- Plant Developmental Biology, Plant Sciences, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Ikram Blilou
- Plant Developmental Biology, Plant Sciences, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands.
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Franssen HJ, Xiao TT, Kulikova O, Wan X, Bisseling T, Scheres B, Heidstra R. Root developmental programs shape the Medicago truncatula nodule meristem. Development 2015; 142:2941-50. [DOI: 10.1242/dev.120774] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 07/24/2015] [Indexed: 02/03/2023]
Abstract
Nodules on the roots of legume plants host nitrogen-fixing rhizobium bacteria. Several lines of evidence indicate that nodules are evolutionary related to roots. We determined whether developmental control of the Medicago truncatula nodule meristem bears resemblance to that in root meristems through analyses of root meristem expressed PLETHORA genes. In nodules, MtPLETHORA1 and 2 genes are preferentially expressed in cells positioned at the periphery of the meristem abutting nodule vascular bundles. Their expression overlaps with an auxin response maximum and MtWOX5 that is a marker for the root quiescent centre. Strikingly, the cells in the central part of the nodule meristem have a high level of cytokinin and display MtPLETHORA 3 and 4 gene expression. Nodule-specific knock-down of MtPLETHORA genes results in reduced number of nodules and/or in nodules in which meristem activity has ceased. Our nodule gene expression map indicates that the nodule meristem is composed of two distinct domains in which different MtPLETHORA gene subsets are expressed. Our mutant studies show that MtPLETHORA genes redundantly function in nodule meristem maintenance. This indicates that Rhizobium has recruited root developmental programs for nodule formation
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Affiliation(s)
- Henk J. Franssen
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Ting Ting Xiao
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Olga Kulikova
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Xi Wan
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Present address: NOVOGENE Bioinformatics technology, 38 Xueqing Road, Haidian district, Beijing, China
| | - Ton Bisseling
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- College of Science, King Saud University, Post Office Box 2455, Riyadh 11451, Saudi Arabia
| | - Ben Scheres
- Department of Plant Sciences, Plant Developmental Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands, telephone: +31-317483264
| | - Renze Heidstra
- Department of Plant Sciences, Plant Developmental Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands, telephone: +31-317483264
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39
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Matos JL, Lau OS, Hachez C, Cruz-Ramírez A, Scheres B, Bergmann DC. Irreversible fate commitment in the Arabidopsis stomatal lineage requires a FAMA and RETINOBLASTOMA-RELATED module. eLife 2014; 3. [PMID: 25303364 PMCID: PMC4225492 DOI: 10.7554/elife.03271] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 10/09/2014] [Indexed: 12/17/2022] Open
Abstract
The presumed totipotency of plant cells leads to questions about how specific stem cell lineages and terminal fates could be established. In the Arabidopsis stomatal lineage, a transient self-renewing phase creates precursors that differentiate into one of two epidermal cell types, guard cells or pavement cells. We found that irreversible differentiation of guard cells involves RETINOBLASTOMA-RELATED (RBR) recruitment to regulatory regions of master regulators of stomatal initiation, facilitated through interaction with a terminal stomatal lineage transcription factor, FAMA. Disrupting physical interactions between FAMA and RBR preferentially reveals the role of RBR in enforcing fate commitment over its role in cell-cycle control in this developmental context. Analysis of the phenotypes linked to the modulation of FAMA and RBR sheds new light on the way iterative divisions and terminal differentiation are coordinately regulated in a plant stem-cell lineage. DOI:http://dx.doi.org/10.7554/eLife.03271.001 Stem cells in animals and plants help to make and replenish the tissues of the body by dividing and becoming specialized types of cells. Once specialized for a certain function, it is important that a cell keeps that function. In plant leaves, one type of stem cell makes two different types of specialized cells: pavement cells and stomatal guard cells. Pavement cells lock together to form a waterproof barrier to the outside, while guard cells surround the small pores that open and close to allow the plant to exchange water, oxygen and carbon dioxide with the atmosphere. Once a cell becomes a pavement cell or a guard cell, it does not change its identity again. However, if a single cell is removed from a plant, it can revert to a stem cell and a whole new plant can be grown from it. This poses the question of how, in intact plants, specialized cells like pavement cells and guard cells are prevented from reverting to stem cells. In Arabidopsis thaliana, a small flowering plant that is widely used as a model organism in research, a protein called FAMA is responsible for controlling a set of genes that turn stem cells into guard cells. Matos et al. have now found that FAMA needs to bind to another protein called RBR to control this process. It seems that these two proteins make the transition from stem cell to guard cell permanent by changing the structure of DNA in regions that control stem cell genes. RBR is similar to a human protein called Retinoblastoma that helps prevent tumors and regulate stem cells, but how it actually performs these functions in humans is still debated. Because stem cells and guard cells are displayed on the surface of plant leaves and leave behind clues of their past, Matos et al. were able to watch stem cells grow up to be mature guard cells. When the partnership between FAMA and RBR was broken, it was possible to watch those same guard cells revert backwards into stem cells. Seeing development ‘rewind’ could provide useful insights into the way in which cell identity is controlled in both plants and animals. DOI:http://dx.doi.org/10.7554/eLife.03271.002
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Affiliation(s)
- Juliana L Matos
- Department of Biology, Stanford University, Stanford, United States
| | - On Sun Lau
- Department of Biology, Stanford University, Stanford, United States
| | - Charles Hachez
- Department of Biology, Stanford University, Stanford, United States
| | | | - Ben Scheres
- Department of Molecular Genetics, Utrecht University, Utrecht, Netherlands
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40
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Abstract
The regulation of columella stem cell activity in the Arabidopsis root cap by a nearby organizing centre, the quiescent centre, has been a key example of the stem cell niche paradigm in plants. Here, we investigate interactions between transcription factors that have been shown to regulate columella stem cells using a simple quantification method for stem cell activity in the root cap. Genetic and expression analyses reveal that the RETINOBLASTOMA-RELATED protein, the FEZ and SOMBRERO NAC-domain transcription factors, the ARF10 and ARF16 auxin response factors and the quiescent centre-expressed WOX5 homeodomain protein each provide independent inputs to regulate the number of columella stem cells. Given the tight control of columella development, we found that these inputs act in a surprisingly parallel manner. Nevertheless, important points of interaction exist; for example, we demonstrate the repression of SMB activity by non-autonomous action of WOX5. Our results suggest that the developmental progression of columella stem cells may be quantitatively regulated by several more broadly acting transcription factors rather than by a single intrinsic stem cell factor, which raises questions about the special nature of the stem cell state in plants.
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Affiliation(s)
- Tom Bennett
- Department of Molecular Genetics, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Albert van den Toorn
- Department of Molecular Genetics, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands Plant Developmental Biology, Wageningen University Research, Wageningen 6708 PB, The Netherlands
| | - Viola Willemsen
- Department of Molecular Genetics, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands Plant Developmental Biology, Wageningen University Research, Wageningen 6708 PB, The Netherlands
| | - Ben Scheres
- Department of Molecular Genetics, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands Plant Developmental Biology, Wageningen University Research, Wageningen 6708 PB, The Netherlands
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41
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Dhonukshe P, Tanaka H, Goh T, Ebine K, Mähönen AP, Prasad K, Blilou I, Geldner N, Xu J, Uemura T, Chory J, Ueda T, Nakano A, Scheres B, Friml J. Retraction: Generation of cell polarity in plants links endocytosis, auxin distribution and cell fate decisions. Nature 2014; 511:370. [PMID: 25030176 DOI: 10.1038/nature13549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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43
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Kakar K, Zhang H, Scheres B, Dhonukshe P. Correction: Retraction: CLASP-mediated cortical microtubule organization guides PIN polarization axis. Nature 2014; 508:274. [DOI: 10.1038/nature13183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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44
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Dhonukshe P, Weits D, Cruz-Ramirez A, Deinum E, Tindemans S, Kakar K, Prasad K, Mähönen A, Ambrose C, Sasabe M, Wachsmann G, Luijten M, Bennett T, Machida Y, Heidstra R, Wasteneys G, Mulder B, Scheres B. Retraction Notice to: A PLETHORA-auxin transcription module controls cell division plane rotation through MAP65 and CLASP. Cell 2014; 155:1189. [PMID: 24267897 DOI: 10.1016/j.cell.2013.10.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A PLETHORA-Auxin Transcription Module Controls Cell Division Plane Rotation through MAP65 and CLASP --Cell, Volume 149, Issue 2, 13 April 2012, Pages 383-396. Our paper reported that Arabidopsis PLETHORA transcription factors regulate cell division planes by transcriptional activation of MAP65, which interacts with the CLASP protein to guide microtubule orientation. We recently identified mistakes affecting Figures 4N, S4B, and S6E in which original data were processed inappropriately such that the panels do not accurately report the original data. At least in one case, the original data did not support the figure's conclusion. We believe that the most responsible course of action is to retract the paper. We sincerely apologize to the scientific community for any inconvenience that this might cause.
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Cruz-Ramírez A, Díaz-Triviño S, Wachsman G, Du Y, Arteága-Vázquez M, Zhang H, Benjamins R, Blilou I, Neef AB, Chandler V, Scheres B. A SCARECROW-RETINOBLASTOMA protein network controls protective quiescence in the Arabidopsis root stem cell organizer. PLoS Biol 2013; 11:e1001724. [PMID: 24302889 PMCID: PMC3841101 DOI: 10.1371/journal.pbio.1001724] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 10/22/2013] [Indexed: 01/17/2023] Open
Abstract
Ben Scheres and colleagues report that in the growing tip of plant roots, a gene regulatory network that includes the plant homologue of Retinoblastoma regulates the divisions of long-term stem cells to replenish tissue and to protect the root stem cell niche. Quiescent long-term somatic stem cells reside in plant and animal stem cell niches. Within the Arabidopsis root stem cell population, the Quiescent Centre (QC), which contains slowly dividing cells, maintains surrounding short-term stem cells and may act as a long-term reservoir for stem cells. The RETINOBLASTOMA-RELATED (RBR) protein cell-autonomously reinforces mitotic quiescence in the QC. RBR interacts with the stem cell transcription factor SCARECROW (SCR) through an LxCxE motif. Disruption of this interaction by point mutation in SCR or RBR promotes asymmetric divisions in the QC that renew short-term stem cells. Analysis of the in vivo role of quiescence in the root stem cell niche reveals that slow cycling within the QC is not needed for structural integrity of the niche but allows the growing root to cope with DNA damage. In the plant Arabidposis thaliana, root meristems (in the growing tip of the root) contain slowly dividing cells that act as an organizing center for the root stem cells that surround them. This centre is called the quiescent centre (QC). In this study, we show that the slow rate of division in the QC is regulated by the interaction between two proteins: Retinoblastoma homolog (RBR) and SCARECROW (SCR), a transcription factor that controls stem cell maintenance. RBR and SCR regulate quiescence in the QC by repressing an asymmetric cell division that generates short-term stem cells. Here we genetically manipulate the cells in the QC to alter their quiescence by regulating the RBR/SCR interaction to demonstrate that quiescence is not needed for the organizing capacity of the QC but instead provides cells with a higher resistance to genotoxic stress, allowing stem cells in the QC to survive even if more rapidly cycling stem cells are damaged. A role for mitotic quiescence has been reported in animal stem cells, in which Rb has been implicated. These findings indicate that it might serve a similar role in plant stem cells.
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Affiliation(s)
- Alfredo Cruz-Ramírez
- Department of Molecular Genetics, Utrecht University, Utrecht, The Netherlands
- Laboratorio Nacional de Genmica para la Biodiversidad, Cinvestav Sede Irapuato, Irapuato, Mexico
| | - Sara Díaz-Triviño
- Department of Molecular Genetics, Utrecht University, Utrecht, The Netherlands
| | - Guy Wachsman
- Department of Molecular Genetics, Utrecht University, Utrecht, The Netherlands
| | - Yujuan Du
- Department of Molecular Genetics, Utrecht University, Utrecht, The Netherlands
| | - Mario Arteága-Vázquez
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Xalapa, Veracruz, Mexico
| | - Hongtao Zhang
- Department of Molecular Genetics, Utrecht University, Utrecht, The Netherlands
| | - Rene Benjamins
- Department of Molecular Genetics, Utrecht University, Utrecht, The Netherlands
| | - Ikram Blilou
- Department of Molecular Genetics, Utrecht University, Utrecht, The Netherlands
| | - Anne B. Neef
- Institute of Organic Chemistry, University of Zurich, Zurich, Switzerland
| | - Vicki Chandler
- BIO5 Institute and Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Ben Scheres
- Department of Molecular Genetics, Utrecht University, Utrecht, The Netherlands
- * E-mail:
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46
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Perilli S, Perez-Perez JM, Di Mambro R, Peris CL, Díaz-Triviño S, Del Bianco M, Pierdonati E, Moubayidin L, Cruz-Ramírez A, Costantino P, Scheres B, Sabatini S. RETINOBLASTOMA-RELATED protein stimulates cell differentiation in the Arabidopsis root meristem by interacting with cytokinin signaling. Plant Cell 2013; 25:4469-78. [PMID: 24285791 PMCID: PMC3875730 DOI: 10.1105/tpc.113.116632] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 11/04/2013] [Accepted: 11/14/2013] [Indexed: 05/23/2023]
Abstract
Maintenance of mitotic cell clusters such as meristematic cells depends on their capacity to maintain the balance between cell division and cell differentiation necessary to control organ growth. In the Arabidopsis thaliana root meristem, the antagonistic interaction of two hormones, auxin and cytokinin, regulates this balance by positioning the transition zone, where mitotically active cells lose their capacity to divide and initiate their differentiation programs. In animals, a major regulator of both cell division and cell differentiation is the tumor suppressor protein RETINOBLASTOMA. Here, we show that similarly to its homolog in animal systems, the plant RETINOBLASTOMA-RELATED (RBR) protein regulates the differentiation of meristematic cells at the transition zone by allowing mRNA accumulation of AUXIN RESPONSE FACTOR19 (ARF19), a transcription factor involved in cell differentiation. We show that both RBR and the cytokinin-dependent transcription factor ARABIDOPSIS RESPONSE REGULATOR12 are required to activate the transcription of ARF19, which is involved in promoting cell differentiation and thus root growth.
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Affiliation(s)
- Serena Perilli
- Department of Biology and Biotechnology, Laboratories of Functional Genomics and Proteomics of Model Systems, University of Rome Sapienza, 00185 Rome, Italy
| | - José Manuel Perez-Perez
- Molecular Genetics, Department of Biology, University of Utrecht, 3584 CH Utrecht, The Netherlands
| | - Riccardo Di Mambro
- Department of Biology and Biotechnology, Laboratories of Functional Genomics and Proteomics of Model Systems, University of Rome Sapienza, 00185 Rome, Italy
| | - Cristina Llavata Peris
- Department of Biology and Biotechnology, Laboratories of Functional Genomics and Proteomics of Model Systems, University of Rome Sapienza, 00185 Rome, Italy
| | - Sara Díaz-Triviño
- Molecular Genetics, Department of Biology, University of Utrecht, 3584 CH Utrecht, The Netherlands
| | - Marta Del Bianco
- Department of Biology and Biotechnology, Laboratories of Functional Genomics and Proteomics of Model Systems, University of Rome Sapienza, 00185 Rome, Italy
| | - Emanuela Pierdonati
- Department of Biology and Biotechnology, Laboratories of Functional Genomics and Proteomics of Model Systems, University of Rome Sapienza, 00185 Rome, Italy
| | - Laila Moubayidin
- Department of Biology and Biotechnology, Laboratories of Functional Genomics and Proteomics of Model Systems, University of Rome Sapienza, 00185 Rome, Italy
| | - Alfredo Cruz-Ramírez
- Molecular Genetics, Department of Biology, University of Utrecht, 3584 CH Utrecht, The Netherlands
| | - Paolo Costantino
- Department of Biology and Biotechnology, Laboratories of Functional Genomics and Proteomics of Model Systems, University of Rome Sapienza, 00185 Rome, Italy
| | - Ben Scheres
- Molecular Genetics, Department of Biology, University of Utrecht, 3584 CH Utrecht, The Netherlands
| | - Sabrina Sabatini
- Department of Biology and Biotechnology, Laboratories of Functional Genomics and Proteomics of Model Systems, University of Rome Sapienza, 00185 Rome, Italy
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47
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Abstract
Spatial patterns of the hormone auxin are important drivers of plant development. The observed feedback between the active, directed transport that generates auxin patterns and the auxin distribution that influences transport orientation has rendered this a popular subject for modelling studies. Here we propose a new mathematical framework for the analysis of polar auxin transport and present a detailed mathematical analysis of published models. We show that most models allow for self-organised patterning for similar biological assumptions, and find that the pattern generated is typically unidirectional, unless additional assumptions or mechanisms are incorporated. Our analysis thus suggests that current models cannot explain the bidirectional fountain-type patterns found in plant meristems in a fully self-organised manner, and we discuss future research directions to address the gaps in our understanding of auxin transport mechanisms.
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Affiliation(s)
- Klaartje van Berkel
- Molecular Genetics Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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48
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Kakar K, Zhang H, Scheres B, Dhonukshe P. CLASP-mediated cortical microtubule organization guides PIN polarization axis. Nature 2013; 495:529-33. [PMID: 23515161 DOI: 10.1038/nature11980] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 01/31/2013] [Indexed: 01/17/2023]
Abstract
Recent evidence indicates a correlation between orientation of the plant cortical microtubule cytoskeleton and localization of polar cargoes. However, the molecules and mechanisms that create this correlation have remained unknown. Here we show that, in Arabidopsis thaliana, the microtubule orientation regulators CLASP and MAP65 (refs 3, 4) control the abundance of polarity regulator PINOID kinase at the plasma membrane. By localized upregulation of clathrin-dependent endocytosis at cortical microtubule- and clathrin-rich domains orthogonal to the axis of polarity, PINOID accelerates the removal of auxin transporter PIN proteins from those sites. This mechanism links directional microtubule organization to the polar localization of auxin transporter PIN proteins, and clarifies how microtubule-enriched cell sides are kept distinct from polar delivery domains. Our results identify the molecular machinery that connects microtubule organization to the regulation of the axis of PIN polarization.
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Affiliation(s)
- Klementina Kakar
- Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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49
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Abstract
In 1993, we published a paper in Development detailing the anatomical structure of the Arabidopsis root. The paper described how root growth was maintained by the precisely tuned activity of a small set of 'initials', which acted as the source of dividing and differentiating cells, and how these stem cell-like cells surrounded a few infrequently dividing cells. This work underpinned subsequent research on root developmental biology and sparked a detailed molecular analysis of how stem cell groups are positioned and maintained in plants.
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Affiliation(s)
- Ben Scheres
- Plant Developmental Biology, Wageningen University Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
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Zhang H, Zhou H, Berke L, Heck AJR, Mohammed S, Scheres B, Menke FLH. Quantitative phosphoproteomics after auxin-stimulated lateral root induction identifies an SNX1 protein phosphorylation site required for growth. Mol Cell Proteomics 2013; 12:1158-69. [PMID: 23328941 DOI: 10.1074/mcp.m112.021220] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein phosphorylation is instrumental to early signaling events. Studying system-wide phosphorylation in relation to processes under investigation requires a quantitative proteomics approach. In Arabidopsis, auxin application can induce pericycle cell divisions and lateral root formation. Initiation of lateral root formation requires transcriptional reprogramming following auxin-mediated degradation of transcriptional repressors. The immediate early signaling events prior to this derepression are virtually uncharacterized. To identify the signal molecules responding to auxin application, we used a lateral root-inducible system that was previously developed to trigger synchronous division of pericycle cells. To identify and quantify the early signaling events following this induction, we combined (15)N-based metabolic labeling and phosphopeptide enrichment and applied a mass spectrometry-based approach. In total, 3068 phosphopeptides were identified from auxin-treated root tissue. This root proteome dataset contains largely phosphopeptides not previously reported and represents one of the largest quantitative phosphoprotein datasets from Arabidopsis to date. Key proteins responding to auxin treatment included the multidrug resistance-like and PIN2 auxin carriers, auxin response factor2 (ARF2), suppressor of auxin resistance 3 (SAR3), and sorting nexin1 (SNX1). Mutational analysis of serine 16 of SNX1 showed that overexpression of the mutated forms of SNX1 led to retarded growth and reduction of lateral root formation due to the reduced outgrowth of the primordium, showing proof of principle for our approach.
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Affiliation(s)
- Hongtao Zhang
- Bijvoet Center for Biomolecular Research, and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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