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Nimchuk ZL, Blilou I. Editorial Overview: Plant Growth and Development: building a plant brick by brick. Curr Opin Plant Biol 2024; 78:102525. [PMID: 38428320 DOI: 10.1016/j.pbi.2024.102525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Affiliation(s)
| | - Ikram Blilou
- King Abdullah University of Science and Technology, Saudi Arabia.
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2
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Smith ES, Nimchuk ZL. What a tangled web it weaves: auxin coordination of stem cell maintenance and flower production. J Exp Bot 2023; 74:6950-6963. [PMID: 37661937 PMCID: PMC10690728 DOI: 10.1093/jxb/erad340] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 03/31/2023] [Accepted: 08/25/2023] [Indexed: 09/05/2023]
Abstract
Robust agricultural yields require consistent flower production throughout fluctuating environmental conditions. Floral primordia are produced in the inflorescence meristem, which contains a pool of continuously dividing stem cells. Daughter cells of these divisions either retain stem cell identity or are pushed to the SAM periphery, where they become competent to develop into floral primordia after receiving the appropriate signal. Thus, flower production is inherently linked to regulation of the stem cell pool. The plant hormone auxin promotes flower development throughout its early phases and has been shown to interact with the molecular pathways regulating stem cell maintenance. Here, we will summarize how auxin signaling contributes to stem cell maintenance and promotes flower development through the early phases of initiation, outgrowth, and floral fate establishment. Recent advances in this area suggest that auxin may serve as a signal that integrates stem cell maintenance and new flower production.
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Affiliation(s)
- Elizabeth Sarkel Smith
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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3
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John A, Smith ES, Jones DS, Soyars CL, Nimchuk ZL. A network of CLAVATA receptors buffers auxin-dependent meristem maintenance. Nat Plants 2023; 9:1306-1317. [PMID: 37550370 PMCID: PMC11070199 DOI: 10.1038/s41477-023-01485-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/07/2023] [Indexed: 08/09/2023]
Abstract
Plant body plans are elaborated in response to both environmental and endogenous cues. How these inputs intersect to promote growth and development remains poorly understood. During reproductive development, central zone stem cell proliferation in inflorescence meristems is negatively regulated by the CLAVATA3 (CLV3) peptide signalling pathway. In contrast, floral primordia formation on meristem flanks requires the hormone auxin. Here we show that CLV3 signalling is also necessary for auxin-dependent floral primordia generation and that this function is partially masked by both inflorescence fasciation and heat-induced auxin biosynthesis. Stem cell regulation by CLAVATA signalling is separable from primordia formation but is also sensitized to temperature and auxin levels. In addition, we uncover a novel role for the CLV3 receptor CLAVATA1 in auxin-dependent meristem maintenance in cooler environments. As such, CLV3 signalling buffers multiple auxin-dependent shoot processes across divergent thermal environments, with opposing effects on cell proliferation in different meristem regions.
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Affiliation(s)
- Amala John
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elizabeth Sarkel Smith
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Daniel S Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Cara L Soyars
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Thermo Fisher Scientific, Raleigh, NC, USA
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Burr CA, Sun J, Yamburenko MV, Willoughby A, Hodgens C, Boeshore SL, Elmore A, Atkinson J, Nimchuk ZL, Bishopp A, Schaller GE, Kieber JJ. Correction: The HK5 and HK6 cytokinin receptors mediate diverse developmental pathways in rice. Development 2023; 150:dev202221. [PMID: 37526652 DOI: 10.1242/dev.202221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
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5
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Stegmann M, Zecua-Ramirez P, Ludwig C, Lee HS, Peterson B, Nimchuk ZL, Belkhadir Y, Hückelhoven R. RGI-GOLVEN signaling promotes cell surface immune receptor abundance to regulate plant immunity. EMBO Rep 2022; 23:e53281. [PMID: 35229426 PMCID: PMC9066070 DOI: 10.15252/embr.202153281] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 05/17/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 11/26/2022] Open
Abstract
Plant immune responses must be tightly controlled for proper allocation of resources for growth and development. In plants, endogenous signaling peptides regulate developmental and growth‐related processes. Recent research indicates that some of these peptides also have regulatory functions in the control of plant immune responses. This classifies these peptides as phytocytokines as they show analogies with metazoan cytokines. However, the mechanistic basis for phytocytokine‐mediated regulation of plant immunity remains largely elusive. Here, we identify GOLVEN2 (GLV2) peptides as phytocytokines in Arabidopsis thaliana. GLV2 signaling enhances sensitivity of plants to elicitation with immunogenic bacterial elicitors and contributes to resistance against virulent bacterial pathogens. GLV2 is perceived by ROOT MERISTEM GROWTH FACTOR 1 INSENSITIVE (RGI) receptors. RGI mutants show reduced elicitor sensitivity and enhanced susceptibility to bacterial infection. RGI3 forms ligand‐induced complexes with the pattern recognition receptor (PRR) FLAGELLIN SENSITIVE 2 (FLS2), suggesting that RGIs are part of PRR signaling platforms. GLV2‐RGI signaling promotes PRR abundance independent of transcriptional regulation and controls plant immunity via a previously undescribed mechanism of phytocytokine activity.
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Affiliation(s)
- Martin Stegmann
- Phytopathology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Patricia Zecua-Ramirez
- Phytopathology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Ho-Seok Lee
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Brenda Peterson
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Youssef Belkhadir
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Ralph Hückelhoven
- Phytopathology, School of Life Sciences, Technical University of Munich, Freising, Germany
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6
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Stegmann M, Zecua-Ramirez P, Ludwig C, Lee HS, Peterson B, Nimchuk ZL, Belkhadir Y, Hückelhoven R. RGI-GOLVEN signaling promotes cell surface immune receptor abundance to regulate plant immunity. EMBO Rep 2022; 23:e53281. [PMID: 35229426 DOI: 10.1101/2021.01.29.428839] [Citation(s) in RCA: 4] [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: 05/17/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 05/23/2023] Open
Abstract
Plant immune responses must be tightly controlled for proper allocation of resources for growth and development. In plants, endogenous signaling peptides regulate developmental and growth-related processes. Recent research indicates that some of these peptides also have regulatory functions in the control of plant immune responses. This classifies these peptides as phytocytokines as they show analogies with metazoan cytokines. However, the mechanistic basis for phytocytokine-mediated regulation of plant immunity remains largely elusive. Here, we identify GOLVEN2 (GLV2) peptides as phytocytokines in Arabidopsis thaliana. GLV2 signaling enhances sensitivity of plants to elicitation with immunogenic bacterial elicitors and contributes to resistance against virulent bacterial pathogens. GLV2 is perceived by ROOT MERISTEM GROWTH FACTOR 1 INSENSITIVE (RGI) receptors. RGI mutants show reduced elicitor sensitivity and enhanced susceptibility to bacterial infection. RGI3 forms ligand-induced complexes with the pattern recognition receptor (PRR) FLAGELLIN SENSITIVE 2 (FLS2), suggesting that RGIs are part of PRR signaling platforms. GLV2-RGI signaling promotes PRR abundance independent of transcriptional regulation and controls plant immunity via a previously undescribed mechanism of phytocytokine activity.
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Affiliation(s)
- Martin Stegmann
- Phytopathology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Patricia Zecua-Ramirez
- Phytopathology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Ho-Seok Lee
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Brenda Peterson
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Youssef Belkhadir
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Ralph Hückelhoven
- Phytopathology, School of Life Sciences, Technical University of Munich, Freising, Germany
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DeFalco TA, Anne P, James SR, Willoughby AC, Schwanke F, Johanndrees O, Genolet Y, Derbyshire P, Wang Q, Rana S, Pullen AM, Menke FLH, Zipfel C, Hardtke CS, Nimchuk ZL. A conserved module regulates receptor kinase signalling in immunity and development. Nat Plants 2022; 8:356-365. [PMID: 35422079 PMCID: PMC9639402 DOI: 10.1038/s41477-022-01134-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/14/2022] [Indexed: 06/01/2023]
Abstract
Ligand recognition by cell-surface receptors underlies development and immunity in both animals and plants. Modulating receptor signalling is critical for appropriate cellular responses but the mechanisms ensuring this are poorly understood. Here, we show that signalling by plant receptors for pathogen-associated molecular patterns (PAMPs) in immunity and CLAVATA3/EMBRYO SURROUNDING REGION-RELATED peptides (CLEp) in development uses a similar regulatory module. In the absence of ligand, signalling is dampened through association with specific type-2C protein phosphatases. Upon activation, PAMP and CLEp receptors phosphorylate divergent cytosolic kinases, which, in turn, phosphorylate the phosphatases, thereby promoting receptor signalling. Our work reveals a regulatory circuit shared between immune and developmental receptor signalling, which may have broader important implications for plant receptor kinase-mediated signalling in general.
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Affiliation(s)
- Thomas A DeFalco
- Institute of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, Zurich, Switzerland
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Pauline Anne
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Sean R James
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andrew C Willoughby
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Florian Schwanke
- Institute of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, Zurich, Switzerland
| | - Oliver Johanndrees
- Institute of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, Zurich, Switzerland
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Yasmine Genolet
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Paul Derbyshire
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Qian Wang
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Surbhi Rana
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Anne-Marie Pullen
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Frank L H Menke
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Cyril Zipfel
- Institute of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, Zurich, Switzerland.
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Christian S Hardtke
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland.
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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8
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DeFalco TA, Anne P, James SR, Willoughby AC, Schwanke F, Johanndrees O, Genolet Y, Derbyshire P, Wang Q, Rana S, Pullen AM, Menke FLH, Zipfel C, Hardtke CS, Nimchuk ZL. A conserved module regulates receptor kinase signalling in immunity and development. Nat Plants 2022; 8:356-365. [PMID: 35422079 DOI: 10.1101/2021.01.19.427293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/14/2022] [Indexed: 05/22/2023]
Abstract
Ligand recognition by cell-surface receptors underlies development and immunity in both animals and plants. Modulating receptor signalling is critical for appropriate cellular responses but the mechanisms ensuring this are poorly understood. Here, we show that signalling by plant receptors for pathogen-associated molecular patterns (PAMPs) in immunity and CLAVATA3/EMBRYO SURROUNDING REGION-RELATED peptides (CLEp) in development uses a similar regulatory module. In the absence of ligand, signalling is dampened through association with specific type-2C protein phosphatases. Upon activation, PAMP and CLEp receptors phosphorylate divergent cytosolic kinases, which, in turn, phosphorylate the phosphatases, thereby promoting receptor signalling. Our work reveals a regulatory circuit shared between immune and developmental receptor signalling, which may have broader important implications for plant receptor kinase-mediated signalling in general.
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Affiliation(s)
- Thomas A DeFalco
- Institute of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, Zurich, Switzerland
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Pauline Anne
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Sean R James
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andrew C Willoughby
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Florian Schwanke
- Institute of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, Zurich, Switzerland
| | - Oliver Johanndrees
- Institute of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, Zurich, Switzerland
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Yasmine Genolet
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Paul Derbyshire
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Qian Wang
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Surbhi Rana
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Anne-Marie Pullen
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Frank L H Menke
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Cyril Zipfel
- Institute of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, Zurich, Switzerland.
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Christian S Hardtke
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland.
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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9
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Willoughby AC, Nimchuk ZL. WOX going on: CLE peptides in plant development. Curr Opin Plant Biol 2021; 63:102056. [PMID: 34077886 PMCID: PMC8545713 DOI: 10.1016/j.pbi.2021.102056] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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: 03/11/2021] [Revised: 04/14/2021] [Accepted: 04/19/2021] [Indexed: 05/11/2023]
Abstract
The development of plant tissues requires cell-cell communication facilitated by chemical and peptide hormones, including small signaling peptides in the CLAVATA3/EMBRYO-SURROUNDING REGION (CLE) family. The paradigmatic CLE signaling peptide CLAVATA3 regulates the size of the shoot apical meristem and the expression of the stem cell-promoting WUSCHEL transcription factor through an unknown mechanism. This review discusses recent advances in CLE signaling, showing that CLE pathways are conserved in bryophytes, that CLE peptides in Arabidopsis thaliana regulate stem cell identity and cell division in root tissues, and connections to auxin biosynthesis in regulating flower and leaf development. These advances shed light on potential WUSCHEL family-independent aspects of CLE signaling and the overlap between CLE and auxin signaling.
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Affiliation(s)
- Andrew C Willoughby
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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10
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Marquès-Bueno MM, Armengot L, Noack LC, Bareille J, Rodriguez L, Platre MP, Bayle V, Liu M, Opdenacker D, Vanneste S, Möller BK, Nimchuk ZL, Beeckman T, Caño-Delgado AI, Friml J, Jaillais Y. Auxin-Regulated Reversible Inhibition of TMK1 Signaling by MAKR2 Modulates the Dynamics of Root Gravitropism. Curr Biol 2020; 31:228-237.e10. [PMID: 33157019 PMCID: PMC7809621 DOI: 10.1016/j.cub.2020.10.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 06/27/2019] [Revised: 09/04/2020] [Accepted: 10/07/2020] [Indexed: 12/14/2022]
Abstract
Plants are able to orient their growth according to gravity, which ultimately controls both shoot and root architecture.1 Gravitropism is a dynamic process whereby gravistimulation induces the asymmetric distribution of the plant hormone auxin, leading to asymmetric growth, organ bending, and subsequent reset of auxin distribution back to the original pre-gravistimulation situation.1, 2, 3 Differential auxin accumulation during the gravitropic response depends on the activity of polarly localized PIN-FORMED (PIN) auxin-efflux carriers.1, 2, 3, 4 In particular, the timing of this dynamic response is regulated by PIN2,5,6 but the underlying molecular mechanisms are poorly understood. Here, we show that MEMBRANE ASSOCIATED KINASE REGULATOR2 (MAKR2) controls the pace of the root gravitropic response. We found that MAKR2 is required for the PIN2 asymmetry during gravitropism by acting as a negative regulator of the cell-surface signaling mediated by the receptor-like kinase TRANSMEMBRANE KINASE1 (TMK1).2,7, 8, 9, 10 Furthermore, we show that the MAKR2 inhibitory effect on TMK1 signaling is antagonized by auxin itself, which triggers rapid MAKR2 membrane dissociation in a TMK1-dependent manner. Our findings suggest that the timing of the root gravitropic response is orchestrated by the reversible inhibition of the TMK1 signaling pathway at the cell surface. MAKR2 is co-expressed with PIN2 and regulates the pace of root gravitropism MAKR2 controls PIN2 asymmetric accumulation at the root level during gravitropism MAKR2 binds to and is a negative regulator of the TMK1 receptor kinase Auxin antagonizes the MAKR2 inhibition of TMK1 by delocalizing MAKR2 in the cytosol
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Affiliation(s)
- Maria Mar Marquès-Bueno
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France; Department of Molecular Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - Laia Armengot
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France
| | - Lise C Noack
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France
| | - Joseph Bareille
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France
| | - Lesia Rodriguez
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Matthieu Pierre Platre
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France
| | - Vincent Bayle
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France
| | - Mengying Liu
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France
| | - Davy Opdenacker
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Steffen Vanneste
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Lab of Plant Growth Analysis, Ghent University Global Campus, Songdomunhwa-Ro, 119, Yeonsu-gu, Incheon 21985, Republic of Korea
| | - Barbara K Möller
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tom Beeckman
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Ana I Caño-Delgado
- Department of Molecular Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - Jiří Friml
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France.
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11
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Jones DS, John A, VanDerMolen KR, Nimchuk ZL. CLAVATA Signaling Ensures Reproductive Development in Plants across Thermal Environments. Curr Biol 2020; 31:220-227.e5. [PMID: 33157018 DOI: 10.1016/j.cub.2020.10.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 04/10/2020] [Revised: 09/03/2020] [Accepted: 10/05/2020] [Indexed: 11/29/2022]
Abstract
The ability to thrive in diverse environments requires that species maintain development and reproduction despite dynamic conditions. Many developmental processes are stabilized through robust signaling pathways that cooperatively ensure proper development.1 During reproduction, plants like Arabidopsis thaliana continuously generate flowers on growing indeterminate inflorescences.2 Flower primordia initiation and outgrowth depends on the hormone auxin and is robust across diverse environments.3-6 Here, we show that reproductive development under different thermal conditions requires the integration of multiple pathways regulating auxin-dependent flower production. In colder/ambient temperatures, the receptor complex CLAVATA2/CORYNE (CLV2/CRN) is necessary for continuous flower outgrowth during inflorescence development. CLV2/CRN signaling is independent of CLAVATA1 (CLV1)-related receptor signaling but involves the CLAVATA3 INSENSITIVE RECEPTOR KINASE (CIK) family co-receptors, with higher order cik mutant combinations phenocopying clv2/crn flower outgrowth defects. Developing crn inflorescences display reduced auxin signaling, and restoration of auxin biosynthesis is sufficient to restore flower outgrowth in colder and ambient temperatures. In contrast, at higher temperatures, both clv2/crn signaling and heat-induced auxin biosynthesis via YUCCA family genes are synergistically required to maintain flower development. Our work reveals a novel mechanism integrating peptide hormone and auxin signaling in the regulation of flower development across diverse thermal environments.
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Affiliation(s)
- Daniel S Jones
- Department of Biology, University of North Carolina at Chapel Hill, 250 Bell Tower Drive, Chapel Hill, NC 27599, USA
| | - Amala John
- Department of Biology, University of North Carolina at Chapel Hill, 250 Bell Tower Drive, Chapel Hill, NC 27599, USA
| | - Kylie R VanDerMolen
- Department of Biology, University of North Carolina at Chapel Hill, 250 Bell Tower Drive, Chapel Hill, NC 27599, USA
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, 250 Bell Tower Drive, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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12
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Burr CA, Sun J, Yamburenko MV, Willoughby A, Hodgens C, Boeshore SL, Elmore A, Atkinson J, Nimchuk ZL, Bishopp A, Schaller GE, Kieber JJ. The HK5 and HK6 cytokinin receptors mediate diverse developmental pathways in rice. Development 2020; 147:dev191734. [PMID: 33028608 PMCID: PMC7648598 DOI: 10.1242/dev.191734] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 04/17/2020] [Accepted: 09/23/2020] [Indexed: 12/22/2022]
Abstract
The phytohormone cytokinin regulates diverse aspects of plant growth and development. Our understanding of the metabolism and perception of cytokinin has made great strides in recent years, mostly from studies of the model dicot Arabidopsis Here, we employed a CRISPR/Cas9-based approach to disrupt a subset of cytokinin histidine kinase (HK) receptors in rice (Oryza sativa) in order to explore the role of cytokinin in a monocot species. In hk5 and hk6 single mutants, the root growth, leaf width, inflorescence architecture and/or floral development were affected. The double hk5 hk6 mutant showed more substantial defects, including severely reduced root and shoot growth, a smaller shoot apical meristem, and an enlarged root cap. Flowering was delayed in the hk5 hk6 mutant and the panicle was significantly reduced in size and infertile due to multiple defects in floral development. The hk5 hk6 mutant also exhibited a severely reduced cytokinin response, consistent with the developmental phenotypes arising from a defect in cytokinin signaling. These results indicate that HK5 and HK6 act as cytokinin receptors, with overlapping functions to regulate diverse aspects of rice growth and development.
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Affiliation(s)
- Christian A Burr
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jinjing Sun
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | - Andrew Willoughby
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Charles Hodgens
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | - Agustus Elmore
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jonathan Atkinson
- School of Bioscience, University of Nottingham, Nottingham LE12 5RD, UK
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Anthony Bishopp
- School of Bioscience, University of Nottingham, Nottingham LE12 5RD, UK
| | - G Eric Schaller
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755
| | - Joseph J Kieber
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
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13
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Whitewoods CD, Cammarata J, Venza ZN, Sang S, Crook AD, Aoyama T, Wang XY, Waller M, Kamisugi Y, Cuming AC, Szövényi P, Nimchuk ZL, Roeder AHK, Scanlon MJ, Harrison CJ. CLAVATA Was a Genetic Novelty for the Morphological Innovation of 3D Growth in Land Plants. Curr Biol 2020; 30:2645-2648. [PMID: 32634407 PMCID: PMC7342000 DOI: 10.1016/j.cub.2020.06.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Fernandez AI, Vangheluwe N, Xu K, Jourquin J, Claus LAN, Morales-Herrera S, Parizot B, De Gernier H, Yu Q, Drozdzecki A, Maruta T, Hoogewijs K, Vannecke W, Peterson B, Opdenacker D, Madder A, Nimchuk ZL, Russinova E, Beeckman T. GOLVEN peptide signalling through RGI receptors and MPK6 restricts asymmetric cell division during lateral root initiation. Nat Plants 2020; 6:533-543. [PMID: 32393883 DOI: 10.1038/s41477-020-0645-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 03/24/2020] [Indexed: 05/26/2023]
Abstract
During lateral root initiation, lateral root founder cells undergo asymmetric cell divisions that generate daughter cells with different sizes and fates, a prerequisite for correct primordium organogenesis. An excess of the GLV6/RGF8 peptide disrupts these initial asymmetric cell divisions, resulting in more symmetric divisions and the failure to achieve lateral root organogenesis. Here, we show that loss-of-function GLV6 and its homologue GLV10 increase asymmetric cell divisions during lateral root initiation, and we identified three members of the RGF1 INSENSITIVE/RGF1 receptor subfamily as likely GLV receptors in this process. Through a suppressor screen, we found that MITOGEN-ACTIVATED PROTEIN KINASE6 is a downstream regulator of the GLV pathway. Our data indicate that GLV6 and GLV10 act as inhibitors of asymmetric cell divisions and signal through RGF1 INSENSITIVE receptors and MITOGEN-ACTIVATED PROTEIN KINASE6 to restrict the number of initial asymmetric cell divisions that take place during lateral root initiation.
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Affiliation(s)
- Ana I Fernandez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Nick Vangheluwe
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ke Xu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Joris Jourquin
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lucas Alves Neubus Claus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Stefania Morales-Herrera
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Laboratory of Molecular Cell Biology, KU Leuven, Kasteelpark, Leuven, Belgium
- VIB Center for Microbiology, Kasteelpark, Leuven, Belgium
| | - Boris Parizot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hugues De Gernier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Qiaozhi Yu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Andrzej Drozdzecki
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Takanori Maruta
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Matsue, Japan
| | - Kurt Hoogewijs
- Department of Organic Chemistry and Macromolecular Chemistry, Ghent University, Ghent, Belgium
| | - Willem Vannecke
- Department of Organic Chemistry and Macromolecular Chemistry, Ghent University, Ghent, Belgium
| | - Brenda Peterson
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Davy Opdenacker
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Annemieke Madder
- Department of Organic Chemistry and Macromolecular Chemistry, Ghent University, Ghent, Belgium
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
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15
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Smit ME, McGregor SR, Sun H, Gough C, Bågman AM, Soyars CL, Kroon JT, Gaudinier A, Williams CJ, Yang X, Nimchuk ZL, Weijers D, Turner SR, Brady SM, Etchells JP. A PXY-Mediated Transcriptional Network Integrates Signaling Mechanisms to Control Vascular Development in Arabidopsis. Plant Cell 2020; 32:319-335. [PMID: 31806676 PMCID: PMC7008486 DOI: 10.1105/tpc.19.00562] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/12/2019] [Accepted: 12/05/2019] [Indexed: 05/18/2023]
Abstract
The cambium and procambium generate the majority of biomass in vascular plants. These meristems constitute a bifacial stem cell population from which xylem and phloem are specified on opposing sides by positional signals. The PHLOEM INTERCALATED WITH XYLEM (PXY) receptor kinase promotes vascular cell division and organization. However, how these functions are specified and integrated is unknown. Here, we mapped a putative PXY-mediated transcriptional regulatory network comprising 690 transcription factor-promoter interactions in Arabidopsis (Arabidopsis thaliana). Among these interactions was a feedforward loop containing transcription factors WUSCHEL HOMEOBOX RELATED14 (WOX14) and TARGET OF MONOPTEROS6 (TMO6), each of which regulates the expression of the gene encoding a third transcription factor, LATERAL ORGAN BOUNDARIES DOMAIN4 (LBD4). PXY signaling in turn regulates the WOX14, TMO6, and LBD4 feedforward loop to control vascular proliferation. Genetic interaction between LBD4 and PXY suggests that LBD4 marks the phloem-procambium boundary, thus defining the shape of the vascular bundle. These data collectively support a mechanism that influences the recruitment of cells into the phloem lineage, and they define the role of PXY signaling in this context in determining the arrangement of vascular tissue.
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Affiliation(s)
- Margot E Smit
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Shauni R McGregor
- Department of Biosciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Heng Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Catherine Gough
- Department of Biosciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Anne-Maarit Bågman
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Cara L Soyars
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Johannes T Kroon
- Department of Biosciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Allison Gaudinier
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Clara J Williams
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Simon R Turner
- School of Biological Science, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Siobhán M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - J Peter Etchells
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
- Department of Biosciences, Durham University, Durham DH1 3LE, United Kingdom
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16
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John A, Nimchuk ZL. A little goes a long way: CLE peptides mediate phloem initiation. J Integr Plant Biol 2019; 61:1034-1035. [PMID: 31456292 DOI: 10.1111/jipb.12868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 08/23/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Amala John
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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17
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Worthen JM, Yamburenko MV, Lim J, Nimchuk ZL, Kieber JJ, Schaller GE. Type-B response regulators of rice play key roles in growth, development and cytokinin signaling. Development 2019; 146:dev.174870. [PMID: 31160418 DOI: 10.1242/dev.174870] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 05/23/2019] [Indexed: 12/20/2022]
Abstract
Cytokinins are plant hormones with crucial roles in growth and development. Although cytokinin signaling is well characterized in the model dicot Arabidopsis, we are only beginning to understand its role in monocots, such as rice (Oryza sativa) and other cereals of agronomic importance. Here, we used primarily a CRISPR/Cas9 gene-editing approach to characterize the roles of a key family of transcription factors, the type-B response regulators (RRs), in cytokinin signaling in rice. Results from the analysis of single rr mutants as well as higher-order rr21/22/23 mutant lines revealed functional overlap as well as subfunctionalization within members of the gene family. Mutant phenotypes associated with decreased activity of rice type-B RRs included effects on leaf and root growth, inflorescence architecture, flower development and fertilization, trichome formation and cytokinin sensitivity. Development of the stigma brush involved in pollen capture was compromised in the rr21/22/23 mutant, whereas anther development was compromised in the rr24 mutant. Novel as well as conserved roles for type-B RRs in the growth and development of a monocot compared with dicots were identified.
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Affiliation(s)
- Jennifer M Worthen
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Maria V Yamburenko
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Jeewoo Lim
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Joseph J Kieber
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - G Eric Schaller
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
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18
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Rodriguez-Leal D, Xu C, Kwon CT, Soyars C, Demesa-Arevalo E, Man J, Liu L, Lemmon ZH, Jones DS, Van Eck J, Jackson DP, Bartlett ME, Nimchuk ZL, Lippman ZB. Evolution of buffering in a genetic circuit controlling plant stem cell proliferation. Nat Genet 2019; 51:786-792. [PMID: 30988512 DOI: 10.1038/s41588-019-0389-8] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 03/07/2019] [Indexed: 01/19/2023]
Abstract
Precise control of plant stem cell proliferation is necessary for the continuous and reproducible development of plant organs1,2. The peptide ligand CLAVATA3 (CLV3) and its receptor protein kinase CLAVATA1 (CLV1) maintain stem cell homeostasis within a deeply conserved negative feedback circuit1,2. In Arabidopsis, CLV1 paralogs also contribute to homeostasis, by compensating for the loss of CLV1 through transcriptional upregulation3. Here, we show that compensation4,5 operates in diverse lineages for both ligands and receptors, but while the core CLV signaling module is conserved, compensation mechanisms have diversified. Transcriptional compensation between ligand paralogs operates in tomato, facilitated by an ancient gene duplication that impacted the domestication of fruit size. In contrast, we found little evidence for transcriptional compensation between ligands in Arabidopsis and maize, and receptor compensation differs between tomato and Arabidopsis. Our findings show that compensation among ligand and receptor paralogs is critical for stem cell homeostasis, but that diverse genetic mechanisms buffer conserved developmental programs.
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Affiliation(s)
- Daniel Rodriguez-Leal
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Inari Agriculture, Cambridge, MA, USA
| | - Cao Xu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Choon-Tak Kwon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Cara Soyars
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Jarrett Man
- Biology Department, University of Massachusetts Amherst, Amherst, MA, USA
| | - Lei Liu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Zachary H Lemmon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Inari Agriculture, Cambridge, MA, USA
| | - Daniel S Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joyce Van Eck
- Boyce Thompson Institute for Plant Science, Ithaca, NY, USA.,Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | | | | | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. .,Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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19
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Vatén A, Soyars CL, Tarr PT, Nimchuk ZL, Bergmann DC. Modulation of Asymmetric Division Diversity through Cytokinin and SPEECHLESS Regulatory Interactions in the Arabidopsis Stomatal Lineage. Dev Cell 2018; 47:53-66.e5. [PMID: 30197241 PMCID: PMC6177308 DOI: 10.1016/j.devcel.2018.08.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [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: 05/25/2017] [Revised: 06/06/2018] [Accepted: 08/08/2018] [Indexed: 11/18/2022]
Abstract
Coordinated growth of organs requires communication among cells within and between tissues. In plants, leaf growth is largely dictated by the epidermis; here, asymmetric and self-renewing divisions of the stomatal lineage create two essential cell types-pavement cells and guard cells-in proportions reflecting inputs from local, systemic, and environmental cues. The transcription factor SPEECHLESS (SPCH) is the prime regulator of divisions, but whether and how it is influenced by external cues to provide flexible development is enigmatic. Here, we show that the phytohormone cytokinin (CK) can act as an endogenous signal to affect the extent and types of stomatal lineage divisions and forms a regulatory circuit with SPCH. Local domains of low CK signaling are created by SPCH-dependent cell-type-specific activity of two repressive type-A ARABIDOPSIS RESPONSE REGULATORs (ARRs), ARR16 and ARR17, and two secreted peptides, CLE9 and CLE10, which, together with SPCH, can customize epidermal cell-type composition.
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Affiliation(s)
- Anne Vatén
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA
| | - Cara L Soyars
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Paul T Tarr
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Dominique C Bergmann
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA.
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20
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Whitewoods CD, Cammarata J, Nemec Venza Z, Sang S, Crook AD, Aoyama T, Wang XY, Waller M, Kamisugi Y, Cuming AC, Szövényi P, Nimchuk ZL, Roeder AHK, Scanlon MJ, Harrison CJ. CLAVATA Was a Genetic Novelty for the Morphological Innovation of 3D Growth in Land Plants. Curr Biol 2018; 28:2365-2376.e5. [PMID: 30033333 PMCID: PMC6089843 DOI: 10.1016/j.cub.2018.05.068] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/10/2018] [Accepted: 05/23/2018] [Indexed: 11/24/2022]
Abstract
How genes shape diverse plant and animal body forms is a key question in biology. Unlike animal cells, plant cells are confined by rigid cell walls, and cell division plane orientation and growth rather than cell movement determine overall body form. The emergence of plants on land coincided with a new capacity to rotate stem cell divisions through multiple planes, and this enabled three-dimensional (3D) forms to arise from ancestral forms constrained to 2D growth. The genes involved in this evolutionary innovation are largely unknown. The evolution of 3D growth is recapitulated during the development of modern mosses when leafy shoots arise from a filamentous (2D) precursor tissue. Here, we show that a conserved, CLAVATA peptide and receptor-like kinase pathway originated with land plants and orients stem cell division planes during the transition from 2D to 3D growth in a moss, Physcomitrella. We find that this newly identified role for CLAVATA in regulating cell division plane orientation is shared between Physcomitrella and Arabidopsis. We report that roles for CLAVATA in regulating cell proliferation and cell fate are also shared and that CLAVATA-like peptides act via conserved receptor components in Physcomitrella. Our results suggest that CLAVATA was a genetic novelty enabling the morphological innovation of 3D growth in land plants.
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Affiliation(s)
- Chris D Whitewoods
- Plant Sciences Department, Cambridge University, Downing Street, Cambridge CB2 3EA, UK
| | - Joseph Cammarata
- Plant Sciences Department, Cambridge University, Downing Street, Cambridge CB2 3EA, UK; Plant Biology Section, School of Integrative Plant Science, Cornell University, Tower Road, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Zoe Nemec Venza
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Stephanie Sang
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Ashley D Crook
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tsuyoshi Aoyama
- Plant Sciences Department, Cambridge University, Downing Street, Cambridge CB2 3EA, UK; School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Xiao Y Wang
- Plant Sciences Department, Cambridge University, Downing Street, Cambridge CB2 3EA, UK
| | - Manuel Waller
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Andrew C Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Adrienne H K Roeder
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Tower Road, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Michael J Scanlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Tower Road, Ithaca, NY 14853, USA
| | - C Jill Harrison
- Plant Sciences Department, Cambridge University, Downing Street, Cambridge CB2 3EA, UK; School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.
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21
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Soyars CL, Peterson BA, Burr CA, Nimchuk ZL. Cutting Edge Genetics: CRISPR/Cas9 Editing of Plant Genomes. Plant Cell Physiol 2018; 59:1608-1620. [PMID: 29912402 DOI: 10.1093/pcp/pcy079] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 04/11/2018] [Indexed: 05/22/2023]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9) system is a genome editing technology transforming the field of plant biology by virtue of the system's efficiency and specificity. The system has quickly evolved for many diverse applications including multiplex gene mutation, gene replacement and transcriptional control. As CRISPR/Cas9 is increasingly applied to plants, it is becoming clear that each component of the system can be modified to improve editing results. This review aims to highlight common considerations and options when conducting CRISPR/Cas9 experiments.
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Affiliation(s)
- Cara L Soyars
- Department of Biology and Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, 4155 Genome Sciences Building, 250 Bell Tower Drive, Chapel Hill, NC, USA
| | - Brenda A Peterson
- Department of Biology and Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, 4155 Genome Sciences Building, 250 Bell Tower Drive, Chapel Hill, NC, USA
| | - Christian A Burr
- Department of Biology and Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, 4155 Genome Sciences Building, 250 Bell Tower Drive, Chapel Hill, NC, USA
| | - Zachary L Nimchuk
- Department of Biology and Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, 4155 Genome Sciences Building, 250 Bell Tower Drive, Chapel Hill, NC, USA
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22
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Moody LA, Kelly S, Coudert Y, Nimchuk ZL, Harrison CJ, Langdale JA. Somatic hybridization provides segregating populations for the identification of causative mutations in sterile mutants of the moss Physcomitrella patens. New Phytol 2018; 218:1270-1277. [PMID: 29498048 DOI: 10.1111/nph.15069] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 11/20/2017] [Accepted: 01/20/2018] [Indexed: 06/08/2023]
Abstract
Forward genetics is now straightforward in the moss Physcomitrella patens, and large mutant populations can be screened relatively easily. However, perturbation of development before the formation of gametes currently leaves no route to gene discovery. Somatic hybridization has previously been used to rescue sterile mutants and to assign P. patens mutations to complementation groups, but the cellular basis of the fusion process could not be monitored, and there was no tractable way to identify causative mutations. Here we use fluorescently tagged lines to generate somatic hybrids between Gransden (Gd) and Villersexel (Vx) strains of P. patens, and show that hybridization produces fertile diploid gametophytes that form phenotypically normal tetraploid sporophytes. Quantification of genetic variation between the two parental strains reveals single nucleotide polymorphisms at a frequency of 1/286 bp. Given that the genetic distinction between Gd and Vx strains exceeds that found between pairs of strains that are commonly used for genetic mapping in other plant species, the spore populations derived from hybrid sporophytes provide suitable material for bulk segregant analysis and gene identification by genome sequencing.
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Affiliation(s)
- Laura A Moody
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Yoan Coudert
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
- Laboratoire Reproduction et Développement des Plantes, Ecole Normale Supérieure de Lyon, CNRS, INRA, Université Claude Bernard Lyon 1, 46 Allée d'Italie, Lyon, 69007, France
| | - Zachary L Nimchuk
- Department of Biology, UNC, Coker Hall, 120 South Road, Chapel Hill, NC, 27599-3280, USA
| | - C Jill Harrison
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Jane A Langdale
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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23
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Liu H, Soyars CL, Li J, Fei Q, He G, Peterson BA, Meyers BC, Nimchuk ZL, Wang X. CRISPR/Cas9-mediated resistance to cauliflower mosaic virus. Plant Direct 2018; 2:e00047. [PMID: 31245713 PMCID: PMC6508564 DOI: 10.1002/pld3.47] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/25/2018] [Accepted: 02/06/2018] [Indexed: 05/03/2023]
Abstract
Viral diseases are a leading cause of worldwide yield losses in crop production. Breeding of resistance genes (R gene) into elite crop cultivars has been the standard and most cost-effective practice. However, R gene-mediated resistance is limited by the available R genes within genetic resources and in many cases, by strain specificity. Therefore, it is important to generate new and broad-spectrum antiviral strategies. The CRISPR-Cas9 (clustered regularly interspaced palindromic repeat, CRISPR-associated) editing system has been employed to confer resistance to human viruses and several plant single-stranded DNA geminiviruses, pointing out the possible application of the CRISPR-Cas9 system for virus control. Here, we demonstrate that strong viral resistance to cauliflower mosaic virus (CaMV), a pararetrovirus with a double-stranded DNA genome, can be achieved through Cas9-mediated multiplex targeting of the viral coat protein sequence. We further show that small interfering RNAs (siRNA) are produced and mostly map to the 3' end of single-guide RNAs (sgRNA), although very low levels of siRNAs map to the spacer region as well. However, these siRNAs are not responsible for the inhibited CaMV infection because there is no resistance if Cas9 is not present. We have also observed edited viruses in systematically infected leaves in some transgenic plants, with short deletions or insertions consistent with Cas9-induced DNA breaks at the sgRNA target sites in coat protein coding sequence. These edited coat proteins, in most cases, led to earlier translation stop and thus, nonfunctional coat proteins. We also recovered wild-type CP sequence in these infected transgenic plants, suggesting these edited viral genomes were packaged by wild-type coat proteins. Our data demonstrate that the CRISPR-Cas9 system can be used for virus control against plant pararetroviruses with further modifications.
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Affiliation(s)
- Haijie Liu
- Department of Plant Pathology, Physiology and Weed ScienceVirginia TechBlacksburgVAUSA
| | - Cara L. Soyars
- Department of Biological SciencesVirginia TechBlacksburgVAUSA
- Department of BiologyUniversity of North Carolina at Chapel HillChapel HillNCUSA
| | - Jianhui Li
- Department of Plant Pathology, Physiology and Weed ScienceVirginia TechBlacksburgVAUSA
| | - Qili Fei
- Department of Plant & Soil SciencesDelaware Biotechnology InstituteUniversity of DelawareNewarkDEUSA
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Guijuan He
- Department of Plant Pathology, Physiology and Weed ScienceVirginia TechBlacksburgVAUSA
| | - Brenda A. Peterson
- Department of Biological SciencesVirginia TechBlacksburgVAUSA
- Department of BiologyUniversity of North Carolina at Chapel HillChapel HillNCUSA
| | - Blake C. Meyers
- Department of Plant & Soil SciencesDelaware Biotechnology InstituteUniversity of DelawareNewarkDEUSA
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Division of Plant SciencesUniversity of Missouri – ColumbiaColumbiaMOUSA
| | - Zachary L. Nimchuk
- Department of Biological SciencesVirginia TechBlacksburgVAUSA
- Department of BiologyUniversity of North Carolina at Chapel HillChapel HillNCUSA
- Faculty of Health SciencesVirginia TechBlacksburgVAUSA
- Curriculum in Genetics and Molecular BiologyUniversity of North Carolina at Chapel HillChapel HillNCUSA
| | - Xiaofeng Wang
- Department of Plant Pathology, Physiology and Weed ScienceVirginia TechBlacksburgVAUSA
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24
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Hodgens C, Nimchuk ZL, Kieber JJ. indCAPS: A tool for designing screening primers for CRISPR/Cas9 mutagenesis events. PLoS One 2017; 12:e0188406. [PMID: 29141013 PMCID: PMC5687723 DOI: 10.1371/journal.pone.0188406] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/06/2017] [Indexed: 11/25/2022] Open
Abstract
Genetic manipulation of organisms using CRISPR/Cas9 technology generally produces small insertions/deletions (indels) that can be difficult to detect. Here, we describe a technique to easily and rapidly identify such indels. Sequence-identified mutations that alter a restriction enzyme recognition site can be readily distinguished from wild-type alleles using a cleaved amplified polymorphic sequence (CAPS) technique. If a restriction site is created or altered by the mutation such that only one allele contains the restriction site, a polymerase chain reaction (PCR) followed by a restriction digest can be used to distinguish the two alleles. However, in the case of most CRISPR-induced alleles, no such restriction sites are present in the target sequences. In this case, a derived CAPS (dCAPS) approach can be used in which mismatches are purposefully introduced in the oligonucleotide primers to create a restriction site in one, but not both, of the amplified templates. Web-based tools exist to aid dCAPS primer design, but when supplied sequences that include indels, the current tools often fail to suggest appropriate primers. Here, we report the development of a Python-based, species-agnostic web tool, called indCAPS, suitable for the design of PCR primers used in dCAPS assays that is compatible with indels. This tool should have wide utility for screening editing events following CRISPR/Cas9 mutagenesis as well as for identifying specific editing events in a pool of CRISPR-mediated mutagenesis events. This tool was field-tested in a CRISPR mutagenesis experiment targeting a cytokinin receptor (AHK3) in Arabidopsis thaliana. The tool suggested primers that successfully distinguished between wild-type and edited alleles of a target locus and facilitated the isolation of two novel ahk3 null alleles. Users can access indCAPS and design PCR primers to employ dCAPS to identify CRISPR/Cas9 alleles at http://indcaps.kieber.cloudapps.unc.edu/.
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Affiliation(s)
- Charles Hodgens
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Zachary L. Nimchuk
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Joseph J. Kieber
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail:
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25
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Moussu S, Doll NM, Chamot S, Brocard L, Creff A, Fourquin C, Widiez T, Nimchuk ZL, Ingram G. ZHOUPI and KERBEROS Mediate Embryo/Endosperm Separation by Promoting the Formation of an Extracuticular Sheath at the Embryo Surface. Plant Cell 2017; 29:1642-1656. [PMID: 28696222 PMCID: PMC5559742 DOI: 10.1105/tpc.17.00016] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 05/23/2017] [Accepted: 07/09/2017] [Indexed: 05/18/2023]
Abstract
Arabidopsis thaliana seed development requires the concomitant development of two zygotic compartments, the embryo and the endosperm. Following fertilization, the endosperm expands and the embryo grows invasively through the endosperm, which breaks down. Here, we describe a structure we refer to as the embryo sheath that forms on the surface of the embryo as it starts to elongate. The sheath is deposited outside the embryonic cuticle and incorporates endosperm-derived material rich in extensin-like molecules. Sheath production is dependent upon the activity of ZHOUPI, an endosperm-specific transcription factor necessary for endosperm degradation, embryo growth, embryo-endosperm separation, and normal embryo cuticle formation. We show that the peptide KERBEROS, whose expression is ZHOUPI dependent, is necessary both for the formation of a normal embryo sheath and for embryo-endosperm separation. Finally, we show that the receptor-like kinases GSO1 and GSO2 are required for sheath deposition at the embryo surface but not for production of sheath material in the endosperm. We present a model in which sheath formation depends on the coordinated production of material in the endosperm and signaling within the embryo, highlighting the complex molecular interaction between these two tissues during early seed development.
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Affiliation(s)
- Steven Moussu
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
| | - Nicolas M Doll
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
| | - Sophy Chamot
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
| | - Lysiane Brocard
- Centre National de la Recherche Scientifique/University of Bordeaux, Plant Imaging Platform of Bordeaux Imaging Center, UMS 3420, F-33000 Bordeaux, France
- Université de Bordeaux, Laboratoire de Biogenèse Membranaire, UMR5200, F-33000 Bordeaux, France
- Centre National de la Recherche Scientifique, Laboratoire de Biogenèse Membranaire, UMR5200, F-33000 Bordeaux, France
| | - Audrey Creff
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
| | - Chloé Fourquin
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
| | - Thomas Widiez
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280
| | - Gwyneth Ingram
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
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26
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Nimchuk ZL, Perdue TD. Live Imaging of Shoot Meristems on an Inverted Confocal Microscope Using an Objective Lens Inverter Attachment. Front Plant Sci 2017; 8:773. [PMID: 28579995 PMCID: PMC5437170 DOI: 10.3389/fpls.2017.00773] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/25/2017] [Indexed: 05/30/2023]
Abstract
Live imaging of above ground meristems can lead to new insights in plant development not possible from static imaging of fixed tissue. The use of an upright confocal microscope offers several technical and biological advantages for live imaging floral or shoot meristems. However, many departments and core facilities possess only inverted confocal microscopes and lack the funding for an additional upright confocal microscope. Here we show that imaging of living apical meristems can be performed on existing inverted confocal microscopes with the use of an affordable and detachable InverterScope accessory.
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Affiliation(s)
- Zachary L. Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel HillNC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel HillNC, USA
| | - Tony D. Perdue
- Department of Biology, University of North Carolina at Chapel Hill, Chapel HillNC, USA
- Biology Microscope Core, University of North Carolina at Chapel Hill, Chapel HillNC, USA
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27
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Nimchuk ZL. CLAVATA1 controls distinct signaling outputs that buffer shoot stem cell proliferation through a two-step transcriptional compensation loop. PLoS Genet 2017; 13:e1006681. [PMID: 28355208 PMCID: PMC5371295 DOI: 10.1371/journal.pgen.1006681] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [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: 01/23/2017] [Accepted: 03/09/2017] [Indexed: 02/07/2023] Open
Abstract
The regulation of stem cell proliferation in plants is controlled by intercellular signaling pathways driven by the diffusible CLAVATA3 (CLV3p) peptide. CLV3p perception is thought to be mediated by an overlapping array of receptors in the stem cell niche including the transmembrane receptor kinase CLV1, Receptor-Like Protein Kinase 2 (RPK2), and a dimer of the receptor-like protein CLV2 and the CORYNE (CRN) pseudokinase. Mutations in these receptors have qualitatively similar effects on stem cell function but it is unclear if this represents common or divergent signaling outputs. Previous work in heterologous systems has suggested that CLV1, RPK2 and CLV2/CRN could form higher order complexes but it is also unclear what relevance these putative complexes have to in vivo receptor functions. Here I use the in vivo regulation of a specific transcriptional target of CLV1 signaling in Arabidopsis to demonstrate that, despite the phenotypic similarities between the different receptor mutants, CLV1 controls distinct signaling outputs in living stem cell niches independent of other receptors. This regulation is separable from stem cell proliferation driven by WUSCHEL, a proposed common transcriptional target of CLV3p signaling. In addition, in the absence of CLV1, CLV1-related receptor kinases are ectopically expressed but also buffer stem cell proliferation through the auto-repression of their own expression. Collectively these data reveal a unique in vivo role for CLV1 separable from other stem cell receptors and provides a framework for dissecting the signaling outputs in stem cell regulation. The proliferation of plant stem cells in above ground tissues is controlled by a suite of receptors in response to the CLAVATA3 peptide ligand. Receptor signaling in response to CLAVATA3 prevents over-proliferation of stem cells. It is unclear what the functional relationship is between the proposed CLAVATA3 receptors or if they impact common signaling outputs. Here I demonstrate that CLAVATA1 signals independently of the other receptors kinases to control distinct transcriptional outputs independent of stem cell proliferation. Stem cell proliferation is buffered by a two-step mechanism which transcriptionally regulates receptor levels in the stem cell niche. This mechanism helps explain the strict control of stem cell proliferation and could provide new avenues for improving plant growth.
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Affiliation(s)
- Zachary L. Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- * E-mail:
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28
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Nishimura MT, Anderson RG, Cherkis KA, Law TF, Liu QL, Machius M, Nimchuk ZL, Yang L, Chung EH, El Kasmi F, Hyunh M, Osborne Nishimura E, Sondek JE, Dangl JL. TIR-only protein RBA1 recognizes a pathogen effector to regulate cell death in Arabidopsis. Proc Natl Acad Sci U S A 2017; 114:E2053-E2062. [PMID: 28137883 PMCID: PMC5347586 DOI: 10.1073/pnas.1620973114] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [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] [Indexed: 01/19/2023] Open
Abstract
Detection of pathogens by plants is mediated by intracellular nucleotide-binding site leucine-rich repeat (NLR) receptor proteins. NLR proteins are defined by their stereotypical multidomain structure: an N-terminal Toll-interleukin receptor (TIR) or coiled-coil (CC) domain, a central nucleotide-binding (NB) domain, and a C-terminal leucine-rich repeat (LRR). The plant innate immune system contains a limited NLR repertoire that functions to recognize all potential pathogens. We isolated Response to the bacterial type III effector protein HopBA1 (RBA1), a gene that encodes a TIR-only protein lacking all other canonical NLR domains. RBA1 is sufficient to trigger cell death in response to HopBA1. We generated a crystal structure for HopBA1 and found that it has similarity to a class of proteins that includes esterases, the heme-binding protein ChaN, and an uncharacterized domain of Pasteurella multocida toxin. Self-association, coimmunoprecipitation with HopBA1, and function of RBA1 require two previously identified TIR-TIR dimerization interfaces. Although previously described as distinct in other TIR proteins, in RBA1 neither of these interfaces is sufficient when the other is disrupted. These data suggest that oligomerization of RBA1 is required for function. Our identification of RBA1 demonstrates that "truncated" NLRs can function as pathogen sensors, expanding our understanding of both receptor architecture and the mechanism of activation in the plant immune system.
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Affiliation(s)
- Marc T Nishimura
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599;
- Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599
| | - Ryan G Anderson
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Karen A Cherkis
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Terry F Law
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
- Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599
| | - Qingli L Liu
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Mischa Machius
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Li Yang
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Eui-Hwan Chung
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
- Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599
| | - Farid El Kasmi
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Michael Hyunh
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Erin Osborne Nishimura
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
| | - John E Sondek
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599;
- Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599
- Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC 27599
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599
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29
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Denbow CJ, Lapins S, Dietz N, Scherer R, Nimchuk ZL, Okumoto S. Gateway-Compatible CRISPR-Cas9 Vectors and a Rapid Detection by High-Resolution Melting Curve Analysis. Front Plant Sci 2017; 8:1171. [PMID: 28725235 PMCID: PMC5496963 DOI: 10.3389/fpls.2017.01171] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 06/19/2017] [Indexed: 05/06/2023]
Abstract
CRISPR-Cas9 system rapidly became an indispensable tool in plant biology to perform targeted mutagenesis. A CRISPR-Cas9-mediated double strand break followed by non-homologous end joining (NHEJ) repair most frequently results in a single base pair deletion or insertions (indels), which is hard to detect using methods based on enzymes that detect heteroduplex DNA. In addition, somatic tissues of the T1 generation inevitably contain a mosaic population, in which the portion of cells carrying the mutation can be too small to be detected by the enzyme-based methods. Here we report an optimized experimental protocol for detecting Arabidopsis mutants carrying a CRISPR-Cas9 mediated mutation, using high-resolution melting (HRM) curve analysis. Single-base pair insertion or deletion (indel) can be easily detected using this method. We have also examined the detection limit for the template containing a one bp indel compared to the WT genome. Our results show that <5% of mutant DNA containing one bp indel can be detected using this method. The vector developed in this study can be used with a Gateway technology-compatible derivative of pCUT vectors, with which off-target mutations could not be detected even by a whole genome sequencing.
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Affiliation(s)
- Cynthia J. Denbow
- Department of Plant Pathology, Physiology and Weed ScienceBlacksburg, VA, United States
| | - Samantha Lapins
- Department of Plant Pathology, Physiology and Weed ScienceBlacksburg, VA, United States
| | - Nick Dietz
- Department of Plant Pathology, Physiology and Weed ScienceBlacksburg, VA, United States
| | - Raelynn Scherer
- Department of Plant Pathology, Physiology and Weed ScienceBlacksburg, VA, United States
| | - Zachary L. Nimchuk
- Department of Biology, University of North CarolinaChapel Hill, NC, United States
| | - Sakiko Okumoto
- Department of Plant Pathology, Physiology and Weed ScienceBlacksburg, VA, United States
- Department of Soil and Crop Science, Texas A&M UniversityCollege Station, TX, United States
- *Correspondence: Sakiko Okumoto
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30
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Liu Y, Miao J, Traore S, Kong D, Liu Y, Zhang X, Nimchuk ZL, Liu Z, Zhao B. SacB-SacR Gene Cassette As the Negative Selection Marker to Suppress Agrobacterium Overgrowth in Agrobacterium-Mediated Plant Transformation. Front Mol Biosci 2016; 3:70. [PMID: 27833912 PMCID: PMC5080373 DOI: 10.3389/fmolb.2016.00070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 06/30/2016] [Accepted: 10/07/2016] [Indexed: 11/13/2022] Open
Abstract
Agrobacterium overgrowth is a common problem in Agrobacterium-mediated plant transformation. To suppress the Agrobacterium overgrowth, various antibiotics have been used during plant tissue culture steps. The antibiotics are expensive and may adversely affect plant cell differentiation and reduce plant transformation efficiency. The SacB-SacR proteins are toxic to most Agrobacterium tumefaciens strains when they are grown on culture medium supplemented with sucrose. Therefore, SacB-SacR genes can be used as negative selection markers to suppress the overgrowth of A. tumefaciens in the plant tissue culture process. We generated a mutant A. tumefaciens strain GV2260 (recA-SacB/R) that has the SacB-SacR cassette inserted into the bacterial genome at the recA gene locus. The mutant Agrobacterium strain is sensitive to sucrose but maintains its ability to transform plant cells in both transient and stable transformation assays. We demonstrated that the mutant strain GV2260 (recA-SacB/R) can be inhibited by sucrose that reduces the overgrowth of Agrobacterium and therefore improves the plant transformation efficiency. We employed GV2260 (recA-SacB/R) to generate stable transgenic N. benthamiana plants expressing a CRISPR-Cas9 for knocking out a WRKY transcription factor.
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Affiliation(s)
- Yiming Liu
- Department of Crop and Soil Environmental Science, Virginia TechBlacksburg, VA, USA; Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Tropical Crops Genetic Resources Institute, Ministry of AgricultureDanzhou, China
| | - Jiamin Miao
- Department of Horticulture, Virginia Tech Blacksburg, VA, USA
| | - Sy Traore
- Department of Horticulture, Virginia Tech Blacksburg, VA, USA
| | - Danyu Kong
- Department of Horticulture, Virginia Tech Blacksburg, VA, USA
| | - Yi Liu
- Department of Horticulture, Virginia Tech Blacksburg, VA, USA
| | - Xunzhong Zhang
- Department of Crop and Soil Environmental Science, Virginia Tech Blacksburg, VA, USA
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Zongrang Liu
- USDA-ARS-Appalachian Fruit Research Station Kearneysville, WV, USA
| | - Bingyu Zhao
- Department of Horticulture, Virginia Tech Blacksburg, VA, USA
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31
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Peterson BA, Haak DC, Nishimura MT, Teixeira PJPL, James SR, Dangl JL, Nimchuk ZL. Genome-Wide Assessment of Efficiency and Specificity in CRISPR/Cas9 Mediated Multiple Site Targeting in Arabidopsis. PLoS One 2016; 11:e0162169. [PMID: 27622539 PMCID: PMC5021288 DOI: 10.1371/journal.pone.0162169] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/18/2016] [Indexed: 11/18/2022] Open
Abstract
Simultaneous multiplex mutation of large gene families using Cas9 has the potential to revolutionize agriculture and plant sciences. The targeting of multiple genomic sites at once raises concerns about the efficiency and specificity in targeting. The model Arabidopsis thaliana is widely used in basic plant research. Previous work has suggested that the Cas9 off-target rate in Arabidopsis is undetectable. Here we use deep sequencing on pooled plants simultaneously targeting 14 distinct genomic loci to demonstrate that multiplex targeting in Arabidopsis is highly specific to on-target sites with no detectable off-target events. In addition, chromosomal translocations are extremely rare. The high specificity of Cas9 in Arabidopsis makes this a reliable method for clean mutant generation with no need to enhance specificity or adopt alternate Cas9 variants.
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Affiliation(s)
- Brenda A Peterson
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America.,Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States of America
| | - David C Haak
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, United States of America
| | - Marc T Nishimura
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Paulo J P L Teixeira
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Sean R James
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America.,Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States of America
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America.,Curriculum in Genetics and Molecular Biology, Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America.,Curriculum in Genetics and Molecular Biology, Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America.,Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States of America
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32
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Soyars CL, James SR, Nimchuk ZL. Ready, aim, shoot: stem cell regulation of the shoot apical meristem. Curr Opin Plant Biol 2016; 29:163-8. [PMID: 26803586 DOI: 10.1016/j.pbi.2015.12.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 12/01/2015] [Accepted: 12/07/2015] [Indexed: 05/13/2023]
Abstract
Plant shoot meristems contain stem cells that are continuously renewed to replenish cells that exit and differentiate during lateral organ formation. Complex cell-to-cell signaling systems balance division and differentiation. These center on ligand-receptor networks, hormone pathways, and transcriptional regulators that function in an integrated manner. In this review, we aim to highlight new findings in shoot stem cell regulation across species.
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Affiliation(s)
- Cara L Soyars
- Department of Biology, University of North Carolina at Chapel Hill, 4155 Genome Sciences Building, 250 Bell Tower Drive, Chapel Hill, NC 27599, United States
| | - Sean R James
- Department of Biology, University of North Carolina at Chapel Hill, 4155 Genome Sciences Building, 250 Bell Tower Drive, Chapel Hill, NC 27599, United States
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, 4155 Genome Sciences Building, 250 Bell Tower Drive, Chapel Hill, NC 27599, United States.
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Nimchuk ZL, Zhou Y, Tarr PT, Peterson BA, Meyerowitz EM. Plant stem cell maintenance by transcriptional cross-regulation of related receptor kinases. Development 2015; 142:1043-9. [PMID: 25758219 DOI: 10.1242/dev.119677] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The CLAVATA3 (CLV3)-CLAVATA1 (CLV1) ligand-receptor kinase pair negatively regulates shoot stem cell proliferation in plants. clv1 null mutants are weaker in phenotype than clv3 mutants, but the clv1 null phenotype is enhanced by mutations in the related receptor kinases BARELY ANY MERISTEM 1, 2 and 3 (BAM1, 2 and 3). The basis of this genetic redundancy is unknown. Here, we demonstrate that the apparent redundancy in the CLV1 clade is in fact due to the transcriptional repression of BAM genes by CLV1 signaling. CLV1 signaling in the rib meristem (RM) of the shoot apical meristem is necessary and sufficient for stem cell regulation. CLV3-CLV1 signaling in the RM represses BAM expression in wild-type Arabidopsis plants. In clv1 mutants, ectopic BAM expression in the RM partially complements the loss of CLV1. BAM regulation by CLV1 is distinct from CLV1 regulation of WUSCHEL, a proposed CLV1 target gene. In addition, quadruple receptor mutants are stronger in phenotype than clv3, pointing to the existence of additional CLV1/BAM ligands. These data provide an explanation for the genetic redundancy seen in the CLV1 clade and reveal a novel feedback operating in the control of plant stem cells.
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Affiliation(s)
- Zachary L Nimchuk
- Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Yun Zhou
- Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Paul T Tarr
- Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Brenda A Peterson
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Elliot M Meyerowitz
- Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
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Segonzac C, Nimchuk ZL, Beck M, Tarr PT, Robatzek S, Meyerowitz EM, Zipfel C. The shoot apical meristem regulatory peptide CLV3 does not activate innate immunity. Plant Cell 2012; 24:3186-92. [PMID: 22923673 PMCID: PMC3462624 DOI: 10.1105/tpc.111.091264] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 01/24/2012] [Accepted: 08/01/2012] [Indexed: 05/20/2023]
Abstract
The Arabidopsis thaliana leucine-rich repeat receptor kinase FLAGELLIN SENSING2 (FLS2) is required for the recognition of bacterial flagellin in innate immunity. Recently, FLS2 was proposed to act as a multispecific receptor recognizing unrelated exogenous and endogenous peptide ligands, including CLAVATA3 (CLV3), a key regulator of shoot meristem stem cell production. Here, we report experimental evidence demonstrating that FLS2 does not recognize CLV3 and that the shoot apical meristem is immune to bacteria independently of CLV3 perception.
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Affiliation(s)
- Cécile Segonzac
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Zachary L. Nimchuk
- Division of Biology, California Institute of Technology, Pasadena, California 91125
| | - Martina Beck
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Paul T. Tarr
- Division of Biology, California Institute of Technology, Pasadena, California 91125
| | - Silke Robatzek
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Elliot M. Meyerowitz
- Division of Biology, California Institute of Technology, Pasadena, California 91125
- The Sainsbury Laboratory–University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Cyril Zipfel
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom
- Address correspondence to
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Jaillais Y, Hothorn M, Belkhadir Y, Dabi T, Nimchuk ZL, Meyerowitz EM, Chory J. Tyrosine phosphorylation controls brassinosteroid receptor activation by triggering membrane release of its kinase inhibitor. Genes Dev 2011; 25:232-7. [PMID: 21289069 DOI: 10.1101/gad.2001911] [Citation(s) in RCA: 196] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Receptor tyrosine kinases control many critical processes in metazoans, but these enzymes appear to be absent in plants. Recently, two Arabidopsis receptor kinases--BRASSINOSTEROID INSENSITIVE 1 (BRI1) and BRI1-ASSOCIATED KINASE1 (BAK1), the receptor and coreceptor for brassinosteroids--were shown to autophosphorylate on tyrosines. However, the cellular roles for tyrosine phosphorylation in plants remain poorly understood. Here, we report that the BRI1 KINASE INHIBITOR 1 (BKI1) is tyrosine phosphorylated in response to brassinosteroid perception. Phosphorylation occurs within a reiterated [KR][KR] membrane targeting motif, releasing BKI1 into the cytosol and enabling formation of an active signaling complex. Our work reveals that tyrosine phosphorylation is a conserved mechanism controlling protein localization in all higher organisms.
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Affiliation(s)
- Yvon Jaillais
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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Nimchuk ZL, Tarr PT, Meyerowitz EM. An evolutionarily conserved pseudokinase mediates stem cell production in plants. Plant Cell 2011; 23:851-4. [PMID: 21398569 PMCID: PMC3082267 DOI: 10.1105/tpc.110.075622] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 02/10/2011] [Accepted: 02/23/2011] [Indexed: 05/20/2023]
Abstract
Sequence comparisons, biochemical experiments, and studies with mutants in transgenic plants show that the Arabidopsis protein CORYNE, currently thought to be a kinase that acts as part of a receptor kinase complex, is likely to be a pseudokinase and not a kinase.
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Nimchuk ZL, Tarr PT, Ohno C, Qu X, Meyerowitz EM. Plant stem cell signaling involves ligand-dependent trafficking of the CLAVATA1 receptor kinase. Curr Biol 2011; 21:345-52. [PMID: 21333538 DOI: 10.1016/j.cub.2011.01.039] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [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] [Received: 04/07/2010] [Revised: 11/03/2010] [Accepted: 01/10/2011] [Indexed: 11/18/2022]
Abstract
BACKGROUND Cell numbers in above-ground meristems of plants are thought to be maintained by a feedback loop driven by perception of the glycopeptide ligand CLAVATA3 (CLV3) by the CLAVATA1 (CLV1) receptor kinase and the CLV2/CORYNE (CRN) receptor-like complex. CLV3 produced in the stem cells at the meristem apex limits the expression level of the stem cell-promoting homeodomain protein WUSCHEL (WUS) in the cells beneath, where CLV1 and WUS RNA are localized. WUS downregulation nonautonomously reduces stem cell proliferation. Overexpression of CLV3 eliminates the stem cells, causing meristem termination, and loss of CLV3 function allows meristem overproliferation. There are many questions regarding the CLV3/CLV1 interaction, including where in the meristem it occurs, how it is regulated, and how it is that a large range of CLV3 concentrations gives no meristem size phenotype. RESULTS Here we use genetics and live imaging to examine the cell biology of CLV1 in Arabidopsis meristematic tissue. We demonstrate that plasma membrane-localized CLV1 is reduced in concentration by CLV3, which causes trafficking of CLV1 to lytic vacuoles. We find that changes in CLV2 activity have no detectable effects on CLV1 levels. We also find that CLV3 appears to diffuse broadly in meristems, contrary to a recent sequestration model. CONCLUSIONS This study provides a new model for CLV1 function in plant stem cell maintenance and suggests that downregulation of plasma membrane-localized CLV1 by its CLV3 ligand can account for the buffering of CLV3 signaling in the maintenance of stem cell pools in plants.
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Affiliation(s)
- Zachary L Nimchuk
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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Nimchuk ZL, Fisher EJ, Desveaux D, Chang JH, Dangl JL. The HopX (AvrPphE) family of Pseudomonas syringae type III effectors require a catalytic triad and a novel N-terminal domain for function. Mol Plant Microbe Interact 2007; 20:346-57. [PMID: 17427805 DOI: 10.1094/mpmi-20-4-0346] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Many gram-negative plant pathogenic bacteria employ type III secretion systems to deliver effector proteins directly into the host cell during infection. On susceptible hosts, type III effectors aid pathogen growth by manipulating host defense pathways. On resistant hosts, some effectors can activate specific host disease resistance (R) genes, leading to generation of rapid and effective immune responses. The biochemical basis of these processes is poorly understood. The HopX (AvrPphE) family is a widespread type III effector among phytopathogenic bacteria. We determined that HopX family members are modular proteins composed of a conserved putative cysteine-based catalytic triad and a conserved potential target/cofactor interaction domain. HopX is soluble in host cells. Putative catalytic triad residues are required for avirulence activity on resistant bean hosts and for the generation of a cell-death response in specific Arabidopsis genotypes. The putative target/cofactor interaction domain is also required for these activities. Our data suggest that specific interaction with and modification of a cytosolic host target drives HopX recognition in resistant hosts and may contribute to virulence in susceptible hosts. Surprisingly, the Legionella pneumophila genome was found to contain a protein with similarity to HopX in sequence and domain arrangement, suggesting that these proteins might also contribute to animal pathogenesis and could be delivered to plant and animal hosts by diverse secretion systems.
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Affiliation(s)
- Zachary L Nimchuk
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
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