1
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Romani F, Sauret-Güeto S, Rebmann M, Annese D, Bonter I, Tomaselli M, Dierschke T, Delmans M, Frangedakis E, Silvestri L, Rever J, Bowman JL, Romani I, Haseloff J. The landscape of transcription factor promoter activity during vegetative development in Marchantia. THE PLANT CELL 2024; 36:2140-2159. [PMID: 38391349 PMCID: PMC11132968 DOI: 10.1093/plcell/koae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 12/08/2023] [Accepted: 12/22/2023] [Indexed: 02/24/2024]
Abstract
Transcription factors (TFs) are essential for the regulation of gene expression and cell fate determination. Characterizing the transcriptional activity of TF genes in space and time is a critical step toward understanding complex biological systems. The vegetative gametophyte meristems of bryophytes share some characteristics with the shoot apical meristems of flowering plants. However, the identity and expression profiles of TFs associated with gametophyte organization are largely unknown. With only ∼450 putative TF genes, Marchantia (Marchantia polymorpha) is an outstanding model system for plant systems biology. We have generated a near-complete collection of promoter elements derived from Marchantia TF genes. We experimentally tested reporter fusions for all the TF promoters in the collection and systematically analyzed expression patterns in Marchantia gemmae. This allowed us to build a map of expression domains in early vegetative development and identify a set of TF-derived promoters that are active in the stem-cell zone. The cell markers provide additional tools and insight into the dynamic regulation of the gametophytic meristem and its evolution. In addition, we provide an online database of expression patterns for all promoters in the collection. We expect that these promoter elements will be useful for cell-type-specific expression, synthetic biology applications, and functional genomics.
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Affiliation(s)
- Facundo Romani
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | | | - Marius Rebmann
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Davide Annese
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Ignacy Bonter
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Marta Tomaselli
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Clayton, Melbourne, VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Mihails Delmans
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | | | - Linda Silvestri
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Jenna Rever
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - John L Bowman
- School of Biological Sciences, Monash University, Clayton, Melbourne, VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Ignacio Romani
- Departamento de Ciencias Sociales, Universidad Nacional de Quilmes, Bernal, Buenos Aires 1876, Argentina
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
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2
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Arnoux-Courseaux M, Coudert Y. Re-examining meristems through the lens of evo-devo. TRENDS IN PLANT SCIENCE 2024; 29:413-427. [PMID: 38040554 DOI: 10.1016/j.tplants.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 12/03/2023]
Abstract
The concept of the meristem was introduced in 1858 to characterize multicellular, formative, and proliferative tissues that give rise to the entire plant body, based on observations of vascular plants. Although its original definition did not encompass bryophytes, this concept has been used and continuously refined over the past 165 years to describe the diverse apices of all land plants. Here, we re-examine this matter in light of recent evo-devo research and show that, despite displaying high anatomical diversity, land plant meristems are unified by shared genetic control. We also propose a modular view of meristem function and highlight multiple evolutionary mechanisms that are likely to have contributed to the assembly and diversification of the varied meristems during the course of plant evolution.
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Affiliation(s)
- Moïra Arnoux-Courseaux
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, INRIA, Lyon 69007, France; Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des Martyrs, F-38054, Grenoble, France
| | - Yoan Coudert
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, INRIA, Lyon 69007, France.
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3
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Kean-Galeno T, Lopez-Arredondo D, Herrera-Estrella L. The Shoot Apical Meristem: An Evolutionary Molding of Higher Plants. Int J Mol Sci 2024; 25:1519. [PMID: 38338798 PMCID: PMC10855264 DOI: 10.3390/ijms25031519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/27/2023] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
The shoot apical meristem (SAM) gives rise to the aerial structure of plants by producing lateral organs and other meristems. The SAM is responsible for plant developmental patterns, thus determining plant morphology and, consequently, many agronomic traits such as the number and size of fruits and flowers and kernel yield. Our current understanding of SAM morphology and regulation is based on studies conducted mainly on some angiosperms, including economically important crops such as maize (Zea mays) and rice (Oryza sativa), and the model species Arabidopsis (Arabidopsis thaliana). However, studies in other plant species from the gymnosperms are scant, making difficult comparative analyses that help us understand SAM regulation in diverse plant species. This limitation prevents deciphering the mechanisms by which evolution gave rise to the multiple plant structures within the plant kingdom and determines the conserved mechanisms involved in SAM maintenance and operation. This review aims to integrate and analyze the current knowledge of SAM evolution by combining the morphological and molecular information recently reported from the plant kingdom.
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Affiliation(s)
- Tania Kean-Galeno
- Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, Lubbock, TX 79409, USA; (T.K.-G.); (D.L.-A.)
| | - Damar Lopez-Arredondo
- Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, Lubbock, TX 79409, USA; (T.K.-G.); (D.L.-A.)
| | - Luis Herrera-Estrella
- Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, Lubbock, TX 79409, USA; (T.K.-G.); (D.L.-A.)
- Unidad de Genómica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato 36821, Mexico
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4
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Zhang H, Mu Y, Zhang H, Yu C. Maintenance of stem cell activity in plant development and stress responses. FRONTIERS IN PLANT SCIENCE 2023; 14:1302046. [PMID: 38155857 PMCID: PMC10754534 DOI: 10.3389/fpls.2023.1302046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/28/2023] [Indexed: 12/30/2023]
Abstract
Stem cells residing in plant apical meristems play an important role during postembryonic development. These stem cells are the wellspring from which tissues and organs of the plant emerge. The shoot apical meristem (SAM) governs the aboveground portions of a plant, while the root apical meristem (RAM) orchestrates the subterranean root system. In their sessile existence, plants are inextricably bound to their environment and must adapt to various abiotic stresses, including osmotic stress, drought, temperature fluctuations, salinity, ultraviolet radiation, and exposure to heavy metal ions. These environmental challenges exert profound effects on stem cells, potentially causing severe DNA damage and disrupting the equilibrium of reactive oxygen species (ROS) and Ca2+ signaling in these vital cells, jeopardizing their integrity and survival. In response to these challenges, plants have evolved mechanisms to ensure the preservation, restoration, and adaptation of the meristematic stem cell niche. This enduring response allows plants to thrive in their habitats over extended periods. Here, we presented a comprehensive overview of the cellular and molecular intricacies surrounding the initiation and maintenance of the meristematic stem cell niche. We also delved into the mechanisms employed by stem cells to withstand and respond to abiotic stressors.
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Affiliation(s)
- Huankai Zhang
- College of Life Sciences, Zaozhuang University, Zaozhuang, China
| | - Yangwei Mu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Hui Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Caiyu Yu
- College of Life Sciences, Zaozhuang University, Zaozhuang, China
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5
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Takahashi G, Kiyosue T, Hirakawa Y. Control of stem cell behavior by CLE-JINGASA signaling in the shoot apical meristem in Marchantia polymorpha. Curr Biol 2023; 33:5121-5131.e6. [PMID: 37977139 DOI: 10.1016/j.cub.2023.10.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/14/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023]
Abstract
Land plants undergo indeterminate growth by the activity of meristems in both gametophyte (haploid) and sporophyte (diploid) generations. In the sporophyte of the flowering plant Arabidopsis thaliana, the apical meristems are located at the shoot and root tips in which a number of regulatory gene homologs are shared for their development, implying deep evolutionary origins. However, little is known about their functional conservation with gametophytic meristems in distantly related land plants such as bryophytes, even though genomic studies have revealed that the subfamily-level diversity of regulatory genes is mostly conserved throughout land plants. Here, we show that a NAM/ATAF/CUC (NAC) domain transcription factor, JINGASA (MpJIN), acts downstream of CLAVATA3 (CLV3)/ESR-related (CLE) peptide signaling and controls stem cell behavior in the gametophytic shoot apical meristem of the liverwort Marchantia polymorpha. In the meristem, strong MpJIN expression was associated with the periclinal cell division at the periphery of the stem cell zone (SCZ), whereas faint MpJIN expression was found at the center of the SCZ. Time course observation indicates that the MpJIN-negative cells are lost from the SCZ and respecified de novo at two separate positions during the dichotomous branching event. Consistently, the induction of MpJIN results in ectopic periclinal cell division in the SCZ and meristem termination. Based on the comparative expression data, we speculate that the function of JIN/FEZ subfamily genes was shared among the shoot apical meristems in the gametophyte and sporophyte generations in early land plants but was lost in certain lineages, including the flowering plant A. thaliana.
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Affiliation(s)
- Go Takahashi
- Department of Life Science, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Tokyo 171-8588, Japan
| | - Tomohiro Kiyosue
- Department of Life Science, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Tokyo 171-8588, Japan
| | - Yuki Hirakawa
- Department of Life Science, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Tokyo 171-8588, Japan.
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6
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Yadav S, Kumar H, Mahajan M, Sahu SK, Singh SK, Yadav RK. Local auxin biosynthesis promotes shoot patterning and stem cell differentiation in Arabidopsis shoot apex. Development 2023; 150:dev202014. [PMID: 38054970 DOI: 10.1242/dev.202014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/19/2023] [Indexed: 12/07/2023]
Abstract
The shoot apical meristem (SAM) of higher plants comprises distinct functional zones. The central zone (CZ) is located at the meristem summit and harbors pluripotent stem cells. Stem cells undergo cell division within the CZ and give rise to descendants, which enter the peripheral zone (PZ) and become recruited into lateral organs. Stem cell daughters that are pushed underneath the CZ form rib meristem (RM). To unravel the mechanism of meristem development, it is essential to know how stem cells adopt distinct cell fates in the SAM. Here, we show that meristem patterning and floral organ primordia formation, besides auxin transport, are regulated by auxin biosynthesis mediated by two closely related genes of the TRYPTOPHAN AMINOTRANSFERASE family. In Arabidopsis SAM, TAA1 and TAR2 played a role in maintaining auxin responses and the identity of PZ cell types. In the absence of auxin biosynthesis and transport, the expression pattern of the marker genes linked to the patterning of the SAM is perturbed. Our results prove that local auxin biosynthesis, in concert with transport, controls the patterning of the SAM into the CZ, PZ and RM.
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Affiliation(s)
- Shalini Yadav
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Punjab 140306, India
| | - Harish Kumar
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Punjab 140306, India
| | - Monika Mahajan
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Punjab 140306, India
| | - Sangram Keshari Sahu
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Punjab 140306, India
| | - Sharad Kumar Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Punjab 140306, India
| | - Ram Kishor Yadav
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Punjab 140306, India
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7
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Selby R, Jones DS. Complex peptide hormone signaling in plant stem cells. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102442. [PMID: 37672866 DOI: 10.1016/j.pbi.2023.102442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/26/2023] [Accepted: 08/09/2023] [Indexed: 09/08/2023]
Abstract
Peptide hormones influence diverse aspects of plant development through highly coordinated cell-cell signaling pathways. Many peptide hormone families play key roles in stem cell maintenance across land plants. In this review, we focus on recent work in two conserved peptide hormone families, CLAVATA3/EMBRYO-SURROUNDING REGION (CLEs) and ROOT MERISTEM GROWTH FACTOR (RGFs), and their roles in regulating plant stem cells. We discuss recent work establishing downstream crosstalk between peptide hormones and other conserved signaling mechanisms in meristem maintenance as well as highlight advances in peptide hormone gene identification that provide important context for CLE/RGF family evolution across diverse plant lineages. CLE and RGF gene families have greatly expanded in angiosperms, contributing to the complex genetic regulation of stem cell homeostasis observed in model systems over the last 30 years. Peptide hormone duplications have resulted in genetic compensation mechanisms that ensure robust development through the function of paralogous genes. Broad conservation of genetic compensation across angiosperms highlights the importance of these mechanisms in developmental signaling and understanding their regulation could inform broader understanding of morphological diversity and evolutionary innovation.
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Affiliation(s)
- Reid Selby
- Department of Biological Sciences, Auburn University, 36849, Auburn, AL, USA
| | - Daniel S Jones
- Department of Biological Sciences, Auburn University, 36849, Auburn, AL, USA.
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8
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Donà M, Bradamante G, Bogojevic Z, Gutzat R, Streubel S, Mosiolek M, Dolan L, Mittelsten Scheid O. A versatile CRISPR-based system for lineage tracing in living plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1169-1184. [PMID: 37403571 DOI: 10.1111/tpj.16378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/09/2023] [Accepted: 06/22/2023] [Indexed: 07/06/2023]
Abstract
Individual cells give rise to diverse cell lineages during the development of multicellular organisms. Understanding the contribution of these lineages to mature organisms is a central question of developmental biology. Several techniques to document cell lineages have been used, from marking single cells with mutations that express a visible marker to generating molecular bar codes by CRISPR-induced mutations and subsequent single-cell analysis. Here, we exploit the mutagenic activity of CRISPR to allow lineage tracing within living plants with a single reporter. Cas9-induced mutations are directed to correct a frameshift mutation that restores expression of a nuclear fluorescent protein, labelling the initial cell and all progenitor cells with a strong signal without modifying other phenotypes of the plants. Spatial and temporal control of Cas9 activity can be achieved using tissue-specific and/or inducible promoters. We provide proof of principle for the function of lineage tracing in two model plants. The conserved features of the components and the versatile cloning system, allowing for easy exchange of promoters, are expected to make the system widely applicable.
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Affiliation(s)
- Mattia Donà
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
| | - Gabriele Bradamante
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
| | - Zorana Bogojevic
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
| | - Ruben Gutzat
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
| | - Susanna Streubel
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
| | - Magdalena Mosiolek
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
| | - Liam Dolan
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
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9
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Reinhardt D, Gola EM. Law and order in plants - the origin and functional relevance of phyllotaxis. TRENDS IN PLANT SCIENCE 2022; 27:1017-1032. [PMID: 35643801 DOI: 10.1016/j.tplants.2022.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/31/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
The regular arrangement of organs (phyllotaxis) in vegetative shoots and flowers is one of the most stunning features of plants. Spiral patterns characterized by Fibonacci numbers have attracted the particular interest of natural scientists and mathematicians. Numerous reviews have dealt with the molecular genetic mechanisms underlying phyllotaxis, and modeling studies have sought to recreate phyllotaxis according to mathematical, biochemical, or physical laws. However, what is the functional significance of regular plant architecture, and how did it evolve? We discuss the developmental constraints and selective forces that may have favored the selection of phyllotaxis, and we argue that a central driver of regular phyllotaxis may have been limitations in the allocation of founder cells and metabolic resources to the different tissues in the shoot apex.
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Affiliation(s)
- Didier Reinhardt
- Department of Biology, Route Albert Gockel 3, University of Fribourg, 1700 Fribourg, Switzerland.
| | - Edyta M Gola
- Department of Plant Developmental Biology, Faculty of Plant Sciences, University of Wroclaw, Kanonia 6/8, 50-328, Wroclaw, Poland
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10
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Hirakawa Y. Evolution of meristem zonation by CLE gene duplication in land plants. NATURE PLANTS 2022; 8:735-740. [PMID: 35854003 DOI: 10.1038/s41477-022-01199-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
In angiosperms, a negative feedback pathway involving CLAVATA3 (CLV3) peptide and WUSCHEL transcription factor maintains the stem-cell population in the shoot apical meristem and is central for continued shoot growth and organogenesis. An intriguing question is how this cell-signalling system was established during the evolution of land plants. On the basis of two recent studies on CLV3/ESR-related (CLE) genes, this paper proposes a model for the evolution of meristem zonation. The model suggests that a stem-cell-limiting CLV3 pathway is derived from stem-cell-promoting CLE pathways conserved in land pants by gene duplication in the angiosperm lineage. The model can be examined in the future by genomic and developmental studies on diverse plant species.
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Affiliation(s)
- Yuki Hirakawa
- Department of Life Science, Faculty of Science, Gakushuin University, Tokyo, Japan.
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11
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Geng Y, Yan A, Zhou Y. Positional cues and cell division dynamics drive meristem development and archegonium formation in Ceratopteris gametophytes. Commun Biol 2022; 5:650. [PMID: 35778477 PMCID: PMC9249879 DOI: 10.1038/s42003-022-03627-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 06/22/2022] [Indexed: 11/17/2022] Open
Abstract
Fern gametophytes are autotrophic and independent of sporophytes, and they develop pluripotent meristems that drive prothallus development and sexual reproduction. To reveal cellular dynamics during meristem development in fern gametophytes, we performed long-term time-lapse imaging and determined the real-time lineage, identity and division activity of each single cell from meristem initiation to establishment in gametophytes of the fern Ceratopteris richardii. Our results demonstrate that in Ceratopteris gametophytes, only a few cell lineages originated from the marginal layer contribute to meristem initiation and proliferation, and the meristem lacks a distinguishable central zone or apical cell with low division activity. Within the meristem, cell division is independent of cell lineages and cells at the marginal layer are more actively dividing than inner cells. Furthermore, the meristem triggers differentiation of adjacent cells into egg-producing archegonia in a position-dependent manner. These findings advance the understanding of diversified meristem and gametophyte development in land plants. Time-lapse imaging of the fern Ceratopteris richardii during meristem initiation and proliferation provides insights into the lineage, identity and division activity of each cell throughout the growth of gametophytes.
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Affiliation(s)
- Yuan Geng
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - An Yan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA. .,Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA.
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12
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Yang S, Zhang T, Wang Z, Zhao X, Li R, Li J. Nitrilases NIT1/2/3 Positively Regulate Flowering by Inhibiting MAF4 Expression in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:889460. [PMID: 35665187 PMCID: PMC9157433 DOI: 10.3389/fpls.2022.889460] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/18/2022] [Indexed: 06/15/2023]
Abstract
Three of the nitrilases (NITs), NIT1, NIT2, and NIT3, are ubiquitously existing in plant kingdom, which catalyze indole-3-acetonitrile into the most important auxin indole-3-acetic acid. Auxin is an indispensable hormone, which plays the important roles in almost all processes of plant growth and development. However, there are few reports on the regulation of flowering-time mediated by auxin. Here, we found that in Arabidopsis, nit1/2/3 showed a late flowering phenotype in short days. To explore the molecular mechanism by which NIT1/2/3 regulate flowering time, we performed transcriptome sequencing of nit1/2/3. The results showed that the expression of a MADS-box transcription factor gene MADS AFFECTING FLOWERING4 (MAF4) was dramatically increased in nit1/2/3 comparing to wild type (WT). MAF4 is one of the paralogs of the potent flowering inhibitor FLOWERING LOCUS C (FLC). There are four other paralogs in FLC clade in Arabidopsis, including FLOWERING LOCUS M (FLM/MAF1), MAF2, MAF3, and MAF5. The late flowering phenotype of nit1/2/3 could not be observed in the maf4 background, indicating that the phenotype was specifically dependent on MAF4 rather than other FLC clade members. Interestingly, the expression of a lncRNA gene MAS, which is transcribed in the opposite direction of MAF4, was found significantly increased in nit1/2/3. Also, MAS has been reported to activate MAF4 transcription by promoting histone 3 lysine 4 trimethylation (H3K4me3). As expected, H3K4me3 deposition at MAF4 locus in nit1/2/3 was highly enriched and significantly higher than that of WT. In summary, we show that NITs, NIT1/2/3, positively regulate flowering by repressing MAF4 through manipulating H3K4me3 modification. Further study needs to be performed to explore the largely unknown mechanisms behind it.
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13
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Beyond Photoprotection: The Multifarious Roles of Flavonoids in Plant Terrestrialization. Int J Mol Sci 2022; 23:ijms23095284. [PMID: 35563675 PMCID: PMC9101737 DOI: 10.3390/ijms23095284] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/29/2022] [Accepted: 05/06/2022] [Indexed: 02/01/2023] Open
Abstract
Plants evolved an impressive arsenal of multifunctional specialized metabolites to cope with the novel environmental pressures imposed by the terrestrial habitat when moving from water. Here we examine the multifarious roles of flavonoids in plant terrestrialization. We reason on the environmental drivers, other than the increase in UV-B radiation, that were mostly responsible for the rise of flavonoid metabolism and how flavonoids helped plants in land conquest. We are reasonably based on a nutrient-deficiency hypothesis for the replacement of mycosporine-like amino acids, typical of streptophytic algae, with the flavonoid metabolism during the water-to-land transition. We suggest that flavonoids modulated auxin transport and signaling and promoted the symbiosis between plants and fungi (e.g., arbuscular mycorrhizal, AM), a central event for the conquest of land by plants. AM improved the ability of early plants to take up nutrients and water from highly impoverished soils. We offer evidence that flavonoids equipped early land plants with highly versatile “defense compounds”, essential for the new set of abiotic and biotic stressors imposed by the terrestrial environment. We conclude that flavonoids have been multifunctional since the appearance of plants on land, not only acting as UV filters but especially improving both nutrient acquisition and biotic stress defense.
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14
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Ishikawa M, Hasebe M. Molecular mechanisms of reprogramming of differentiated cells into stem cells in the moss Physcomitrium patens. CURRENT OPINION IN PLANT BIOLOGY 2022; 65:102123. [PMID: 34735974 DOI: 10.1016/j.pbi.2021.102123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/14/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Plant and animal stem cells can self-renew and give rise to differentiated cells to form tissues or organs. Unlike differentiated cells in animals, those in land plants can be readily reprogrammed into stem cells, reflecting the plasticity of plant cell identity. The moss Physcomitrium patens (synonym: Physcomitrella patens) is highly regenerable, and its leaf cells can be reprogrammed into stem cells in response to wounding or by transient DNA damage without wounding. Wounding and DNA damage induce STEM CELL-INDUCING FACTOR 1, an APETALA2/ETHYLENE RESPONSE FACTOR. Here, we summarize the genetic networks that regulate cellular reprogramming in P. patens and the roles of STEMIN1 and discuss the generality and divergence of the molecular mechanisms underlying cellular reprogramming in land plants and animals.
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Affiliation(s)
- Masaki Ishikawa
- National Institute for Basic Biology, Okazaki, 444-8585, Japan; School of Life Science, The Graduate University for Advanced Studies, Okazaki, 444-8585, Japan.
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, Okazaki, 444-8585, Japan; School of Life Science, The Graduate University for Advanced Studies, Okazaki, 444-8585, Japan.
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Naramoto S, Hata Y, Fujita T, Kyozuka J. The bryophytes Physcomitrium patens and Marchantia polymorpha as model systems for studying evolutionary cell and developmental biology in plants. THE PLANT CELL 2022; 34:228-246. [PMID: 34459922 PMCID: PMC8773975 DOI: 10.1093/plcell/koab218] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/25/2021] [Indexed: 05/03/2023]
Abstract
Bryophytes are nonvascular spore-forming plants. Unlike in flowering plants, the gametophyte (haploid) generation of bryophytes dominates the sporophyte (diploid) generation. A comparison of bryophytes with flowering plants allows us to answer some fundamental questions raised in evolutionary cell and developmental biology. The moss Physcomitrium patens was the first bryophyte with a sequenced genome. Many cell and developmental studies have been conducted in this species using gene targeting by homologous recombination. The liverwort Marchantia polymorpha has recently emerged as an excellent model system with low genomic redundancy in most of its regulatory pathways. With the development of molecular genetic tools such as efficient genome editing, both P. patens and M. polymorpha have provided many valuable insights. Here, we review these advances with a special focus on polarity formation at the cell and tissue levels. We examine current knowledge regarding the cellular mechanisms of polarized cell elongation and cell division, including symmetric and asymmetric cell division. We also examine the role of polar auxin transport in mosses and liverworts. Finally, we discuss the future of evolutionary cell and developmental biological studies in plants.
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Affiliation(s)
| | - Yuki Hata
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Tomomichi Fujita
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
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16
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Wu X, Yan A, Liu X, Zhang S, Zhou Y. Quantitative live-imaging reveals the dynamics of apical cells during gametophyte development in ferns. QUANTITATIVE PLANT BIOLOGY 2022; 3:e25. [PMID: 37077984 PMCID: PMC10095955 DOI: 10.1017/qpb.2022.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/19/2022] [Accepted: 10/08/2022] [Indexed: 05/02/2023]
Abstract
Meristems in land plants share conserved functions but develop highly variable structures. Meristems in seed-free plants, including ferns, usually contain one or a few pyramid-/wedge-shaped apical cells (ACs) as initials, which are lacking in seed plants. It remained unclear how ACs promote cell proliferation in fern gametophytes and whether any persistent AC exists to sustain fern gametophyte development continuously. Here, we uncovered previously undefined ACs maintained even at late developmental stages in fern gametophytes. Through quantitative live-imaging, we determined division patterns and growth dynamics that maintain the persistent AC in Sphenomeris chinensis, a representative fern. The AC and its immediate progenies form a conserved cell packet, driving cell proliferation and prothallus expansion. At the apical centre of gametophytes, the AC and its adjacent progenies display small dimensions resulting from active cell division instead of reduced cell expansion. These findings provide insight into diversified meristem development in land plants.
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Affiliation(s)
- Xiao Wu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana47907, USA
- Purdue Centre for Plant Biology, Purdue University, West Lafayette, Indiana47907, USA
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - An Yan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California91125, USA
| | - Xing Liu
- Purdue Centre for Plant Biology, Purdue University, West Lafayette, Indiana47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, Indiana47907, USA
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Authors for correspondence: S. Zhang, Y. Zhou, E-mail: ;
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana47907, USA
- Purdue Centre for Plant Biology, Purdue University, West Lafayette, Indiana47907, USA
- Authors for correspondence: S. Zhang, Y. Zhou, E-mail: ;
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17
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Fujita T, Nogué F, Rensing SA, Takezawa D, Vidali L. Molecular biology of mosses. PLANT MOLECULAR BIOLOGY 2021; 107:209-211. [PMID: 34843031 DOI: 10.1007/s11103-021-01218-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Tomomichi Fujita
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, 060-0810, Japan.
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Route de St Cyr, 78026, Versailles, France
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Daisuke Takezawa
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Luis Vidali
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
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18
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Schlegel J, Denay G, Wink R, Pinto KG, Stahl Y, Schmid J, Blümke P, Simon RGW. Control of Arabidopsis shoot stem cell homeostasis by two antagonistic CLE peptide signalling pathways. eLife 2021; 10:e70934. [PMID: 34643181 PMCID: PMC8594942 DOI: 10.7554/elife.70934] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/30/2021] [Indexed: 11/28/2022] Open
Abstract
Stem cell homeostasis in plant shoot meristems requires tight coordination between stem cell proliferation and cell differentiation. In Arabidopsis, stem cells express the secreted dodecapeptide CLAVATA3 (CLV3), which signals through the leucine-rich repeat (LRR)-receptor kinase CLAVATA1 (CLV1) and related CLV1-family members to downregulate expression of the homeodomain transcription factor WUSCHEL (WUS). WUS protein moves from cells below the stem cell domain to the meristem tip and promotes stem cell identity, together with CLV3 expression, generating a negative feedback loop. How stem cell activity in the meristem centre is coordinated with organ initiation and cell differentiation at the periphery is unknown. We show here that the CLE40 gene, encoding a secreted peptide closely related to CLV3, is expressed in the SAM in differentiating cells in a pattern complementary to that of CLV3. CLE40 promotes WUS expression via BAM1, a CLV1-family receptor, and CLE40 expression is in turn repressed in a WUS-dependent manner. Together, CLE40-BAM1-WUS establish a second negative feedback loop. We propose that stem cell homeostasis is achieved through two intertwined pathways that adjust WUS activity and incorporate information on the size of the stem cell domain, via CLV3-CLV1, and on cell differentiation via CLE40-BAM1.
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Affiliation(s)
- Jenia Schlegel
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| | - Gregoire Denay
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| | - Rene Wink
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| | - Karine Gustavo Pinto
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| | - Yvonne Stahl
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| | - Julia Schmid
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| | - Patrick Blümke
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| | - Rüdiger GW Simon
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
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Furumizu C, Krabberød AK, Hammerstad M, Alling RM, Wildhagen M, Sawa S, Aalen RB. The sequenced genomes of non-flowering land plants reveal the innovative evolutionary history of peptide signaling. THE PLANT CELL 2021; 33:2915-2934. [PMID: 34240188 PMCID: PMC8462819 DOI: 10.1093/plcell/koab173] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/08/2021] [Indexed: 12/20/2022]
Abstract
An understanding of land plant evolution is a prerequisite for in-depth knowledge of plant biology. Here we extract and explore information hidden in the increasing number of sequenced plant genomes, from bryophytes to angiosperms, to elucidate a specific biological question - how peptide signaling evolved. To conquer land and cope with changing environmental conditions, plants have gone through transformations that must have required innovations in cell-to-cell communication. We discuss peptides mediating endogenous and exogenous changes by interaction with receptors activating intracellular molecular signaling. Signaling peptides were discovered in angiosperms and operate in tissues and organs such as flowers, seeds, vasculature, and 3D meristems that are not universally conserved across land plants. Nevertheless, orthologs of angiosperm peptides and receptors have been identified in non-angiosperms. These discoveries provoke questions regarding co-evolution of ligands and their receptors, and whether de novo interactions in peptide signaling pathways may have contributed to generate novel traits in land plants. The answers to such questions will have profound implications for the understanding of the evolution of cell-to-cell communication and the wealth of diversified terrestrial plants. Under this perspective we have generated, analyzed, and reviewed phylogenetic, genomic, structural, and functional data to elucidate the evolution of peptide signaling.
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Affiliation(s)
- Chihiro Furumizu
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Anders K Krabberød
- Section for Evolutionary Biology and Genetics, Department of Biosciences, University of Oslo, Norway
| | - Marta Hammerstad
- Section for Biochemistry and Molecular Biology, Department of Biosciences, University of Oslo, Norway
| | - Renate M Alling
- Section for Evolutionary Biology and Genetics, Department of Biosciences, University of Oslo, Norway
| | - Mari Wildhagen
- Section for Evolutionary Biology and Genetics, Department of Biosciences, University of Oslo, Norway
| | - Shinichiro Sawa
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Reidunn B Aalen
- Section for Evolutionary Biology and Genetics, Department of Biosciences, University of Oslo, Norway
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