1
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Konstantinova N, von der Mark C, De Rybel B. Intrinsic cues guiding changes in division orientation in the Arabidopsis root meristem: a formative experience. JOURNAL OF EXPERIMENTAL BOTANY 2025; 76:1546-1552. [PMID: 39688908 DOI: 10.1093/jxb/erae509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2024] [Accepted: 12/16/2024] [Indexed: 12/18/2024]
Abstract
The orientation of cell division is crucial for normal development of all plant organs throughout their life cycle. Despite the importance of understanding the intricate molecular mechanisms guiding this process, relatively few pathways have been characterized to date. Here we want to outline what is known about the molecular regulation guiding changes in division orientation in the root apical meristem of the model plant Arabidopsis thaliana, from the upstream transcriptional modules to the downstream executors that lead to division plane establishment. We specifically focus on the gaps in our knowledge about this highly coordinated process and propose that a new approach should be taken to characterize how changes in division orientation are controlled in more holistic detail.
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Affiliation(s)
- Nataliia Konstantinova
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Claudia von der Mark
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Bert De Rybel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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2
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Cai X, Zhang H, Mu C, Chen Y, He C, Liu M, Laux T, Pi L. A mobile miR160-triggered transcriptional axis controls root stem cell niche maintenance and regeneration in Arabidopsis. Dev Cell 2025; 60:459-471.e5. [PMID: 39488206 DOI: 10.1016/j.devcel.2024.10.006] [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: 02/08/2024] [Revised: 07/23/2024] [Accepted: 10/08/2024] [Indexed: 11/04/2024]
Abstract
In multicellular organisms, communication between cells is vital for their fate determination. In plants, the quiescent center (QC) signals to adjacent stem cells to maintain them undifferentiated. However, how surrounding stem cells instruct the QC remains poorly understood. Here, we show that in the Arabidopsis root, microRNA160 (miR160) moves from stele stem cells (SSCs) to the QC, where it degrades the mRNAs of two auxin response factors, ARF10 and ARF17. This degradation relieves BRAVO from direct transcriptional repression, maintaining QC quiescence. We further identify that blocking miR160 movement due to DNA damage-induced SSC death and restricted symplastic transport reduces BRAVO and WOX5 expression, leading to QC division to replenish damaged stem cells during root regeneration. Together, our results demonstrate that a transcriptional axis initiated by mobile miR160 regulates the QC and stem cell behavior, advancing our understanding of the communication between stem cells and their surrounding cellular environment.
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Affiliation(s)
- Xixi Cai
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Hang Zhang
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Changqing Mu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Yanjun Chen
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, School of Medicine, Wuhan University, Wuhan 430072, China
| | - Chongzhen He
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Mingyu Liu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Thomas Laux
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Limin Pi
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies, Wuhan University, Wuhan 430072, China.
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3
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Zhang N, Bitterli P, Oluoch P, Hermann M, Aichinger E, Groot EP, Laux T. Deciphering the molecular logic of WOX5 function in the root stem cell organizer. EMBO J 2025; 44:281-303. [PMID: 39558109 PMCID: PMC11696986 DOI: 10.1038/s44318-024-00302-2] [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: 06/09/2024] [Revised: 10/17/2024] [Accepted: 10/25/2024] [Indexed: 11/20/2024] Open
Abstract
Plant and animal stem cells receive signals from their surrounding cells to stay undifferentiated. In the Arabidopsis root, the quiescent center (QC) acts as a stem cell organizer, signaling to the neighboring stem cells. WOX5 is a central transcription factor regulating QC function. However, due to the scarcity of QC cells, WOX5 functions in the QC are largely unexplored at a genomic scale. Here, we unveil the transcriptional and epigenetic landscapes of the QC and the role of WOX5 within them. We find that WOX5 functions both as a transcriptional repressor and activator, affecting histone modifications and chromatin accessibility. Our data expand on known WOX5 functions, such as the regulation of differentiation, cell division, and auxin biosynthesis. We also uncover unexpected WOX5-regulated pathways involved in nitrate transport and the regulation of basal expression levels of genes associated with mature root tissues. These data suggest a role for QC cells as reserve stem cells and primed cells for prospective progenitor fates. Taken together, these findings offer insights into the role of WOX5 at the QC and provide a basis for further analyses to advance our understanding of the nature of plant stem cell organizers.
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Affiliation(s)
- Ning Zhang
- State Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, 271018, Tai'an, Shandong, China.
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany.
| | - Pamela Bitterli
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Peter Oluoch
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Marita Hermann
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Ernst Aichinger
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Edwin P Groot
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
- Sino-German Joint Research Center on Agricultural Biology, Shandong Agricultural University, Tai'an, Shandong, China
| | - Thomas Laux
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany.
- Sino-German Joint Research Center on Agricultural Biology, Shandong Agricultural University, Tai'an, Shandong, China.
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4
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Zhang H, Tian L, Ma Y, Xu J, Bai T, Wang Q, Liu X, Guo L. Not only the top: Type I topoisomerases function in multiple tissues and organs development in plants. J Adv Res 2024:S2090-1232(24)00588-5. [PMID: 39662729 DOI: 10.1016/j.jare.2024.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 11/24/2024] [Accepted: 12/07/2024] [Indexed: 12/13/2024] Open
Abstract
BACKGROUND DNA topoisomerases (TOPs) are essential components in a diverse range of biological processes including DNA replication, transcription and genome integrity. Although the functions and mechanisms of TOPs, particularly type I TOP (TOP1s), have been extensively studied in bacteria, yeast and animals, researches on these proteins in plants have only recently commenced. AIM OF REVIEW In this review, the function and mechanism studies of TOP1s in plants and the structural biology of plant TOP1 are presented, providing readers with a comprehensive understanding of the current research status of this essential enzyme.The future research directions for exploring the working mechanism of plant TOP1s are also discussed. KEY SCIENTIFIC CONCEPTS OF REVIEW Over the past decade, it has been discovered TOP1s play a vital role in multiphasic processes of plant development, such as maintaining meristem activity, gametogenesis, flowering time, gravitropic response and so on. Plant TOP1s affects gene transcription by modulating chromatin status, including chromatin accessibility, DNA/RNA structure, and nucleosome positioning. However, the function and mechanism of this vital enzyme is poorly summarized although it has been systematically summarized in other species. This review summarized the research progresses of plant TOP1s according to the diverse functions and working mechanism in different tissues.
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Affiliation(s)
- Hao Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, 050024, Shijiazhuang, China.
| | - Lirong Tian
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, 050024, Shijiazhuang, China.
| | - Yuru Ma
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, 050024, Shijiazhuang, China.
| | - Jiahui Xu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, 050024, Shijiazhuang, China.
| | - Tianyu Bai
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, 050024, Shijiazhuang, China.
| | - Qian Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, 050024, Shijiazhuang, China.
| | - Xigang Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, 050024, Shijiazhuang, China.
| | - Lin Guo
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, 050024, Shijiazhuang, China.
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5
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Chu Y, Duan R, Song H, Zhang W, Zhou Y, Ma Y, Yin X, Tian L, Ausin I, Han Z. AtHD2D is involved in regulating lateral root development and participates in abiotic stress response in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2024; 297:154242. [PMID: 38614048 DOI: 10.1016/j.jplph.2024.154242] [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: 10/19/2023] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/15/2024]
Abstract
Roots are essential to terrestrial plants, as their growth and morphology are crucial for plant development. The growth of the roots is affected and regulated by several internal and external environmental signals and metabolic pathways. Among them, chromatin modification plays an important regulatory role. In this study, we explore the potential roles of the histone deacetylase AtHD2D in root development and lay the foundation for further research on the biological processes and molecular mechanisms of AtHD2D in the future. Our study indicates that AtHD2D affects the root tip microenvironment homeostasis by affecting the gene transcription levels required to maintain the root tip microenvironment. In addition, we confirmed that AtHD2D is involved in regulating Arabidopsis lateral root development and further explained the possible role of AtHD2D in auxin-mediated lateral root development. AtHD2D can effectively enhance the resistance of Arabidopsis thaliana to abiotic stress. We believe that AtHD2D is involved in coping with abiotic stress by promoting the development of lateral roots. Overexpression of AtHD2D promotes the accumulation of reactive oxygen species (ROS) in roots, indicating that AtHD2D is also involved in developing lateral roots mediated by ROS. Previous studies have shown that the overexpression of AtHD2D can effectively enhance the resistance of Arabidopsis thaliana to abiotic stress. Based on our data, we believe that AtHD2D participates in the response to abiotic stress by promoting the development of lateral roots. AtHD2D-mediated lateral root development provides new ideas for studying the mechanism of HDAC protein in regulating root development.
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Affiliation(s)
- Yueyang Chu
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Ruochen Duan
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Haoran Song
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Wenshuo Zhang
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Yuxuan Zhou
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Yutong Ma
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Xiaotong Yin
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Lining Tian
- London Research and Development Centre, Agriculture and Agri-food Canada, London, Ontario, N5V 4T3, Canada
| | - Israel Ausin
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Zhaofen Han
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China.
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6
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Possenti M, Sessa G, Alfè A, Turchi L, Ruzza V, Sassi M, Morelli G, Ruberti I. HD-Zip II transcription factors control distal stem cell fate in Arabidopsis roots by linking auxin signaling to the FEZ/SOMBRERO pathway. Development 2024; 151:dev202586. [PMID: 38563568 DOI: 10.1242/dev.202586] [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: 12/06/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024]
Abstract
In multicellular organisms, specialized tissues are generated by specific populations of stem cells through cycles of asymmetric cell divisions, where one daughter undergoes differentiation and the other maintains proliferative properties. In Arabidopsis thaliana roots, the columella - a gravity-sensing tissue that protects and defines the position of the stem cell niche - represents a typical example of a tissue whose organization is exclusively determined by the balance between proliferation and differentiation. The columella derives from a single layer of stem cells through a binary cell fate switch that is precisely controlled by multiple, independent regulatory inputs. Here, we show that the HD-Zip II transcription factors (TFs) HAT3, ATHB4 and AHTB2 redundantly regulate columella stem cell fate and patterning in the Arabidopsis root. The HD-Zip II TFs promote columella stem cell proliferation by acting as effectors of the FEZ/SMB circuit and, at the same time, by interfering with auxin signaling to counteract hormone-induced differentiation. Overall, our work shows that HD-Zip II TFs connect two opposing parallel inputs to fine-tune the balance between proliferation and differentiation in columella stem cells.
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Affiliation(s)
- Marco Possenti
- Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), Rome 00178, Italy
| | - Giovanna Sessa
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Altea Alfè
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Luana Turchi
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Valentino Ruzza
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Massimiliano Sassi
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Giorgio Morelli
- Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), Rome 00178, Italy
| | - Ida Ruberti
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
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7
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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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8
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Wang L, Tian T, Liang J, Li R, Xin X, Qi Y, Zhou Y, Fan Q, Ning G, Becana M, Duanmu D. A transcription factor of the NAC family regulates nitrate-induced legume nodule senescence. THE NEW PHYTOLOGIST 2023; 238:2113-2129. [PMID: 36945893 DOI: 10.1111/nph.18896] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/12/2023] [Indexed: 05/04/2023]
Abstract
Legumes establish symbioses with rhizobia by forming nitrogen-fixing nodules. Nitrate is a major environmental factor that affects symbiotic functioning. However, the molecular mechanism of nitrate-induced nodule senescence is poorly understood. Comparative transcriptomic analysis reveals an NAC-type transcription factor in Lotus japonicus, LjNAC094, that acts as a positive regulator in nitrate-induced nodule senescence. Stable overexpression and mutant lines of NAC094 were constructed and used for phenotypic characterization. DNA-affinity purification sequencing was performed to identify NAC094 targeting genes and results were confirmed by electrophoretic mobility shift and transactivation assays. Overexpression of NAC094 induces premature nodule senescence. Knocking out NAC094 partially relieves nitrate-induced degradation of leghemoglobins and abolishes nodule expression of senescence-associated genes (SAGs) that contain a conserved binding motif for NAC094. Nitrate-triggered metabolic changes in wild-type nodules are largely affected in nac094 mutant nodules. Induction of NAC094 and its targeting SAGs was almost blocked in the nitrate-insensitive nlp1, nlp4, and nlp1 nlp4 mutants. We conclude that NAC094 functions downstream of NLP1 and NLP4 by regulating nitrate-induced expression of SAGs. Our study fills in a key gap between nitrate and the execution of nodule senescence, and provides a potential strategy to improve nitrogen fixation and stress tolerance of legumes.
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Affiliation(s)
- Longlong Wang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tao Tian
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianjun Liang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Runhui Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xian Xin
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Yongmei Qi
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yumiao Zhou
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiuling Fan
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guogui Ning
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
| | - Manuel Becana
- Departamento de Biología Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Avenida Montañana 1005, 50059, Zaragoza, Spain
| | - Deqiang Duanmu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
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9
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Zhang Y, Xu T, Dong J. Asymmetric cell division in plant development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:343-370. [PMID: 36610013 PMCID: PMC9975081 DOI: 10.1111/jipb.13446] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/05/2023] [Indexed: 05/03/2023]
Abstract
Asymmetric cell division (ACD) is a fundamental process that generates new cell types during development in eukaryotic species. In plant development, post-embryonic organogenesis driven by ACD is universal and more important than in animals, in which organ pattern is preset during embryogenesis. Thus, plant development provides a powerful system to study molecular mechanisms underlying ACD. During the past decade, tremendous progress has been made in our understanding of the key components and mechanisms involved in this important process in plants. Here, we present an overview of how ACD is determined and regulated in multiple biological processes in plant development and compare their conservation and specificity among different model cell systems. We also summarize the molecular roles and mechanisms of the phytohormones in the regulation of plant ACD. Finally, we conclude with the overarching paradigms and principles that govern plant ACD and consider how new technologies can be exploited to fill the knowledge gaps and make new advances in the field.
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Affiliation(s)
- Yi Zhang
- Plant Synthetic Biology Center, Haixia Institute of Science and Technology, and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- The Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Tongda Xu
- Plant Synthetic Biology Center, Haixia Institute of Science and Technology, and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Juan Dong
- The Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Plant Biology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08891, USA
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10
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Teh OK, Singh P, Ren J, Huang LT, Ariyarathne M, Salamon BP, Wang Y, Kotake T, Fujita T. Surface-localized glycoproteins act through class C ARFs to fine-tune gametophore initiation in Physcomitrium patens. Development 2022; 149:282110. [PMID: 36520083 DOI: 10.1242/dev.200370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 10/17/2022] [Indexed: 12/23/2022]
Abstract
Arabinogalactan proteins are functionally diverse cell wall structural glycoproteins that have been implicated in cell wall remodeling, although the mechanistic actions remain elusive. Here, we identify and characterize two AGP glycoproteins, SLEEPING BEAUTY (SB) and SB-like (SBL), that negatively regulate the gametophore bud initiation in Physcomitrium patens by dampening cell wall loosening/softening. Disruption of SB and SBL led to accelerated gametophore formation and altered cell wall compositions. The function of SB is glycosylation dependent and genetically connected with the class C auxin response factor (ARF) transcription factors PpARFC1B and PpARFC2. Transcriptomics profiling showed that SB upregulates PpARFC2, which in turn suppresses a range of cell wall-modifying genes that are required for cell wall loosening/softening. We further show that PpARFC2 binds directly to multiple AuxRE motifs on the cis-regulatory sequences of PECTIN METHYLESTERASE to suppress its expression. Hence, our results demonstrate a mechanism by which the SB modulates the strength of intracellular auxin signaling output, which is necessary to fine-tune the timing of gametophore initials formation.
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Affiliation(s)
- Ooi Kock Teh
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec.2, Academia Rd., Nankang, Taipei 11529, Taiwan.,Department of Biological Sciences, Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Prerna Singh
- Graduate School of Life Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Junling Ren
- Graduate School of Life Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Lin Tzu Huang
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec.2, Academia Rd., Nankang, Taipei 11529, Taiwan
| | - Menaka Ariyarathne
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec.2, Academia Rd., Nankang, Taipei 11529, Taiwan
| | - Benjamin Prethiviraj Salamon
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec.2, Academia Rd., Nankang, Taipei 11529, Taiwan
| | - Yu Wang
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec.2, Academia Rd., Nankang, Taipei 11529, Taiwan
| | - Toshihisa Kotake
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, 225 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Tomomichi Fujita
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
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11
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Zhao Y, Liu Z, Wang L, Liu H. Fumonisin B1 as a Tool to Explore Sphingolipid Roles in Arabidopsis Primary Root Development. Int J Mol Sci 2022; 23:12925. [PMID: 36361715 PMCID: PMC9654530 DOI: 10.3390/ijms232112925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 03/28/2024] Open
Abstract
Fumonisin B1 is a mycotoxin that is structurally analogous to sphinganine and sphingosine and inhibits the biosynthesis of complex sphingolipids by repressing ceramide synthase. Based on the connection between FB1 and sphingolipid metabolism, FB1 has been widely used as a tool to explore the multiple functions of sphingolipids in mammalian and plant cells. The aim of this work was to determine the effect of sphingolipids on primary root development by exposing Arabidopsis (Arabidopsis thaliana) seedlings to FB1. We show that FB1 decreases the expression levels of several PIN-FORMED (PIN) genes and the key stem cell niche (SCN)-defining transcription factor genes WUSCHEL-LIKE HOMEOBOX5 (WOX5) and PLETHORAs (PLTs), resulting in the loss of quiescent center (QC) identity and SCN maintenance, as well as stunted root growth. In addition, FB1 induces cell death at the root apical meristem in a non-cell-type-specific manner. We propose that sphingolipids play a key role in primary root growth through the maintenance of the root SCN and the amelioration of cell death in Arabidopsis.
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Affiliation(s)
- Yanxue Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475000, China
| | - Zhongjie Liu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Lei Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475000, China
| | - Hao Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475000, China
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12
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Ortigosa F, Lobato-Fernández C, Shikano H, Ávila C, Taira S, Cánovas FM, Cañas RA. Ammonium regulates the development of pine roots through hormonal crosstalk and differential expression of transcription factors in the apex. PLANT, CELL & ENVIRONMENT 2022; 45:915-935. [PMID: 34724238 DOI: 10.1111/pce.14214] [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: 07/21/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
Ammonium is a prominent source of inorganic nitrogen for plant nutrition, but excessive amounts can be toxic for many species. However, most conifers are tolerant to ammonium, a relevant physiological feature of this ancient evolutionary lineage. For a better understanding of the molecular basis of this trait, ammonium-induced changes in the transcriptome of maritime pine (Pinus pinaster Ait.) root apex have been determined by laser capture microdissection and RNA sequencing. Ammonium promoted changes in the transcriptional profiles of multiple transcription factors, such as SHORT-ROOT, and phytohormone-related transcripts, such as ACO, involved in the development of the root meristem. Nano-PALDI-MSI and transcriptomic analyses showed that the distributions of IAA and CKs were altered in the root apex in response to ammonium nutrition. Taken together, the data suggest that this early response is involved in the increased lateral root branching and principal root growth, which characterize the long-term response to ammonium supply in pine. All these results suggest that ammonium induces changes in the root system architecture through the IAA-CK-ET phytohormone crosstalk and transcriptional regulation.
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Affiliation(s)
- Francisco Ortigosa
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
| | - César Lobato-Fernández
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
| | - Hitomi Shikano
- Faculty of Food and Agricultural Sciences, Fukushima University, Kanayagawa, Fukushima, Japan
| | - Concepción Ávila
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
| | - Shu Taira
- Faculty of Food and Agricultural Sciences, Fukushima University, Kanayagawa, Fukushima, Japan
| | - Francisco M Cánovas
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
| | - Rafael A Cañas
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
- Integrative Molecular Biology Lab, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
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13
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Siqueira JA, Otoni WC, Araújo WL. The hidden half comes into the spotlight: Peeking inside the black box of root developmental phases. PLANT COMMUNICATIONS 2022; 3:100246. [PMID: 35059627 PMCID: PMC8760039 DOI: 10.1016/j.xplc.2021.100246] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/13/2021] [Accepted: 09/18/2021] [Indexed: 05/30/2023]
Abstract
Efficient use of natural resources (e.g., light, water, and nutrients) can be improved with a tailored developmental program that maximizes the lifetime and fitness of plants. In plant shoots, a developmental phase represents a time window in which the meristem triggers the development of unique morphological and physiological traits, leading to the emergence of leaves, flowers, and fruits. Whereas developmental phases in plant shoots have been shown to enhance food production in crops, this phenomenon has remained poorly investigated in roots. In light of recent advances, we suggest that root development occurs in three main phases: root apical meristem appearance, foraging, and senescence. We provide compelling evidence suggesting that these phases are regulated by at least four developmental pathways: autonomous, non-autonomous, hormonal, and periodic. Root developmental pathways differentially coordinate organ plasticity, promoting morphological alterations, tissue regeneration, and cell death regulation. Furthermore, we suggest how nutritional checkpoints may allow progression through the developmental phases, thus completing the root life cycle. These insights highlight novel and exciting advances in root biology that may help maximize the productivity of crops through more sustainable agriculture and the reduced use of chemical fertilizers.
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14
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Betegón‐Putze I, Mercadal J, Bosch N, Planas‐Riverola A, Marquès‐Bueno M, Vilarrasa‐Blasi J, Frigola D, Burkart RC, Martínez C, Conesa A, Sozzani R, Stahl Y, Prat S, Ibañes M, Caño‐Delgado AI. Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots. Mol Syst Biol 2021; 17:e9864. [PMID: 34132490 PMCID: PMC8207686 DOI: 10.15252/msb.20209864] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 11/29/2022] Open
Abstract
Understanding stem cell regulatory circuits is the next challenge in plant biology, as these cells are essential for tissue growth and organ regeneration in response to stress. In the Arabidopsis primary root apex, stem cell-specific transcription factors BRAVO and WOX5 co-localize in the quiescent centre (QC) cells, where they commonly repress cell division so that these cells can act as a reservoir to replenish surrounding stem cells, yet their molecular connection remains unknown. Genetic and biochemical analysis indicates that BRAVO and WOX5 form a transcription factor complex that modulates gene expression in the QC cells to preserve overall root growth and architecture. Furthermore, by using mathematical modelling we establish that BRAVO uses the WOX5/BRAVO complex to promote WOX5 activity in the stem cells. Our results unveil the importance of transcriptional regulatory circuits in plant stem cell development.
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Affiliation(s)
- Isabel Betegón‐Putze
- Department of Molecular GeneticsCentre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UAB (Cerdanyola del Vallès)BarcelonaSpain
| | - Josep Mercadal
- Departament de Matèria CondensadaFacultat de FísicaUniversitat de BarcelonaBarcelonaSpain
- Universitat de Barcelona Institute of Complex Systems (UBICS)BarcelonaSpain
| | - Nadja Bosch
- Department of Molecular GeneticsCentre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UAB (Cerdanyola del Vallès)BarcelonaSpain
| | - Ainoa Planas‐Riverola
- Department of Molecular GeneticsCentre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UAB (Cerdanyola del Vallès)BarcelonaSpain
| | - Mar Marquès‐Bueno
- Department of Molecular GeneticsCentre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UAB (Cerdanyola del Vallès)BarcelonaSpain
| | - Josep Vilarrasa‐Blasi
- Department of Molecular GeneticsCentre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UAB (Cerdanyola del Vallès)BarcelonaSpain
- Present address:
Department of BiologyStanford UniversityStanfordCAUSA
| | - David Frigola
- Departament de Matèria CondensadaFacultat de FísicaUniversitat de BarcelonaBarcelonaSpain
| | - Rebecca C Burkart
- Institute for Developmental GeneticsHeinrich‐Heine UniversityDüsseldorfGermany
| | - Cristina Martínez
- Department of Plant Molecular GeneticsCentro Nacional de Biotecnología (CNB)MadridSpain
| | - Ana Conesa
- Microbiology and Cell ScienceInstitute for Food and Agricultural ResearchGenetics InstituteUniversity of FloridaGainesvilleFLUSA
| | - Rosangela Sozzani
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Yvonne Stahl
- Institute for Developmental GeneticsHeinrich‐Heine UniversityDüsseldorfGermany
| | - Salomé Prat
- Department of Plant Molecular GeneticsCentro Nacional de Biotecnología (CNB)MadridSpain
| | - Marta Ibañes
- Departament de Matèria CondensadaFacultat de FísicaUniversitat de BarcelonaBarcelonaSpain
- Universitat de Barcelona Institute of Complex Systems (UBICS)BarcelonaSpain
| | - Ana I Caño‐Delgado
- Department of Molecular GeneticsCentre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UAB (Cerdanyola del Vallès)BarcelonaSpain
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15
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Zluhan-Martínez E, López-Ruíz BA, García-Gómez ML, García-Ponce B, de la Paz Sánchez M, Álvarez-Buylla ER, Garay-Arroyo A. Integrative Roles of Phytohormones on Cell Proliferation, Elongation and Differentiation in the Arabidopsis thaliana Primary Root. FRONTIERS IN PLANT SCIENCE 2021; 12:659155. [PMID: 33981325 PMCID: PMC8107238 DOI: 10.3389/fpls.2021.659155] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/24/2021] [Indexed: 05/17/2023]
Abstract
The growth of multicellular organisms relies on cell proliferation, elongation and differentiation that are tightly regulated throughout development by internal and external stimuli. The plasticity of a growth response largely depends on the capacity of the organism to adjust the ratio between cell proliferation and cell differentiation. The primary root of Arabidopsis thaliana offers many advantages toward understanding growth homeostasis as root cells are continuously produced and move from cell proliferation to elongation and differentiation that are processes spatially separated and could be studied along the longitudinal axis. Hormones fine tune plant growth responses and a huge amount of information has been recently generated on the role of these compounds in Arabidopsis primary root development. In this review, we summarized the participation of nine hormones in the regulation of the different zones and domains of the Arabidopsis primary root. In some cases, we found synergism between hormones that function either positively or negatively in proliferation, elongation or differentiation. Intriguingly, there are other cases where the interaction between hormones exhibits unexpected results. Future analysis on the molecular mechanisms underlying crosstalk hormone action in specific zones and domains will unravel their coordination over PR development.
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Affiliation(s)
- Estephania Zluhan-Martínez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Brenda Anabel López-Ruíz
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Mónica L. García-Gómez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- *Correspondence: Adriana Garay-Arroyo,
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16
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Desvoyes B, Gutierrez C. Roles of plant retinoblastoma protein: cell cycle and beyond. EMBO J 2020; 39:e105802. [PMID: 32865261 PMCID: PMC7527812 DOI: 10.15252/embj.2020105802] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/16/2020] [Accepted: 08/06/2020] [Indexed: 12/16/2022] Open
Abstract
The human retinoblastoma (RB1) protein is a tumor suppressor that negatively regulates cell cycle progression through its interaction with members of the E2F/DP family of transcription factors. However, RB-related (RBR) proteins are an early acquisition during eukaryote evolution present in plant lineages, including unicellular algae, ancient plants (ferns, lycophytes, liverworts, mosses), gymnosperms, and angiosperms. The main RBR protein domains and interactions with E2Fs are conserved in all eukaryotes and not only regulate the G1/S transition but also the G2/M transition, as part of DREAM complexes. RBR proteins are also important for asymmetric cell division, stem cell maintenance, and the DNA damage response (DDR). RBR proteins play crucial roles at every developmental phase transition, in association with chromatin factors, as well as during the reproductive phase during female and male gametes production and embryo development. Here, we review the processes where plant RBR proteins play a role and discuss possible avenues of research to obtain a full picture of the multifunctional roles of RBR for plant life.
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17
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Kumar N, Iyer-Pascuzzi AS. Shedding the Last Layer: Mechanisms of Root Cap Cell Release. PLANTS 2020; 9:plants9030308. [PMID: 32121604 PMCID: PMC7154840 DOI: 10.3390/plants9030308] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 01/06/2023]
Abstract
The root cap, a small tissue at the tip of the root, protects the root from environmental stress and functions in gravity perception. To perform its functions, the position and size of the root cap remains stable throughout root growth. This occurs due to constant root cap cell turnover, in which the last layer of the root cap is released, and new root cap cells are produced. Cells in the last root cap layer are known as border cells or border-like cells, and have important functions in root protection against bacterial and fungal pathogens. Despite the importance of root cap cell release to root health and plant growth, the mechanisms regulating this phenomenon are not well understood. Recent work identified several factors including transcription factors, auxin, and small peptides with roles in the production and release of root cap cells. Here, we review the involvement of the known players in root cap cell release, compare the release of border-like cells and border cells, and discuss the importance of root cap cell release to root health and survival.
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18
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Lv B, Yu Q, Liu J, Wen X, Yan Z, Hu K, Li H, Kong X, Li C, Tian H, De Smet I, Zhang X, Ding Z. Non-canonical AUX/IAA protein IAA33 competes with canonical AUX/IAA repressor IAA5 to negatively regulate auxin signaling. EMBO J 2020; 39:e101515. [PMID: 31617603 PMCID: PMC6939196 DOI: 10.15252/embj.2019101515] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 09/05/2019] [Accepted: 09/10/2019] [Indexed: 11/09/2022] Open
Abstract
The phytohormone auxin controls plant growth and development via TIR1-dependent protein degradation of canonical AUX/IAA proteins, which normally repress the activity of auxin response transcription factors (ARFs). IAA33 is a non-canonical AUX/IAA protein lacking a TIR1-binding domain, and its role in auxin signaling and plant development is not well understood. Here, we show that IAA33 maintains root distal stem cell identity and negatively regulates auxin signaling by interacting with ARF10 and ARF16. IAA33 competes with the canonical AUX/IAA repressor IAA5 for binding to ARF10/16 to protect them from IAA5-mediated inhibition. In contrast to auxin-dependent degradation of canonical AUX/IAA proteins, auxin stabilizes IAA33 protein via MITOGEN-ACTIVATED PROTEIN KINASE 14 (MPK14) and does not affect IAA33 gene expression. Taken together, this study provides insight into the molecular functions of non-canonical AUX/IAA proteins in auxin signaling transduction.
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Affiliation(s)
- Bingsheng Lv
- The Key Laboratory of Plant Development and Environmental Adaptation BiologyMinistry of EducationSchool of Life SciencesShandong UniversityQingdaoShandongChina
| | - Qianqian Yu
- The Key Laboratory of Plant Development and Environmental Adaptation BiologyMinistry of EducationSchool of Life SciencesShandong UniversityQingdaoShandongChina
- College of Life SciencesLiaocheng UniversityLiaochengShandongChina
| | - Jiajia Liu
- The Key Laboratory of Plant Development and Environmental Adaptation BiologyMinistry of EducationSchool of Life SciencesShandong UniversityQingdaoShandongChina
| | - Xuejing Wen
- The Key Laboratory of Plant Development and Environmental Adaptation BiologyMinistry of EducationSchool of Life SciencesShandong UniversityQingdaoShandongChina
| | - Zhenwei Yan
- The Key Laboratory of Plant Development and Environmental Adaptation BiologyMinistry of EducationSchool of Life SciencesShandong UniversityQingdaoShandongChina
| | - Kongqin Hu
- The Key Laboratory of Plant Development and Environmental Adaptation BiologyMinistry of EducationSchool of Life SciencesShandong UniversityQingdaoShandongChina
| | - Hanbing Li
- Department of BiochemistryUniversity of MissouriColumbiaMOUSA
| | - Xiangpei Kong
- The Key Laboratory of Plant Development and Environmental Adaptation BiologyMinistry of EducationSchool of Life SciencesShandong UniversityQingdaoShandongChina
| | - Cuiling Li
- The Key Laboratory of Plant Development and Environmental Adaptation BiologyMinistry of EducationSchool of Life SciencesShandong UniversityQingdaoShandongChina
| | - Huiyu Tian
- The Key Laboratory of Plant Development and Environmental Adaptation BiologyMinistry of EducationSchool of Life SciencesShandong UniversityQingdaoShandongChina
| | - Ive De Smet
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Xian‐Sheng Zhang
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai’ anShandongChina
| | - Zhaojun Ding
- The Key Laboratory of Plant Development and Environmental Adaptation BiologyMinistry of EducationSchool of Life SciencesShandong UniversityQingdaoShandongChina
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19
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Roué J, Chauvet H, Brunel-Michac N, Bizet F, Moulia B, Badel E, Legué V. Root cap size and shape influence responses to the physical strength of the growth medium in Arabidopsis thaliana primary roots. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:126-137. [PMID: 31682268 DOI: 10.1093/jxb/erz418] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 10/11/2019] [Indexed: 06/10/2023]
Abstract
During the progression of root in soil, root cap cells are the first to encounter obstacles and are known to sense environmental cues, thus making the root cap a potential mechanosensing site. In this study, a two-layered growth medium system was developed in order to study root responses to variations in the physical strength of the medium and the importance of the root cap in the establishment of these responses. Root growth and trajectory of primary roots of Arabidopsis seedlings were investigated using in vivo image analysis. After contact with the harder layer of the medium, the root either penetrated it or underwent rapid curvature, thus enabling reorientation of growth. We initially hypothesized that the root-cap structure would affect apex penetration and reorientation, with pointed caps facilitating and domed caps impeding root penetration. This hypothesis was investigated by analysing the responses of Arabidopsis mutants with altered root caps. The primary root of lines of the fez-2 mutant, which has fewer root-cap cell layers and a more pointed root cap than wild-type roots, showed impaired penetration ability. Conversely, smb-3 roots, which display a rectangular-shaped cap, showed enhanced penetration abilities. These results, which contradict our original hypothesis, reveal a role for resistance to buckling in determining root penetration abilities.
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Affiliation(s)
- J Roué
- Université Clermont Auvergne, INRA, PIAF, Clermont-Ferrand, France
| | - H Chauvet
- Université Clermont Auvergne, INRA, PIAF, Clermont-Ferrand, France
| | - N Brunel-Michac
- Université Clermont Auvergne, INRA, PIAF, Clermont-Ferrand, France
| | - F Bizet
- Université Clermont Auvergne, INRA, PIAF, Clermont-Ferrand, France
| | - B Moulia
- Université Clermont Auvergne, INRA, PIAF, Clermont-Ferrand, France
| | - E Badel
- Université Clermont Auvergne, INRA, PIAF, Clermont-Ferrand, France
| | - V Legué
- Université Clermont Auvergne, INRA, PIAF, Clermont-Ferrand, France
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20
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Method to Study Gene Expression Patterns During De Novo Root Regeneration from Arabidopsis Leaf Explants. Methods Mol Biol 2019. [PMID: 31797288 DOI: 10.1007/978-1-0716-0183-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
De novo root regeneration (DNRR) is the process in which adventitious roots are regenerated from damaged plant tissues or organs. We have developed a simple DNRR system in which adventitious roots are formed from detached leaf explants of Arabidopsis (Arabidopsis thaliana) on B5 medium without external hormones. In this chapter, we introduce the methods used to observe gene expression patterns during rooting from leaf explants. Usually, β-glucuronidase (GUS) staining is used to visualize gene expression patterns, since fluorescent proteins are difficult to observe because of the high autofluorescence in leaf explants. Here, we describe the use of the ClearSee technique with Congo red staining for deep imaging to observe fluorescent proteins. This method diminishes autofluorescence in leaf explants and preserves the stability of fluorescent proteins, thus allowing us to investigate the endogenous molecular actions guiding DNRR.
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21
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Chen D, Wang Q, Feng J, Ruan Y, Shen WH. Arabidopsis ZUOTIN RELATED FACTOR1 Proteins Are Required for Proper Embryonic and Post-Embryonic Root Development. FRONTIERS IN PLANT SCIENCE 2019; 10:1498. [PMID: 31824531 PMCID: PMC6882920 DOI: 10.3389/fpls.2019.01498] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/29/2019] [Indexed: 06/10/2023]
Abstract
The H2A/UBIQUITIN-binding proteins AtZRF1a/b have been reported as key regulators involved in multiple processes of Arabidopsis plant growth and development. Yet, the cellular and molecular mechanisms underlying the mutant phenotype remain largely elusive. Here we show that loss-of-function of AtZRF1a/b causes defective root elongation and deformed root apical meristem organization in seedlings. The premature termination of the primary root in the atzrf1a;atzrf1b double mutant is associated with an advanced onset of endoreduplication and subsequent consumption of reservoir stem cells. Cytological analyses using cell type-specific markers and florescent dyes indicate that AtZRF1a/b are involved in maintenance of proper cell layer organization, determinacy of cell identity, and establishment of auxin gradient and maximum at the root tip. During embryogenesis AtZRF1a/b act dominantly in regulating the maintenance of ground tissue initial cells and production of lateral root cap. Lastly, quantitative real-time polymerase chain reaction analysis shows mis-expression of some key genes involved in regulating cell patterning, cell proliferation and/or hormone pathways. Our results provide important insight into AtZRF1a/b function in cell fate determinacy and in establishment and maintenance of proper stem cell reservoir during embryonic and post-embryonic root development.
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Affiliation(s)
- Donghong Chen
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 CNRS, Université de Strasbourg, Strasbourg, France
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Hunan Agricultural University, Changsha, China
| | - Qiannan Wang
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 CNRS, Université de Strasbourg, Strasbourg, France
| | - Jing Feng
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 CNRS, Université de Strasbourg, Strasbourg, France
| | - Ying Ruan
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Hunan Agricultural University, Changsha, China
| | - Wen-Hui Shen
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 CNRS, Université de Strasbourg, Strasbourg, France
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22
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Maeda K, Kunieda T, Tamura K, Hatano K, Hara-Nishimura I, Shimada T. Identification of Periplasmic Root-Cap Mucilage in Developing Columella Cells of Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2019; 60:1296-1303. [PMID: 30892660 DOI: 10.1093/pcp/pcz047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 03/06/2019] [Indexed: 06/09/2023]
Abstract
Plant roots secrete various substances with diverse functions against both plants and microbes in the rhizosphere. A major secretory substance is root-cap mucilage, whose functions have been well characterized, albeit mainly in crops. However, little is currently known about the developmental mechanisms of root-cap mucilage. Here, we show the accumulation and extrusion of root-cap mucilage in Arabidopsis. We found propidium iodide (PI) stainable structures between the plasma membrane and cell wall in the sixth layer of columella cells (c6) from the quiescent center. Ruthenium red staining and PI staining with calcium ions suggested that the structure comprises in part pectin polysaccharides. Electron microscopy revealed that the structure had a meshwork of electron-dense filaments that resembled periplasmic mucilage in other plants. In the c6 cells, we also observed many large vesicles with denser meshwork filaments to periplasmic mucilage, which likely mediate the transport of mucilage components. Extruded mucilage was observed outside a partially degraded cell wall in the c7 cells. Moreover, we found that the Class IIB NAC transcription factors BEARSKIN1 (BRN1) and BRN2, which are known to regulate the terminal differentiation of columella cells, were required for the efficient accumulation of root-cap mucilage in Arabidopsis. Taken together, our findings reveal the accumulation of and dynamic changes in periplasmic mucilage during columella cell development in Arabidopsis.
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Affiliation(s)
- Kazuki Maeda
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Tadashi Kunieda
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Kentaro Tamura
- Department of Environmental and Life Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kyoko Hatano
- Department of Interdisciplinary Environment, Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Ikuko Hara-Nishimura
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan
| | - Tomoo Shimada
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan
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Xiao TT, van Velzen R, Kulikova O, Franken C, Bisseling T. Lateral root formation involving cell division in both pericycle, cortex and endodermis is a common and ancestral trait in seed plants. Development 2019; 146:dev.182592. [DOI: 10.1242/dev.182592] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 09/23/2019] [Indexed: 01/29/2023]
Abstract
Studies on the model plant Arabidopsis have led to the common view that lateral roots are exclusively formed from pericycle cells and that the latter are unique in their ability to be reprogrammed into stem cells. By analysing lateral root formation in an evolutionary context, we show that lateral root primordium formation in which cortex, endodermis and pericycle are mitotically activated, is a common and ancestral trait in seed plants, whereas the exclusive involvement of pericycle evolved in the Brassicaceae. Further, also the endodermis can be reprogrammed into stem cells in some species.
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Affiliation(s)
- Ting Ting Xiao
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Robin van Velzen
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Olga Kulikova
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Carolien Franken
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Ton Bisseling
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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24
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Shi CL, von Wangenheim D, Herrmann U, Wildhagen M, Kulik I, Kopf A, Ishida T, Olsson V, Anker MK, Albert M, Butenko MA, Felix G, Sawa S, Claassen M, Friml J, Aalen RB. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. NATURE PLANTS 2018; 4:596-604. [PMID: 30061750 DOI: 10.1038/s41477-018-0212-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/03/2018] [Indexed: 12/21/2022]
Abstract
The root cap protects the stem cell niche of angiosperm roots from damage. In Arabidopsis, lateral root cap (LRC) cells covering the meristematic zone are regularly lost through programmed cell death, while the outermost layer of the root cap covering the tip is repeatedly sloughed. Efficient coordination with stem cells producing new layers is needed to maintain a constant size of the cap. We present a signalling pair, the peptide IDA-LIKE1 (IDL1) and its receptor HAESA-LIKE2 (HSL2), mediating such communication. Live imaging over several days characterized this process from initial fractures in LRC cell files to full separation of a layer. Enhanced expression of IDL1 in the separating root cap layers resulted in increased frequency of sloughing, balanced with generation of new layers in a HSL2-dependent manner. Transcriptome analyses linked IDL1-HSL2 signalling to the transcription factors BEARSKIN1/2 and genes associated with programmed cell death. Mutations in either IDL1 or HSL2 slowed down cell division, maturation and separation. Thus, IDL1-HSL2 signalling potentiates dynamic regulation of the homeostatic balance between stem cell division and sloughing activity.
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Affiliation(s)
- Chun-Lin Shi
- Section of Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Daniel von Wangenheim
- Institute of Science and Technology Austria, Klosterneuburg, Austria
- Centre for Plant Integrative Biology, University of Nottingham, Loughborough, UK
| | - Ullrich Herrmann
- Section of Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Plant Developmental Biology and Plant Physiology, University of Kiel, Kiel, Germany
| | - Mari Wildhagen
- Section of Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ivan Kulik
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Andreas Kopf
- ETH Zurich, HPT E 73, Auguste-Piccard-Hof 1, Zürich, Switzerland
| | - Takashi Ishida
- International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, Kumamoto, Japan
| | - Vilde Olsson
- Section of Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Mari Kristine Anker
- Section of Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Markus Albert
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Melinka A Butenko
- Section of Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Georg Felix
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Shinichiro Sawa
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Manfred Claassen
- ETH Zurich, HPT E 73, Auguste-Piccard-Hof 1, Zürich, Switzerland
| | - Jiří Friml
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Reidunn B Aalen
- Section of Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway.
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25
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Flores-Sandoval E, Eklund DM, Hong SF, Alvarez JP, Fisher TJ, Lampugnani ER, Golz JF, Vázquez-Lobo A, Dierschke T, Lin SS, Bowman JL. Class C ARFs evolved before the origin of land plants and antagonize differentiation and developmental transitions in Marchantia polymorpha. THE NEW PHYTOLOGIST 2018; 218:1612-1630. [PMID: 29574879 DOI: 10.1111/nph.15090] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 02/05/2018] [Indexed: 05/08/2023]
Abstract
A plethora of developmental and physiological processes in land plants is influenced by auxin, to a large extent via alterations in gene expression by AUXIN RESPONSE FACTORs (ARFs). The canonical auxin transcriptional response system is a land plant innovation, however, charophycean algae possess orthologues of at least some classes of ARF and AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) genes, suggesting that elements of the canonical land plant system existed in an ancestral alga. We reconstructed the phylogenetic relationships between streptophyte ARF and AUX/IAA genes and functionally characterized the solitary class C ARF, MpARF3, in Marchantia polymorpha. Phylogenetic analyses indicate that multiple ARF classes, including class C ARFs, existed in an ancestral alga. Loss- and gain-of-function MpARF3 alleles result in pleiotropic effects in the gametophyte, with MpARF3 inhibiting differentiation and developmental transitions in multiple stages of the life cycle. Although loss-of-function Mparf3 and Mpmir160 alleles respond to exogenous auxin treatments, strong miR-resistant MpARF3 alleles are auxin-insensitive, suggesting that class C ARFs act in a context-dependent fashion. We conclude that two modules independently evolved to regulate a pre-existing ARF transcriptional network. Whereas the auxin-TIR1-AUX/IAA pathway evolved to repress class A/B ARF activity, miR160 evolved to repress class C ARFs in a dynamic fashion.
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Affiliation(s)
- Eduardo Flores-Sandoval
- School of Biological Sciences, Monash University, Clayton, Melbourne, Victoria, 3800, Australia
| | - D Magnus Eklund
- School of Biological Sciences, Monash University, Clayton, Melbourne, Victoria, 3800, Australia
| | - Syuan-Fei Hong
- Institute of Biotechnology, National Taiwan University, 81, Chang-Xing ST., Taipei, 106, Taiwan
| | - John P Alvarez
- School of Biological Sciences, Monash University, Clayton, Melbourne, Victoria, 3800, Australia
| | - Tom J Fisher
- School of Biological Sciences, Monash University, Clayton, Melbourne, Victoria, 3800, Australia
| | - Edwin R Lampugnani
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - John F Golz
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Alejandra Vázquez-Lobo
- CIByC, Universidad Autónoma del Estado de Morelos, Av. Universidad No. 1001, Colonia Chamilpa, CP 62209, Cuernavaca, Morelos, México
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Clayton, Melbourne, Victoria, 3800, Australia
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, 81, Chang-Xing ST., Taipei, 106, Taiwan
| | - John L Bowman
- School of Biological Sciences, Monash University, Clayton, Melbourne, Victoria, 3800, Australia
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26
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Spatial specificity of auxin responses coordinates wood formation. Nat Commun 2018; 9:875. [PMID: 29491423 PMCID: PMC5830446 DOI: 10.1038/s41467-018-03256-2] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 01/31/2018] [Indexed: 12/21/2022] Open
Abstract
Spatial organization of signalling events of the phytohormone auxin is fundamental for maintaining a dynamic transition from plant stem cells to differentiated descendants. The cambium, the stem cell niche mediating wood formation, fundamentally depends on auxin signalling but its exact role and spatial organization is obscure. Here we show that, while auxin signalling levels increase in differentiating cambium descendants, a moderate level of signalling in cambial stem cells is essential for cambium activity. We identify the auxin-dependent transcription factor ARF5/MONOPTEROS to cell-autonomously restrict the number of stem cells by directly attenuating the activity of the stem cell-promoting WOX4 gene. In contrast, ARF3 and ARF4 function as cambium activators in a redundant fashion from outside of WOX4-expressing cells. Our results reveal an influence of auxin signalling on distinct cambium features by specific signalling components and allow the conceptual integration of plant stem cell systems with distinct anatomies. Auxin activity controls plant stem cell function. Here the authors show that in the cambium, moderate auxin activity restricts cambial stem cell number via ARF5-dependent repression of the stem‐cell‐promoting factor WOX4, while ARF3 and ARF4 promote cambial activity outside of the WOX4‐expression domain.
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27
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Augstein F, Carlsbecker A. Getting to the Roots: A Developmental Genetic View of Root Anatomy and Function From Arabidopsis to Lycophytes. FRONTIERS IN PLANT SCIENCE 2018; 9:1410. [PMID: 30319672 PMCID: PMC6167918 DOI: 10.3389/fpls.2018.01410] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 09/05/2018] [Indexed: 05/11/2023]
Abstract
Roots attach plants to the ground and ensure efficient and selective uptake of water and nutrients. These functions are facilitated by the morphological and anatomical structures of the root, formed by the activity of the root apical meristem (RAM) and consecutive patterning and differentiation of specific tissues with distinct functions. Despite the importance of this plant organ, its evolutionary history is not clear, but fossils suggest that roots evolved at least twice, in the lycophyte (clubmosses and their allies) and in the euphyllophyte (ferns and seed plants) lineages. Both lycophyte and euphyllophyte roots grow indeterminately by the action of an apical meristem, which is protected by a root cap. They produce root hairs, and in most species the vascular stele is guarded by a specialized endodermal cell layer. Hence, most of these traits must have evolved independently in these lineages. This raises the question if the development of these apparently analogous tissues is regulated by distinct or homologous genes, independently recruited from a common ancestor of lycophytes and euphyllophytes. Currently, there are few studies of the genetic and molecular regulation of lycophyte and fern roots. Therefore, in this review, we focus on key regulatory networks that operate in root development in the model angiosperm Arabidopsis. We describe current knowledge of the mechanisms governing RAM maintenance as well as patterning and differentiation of tissues, such as the endodermis and the vasculature, and compare with other species. We discuss the importance of comparative analyses of anatomy and morphology of extant and extinct species, along with analyses of gene regulatory networks and, ultimately, gene function in plants holding key phylogenetic positions to test hypotheses of root evolution.
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28
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Kamiya M, Higashio SY, Isomoto A, Kim JM, Seki M, Miyashima S, Nakajima K. Control of root cap maturation and cell detachment by BEARSKIN transcription factors in Arabidopsis. Development 2017; 143:4063-4072. [PMID: 27803060 DOI: 10.1242/dev.142331] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/19/2016] [Indexed: 01/29/2023]
Abstract
The root cap supports root growth by protecting the root meristem, sensing gravity and interacting with the rhizosphere through metabolite secretion and cell dispersal. Sustained root cap functions therefore rely on balanced proliferation of proximal stem cells and regulated detachment of distal mature cells. Although the gene regulatory network that governs stem cell activity in the root cap has been extensively studied in Arabidopsis, the mechanisms by which root cap cells mature and detach from the root tip are poorly understood. We performed a detailed expression analysis of three regulators of root cap differentiation, SOMBRERO, BEARSKIN1 and BEARSKIN2, and identified their downstream genes. Our results indicate that expression of BEARSKIN1 and BEARSKIN2 is associated with cell positioning on the root surface. We identified a glycosyl hydrolase 28 (GH28) family polygalacturonase (PG) gene as a direct target of BEARSKIN1. Overexpression and loss-of-function analyses demonstrated that the protein encoded by this PG gene facilitates cell detachment. We thus revealed a molecular link between the key regulators of root cap differentiation and the cellular events underlying root cap-specific functions.
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Affiliation(s)
- Masako Kamiya
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Shin-Ya Higashio
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Atsushi Isomoto
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Jong-Myong Kim
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Motoaki Seki
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shunsuke Miyashima
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Keiji Nakajima
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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29
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Zhang Y, Jiao Y, Jiao H, Zhao H, Zhu YX. Two-Step Functional Innovation of the Stem-Cell Factors WUS/WOX5 during Plant Evolution. Mol Biol Evol 2017; 34:640-653. [PMID: 28053005 PMCID: PMC5400392 DOI: 10.1093/molbev/msw263] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
WUS and WOX5, which are expressed, respectively, in the organizing center (OC) and the quiescent center (QC), are essential for shoot/root apical stem-cell maintenance in flowering plants. However, little is known about how these stem-cell factors evolved their functions in flowering plants. Here, we show that the WUS/WOX5 proteins acquired two distinct capabilities by a two-step functional innovation process in the course of plant evolution. The first-step is the apical stem-cell maintenance activity of WUS/WOX5, which originated in the common ancestor of ferns and seed plants, as evidenced by the interspecies complementation experiments, showing that ectopic expression of fern Ceratopteris richardii WUS-like (CrWUL) surrounding OC/QC, or exclusive OC-/QC-expressed gymnosperms/angiosperms WUS/WOX5 in Arabidopsis wus-1 and wox5-1 mutants, could rescue their phenotypes. The second-step is the intercellular mobility that emerged in the common ancestor of seed plants after divergence from the ferns. Evidence for this includes confocal imaging of GFP fusion proteins, showing that WUS/WOX5 from seed plants, rather than from the fern CrWUL, can migrate into cells adjacent to the OC/QC. Evolutionary analysis showed that the WUS-like gene was duplicated into two copies prior to the divergence of gymnosperms/angiosperms. Then the two gene copies (WUS and WOX5) have undergone similar levels of purifying selection, which is consistent with their conserved functions in angiosperm shoot/root stem-cell maintenance and floral organ formation. Our results highlight the critical roles and the essential prerequisites that the two-step functional innovation of these genes performs and represents in the origin of flowering plants.
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Affiliation(s)
- Yuzhou Zhang
- Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Yue Jiao
- Development Center for Science and Technology, Ministry of Agriculture, Beijing, China
| | - Hengwu Jiao
- Department of Ecology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Huabin Zhao
- Department of Ecology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yu-Xian Zhu
- Institute for Advanced Studies, Wuhan University, Wuhan, China.,Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan, China
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30
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Zhu C, Wang L, Chen J, Liu C, Zeng H, Wang H. Over-expression of KdSOC1 gene affected plantlet morphogenesis in Kalanchoe daigremontiana. Sci Rep 2017; 7:5629. [PMID: 28717174 PMCID: PMC5514138 DOI: 10.1038/s41598-017-04387-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 05/15/2017] [Indexed: 11/19/2022] Open
Abstract
Kalanchoe daigremontiana reproduces asexually by producing plantlets along the leaf margin. The aim of this study was to identify the function of the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 gene in Kalanchoe daigremontiana (KdSOC1) during plantlet morphogenesis. In this study, KdSOC1 gene expression was detected at stem cell niche during in vitro somatic embryogenesis and plantlet morphogenesis. Disrupting endogenous auxin transportation suppressed the KdSOC1 gene response. Knockdown of the KdSOC1 gene caused a defect in cotyledon formation during the early heart stage of somatic embryogenesis. Over-expression (OE) of the KdSOC1 gene resulted in asymmetric plantlet distribution, a reduced number of plantlets, thicker leaves, and thicker vascular fibers. Higher KdPIN1 gene expression and auxin content were found in OE plant compared to those of wild-type plant leaves, which indicated possible KdSOC1 gene role in affecting auxin distribution and accumulation. KdSOC1 gene OE in DR5-GUS Arabidopsis reporting lines resulted in an abnormal auxin response pattern during different stages of somatic embryogenesis. In summary, the KdSOC1 gene OE might alter auxin distribution and accumulation along leaf margin to initiate plantlet formation and distribution, which is crucial for plasticity during plantlet formation under various environmental conditions.
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Affiliation(s)
- Chen Zhu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Li Wang
- Sivilculture Forestry department, College of Forestry, Beijing Forestry University, Beijing, China
| | - Jinhua Chen
- Turfgrass Management department, College of Forestry, Beijing forestry university, Beijing, China
| | - Chenglan Liu
- Turfgrass Management department, College of Forestry, Beijing forestry university, Beijing, China
| | - Huiming Zeng
- Turfgrass Management department, College of Forestry, Beijing forestry university, Beijing, China.
| | - Huafang Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
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31
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Hong JH, Savina M, Du J, Devendran A, Kannivadi Ramakanth K, Tian X, Sim WS, Mironova VV, Xu J. A Sacrifice-for-Survival Mechanism Protects Root Stem Cell Niche from Chilling Stress. Cell 2017. [PMID: 28648662 DOI: 10.1016/j.cell.2017.06.002] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Temperature has a profound influence on plant and animal development, but its effects on stem cell behavior and activity remain poorly understood. Here, we characterize the responses of the Arabidopsis root to chilling (low but above-freezing) temperature. Chilling stress at 4°C leads to DNA damage predominantly in root stem cells and their early descendants. However, only newly generated/differentiating columella stem cell daughters (CSCDs) preferentially die in a programmed manner. Inhibition of the DNA damage response in these CSCDs prevents their death but makes the stem cell niche more vulnerable to chilling stress. Mathematical modeling and experimental validation indicate that CSCD death results in the re-establishment of the auxin maximum in the quiescent center (QC) and the maintenance of functional stem cell niche activity under chilling stress. This mechanism improves the root's ability to withstand the accompanying environmental stresses and to resume growth when optimal temperatures are restored.
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Affiliation(s)
- Jing Han Hong
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Maria Savina
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; Novosibirsk State University, LCT&EB, Novosibirsk 630090, Russia
| | - Jing Du
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Ajay Devendran
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Karthikbabu Kannivadi Ramakanth
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Xin Tian
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Wei Shi Sim
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Victoria V Mironova
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; Novosibirsk State University, LCT&EB, Novosibirsk 630090, Russia
| | - Jian Xu
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore.
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32
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García-Gómez ML, Azpeitia E, Álvarez-Buylla ER. A dynamic genetic-hormonal regulatory network model explains multiple cellular behaviors of the root apical meristem of Arabidopsis thaliana. PLoS Comput Biol 2017; 13:e1005488. [PMID: 28426669 PMCID: PMC5417714 DOI: 10.1371/journal.pcbi.1005488] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 05/04/2017] [Accepted: 03/30/2017] [Indexed: 11/18/2022] Open
Abstract
The study of the concerted action of hormones and transcription factors is fundamental to understand cell differentiation and pattern formation during organ development. The root apical meristem of Arabidopsis thaliana is a useful model to address this. It has a stem cell niche near its tip conformed of a quiescent organizer and stem or initial cells around it, then a proliferation domain followed by a transition domain, where cells diminish division rate before transiting to the elongation zone; here, cells grow anisotropically prior to their final differentiation towards the plant base. A minimal model of the gene regulatory network that underlies cell-fate specification and patterning at the root stem cell niche was proposed before. In this study, we update and couple such network with both the auxin and cytokinin hormone signaling pathways to address how they collectively give rise to attractors that correspond to the genetic and hormonal activity profiles that are characteristic of different cell types along A. thaliana root apical meristem. We used a Boolean model of the genetic-hormonal regulatory network to integrate known and predicted regulatory interactions into alternative models. Our analyses show that, after adding some putative missing interactions, the model includes the necessary and sufficient components and regulatory interactions to recover attractors characteristic of the root cell types, including the auxin and cytokinin activity profiles that correlate with different cellular behaviors along the root apical meristem. Furthermore, the model predicts the existence of activity configurations that could correspond to the transition domain. The model also provides a possible explanation for apparently paradoxical cellular behaviors in the root meristem. For example, how auxin may induce and at the same time inhibit WOX5 expression. According to the model proposed here the hormonal regulation of WOX5 might depend on the cell type. Our results illustrate how non-linear multi-stable qualitative network models can aid at understanding how transcriptional regulators and hormonal signaling pathways are dynamically coupled and may underlie both the acquisition of cell fate and the emergence of hormonal activity profiles that arise during complex organ development.
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Affiliation(s)
- Mónica L. García-Gómez
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Eugenio Azpeitia
- INRIA project-team Virtual Plants, joint with CIRAD and INRA, Montpellier, France
| | - Elena R. Álvarez-Buylla
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
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33
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Babiychuk E, Hoang KT, Vandepoele K, Van De Slijke E, Geelen D, De Jaeger G, Obokata J, Kushnir S. The mutation nrpb1-A325V in the largest subunit of RNA polymerase II suppresses compromised growth of Arabidopsis plants deficient in a function of the general transcription factor IIF. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:730-745. [PMID: 27862530 DOI: 10.1111/tpj.13417] [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: 08/18/2016] [Accepted: 10/31/2016] [Indexed: 06/06/2023]
Abstract
The evolutionarily conserved 12-subunit RNA polymerase II (Pol II) is a central catalytic component that drives RNA synthesis during the transcription cycle that consists of transcription initiation, elongation, and termination. A diverse set of general transcription factors, including a multifunctional TFIIF, govern Pol II selectivity, kinetic properties, and transcription coupling with posttranscriptional processes. Here, we show that TFIIF of Arabidopsis (Arabidopsis thaliana) resembles the metazoan complex that is composed of the TFIIFα and TFIIFβ polypeptides. Arabidopsis has two TFIIFβ subunits, of which TFIIFβ1/MAN1 is essential and TFIIFβ2/MAN2 is not. In the partial loss-of-function mutant allele man1-1, the winged helix domain of Arabidopsis TFIIFβ1/MAN1 was dispensable for plant viability, whereas the cellular organization of the shoot and root apical meristems were abnormal. Forward genetic screening identified an epistatic interaction between the largest Pol II subunit nrpb1-A325V variant and the man1-1 mutation. The suppression of the man1-1 mutant developmental defects by a mutation in Pol II suggests a link between TFIIF functions in Arabidopsis transcription cycle and the maintenance of cellular organization in the shoot and root apical meristems.
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Affiliation(s)
- Elena Babiychuk
- Vale Institute of Technology Sustainable Development, 66055-090, Belém, Pará, Brazil
| | - Khai Trinh Hoang
- Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium
- Department of Agriculture and Applied Sciences, Can Tho Technical Economic College, Can Tho, Vietnam
| | - Klaas Vandepoele
- Department of Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - Eveline Van De Slijke
- Department of Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - Danny Geelen
- Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - Junichi Obokata
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, 606-8522, Japan
| | - Sergei Kushnir
- Vale Institute of Technology Sustainable Development, 66055-090, Belém, Pará, Brazil
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34
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Pillitteri LJ, Guo X, Dong J. Asymmetric cell division in plants: mechanisms of symmetry breaking and cell fate determination. Cell Mol Life Sci 2016; 73:4213-4229. [PMID: 27286799 PMCID: PMC5522748 DOI: 10.1007/s00018-016-2290-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 06/02/2016] [Accepted: 06/02/2016] [Indexed: 02/07/2023]
Abstract
Asymmetric cell division is a fundamental mechanism that generates cell diversity while maintaining self-renewing stem cell populations in multicellular organisms. Both intrinsic and extrinsic mechanisms underpin symmetry breaking and differential daughter cell fate determination in animals and plants. The emerging picture suggests that plants deal with the problem of symmetry breaking using unique cell polarity proteins, mobile transcription factors, and cell wall components to influence asymmetric divisions and cell fate. There is a clear role for altered auxin distribution and signaling in distinguishing two daughter cells and an emerging role for epigenetic modifications through chromatin remodelers and DNA methylation in plant cell differentiation. The importance of asymmetric cell division in determining final plant form provides the impetus for its study in the areas of both basic and applied science.
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Affiliation(s)
- Lynn Jo Pillitteri
- Department of Biology, Western Washington University, Bellingham, WA, 98225, USA
| | - Xiaoyu Guo
- Waksman Institute of Microbiology, Rutgers the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Juan Dong
- Waksman Institute of Microbiology, Rutgers the State University of New Jersey, Piscataway, NJ, 08854, USA.
- Department of Plant Biology and Pathology, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA.
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35
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Rahni R, Efroni I, Birnbaum KD. A Case for Distributed Control of Local Stem Cell Behavior in Plants. Dev Cell 2016; 38:635-42. [PMID: 27676436 PMCID: PMC5076558 DOI: 10.1016/j.devcel.2016.08.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/11/2016] [Accepted: 08/26/2016] [Indexed: 12/11/2022]
Abstract
The root meristem has a centrally located group of mitotically quiescent cells, to which current models assign a stem cell organizer function. However, evidence is emerging for decentralized control of stem cell activity, whereby self-renewing behavior emerges from the lack of cell displacement at the border of opposing differentiation gradients. We term this a "stagnation" model due to its reliance on passive mechanics. The position of stem cells is established by two opposing axes that reciprocally control each other's differentiation. Such broad tissue organization programs would allow plants, like some animal systems, to rapidly reconstitute stem cells from non-stem-cell tissues.
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Affiliation(s)
- Ramin Rahni
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Idan Efroni
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University, Rehovot 76100, Israel
| | - Kenneth D Birnbaum
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA.
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36
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Abstract
Single-cell transcriptomics has been employed in a growing number of animal studies, but the technique has yet to be widely used in plants. Nonetheless, early studies indicate that single-cell RNA-seq protocols developed for animal cells produce informative datasets in plants. We argue that single-cell transcriptomics has the potential to provide a new perspective on plant problems, such as the nature of the stem cells or initials, the plasticity of plant cells, and the extent of localized cellular responses to environmental inputs. Single-cell experimental outputs require different analytical approaches compared with pooled cell profiles and new tools tailored to single-cell assays are being developed. Here, we highlight promising new single-cell profiling approaches, their limitations as applied to plants, and their potential to address fundamental questions in plant biology.
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Affiliation(s)
- Idan Efroni
- The Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA.,Present address: The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University, Rehovot, 76100, Israel
| | - Kenneth D Birnbaum
- The Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA.
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37
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Fisher AP, Sozzani R. Uncovering the networks involved in stem cell maintenance and asymmetric cell division in the Arabidopsis root. CURRENT OPINION IN PLANT BIOLOGY 2016; 29:38-43. [PMID: 26707611 DOI: 10.1016/j.pbi.2015.11.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 11/02/2015] [Accepted: 11/04/2015] [Indexed: 06/05/2023]
Abstract
Stem cells are the source of different cell types and tissues in all multicellular organisms. In plants, the balance between stem cell self-renewal and differentiation of their progeny is crucial for correct tissue and organ formation. How transcriptional programs precisely control stem cell maintenance and identity, and what are the regulatory programs influencing stem cell asymmetric cell division (ACD), are key questions that researchers have sought to address for the past decade. Successful efforts in genetic, molecular, and developmental biology, along with mathematical modeling, have identified some of the players involved in stem cell regulation. In this review, we will discuss several studies that characterized many of the genetic programs and molecular mechanisms regulating stem cell ACD and their identity in the Arabidopsis root. We will also highlight how the growing use of mathematical modeling provides a comprehensive and quantitative perspective on the design rules governing stem cell ACDs.
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Affiliation(s)
- Adam P Fisher
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States.
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38
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Wei Z, Li J. Brassinosteroids Regulate Root Growth, Development, and Symbiosis. MOLECULAR PLANT 2016; 9:86-100. [PMID: 26700030 DOI: 10.1016/j.molp.2015.12.003] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 10/29/2015] [Accepted: 12/07/2015] [Indexed: 05/19/2023]
Abstract
Brassinosteroids (BRs) are natural plant hormones critical for growth and development. BR deficient or signaling mutants show significantly shortened root phenotypes. However, for a long time, it was thought that these phenotypes were solely caused by reduced cell elongation in the mutant roots. Functions of BRs in regulating root development have been largely neglected. Nonetheless, recent detailed analyses, revealed that BRs are not only involved in root cell elongation but are also involved in many aspects of root development, such as maintenance of meristem size, root hair formation, lateral root initiation, gravitropic response, mycorrhiza formation, and nodulation in legume species. In this review, current findings on the functions of BRs in mediating root growth, development, and symbiosis are discussed.
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Affiliation(s)
- Zhuoyun Wei
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jia Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
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39
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Gaillochet C, Lohmann JU. The never-ending story: from pluripotency to plant developmental plasticity. Development 2015; 142:2237-49. [PMID: 26130755 PMCID: PMC4510588 DOI: 10.1242/dev.117614] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Plants are sessile organisms, some of which can live for over a thousand years. Unlike most animals, plants employ a post-embryonic mode of development driven by the continuous activity of pluripotent stem cells. Consequently, plants are able to initiate new organs over extended periods of time, and many species can readily replace lost body structures by de novo organogenesis. Classical studies have also shown that plant tissues have a remarkable capacity to undergo de-differentiation and proliferation in vitro, highlighting the fact that plant cell fate is highly plastic. This suggests that the mechanisms regulating fate transitions must be continuously active in most plant cells and that the control of cellular pluripotency lies at the core of diverse developmental programs. Here, we review how pluripotency is established in plant stem cell systems, how it is maintained during development and growth and re-initiated during regeneration, and how these mechanisms eventually contribute to the amazing developmental plasticity of plants.
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Affiliation(s)
- Christophe Gaillochet
- Department of Stem Cell Biology, Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
| | - Jan U Lohmann
- Department of Stem Cell Biology, Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
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40
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Kumpf RP, Nowack MK. The root cap: a short story of life and death. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5651-62. [PMID: 26068468 DOI: 10.1093/jxb/erv295] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Over 130 years ago, Charles Darwin recognized that sensory functions in the root tip influence directional root growth. Modern plant biology has unravelled that many of the functions that Darwin attributed to the root tip are actually accomplished by a particular organ-the root cap. The root cap surrounds and protects the meristematic stem cells at the growing root tip. Due to this vanguard position, the root cap is predisposed to receive and transmit environmental information to the root proper. In contrast to other plant organs, the root cap shows a rapid turnover of short-lived cells regulated by an intricate balance of cell generation, differentiation, and degeneration. Thanks to these particular features, the root cap is an excellent developmental model system, in which generation, differentiation, and degeneration of cells can be investigated in a conveniently compact spatial and temporal frame. In this review, we give an overview of the current knowledge and concepts of root cap biology, focusing on the model plant Arabidopsis thaliana.
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Affiliation(s)
- Robert P Kumpf
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Moritz K Nowack
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
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41
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Boyer F, Simon R. Asymmetric cell divisions constructing Arabidopsis stem cell niches: the emerging role of protein phosphatases. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:935-45. [PMID: 26012742 DOI: 10.1111/plb.12352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/18/2015] [Indexed: 05/07/2023]
Abstract
Plant stem cell niches (SCNs) can be maintained in time through asymmetric cell divisions (ACDs) that allow the production of new cell types while constantly renewing the pools of stem cells (SCs). ACDs in plants require the asymmetric distribution of molecular components inside the cells as well as external asymmetric positional information. These two types of asymmetric information are controlled by inter- and intracellular signalling events. Phosphorylation of proteins is a major intermediate step in these signalling events, serving either as an activator or repressor of signalling, via fast auto- and trans-phosphorylation mechanisms. Whereas protein kinases, which phosphorylate proteins on serine, threonine or tyrosine residues, have been thoroughly studied, less attention has been given to protein phosphatases, which de-phosphorylate their protein targets on these same residues. Phosphatases modulate the activity of signalling pathways by balancing the action of kinases, and are therefore critical in the regulation of ACDs in plants. In this review, we first present the different types of ACDs that operate during Arabidopsis embryonic and post-embryonic development and participate in the construction and maintenance of its root and shoot SCNs; we then give a brief description of the main protein phosphatases so far described in the Arabidopsis genome; and finally discuss their functions toward the regulation of the ACDs introduced in the first part of the paper.
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Affiliation(s)
- F Boyer
- Institute of Developmental Genetics, Heinrich Heine University, Düsseldorf, Germany
| | - R Simon
- Institute of Developmental Genetics, Heinrich Heine University, Düsseldorf, Germany
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42
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Richards S, Wink RH, Simon R. Mathematical modelling of WOX5- and CLE40-mediated columella stem cell homeostasis in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5375-84. [PMID: 26019259 PMCID: PMC4526915 DOI: 10.1093/jxb/erv257] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The root meristem of Arabidopsis thaliana harbours a pool of stem cells, which divide to give rise to the differentiated cells of the various root tissues. Regulatory networks of inter-cellular signalling molecules control the homeostasis of stem cell number and position so that both stem and differentiated cells are consistently available. This work focuses on the transcription factor WUSCHEL-RELATED HOMEOBOX 5 (WOX5), the signalling peptide CLAVATA3/EMBRYO-SURROUNDING REGION 40 (CLE40) and the feedback loops involving them, which maintain the columella stem cells (CSCs). WOX5 signals from the quiescent centre (QC) to promote stem cell fate, while CLE40 is secreted from the differentiated columella cells (CCs) to promote differentiation. Our analyses of mathematical models of this network show that, when cell fate is controlled primarily by antagonistic factors, homeostasis requires a spatial component and inter-cellular signalling. We have also found that WOX5 contributes to, but is not absolutely necessary for, CSC maintenance. Furthermore, our modelling led us to postulate an additional signalling molecule that promotes CSC maintenance. We propose that this WOX5-independent signal originates in the QC, is targeted by CLE40 signalling and is capable of maintaining CSCs.
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Affiliation(s)
- Sarah Richards
- Institute of Developmental Genetics, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Rene H Wink
- Institute of Developmental Genetics, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Rüdiger Simon
- Institute of Developmental Genetics, Heinrich Heine University, 40225 Düsseldorf, Germany
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43
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Meyer MR, Shah S, Zhang J, Rohrs H, Rao AG. Evidence for intermolecular interactions between the intracellular domains of the arabidopsis receptor-like kinase ACR4, its homologs and the Wox5 transcription factor. PLoS One 2015; 10:e0118861. [PMID: 25756623 PMCID: PMC4355418 DOI: 10.1371/journal.pone.0118861] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/07/2015] [Indexed: 11/23/2022] Open
Abstract
Arabidopsis CRINKLY4 (ACR4) is a receptor-like kinase (RLK) involved in the global development of the plant. The Arabidopsis genome encodes four homologs of ACR4 that contain sequence similarity and analogous architectural elements to ACR4, termed Arabidopsis CRINKLY4 Related (AtCRRs) proteins. Additionally, a signaling module has been previously proposed including a postulated peptide ligand, CLE40, the ACR4 RLK, and the WOX5 transcription factor that engage in a possible feedback mechanism controlling stem cell differentiation. However, little biochemical evidence is available to ascertain the molecular aspects of receptor heterodimerization and the role of phosphorylation in these interactions. Therefore, we have undertaken an investigation of the in vitro interactions between the intracellular domains (ICD) of ACR4, the CRRs and WOX5. We demonstrate that interaction can occur between ACR4 and all four CRRs in the unphosphorylated state. However, phosphorylation dependency is observed for the interaction between ACR4 and CRR3. Furthermore, sequence analysis of the ACR4 gene family has revealed a conserved ‘KDSAF’ motif that may be involved in protein-protein interactions among the receptor family. We demonstrate that peptides harboring this conserved motif in CRR3 and CRK1are able to bind to the ACR4 kinase domain. Our investigations also indicate that the ACR4 ICD can interact with and phosphorylate the transcription factor WOX5.
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Affiliation(s)
- Matthew R. Meyer
- Department of Medicine, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO 63130, United States of America
| | - Shweta Shah
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States of America
| | - J. Zhang
- NIH NCRR Center for Biomedical and Bio-Organic Mass Spectrometry, Dept. of Chemistry, Washington University, St. Louis, MO 63130, United States of America
| | - Henry Rohrs
- NIH NCRR Center for Biomedical and Bio-Organic Mass Spectrometry, Dept. of Chemistry, Washington University, St. Louis, MO 63130, United States of America
| | - A. Gururaj Rao
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States of America
- * E-mail:
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44
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Hong JH, Chu H, Zhang C, Ghosh D, Gong X, Xu J. A quantitative analysis of stem cell homeostasis in the Arabidopsis columella root cap. FRONTIERS IN PLANT SCIENCE 2015; 6:206. [PMID: 25870608 PMCID: PMC4375977 DOI: 10.3389/fpls.2015.00206] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/15/2015] [Indexed: 05/20/2023]
Abstract
The Lugol's staining method has been widely used to detect changes in the maintenance of stem cell fate in the columella root cap of Arabidopsis roots since the late 1990s. However, various limitations of this method demand for additional or complementary new approaches. For instance, it is unable to reveal the division rate of columella root cap stem cells. Here we report that, by labeling dividing stem cells with 5-ethynyl-2'-deoxyuridine (EdU), the number and distribution of their labeled progeny can be studied so that the division rate of stem cells can be measured quantitatively and in addition, that the progression of stem cell progeny differentiation can be assessed in combination with Lugol's staining. EdU staining takes few hours and visualization of the stain characteristics of columella root cap can be performed easily under confocal microscopes. This simple technology, when used together with Lugol's staining, provides a novel quantitative method to study the dynamics of stem cell behavior that govern homeostasis in the Arabidopsis columella root cap.
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Affiliation(s)
- Jing Han Hong
- Department of Biological Sciences, National University of Singapore, Singapore
- NUS Centre for BioImaging Sciences, National University of Singapore, Singapore
| | - Huangwei Chu
- Department of Biological Sciences, National University of Singapore, Singapore
- NUS Centre for BioImaging Sciences, National University of Singapore, Singapore
| | - Chen Zhang
- Department of Biological Sciences, National University of Singapore, Singapore
- NUS Centre for BioImaging Sciences, National University of Singapore, Singapore
| | - Dipanjana Ghosh
- Department of Biological Sciences, National University of Singapore, Singapore
- NUS Centre for BioImaging Sciences, National University of Singapore, Singapore
| | - Ximing Gong
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Jian Xu
- Department of Biological Sciences, National University of Singapore, Singapore
- NUS Centre for BioImaging Sciences, National University of Singapore, Singapore
- *Correspondence: Jian Xu, Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
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45
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Drisch RC, Stahl Y. Function and regulation of transcription factors involved in root apical meristem and stem cell maintenance. FRONTIERS IN PLANT SCIENCE 2015; 6:505. [PMID: 26217359 PMCID: PMC4491714 DOI: 10.3389/fpls.2015.00505] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 06/23/2015] [Indexed: 05/20/2023]
Abstract
Plant roots are essential for overall plant development, growth, and performance by providing anchorage in the soil and uptake of nutrients and water. The primary root of higher plants derives from a group of pluripotent, mitotically active stem cells residing in the root apical meristem (RAM) which provides the basis for growth, development, and regeneration of the root. The stem cells in the Arabidopsis thaliana RAM are surrounding the quiescent center (QC), which consists of a group of rarely dividing cells. The QC maintains the stem cells in a non-cell-autonomous manner and prevents them from differentiation. The necessary dynamic but also tight regulation of the transition from stem cell fate to differentiation most likely requires complex regulatory mechanisms to integrate external and internal cues. Transcription factors play a central role in root development and are regulated by phytohormones, small signaling molecules, and miRNAs. In this review we give a comprehensive overview about the function and regulation of specific transcription factors controlling stem cell fate and root apical meristem maintenance and discuss the possibility of TF complex formation, subcellular translocations and cell-to-cell movement functioning as another level of regulation.
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Affiliation(s)
| | - Yvonne Stahl
- *Correspondence: Yvonne Stahl, Institute for Developmental Genetics, Heinrich-Heine-University, Universitätsstrasse 1, Düsseldorf, NRW, Germany,
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