101
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Denyer T, Timmermans MCP. High-throughput single-cell RNA sequencing. TRENDS IN PLANT SCIENCE 2022; 27:104-105. [PMID: 34598882 DOI: 10.1016/j.tplants.2021.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Tom Denyer
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Marja C P Timmermans
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany.
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102
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Sanden NC, Schulz A. Identification of new proteins in mature sieve elements. PHYSIOLOGIA PLANTARUM 2022; 174:e13634. [PMID: 35060148 DOI: 10.1111/ppl.13634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
The phloem enables vascular plants to transport photoassimilates from source tissues to heterotrophic sink tissues. In the phloem, unbroken strings of enucleated sieve elements, which lose the majority of their cellular contents upon maturation, provide a low resistance path for mass flow. The protein machinery in mature sieve elements performs vital functions to maintain the flow, transmit systemic signals and defend the sugar stream against pests. However, our knowledge of this particular protein population is very limited since mature sieve elements are difficult to isolate and not amenable to transcriptomic analysis due to their enucleate nature. Here, we used co-expression analysis and published gene clusters from transcriptomic studies to generate a list of sieve element proteins that potentially survive the enucleation process to reside in mature sieve elements. We selected seven candidates and show that they all localize in sieve elements in Arabidopsis roots and six of them in bolting stems. Our results support the idea that nascent sieve elements prior to enucleation translate part of the protein machinery found in mature sieve elements. Our co-expression list and the publicly available gene clusters expressed in late proto- and meta-phloem sieve elements are valuable resources for uncharacterized genes that may function in mature sieve elements.
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Affiliation(s)
- Niels Christian Sanden
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- Section for Transport biology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Alexander Schulz
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- Section for Transport biology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
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103
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Verslues PE, Longkumer T. Size and activity of the root meristem: A key for drought resistance and a key model of drought-related signaling. PHYSIOLOGIA PLANTARUM 2022; 174:e13622. [PMID: 34988997 DOI: 10.1111/ppl.13622] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/17/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
Plants make many adjustments to their growth and development in response to even small changes in water availability. Under such conditions, root elongation can be actively restricted by stress-related signaling mechanisms. Here we look at how the Arabidopsis thaliana root meristem can be affected by moderate water limitation (low water potential, ψw ). Recent characterization of the clade E Growth-Regulating (EGR) protein phosphatases and Microtubule Associated Stress Protein 1 (MASP1) provides an example of how active restriction of root meristem size allows the plant to downregulate root elongation during low ψw stress. EGR2 protein accumulation in cortex cells of the transition zone at the distal end of the root meristem illustrates how the balance of cell division versus cell expansion signals at this critical location can determine meristem size and root elongation during low ψw . These characteristics of EGRs also raise the question of whether they may also be involved in hydrotropism, and, more broadly, whether hydrotropism is a distinct response or a specific manifestation of more general mechanisms used to adjust root growth under moderate severity low ψw whether or not a gradient of water availability is present. These questions, as well as a better understanding of how specific cell layers (cortex and endodermis) seem to have an outsized role in growth regulation and better understanding the roles of plasma membrane-based signaling and polar-localized proteins in the regulation of root meristem size and cell division activity are key to elucidating the cellular mechanisms that determine root growth behavior during soil drying.
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Affiliation(s)
- Paul E Verslues
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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104
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Roszak P, Heo JO, Blob B, Toyokura K, Sugiyama Y, de Luis Balaguer MA, Lau WWY, Hamey F, Cirrone J, Madej E, Bouatta AM, Wang X, Guichard M, Ursache R, Tavares H, Verstaen K, Wendrich J, Melnyk CW, Oda Y, Shasha D, Ahnert SE, Saeys Y, De Rybel B, Heidstra R, Scheres B, Grossmann G, Mähönen AP, Denninger P, Göttgens B, Sozzani R, Birnbaum KD, Helariutta Y. Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization. Science 2021; 374:eaba5531. [PMID: 34941412 PMCID: PMC8730638 DOI: 10.1126/science.aba5531] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In the plant meristem, tissue-wide maturation gradients are coordinated with specialized cell networks to establish various developmental phases required for indeterminate growth. Here, we used single-cell transcriptomics to reconstruct the protophloem developmental trajectory from the birth of cell progenitors to terminal differentiation in the Arabidopsis thaliana root. PHLOEM EARLY DNA-BINDING-WITH-ONE-FINGER (PEAR) transcription factors mediate lineage bifurcation by activating guanosine triphosphatase signaling and prime a transcriptional differentiation program. This program is initially repressed by a meristem-wide gradient of PLETHORA transcription factors. Only the dissipation of PLETHORA gradient permits activation of the differentiation program that involves mutual inhibition of early versus late meristem regulators. Thus, for phloem development, broad maturation gradients interface with cell-type-specific transcriptional regulators to stage cellular differentiation.
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Affiliation(s)
- Pawel Roszak
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Jung-Ok Heo
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Institute of Biotechnology, HiLIFE/Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Bernhard Blob
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Koichi Toyokura
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
- Faculty of Science and Engineering, Konan University, Kobe, Japan
- GRA&GREEN Inc., Incubation Facility, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Yuki Sugiyama
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
| | | | - Winnie W Y Lau
- Wellcome Trust and MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK
| | - Fiona Hamey
- Wellcome Trust and MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK
| | - Jacopo Cirrone
- Computer Science Department, Courant Institute for Mathematical Sciences, New York University, New York, NY, USA
| | - Ewelina Madej
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Alida M Bouatta
- Plant Systems Biology, Technical University of Munich, Freising, Germany
| | - Xin Wang
- Institute of Biotechnology, HiLIFE/Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Marjorie Guichard
- Institute of Cell and Interaction Biology, CEPLAS, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Robertas Ursache
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Hugo Tavares
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Bioinformatics Training Facility, Department of Genetics, University of Cambridge, Cambridge, UK
| | - Kevin Verstaen
- Data Mining and Modelling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Jos Wendrich
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Charles W Melnyk
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Yoshihisa Oda
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
- Department of Genetics, the Graduate University for Advanced Studies, SOKENDAI, Mishima, Japan
| | - Dennis Shasha
- Computer Science Department, Courant Institute for Mathematical Sciences, New York University, New York, NY, USA
| | - Sebastian E Ahnert
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- The Alan Turing Institute, British Library, London, UK
| | - Yvan Saeys
- Data Mining and Modelling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Renze Heidstra
- Department of Plant Sciences, Wageningen University and Research, Wageningen, Netherlands
| | - Ben Scheres
- Department of Plant Sciences, Wageningen University and Research, Wageningen, Netherlands
- Rijk Zwaan R&D, 4793 Fijnaart, Netherlands
| | - Guido Grossmann
- Institute of Cell and Interaction Biology, CEPLAS, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Ari Pekka Mähönen
- Institute of Biotechnology, HiLIFE/Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Philipp Denninger
- Plant Systems Biology, Technical University of Munich, Freising, Germany
| | - Berthold Göttgens
- Wellcome Trust and MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK
| | - Rosangela Sozzani
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, USA
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Yrjö Helariutta
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Institute of Biotechnology, HiLIFE/Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
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105
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Graeff M, Rana S, Wendrich JR, Dorier J, Eekhout T, Aliaga Fandino AC, Guex N, Bassel GW, De Rybel B, Hardtke CS. A single-cell morpho-transcriptomic map of brassinosteroid action in the Arabidopsis root. MOLECULAR PLANT 2021; 14:1985-1999. [PMID: 34358681 PMCID: PMC8674818 DOI: 10.1016/j.molp.2021.07.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/03/2021] [Accepted: 07/29/2021] [Indexed: 05/05/2023]
Abstract
The effects of brassinosteroid signaling on shoot and root development have been characterized in great detail but a simple consistent positive or negative impact on a basic cellular parameter was not identified. In this study, we combined digital 3D single-cell shape analysis and single-cell mRNA sequencing to characterize root meristems and mature root segments of brassinosteroid-blind mutants and wild type. The resultant datasets demonstrate that brassinosteroid signaling affects neither cell volume nor cell proliferation capacity. Instead, brassinosteroid signaling is essential for the precise orientation of cell division planes and the extent and timing of anisotropic cell expansion. Moreover, we found that the cell-aligning effects of brassinosteroid signaling can propagate to normalize the anatomy of both adjacent and distant brassinosteroid-blind cells through non-cell-autonomous functions, which are sufficient to restore growth vigor. Finally, single-cell transcriptome data discern directly brassinosteroid-responsive genes from genes that can react non-cell-autonomously and highlight arabinogalactans as sentinels of brassinosteroid-dependent anisotropic cell expansion.
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Affiliation(s)
- Moritz Graeff
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Surbhi Rana
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Jos R Wendrich
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9000 Ghent, Belgium
| | - Julien Dorier
- Bioinformatics Competence Center, University of Lausanne, Genopode Building, 1015 Lausanne, Switzerland
| | - Thomas Eekhout
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9000 Ghent, Belgium
| | - Ana Cecilia Aliaga Fandino
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Genopode Building, 1015 Lausanne, Switzerland
| | - George W Bassel
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK
| | - Bert De Rybel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9000 Ghent, Belgium
| | - Christian S Hardtke
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland.
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106
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Kim JY, Loo EPI, Pang TY, Lercher M, Frommer WB, Wudick MM. Cellular export of sugars and amino acids: role in feeding other cells and organisms. PLANT PHYSIOLOGY 2021; 187:1893-1914. [PMID: 34015139 PMCID: PMC8644676 DOI: 10.1093/plphys/kiab228] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/29/2021] [Indexed: 05/20/2023]
Abstract
Sucrose, hexoses, and raffinose play key roles in the plant metabolism. Sucrose and raffinose, produced by photosynthesis, are translocated from leaves to flowers, developing seeds and roots. Translocation occurs in the sieve elements or sieve tubes of angiosperms. But how is sucrose loaded into and unloaded from the sieve elements? There seem to be two principal routes: one through plasmodesmata and one via the apoplasm. The best-studied transporters are the H+/SUCROSE TRANSPORTERs (SUTs) in the sieve element-companion cell complex. Sucrose is delivered to SUTs by SWEET sugar uniporters that release these key metabolites into the apoplasmic space. The H+/amino acid permeases and the UmamiT amino acid transporters are hypothesized to play analogous roles as the SUT-SWEET pair to transport amino acids. SWEETs and UmamiTs also act in many other important processes-for example, seed filling, nectar secretion, and pollen nutrition. We present information on cell type-specific enrichment of SWEET and UmamiT family members and propose several members to play redundant roles in the efflux of sucrose and amino acids across different cell types in the leaf. Pathogens hijack SWEETs and thus represent a major susceptibility of the plant. Here, we provide an update on the status of research on intercellular and long-distance translocation of key metabolites such as sucrose and amino acids, communication of the plants with the root microbiota via root exudates, discuss the existence of transporters for other important metabolites and provide potential perspectives that may direct future research activities.
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Affiliation(s)
- Ji-Yun Kim
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Eliza P -I Loo
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Tin Yau Pang
- Institute for Computer Science and Department of Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Martin Lercher
- Institute for Computer Science and Department of Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Wolf B Frommer
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Michael M Wudick
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Author for communication:
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107
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DeMott L, Oblessuc PR, Pierce A, Student J, Melotto M. Spatiotemporal regulation of JAZ4 expression and splicing contribute to ethylene- and auxin-mediated responses in Arabidopsis roots. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1266-1282. [PMID: 34562337 DOI: 10.1111/tpj.15508] [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: 12/28/2020] [Revised: 08/26/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Jasmonic acid (JA) signaling controls several processes related to plant growth, development, and defense, which are modulated by the transcription regulator and receptor JASMONATE-ZIM DOMAIN (JAZ) proteins. We recently discovered that a member of the JAZ family, JAZ4, has a prominent function in canonical JA signaling as well as other mechanisms. Here, we discovered the existence of two naturally occurring splice variants (SVs) of JAZ4 in planta, JAZ4.1 and JAZ4.2, and employed biochemical and pharmacological approaches to determine protein stability and repression capability of these SVs within JA signaling. We then utilized quantitative and qualitative transcriptional studies to determine spatiotemporal expression and splicing patterns in vivo, which revealed developmental-, tissue-, and organ-specific regulation. Detailed phenotypic and expression analyses suggest a role of JAZ4 in ethylene (ET) and auxin signaling pathways differentially within the zones of root development in seedlings. These results support a model in which JAZ4 functions as a negative regulator of ET signaling and auxin signaling in root tissues above the apex. However, in the root apex JAZ4 functions as a positive regulator of auxin signaling possibly independently of ET. Collectively, our data provide insight into the complexity of spatiotemporal regulation of JAZ4 and how this impacts hormone signaling specificity and diversity in Arabidopsis roots.
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Affiliation(s)
- Logan DeMott
- Department of Plant Sciences, University of California, Davis, CA, USA
- Plant Pathology Graduate Group, University of California, Davis, CA, USA
| | - Paula R Oblessuc
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Alice Pierce
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Joseph Student
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Maeli Melotto
- Department of Plant Sciences, University of California, Davis, CA, USA
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108
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Xie J, Dawwam GE, Sehim AE, Li X, Wu J, Chen S, Zhang D. Drought Stress Triggers Shifts in the Root Microbial Community and Alters Functional Categories in the Microbial Gene Pool. Front Microbiol 2021; 12:744897. [PMID: 34745045 PMCID: PMC8566882 DOI: 10.3389/fmicb.2021.744897] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Abstract
Drought is a major threat to crop productivity and causes decreased plant growth, poor yields, and crop failure. Nevertheless, the frequency of droughts is expected to increase in the coming decades. The microbial communities associated with crop plants can influence how plants respond to various stresses; hence, microbiome manipulation is fast becoming an effective strategy for improving the stress tolerance of plants. The effect of drought stress on the root microbiome of perennial woody plants is currently poorly understood. Using Populus trees as a model ecosystem, we found that the diversity of the root microbial community decreased during drought treatment and that compositional shifts in microbes during drought stress were driven by the relative abundances of a large number of dominant phyla, including Actinobacteria, Firmicutes, and Proteobacteria. A subset of microbes, including Streptomyces rochei, Bacillus arbutinivorans, B. endophyticus, B. megaterium, Aspergillus terreus, Penicillium raperi, Trichoderma ghanense, Gongronella butleri, and Rhizopus stolonifer, was isolated from the drought-treated poplar rhizosphere soils, which have potentially beneficial to plant fitness. Further controlled inoculation experiments showed that the isolated bacterial and fungal isolates positively impacted plant growth and drought tolerance. Collectively, our results demonstrate the impact of drought on root microbiome structure and provide a novel example of manipulating root microbiomes to improve plant tolerance.
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Affiliation(s)
- Jianbo Xie
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Ghada E Dawwam
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Botany and Microbiology Department, Faculty of Science, Benha University, Benha, Egypt
| | - Amira E Sehim
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Botany and Microbiology Department, Faculty of Science, Benha University, Benha, Egypt
| | - Xian Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jiadong Wu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Sisi Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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109
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Villaécija-Aguilar JA, Körösy C, Maisch L, Hamon-Josse M, Petrich A, Magosch S, Chapman P, Bennett T, Gutjahr C. KAI2 promotes Arabidopsis root hair elongation at low external phosphate by controlling local accumulation of AUX1 and PIN2. Curr Biol 2021; 32:228-236.e3. [PMID: 34758285 DOI: 10.1016/j.cub.2021.10.044] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/17/2021] [Accepted: 10/20/2021] [Indexed: 11/30/2022]
Abstract
Root hair (RH) growth to increase the absorptive root surface area is a key adaptation of plants to limiting phosphate availability in soils. Despite the importance of this trait, especially for seedling survival, little is known about the molecular events connecting phosphate starvation sensing and RH growth regulation. KARRIKIN INSENSITIVE2 (KAI2), an α/β-hydrolase receptor of a yet-unknown plant hormone ("KAI2-ligand" [KL]), is required for RH elongation.1 KAI2 interacts with the F-box protein MORE AXILLIARY BRANCHING2 (MAX2) to target regulatory proteins of the SUPPRESSOR of MAX2 1 (SMAX1) family for degradation.2 Here, we demonstrate that Pi starvation increases KL signaling in Arabidopsis roots through transcriptional activation of KAI2 and MAX2. Both genes are required for RH elongation under these conditions, while smax1 smxl2 mutants have constitutively long RHs, even at high Pi availability. Attenuated RH elongation in kai2 mutants is explained by reduced shootward auxin transport from the root tip resulting in reduced auxin signaling in the RH zone, caused by an inability to increase localized accumulation of the auxin importer AUXIN TRANSPORTER PROTEIN1 (AUX1) and the auxin exporter PIN-FORMED2 (PIN2) upon Pi starvation. Consistent with AUX1 and PIN2 accumulation being mediated via ethylene signaling,3 expression of 1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE 7 (ACS7) is increased at low Pi in a KAI2-dependent manner, and treatment with an ethylene precursor restores RH elongation of acs7, but not of aux1 and pin2. Thus, KAI2 signaling is increased by phosphate starvation to trigger an ethylene- AUX1/PIN2-auxin cascade required for RH elongation.
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Affiliation(s)
- José Antonio Villaécija-Aguilar
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, 85354 Freising, Germany
| | - Caroline Körösy
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, 85354 Freising, Germany
| | - Lukas Maisch
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, 85354 Freising, Germany
| | - Maxime Hamon-Josse
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Andrea Petrich
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, 85354 Freising, Germany
| | - Sonja Magosch
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, 85354 Freising, Germany
| | - Philipp Chapman
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, 85354 Freising, Germany
| | - Tom Bennett
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Caroline Gutjahr
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, 85354 Freising, Germany.
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110
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Hawkins C, Ginzburg D, Zhao K, Dwyer W, Xue B, Xu A, Rice S, Cole B, Paley S, Karp P, Rhee SY. Plant Metabolic Network 15: A resource of genome-wide metabolism databases for 126 plants and algae. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1888-1905. [PMID: 34403192 DOI: 10.1111/jipb.13163] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/14/2021] [Indexed: 05/18/2023]
Abstract
To understand and engineer plant metabolism, we need a comprehensive and accurate annotation of all metabolic information across plant species. As a step towards this goal, we generated genome-scale metabolic pathway databases of 126 algal and plant genomes, ranging from model organisms to crops to medicinal plants (https://plantcyc.org). Of these, 104 have not been reported before. We systematically evaluated the quality of the databases, which revealed that our semi-automated validation pipeline dramatically improves the quality. We then compared the metabolic content across the 126 organisms using multiple correspondence analysis and found that Brassicaceae, Poaceae, and Chlorophyta appeared as metabolically distinct groups. To demonstrate the utility of this resource, we used recently published sorghum transcriptomics data to discover previously unreported trends of metabolism underlying drought tolerance. We also used single-cell transcriptomics data from the Arabidopsis root to infer cell type-specific metabolic pathways. This work shows the quality and quantity of our resource and demonstrates its wide-ranging utility in integrating metabolism with other areas of plant biology.
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Affiliation(s)
- Charles Hawkins
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Daniel Ginzburg
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Kangmei Zhao
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - William Dwyer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Bo Xue
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Angela Xu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Selena Rice
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Benjamin Cole
- DOE-Joint Genome Institute, Lawrence Berkeley Laboratory, Berkeley, California, 94720, USA
| | - Suzanne Paley
- SRI International, Menlo Park, California, 94025, USA
| | - Peter Karp
- SRI International, Menlo Park, California, 94025, USA
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
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111
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Yang B, Minne M, Brunoni F, Plačková L, Petřík I, Sun Y, Nolf J, Smet W, Verstaen K, Wendrich JR, Eekhout T, Hoyerová K, Van Isterdael G, Haustraete J, Bishopp A, Farcot E, Novák O, Saeys Y, De Rybel B. Non-cell autonomous and spatiotemporal signalling from a tissue organizer orchestrates root vascular development. NATURE PLANTS 2021; 7:1485-1494. [PMID: 34782768 PMCID: PMC7612341 DOI: 10.1038/s41477-021-01017-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 10/06/2021] [Indexed: 05/28/2023]
Abstract
During plant development, a precise balance of cytokinin is crucial for correct growth and patterning, but it remains unclear how this is achieved across different cell types and in the context of a growing organ. Here we show that in the root apical meristem, the TMO5/LHW complex increases active cytokinin levels via two cooperatively acting enzymes. By profiling the transcriptomic changes of increased cytokinin at single-cell level, we further show that this effect is counteracted by a tissue-specific increase in CYTOKININ OXIDASE 3 expression via direct activation of the mobile transcription factor SHORTROOT. In summary, we show that within the root meristem, xylem cells act as a local organizer of vascular development by non-autonomously regulating cytokinin levels in neighbouring procambium cells via sequential induction and repression modules.
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Affiliation(s)
- BaoJun Yang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
| | - Max Minne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Federica Brunoni
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Lenka Plačková
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Ivan Petřík
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Yanbiao Sun
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Jonah Nolf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Wouter Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Kevin Verstaen
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
- VIB Center for Inflammation Research, Data Mining and Modelling for Biomedicine, Ghent, Belgium
| | - Jos R Wendrich
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Klára Hoyerová
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic
| | - Gert Van Isterdael
- VIB Flow Core, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Jurgen Haustraete
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- VIB Protein Service Facility, VIB Center for Inflammation Research, Ghent, Belgium
| | - Anthony Bishopp
- School of Biosciences, University of Nottingham, Loughborough, UK
| | - Etienne Farcot
- School of Mathematical Sciences, University of Nottingham, Nottingham, UK
| | - Ondřej Novák
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Yvan Saeys
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
- VIB Center for Inflammation Research, Data Mining and Modelling for Biomedicine, Ghent, Belgium
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
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112
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Desvoyes B, Echevarría C, Gutierrez C. A perspective on cell proliferation kinetics in the root apical meristem. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6708-6715. [PMID: 34159378 PMCID: PMC8513163 DOI: 10.1093/jxb/erab303] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/22/2021] [Indexed: 06/13/2023]
Abstract
Organogenesis in plants is primarily postembryonic and relies on a strict balance between cell division and cell expansion. The root is a particularly well-suited model to study cell proliferation in detail since the two processes are spatially and temporally separated for all the different tissues. In addition, the root is amenable to detailed microscopic analysis to identify cells progressing through the cell cycle. While it is clear that cell proliferation activity is restricted to the root apical meristem (RAM), understanding cell proliferation kinetics and identifying its parameters have required much effort over many years. Here, we review the main concepts, experimental settings, and findings aimed at obtaining a detailed knowledge of how cells proliferate within the RAM. The combination of novel tools, experimental strategies, and mathematical models has contributed to our current view of cell proliferation in the RAM. We also discuss several lines of research that need to be explored in the future.
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Affiliation(s)
- Bénédicte Desvoyes
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Clara Echevarría
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
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113
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Shahan R, Nolan TM, Benfey PN. Single-cell analysis of cell identity in the Arabidopsis root apical meristem: insights and opportunities. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6679-6686. [PMID: 34018001 PMCID: PMC8513161 DOI: 10.1093/jxb/erab228] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/18/2021] [Indexed: 05/06/2023]
Abstract
A fundamental question in developmental biology is how the progeny of stem cells become differentiated tissues. The Arabidopsis root is a tractable model to address this question due to its simple organization and defined cell lineages. In particular, the zone of dividing cells at the root tip-the root apical meristem-presents an opportunity to map the gene regulatory networks underlying stem cell niche maintenance, tissue patterning, and cell identity acquisition. To identify molecular regulators of these processes, studies over the last 20 years employed global profiling of gene expression patterns. However, these technologies are prone to information loss due to averaging gene expression signatures over multiple cell types and/or developmental stages. Recently developed high-throughput methods to profile gene expression at single-cell resolution have been successfully applied to plants. Here, we review insights from the first published single-cell mRNA sequencing and chromatin accessibility datasets generated from Arabidopsis roots. These studies successfully reconstruct developmental trajectories, phenotype cell identity mutants at unprecedented resolution, and reveal cell type-specific responses to environmental stimuli. The experimental insight gained from Arabidopsis paves the way to profile roots from additional species.
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Affiliation(s)
- Rachel Shahan
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Trevor M Nolan
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Philip N Benfey
- Department of Biology, Duke University, Durham, NC 27708, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
- Correspondence:
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114
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Shojaee A, Saavedra M, Huang SSC. Potentials of single-cell genomics in deciphering cellular phenotypes. CURRENT OPINION IN PLANT BIOLOGY 2021; 63:102059. [PMID: 34116424 PMCID: PMC8545747 DOI: 10.1016/j.pbi.2021.102059] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/26/2021] [Accepted: 04/25/2021] [Indexed: 06/05/2023]
Abstract
Single-cell genomics, particularly single-cell transcriptome profiling by RNA sequencing have transformed the possibilities to relate genes to functions, structures, and eventually phenotypes. We can now observe changes in each cell's transcriptome and among its neighborhoods, interrogate the sequence of transcriptional events, and assess their influence on subsequent events. This paradigm shift in biology enables us to infer causal relationships in these events with high accuracy. Here we review the latest single-cell studies in plants that uncover how cellular phenotypes emerge as a result of the transcriptome process such as waves of expression, trajectories of development and responses to the environment, and spatial information. With an eye on the advances made in animal and human studies, we further highlight some of the needed areas for future research and development, including computational methods.
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Affiliation(s)
- Abbas Shojaee
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Pl, New York, NY 10003, United States
| | - Michelle Saavedra
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Pl, New York, NY 10003, United States
| | - Shao-Shan Carol Huang
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Pl, New York, NY 10003, United States.
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115
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Abstract
High-throughput single-cell transcriptomic approaches have revolutionized our view of gene expression at the level of individual cells, providing new insights into their heterogeneity, identities, and functions. Recently, technical challenges to the application of single-cell transcriptomics to plants have been overcome, and many plant organs and tissues have now been subjected to analyses at single-cell resolution. In this review, we describe these studies and their impact on our understanding of the diversity, differentiation, and activities of plant cells. We particularly highlight their impact on plant cell identity, including unprecedented views of cell transitions and definitions of rare and novel cell types. We also point out current challenges and future opportunities for the application and analyses of single-cell transcriptomics in plants. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Kook Hui Ryu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; , ,
| | - Yan Zhu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; , ,
| | - John Schiefelbein
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; , ,
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116
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Li H, Testerink C, Zhang Y. How roots and shoots communicate through stressful times. TRENDS IN PLANT SCIENCE 2021; 26:940-952. [PMID: 33896687 DOI: 10.1016/j.tplants.2021.03.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 02/19/2021] [Accepted: 03/16/2021] [Indexed: 05/06/2023]
Abstract
When plants face an environmental stress such as water deficit, soil salinity, high temperature, or shade, good communication between above- and belowground organs is necessary to coordinate growth and development. Various signals including hormones, peptides, proteins, hydraulic signals, and metabolites are transported mostly through the vasculature to distant tissues. How shoots and roots synchronize their response to stress using mobile signals is an emerging field of research. We summarize recent advances on mobile signals regulating shoot stomatal movement and root development in response to highly localized environmental cues. In addition, we highlight how the vascular system is not only a conduit but is also flexible in its development in response to abiotic stress.
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Affiliation(s)
- Hongfei Li
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Christa Testerink
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, 6708PB Wageningen, The Netherlands.
| | - Yanxia Zhang
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, 6708PB Wageningen, The Netherlands.
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117
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Phua SY, De Smet B, Remacle C, Chan KX, Van Breusegem F. Reactive oxygen species and organellar signaling. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5807-5824. [PMID: 34009340 DOI: 10.1093/jxb/erab218] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/14/2021] [Indexed: 05/07/2023]
Abstract
The evolution of photosynthesis and its associated metabolic pathways has been crucial to the successful establishment of plants, but has also challenged plant cells in the form of production of reactive oxygen species (ROS). Intriguingly, multiple forms of ROS are generated in virtually every plant cell compartment through diverse pathways. As a result, a sophisticated network of ROS detoxification and signaling that is simultaneously tailored to individual organelles and safeguards the entire cell is necessary. Here we take an organelle-centric view on the principal sources and sinks of ROS across the plant cell and provide insights into the ROS-induced organelle to nucleus retrograde signaling pathways needed for operational readjustments during environmental stresses.
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Affiliation(s)
- Su Yin Phua
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent,Belgium
- Center for Plant Systems Biology, VIB, Ghent,Belgium
| | - Barbara De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent,Belgium
- Center for Plant Systems Biology, VIB, Ghent,Belgium
| | - Claire Remacle
- Genetics and Physiology of Microalgae, InBios/Phytosystems, Université de Liège, Liège,Belgium
| | - Kai Xun Chan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent,Belgium
- Center for Plant Systems Biology, VIB, Ghent,Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent,Belgium
- Center for Plant Systems Biology, VIB, Ghent,Belgium
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118
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Abstract
Nutrients are vital to life through intertwined sensing, signaling, and metabolic processes. Emerging research focuses on how distinct nutrient signaling networks integrate and coordinate gene expression, metabolism, growth, and survival. We review the multifaceted roles of sugars, nitrate, and phosphate as essential plant nutrients in controlling complex molecular and cellular mechanisms of dynamic signaling networks. Key advances in central sugar and energy signaling mechanisms mediated by the evolutionarily conserved master regulators HEXOKINASE1 (HXK1), TARGET OF RAPAMYCIN (TOR), and SNF1-RELATED PROTEIN KINASE1 (SNRK1) are discussed. Significant progress in primary nitrate sensing, calcium signaling, transcriptome analysis, and root-shoot communication to shape plant biomass and architecture are elaborated. Discoveries on intracellular and extracellular phosphate signaling and the intimate connections with nitrate and sugar signaling are examined. This review highlights the dynamic nutrient, energy, growth, and stress signaling networks that orchestrate systemwide transcriptional, translational, and metabolic reprogramming, modulate growth and developmental programs, and respond to environmental cues. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Lei Li
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA; ,
| | - Kun-Hsiang Liu
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA; , .,State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, and Institute of Future Agriculture, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China
| | - Jen Sheen
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA; ,
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119
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Thibivilliers S, Libault M. Enhancing Our Understanding of Plant Cell-to-Cell Interactions Using Single-Cell Omics. FRONTIERS IN PLANT SCIENCE 2021; 12:696811. [PMID: 34421948 PMCID: PMC8375048 DOI: 10.3389/fpls.2021.696811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/07/2021] [Indexed: 05/05/2023]
Abstract
Plants are composed of cells that physically interact and constantly adapt to their environment. To reveal the contribution of each plant cells to the biology of the entire organism, their molecular, morphological, and physiological attributes must be quantified and analyzed in the context of the morphology of the plant organs. The emergence of single-cell/nucleus omics technologies now allows plant biologists to access different modalities of individual cells including their epigenome and transcriptome to reveal the unique molecular properties of each cell composing the plant and their dynamic regulation during cell differentiation and in response to their environment. In this manuscript, we provide a perspective regarding the challenges and strategies to collect plant single-cell biological datasets and their analysis in the context of cellular interactions. As an example, we provide an analysis of the transcriptional regulation of the Arabidopsis genes controlling the differentiation of the root hair cells at the single-cell level. We also discuss the perspective of the use of spatial profiling to complement existing plant single-cell omics.
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Affiliation(s)
| | - Marc Libault
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
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120
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Mochdia K, Tamaki S. Transcription Factor-Based Genetic Engineering in Microalgae. PLANTS 2021; 10:plants10081602. [PMID: 34451646 PMCID: PMC8399792 DOI: 10.3390/plants10081602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/16/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022]
Abstract
Sequence-specific DNA-binding transcription factors (TFs) are key components of gene regulatory networks. Advances in high-throughput sequencing have facilitated the rapid acquisition of whole genome assembly and TF repertoires in microalgal species. In this review, we summarize recent advances in gene discovery and functional analyses, especially for transcription factors in microalgal species. Specifically, we provide examples of the genome-scale identification of transcription factors in genome-sequenced microalgal species and showcase their application in the discovery of regulators involved in various cellular functions. Herein, we highlight TF-based genetic engineering as a promising framework for designing microalgal strains for microalgal-based bioproduction.
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Affiliation(s)
- Keiichi Mochdia
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama 244-0813, Japan
- RIKEN Baton Zone Program, Tsurumi-ku, Yokohama 230-0045, Japan;
- School of Information and Data Sciences, Nagasaki University, Bunkyo-machi, Nagasaki 852-8521, Japan
- Correspondence: ; Tel.: +81-045-503-9111
| | - Shun Tamaki
- RIKEN Baton Zone Program, Tsurumi-ku, Yokohama 230-0045, Japan;
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121
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Graeff M, Hardtke CS. Metaphloem development in the Arabidopsis root tip. Development 2021; 148:270791. [PMID: 34224570 DOI: 10.1242/dev.199766] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/29/2021] [Indexed: 11/20/2022]
Abstract
The phloem transport network is a major evolutionary innovation that enabled plants to dominate terrestrial ecosystems. In the growth apices, the meristems, apical stem cells continuously produce early 'protophloem'. This is easily observed in Arabidopsis root meristems, in which the differentiation of individual protophloem sieve element precursors into interconnected conducting sieve tubes is laid out in a spatio-temporal gradient. The mature protophloem eventually collapses as the neighboring metaphloem takes over its function further distal from the stem cell niche. Compared with protophloem, metaphloem ontogenesis is poorly characterized, primarily because its visualization is challenging. Here, we describe the improved TetSee protocol to investigate metaphloem development in Arabidopsis root tips in combination with a set of molecular markers. We found that mature metaphloem sieve elements are only observed in the late post-meristematic root, although their specification is initiated as soon as protophloem sieve elements enucleate. Moreover, unlike protophloem sieve elements, metaphloem sieve elements only differentiate once they have fully elongated. Finally, our results suggest that metaphloem differentiation is not directly controlled by protophloem-derived cues but rather follows a distinct, robust developmental trajectory.
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Affiliation(s)
- Moritz Graeff
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Christian S Hardtke
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
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122
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Gogolev YV, Ahmar S, Akpinar BA, Budak H, Kiryushkin AS, Gorshkov VY, Hensel G, Demchenko KN, Kovalchuk I, Mora-Poblete F, Muslu T, Tsers ID, Yadav NS, Korzun V. OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security. PLANTS (BASEL, SWITZERLAND) 2021; 10:1423. [PMID: 34371624 PMCID: PMC8309286 DOI: 10.3390/plants10071423] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022]
Abstract
The incredible success of crop breeding and agricultural innovation in the last century greatly contributed to the Green Revolution, which significantly increased yields and ensures food security, despite the population explosion. However, new challenges such as rapid climate change, deteriorating soil, and the accumulation of pollutants require much faster responses and more effective solutions that cannot be achieved through traditional breeding. Further prospects for increasing the efficiency of agriculture are undoubtedly associated with the inclusion in the breeding strategy of new knowledge obtained using high-throughput technologies and new tools in the future to ensure the design of new plant genomes and predict the desired phenotype. This article provides an overview of the current state of research in these areas, as well as the study of soil and plant microbiomes, and the prospective use of their potential in a new field of microbiome engineering. In terms of genomic and phenomic predictions, we also propose an integrated approach that combines high-density genotyping and high-throughput phenotyping techniques, which can improve the prediction accuracy of quantitative traits in crop species.
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Affiliation(s)
- Yuri V. Gogolev
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russia;
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile; (S.A.); (F.M.-P.)
| | | | - Hikmet Budak
- Montana BioAg Inc., Missoula, MT 59802, USA; (B.A.A.); (H.B.)
| | - Alexey S. Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (A.S.K.); (K.N.D.)
| | - Vladimir Y. Gorshkov
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russia;
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, 40225 Dusseldorf, Germany;
- Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, 78371 Olomouc, Czech Republic
| | - Kirill N. Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (A.S.K.); (K.N.D.)
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; (I.K.); (N.S.Y.)
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile; (S.A.); (F.M.-P.)
| | - Tugdem Muslu
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey;
| | - Ivan D. Tsers
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Narendra Singh Yadav
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; (I.K.); (N.S.Y.)
| | - Viktor Korzun
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
- KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37555 Einbeck, Germany
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Tripathi RK, Wilkins O. Single cell gene regulatory networks in plants: Opportunities for enhancing climate change stress resilience. PLANT, CELL & ENVIRONMENT 2021; 44:2006-2017. [PMID: 33522607 PMCID: PMC8359182 DOI: 10.1111/pce.14012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 05/05/2023]
Abstract
Global warming poses major challenges for plant survival and agricultural productivity. Thus, efforts to enhance stress resilience in plants are key strategies for protecting food security. Gene regulatory networks (GRNs) are a critical mechanism conferring stress resilience. Until recently, predicting GRNs of the individual cells that make up plants and other multicellular organisms was impeded by aggregate population scale measurements of transcriptome and other genome-scale features. With the advancement of high-throughput single cell RNA-seq and other single cell assays, learning GRNs for individual cells is now possible, in principle. In this article, we report on recent advances in experimental and analytical methodologies for single cell sequencing assays especially as they have been applied to the study of plants. We highlight recent advances and ongoing challenges for scGRN prediction, and finally, we highlight the opportunity to use scGRN discovery for studying and ultimately enhancing abiotic stress resilience in plants.
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Affiliation(s)
- Rajiv K. Tripathi
- Department of Biological SciencesUniversity of ManitobaWinnipegManitobaCanada
| | - Olivia Wilkins
- Department of Biological SciencesUniversity of ManitobaWinnipegManitobaCanada
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124
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Wang Y, Huan Q, Li K, Qian W. Single-cell transcriptome atlas of the leaf and root of rice seedlings. J Genet Genomics 2021; 48:881-898. [PMID: 34340913 DOI: 10.1016/j.jgg.2021.06.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/14/2022]
Abstract
As a multicellular organism, rice flourishes relying on gene expression diversity among cells of various functions. However, cellular-resolution transcriptome features are yet to be fully recognized, let alone cell-specific transcriptional responses to environmental stimuli. In this study, we apply single-cell RNA sequencing to both shoot and root of rice seedlings growing in Kimura B nutrient solution or exposed to various abiotic stresses and characterize transcriptomes for a total of 237,431 individual cells. We identify 15 and nine cell types in the leaf and root, respectively, and observe that common transcriptome features are often shared between leaves and roots in the same tissue layer, except for endodermis or epidermis. Abiotic stress stimuli alter gene expression largely in a cell type-specific manner, but for a given cell type, different stresses often trigger transcriptional regulation of roughly the same set of genes. Besides, we detect proportional changes in cell populations in response to abiotic stress and investigate the underlying molecular mechanisms through single-cell reconstruction of the developmental trajectory. Collectively, our study represents a benchmark-setting data resource of single-cell transcriptome atlas for rice seedlings and an illustration of exploiting such resources to drive discoveries in plant biology.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing Huan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Ke Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenfeng Qian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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125
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Seyfferth C, Renema J, Wendrich JR, Eekhout T, Seurinck R, Vandamme N, Blob B, Saeys Y, Helariutta Y, Birnbaum KD, De Rybel B. Advances and Opportunities in Single-Cell Transcriptomics for Plant Research. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:847-866. [PMID: 33730513 PMCID: PMC7611048 DOI: 10.1146/annurev-arplant-081720-010120] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Single-cell approaches are quickly changing our view on biological systems by increasing the spatiotemporal resolution of our analyses to the level of the individual cell. The field of plant biology has fully embraced single-cell transcriptomics and is rapidly expanding the portfolio of available technologies and applications. In this review, we give an overview of the main advances in plant single-cell transcriptomics over the past few years and provide the reader with an accessible guideline covering all steps, from sample preparation to data analysis. We end by offering a glimpse of how these technologies will shape and accelerate plant-specific research in the near future.
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Affiliation(s)
- Carolin Seyfferth
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jim Renema
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jos R Wendrich
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Ruth Seurinck
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, 9052 Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium
| | - Niels Vandamme
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, 9052 Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium
| | - Bernhard Blob
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
- Viikki Plant Science Centre, HiLIFE/Organismal and Evolutionary Biology Research Program, Institute of Biotechnology, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Yvan Saeys
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, 9052 Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium
| | - Yrjo Helariutta
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
- Viikki Plant Science Centre, HiLIFE/Organismal and Evolutionary Biology Research Program, Institute of Biotechnology, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA;
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
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126
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Lhamo D, Luan S. Potential Networks of Nitrogen-Phosphorus-Potassium Channels and Transporters in Arabidopsis Roots at a Single Cell Resolution. FRONTIERS IN PLANT SCIENCE 2021; 12:689545. [PMID: 34220911 PMCID: PMC8242960 DOI: 10.3389/fpls.2021.689545] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/24/2021] [Indexed: 05/08/2023]
Abstract
Nitrogen (N), phosphorus (P), and potassium (K) are three major macronutrients essential for plant life. These nutrients are acquired and transported by several large families of transporters expressed in plant roots. However, it remains largely unknown how these transporters are distributed in different cell-types that work together to transfer the nutrients from the soil to different layers of root cells and eventually reach vasculature for massive flow. Using the single cell transcriptomics data from Arabidopsis roots, we profiled the transcriptional patterns of putative nutrient transporters in different root cell-types. Such analyses identified a number of uncharacterized NPK transporters expressed in the root epidermis to mediate NPK uptake and distribution to the adjacent cells. Some transport genes showed cortex- and endodermis-specific expression to direct the nutrient flow toward the vasculature. For long-distance transport, a variety of transporters were shown to express and potentially function in the xylem and phloem. In the context of subcellular distribution of mineral nutrients, the NPK transporters at subcellular compartments were often found to show ubiquitous expression patterns, which suggests function in house-keeping processes. Overall, these single cell transcriptomic analyses provide working models of nutrient transport from the epidermis across the cortex to the vasculature, which can be further tested experimentally in the future.
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Affiliation(s)
- Dhondup Lhamo
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
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127
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Gross A, Tiwari S, Shtein I, Erel R. Direct foliar uptake of phosphorus from desert dust. THE NEW PHYTOLOGIST 2021; 230:2213-2225. [PMID: 33721337 DOI: 10.1111/nph.17344] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/09/2021] [Indexed: 05/02/2023]
Abstract
Phosphorus (P) scarcity constrains plant growth in many ecosystems worldwide. In P-poor ecosystems, the biogeochemical paradigm links plant productivity with the deposition of P-rich dust originating from desert storms. However, dust P usually has low bioavailability and is thought to be utilized solely via roots. We applied desert dust on the leaf surface of P-deficient and P-sufficient wheat, chickpea and maize to test the feasibility of direct foliar uptake of dust-P and investigate its related acquisition mechanisms. Foliar dust doubled the growth of P-deficient chickpea and wheat, crops originating near the Syrian Desert. P deficiency stimulated several leaf modifications that enabled acquisition of up to 30% of the sparingly soluble dust-P that is conventionally perceived as unavailable. These modifications increased foliar dust capture, acidified the leaf surface and, in chickpea, enhanced exudation of P-solubilizing organic acids. Maize (originating far from deserts) displayed only a marginal response to dust. The dramatic response of chickpea and wheat in comparison to maize suggests that plants that evolved in dust-rich ecosystems adopted specialized utilization strategies. Interestingly, the abovementioned foliar responses are comparable to known P uptake root responses. Given that P limitation is almost universal, a foliar P uptake pathway will have significant ecological and agricultural implications.
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Affiliation(s)
- Avner Gross
- Department of Geography and Environmental Development, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Sudeep Tiwari
- Department of Geography and Environmental Development, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
- Institute of Soil, Water and Environmental Sciences, Gilat Research Center, Agricultural Research Organization, 85820, Israel
| | - Ilana Shtein
- Eastern Region Research and Development Center, Ariel, 40700, Israel
| | - Ran Erel
- Institute of Soil, Water and Environmental Sciences, Gilat Research Center, Agricultural Research Organization, 85820, Israel
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128
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Perotti MF, Arce AL, Chan RL. The underground life of homeodomain-leucine zipper transcription factors. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4005-4021. [PMID: 33713412 DOI: 10.1093/jxb/erab112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
Roots are the anchorage organs of plants, responsible for water and nutrient uptake, exhibiting high plasticity. Root architecture is driven by the interactions of biomolecules, including transcription factors and hormones that are crucial players regulating root plasticity. Multiple transcription factor families are involved in root development; some, such as ARFs and LBDs, have been well characterized, whereas others remain less well investigated. In this review, we synthesize the current knowledge about the involvement of the large family of homeodomain-leucine zipper (HD-Zip) transcription factors in root development. This family is divided into four subfamilies (I-IV), mainly according to structural features, such as additional motifs aside from HD-Zip, as well as their size, gene structure, and expression patterns. We explored and analyzed public databases and the scientific literature regarding HD-Zip transcription factors in Arabidopsis and other species. Most members of the four HD-Zip subfamilies are expressed in specific cell types and several individuals from each group have assigned functions in root development. Notably, a high proportion of the studied proteins are part of intricate regulation pathways involved in primary and lateral root growth and development.
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Affiliation(s)
- María Florencia Perotti
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, FBCB, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe,Argentina
| | - Agustín Lucas Arce
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, FBCB, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe,Argentina
| | - Raquel Lía Chan
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, FBCB, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe,Argentina
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129
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Ke Y, Podio M, Conner J, Ozias-Akins P. Single-cell transcriptome profiling of buffelgrass (Cenchrus ciliaris) eggs unveils apomictic parthenogenesis signatures. Sci Rep 2021; 11:9880. [PMID: 33972603 PMCID: PMC8110759 DOI: 10.1038/s41598-021-89170-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/15/2021] [Indexed: 12/04/2022] Open
Abstract
Apomixis, a type of asexual reproduction in angiosperms, results in progenies that are genetically identical to the mother plant. It is a highly desirable trait in agriculture due to its potential to preserve heterosis of F1 hybrids through subsequent generations. However, no major crops are apomictic. Deciphering mechanisms underlying apomixis becomes one of the alternatives to engineer self-reproducing capability into major crops. Parthenogenesis, a major component of apomixis, commonly described as the ability to initiate embryo formation from the egg cell without fertilization, also can be valuable in plant breeding for doubled haploid production. A deeper understanding of transcriptional differences between parthenogenetic and sexual or non-parthenogenetic eggs can assist with pathway engineering. By conducting laser capture microdissection-based RNA-seq on sexual and parthenogenetic egg cells on the day of anthesis, a de novo transcriptome for the Cenchrus ciliaris egg cells was created, transcriptional profiles that distinguish the parthenogenetic egg from its sexual counterpart were identified, and functional roles for a few transcription factors in promoting natural parthenogenesis were suggested. These transcriptome data expand upon previous gene expression studies and will be a resource for future research on the transcriptome of egg cells in parthenogenetic and sexual genotypes.
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Affiliation(s)
- Yuji Ke
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA, 31793, USA
| | - Maricel Podio
- Department of Horticulture, University of Georgia, Tifton, GA, 31793, USA
| | - Joann Conner
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA, 31793, USA.,Department of Horticulture, University of Georgia, Tifton, GA, 31793, USA
| | - Peggy Ozias-Akins
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA, 31793, USA. .,Department of Horticulture, University of Georgia, Tifton, GA, 31793, USA.
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130
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Eckardt NA. Sweeter than SWEET: a single-cell leaf vasculature transcriptome atlas. THE PLANT CELL 2021; 33:445-446. [PMID: 33793847 PMCID: PMC8136873 DOI: 10.1093/plcell/koaa059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
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131
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Kim JY, Symeonidi E, Pang TY, Denyer T, Weidauer D, Bezrutczyk M, Miras M, Zöllner N, Hartwig T, Wudick MM, Lercher M, Chen LQ, Timmermans MCP, Frommer WB. Distinct identities of leaf phloem cells revealed by single cell transcriptomics. THE PLANT CELL 2021; 33:511-530. [PMID: 33955487 PMCID: PMC8136902 DOI: 10.1093/plcell/koaa060] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/18/2020] [Indexed: 05/20/2023]
Abstract
The leaf vasculature plays a key role in solute translocation. Veins consist of at least seven distinct cell types, with specific roles in transport, metabolism, and signaling. Little is known about leaf vascular cells, in particular the phloem parenchyma (PP). PP effluxes sucrose into the apoplasm as a basis for phloem loading, yet PP has been characterized only microscopically. Here, we enriched vascular cells from Arabidopsis leaves to generate a single-cell transcriptome atlas of leaf vasculature. We identified at least 19 cell clusters, encompassing epidermis, guard cells, hydathodes, mesophyll, and all vascular cell types, and used metabolic pathway analysis to define their roles. Clusters comprising PP cells were enriched for transporters, including SWEET11 and SWEET12 sucrose and UmamiT amino acid efflux carriers. We provide evidence that PP development occurs independently from ALTERED PHLOEM DEVELOPMENT, a transcription factor required for phloem differentiation. PP cells have a unique pattern of amino acid metabolism activity distinct from companion cells (CCs), explaining differential distribution/metabolism of amino acids in veins. The kinship relation of the vascular clusters is strikingly similar to the vein morphology, except for a clear separation of CC from the other vascular cells including PP. In summary, our single-cell RNA-sequencing analysis provides a wide range of information into the leaf vasculature and the role and relationship of the leaf cell types.
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Affiliation(s)
- Ji-Yun Kim
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Author for correspondence: (W.B.F.), (J.-Y.K.)
| | - Efthymia Symeonidi
- Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
| | - Tin Yau Pang
- Institute for Computer Science and Department of Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Tom Denyer
- Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
| | - Diana Weidauer
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Margaret Bezrutczyk
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Manuel Miras
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Nora Zöllner
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Thomas Hartwig
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Michael M Wudick
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Martin Lercher
- Institute for Computer Science and Department of Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Li-Qing Chen
- Department of Plant Biology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Marja C P Timmermans
- Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
| | - Wolf B Frommer
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan
- Author for correspondence: (W.B.F.), (J.-Y.K.)
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132
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Holbein J, Shen D, Andersen TG. The endodermal passage cell - just another brick in the wall? THE NEW PHYTOLOGIST 2021; 230:1321-1328. [PMID: 33438208 DOI: 10.1111/nph.17182] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
The endodermis surrounds and protects the vasculature partly by depositing hydrophobic suberin in the cell walls. Yet, some cells remain unsuberised. These historically termed 'passage cells' are assumed to provide a low-resistance pathway to the xylem. Only recently have we started to gain molecular insights into these cells, which allow us to probe how roots coordinate communication with the environment across barriers with single-cell precision. Increased understanding of root physiology at a high-resolution is intriguing, as it is likely to provide us with new tools to improve overall plant health. With this in mind, we here provide a brief overview of passage cells, their presence across plant species, as well as a molecular update and future directions for passage cell-related research.
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Affiliation(s)
- Julia Holbein
- Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Defeng Shen
- Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
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133
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Shi D, Jouannet V, Agustí J, Kaul V, Levitsky V, Sanchez P, Mironova VV, Greb T. Tissue-specific transcriptome profiling of the Arabidopsis inflorescence stem reveals local cellular signatures. THE PLANT CELL 2021; 33:200-223. [PMID: 33582756 PMCID: PMC8136906 DOI: 10.1093/plcell/koaa019] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/02/2020] [Indexed: 05/06/2023]
Abstract
Genome-wide gene expression maps with a high spatial resolution have substantially accelerated plant molecular science. However, the number of characterized tissues and growth stages is still small due to the limited accessibility of most tissues for protoplast isolation. Here, we provide gene expression profiles of the mature inflorescence stem of Arabidopsis thaliana covering a comprehensive set of distinct tissues. By combining fluorescence-activated nucleus sorting and laser-capture microdissection with next-generation RNA sequencing, we characterized the transcriptomes of xylem vessels, fibers, the proximal and distal cambium, phloem, phloem cap, pith, starch sheath, and epidermis cells. Our analyses classified more than 15,000 genes as being differentially expressed among different stem tissues and revealed known and novel tissue-specific cellular signatures. By determining overrepresented transcription factor binding regions in the promoters of differentially expressed genes, we identified candidate tissue-specific transcriptional regulators. Our datasets predict the expression profiles of an exceptional number of genes and allow hypotheses to be generated about the spatial organization of physiological processes. Moreover, we demonstrate that information about gene expression in a broad range of mature plant tissues can be established at high spatial resolution by nuclear mRNA profiling. Tissue-specific gene expression values can be accessed online at https://arabidopsis-stem.cos.uni-heidelberg.de/.
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Affiliation(s)
- Dongbo Shi
- Department of Developmental Physiology, Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
- Japan Science and Technology Agency (JST), Saitama, Kawaguchi, Japan
| | - Virginie Jouannet
- Department of Developmental Physiology, Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Javier Agustí
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), C/Enginyer Fausto Elio S/N. 46011 Valencia, Spain
| | - Verena Kaul
- Department of Developmental Physiology, Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Victor Levitsky
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk, 630090, Russia
- Department of Systems Biology, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Pablo Sanchez
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Victoria V Mironova
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk, 630090, Russia
- Department of Systems Biology, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Thomas Greb
- Department of Developmental Physiology, Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
- Author for correspondence:
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134
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A single-cell analysis of the Arabidopsis vegetative shoot apex. Dev Cell 2021; 56:1056-1074.e8. [PMID: 33725481 DOI: 10.1016/j.devcel.2021.02.021] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 12/06/2020] [Accepted: 02/19/2021] [Indexed: 01/13/2023]
Abstract
The shoot apical meristem allows for reiterative formation of new aerial structures throughout the life cycle of a plant. We use single-cell RNA sequencing to define the cellular taxonomy of the Arabidopsis vegetative shoot apex at the transcriptome level. We find that the shoot apex is composed of highly heterogeneous cells, which can be partitioned into 7 broad populations with 23 transcriptionally distinct cell clusters. We delineate cell-cycle continuums and developmental trajectories of epidermal cells, vascular tissue, and leaf mesophyll cells and infer transcription factors and gene expression signatures associated with cell fate decisions. Integrative analysis of shoot and root apical cell populations further reveals common and distinct features of epidermal and vascular tissues. Our results, thus, offer a valuable resource for investigating the basic principles underlying cell division and differentiation in plants at single-cell resolution.
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135
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Long Y, Liu Z, Jia J, Mo W, Fang L, Lu D, Liu B, Zhang H, Chen W, Zhai J. FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants. Genome Biol 2021; 22:66. [PMID: 33608047 PMCID: PMC7893963 DOI: 10.1186/s13059-021-02288-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 02/03/2021] [Indexed: 12/17/2022] Open
Abstract
The broad application of single-cell RNA profiling in plants has been hindered by the prerequisite of protoplasting that requires digesting the cell walls from different types of plant tissues. Here, we present a protoplasting-free approach, flsnRNA-seq, for large-scale full-length RNA profiling at a single-nucleus level in plants using isolated nuclei. Combined with 10x Genomics and Nanopore long-read sequencing, we validate the robustness of this approach in Arabidopsis root cells and the developing endosperm. Sequencing results demonstrate that it allows for uncovering alternative splicing and polyadenylation-related RNA isoform information at the single-cell level, which facilitates characterizing cell identities.
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Affiliation(s)
- Yanping Long
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Zhijian Liu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jinbu Jia
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Weipeng Mo
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Liang Fang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Dongdong Lu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Bo Liu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Hong Zhang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Wei Chen
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jixian Zhai
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China.
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China.
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Shaw R, Tian X, Xu J. Single-Cell Transcriptome Analysis in Plants: Advances and Challenges. MOLECULAR PLANT 2021; 14:115-126. [PMID: 33152518 DOI: 10.1016/j.molp.2020.10.012] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/08/2020] [Accepted: 10/30/2020] [Indexed: 05/22/2023]
Abstract
The rapid and enthusiastic adoption of single-cell RNA sequencing (scRNA-seq) has demonstrated that this technology is far more than just another way to perform transcriptome analysis. It is not an exaggeration to say that the advent of scRNA-seq is revolutionizing the details of whole-transcriptome snapshots from a tissue to a cell. With this disruptive technology, it is now possible to mine heterogeneity between tissue types and within cells like never before. This enables more rapid identification of rare and novel cell types, simultaneous characterization of multiple different cell types and states, more accurate and integrated understanding of their roles in life processes, and more. However, we are only at the beginning of unlocking the full potential of scRNA-seq applications. This is particularly true for plant sciences, where single-cell transcriptome profiling is in its early stage and has many exciting challenges to overcome. In this review, we compare and evaluate recent pioneering studies using the Arabidopsis root model, which has established new paradigms for scRNA-seq studies in plants. We also explore several new and promising single-cell analysis tools that are available to those wishing to study plant development and physiology at unprecedented resolution and scale. In addition, we propose some future directions on the use of scRNA-seq technology to tackle some of the critical challenges in plant research and breeding.
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Affiliation(s)
- Rahul Shaw
- Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Xin Tian
- Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Jian Xu
- Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore.
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Nenadić M, Vermeer JEM. Dynamic cytokinin signalling landscapes during lateral root formation in Arabidopsis. QUANTITATIVE PLANT BIOLOGY 2021; 2:e13. [PMID: 37077210 PMCID: PMC10095801 DOI: 10.1017/qpb.2021.13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 10/04/2021] [Accepted: 10/20/2021] [Indexed: 05/03/2023]
Abstract
By forming lateral roots, plants expand their root systems to improve anchorage and absorb more water and nutrients from the soil. Each phase of this developmental process in Arabidopsis is tightly regulated by dynamic and continuous signalling of the phytohormones cytokinin and auxin. While the roles of auxin in lateral root organogenesis and spatial accommodation by overlying cell layers have been well studied, insights on the importance of cytokinin is still somewhat limited. Cytokinin is a negative regulator of lateral root formation with versatile modes of action being activated at different root developmental zones. Here, we review the latest progress made towards our understanding of these spatially separated mechanisms of cytokinin-mediated signalling that shape lateral root initiation, outgrowth and emergence and highlight some of the enticing open questions.
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Affiliation(s)
- Milica Nenadić
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Centre, University of Zurich, Zurich, Switzerland
| | - Joop E. M. Vermeer
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Centre, University of Zurich, Zurich, Switzerland
- Laboratory of Cell and Molecular Biology, University of Neuchâtel, Neuchâtel, Switzerland
- Author for correspondence: Joop E. M. Vermeer, E-mail:
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138
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Ma Z, Wang J, Li C, Ren P, Yao L, Li B, Meng Y, Ma X, Si E, Yang K, Shang X, Wang H. Global Profiling of Phosphorylation Reveals the Barley Roots Response to Phosphorus Starvation and Resupply. FRONTIERS IN PLANT SCIENCE 2021; 12:676432. [PMID: 34335649 PMCID: PMC8317692 DOI: 10.3389/fpls.2021.676432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/09/2021] [Indexed: 05/04/2023]
Abstract
Phosphorus (P) deficiency is a major threat to the crop production, and for understanding the response mechanism of plant roots, P stress may facilitate the development of crops with increased tolerance. Phosphorylation plays a critical role in the regulation of proteins for plant responses to biotic and abiotic stress; however, its functions in P starvation/resupply are largely unknown for barley (Hordeum vulgare) growth. Here, we performed a global review of phosphorylation in barley roots treated by P starvation/resupply. We identified 7,710 phosphorylation sites on 3,373 proteins, of which 76 types of conserved motifs were extracted from 10,428 phosphorylated peptides. Most phosphorylated proteins were located in the nucleus (36%) and chloroplast (32%). Compared with the control, 186 and 131 phosphorylated proteins under P starvation condition and 156 and 111 phosphorylated proteins under P resupply condition showed significant differences at 6 and 48 h, respectively. These proteins mainly participated in carbohydrate metabolism, phytohormones, signal transduction, cell wall stress, and oxidases stress. Moreover, the pathways of the ribosome, RNA binding, protein transport, and metal binding were significantly enriched under P starvation, and only two pathways of ribosome and RNA binding were greatly enriched under Pi resupply according to the protein-protein interaction analysis. The results suggested that the phosphorylation proteins might play important roles in the metabolic processes of barley roots in response to Pi deficiency/resupply. The data not only provide unique access to phosphorylation reprogramming of plant roots under deficiency/resupply but also demonstrate the close cooperation between these phosphorylation proteins and key metabolic functions.
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Affiliation(s)
- Zengke Ma
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Juncheng Wang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Chengdao Li
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Panrong Ren
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Lirong Yao
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Baochun Li
- Department of Botany, College of Life Sciences and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yaxiong Meng
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xiaole Ma
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Erjing Si
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Ke Yang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xunwu Shang
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Huajun Wang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Huajun Wang
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Yu F, Wang S, Zhang W, Wang H, Yu L, Fei Z, Li J. An R2R3-type myeloblastosis transcription factor MYB103 is involved in phosphorus remobilization. FOOD PRODUCTION, PROCESSING AND NUTRITION 2020. [DOI: 10.1186/s43014-020-00038-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
The members of myeloblastosis transcription factor (MYB TF) family are involved in the regulation of biotic and abiotic stresses in plants. However, the role of MYB TF in phosphorus remobilization remains largely unexplored. In the present study, we show that an R2R3 type MYB transcription factor, MYB103, is involved in phosphorus (P) remobilization. MYB103 was remarkably induced by P deficiency in cabbage (Brassica oleracea var. capitata L.). As cabbage lacks the proper mutant for elucidating the mechanism of MYB103 in P deficiency, another member of the crucifer family, Arabidopsis thaliana was chosen for further study. The transcript of its homologue AtMYB103 was also elevated in response to P deficiency in A. thaliana, while disruption of AtMYB103 (myb103) exhibited increased sensitivity to P deficiency, accompanied with decreased tissue biomass and soluble P concentration. Furthermore, AtMYB103 was involved in the P reutilization from cell wall, as less P was released from the cell wall in myb103 than in wildtype, coinciding with the reduction of ethylene production. Taken together, our results uncover an important role of MYB103 in the P remobilization, presumably through ethylene signaling.
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Zlotorynski E. The secret of increased (root) hair density. Nat Rev Mol Cell Biol 2020; 21:657. [PMID: 32994551 DOI: 10.1038/s41580-020-00302-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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