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Motte H, Parizot B, Xuan W, Chen Q, Maere S, Bensmihen S, Beeckman T. Interspecies co-expression analysis of lateral root development using inducible systems in rice, Medicago, and Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1052-1063. [PMID: 37793018 DOI: 10.1111/tpj.16481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/30/2023] [Accepted: 09/13/2023] [Indexed: 10/06/2023]
Abstract
Lateral roots are crucial for plant growth and development, making them an important target for research aiming to improve crop yields and food security. However, their endogenous ontogeny and, as it were, stochastic appearance challenge their study. Lateral Root Inducible Systems (LRIS) can be used to overcome these challenges by inducing lateral roots massively and synchronously. The combination of LRISs with transcriptomic approaches significantly advanced our insights in the molecular control of lateral root formation, in particular for Arabidopsis. Despite this success, LRISs have been underutilized for other plant species or for lateral root developmental stages later than the initiation. In this study, we developed and/or adapted LRISs in rice, Medicago, and Arabidopsis to perform RNA-sequencing during time courses that cover different developmental stages of lateral root formation and primordium development. As such, our study provides three extensive datasets of gene expression profiles during lateral root development in three different plant species. The three LRISs are highly effective but timing and spatial distribution of lateral root induction vary among the species. Detailed characterization of the stages in time and space in the respective species enabled an interspecies co-expression analysis to identify conserved players involved in lateral root development, as illustrated for the AUX/IAA and LBD gene families. Overall, our results provide a valuable resource to identify potentially conserved regulatory mechanisms in lateral root development, and as such will contribute to a better understanding of the complex regulatory network underlying lateral root development.
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Affiliation(s)
- Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Boris Parizot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Wei Xuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qian Chen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Steven Maere
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Sandra Bensmihen
- INRAE, CNRS, LIPME, Université de Toulouse, F-31326, Castanet-Tolosan, France
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
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2
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Otero S, Gildea I, Roszak P, Lu Y, Di Vittori V, Bourdon M, Kalmbach L, Blob B, Heo JO, Peruzzo F, Laux T, Fernie AR, Tavares H, Helariutta Y. A root phloem pole cell atlas reveals common transcriptional states in protophloem-adjacent cells. NATURE PLANTS 2022; 8:954-970. [PMID: 35927456 DOI: 10.1038/s41477-022-01178-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Single-cell sequencing has recently allowed the generation of exhaustive root cell atlases. However, some cell types are elusive and remain underrepresented. Here we use a second-generation single-cell approach, where we zoom in on the root transcriptome sorting with specific markers to profile the phloem poles at an unprecedented resolution. Our data highlight the similarities among the developmental trajectories and gene regulatory networks common to protophloem sieve element (PSE)-adjacent lineages in relation to PSE enucleation, a key event in phloem biology. As a signature for early PSE-adjacent lineages, we have identified a set of DNA-binding with one finger (DOF) transcription factors, the PINEAPPLEs (PAPL), that act downstream of PHLOEM EARLY DOF (PEAR) genes and are important to guarantee a proper root nutrition in the transition to autotrophy. Our data provide a holistic view of the phloem poles that act as a functional unit in root development.
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Affiliation(s)
- Sofia Otero
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Iris Gildea
- 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
- Department of Plant Biology and Genome Center, University of California, Davis, CA, USA
| | - Pawel Roszak
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Yipeng Lu
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Valerio Di Vittori
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Matthieu Bourdon
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Lothar Kalmbach
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Bernhard Blob
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Jung-Ok Heo
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | | | - Thomas Laux
- Signalling Research Centres BIOSS and CIBSS, Freiburg, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Hugo Tavares
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
| | - Yka 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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3
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Gala HP, Lanctot A, Jean-Baptiste K, Guiziou S, Chu JC, Zemke JE, George W, Queitsch C, Cuperus JT, Nemhauser JL. A single-cell view of the transcriptome during lateral root initiation in Arabidopsis thaliana. THE PLANT CELL 2021; 33:2197-2220. [PMID: 33822225 PMCID: PMC8364244 DOI: 10.1093/plcell/koab101] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/31/2021] [Indexed: 05/20/2023]
Abstract
Root architecture is a major determinant of plant fitness and is under constant modification in response to favorable and unfavorable environmental stimuli. Beyond impacts on the primary root, the environment can alter the position, spacing, density, and length of secondary or lateral roots. Lateral root development is among the best-studied examples of plant organogenesis, yet there are still many unanswered questions about its earliest steps. Among the challenges faced in capturing these first molecular events is the fact that this process occurs in a small number of cells with unpredictable timing. Single-cell sequencing methods afford the opportunity to isolate the specific transcriptional changes occurring in cells undergoing this fate transition. Using this approach, we successfully captured the transcriptomes of initiating lateral root primordia in Arabidopsis thaliana and discovered many upregulated genes associated with this process. We developed a method to selectively repress target gene transcription in the xylem pole pericycle cells where lateral roots originate and demonstrated that the expression of several of these targets is required for normal root development. We also discovered subpopulations of cells in the pericycle and endodermal cell files that respond to lateral root initiation, highlighting the coordination across cell files required for this fate transition.
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Affiliation(s)
- Hardik P. Gala
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Amy Lanctot
- Department of Biology, University of Washington, Seattle, WA 98195, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Ken Jean-Baptiste
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Sarah Guiziou
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Jonah C. Chu
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Joseph E. Zemke
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Wesley George
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Josh T. Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Author for correspondence: (J.T.C.); (J.L.N.)
| | - Jennifer L. Nemhauser
- Department of Biology, University of Washington, Seattle, WA 98195, USA
- Author for correspondence: (J.T.C.); (J.L.N.)
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4
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Rich-Griffin C, Eichmann R, Reitz MU, Hermann S, Woolley-Allen K, Brown PE, Wiwatdirekkul K, Esteban E, Pasha A, Kogel KH, Provart NJ, Ott S, Schäfer P. Regulation of Cell Type-Specific Immunity Networks in Arabidopsis Roots. THE PLANT CELL 2020; 32:2742-2762. [PMID: 32699170 PMCID: PMC7474276 DOI: 10.1105/tpc.20.00154] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/07/2020] [Accepted: 07/20/2020] [Indexed: 05/04/2023]
Abstract
While root diseases are among the most devastating stresses in global crop production, our understanding of root immunity is still limited relative to our knowledge of immune responses in leaves. Considering that root performance is based on the concerted functions of its different cell types, we undertook a cell type-specific transcriptome analysis to identify gene networks activated in epidermis, cortex, and pericycle cells of Arabidopsis (Arabidopsis thaliana) roots challenged with two immunity elicitors, the bacterial flagellin-derived flg22 and the endogenous Pep1 peptide. Our analyses revealed distinct immunity gene networks in each cell type. To further substantiate our understanding of regulatory patterns underlying these cell type-specific immunity networks, we developed a tool to analyze paired transcription factor binding motifs in the promoters of cell type-specific genes. Our study points toward a connection between cell identity and cell type-specific immunity networks that might guide cell types in launching immune response according to the functional capabilities of each cell type.
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Affiliation(s)
| | - Ruth Eichmann
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
- Institute of Molecular Botany, Ulm University, 89069 Ulm, Germany
| | - Marco U Reitz
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Sophie Hermann
- Institute of Phytopathology, Justus Liebig University, 35392 Giessen, Germany
| | | | - Paul E Brown
- Bioinformatics Research Technology Platform, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Kate Wiwatdirekkul
- Department of Computer Science, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Karl-Heinz Kogel
- Institute of Phytopathology, Justus Liebig University, 35392 Giessen, Germany
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Sascha Ott
- Department of Computer Science, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Patrick Schäfer
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
- Institute of Molecular Botany, Ulm University, 89069 Ulm, Germany
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
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5
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Guo N, Hu J, Yan M, Qu H, Luo L, Tegeder M, Xu G. Oryza sativa Lysine-Histidine-type Transporter 1 functions in root uptake and root-to-shoot allocation of amino acids in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:395-411. [PMID: 32159895 DOI: 10.1111/tpj.14742] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 02/02/2020] [Accepted: 02/11/2020] [Indexed: 05/03/2023]
Abstract
In agricultural soils, amino acids can represent vital nitrogen (N) sources for crop growth and yield. However, the molecular mechanisms underlying amino acid uptake and allocation are poorly understood in crop plants. This study shows that rice (Oryza sativa L.) roots can acquire aspartate at soil concentration, and that japonica subspecies take up this acidic amino acid 1.5-fold more efficiently than indica subspecies. Genetic association analyses with 68 representative japonica or indica germplasms identified rice Lysine-Histidine-type Transporter 1 (OsLHT1) as a candidate gene associated with the aspartate uptake trait. When expressed in yeast, OsLHT1 supported cell growth on a broad spectrum of amino acids, and effectively transported aspartate, asparagine and glutamate. OsLHT1 is localized throughout the rice root, including root hairs, epidermis, cortex and stele, and to the leaf vasculature. Knockout of OsLHT1 in japonica resulted in reduced root uptake of amino acids. Furthermore, in 15 N-amino acid-fed mutants versus wild-type, a higher percentage of 15 N remained in roots instead of being allocated to the shoot. 15 N-ammonium uptake and subsequently the delivery of root-synthesized amino acids to Oslht1 shoots were also significantly decreased, which was accompanied by reduced shoot growth. These results together provide evidence that OsLHT1 functions in both root uptake and root to shoot allocation of a broad spectrum of amino acids in rice.
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Affiliation(s)
- Nan Guo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Jinqi Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ming Yan
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
| | - Hongye Qu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
| | - Le Luo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mechthild Tegeder
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
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6
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Kortz A, Hochholdinger F, Yu P. Cell Type-Specific Transcriptomics of Lateral Root Formation and Plasticity. FRONTIERS IN PLANT SCIENCE 2019; 10:21. [PMID: 30809234 PMCID: PMC6379339 DOI: 10.3389/fpls.2019.00021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/08/2019] [Indexed: 05/25/2023]
Abstract
Lateral roots are a major determinant of root architecture and are instrumental for the efficient uptake of water and nutrients. Lateral roots consist of multiple cell types each expressing a unique transcriptome at a given developmental stage. Therefore, transcriptome analyses of complete lateral roots provide only average gene expression levels integrated over all cell types. Such analyses have the risk to mask genes, pathways and networks specifically expressed in a particular cell type during lateral root formation. Cell type-specific transcriptomics paves the way for a holistic understanding of the programming and re-programming of cells such as pericycle cells, involved in lateral root initiation. Recent discoveries have advanced the molecular understanding of the intrinsic genetic control of lateral root initiation and elongation. Moreover, the impact of nitrate availability on the transcriptional regulation of lateral root formation in Arabidopsis and cereals has been studied. In this review, we will focus on the systemic dissection of lateral root formation and its interaction with environmental nitrate through cell type-specific transcriptome analyses. These novel discoveries provide a better mechanistic understanding of postembryonic lateral root development in plants.
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Affiliation(s)
| | | | - Peng Yu
- *Correspondence: Frank Hochholdinger, Peng Yu,
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7
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Motte H, Beeckman T. The evolution of root branching: increasing the level of plasticity. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:785-793. [PMID: 30481325 DOI: 10.1093/jxb/ery409] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/07/2018] [Indexed: 05/26/2023]
Abstract
Plant roots and root systems are indispensable for water and nutrient foraging, and are a major evolutionary achievement for plants to cope with dry land conditions. The ability of roots to branch contributes substantially to their capacity to explore the soil for water and nutrients, and led ~400 million years ago to the successful colonization of land by plants, eventually even in arid regions. During this colonization, different forms of root branching evolved, reinforcing step by step the phenotypic plasticity of the root system. Whereas the lycophytes, the most ancient land plants with roots, only branch at the root tip, ferns are able to form roots laterally in a fixed pattern along the main root. Finally, roots of seed plants show the highest phenotypic plasticity, because lateral roots can possibly, dependent on internal and/or external signals, be produced at almost any position along the main root. The competence to form lateral roots in seed plants is based on the presence of internal cell files with stem cell-like features. Despite the dissimilarities between the different clades, a number of genetic modules seem to be co-opted in order to acquire root branching capacity. In this review, starting from the lateral root pathways in seed plants, we review root branching in the different land plant lineages and discuss the hitherto described genetic modules that contribute to their root branching capacity. We try to obtain insight into how land plants have acquired an increasing root branching plasticity during evolution that contributed to the successful colonization of our planet by seed plants.
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Affiliation(s)
- Hans Motte
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Tom Beeckman
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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8
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Aubry E, Dinant S, Vilaine F, Bellini C, Le Hir R. Lateral Transport of Organic and Inorganic Solutes. PLANTS (BASEL, SWITZERLAND) 2019; 8:E20. [PMID: 30650538 PMCID: PMC6358943 DOI: 10.3390/plants8010020] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/10/2019] [Accepted: 01/11/2019] [Indexed: 12/20/2022]
Abstract
Organic (e.g., sugars and amino acids) and inorganic (e.g., K⁺, Na⁺, PO₄2-, and SO₄2-) solutes are transported long-distance throughout plants. Lateral movement of these compounds between the xylem and the phloem, and vice versa, has also been reported in several plant species since the 1930s, and is believed to be important in the overall resource allocation. Studies of Arabidopsis thaliana have provided us with a better knowledge of the anatomical framework in which the lateral transport takes place, and have highlighted the role of specialized vascular and perivascular cells as an interface for solute exchanges. Important breakthroughs have also been made, mainly in Arabidopsis, in identifying some of the proteins involved in the cell-to-cell translocation of solutes, most notably a range of plasma membrane transporters that act in different cell types. Finally, in the future, state-of-art imaging techniques should help to better characterize the lateral transport of these compounds on a cellular level. This review brings the lateral transport of sugars and inorganic solutes back into focus and highlights its importance in terms of our overall understanding of plant resource allocation.
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Affiliation(s)
- Emilie Aubry
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France.
| | - Sylvie Dinant
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France.
| | - Françoise Vilaine
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France.
| | - Catherine Bellini
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France.
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90183 Umeå, Sweden.
| | - Rozenn Le Hir
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France.
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9
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Liu C, Zhang C, Fan M, Ma W, Chen M, Cai F, Liu K, Lin F. GmIDL2a and GmIDL4a, Encoding the Inflorescence Deficient in Abscission-Like Protein, Are Involved in Soybean Cell Wall Degradation during Lateral Root Emergence. Int J Mol Sci 2018; 19:E2262. [PMID: 30072588 PMCID: PMC6121880 DOI: 10.3390/ijms19082262] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/19/2018] [Accepted: 07/22/2018] [Indexed: 11/23/2022] Open
Abstract
The number of lateral roots (LRs) of a plant determines the efficiency of water and nutrient uptake. Soybean is a typical taproot crop which is deficient in LRs. The number of LRs is therefore an important agronomic trait in soybean breeding. It is reported that the inflorescence deficient in abscission (IDA) protein plays an important role in the emergence of Arabidopsis LRs. Previously, the genes which encode IDA-like (IDL) proteins have been identified in the soybean genome. However, the functions of these genes in LR development are unknown. Therefore, it is of great value to investigate the function of IDL genes in soybean. In the present study, the functions of two root-specific expressed IDL genes, GmIDL2a and GmIDL4a, are investigated. The expressions of GmIDL2a and GmIDL4a, induced by auxin, are located in the overlaying tissue, where LRs are initiated. Overexpression of GmIDL2a and GmIDL4a increases the LR densities of the primary roots, but not in the elder root. Abnormal cell layer separation has also been observed in GmIDL2a- and GmIDL4a-overexpressing roots. These results suggest that the overlaying tissues of GmIDL2a- and GmIDL4a-overexpressing roots are looser and are suitable for the emergence of the LR primordium. Further investigation shows that the expression of some of the cell wall remodeling (CWR) genes, such as xyloglucan endotransglucosylase/hydrolases, expansins, and polygalacturonases, are increased when GmIDL2a and GmIDL4a are overexpressed in hairy roots. Here, we conclude that GmIDL2a and GmIDL4a function in LR emergence through regulating soybean CWR gene expression.
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Affiliation(s)
- Chen Liu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110086, China.
| | - Chunyu Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110086, China.
| | - Mingxia Fan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110086, China.
| | - Wenjuan Ma
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110086, China.
| | - Meiming Chen
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110086, China.
| | - Fengchun Cai
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110086, China.
| | - Kuichen Liu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110086, China.
| | - Feng Lin
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110086, China.
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10
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Ross-Elliott TJ, Jensen KH, Haaning KS, Wager BM, Knoblauch J, Howell AH, Mullendore DL, Monteith AG, Paultre D, Yan D, Otero S, Bourdon M, Sager R, Lee JY, Helariutta Y, Knoblauch M, Oparka KJ. Phloem unloading in Arabidopsis roots is convective and regulated by the phloem-pole pericycle. eLife 2017; 6. [PMID: 28230527 PMCID: PMC5365319 DOI: 10.7554/elife.24125] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 02/17/2017] [Indexed: 02/05/2023] Open
Abstract
In plants, a complex mixture of solutes and macromolecules is transported by the phloem. Here, we examined how solutes and macromolecules are separated when they exit the phloem during the unloading process. We used a combination of approaches (non-invasive imaging, 3D-electron microscopy, and mathematical modelling) to show that phloem unloading of solutes in Arabidopsis roots occurs through plasmodesmata by a combination of mass flow and diffusion (convective phloem unloading). During unloading, solutes and proteins are diverted into the phloem-pole pericycle, a tissue connected to the protophloem by a unique class of ‘funnel plasmodesmata’. While solutes are unloaded without restriction, large proteins are released through funnel plasmodesmata in discrete pulses, a phenomenon we refer to as ‘batch unloading’. Unlike solutes, these proteins remain restricted to the phloem-pole pericycle. Our data demonstrate a major role for the phloem-pole pericycle in regulating phloem unloading in roots. DOI:http://dx.doi.org/10.7554/eLife.24125.001 A mechanism called photosynthesis allows plants to use energy from sunlight to make sugars from carbon dioxide gas and water. These sugars can then be used as fuel, or as building blocks for wood and other plant structures. Every part of the plant requires sugars, but most photosynthesis happens in the leaves and stems, so the sugars need to be able to move around the plant to wherever they are needed. Phloem tubes form a network that transports sugar, proteins and other molecules around the plant within a fluid known as sap. Because this network is so extensive, it is very difficult to study, which has left researchers with major questions about how it works. For example, it is not clear how the sugar and other molecules leave the phloem when they reach their destination. Ross-Elliot et al. used a combination of microscopy and mathematical modeling to investigate how sugars and other molecules leave the phloem in the roots of a plant called Arabidopsis thaliana. The experiments show that these molecules move directly into cells within a neighboring tissue called the phloem-pole pericycle via pores known as funnel plasmodesmata. Ross-Elliot et al. incorporated the experimental data into a mathematical model of phloem unloading. This model suggests that sugars and other small molecules move freely through the funnel plasmodesmata, but large proteins pass through these pores in pulses. Future challenges include finding out exactly how plants control phloem unloading and to investigate whether it is possible to modify the delivery of specific molecules to particular parts of the plant. DOI:http://dx.doi.org/10.7554/eLife.24125.002
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Affiliation(s)
| | - Kaare H Jensen
- Department of Physics, Technical University of Denmark, Lyngby, Denmark
| | - Katrine S Haaning
- Department of Physics, Technical University of Denmark, Lyngby, Denmark
| | - Brittney M Wager
- School of Biological Sciences, Washington State University, Pullman, United States
| | - Jan Knoblauch
- School of Biological Sciences, Washington State University, Pullman, United States
| | - Alexander H Howell
- School of Biological Sciences, Washington State University, Pullman, United States
| | - Daniel L Mullendore
- School of Biological Sciences, Washington State University, Pullman, United States
| | - Alexander G Monteith
- Department of Biological and Medical Sciences, Oxford Brookes University, Headington, Oxford, United Kingdom
| | - Danae Paultre
- Institute of Molecular Plant Science, University of Edinburgh, Edinburgh, United Kingdom
| | - Dawei Yan
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Sofia Otero
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Matthieu Bourdon
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Ross Sager
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, United States
| | - Jung-Youn Lee
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, United States
| | - Ykä Helariutta
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Michael Knoblauch
- School of Biological Sciences, Washington State University, Pullman, United States
| | - Karl J Oparka
- Institute of Molecular Plant Science, University of Edinburgh, Edinburgh, United Kingdom
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11
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Besnard J, Pratelli R, Zhao C, Sonawala U, Collakova E, Pilot G, Okumoto S. UMAMIT14 is an amino acid exporter involved in phloem unloading in Arabidopsis roots. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:6385-6397. [PMID: 27856708 PMCID: PMC5181585 DOI: 10.1093/jxb/erw412] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Amino acids are the main form of nitrogen transported between the plant organs. Transport of amino acids across membranes is mediated by specialized proteins: importers, exporters, and facilitators. Unlike amino acid importers, amino acid exporters have not been thoroughly studied, partly due to a lack of high-throughput techniques enabling their isolation. Usually Multiple Acids Move In and out Transporters 14 (UMAMIT14) from Arabidopsis shares sequence similarity to the amino acid facilitator Silique Are Red1 (UMAMIT18), and has been shown to be involved in amino acid transfer to the seeds. We show here that UMAMIT14 is also expressed in root pericycle and phloem cells and mediates export of a broad range of amino acids in yeast. Loss-of-function of UMAMIT14 leads to a reduced shoot-to-root and root-to-medium transfer of amino acids originating from the leaves. These fluxes were further reduced in an umamti14 umamit18 double loss-of-function mutant. This study suggests that UMAMIT14 is involved in phloem unloading of amino acids in roots, and that UMAMIT14 and UMAMIT18 are involved in the radial transport of amino acids in roots, which is essential for maintaining amino acid secretion to the soil.
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Affiliation(s)
- Julien Besnard
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061, VA, USA
| | - Réjane Pratelli
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061, VA, USA
| | - Chengsong Zhao
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061, VA, USA
| | - Unnati Sonawala
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061, VA, USA
| | - Eva Collakova
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061, VA, USA
| | - Guillaume Pilot
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061, VA, USA
| | - Sakiko Okumoto
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061, VA, USA
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12
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Bouché F, D’Aloia M, Tocquin P, Lobet G, Detry N, Périlleux C. Integrating roots into a whole plant network of flowering time genes in Arabidopsis thaliana. Sci Rep 2016; 6:29042. [PMID: 27352932 PMCID: PMC4926122 DOI: 10.1038/srep29042] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 06/10/2016] [Indexed: 11/21/2022] Open
Abstract
Molecular data concerning the involvement of roots in the genetic pathways regulating floral transition are lacking. In this study, we performed global analyses of the root transcriptome in Arabidopsis in order to identify flowering time genes that are expressed in the roots and genes that are differentially expressed in the roots during the induction of flowering. Data mining of public microarray experiments uncovered that about 200 genes whose mutations are reported to alter flowering time are expressed in the roots (i.e. were detected in more than 50% of the microarrays). However, only a few flowering integrator genes passed the analysis cutoff. Comparison of root transcriptome in short days and during synchronized induction of flowering by a single 22-h long day revealed that 595 genes were differentially expressed. Enrichment analyses of differentially expressed genes in root tissues, gene ontology categories, and cis-regulatory elements converged towards sugar signaling. We concluded that roots are integrated in systemic signaling, whereby carbon supply coordinates growth at the whole plant level during the induction of flowering. This coordination could involve the root circadian clock and cytokinin biosynthesis as a feed forward loop towards the shoot.
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Affiliation(s)
- Frédéric Bouché
- InBioS, PhytoSYSTEMS, Laboratory of Plant Physiology, University of Liège, Quartier Vallée 1 Sart Tilman Campus, Chemin de la Vallée no. 4, B-4000 Liège, Belgium
| | - Maria D’Aloia
- InBioS, PhytoSYSTEMS, Laboratory of Plant Physiology, University of Liège, Quartier Vallée 1 Sart Tilman Campus, Chemin de la Vallée no. 4, B-4000 Liège, Belgium
| | - Pierre Tocquin
- InBioS, PhytoSYSTEMS, Laboratory of Plant Physiology, University of Liège, Quartier Vallée 1 Sart Tilman Campus, Chemin de la Vallée no. 4, B-4000 Liège, Belgium
| | - Guillaume Lobet
- InBioS, PhytoSYSTEMS, Laboratory of Plant Physiology, University of Liège, Quartier Vallée 1 Sart Tilman Campus, Chemin de la Vallée no. 4, B-4000 Liège, Belgium
| | - Nathalie Detry
- InBioS, PhytoSYSTEMS, Laboratory of Plant Physiology, University of Liège, Quartier Vallée 1 Sart Tilman Campus, Chemin de la Vallée no. 4, B-4000 Liège, Belgium
| | - Claire Périlleux
- InBioS, PhytoSYSTEMS, Laboratory of Plant Physiology, University of Liège, Quartier Vallée 1 Sart Tilman Campus, Chemin de la Vallée no. 4, B-4000 Liège, Belgium
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13
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Ghorbani S, Lin YC, Parizot B, Fernandez A, Njo MF, Van de Peer Y, Beeckman T, Hilson P. Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5257-69. [PMID: 26195730 PMCID: PMC4526923 DOI: 10.1093/jxb/erv346] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plant genomes encode numerous small secretory peptides (SSPs) whose functions have yet to be explored. Based on structural features that characterize SSP families known to take part in postembryonic development, this comparative genome analysis resulted in the identification of genes coding for oligopeptides potentially involved in cell-to-cell communication. Because genome annotation based on short sequence homology is difficult, the criteria for the de novo identification and aggregation of conserved SSP sequences were first benchmarked across five reference plant species. The resulting gene families were then extended to 32 genome sequences, including major crops. The global phylogenetic pattern common to the functionally characterized SSP families suggests that their apparition and expansion coincide with that of the land plants. The SSP families can be searched online for members, sequences and consensus (http://bioinformatics.psb.ugent.be/webtools/PlantSSP/). Looking for putative regulators of root development, Arabidopsis thaliana SSP genes were further selected through transcriptome meta-analysis based on their expression at specific stages and in specific cell types in the course of the lateral root formation. As an additional indication that formerly uncharacterized SSPs may control development, this study showed that root growth and branching were altered by the application of synthetic peptides matching conserved SSP motifs, sometimes in very specific ways. The strategy used in the study, combining comparative genomics, transcriptome meta-analysis and peptide functional assays in planta, pinpoints factors potentially involved in non-cell-autonomous regulatory mechanisms. A similar approach can be implemented in different species for the study of a wide range of developmental programmes.
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Affiliation(s)
- Sarieh Ghorbani
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Yao-Cheng Lin
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Boris Parizot
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Ana Fernandez
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Maria Fransiska Njo
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria 0028, South Africa
| | - Tom Beeckman
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Pierre Hilson
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Saclay Plant Sciences, INRA, route de Saint-Cyr, 78026 Versailles, France
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14
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Czyzewicz N, Shi CL, Vu LD, Van De Cotte B, Hodgman C, Butenko MA, De Smet I. Modulation of Arabidopsis and monocot root architecture by CLAVATA3/EMBRYO SURROUNDING REGION 26 peptide. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5229-43. [PMID: 26188203 PMCID: PMC4526925 DOI: 10.1093/jxb/erv360] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Plant roots are important for a wide range of processes, including nutrient and water uptake, anchoring and mechanical support, storage functions, and as the major interface with the soil environment. Several small signalling peptides and receptor kinases have been shown to affect primary root growth, but very little is known about their role in lateral root development. In this context, the CLE family, a group of small signalling peptides that has been shown to affect a wide range of developmental processes, were the focus of this study. Here, the expression pattern during lateral root initiation for several CLE family members is explored and to what extent CLE1, CLE4, CLE7, CLE26, and CLE27, which show specific expression patterns in the root, are involved in regulating root architecture in Arabidopsis thaliana is assessed. Using chemically synthesized peptide variants, it was found that CLE26 plays an important role in regulating A. thaliana root architecture and interacts with auxin signalling. In addition, through alanine scanning and in silico structural modelling, key residues in the CLE26 peptide sequence that affect its activity are pinpointed. Finally, some interesting similarities and differences regarding the role of CLE26 in regulating monocot root architecture are presented.
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Affiliation(s)
- Nathan Czyzewicz
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Leicestershire LE12 5RD, UK
| | - Chun-Lin Shi
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, N-0316 Oslo, Norway
| | - Lam Dai Vu
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Genetics, Ghent University, B-9052 Ghent, Belgium Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Brigitte Van De Cotte
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Genetics, Ghent University, B-9052 Ghent, Belgium
| | - Charlie Hodgman
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Leicestershire LE12 5RD, UK
| | - Melinka A Butenko
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, N-0316 Oslo, Norway
| | - Ive De Smet
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Leicestershire LE12 5RD, UK Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Genetics, Ghent University, B-9052 Ghent, Belgium Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Leicestershire LE12 5RD, UK
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15
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Affiliation(s)
- Tom Beeckman
- Department of Plant Systems Biology, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium.
| | - Ive De Smet
- Department of Plant Systems Biology, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium; Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.
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16
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Kajala K, Ramakrishna P, Fisher A, C. Bergmann D, De Smet I, Sozzani R, Weijers D, Brady SM. Omics and modelling approaches for understanding regulation of asymmetric cell divisions in arabidopsis and other angiosperm plants. ANNALS OF BOTANY 2014; 113:1083-1105. [PMID: 24825294 PMCID: PMC4030820 DOI: 10.1093/aob/mcu065] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 03/06/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND Asymmetric cell divisions are formative divisions that generate daughter cells of distinct identity. These divisions are coordinated by either extrinsic ('niche-controlled') or intrinsic regulatory mechanisms and are fundamentally important in plant development. SCOPE This review describes how asymmetric cell divisions are regulated during development and in different cell types in both the root and the shoot of plants. It further highlights ways in which omics and modelling approaches have been used to elucidate these regulatory mechanisms. For example, the regulation of embryonic asymmetric divisions is described, including the first divisions of the zygote, formative vascular divisions and divisions that give rise to the root stem cell niche. Asymmetric divisions of the root cortex endodermis initial, pericycle cells that give rise to the lateral root primordium, procambium, cambium and stomatal cells are also discussed. Finally, a perspective is provided regarding the role of other hormones or regulatory molecules in asymmetric divisions, the presence of segregated determinants and the usefulness of modelling approaches in understanding network dynamics within these very special cells. CONCLUSIONS Asymmetric cell divisions define plant development. High-throughput genomic and modelling approaches can elucidate their regulation, which in turn could enable the engineering of plant traits such as stomatal density, lateral root development and wood formation.
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Affiliation(s)
- Kaisa Kajala
- Department of Plant Biology and Genome Center, UC Davis, Davis, CA 95616, USA
| | - Priya Ramakrishna
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Adam Fisher
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Dominique C. Bergmann
- Howard Hughes Medical Institute and Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Ive De Smet
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703HA Wageningen, The Netherlands
| | - Siobhan M. Brady
- Department of Plant Biology and Genome Center, UC Davis, Davis, CA 95616, USA
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17
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Jansen L, Hollunder J, Roberts I, Forestan C, Fonteyne P, Van Quickenborne C, Zhen RG, McKersie B, Parizot B, Beeckman T. Comparative transcriptomics as a tool for the identification of root branching genes in maize. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:1092-102. [PMID: 23941360 DOI: 10.1111/pbi.12104] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 07/09/2013] [Indexed: 05/09/2023]
Abstract
The root system is fundamental for plant development, is crucial for overall plant growth and is recently being recognized as the key for future crop productivity improvement. A major determinant of root system architecture is the initiation of lateral roots. While knowledge of the genetic and molecular mechanisms regulating lateral root initiation has mainly been achieved in the dicotyledonous plant Arabidopsis thaliana, only scarce data are available for major crop species, generally monocotyledonous plants. The existence of both similarities and differences at the morphological and anatomical level between plant species from both clades raises the question whether regulation of lateral root initiation may or may not be conserved through evolution. Here, we performed a targeted genome-wide transcriptome analysis during lateral root initiation both in primary and in adventitious roots of Zea mays and found evidence for the existence of common transcriptional regulation. Further, based on a comparative analysis with Arabidopsis transcriptome data, a core of genes putatively conserved across angiosperms could be identified. Therefore, it is plausible that common regulatory mechanisms for lateral root initiation are at play in maize and Arabidopsis, a finding that might encourage the extrapolation of knowledge obtained in Arabidopsis to crop species at the level of root system architecture.
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Affiliation(s)
- Leentje Jansen
- Integrative Plant Biology division, Department of Plant Systems Biology, VIB, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
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18
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Lavenus J, Goh T, Roberts I, Guyomarc'h S, Lucas M, De Smet I, Fukaki H, Beeckman T, Bennett M, Laplaze L. Lateral root development in Arabidopsis: fifty shades of auxin. TRENDS IN PLANT SCIENCE 2013; 18:450-8. [PMID: 23701908 DOI: 10.1016/j.tplants.2013.04.006] [Citation(s) in RCA: 376] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/08/2013] [Accepted: 04/15/2013] [Indexed: 05/18/2023]
Abstract
The developmental plasticity of the root system represents a key adaptive trait enabling plants to cope with abiotic stresses such as drought and is therefore important in the current context of global changes. Root branching through lateral root formation is an important component of the adaptability of the root system to its environment. Our understanding of the mechanisms controlling lateral root development has progressed tremendously in recent years through research in the model plant Arabidopsis thaliana (Arabidopsis). These studies have revealed that the phytohormone auxin acts as a common integrator to many endogenous and environmental signals regulating lateral root formation. Here, we review what has been learnt about the myriad roles of auxin during lateral root formation in Arabidopsis.
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Affiliation(s)
- Julien Lavenus
- Institut de Recherche pour le Développement (IRD), UMR DIADE (IRD/UM2), 911 Avenue Agropolis, 34394 Montpellier cedex 5, France
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19
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Laskowski M. Lateral root initiation is a probabilistic event whose frequency is set by fluctuating levels of auxin response. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:2609-17. [PMID: 23709673 DOI: 10.1093/jxb/ert155] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The locations in which lateral roots arise are determined by local peaks of auxin response driven by whole-plant physiology. The architecture of a plant root system adapts it to the conditions in which it grows: large shoot systems demand large root systems, and growth in soils that have low or patchy nutrient distributions is often best managed by non-uniform patterns of root branching. It is not surprising then that the regulation of lateral root spacing is responsive to a wide array of stimuli. Molecular genetic studies have outlined a mechanism by which multiple modules of auxin response in specific cell types drive lateral root initiation. These peaks of auxin responsiveness are functionally controlled by the growth of the plant and the changing environmental conditions it experiences. Thus, the process of lateral root initiation, which depends on strong local auxin response, is globally mediated.
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Affiliation(s)
- Marta Laskowski
- Department of Biology, Oberlin College, Oberlin, OH 44074, USA.
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20
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Smith S, De Smet I. Root system architecture: insights from Arabidopsis and cereal crops. Philos Trans R Soc Lond B Biol Sci 2012; 367:1441-52. [PMID: 22527386 DOI: 10.1098/rstb.2011.0234] [Citation(s) in RCA: 234] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Roots are important to plants for a wide variety of processes, including nutrient and water uptake, anchoring and mechanical support, storage functions, and as the major interface between the plant and various biotic and abiotic factors in the soil environment. Understanding the development and architecture of roots holds potential for the exploitation and manipulation of root characteristics to both increase food plant yield and optimize agricultural land use. This theme issue highlights the importance of investigating specific aspects of root architecture in both the model plant Arabidopsis thaliana and (cereal) crops, presents novel insights into elements that are currently hardly addressed and provides new tools and technologies to study various aspects of root system architecture. This introduction gives a broad overview of the importance of the root system and provides a snapshot of the molecular control mechanisms associated with root branching and responses to the environment in A. thaliana and cereal crops.
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Affiliation(s)
- Stephanie Smith
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
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