1
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Zhang F, Wang J, Ding T, Lin X, Hu H, Ding Z, Tian H. MYB2 and MYB108 regulate lateral root development by interacting with LBD29 in Arabidopsis thaliana. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 38923126 DOI: 10.1111/jipb.13720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 05/15/2024] [Indexed: 06/28/2024]
Abstract
AUXIN RESPONSE FACTOR 7 (ARF7)-mediated auxin signaling plays a key role in lateral root (LR) development by regulating downstream LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factor genes, including LBD16, LBD18, and LBD29. LBD proteins are believed to regulate the transcription of downstream genes as homodimers or heterodimers. However, whether LBD29 forms dimers with other proteins to regulate LR development remains unknown. Here, we determined that the Arabidopsis thaliana (L.) Heynh. MYB transcription factors MYB2 and MYB108 interact with LBD29 and regulate auxin-induced LR development. Both MYB2 and MYB108 were induced by auxin in an ARF7-dependent manner. Disruption of MYB2 by fusion with an SRDX domain severely affected auxin-induced LR formation and the ability of LBD29 to induce LR development. By contrast, overexpression of MYB2 or MYB108 resulted in greater LR numbers, except in the lbd29 mutant background. These findings underscore the interdependence and importance of MYB2, MYB108, and LBD29 in regulating LR development. In addition, MYB2-LBD29 and MYB108-LBD29 complexes promoted the expression of CUTICLE DESTRUCTING FACTOR 1 (CDEF1), a member of the GDSL (Gly-Asp-Ser-Leu) lipase/esterase family involved in LR development. In summary, this study identified MYB2-LBD29 and MYB108-LBD29 regulatory modules that act downstream of ARF7 and intricately control auxin-mediated LR development.
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Affiliation(s)
- Feng Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Junxia Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Tingting Ding
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
- Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Xuefeng Lin
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Haiying Hu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Zhaojun Ding
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Huiyu Tian
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
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2
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Zhang Y, Li Y, de Zeeuw T, Duijts K, Kawa D, Lamers J, Munzert KS, Li H, Zou Y, Meyer AJ, Yan J, Verstappen F, Wang Y, Gijsberts T, Wang J, Gigli-Bisceglia N, Engelsdorf T, van Dijk ADJ, Testerink C. Root branching under high salinity requires auxin-independent modulation of LATERAL ORGAN BOUNDARY DOMAIN 16 function. THE PLANT CELL 2024; 36:899-918. [PMID: 38142228 PMCID: PMC10980347 DOI: 10.1093/plcell/koad317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/17/2023] [Accepted: 12/08/2023] [Indexed: 12/25/2023]
Abstract
Salinity stress constrains lateral root (LR) growth and severely affects plant growth. Auxin signaling regulates LR formation, but the molecular mechanism by which salinity affects root auxin signaling and whether salt induces other pathways that regulate LR development remains unknown. In Arabidopsis thaliana, the auxin-regulated transcription factor LATERAL ORGAN BOUNDARY DOMAIN 16 (LBD16) is an essential player in LR development under control conditions. Here, we show that under high-salt conditions, an alternative pathway regulates LBD16 expression. Salt represses auxin signaling but, in parallel, activates ZINC FINGER OF ARABIDOPSIS THALIANA 6 (ZAT6), a transcriptional activator of LBD16. ZAT6 activates LBD16 expression, thus contributing to downstream cell wall remodeling and promoting LR development under high-salt conditions. Our study thus shows that the integration of auxin-dependent repressive and salt-activated auxin-independent pathways converging on LBD16 modulates root branching under high-salt conditions.
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Affiliation(s)
- Yanxia Zhang
- Laboratory of Plant Physiology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
- Plant Cell Biology, Faculty of Science, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE Amsterdam, The Netherlands
- College of Agriculture, South China Agricultural University, 510642 Guangzhou, China
| | - Yiyun Li
- Laboratory of Plant Physiology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Thijs de Zeeuw
- Laboratory of Plant Physiology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Kilian Duijts
- Laboratory of Plant Physiology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Dorota Kawa
- Plant Cell Biology, Faculty of Science, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - Jasper Lamers
- Laboratory of Plant Physiology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Kristina S Munzert
- Molecular Plant Physiology, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Hongfei Li
- Laboratory of Plant Physiology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Yutao Zou
- Laboratory of Plant Physiology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - A Jessica Meyer
- Laboratory of Plant Physiology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Jinxuan Yan
- Laboratory of Plant Physiology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Francel Verstappen
- Laboratory of Plant Physiology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Yixuan Wang
- Laboratory of Plant Physiology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Tom Gijsberts
- Laboratory of Plant Physiology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Jielin Wang
- Laboratory of Plant Physiology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Nora Gigli-Bisceglia
- Laboratory of Plant Physiology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Timo Engelsdorf
- Molecular Plant Physiology, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Christa Testerink
- Laboratory of Plant Physiology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
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3
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Wang J, Song Y, Wang Z, Shi L, Yu S, Xu Y, Wang G, He D, Jiang L, Shang W, He S. RNA Sequencing Analysis and Verification of Paeonia ostii 'Fengdan' CuZn Superoxide Dismutase ( PoSOD) Genes in Root Development. PLANTS (BASEL, SWITZERLAND) 2024; 13:421. [PMID: 38337954 PMCID: PMC10856844 DOI: 10.3390/plants13030421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/28/2024] [Accepted: 01/28/2024] [Indexed: 02/12/2024]
Abstract
Tree peony (Paeonia suffruticosa) is a significant medicinal plant. However, the low rooting number is a bottleneck problem in the micropropagation protocols of P. ostii 'Fengdan'. The activity of superoxide dismutase (SOD) is closely related to root development. But research on the SOD gene's impact on rooting is still lacking. In this study, RNA sequencing (RNA-seq) was used to analyze the four crucial stages of root development in P. ostii 'Fengdan' seedlings, including the early root primordium formation stage (Gmfq), root primordium formation stage (Gmf), root protrusion stage (Gtq), and root outgrowth stage (Gzc). A total of 141.77 GB of data were obtained; 71,718, 29,804, and 24,712 differentially expressed genes (DEGs) were identified in the comparison groups of Gmfq vs. Gmf, Gmf vs. Gtq, and Gtq vs. Gzc, respectively. Among the 20 most highly expressed DEGs in the three comparison groups, only the CuZnSOD gene (SUB13202229, PoSOD) was found to be significantly expressed in Gtq vs. Gzc. The overexpression of PoSOD increased the number of adventitious roots and promoted the activities of peroxidase (POD) and SOD in P. ostii 'Fengdan'. The gene ADVENTITIOUS ROOTING RELATED OXYGENASE1 (PoARRO-1), which is closely associated with the development of adventitious roots, was also significantly upregulated in overexpressing PoSOD plants. Furthermore, PoSOD interacted with PoARRO-1 in yeast two-hybrid (Y2H) and biomolecular luminescence complementation (BiFC) assays. In conclusion, PoSOD could interact with PoARRO-1 and enhance the root development of tube plantlets in P. ostii 'Fengdan'. This study will help us to preliminarily understand the molecular mechanism of adventitious root formation and improve the root quality of tree peony and other medicinal plants.
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Affiliation(s)
- Jiange Wang
- Zhengzhou Key Laboratory for Research and Development of Regional Plants, College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China; (J.W.); (Y.S.); (Z.W.); (L.S.); (Y.X.); (G.W.); (D.H.)
| | - Yinglong Song
- Zhengzhou Key Laboratory for Research and Development of Regional Plants, College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China; (J.W.); (Y.S.); (Z.W.); (L.S.); (Y.X.); (G.W.); (D.H.)
| | - Zheng Wang
- Zhengzhou Key Laboratory for Research and Development of Regional Plants, College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China; (J.W.); (Y.S.); (Z.W.); (L.S.); (Y.X.); (G.W.); (D.H.)
| | - Liyun Shi
- Zhengzhou Key Laboratory for Research and Development of Regional Plants, College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China; (J.W.); (Y.S.); (Z.W.); (L.S.); (Y.X.); (G.W.); (D.H.)
| | - Shuiyan Yu
- Shanghai Chen Shan Botanical Garden, Shanghai 201602, China;
| | - Yufeng Xu
- Zhengzhou Key Laboratory for Research and Development of Regional Plants, College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China; (J.W.); (Y.S.); (Z.W.); (L.S.); (Y.X.); (G.W.); (D.H.)
| | - Guiqing Wang
- Zhengzhou Key Laboratory for Research and Development of Regional Plants, College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China; (J.W.); (Y.S.); (Z.W.); (L.S.); (Y.X.); (G.W.); (D.H.)
| | - Dan He
- Zhengzhou Key Laboratory for Research and Development of Regional Plants, College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China; (J.W.); (Y.S.); (Z.W.); (L.S.); (Y.X.); (G.W.); (D.H.)
| | - Liwei Jiang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China;
| | - Wenqian Shang
- Zhengzhou Key Laboratory for Research and Development of Regional Plants, College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China; (J.W.); (Y.S.); (Z.W.); (L.S.); (Y.X.); (G.W.); (D.H.)
| | - Songlin He
- Zhengzhou Key Laboratory for Research and Development of Regional Plants, College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China; (J.W.); (Y.S.); (Z.W.); (L.S.); (Y.X.); (G.W.); (D.H.)
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China
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4
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Zhang Y, Ma Y, Zhang H, Xu J, Gao X, Zhang T, Liu X, Guo L, Zhao D. Environmental F actors coordinate circadian clock function and rhythm to regulate plant development. PLANT SIGNALING & BEHAVIOR 2023; 18:2231202. [PMID: 37481743 PMCID: PMC10364662 DOI: 10.1080/15592324.2023.2231202] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 07/25/2023]
Abstract
Changes in the external environment necessitate plant growth plasticity, with environmental signals such as light, temperature, and humidity regulating growth and development. The plant circadian clock is a biological time keeper that can be "reset" to adjust internal time to changes in the external environment. Exploring the regulatory mechanisms behind plant acclimation to environmental factors is important for understanding how plant growth and development are shaped and for boosting agricultural production. In this review, we summarize recent insights into the coordinated regulation of plant growth and development by environmental signals and the circadian clock, further discussing the potential of this knowledge.
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Affiliation(s)
- Ying Zhang
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- Institute of Biotechnology and Food Science, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Yuru Ma
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Hao Zhang
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Jiahui Xu
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Xiaokuan Gao
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
| | - Tengteng Zhang
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Xigang Liu
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Lin Guo
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Dan Zhao
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
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5
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Ikeda H, Uchikawa T, Kondo Y, Takahashi N, Shishikui T, Watahiki MK, Kubota A, Endo M. Circadian Clock Controls Root Hair Elongation through Long-Distance Communication. PLANT & CELL PHYSIOLOGY 2023; 64:1289-1300. [PMID: 37552691 DOI: 10.1093/pcp/pcad076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/06/2023] [Accepted: 07/13/2023] [Indexed: 08/10/2023]
Abstract
Plants adapt to periodic environmental changes, such as day and night, by using circadian clocks. Cell division and elongation are primary steps to adjust plant development according to their environments. In Arabidopsis, hypocotyl elongation has been studied as a representative model to understand how the circadian clock regulates cell elongation. However, it remains unknown whether similar phenomena exist in other organs, such as roots, where circadian clocks regulate physiological responses. Here, we show that root hair elongation is controlled by both light and the circadian clock. By developing machine-learning models to automatically analyze the images of root hairs, we found that genes encoding major components of the central oscillator, such as TIMING OF CAB EXPRESSION1 (TOC1) or CIRCADIAN CLOCK ASSOCIATED1 (CCA1), regulate the rhythmicity of root hair length. The partial illumination of light to either shoots or roots suggested that light received in shoots is mainly responsible for the generation of root hair rhythmicity. Furthermore, grafting experiments between wild-type (WT) and toc1 plants demonstrated that TOC1 in shoots is responsible for the generation of root hair rhythmicity. Our results illustrate the combinational effects of long-distance signaling and the circadian clock on the regulation of root hair length.
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Affiliation(s)
- Hikari Ikeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan
| | - Taiga Uchikawa
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan
| | - Yohei Kondo
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, 444-8787 Japan
| | - Nozomu Takahashi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, 332-0012 Japan
| | - Takuma Shishikui
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan
| | - Masaaki K Watahiki
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
- Faculty of Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Akane Kubota
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan
| | - Motomu Endo
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan
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6
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Wang Q, De Gernier H, Duan X, Xie Y, Geelen D, Hayashi KI, Xuan W, Geisler M, Ten Tusscher K, Beeckman T, Vanneste S. GH3-mediated auxin inactivation attenuates multiple stages of lateral root development. THE NEW PHYTOLOGIST 2023; 240:1900-1912. [PMID: 37743759 DOI: 10.1111/nph.19284] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/19/2023] [Indexed: 09/26/2023]
Abstract
Lateral root (LR) positioning and development rely on the dynamic interplay between auxin production, transport but also inactivation. Nonetheless, how the latter affects LR organogenesis remains largely uninvestigated. Here, we systematically analyze the impact of the major auxin inactivation pathway defined by GRETCHEN HAGEN3-type (GH3) auxin conjugating enzymes and DIOXYGENASE FOR AUXIN OXIDATION1 (DAO1) in all stages of LR development using reporters, genetics and inhibitors in Arabidopsis thaliana. Our data demonstrate that the gh3.1/2/3/4/5/6 hextuple (gh3hex) mutants display a higher LR density due to increased LR initiation and faster LR developmental progression, acting epistatically over dao1-1. Grafting and local inhibitor applications reveal that root and shoot GH3 activities control LR formation. The faster LR development in gh3hex is associated with GH3 expression domains in and around developing LRs. The increase in LR initiation is associated with accelerated auxin response oscillations coinciding with increases in apical meristem size and LR cap cell death rates. Our research reveals how GH3-mediated auxin inactivation attenuates LR development. Local GH3 expression in LR primordia attenuates development and emergence, whereas GH3 effects on pre-initiation stages are indirect, by modulating meristem activities that in turn coordinate root growth with LR spacing.
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Affiliation(s)
- Qing Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Hugues De Gernier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Xingliang Duan
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuanming Xie
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Danny Geelen
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, 9000, Belgium
| | - Ken-Ishiro Hayashi
- Department of Bioscience, Okayama University of Science, Okayama, 700-0005, Japan
| | - Wei Xuan
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Markus Geisler
- Department of Biology, University of Fribourg, Fribourg, CH-1700, Switzerland
| | - Kirsten Ten Tusscher
- Computational Developmental Biology Group, Faculty of Science, Utrecht University, Utrecht, 3584 CH, the Netherlands
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Steffen Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, 9000, Belgium
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7
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Salazar-Gutiérrez D, Cruz-Mendívil A, Villicaña C, Heredia JB, Lightbourn-Rojas LA, León-Félix J. Transcriptomic Analysis Reveals the Response Mechanisms of Bell Pepper ( Capsicum annuum) to Phosphorus Deficiency. Metabolites 2023; 13:1078. [PMID: 37887403 PMCID: PMC10609356 DOI: 10.3390/metabo13101078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/18/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
Phosphorus (P) is an important nutritional element needed by plants. Roots obtain P as inorganic phosphate (Pi), mostly in H2PO-4 form. It is vital for plants to have a sufficient supply of Pi since it participates in important processes like photosynthesis, energy transfer, and protein activation, among others. The physicochemical properties and the organic material usually make Pi bioavailability in soil low, causing crops and undomesticated plants to experience variations in accessibility or even a persistent phosphate limitation. In this study, transcriptome data from pepper roots under low-Pi stress was analyzed in order to identify Pi starvation-responsive genes and their relationship with metabolic pathways and functions. Transcriptome data were obtained from pepper roots with Pi deficiency by RNASeq and analyzed with bioinformatic tools. A total of 97 differentially expressed genes (DEGs) were identified; Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment revealed that metabolic pathways, such as porphyrin and chlorophyll metabolism, were down-regulated, and galactose and fatty acid metabolism were up-regulated. The results indicate that bell pepper follows diverse processes related to low Pi tolerance regulation, such as the remobilization of internal Pi, alternative metabolic pathways to generate energy, and regulators of root development.
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Affiliation(s)
- Daizha Salazar-Gutiérrez
- Molecular Biology and Functional Genomics, Centro de Investigación en Alimentación y Desarrollo (CIAD), Culiacán 80110, Sinaloa, Mexico;
| | - Abraham Cruz-Mendívil
- CONAHCYT-Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Guasave 81101, Sinaloa, Mexico;
| | - Claudia Villicaña
- CONAHCYT-Molecular Biology and Functional Genomics, Centro de Investigación en Alimentación y Desarrollo (CIAD), Culiacán 80110, Sinaloa, Mexico;
| | - José Basilio Heredia
- Functional and Nutraceutical Foods, Centro de Investigación en Alimentación y Desarrollo (CIAD), Culiacán 80110, Sinaloa, Mexico;
| | | | - Josefina León-Félix
- Molecular Biology and Functional Genomics, Centro de Investigación en Alimentación y Desarrollo (CIAD), Culiacán 80110, Sinaloa, Mexico;
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8
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Liu W, Cai G, Zhai N, Wang H, Tang T, Zhang Y, Zhang Z, Sun L, Zhang Y, Beeckman T, Xu L. Genome and transcriptome of Selaginella kraussiana reveal evolution of root apical meristems in vascular plants. Curr Biol 2023; 33:4085-4097.e5. [PMID: 37716350 DOI: 10.1016/j.cub.2023.08.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/30/2023] [Accepted: 08/22/2023] [Indexed: 09/18/2023]
Abstract
The evolution of roots allowed vascular plants to adapt to land environments. Fossil evidence indicates that roots evolved independently in euphyllophytes (ferns and seed plants) and lycophytes, the two lineages of extant vascular plants. Based on a high-quality genome assembly, mRNA sequencing (mRNA-seq) data, and single-cell RNA-seq data for the lycophyte Selaginella kraussiana, we show that the two root origin events in lycophytes and euphyllophytes adopted partially similar molecular modules in the regulation of root apical meristem (RAM) development. In S. kraussiana, the RAM initiates from the rhizophore primordium guided by auxin and duplicates itself by dichotomous branching. The auxin signaling pathway directly upregulates euAINTEGUMENTAb (SkeuANTb), and then SkeuANTb directly promotes the expression of SkeuANTa and the WUSCHEL-RELATED HOMEOBOX13b (SkWOX13b) for RAM maintenance, partially similar to the molecular pathway involving the euANT-branch PLETHORA (AtPLT) genes and AtWOX5 in root initiation in the seed plant Arabidopsis thaliana. Other molecular modules, e.g., SHORT-ROOT and SCARECROW, also have partially similar expression patterns in the RAMs of S. kraussiana and A. thaliana. Overall, our study not only provides genome and transcriptome tools of S. kraussiana but also indicates the employment of some common molecular modules in RAMs during root origins in lycophytes and euphyllophytes.
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Affiliation(s)
- Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Gui Cai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Ning Zhai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Hua Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Tengfei Tang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Yuyun Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Zhiyao Zhang
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Lijun Sun
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.
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9
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Ibrahim S, Ahmad N, Kuang L, Li K, Tian Z, Sadau SB, Tajo SM, Wang X, Wang H, Dun X. Transcriptome analysis reveals key regulatory genes for root growth related to potassium utilization efficiency in rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1194914. [PMID: 37546248 PMCID: PMC10400329 DOI: 10.3389/fpls.2023.1194914] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023]
Abstract
Root system architecture (RSA) is the primary predictor of nutrient intake and significantly influences potassium utilization efficiency (KUE). Uncertainty persists regarding the genetic factors governing root growth in rapeseed. The root transcriptome analysis reveals the genetic basis driving crop root growth. In this study, RNA-seq was used to profile the overall transcriptome in the root tissue of 20 Brassica napus accessions with high and low KUE. 71,437 genes in the roots displayed variable expression profiles between the two contrasting genotype groups. The 212 genes that had varied expression levels between the high and low KUE lines were found using a pairwise comparison approach. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classification analysis revealed that the DEGs implicated in hormone and signaling pathways, as well as glucose, lipid, and amino acid metabolism, were all differently regulated in the rapeseed root system. Additionally, we discovered 33 transcription factors (TFs) that control root development were differentially expressed. By combining differential expression analysis, weighted gene co-expression network analysis (WGCNA), and recent genome-wide association study (GWAS) results, four candidate genes were identified as essential hub genes. These potential genes were located fewer than 100 kb from the peak SNPs of QTL clusters, and it was hypothesized that they regulated the formation of the root system. Three of the four hub genes' homologs-BnaC04G0560400ZS, BnaC04G0560400ZS, and BnaA03G0073500ZS-have been shown to control root development in earlier research. The information produced by our transcriptome profiling could be useful in revealing the molecular processes involved in the growth of rapeseed roots in response to KUE.
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Affiliation(s)
- Sani Ibrahim
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Department of Plant Biology, Faculty of Life Sciences, College of Natural and Pharmaceutical Sciences, Bayero University, Kano, Nigeria
| | - Nazir Ahmad
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Lieqiong Kuang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Keqi Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Ze Tian
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Salisu Bello Sadau
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (Institute of Cotton Research (ICR), CAAS), Anyang, China
| | - Sani Muhammad Tajo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (Institute of Cotton Research (ICR), CAAS), Anyang, China
| | - Xinfa Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Hanzhong Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaoling Dun
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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10
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van Zelm E, Bugallo-Alfageme S, Behrouzi P, Meyer AJ, Testerink C, Gommers CMM. Natural variation in salt-induced root growth phases and their contribution to root architecture plasticity. PLANT, CELL & ENVIRONMENT 2023; 46:2174-2186. [PMID: 36912402 DOI: 10.1111/pce.14583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/14/2023] [Accepted: 03/10/2023] [Indexed: 06/08/2023]
Abstract
The root system architecture of a plant changes during salt stress exposure. Different accessions of Arabidopsis thaliana have adopted different strategies in remodelling their root architecture during salt stress. Salt induces a multiphase growth response in roots, consisting of a stop phase, quiescent phase, recovery phase and eventually a new level of homoeostasis. We explored natural variation in the length of and growth rate during these phases in both main and lateral roots and find that some accessions lack the quiescent phase. Using mathematical models and correlation-based network, allowed us to correlate dynamic traits to overall root architecture and discover that both the main root growth rate during homoeostasis and lateral root appearance are the strongest determinants of overall root architecture. In addition, this approach revealed a trade-off between investing in main or lateral root length during salt stress. By studying natural variation in high-resolution temporal root growth using mathematical modelling, we gained new insights in the interactions between dynamic root growth traits and we identified key traits that modulate overall root architecture during salt stress.
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Affiliation(s)
- Eva van Zelm
- Laboratory of Plant Physiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Silvia Bugallo-Alfageme
- Laboratory of Plant Physiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Pariya Behrouzi
- Mathematical-Statistical Method Group, Wageningen University & Research, Wageningen, The Netherlands
| | - A Jessica Meyer
- Laboratory of Plant Physiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Christa Testerink
- Laboratory of Plant Physiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Charlotte M M Gommers
- Laboratory of Plant Physiology, Wageningen University & Research, Wageningen, The Netherlands
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11
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Gombos M, Hapek N, Kozma-Bognár L, Grezal G, Zombori Z, Kiss E, Györgyey J. Limited water stress modulates expression of circadian clock genes in Brachypodium distachyon roots. Sci Rep 2023; 13:1241. [PMID: 36690685 PMCID: PMC9870971 DOI: 10.1038/s41598-022-27287-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 12/29/2022] [Indexed: 01/24/2023] Open
Abstract
Organisms have evolved a circadian clock for the precise timing of their biological processes. Studies primarily on model dicots have shown the complexity of the inner timekeeper responsible for maintaining circadian oscillation in plants and have highlighted that circadian regulation is more than relevant to a wide range of biological processes, especially organ development and timing of flowering. Contribution of the circadian clock to overall plant fitness and yield has also long been known. Nevertheless, the organ- and species-specific functions of the circadian clock and its relation to stress adaptation have only recently been identified. Here we report transcriptional changes of core clock genes of the model monocot Brachypodium distachyon under three different light regimes (18:6 light:dark, 24:0 light and 0:24 dark) in response to mild drought stress in roots and green plant parts. Comparative monitoring of core clock gene expression in roots and green plant parts has shown that both phase and amplitude of expression in the roots of Brachypodium plants differ markedly from those in the green plant parts, even under well-watered conditions. Moreover, circadian clock genes responded to water depletion differently in root and shoot. These results suggest an organ-specific form and functions of the circadian clock in Brachypodium roots.
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Affiliation(s)
- Magdolna Gombos
- Institute of Plant Biology, BRC-Biological Research Centre, Szeged, Hungary
| | - Nóra Hapek
- Institute of Plant Biology, BRC-Biological Research Centre, Szeged, Hungary
- Institute of Biochemistry, BRC-Biological Research Centre, Szeged, Hungary
| | - László Kozma-Bognár
- Institute of Plant Biology, BRC-Biological Research Centre, Szeged, Hungary
- Department of Genetics, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Gábor Grezal
- Institute of Biochemistry, BRC-Biological Research Centre, Szeged, Hungary
| | - Zoltán Zombori
- Institute of Plant Biology, BRC-Biological Research Centre, Szeged, Hungary
| | - Edina Kiss
- Institute of Plant Biology, BRC-Biological Research Centre, Szeged, Hungary
| | - János Györgyey
- Institute of Plant Biology, BRC-Biological Research Centre, Szeged, Hungary.
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12
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Singh A. GIGANTEA regulates lateral root formation by modulating auxin signaling in Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2022; 17:2096780. [PMID: 35822517 PMCID: PMC9291669 DOI: 10.1080/15592324.2022.2096780] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/27/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Lateral root (LR) formation is a vital organogenetic process that determines the root architecture in plants. The number of root branches governs the degree of anchorage, efficiency of nutrients acquisition, and water uptake. The molecular pathways involved in LR formation have been extensively studied in Arabidopsis thaliana (At). A plant hormone, Auxin, is a key regulator of root development and promotes LR formation in plants. A plethora of Arabidopsis genes have been identified to regulate LR initiation, patterning, and emergence processes. Recently, the involvement of flowering time control pathways and circadian clock pathways in LR development has come to light, but the connecting link between these processes is still missing. We have established that GIGANTEA (GI), a key component of photoperiodic flowering, can regulate the formation of LRs in Arabidopsis. GI is known to be involved in red light signaling and circadian clock signaling pathways. Here, we report that over-expression of GI enhances LR formation in red light in At. Real-time PCR analysis shows that GI positively regulates the transcription of TRANSPORT INHIBITOR RESPONSE 1 (TIR1) which is an upstream component of auxin signaling. Furthermore, gi-100 mutant downregulates the LR initiation signaling gene, AUXIN RESPONSE FACTOR 7 (ARF7), and its downstream target gene, LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16). Hence, GI acts as a positive regulator of IAA14-ARF7-LBD16 modules during LR initiation. We have also checked the effect of GI on the expression of NAC1 and AIR3 genes which are controlled by TIR1 during LR formation. Our results show that GI induces the NAC1 transcription and its downstream gene, AIR3 expression, which leads to the enhancement of LR initiation. Taken together, our results suggest that GI controls the expression of TIR1 to govern auxin signaling during LR formation in presence of red light and GI can act as a link between circadian clock signaling, flowering time control pathways, light signaling, and lateral root development pathways.
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Affiliation(s)
- Anamika Singh
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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13
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Luklová M, Novák J, Kopecká R, Kameniarová M, Gibasová V, Brzobohatý B, Černý M. Phytochromes and Their Role in Diurnal Variations of ROS Metabolism and Plant Proteome. Int J Mol Sci 2022; 23:ijms232214134. [PMID: 36430613 PMCID: PMC9695588 DOI: 10.3390/ijms232214134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/12/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022] Open
Abstract
Plants are sessile organisms forced to adapt to environmental variations recurring in a day-night cycle. Extensive research has uncovered the transcriptional control of plants' inner clock and has revealed at least some part of the intricate and elaborate regulatory mechanisms that govern plant diel responses and provide adaptation to the ever-changing environment. Here, we analyzed the proteome of the Arabidopsis thaliana mutant genotypes collected in the middle of the day and the middle of the night, including four mutants in the phytochrome (phyA, phyB, phyC, and phyD) and the circadian clock protein LHY. Our approach provided a novel insight into the diel regulations, identifying 640 significant changes in the night-day protein abundance. The comparison with previous studies confirmed that a large portion of identified proteins was a known target of diurnal regulation. However, more than 300 were novel oscillations hidden under standard growth chamber conditions or not manifested in the wild type. Our results indicated a prominent role for ROS metabolism and phytohormone cytokinin in the observed regulations, and the consecutive analyses confirmed that. The cytokinin signaling significantly increased at night, and in the mutants, the hydrogen peroxide content was lower, and the night-day variation seemed to be lost in the phyD genotype. Furthermore, regulations in the lhy and phyB mutants were partially similar to those found in the catalase mutant cat2, indicating shared ROS-mediated signaling pathways. Our data also shed light on the role of the relatively poorly characterized Phytochrome D, pointing to its connection to glutathione metabolism and the regulation of glutathione S-transferases.
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14
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Newman A, Picot E, Davies S, Hilton S, Carré IA, Bending GD. Circadian rhythms in the plant host influence rhythmicity of rhizosphere microbiota. BMC Biol 2022; 20:235. [PMID: 36266698 PMCID: PMC9585842 DOI: 10.1186/s12915-022-01430-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 09/30/2022] [Indexed: 11/18/2022] Open
Abstract
Background Recent studies demonstrated that microbiota inhabiting the plant rhizosphere exhibit diel changes in abundance. To investigate the impact of plant circadian rhythms on bacterial and fungal rhythms in the rhizosphere, we analysed temporal changes in fungal and bacterial communities in the rhizosphere of Arabidopsis plants overexpressing or lacking function of the circadian clock gene LATE ELONGATED HYPOCOTYL (LHY). Results Under diel light–dark cycles, the knock-out mutant lhy-11 and the gain-of-function mutant lhy-ox both exhibited gene expression rhythms with altered timing and amplitude compared to wild-type plants. Distinct sets of bacteria and fungi were found to display rhythmic changes in abundance in the rhizosphere of both of these mutants, suggesting that abnormal patterns of rhythmicity in the plant host caused temporal reprogramming of the rhizosphere microbiome. This was associated with changes in microbial community structure, including changes in the abundance of fungal guilds known to impact on plant health. Under constant environmental conditions, microbial rhythmicity persisted in the rhizosphere of wild-type plants, indicating control by a circadian oscillator. In contrast, loss of rhythmicity in lhy-ox plants was associated with disrupted rhythms for the majority of rhizosphere microbiota. Conclusions These results show that aberrant function of the plant circadian clock is associated with altered rhythmicity of rhizosphere bacteria and fungi. In the long term, this leads to changes in composition of the rhizosphere microbiome, with potential consequences for plant health. Further research will be required to understand the functional implications of these changes and how they impact on plant health and productivity. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01430-z.
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Affiliation(s)
- Amy Newman
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK.,Present address: National STEM Learning Centre, University of York, York, YO10 5DD, UK
| | - Emma Picot
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK
| | - Sian Davies
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK.,Present address: Micropathology Ltd, Venture Centre, Sir William Lyons Road, Coventry, CV4 7EZ, UK
| | - Sally Hilton
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK.,Present address: Micropathology Ltd, Venture Centre, Sir William Lyons Road, Coventry, CV4 7EZ, UK
| | - Isabelle A Carré
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK.
| | - Gary D Bending
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK
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15
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Davis W, Endo M, Locke JCW. Spatially specific mechanisms and functions of the plant circadian clock. PLANT PHYSIOLOGY 2022; 190:938-951. [PMID: 35640123 PMCID: PMC9516738 DOI: 10.1093/plphys/kiac236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Like many organisms, plants have evolved a genetic network, the circadian clock, to coordinate processes with day/night cycles. In plants, the clock is a pervasive regulator of development and modulates many aspects of physiology. Clock-regulated processes range from the correct timing of growth and cell division to interactions with the root microbiome. Recently developed techniques, such as single-cell time-lapse microscopy and single-cell RNA-seq, are beginning to revolutionize our understanding of this clock regulation, revealing a surprising degree of organ, tissue, and cell-type specificity. In this review, we highlight recent advances in our spatial view of the clock across the plant, both in terms of how it is regulated and how it regulates a diversity of output processes. We outline how understanding these spatially specific functions will help reveal the range of ways that the clock provides a fitness benefit for the plant.
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Affiliation(s)
- William Davis
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Motomu Endo
- Authors for correspondence: (M.E.); (J.C.W.L.)
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16
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Perez-Garcia P, Serrano-Ron L, Moreno-Risueno MA. The nature of the root clock at single cell resolution: Principles of communication and similarities with plant and animal pulsatile and circadian mechanisms. Curr Opin Cell Biol 2022; 77:102102. [DOI: 10.1016/j.ceb.2022.102102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/14/2022] [Accepted: 04/24/2022] [Indexed: 11/30/2022]
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17
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A guiding role of the Arabidopsis circadian clock in cell differentiation revealed by time-series single-cell RNA sequencing. Cell Rep 2022; 40:111059. [PMID: 35830805 DOI: 10.1016/j.celrep.2022.111059] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 04/01/2022] [Accepted: 06/14/2022] [Indexed: 11/21/2022] Open
Abstract
Circadian rhythms and progression of cell differentiation are closely coupled in multicellular organisms. However, whether establishment of circadian rhythms regulates cell differentiation or vice versa has not been elucidated due to technical limitations. Here, we exploit high cell fate plasticity of plant cells to perform single-cell RNA sequencing during the entire process of cell differentiation. By analyzing reconstructed actual time series of the differentiation processes at single-cell resolution using a method we developed (PeakMatch), we find that the expression profile of clock genes is changed prior to cell differentiation, including induction of the clock gene LUX ARRYTHMO (LUX). ChIP sequencing analysis reveals that LUX induction in early differentiating cells directly targets genes involved in cell-cycle progression to regulate cell differentiation. Taken together, these results not only reveal a guiding role of the plant circadian clock in cell differentiation but also provide an approach for time-series analysis at single-cell resolution.
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18
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Hoopes GM, Zarka D, Feke A, Acheson K, Hamilton JP, Douches D, Buell CR, Farré EM. Keeping time in the dark: Potato diel and circadian rhythmic gene expression reveals tissue-specific circadian clocks. PLANT DIRECT 2022; 6:e425. [PMID: 35844780 PMCID: PMC9277033 DOI: 10.1002/pld3.425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 05/15/2022] [Accepted: 06/24/2022] [Indexed: 05/10/2023]
Abstract
The circadian clock is an internal molecular oscillator and coordinates numerous physiological processes through regulation of molecular pathways. Tissue-specific clocks connected by mobile signals have previously been found to run at different speeds in Arabidopsis thaliana tissues. However, tissue variation in circadian clocks in crop species is unknown. In this study, leaf and tuber global gene expression in cultivated potato under cycling and constant environmental conditions was profiled. In addition, we used a circadian-regulated luciferase reporter construct to study tuber gene expression rhythms. Diel and circadian expression patterns were present among 17.9% and 5.6% of the expressed genes in the tuber. Over 500 genes displayed differential tissue specific diel phases. Intriguingly, few core circadian clock genes had circadian expression patterns, while all such genes were circadian rhythmic in cultivated tomato leaves. Furthermore, robust diel and circadian transcriptional rhythms were observed among detached tubers. Our results suggest alternative regulatory mechanisms and/or clock composition is present in potato, as well as the presence of tissue-specific independent circadian clocks. We have provided the first evidence of a functional circadian clock in below-ground storage organs, holding important implications for other storage root and tuberous crops.
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Affiliation(s)
| | - Daniel Zarka
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Ann Feke
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Kaitlyn Acheson
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
| | - John P. Hamilton
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
| | - David Douches
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - C. Robin Buell
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
- Michigan State University AgBioResearchMichigan State UniversityEast LansingMichiganUSA
| | - Eva M. Farré
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
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19
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Bellande K, Trinh DC, Gonzalez AA, Dubois E, Petitot AS, Lucas M, Champion A, Gantet P, Laplaze L, Guyomarc’h S. PUCHI represses early meristem formation in developing lateral roots of Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3496-3510. [PMID: 35224628 PMCID: PMC9162184 DOI: 10.1093/jxb/erac079] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 02/25/2022] [Indexed: 05/21/2023]
Abstract
Lateral root organogenesis is a key process in the development of a plant's root system and its adaptation to the environment. During lateral root formation, an early phase of cell proliferation first produces a four-cell-layered primordium, and only from this stage onwards is a root meristem-like structure, expressing root stem cell niche marker genes, being established in the developing organ. Previous studies reported that the gene regulatory network controlling lateral root formation is organized into two subnetworks whose mutual inhibition may contribute to organ patterning. PUCHI encodes an AP2/ERF transcription factor expressed early during lateral root primordium development and required for correct lateral root formation. To dissect the molecular events occurring during this early phase, we generated time-series transcriptomic datasets profiling lateral root development in puchi-1 mutants and wild types. Transcriptomic and reporter analyses revealed that meristem-related genes were expressed ectopically at early stages of lateral root formation in puchi-1 mutants. We conclude that, consistent with the inhibition of genetic modules contributing to lateral root development, PUCHI represses ectopic establishment of meristematic cell identities at early stages of organ development. These findings shed light on gene network properties that orchestrate correct timing and patterning during lateral root formation.
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Affiliation(s)
| | | | - Anne-Alicia Gonzalez
- Univ Montpellier, CNRS, INSERM, Montpellier, France
- Montpellier GenomiX, France Génomique, Montpellier, France
| | - Emeric Dubois
- Univ Montpellier, CNRS, INSERM, Montpellier, France
- Montpellier GenomiX, France Génomique, Montpellier, France
| | | | - Mikaël Lucas
- DIADE, Univ Montpellier, IRD, Montpellier, France
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20
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Yan H, Lee J, Song Q, Li Q, Schiefelbein J, Zhao B, Li S. Identification of new marker genes from plant single-cell RNA-seq data using interpretable machine learning methods. THE NEW PHYTOLOGIST 2022; 234:1507-1520. [PMID: 35211979 PMCID: PMC9314150 DOI: 10.1111/nph.18053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 02/06/2022] [Indexed: 05/16/2023]
Abstract
An essential step in the analysis of single-cell RNA sequencing data is to classify cells into specific cell types using marker genes. In this study, we have developed a machine learning pipeline called single-cell predictive marker (SPmarker) to identify novel cell-type marker genes in the Arabidopsis root. Unlike traditional approaches, our method uses interpretable machine learning models to select marker genes. We have demonstrated that our method can: assign cell types based on cells that were labelled using published methods; project cell types identified by trajectory analysis from one data set to other data sets; and assign cell types based on internal GFP markers. Using SPmarker, we have identified hundreds of new marker genes that were not identified before. As compared to known marker genes, the new marker genes have more orthologous genes identifiable in the corresponding rice single-cell clusters. The new root hair marker genes also include 172 genes with orthologs expressed in root hair cells in five non-Arabidopsis species, which expands the number of marker genes for this cell type by 35-154%. Our results represent a new approach to identifying cell-type marker genes from scRNA-seq data and pave the way for cross-species mapping of scRNA-seq data in plants.
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Affiliation(s)
- Haidong Yan
- School of Plant and Environmental Sciences (SPES)Virginia TechBlacksburgVA24060USA
| | - Jiyoung Lee
- School of Plant and Environmental Sciences (SPES)Virginia TechBlacksburgVA24060USA
- Graduate Program in Genetics, Bioinformatics and Computational Biology (GBCB)Virginia TechBlacksburgVA24060USA
| | - Qi Song
- School of Plant and Environmental Sciences (SPES)Virginia TechBlacksburgVA24060USA
- Graduate Program in Genetics, Bioinformatics and Computational Biology (GBCB)Virginia TechBlacksburgVA24060USA
| | - Qi Li
- School of Plant and Environmental Sciences (SPES)Virginia TechBlacksburgVA24060USA
| | - John Schiefelbein
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMI48109USA
| | - Bingyu Zhao
- School of Plant and Environmental Sciences (SPES)Virginia TechBlacksburgVA24060USA
| | - Song Li
- School of Plant and Environmental Sciences (SPES)Virginia TechBlacksburgVA24060USA
- Graduate Program in Genetics, Bioinformatics and Computational Biology (GBCB)Virginia TechBlacksburgVA24060USA
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21
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Achom M, Roy P, Lagunas B, Picot E, Richards L, Bonyadi-Pour R, Pardal AJ, Baxter L, Richmond BL, Aschauer N, Fletcher EM, Rowson M, Blackwell J, Rich-Griffin C, Mysore KS, Wen J, Ott S, Carré IA, Gifford ML. Plant circadian clock control of Medicago truncatula nodulation via regulation of nodule cysteine-rich peptides. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2142-2156. [PMID: 34850882 PMCID: PMC8982390 DOI: 10.1093/jxb/erab526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 11/30/2021] [Indexed: 06/13/2023]
Abstract
Legumes house nitrogen-fixing endosymbiotic rhizobia in specialized polyploid cells within root nodules, which undergo tightly regulated metabolic activity. By carrying out expression analysis of transcripts over time in Medicago truncatula nodules, we found that the circadian clock enables coordinated control of metabolic and regulatory processes linked to nitrogen fixation. This involves the circadian clock-associated transcription factor LATE ELONGATED HYPOCOTYL (LHY), with lhy mutants being affected in nodulation. Rhythmic transcripts in root nodules include a subset of nodule-specific cysteine-rich peptides (NCRs) that have the LHY-bound conserved evening element in their promoters. Until now, studies have suggested that NCRs act to regulate bacteroid differentiation and keep the rhizobial population in check. However, these conclusions came from the study of a few members of this very large gene family that has complex diversified spatio-temporal expression. We suggest that rhythmic expression of NCRs may be important for temporal coordination of bacterial activity with the rhythms of the plant host, in order to ensure optimal symbiosis.
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Affiliation(s)
- Mingkee Achom
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Proyash Roy
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Beatriz Lagunas
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Emma Picot
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Luke Richards
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Roxanna Bonyadi-Pour
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Alonso J Pardal
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Laura Baxter
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Bethany L Richmond
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Nadine Aschauer
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Eleanor M Fletcher
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Monique Rowson
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Joseph Blackwell
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Charlotte Rich-Griffin
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Kirankumar S Mysore
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401, USA
| | - Jiangqi Wen
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401, USA
| | - Sascha Ott
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Isabelle A Carré
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Miriam L Gifford
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
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22
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Cabrera J, Conesa CM, Del Pozo JC. May the dark be with roots: a perspective on how root illumination may bias in vitro research on plant-environment interactions. THE NEW PHYTOLOGIST 2022; 233:1988-1997. [PMID: 34942016 DOI: 10.1111/nph.17936] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Roots anchor plants to the soil, providing them with nutrients and water while creating a defence network and facilitating beneficial interactions with a multitude of living organisms and climatological conditions. To facilitate morphological and molecular studies, root research has been conducted using in vitro systems. However, under natural conditions, roots grow in the dark, mainly in the absence of illumination, except for the relatively low illumination of the upper soil surface, and this has been largely ignored. Here, we discuss the results found over the last decade on how experimental exposure of roots to light may bias root development and responses through the alteration of hormonal signalling, cytoskeleton organization, reactive oxygen species or the accumulation of flavonoids, among other factors. Illumination alters the uptake of nutrients or water, and also affects the response of the roots to abiotic stresses and root interactions with the microbiota. Furthermore, we review in vitro systems created to maintain roots in darkness, and provide a comparative analysis of root transcriptomes obtained with these devices. Finally, we identify other experimental variables that should be considered to better mimic soil conditions, whose improvement would benefit studies using in vitro cultivation or enclosed ecosystems.
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Affiliation(s)
- Javier Cabrera
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Consejo Superior de Investigaciones Científicas (UPM-INIA/CSIC), UPM, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Carlos M Conesa
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Consejo Superior de Investigaciones Científicas (UPM-INIA/CSIC), UPM, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
- Escuela Técnica Superior de Ingeniería Agronómica, Agroambiental y de Biosistemas (ETSIAAB), Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Juan C Del Pozo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Consejo Superior de Investigaciones Científicas (UPM-INIA/CSIC), UPM, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
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23
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Stöckle D, Reyes-Hernández BJ, Barro AV, Nenadić M, Winter Z, Marc-Martin S, Bald L, Ursache R, Fujita S, Maizel A, Vermeer JEM. Microtubule-based perception of mechanical conflicts controls plant organ morphogenesis. SCIENCE ADVANCES 2022; 8:eabm4974. [PMID: 35138892 PMCID: PMC8827652 DOI: 10.1126/sciadv.abm4974] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/22/2021] [Indexed: 05/30/2023]
Abstract
Precise coordination between cells and tissues is essential for differential growth in plants. During lateral root formation in Arabidopsis thaliana, the endodermis is actively remodeled to allow outgrowth of the new organ. Here, we show that microtubule arrays facing lateral root founder cells display a higher order compared to arrays on the opposite side of the same cell, and this asymmetry is required for endodermal remodeling and lateral root initiation. We identify that MICROTUBULE ASSOCIATED PROTEIN 70-5 (MAP70-5) is necessary for the establishment of this spatially defined microtubule organization and endodermis remodeling and thus contributes to lateral root morphogenesis. We propose that MAP70-5 and cortical microtubule arrays in the endodermis integrate the mechanical signals generated by lateral root outgrowth, facilitating the channeling of organogenesis.
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Affiliation(s)
- Dorothee Stöckle
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
- Laboratory of Cell and Molecular Biology, Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, CH-2000 Neuchâtel, Switzerland
| | | | - Amaya Vilches Barro
- Center for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Milica Nenadić
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Zsofiá Winter
- Laboratory of Cell and Molecular Biology, Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Sophie Marc-Martin
- Laboratory of Cell and Molecular Biology, Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Lotte Bald
- Center for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Robertas Ursache
- Department of Molecular Plant Biology, University of Lausanne, UNIL-Sorge, 1015 Lausanne, Switzerland
| | - Satoshi Fujita
- Department of Molecular Plant Biology, University of Lausanne, UNIL-Sorge, 1015 Lausanne, Switzerland
| | - Alexis Maizel
- Laboratory of Cell and Molecular Biology, Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Joop EM Vermeer
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
- Laboratory of Cell and Molecular Biology, Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, CH-2000 Neuchâtel, Switzerland
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24
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Jourquin J, Fernandez AI, Parizot B, Xu K, Grunewald W, Mamiya A, Fukaki H, Beeckman T. Two phylogenetically unrelated peptide-receptor modules jointly regulate lateral root initiation via a partially shared signaling pathway in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2022; 233:1780-1796. [PMID: 34913488 PMCID: PMC9302118 DOI: 10.1111/nph.17919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 12/04/2021] [Indexed: 05/06/2023]
Abstract
Peptide-receptor signaling is an important system for intercellular communication, regulating many developmental processes. A single process can be controlled by several distinct signaling peptides. However, since peptide-receptor modules are usually studied separately, their mechanistic interactions remain largely unexplored. Two phylogenetically unrelated peptide-receptor modules, GLV6/GLV10-RGI and TOLS2/PIP2-RLK7, independently described as inhibitors of lateral root initiation, show striking similarities between their expression patterns and gain- and loss-of-function phenotypes, suggesting a common function during lateral root spacing and initiation. The GLV6/GLV10-RGI and TOLS2/PIP2-RLK7 modules trigger similar transcriptional changes, likely in part via WRKY transcription factors. Their overlapping set of response genes includes PUCHI and PLT5, both required for the effect of GLV6/10, as well as TOLS2, on lateral root initiation. Furthermore, both modules require the activity of MPK6 and can independently trigger MPK3/MPK6 phosphorylation. The GLV6/10 and TOLS2/PIP2 signaling pathways seem to converge in the activation of MPK3/MPK6, leading to the induction of a similar transcriptional response in the same target cells, thereby regulating lateral root initiation through a (partially) common mechanism. Convergence of signaling pathways downstream of phylogenetically unrelated peptide-receptor modules adds an additional, and hitherto unrecognized, level of complexity to intercellular communication networks in plants.
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Affiliation(s)
- Joris Jourquin
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
- Center for Plant Systems BiologyVIB‐UGentGhent9052Belgium
| | - Ana Ibis Fernandez
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
- Center for Plant Systems BiologyVIB‐UGentGhent9052Belgium
| | - Boris Parizot
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
- Center for Plant Systems BiologyVIB‐UGentGhent9052Belgium
| | - Ke Xu
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
- Center for Plant Systems BiologyVIB‐UGentGhent9052Belgium
| | - Wim Grunewald
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
- Center for Plant Systems BiologyVIB‐UGentGhent9052Belgium
| | - Akihito Mamiya
- Department of BiologyGraduate School of ScienceKobe UniversityKobe657‐8501Japan
| | - Hidehiro Fukaki
- Department of BiologyGraduate School of ScienceKobe UniversityKobe657‐8501Japan
| | - Tom Beeckman
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
- Center for Plant Systems BiologyVIB‐UGentGhent9052Belgium
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25
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Shimadzu S, Furuya T, Ozawa Y, Fukuda H, Kondo Y. Spatio-temporal imaging of cell fate dynamics in single plant cells using luminescence microscope. QUANTITATIVE PLANT BIOLOGY 2022; 3:e15. [PMID: 37077981 PMCID: PMC10095866 DOI: 10.1017/qpb.2022.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/20/2022] [Accepted: 06/20/2022] [Indexed: 05/03/2023]
Abstract
Stem cell fates are spatio-temporally regulated during plant development. Time-lapse imaging of fluorescence reporters is the most widely used method for spatio-temporal analysis of biological processes. However, excitation light for imaging fluorescence reporters causes autofluorescence and photobleaching. Unlike fluorescence reporters, luminescence proteins do not require excitation light, and therefore offer an alternative reporter for long-term and quantitative spatio-temporal analysis. We established an imaging system for luciferase, which enabled monitoring cell fate marker dynamics during vascular development in a vascular cell induction system called VISUAL. Single cells expressing the cambium marker, proAtHB8:ELUC, had sharp luminescence peaks at different time points. Furthermore, dual-color luminescence imaging revealed spatio-temporal relationships between cells that differentiated into xylem or phloem, and cells that transitioned from procambium to cambium. This imaging system enables not only the detection of temporal gene expression, but also facilitates monitoring of spatio-temporal dynamics of cell identity transitions at the single cell level.
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Affiliation(s)
- Shunji Shimadzu
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Science, Kobe University, Kobe, Japan
| | - Tomoyuki Furuya
- Graduate School of Science, Kobe University, Kobe, Japan
- College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Yasuko Ozawa
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroo Fukuda
- Department of Bioscience and Biotechnology, Faculty of Bioenvironmental Science, Kyoto University of Advanced Science, Kameoka, Japan
| | - Yuki Kondo
- Graduate School of Science, Kobe University, Kobe, Japan
- Author for correspondence: Y. Kondo, E-mail:
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26
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Guyomarc'h S, Lucas M, Laplaze L. Postembryonic Organogenesis in Plants: Experimental Induction of New Shoot and Root Organs. Methods Mol Biol 2022; 2395:79-95. [PMID: 34822150 DOI: 10.1007/978-1-0716-1816-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Postembryonic organogenesis is a critical component in plant root and shoot development and its adaptation to the environment. Decades of scientific analyses have yielded a wealth of experimental data about the cellular and molecular processes orchestrating the postembryonic formation of new shoot and root organs. Among these, distribution and signaling of the plant hormone auxin play a prominent role. Systems biology approaches are now particularly interesting to study the emerging properties of such complex and dynamic regulatory networks. To fully explore the precise kinetics of these organogenesis processes, efficient protocols for the synchronized induction of shoot and root organogenesis are extremely valuable. Two protocols for shoot and root organ induction are detailed.
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Affiliation(s)
| | - Mikaël Lucas
- DIADE, Univ Montpellier, IRD, CIRAD, Montpellier, France
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27
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Karlova R, Boer D, Hayes S, Testerink C. Root plasticity under abiotic stress. PLANT PHYSIOLOGY 2021; 187:1057-1070. [PMID: 34734279 PMCID: PMC8566202 DOI: 10.1093/plphys/kiab392] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/25/2021] [Indexed: 05/08/2023]
Abstract
Abiotic stresses increasingly threaten existing ecological and agricultural systems across the globe. Plant roots perceive these stresses in the soil and adapt their architecture accordingly. This review provides insights into recent discoveries showing the importance of root system architecture (RSA) and plasticity for the survival and development of plants under heat, cold, drought, salt, and flooding stress. In addition, we review the molecular regulation and hormonal pathways involved in controlling RSA plasticity, main root growth, branching and lateral root growth, root hair development, and formation of adventitious roots. Several stresses affect root anatomy by causing aerenchyma formation, lignin and suberin deposition, and Casparian strip modulation. Roots can also actively grow toward favorable soil conditions and avoid environments detrimental to their development. Recent advances in understanding the cellular mechanisms behind these different root tropisms are discussed. Understanding root plasticity will be instrumental for the development of crops that are resilient in the face of abiotic stress.
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Affiliation(s)
- Rumyana Karlova
- Laboratory of Plant Physiology, Wageningen University, 6700 AA Wageningen, The Netherlands
| | - Damian Boer
- Laboratory of Plant Physiology, Wageningen University, 6700 AA Wageningen, The Netherlands
| | - Scott Hayes
- Laboratory of Plant Physiology, Wageningen University, 6700 AA Wageningen, The Netherlands
| | - Christa Testerink
- Laboratory of Plant Physiology, Wageningen University, 6700 AA Wageningen, The Netherlands
- Author for communication:
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28
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Band LR. Auxin fluxes through plasmodesmata. THE NEW PHYTOLOGIST 2021; 231:1686-1692. [PMID: 34053083 DOI: 10.1111/nph.17517] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/29/2021] [Indexed: 05/27/2023]
Abstract
Characterising the processes that control auxin dynamics is essential to understanding how auxin regulates plant development. Over recent years, several studies have investigated auxin diffusion through plasmodesmata, characterising this cell-to-cell diffusion and demonstrating that it affects auxin distributions. Furthermore, studies have shown that plasmodesmatal auxin diffusion affects developmental processes, including phototropism, lateral root emergence and leaf hyponasty. This short Tansley Insight review describes how these studies have contributed to our understanding of auxin dynamics and discusses potential future directions in this area.
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Affiliation(s)
- Leah R Band
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
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29
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Šečić E, Zanini S, Wibberg D, Jelonek L, Busche T, Kalinowski J, Nasfi S, Thielmann J, Imani J, Steinbrenner J, Kogel KH. A novel plant-fungal association reveals fundamental sRNA and gene expression reprogramming at the onset of symbiosis. BMC Biol 2021; 19:171. [PMID: 34429124 PMCID: PMC8385953 DOI: 10.1186/s12915-021-01104-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 07/16/2021] [Indexed: 01/15/2023] Open
Affiliation(s)
- Ena Šečić
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Silvia Zanini
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Daniel Wibberg
- Center for Biotechnology - CeBiTec, Bielefeld University, 33615, Bielefeld, Germany
| | - Lukas Jelonek
- Institute of Bioinformatics and Systems Biology, Justus Liebig University, 35392, Giessen, Germany
| | - Tobias Busche
- Center for Biotechnology - CeBiTec, Bielefeld University, 33615, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology - CeBiTec, Bielefeld University, 33615, Bielefeld, Germany
| | - Sabrine Nasfi
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Jennifer Thielmann
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Jafargholi Imani
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Jens Steinbrenner
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Karl-Heinz Kogel
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany.
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30
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Shin Y, Chane A, Jung M, Lee Y. Recent Advances in Understanding the Roles of Pectin as an Active Participant in Plant Signaling Networks. PLANTS (BASEL, SWITZERLAND) 2021; 10:1712. [PMID: 34451757 PMCID: PMC8399534 DOI: 10.3390/plants10081712] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 01/02/2023]
Abstract
Pectin is an abundant cell wall polysaccharide with essential roles in various biological processes. The structural diversity of pectins, along with the numerous combinations of the enzymes responsible for pectin biosynthesis and modification, plays key roles in ensuring the specificity and plasticity of cell wall remodeling in different cell types and under different environmental conditions. This review focuses on recent progress in understanding various aspects of pectin, from its biosynthetic and modification processes to its biological roles in different cell types. In particular, we describe recent findings that cell wall modifications serve not only as final outputs of internally determined pathways, but also as key components of intercellular communication, with pectin as a major contributor to this process. The comprehensive view of the diverse roles of pectin presented here provides an important basis for understanding how cell wall-enclosed plant cells develop, differentiate, and interact.
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Affiliation(s)
- Yesol Shin
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea; (Y.S.); (A.C.); (M.J.)
| | - Andrea Chane
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea; (Y.S.); (A.C.); (M.J.)
| | - Minjung Jung
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea; (Y.S.); (A.C.); (M.J.)
| | - Yuree Lee
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea; (Y.S.); (A.C.); (M.J.)
- Research Center for Plant Plasticity, Seoul National University, Seoul 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
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31
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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: 70] [Impact Index Per Article: 23.3] [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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32
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Serrano-Ron L, Perez-Garcia P, Sanchez-Corrionero A, Gude I, Cabrera J, Ip PL, Birnbaum KD, Moreno-Risueno MA. Reconstruction of lateral root formation through single-cell RNA sequencing reveals order of tissue initiation. MOLECULAR PLANT 2021; 14:1362-1378. [PMID: 34062316 PMCID: PMC8338891 DOI: 10.1016/j.molp.2021.05.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 05/01/2021] [Accepted: 05/26/2021] [Indexed: 05/13/2023]
Abstract
Postembryonic organogenesis is critical for plant development. Underground, lateral roots (LRs) form the bulk of mature root systems, yet the ontogeny of the LR primordium (LRP) is not clear. In this study, we performed the single-cell RNA sequencing through the first four stages of LR formation in Arabidopsis. Our analysis led to a model in which a single group of precursor cells, with a cell identity different from their pericycle origins, rapidly reprograms and splits into a mixed ground tissue/stem cell niche fate and a vascular precursor fate. The ground tissue and stem cell niche fates soon separate and a subset of more specialized vascular cells form sucrose transporting phloem cells that appear to connect to the primary root. We did not detect cells resembling epidermis or root cap, suggesting that outer tissues may form later, preceding LR emergence. At this stage, some remaining initial precursor cells form the primordium flanks, while the rest create a reservoir of pluripotent cells that are able to replace the LR if damaged. Laser ablation of the central and lateral LRP regions showed that remaining cells restart the sequence of tissue initiation to form a LR. Collectively, our study reveals an ontological hierarchy for LR formation with an early and sequential split of main root tissues and stem cells.
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Affiliation(s)
- Laura Serrano-Ron
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Pablo Perez-Garcia
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain.
| | - Alvaro Sanchez-Corrionero
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Inmaculada Gude
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Javier Cabrera
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Pui-Leng Ip
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Miguel A Moreno-Risueno
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain.
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33
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Wang L, Zhou A, Li J, Yang M, Bu F, Ge L, Chen L, Huang W. Circadian rhythms driving a fast-paced root clock implicate species-specific regulation in Medicago truncatula. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1537-1554. [PMID: 34009694 DOI: 10.1111/jipb.13138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/13/2021] [Indexed: 06/12/2023]
Abstract
Plants have a hierarchical circadian structure comprising multiple tissue-specific oscillators that operate at different speeds and regulate the expression of distinct sets of genes in different organs. However, the identity of the genes differentially regulated by the circadian clock in different organs, such as roots, and how their oscillations create functional specialization remain unclear. Here, we profiled the diurnal and circadian landscapes of the shoots and roots of Medicago truncatula and identified the conserved regulatory sequences contributing to transcriptome oscillations in each organ. We found that the light-dark cycles strongly affect the global transcriptome oscillation in roots, and many clock genes oscillate only in shoots. Moreover, many key genes involved in nitrogen fixation are regulated by circadian rhythms. Surprisingly, the root clock runs faster than the shoot clock, which is contrary to the hierarchical circadian structure showing a slow-paced root clock in both detached and intact Arabidopsis thaliana (L.) Heynh. roots. Our result provides important clues about the species-specific circadian regulatory mechanism, which is often overlooked, and possibly coordinates the timing between shoots and roots independent of the current prevailing model.
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Affiliation(s)
- Liping Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Anqi Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Mingkang Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Fan Bu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Liangfa Ge
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, 510642, China
| | - Liang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Wei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
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34
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Masuda K, Fukuda H. Unstable Phase Response Curves Shown by Spatiotemporal Patterns in the Plant Root Circadian Clock. J Biol Rhythms 2021; 36:432-441. [PMID: 34313451 DOI: 10.1177/07487304211028440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Phase response curves (PRCs) play important roles in the entrainment of periodic environmental cycles. Measuring the PRC is necessary to elucidate the relationship between environmental cues and the circadian clock. Conversely, the PRCs of plant circadian clocks are unstable due to multiple factors such as biotic/abiotic noise, individual differences, changes in amplitude, growth stage, and organ/tissue specificity. However, evaluating the effect of each factor is important because PRCs are commonly obtained by determining the response of many individuals, which include different amplitude states and organs. The plant root circadian clock spontaneously generates a spatiotemporal pattern called a stripe pattern, whereby all phases of the circadian rhythm exist within an individual root. Therefore, stimulating a plant root expressing this pattern enables phase responses at all phases to be measured using an individual root. In this study, we measured PRCs for thermal stimuli using this spatiotemporal pattern method and found that the PRC changed asymmetrically with positive and negative temperature stimuli. Individual differences were observed for weak but not for strong temperature stimuli. The root PRC changed depending on the amplitude of the circadian rhythm. The PRC in the young root near the hypocotyl was more sensitive than those in older roots or near the tip. Simulation with a phase oscillator model revealed the effect of measurement and internal noises on the PRC. These results indicate that instability in the entrainment of the plant circadian clock involves multiple factors, each having different characteristics. These results may help us understand how plant circadian clocks adapt to unstable environments and how plant circadian clocks with different characteristics, such as organ, age, and amplitude, are integrated within individuals.
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Affiliation(s)
- Kosaku Masuda
- Graduate School of Engineering, Osaka Prefecture University, Osaka, Japan.,Japan Society for the Promotion of Science, Tokyo, Japan
| | - Hirokazu Fukuda
- Graduate School of Engineering, Osaka Prefecture University, Osaka, Japan
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35
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Sorkin ML, Nusinow DA. Time Will Tell: Intercellular Communication in the Plant Clock. TRENDS IN PLANT SCIENCE 2021; 26:706-719. [PMID: 33468432 DOI: 10.1016/j.tplants.2020.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/14/2020] [Accepted: 12/20/2020] [Indexed: 05/17/2023]
Abstract
Multicellular organisms have evolved local and long-distance signaling mechanisms to synchronize development and response to stimuli among a complex network of cells, tissues, and organs. Biological timekeeping is one such activity that is suggested to be coordinated within an organism to anticipate and respond to daily and seasonal patterns in the environment. New research into the plant clock suggests circadian rhythms are communicated between cells and across long distances. However, further clarity is required on the nature of the signaling molecules and the mechanisms underlying signal translocation. Here we summarize the roles and properties of tissue-specific circadian rhythms, discuss the evidence for local and long-distance clock communication, and evaluate the potential signaling molecules and transport mechanisms involved in this system.
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Affiliation(s)
- Maria L Sorkin
- Donald Danforth Plant Science Center, St. Louis, MO, USA; Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA
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36
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Serrano-Ron L, Cabrera J, Perez-Garcia P, Moreno-Risueno MA. Unraveling Root Development Through Single-Cell Omics and Reconstruction of Gene Regulatory Networks. FRONTIERS IN PLANT SCIENCE 2021; 12:661361. [PMID: 34017350 PMCID: PMC8129646 DOI: 10.3389/fpls.2021.661361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/25/2021] [Indexed: 05/30/2023]
Abstract
Over the last decades, research on postembryonic root development has been facilitated by "omics" technologies. Among these technologies, microarrays first, and RNA sequencing (RNA-seq) later, have provided transcriptional information on the underlying molecular processes establishing the basis of System Biology studies in roots. Cell fate specification and development have been widely studied in the primary root, which involved the identification of many cell type transcriptomes and the reconstruction of gene regulatory networks (GRN). The study of lateral root (LR) development has not been an exception. However, the molecular mechanisms regulating cell fate specification during LR formation remain largely unexplored. Recently, single-cell RNA-seq (scRNA-seq) studies have addressed the specification of tissues from stem cells in the primary root. scRNA-seq studies are anticipated to be a useful approach to decipher cell fate specification and patterning during LR formation. In this review, we address the different scRNA-seq strategies used both in plants and animals and how we could take advantage of scRNA-seq to unravel new regulatory mechanisms and reconstruct GRN. In addition, we discuss how to integrate scRNA-seq results with previous RNA-seq datasets and GRN. We also address relevant findings obtained through single-cell based studies and how LR developmental studies could be facilitated by scRNA-seq approaches and subsequent GRN inference. The use of single-cell approaches to investigate LR formation could help to decipher fundamental biological mechanisms such as cell memory, synchronization, polarization, or pluripotency.
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Affiliation(s)
| | | | | | - Miguel A. Moreno-Risueno
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
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37
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Paajanen P, Lane de Barros Dantas L, Dodd AN. Layers of crosstalk between circadian regulation and environmental signalling in plants. Curr Biol 2021; 31:R399-R413. [PMID: 33905701 DOI: 10.1016/j.cub.2021.03.046] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Circadian regulation has a pervasive influence upon plant development, physiology and metabolism, impacting upon components of fitness and traits of agricultural importance. Circadian regulation is inextricably connected to the responses of plants to their abiotic environments, from the cellular to whole plant scales. Here, we review the crosstalk that occurs between circadian regulation and responses to the abiotic environment from the intracellular scale through to naturally fluctuating environments. We examine the spatial crosstalk that forms part of plant circadian regulation, at the subcellular, tissue, organ and whole-plant scales. This includes a focus on chloroplast and mitochondrial signalling, alternative splicing, long-distance circadian signalling and circadian regulation within natural environments. We also consider mathematical models for plant circadian regulation, to suggest future areas for advancing understanding of roles for circadian regulation in plant responses to environmental cues.
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Affiliation(s)
- Pirita Paajanen
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Antony N Dodd
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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38
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Ursache R, De Jesus Vieira Teixeira C, Dénervaud Tendon V, Gully K, De Bellis D, Schmid-Siegert E, Grube Andersen T, Shekhar V, Calderon S, Pradervand S, Nawrath C, Geldner N, Vermeer JEM. GDSL-domain proteins have key roles in suberin polymerization and degradation. NATURE PLANTS 2021; 7:353-364. [PMID: 33686223 PMCID: PMC7610369 DOI: 10.1038/s41477-021-00862-9] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 01/25/2021] [Indexed: 05/19/2023]
Abstract
Plant roots acquire nutrients and water while managing interactions with the soil microbiota. The root endodermis provides an extracellular diffusion barrier through a network of lignified cell walls called Casparian strips, supported by subsequent formation of suberin lamellae. Whereas lignification is thought to be irreversible, suberin lamellae display plasticity, which is crucial for root adaptative responses. Although suberin is a major plant polymer, fundamental aspects of its biosynthesis and turnover have remained obscure. Plants shape their root system via lateral root formation, an auxin-induced process requiring local breaking and re-sealing of endodermal lignin and suberin barriers. Here, we show that differentiated endodermal cells have a specific, auxin-mediated transcriptional response dominated by cell wall remodelling genes. We identified two sets of auxin-regulated GDSL lipases. One is required for suberin synthesis, while the other can drive suberin degradation. These enzymes have key roles in suberization, driving root suberin plasticity.
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Affiliation(s)
- Robertas Ursache
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland.
| | | | | | - Kay Gully
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Damien De Bellis
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
| | - Emanuel Schmid-Siegert
- Vital-IT Competence Center, Swiss Institute of Bioinformatics, Lausanne, Switzerland
- NGSAI, Epalinges, Switzerland
| | - Tonni Grube Andersen
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Vinay Shekhar
- Laboratory of Cell and Molecular Biology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Centre, University of Zurich, Zurich, Switzerland
| | - Sandra Calderon
- Vital-IT Competence Center, Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Genomic Technologies Facility, University of Lausanne, Lausanne, Switzerland
| | - Sylvain Pradervand
- Vital-IT Competence Center, Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Genomic Technologies Facility, University of Lausanne, Lausanne, Switzerland
| | - Christiane Nawrath
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Niko Geldner
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland.
| | - Joop E M Vermeer
- Laboratory of Cell and Molecular Biology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Centre, University of Zurich, Zurich, Switzerland.
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39
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Zhang Z, Sun Y, Li Y. Plant rejuvenation: from phenotypes to mechanisms. PLANT CELL REPORTS 2020; 39:1249-1262. [PMID: 32780162 DOI: 10.1007/s00299-020-02577-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/28/2020] [Accepted: 08/01/2020] [Indexed: 06/11/2023]
Abstract
Plant rejuvenation refers to the reversal of the adult phase in plants and the recovery of part or all of juvenile plant characteristics. The growth and reproductive vitality of plants can be increased after rejuvenation. In recent years, research has successfully reversed the development clock in plants by certain methods; created rejuvenated plants and revealed the basic rules of plant morphology, physiology and reproduction. Here, we reconstitute the changes at the morphological and macromolecular levels, including those in RNA, phytohormones and DNA, during plant rejuvenation. In addition, the characteristics of plant phase changes that can be used as references for plant rejuvenation are also summarized. We further propose possible mechanisms for plant rejuvenation, methods for reversing plant development and problems that should be avoided. Overall, this study highlights the physiological and molecular events involved in plant rejuvenation.
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Affiliation(s)
- Zijie Zhang
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Laboratory For Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Yuhan Sun
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Laboratory For Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Yun Li
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Laboratory For Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China.
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40
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Fernandez AI, Vangheluwe N, Xu K, Jourquin J, Claus LAN, Morales-Herrera S, Parizot B, De Gernier H, Yu Q, Drozdzecki A, Maruta T, Hoogewijs K, Vannecke W, Peterson B, Opdenacker D, Madder A, Nimchuk ZL, Russinova E, Beeckman T. GOLVEN peptide signalling through RGI receptors and MPK6 restricts asymmetric cell division during lateral root initiation. NATURE PLANTS 2020; 6:533-543. [PMID: 32393883 DOI: 10.1038/s41477-020-0645-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 03/24/2020] [Indexed: 05/26/2023]
Abstract
During lateral root initiation, lateral root founder cells undergo asymmetric cell divisions that generate daughter cells with different sizes and fates, a prerequisite for correct primordium organogenesis. An excess of the GLV6/RGF8 peptide disrupts these initial asymmetric cell divisions, resulting in more symmetric divisions and the failure to achieve lateral root organogenesis. Here, we show that loss-of-function GLV6 and its homologue GLV10 increase asymmetric cell divisions during lateral root initiation, and we identified three members of the RGF1 INSENSITIVE/RGF1 receptor subfamily as likely GLV receptors in this process. Through a suppressor screen, we found that MITOGEN-ACTIVATED PROTEIN KINASE6 is a downstream regulator of the GLV pathway. Our data indicate that GLV6 and GLV10 act as inhibitors of asymmetric cell divisions and signal through RGF1 INSENSITIVE receptors and MITOGEN-ACTIVATED PROTEIN KINASE6 to restrict the number of initial asymmetric cell divisions that take place during lateral root initiation.
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Affiliation(s)
- Ana I Fernandez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Nick Vangheluwe
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ke Xu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Joris Jourquin
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lucas Alves Neubus Claus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Stefania Morales-Herrera
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Laboratory of Molecular Cell Biology, KU Leuven, Kasteelpark, Leuven, Belgium
- VIB Center for Microbiology, Kasteelpark, Leuven, Belgium
| | - Boris Parizot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hugues De Gernier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Qiaozhi Yu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Andrzej Drozdzecki
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Takanori Maruta
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Matsue, Japan
| | - Kurt Hoogewijs
- Department of Organic Chemistry and Macromolecular Chemistry, Ghent University, Ghent, Belgium
| | - Willem Vannecke
- Department of Organic Chemistry and Macromolecular Chemistry, Ghent University, Ghent, Belgium
| | - Brenda Peterson
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Davy Opdenacker
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Annemieke Madder
- Department of Organic Chemistry and Macromolecular Chemistry, Ghent University, Ghent, Belgium
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
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41
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Mellor NL, Voß U, Janes G, Bennett MJ, Wells DM, Band LR. Auxin fluxes through plasmodesmata modify root-tip auxin distribution. Development 2020; 147:dev181669. [PMID: 32229613 PMCID: PMC7132777 DOI: 10.1242/dev.181669] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 02/17/2020] [Indexed: 01/05/2023]
Abstract
Auxin is a key signal regulating plant growth and development. It is well established that auxin dynamics depend on the spatial distribution of efflux and influx carriers on the cell membranes. In this study, we employ a systems approach to characterise an alternative symplastic pathway for auxin mobilisation via plasmodesmata, which function as intercellular pores linking the cytoplasm of adjacent cells. To investigate the role of plasmodesmata in auxin patterning, we developed a multicellular model of the Arabidopsis root tip. We tested the model predictions using the DII-VENUS auxin response reporter, comparing the predicted and observed DII-VENUS distributions using genetic and chemical perturbations designed to affect both carrier-mediated and plasmodesmatal auxin fluxes. The model revealed that carrier-mediated transport alone cannot explain the experimentally determined auxin distribution in the root tip. In contrast, a composite model that incorporates both carrier-mediated and plasmodesmatal auxin fluxes re-capitulates the root-tip auxin distribution. We found that auxin fluxes through plasmodesmata enable auxin reflux and increase total root-tip auxin. We conclude that auxin fluxes through plasmodesmata modify the auxin distribution created by efflux and influx carriers.
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Affiliation(s)
- Nathan L Mellor
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Ute Voß
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - George Janes
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Malcolm J Bennett
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Darren M Wells
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Leah R Band
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK
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42
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López-Salmerón V, Cho H, Tonn N, Greb T. The Phloem as a Mediator of Plant Growth Plasticity. Curr Biol 2020; 29:R173-R181. [PMID: 30836090 DOI: 10.1016/j.cub.2019.01.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Developmental plasticity, defined as the capacity to respond to changing environmental conditions, is an inherent feature of plant growth. Recent studies have brought the phloem tissue, the quintessential conduit for energy metabolites and inter-organ communication, into focus as an instructive developmental system. Those studies have clarified long-standing questions about essential aspects of phloem development and function, such as the pressure flow hypothesis, mechanisms of phloem unloading, and source-sink relationships. Interestingly, plants with impaired phloem development show characteristic changes in body architecture, thereby highlighting the capacity of the phloem to integrate environmental cues and to fine-tune plant development. Therefore, understanding the plasticity of phloem development provides scenarios of how environmental stimuli are translated into differential plant growth. In this Review, we summarize novel insights into how phloem identity is established and how phloem cells fulfil their core function as transport units. Moreover, we discuss possible interfaces between phloem physiology and development as sites for mediating the plastic growth mode of plants.
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Affiliation(s)
- Vadir López-Salmerón
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Hyunwoo Cho
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Nina Tonn
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Thomas Greb
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany.
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43
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Seo SY, Wi SJ, Park KY. Functional switching of NPR1 between chloroplast and nucleus for adaptive response to salt stress. Sci Rep 2020; 10:4339. [PMID: 32152424 PMCID: PMC7062895 DOI: 10.1038/s41598-020-61379-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 02/13/2020] [Indexed: 02/02/2023] Open
Abstract
Salt stress causes rapid accumulation of nonexpressor of pathogenesis-related genes 1 (NPR1) protein, known as the redox-sensitive transcription coactivator, which in turn elicits many adaptive responses. The NPR1 protein transiently accumulates in chloroplast stroma under salt stress, which attenuates stress-triggered down-regulation of photosynthetic capability. We observed that oligomeric NPR1 in chloroplasts and cytoplasm had chaperone activity, whereas monomeric NPR1 in the nucleus did not. Additionally, NPR1 overexpression resulted in reinforcement of morning-phased and evening-phased circadian clock. NPR1 overexpression also enhanced antioxidant activity and reduced stress-induced reactive oxygen species (ROS) generation at early stage, followed with transcription levels for ROS detoxification. These results suggest a functional switch from a molecular chaperone to a transcriptional coactivator, which is dependent on subcellular localization. Our findings imply that dual localization of NPR1 is related to proteostasis and redox homeostasis in chloroplasts for emergency restoration as well as transcriptional coactivator in the nucleus for adaptation to stress.
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Affiliation(s)
- So Yeon Seo
- Department of Biology, Sunchon National University, Sunchon, Chonnam, Republic of Korea
| | - Soo Jin Wi
- Department of Biology, Sunchon National University, Sunchon, Chonnam, Republic of Korea
| | - Ky Young Park
- Department of Biology, Sunchon National University, Sunchon, Chonnam, Republic of Korea.
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Zhang F, Tao W, Sun R, Wang J, Li C, Kong X, Tian H, Ding Z. PRH1 mediates ARF7-LBD dependent auxin signaling to regulate lateral root development in Arabidopsis thaliana. PLoS Genet 2020; 16:e1008044. [PMID: 32032352 PMCID: PMC7006904 DOI: 10.1371/journal.pgen.1008044] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 12/22/2019] [Indexed: 11/19/2022] Open
Abstract
The development of lateral roots in Arabidopsis thaliana is strongly dependent on signaling directed by the AUXIN RESPONSE FACTOR7 (ARF7), which in turn activates LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors (LBD16, LBD18 and LBD29). Here, the product of PRH1, a PR-1 homolog annotated previously as encoding a pathogen-responsive protein, was identified as a target of ARF7-mediated auxin signaling and also as participating in the development of lateral roots. PRH1 was shown to be strongly induced by auxin treatment, and plants lacking a functional copy of PRH1 formed fewer lateral roots. The transcription of PRH1 was controlled by the binding of both ARF7 and LBDs to its promoter region. In Arabidopsis thaliana AUXIN RESPONSE FACTOR7 (ARF7)-mediated auxin signaling plays a key role in lateral roots (LRs) development. The LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors (LBD16, LBD18 and LBD29) act downstream of ARF7-mediated auxin signaling to control LRs formation. Here, the PR-1 homolog PRH1 was identified as a novel target of both ARF7 and LBDs (especially the LBD29) during auxin induced LRs formation, as both ARF7 and LBDs were able to bind to the PRH1 promoter. This study provides new insights about how auxin regulates lateral root development.
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Affiliation(s)
- Feng Zhang
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Wenqing Tao
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Ruiqi Sun
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Junxia Wang
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Cuiling Li
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Xiangpei Kong
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Huiyu Tian
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Zhaojun Ding
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
- * E-mail:
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45
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Motte H, Parizot B, Fang T, Beeckman T. The evolutionary trajectory of root stem cells. CURRENT OPINION IN PLANT BIOLOGY 2020; 53:23-30. [PMID: 31707318 DOI: 10.1016/j.pbi.2019.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/05/2019] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
Root stem cells are crucial for the establishment of roots and are therefore a major evolutionary innovation that enabled land plants to spread on land. Despite their importance, not too much is known about the origin and the molecular players installing and maintaining them. Although still fragmentary, the recent availability of new data for early land plants can be used to identify and analyze the conservation of key regulators of root meristems. In this review, we evaluate the possible conservation of important root stem cell regulators to suggest pathways that might have been important at the origin of roots.
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Affiliation(s)
- Hans Motte
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Boris Parizot
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Tao Fang
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Tom Beeckman
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
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46
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Escamez S, André D, Sztojka B, Bollhöner B, Hall H, Berthet B, Voß U, Lers A, Maizel A, Andersson M, Bennett M, Tuominen H. Cell Death in Cells Overlying Lateral Root Primordia Facilitates Organ Growth in Arabidopsis. Curr Biol 2020; 30:455-464.e7. [PMID: 31956028 DOI: 10.1016/j.cub.2019.11.078] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/22/2019] [Accepted: 11/26/2019] [Indexed: 02/06/2023]
Abstract
Plant organ growth is widely accepted to be determined by cell division and cell expansion, but, unlike that in animals, the contribution of cell elimination has rarely been recognized. We investigated this paradigm during Arabidopsis lateral root formation, when the lateral root primordia (LRP) must traverse three overlying cell layers within the parent root. A subset of LRP-overlying cells displayed the induction of marker genes for cell types undergoing developmental cell death, and their cell death was detected by electron, confocal, and light sheet microscopy techniques. LRP growth was delayed in cell-death-deficient mutants lacking the positive cell death regulator ORESARA1/ANAC092 (ORE1). LRP growth was restored in ore1-2 knockout plants by genetically inducing cell elimination in cells overlying the LRP or by physically killing LRP-overlying cells by ablation with optical tweezers. Our results support that, in addition to previously discovered mechanisms, cell elimination contributes to regulating lateral root emergence.
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Affiliation(s)
- Sacha Escamez
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
| | - Domenique André
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
| | - Bernadette Sztojka
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
| | - Benjamin Bollhöner
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
| | - Hardy Hall
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
| | - Béatrice Berthet
- Center for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Ute Voß
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 SRD, UK
| | - Amnon Lers
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Rishon LeZion, 7528809, Israel
| | - Alexis Maizel
- Center for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | | | - Malcolm Bennett
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 SRD, UK
| | - Hannele Tuominen
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden.
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47
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Tong M, Lee K, Ezer D, Cortijo S, Jung J, Charoensawan V, Box MS, Jaeger KE, Takahashi N, Mas P, Wigge PA, Seo PJ. The Evening Complex Establishes Repressive Chromatin Domains Via H2A.Z Deposition. PLANT PHYSIOLOGY 2020; 182:612-625. [PMID: 31712305 PMCID: PMC6945876 DOI: 10.1104/pp.19.00881] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/19/2019] [Indexed: 05/07/2023]
Abstract
The Evening Complex (EC) is a core component of the Arabidopsis (Arabidopsis thaliana) circadian clock, which represses target gene expression at the end of the day and integrates temperature information to coordinate environmental and endogenous signals. Here we show that the EC induces repressive chromatin structure to regulate the evening transcriptome. The EC component ELF3 directly interacts with a protein from the SWI2/SNF2-RELATED (SWR1) complex to control deposition of H2A.Z-nucleosomes at the EC target genes. SWR1 components display circadian oscillation in gene expression with a peak at dusk. In turn, SWR1 is required for the circadian clockwork, as defects in SWR1 activity alter morning-expressed genes. The EC-SWR1 complex binds to the loci of the core clock genes PSEUDO-RESPONSE REGULATOR7 (PRR7) and PRR9 and catalyzes deposition of nucleosomes containing the histone variant H2A.Z coincident with the repression of these genes at dusk. This provides a mechanism by which the circadian clock temporally establishes repressive chromatin domains to shape oscillatory gene expression around dusk.
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Affiliation(s)
- Meixuezi Tong
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Kyounghee Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Daphne Ezer
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Sandra Cortijo
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Jaehoon Jung
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Varodom Charoensawan
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Mathew S Box
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Katja E Jaeger
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Nozomu Takahashi
- Center for Research in Agricultural Genomics, Consortium Consejo Superior de Investigaciones Cientificas-Institute of Agrifood Research and Technology-Universitat Autònoma de Barcelona-Universidad de Barcelona, Parc de Recerca Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallés), Barcelona 08193, Spain
| | - Paloma Mas
- Center for Research in Agricultural Genomics, Consortium Consejo Superior de Investigaciones Cientificas-Institute of Agrifood Research and Technology-Universitat Autònoma de Barcelona-Universidad de Barcelona, Parc de Recerca Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallés), Barcelona 08193, Spain
- Consejo Superior de Investigaciones Científicas, Barcelona 08193, Spain
| | - Philip A Wigge
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
- Leibniz-Institut für Gemüse- und Zierpflanzenbau, 14979 Großbeeren, Germany
| | - Pil Joon Seo
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea
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48
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Kawa D, Meyer AJ, Dekker HL, Abd-El-Haliem AM, Gevaert K, Van De Slijke E, Maszkowska J, Bucholc M, Dobrowolska G, De Jaeger G, Schuurink RC, Haring MA, Testerink C. SnRK2 Protein Kinases and mRNA Decapping Machinery Control Root Development and Response to Salt. PLANT PHYSIOLOGY 2020; 182:361-377. [PMID: 31570508 PMCID: PMC6945840 DOI: 10.1104/pp.19.00818] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/17/2019] [Indexed: 05/20/2023]
Abstract
SNF1-RELATED PROTEIN KINASES 2 (SnRK2) are important components of early osmotic and salt stress signaling pathways in plants. The Arabidopsis (Arabidopsis thaliana) SnRK2 family comprises the abscisic acid (ABA)-activated protein kinases SnRK2.2, SnRK2.3, SnRK2.6, SnRK2.7, and SnRK2.8, and the ABA-independent subclass 1 protein kinases SnRK2.1, SnRK2.4, SnRK2.5, SnRK2.9, and SnRK2.10. ABA-independent SnRK2s act at the posttranscriptional level via phosphorylation of VARICOSE (VCS), a member of the mRNA decapping complex, that catalyzes the first step of 5'mRNA decay. Here, we identified VCS and VARICOSE RELATED (VCR) as interactors and phosphorylation targets of SnRK2.5, SnRK2.6, and SnRK2.10. All three protein kinases phosphorylated Ser-645 and Ser-1156 of VCS, whereas SnRK2.6 and SnRK2.10 also phosphorylated VCS Ser-692 and Ser-680 of VCR. We showed that subclass 1 SnRK2s, VCS, and 5' EXORIBONUCLEASE 4 (XRN4) are involved in regulating root growth under control conditions as well as modulating root system architecture in response to salt stress. Our results suggest interesting patterns of redundancy within subclass 1 SnRK2 protein kinases, with SnRK2.1, SnRK2.5, and SnRK2.9 controlling root growth under nonstress conditions and SnRK2.4 and SnRK2.10 acting mostly in response to salinity. We propose that subclass 1 SnRK2s function in root development under salt stress by affecting the transcript levels of aquaporins, as well as CYP79B2, an enzyme involved in auxin biosynthesis.
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Affiliation(s)
- Dorota Kawa
- Plant Cell Biology, University of Amsterdam, Swammerdam Institute for Life Sciences Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - A Jessica Meyer
- Plant Cell Biology, University of Amsterdam, Swammerdam Institute for Life Sciences Amsterdam, 1098 XH Amsterdam, The Netherlands
- Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Henk L Dekker
- Mass Spectrometry of Biomacromolecules, University of Amsterdam, Swammerdam Institute for Life Sciences Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Ahmed M Abd-El-Haliem
- Plant Physiology, University of Amsterdam, Swammerdam Institute for Life Sciences Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, 9000 Gent, Belgium
- VIB Center for Medical Biotechnology, 9000 Gent, Belgium
| | - Eveline Van De Slijke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9000 Gent, Belgium
- VIB Center for Plant Systems Biology, 9052 Gent, Belgium
| | - Justyna Maszkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warszawa, Poland
| | - Maria Bucholc
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warszawa, Poland
| | - Grażyna Dobrowolska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warszawa, Poland
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9000 Gent, Belgium
- VIB Center for Plant Systems Biology, 9052 Gent, Belgium
| | - Robert C Schuurink
- Plant Physiology, University of Amsterdam, Swammerdam Institute for Life Sciences Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Michel A Haring
- Plant Physiology, University of Amsterdam, Swammerdam Institute for Life Sciences Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Christa Testerink
- Plant Cell Biology, University of Amsterdam, Swammerdam Institute for Life Sciences Amsterdam, 1098 XH Amsterdam, The Netherlands
- Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
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49
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Le Gac AL, Laux T. Hypoxia Is a Developmental Regulator in Plant Meristems. MOLECULAR PLANT 2019; 12:1422-1424. [PMID: 31628990 DOI: 10.1016/j.molp.2019.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 10/08/2019] [Accepted: 10/09/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Anne-Laure Le Gac
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Thomas Laux
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany; Sino-German Joint Research Center on Agricultural Biology, Shandong Agricultural University, Tai'an, Shandong, China.
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50
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Xu P, Cai W. Nitrate-responsive OBP4-XTH9 regulatory module controls lateral root development in Arabidopsis thaliana. PLoS Genet 2019; 15:e1008465. [PMID: 31626627 PMCID: PMC6821136 DOI: 10.1371/journal.pgen.1008465] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 10/30/2019] [Accepted: 10/07/2019] [Indexed: 11/19/2022] Open
Abstract
Plant root system architecture in response to nitrate availability represents a notable example to study developmental plasticity, but the underlying mechanism remains largely unknown. Xyloglucan endotransglucosylases (XTHs) play a critical role in cell wall biosynthesis. Here we assessed the gene expression of XTH1-11 belonging to group I of XTHs in lateral root (LR) primordia and found that XTH9 was highly expressed. Correspondingly, an xth9 mutant displayed less LR, while overexpressing XTH9 presented more LR, suggesting the potential function of XTH9 in controlling LR development. XTH9 gene mutation obviously alters the properties of the cell wall. Furthermore, nitrogen signals stimulated the expression of XTH9 to promote LRs. Genetic analysis revealed that the function of XTH9 was dependent on auxin-mediated ARF7/19 and downstream AFB3 in response to nitrogen signals. In addition, we identified another transcription factor, OBP4, that was also induced by nitrogen treatment, but the induction was much slower than that of XTH9. In contrast to XTH9, overexpressing OBP4 caused fewer LRs while OBP4 knockdown with OBP4-RNAi or an artificial miRNA silenced amiOBP4 line produced more LR. We further found OBP4 bound to the promoter of XTH9 to suppress XTH9 expression. In agreement with this, both OBP4-RNAi and crossed OBP4-RNAi & 35S::XTH9 lines led to more LR, but OBP4-RNAi & xth9 produced less LR, similar to xth9. Based on these findings we propose a novel mechanism by which OBP4 antagonistically controls XTH9 expression and the OBP4-XTH9 module elaborately sustains LR development in response to nitrate treatment. Nitrate is not only a nutrient, but also a signal that controls downstream signaling genes at the whole-plant level. In plants, changes in root system architecture in response to nitrate availability represent a notable example of developmental plasticity in response to environmental stimuli. However, the molecular mechanisms underlying nitrate-associated modulation are largely unknown. Here, we identified a nitrogen-responsive signaling module that comprises both xyloglucan endotransglucosylase 9 (XTH9) and the Dof transcription factor OBP4 and controls lateral root (LR) development. We used root gravitropic bending assays to observe the gene expression of group 1 xyloglucan endotransglucosylases (XTHs) involved in LR primordia. The results showed that XTH9 expression patterns were changed and that xth9 knockout mutants displayed altered LR growth. XTH9 was expressed in the LRs and in response to nitrate treatment, and the xth9 mutants were defective in nitrate-promoted LR growth. Moreover, XTH9 overexpression increased LR length and increased tolerance to low-nitrate stress. We found that OBP4 could negatively regulate XTH9 and inhibited root growth. OBP4 and XTH9 worked downstream of ARF7/9. We conclude that OBP4 and XTH9 constitute a regulatory module which contributes to LR growth in response to different environmental nitrate concentration signals.
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Affiliation(s)
- Peipei Xu
- Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Weiming Cai
- Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- * E-mail:
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