1
|
Shang E, Wei K, Lv B, Zhang X, Lin X, Ding Z, Leng J, Tian H, Ding Z. VIK-Mediated Auxin Signaling Regulates Lateral Root Development in Arabidopsis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2402442. [PMID: 38958531 DOI: 10.1002/advs.202402442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/31/2024] [Indexed: 07/04/2024]
Abstract
The crucial role of TIR1-receptor-mediated gene transcription regulation in auxin signaling has long been established. In recent years, the significant role of protein phosphorylation modifications in auxin signal transduction has gradually emerged. To further elucidate the significant role of protein phosphorylation modifications in auxin signaling, a phosphoproteomic analysis in conjunction with auxin treatment has identified an auxin activated Mitogen-activated Protein Kinase Kinase Kinase (MAPKKK) VH1-INTERACTING Kinase (VIK), which plays an important role in auxin-induced lateral root (LR) development. In the vik mutant, auxin-induced LR development is significantly attenuated. Further investigations show that VIK interacts separately with the positive regulator of LR development, LATERAL ORGAN BOUNDARIES-DOMAIN18 (LBD18), and the negative regulator of LR emergence, Ethylene Responsive Factor 13 (ERF13). VIK directly phosphorylates and stabilizes the positive transcription factor LBD18 in LR formation. In the meantime, VIK directly phosphorylates the negative regulator ERF13 at Ser168 and Ser172 sites, causing its degradation and releasing the repression by ERF13 on LR emergence. In summary, VIK-mediated auxin signaling regulates LR development by enhancing the protein stability of LBD18 and inducing the degradation of ERF13, respectively.
Collapse
Affiliation(s)
- Erlei Shang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| | - Kaijing Wei
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| | - Bingsheng Lv
- College of Horticulture, Qingdao Agricultural University, Qingdao, Shandong, 266109, China
| | - Xueli Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| | - Xuefeng Lin
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| | - Zhihui Ding
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| | - Junchen Leng
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| | - Huiyu Tian
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| | - Zhaojun Ding
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Chen Y, Fu Y, Xia Y, Miao Y, Shao J, Xuan W, Liu Y, Xun W, Yan Q, Shen Q, Zhang R. Trichoderma-secreted anthranilic acid promotes lateral root development via auxin signaling and RBOHF-induced endodermal cell wall remodeling. Cell Rep 2024; 43:114030. [PMID: 38551966 DOI: 10.1016/j.celrep.2024.114030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/06/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024] Open
Abstract
Trichoderma spp. have evolved the capacity to communicate with plants by producing various secondary metabolites (SMs). Nonhormonal SMs play important roles in plant root development, while specific SMs from rhizosphere microbes and their underlying mechanisms to control plant root branching are still largely unknown. In this study, a compound, anthranilic acid (2-AA), is identified from T. guizhouense NJAU4742 to promote lateral root development. Further studies demonstrate that 2-AA positively regulates auxin signaling and transport in the canonical auxin pathway. 2-AA also partly rescues the lateral root numbers of CASP1pro:shy2-2, which regulates endodermal cell wall remodeling via an RBOHF-induced reactive oxygen species burst. In addition, our work reports another role for microbial 2-AA in the regulation of lateral root development, which is different from its better-known role in plant indole-3-acetic acid biosynthesis. In summary, this study identifies 2-AA from T. guizhouense NJAU4742, which plays versatile roles in regulating plant root development.
Collapse
Affiliation(s)
- Yu Chen
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Yansong Fu
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanwei Xia
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Youzhi Miao
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiahui Shao
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Xuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunpeng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Weibing Xun
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Qiuyan Yan
- Institute of Wheat Research, Shanxi Agricultural University, Linfen 041000, China
| | - Qirong Shen
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruifu Zhang
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Collins E, Shou H, Mao C, Whelan J, Jost R. Dynamic interactions between SPX proteins, the ubiquitination machinery, and signalling molecules for stress adaptation at a whole-plant level. Biochem J 2024; 481:363-385. [PMID: 38421035 DOI: 10.1042/bcj20230163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 03/02/2024]
Abstract
The plant macronutrient phosphorus is a scarce resource and plant-available phosphate is limiting in most soil types. Generally, a gene regulatory module called the phosphate starvation response (PSR) enables efficient phosphate acquisition by roots and translocation to other organs. Plants growing on moderate to nutrient-rich soils need to co-ordinate availability of different nutrients and repress the highly efficient PSR to adjust phosphate acquisition to the availability of other macro- and micronutrients, and in particular nitrogen. PSR repression is mediated by a small family of single SYG1/Pho81/XPR1 (SPX) domain proteins. The SPX domain binds higher order inositol pyrophosphates that signal cellular phosphorus status and modulate SPX protein interaction with PHOSPHATE STARVATION RESPONSE1 (PHR1), the central transcriptional regulator of PSR. Sequestration by SPX repressors restricts PHR1 access to PSR gene promoters. Here we focus on SPX4 that primarily acts in shoots and sequesters many transcription factors other than PHR1 in the cytosol to control processes beyond the classical PSR, such as nitrate, auxin, and jasmonic acid signalling. Unlike SPX1 and SPX2, SPX4 is subject to proteasomal degradation not only by singular E3 ligases, but also by SCF-CRL complexes. Emerging models for these different layers of control and their consequences for plant acclimation to the environment will be discussed.
Collapse
Affiliation(s)
- Emma Collins
- Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
| | - Huixia Shou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
- Hainan Institute, Zhejiang University, Sanya 572025, China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang 314400, China
| | - Chuanzao Mao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
| | - James Whelan
- Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang 314400, China
| | - Ricarda Jost
- Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, Bundoora, VIC 3086, Australia
| |
Collapse
|
6
|
Zhao J, Shi C, Wang L, Han X, Zhu Y, Liu J, Yang X. Functional Trait Responses of Sophora alopecuroides L. Seedlings to Diverse Environmental Stresses in the Desert Steppe of Ningxia, China. PLANTS (BASEL, SWITZERLAND) 2023; 13:69. [PMID: 38202378 PMCID: PMC10780927 DOI: 10.3390/plants13010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024]
Abstract
The seedling stage of plants is a crucial and vulnerable period in population and community dynamics. Despite this, studies on how plant traits respond to different environmental stresses often tend to overlook this early stage. Our study focused on Sophora alopecuroides L. seedlings in Ningxia Yanchi desert steppe, analyzing the effects of sand burial, salinity, and drought on their key aboveground and belowground traits. The results showed that sand burial significantly negatively affected stem biomass (SB), leaf biomass (LB), stem diameter (SD), leaf length (LL), leaf width (LW), leaf area (LA), and total root volume (RV), but positively influenced total root length (RL). As sand burial depth increased, SB, LB, SD, LL, LW, LA, RV, root biomass (RB), RV, and lateral root numbers (LRN) significantly decreased. Salinity stress negatively affected SB, LB, SD, LL, LW, LA, RB, RL, and RV, with these traits declining as the stress concentration increased. Drought stress had a positive effect on SD and LL, with both traits showing an increase as the intensity of the drought stress intensified; however, it adversely affected RL. In Ningxia Yanchi desert steppe, salinity stress had the most significant effect on the traits of S. alopecuroides seedlings, followed by sand burial, with drought having the least significant effect. This study provides essential theoretical support for understanding how S. alopecuroides seedlings cope with environmental stresses in their early life stages.
Collapse
Affiliation(s)
- Jingdong Zhao
- Breeding Base for State Key Lab. of Land Degradation and Ecological Restoration in Northwestern China/Key Lab. of Restoration and Reconstruction of Degraded Ecosystems in Northwestern China of Ministry of Education, Ningxia University, Yinchuan 750021, China
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing 100091, China
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China
| | - Chaoyi Shi
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing 100091, China
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China
- Inner Mongolia Water Resources Inner Mongolia Water Resources Co., Ltd., Hohhot 010020, China
| | - Le Wang
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing 100091, China
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China
| | - Xuejiao Han
- Forestry and Grassland Work Station of Inner Mongolia, Hohhot 010011, China
| | - Yuanjun Zhu
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing 100091, China
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China
| | - Jiankang Liu
- Breeding Base for State Key Lab. of Land Degradation and Ecological Restoration in Northwestern China/Key Lab. of Restoration and Reconstruction of Degraded Ecosystems in Northwestern China of Ministry of Education, Ningxia University, Yinchuan 750021, China
| | - Xiaohui Yang
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing 100091, China
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China
| |
Collapse
|
7
|
Ahkami AH. Systems biology of root development in Populus: Review and perspectives. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111818. [PMID: 37567482 DOI: 10.1016/j.plantsci.2023.111818] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/28/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023]
Abstract
The root system of plants consists of primary, lateral, and adventitious roots (ARs) (aka shoot-born roots). ARs arise from stem- or leaf-derived cells during post-embryonic development. Adventitious root development (ARD) through stem cuttings is the first requirement for successful establishment and growth of planted trees; however, the details of the molecular mechanisms underlying ARD are poorly understood. This knowledge is important to both basic plant biology and because of its necessary role in the successful propagation of superior cultivars of commercial woody bioenergy crops, like poplar. In this review article, the molecular mechanisms that control both endogenous (auxin) and environmentally (nutrients and microbes) regulated ARD and how these systems interact to control the rooting efficiency of poplar trees are described. Then, potential future studies in employing integrated systems biology approaches at cellular resolutions are proposed to more precisely identify the molecular mechanisms that cause AR. Using genetic transformation and genome editing approaches, this information can be used for improving ARD in economically important plants for which clonal propagation is a requirement.
Collapse
Affiliation(s)
- Amir H Ahkami
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, USA.
| |
Collapse
|
8
|
Uemura Y, Kimura S, Ohta T, Suzuki T, Mase K, Kato H, Sakaoka S, Uefune M, Komine Y, Hotta K, Shimizu M, Morikami A, Tsukagoshi H. A very long chain fatty acid responsive transcription factor, MYB93, regulates lateral root development in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1408-1427. [PMID: 37247130 DOI: 10.1111/tpj.16330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 05/30/2023]
Abstract
Lateral roots (LRs) are critical to root system architecture development in plants. Although the molecular mechanisms by which auxin regulates LR development have been extensively studied, several additional regulatory systems are hypothesized to be involved. Recently, the regulatory role of very long chain fatty acids (VLCFAs) has been shown in LR development. Our analysis showed that LTPG1 and LTPG2, transporters of VLCFAs, are specifically expressed in the developing LR primordium (LRP), while the number of LRs is reduced in the ltpg1/ltpg2 double mutant. Moreover, late LRP development was hindered when the VLCFA levels were reduced by the VLCFA synthesis enzyme mutant, kcs1-5. However, the details of the regulatory mechanisms of LR development controlled by VLCFAs remain unknown. In this study, we propose a novel method to analyze the LRP development stages with high temporal resolution using a deep neural network and identify a VLCFA-responsive transcription factor, MYB93, via transcriptome analysis of kcs1-5. MYB93 showed a carbon chain length-specific expression response following treatment of VLCFAs. Furthermore, myb93 transcriptome analysis suggested that MYB93 regulated the expression of cell wall organization genes. In addition, we also found that LTPG1 and LTPG2 are involved in LR development through the formation of root cap cuticle, which is different from transcriptional regulation by VLCFAs. Our results suggest that VLCFA is a regulator of LRP development through transcription factor-mediated regulation of gene expression and the transportation of VLCFAs is also involved in LR development through root cap cuticle formation.
Collapse
Affiliation(s)
- Yuta Uemura
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Saori Kimura
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Tomomichi Ohta
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 478-8501, Japan
| | - Kosuke Mase
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Hiroyuki Kato
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Satomi Sakaoka
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Masayoshi Uefune
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Yuki Komine
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Kazuhiro Hotta
- Department of Electrical and Electronic Engineering, Faculty of Science and Technology, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Motoyuki Shimizu
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Atsushi Morikami
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Hironaka Tsukagoshi
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| |
Collapse
|
9
|
Lin LY, Chow HX, Chen CH, Mitsuda N, Chou WC, Liu TY. Role of autophagy-related proteins ATG8f and ATG8h in the maintenance of autophagic activity in Arabidopsis roots under phosphate starvation. FRONTIERS IN PLANT SCIENCE 2023; 14:1018984. [PMID: 37434600 PMCID: PMC10331476 DOI: 10.3389/fpls.2023.1018984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 05/23/2023] [Indexed: 07/13/2023]
Abstract
Nutrient starvation-induced autophagy is a conserved process in eukaryotes. Plants defective in autophagy show hypersensitivity to carbon and nitrogen limitation. However, the role of autophagy in plant phosphate (Pi) starvation response is relatively less explored. Among the core autophagy-related (ATG) genes, ATG8 encodes a ubiquitin-like protein involved in autophagosome formation and selective cargo recruitment. The Arabidopsis thaliana ATG8 genes, AtATG8f and AtATG8h, are notably induced in roots under low Pi. In this study, we show that such upregulation correlates with their promoter activities and can be suppressed in the phosphate response 1 (phr1) mutant. Yeast one-hybrid analysis failed to attest the binding of the AtPHR1 transcription factor to the promoter regions of AtATG8f and AtATG8h. Dual luciferase reporter assays in Arabidopsis mesophyll protoplasts also indicated that AtPHR1 could not transactivate the expression of both genes. Loss of AtATG8f and AtATG8h leads to decreased root microsomal-enriched ATG8 but increased ATG8 lipidation. Moreover, atg8f/atg8h mutants exhibit reduced autophagic flux estimated by the vacuolar degradation of ATG8 in the Pi-limited root but maintain normal cellular Pi homeostasis with reduced number of lateral roots. While the expression patterns of AtATG8f and AtATG8h overlap in the root stele, AtATG8f is more strongly expressed in the root apex and root hair and remarkably at sites where lateral root primordia develop. We hypothesize that Pi starvation-induction of AtATG8f and AtATG8h may not directly contribute to Pi recycling but rely on a second wave of transcriptional activation triggered by PHR1 that fine-tunes cell type-specific autophagic activity.
Collapse
Affiliation(s)
- Li-Yen Lin
- Institute of Bioinformatics and Structural Biology, College of Life Sciences and Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Hong-Xuan Chow
- Institute of Bioinformatics and Structural Biology, College of Life Sciences and Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Chih-Hao Chen
- Institute of Bioinformatics and Structural Biology, College of Life Sciences and Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Wen-Chun Chou
- Institute of Bioinformatics and Structural Biology, College of Life Sciences and Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Tzu-Yin Liu
- Institute of Bioinformatics and Structural Biology, College of Life Sciences and Medicine, National Tsing Hua University, Hsinchu, Taiwan
- Department of Life Science, College of Life Sciences and Medicine, National Tsing Hua University, Hsinchu, Taiwan
| |
Collapse
|
10
|
Singh H, Singh Z, Kashyap R, Yadav SR. Lateral root branching: evolutionary innovations and mechanistic divergence in land plants. THE NEW PHYTOLOGIST 2023; 238:1379-1385. [PMID: 36882384 DOI: 10.1111/nph.18864] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
The root system architecture in plants is a result of multiple evolutionary innovations over time in response to changing environmental cues. Dichotomy and endogenous lateral branching in the roots evolved in lycophytes lineage but extant seed plants use lateral branching instead. This has led to the development of complex and adaptive root systems, with lateral roots playing a key role in this process exhibiting conserved and divergent features in different plant species. The study of lateral root branching in diverse plant species can shed light on the orderly yet distinct nature of postembryonic organogenesis in plants. This insight provides an overview of the diversity in lateral root (LR) development in various plant species during the evolution of root system in plants.
Collapse
Affiliation(s)
- Harshita Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
- Center for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
| | - Zeenu Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Rohan Kashyap
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Shri Ram Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| |
Collapse
|
11
|
Ali O, Cheddadi I, Landrein B, Long Y. Revisiting the relationship between turgor pressure and plant cell growth. THE NEW PHYTOLOGIST 2023; 238:62-69. [PMID: 36527246 DOI: 10.1111/nph.18683] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Growth is central to plant morphogenesis. Plant cells are encased in rigid cell walls, and they must overcome physical confinement to grow to specific sizes and shapes. Cell wall tension and turgor pressure are the main mechanical components impacting plant cell growth. Cell wall mechanics has been the focus of most plant biomechanical studies, and turgor pressure was often considered as a constant and largely passive component. Nevertheless, it is increasingly accepted that turgor pressure plays a significant role in plant growth. Numerous theoretical and experimental studies suggest that turgor pressure can be both spatially inhomogeneous and actively modulated during morphogenesis. Here, we revisit the pressure-growth relationship by reviewing recent advances in investigating the interactions between cellular/tissular pressure and growth.
Collapse
Affiliation(s)
- Olivier Ali
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA, Lyon Cedex 07, 69364, France
| | - Ibrahim Cheddadi
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA, Lyon Cedex 07, 69364, France
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000, Grenoble, France
| | - Benoit Landrein
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA, Lyon Cedex 07, 69364, France
| | - Yuchen Long
- Department of Biological Sciences, The National University of Singapore, Singapore, 117543, Singapore
- Mechanobiology Institute, The National University of Singapore, Singapore, 117411, Singapore
| |
Collapse
|
12
|
Qian Y, Wang X, Liu Y, Wang X, Mao T. HY5 inhibits lateral root initiation in Arabidopsis through negative regulation of the microtubule-stabilizing protein TPXL5. THE PLANT CELL 2023; 35:1092-1109. [PMID: 36512471 PMCID: PMC10015163 DOI: 10.1093/plcell/koac358] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
Tight control of lateral root (LR) initiation is vital for root system architecture and function. Regulation of cortical microtubule reorganization is involved in the asymmetric radial expansion of founder cells during LR initiation in Arabidopsis (Arabidopsis thaliana). However, critical genetic evidence on the role of microtubules in LR initiation is lacking and the mechanisms underlying this regulation are poorly understood. Here, we found that the previously uncharacterized microtubule-stabilizing protein TPX2-LIKE5 (TPXL5) participates in LR initiation, which is finely regulated by the transcription factor ELONGATED HYPOCOTYL5 (HY5). In tpxl5 mutants, LR density was decreased and more LR primordia (LRPs) remained in stage I, indicating delayed LR initiation. In particular, the cell width in the peripheral domain of LR founder cells after the first asymmetric cell division was larger in tpxl5 mutants than in the wild-type. Consistently, ordered transverse cortical microtubule arrays were not well generated in tpxl5 mutants. In addition, HY5 directly targeted the promoter of TPXL5 and downregulated TPXL5 expression. The hy5 mutant exhibited higher LR density and fewer stage I LRPs, indicating accelerated LR initiation. Such phenotypes were partially suppressed by TPXL5 knockout. Taken together, our data provide genetic evidence supporting the notion that cortical microtubules are essential for LR initiation and unravel a molecular mechanism underlying HY5 regulation of TPXL5-mediated microtubule reorganization and cell remodeling during LR initiation.
Collapse
Affiliation(s)
- Yanmin Qian
- State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaohong Wang
- State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yimin Liu
- State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiangfeng Wang
- State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Tonglin Mao
- State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| |
Collapse
|
13
|
Miyoshi Y, Soma F, Yin YG, Suzui N, Noda Y, Enomoto K, Nagao Y, Yamaguchi M, Kawachi N, Yoshida E, Tashima H, Yamaya T, Kuya N, Teramoto S, Uga Y. Rice immediately adapts the dynamics of photosynthates translocation to roots in response to changes in soil water environment. FRONTIERS IN PLANT SCIENCE 2023; 13:1024144. [PMID: 36743553 PMCID: PMC9889367 DOI: 10.3389/fpls.2022.1024144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 12/05/2022] [Indexed: 06/18/2023]
Abstract
Rice is susceptible to abiotic stresses such as drought stress. To enhance drought resistance, elucidating the mechanisms by which rice plants adapt to intermittent drought stress that may occur in the field is an important requirement. Roots are directly exposed to changes in the soil water condition, and their responses to these environmental changes are driven by photosynthates. To visualize the distribution of photosynthates in the root system of rice plants under drought stress and recovery from drought stress, we combined X-ray computed tomography (CT) with open type positron emission tomography (OpenPET) and positron-emitting tracer imaging system (PETIS) with 11C tracer. The short half-life of 11C (20.39 min) allowed us to perform multiple experiments using the same plant, and thus photosynthate translocation was visualized as the same plant was subjected to drought stress and then re-irrigation for recovery. The results revealed that when soil is drier, 11C-photosynthates mainly translocated to the seminal roots, likely to promote elongation of the root with the aim of accessing water stored in the lower soil layers. The photosynthates translocation to seminal roots immediately stopped after rewatering then increased significantly in crown roots. We suggest that when rice plant experiencing drought is re-irrigated from the bottom of pot, the destination of 11C-photosynthates translocation immediately switches from seminal root to crown roots. We reveal that rice roots are responsive to changes in soil water conditions and that rice plants differentially adapts the dynamics of photosynthates translocation to crown roots and seminal roots depending on soil conditions.
Collapse
Affiliation(s)
- Yuta Miyoshi
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum Science and Technology (QST), Takasaki, Japan
| | - Fumiyuki Soma
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Yong-Gen Yin
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum Science and Technology (QST), Takasaki, Japan
| | - Nobuo Suzui
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum Science and Technology (QST), Takasaki, Japan
| | - Yusaku Noda
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum Science and Technology (QST), Takasaki, Japan
| | - Kazuyuki Enomoto
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum Science and Technology (QST), Takasaki, Japan
| | - Yuto Nagao
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum Science and Technology (QST), Takasaki, Japan
| | - Mitsutaka Yamaguchi
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum Science and Technology (QST), Takasaki, Japan
| | - Naoki Kawachi
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum Science and Technology (QST), Takasaki, Japan
| | - Eiji Yoshida
- Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology (QST), Chiba, Japan
| | - Hideaki Tashima
- Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology (QST), Chiba, Japan
| | - Taiga Yamaya
- Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology (QST), Chiba, Japan
| | - Noriyuki Kuya
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Shota Teramoto
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Yusaku Uga
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| |
Collapse
|
14
|
Li Y, Jin F, Wu X, Teixeira da Silva JA, Xiong Y, Zhang X, Ma G. Identification and function of miRNA-mRNA interaction pairs during lateral root development of hemi-parasitic Santalum album L. seedlings. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153866. [PMID: 36399836 DOI: 10.1016/j.jplph.2022.153866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Sandalwood (Santalum album L.) is a hemi-parasitic tree species famous for its santalol and santalene, which are extracted from its heartwood and roots. The ability to understand root functionality within its branched root system would benefit the regulation of sandalwood growth and enhance the commercial value of sandalwood. Phenotypic and anatomical evidence in this study indicated that seed germination stage 4 (SG4) seemed pivotal for lateral root (LR) morphogenesis. Small RNA (sRNA) high-throughput sequencing of root tissues at three sub-stages of SG4 (lateral root primordia initiation (LRPI), lateral root primordia development (LRPD), and lateral root primordia emergence (LRPE)) was performed to identify microRNAs (miRNAs) associated with LR development. A total of 135 miRNAs, including 70 differentially expressed miRNAs (DEMs), were screened. Ten DEMs were selected to investigate transcript abundance in different organs or developmental stages. Among 100 negative DEM-mRNA interaction pairs, four targets (Sa-miR166m_2, 408d, 858a, and novel_Sa-miR8) were selected for studying cleavage sites by 5' RLM-RACE validation. The expression mode of the four miRNA-mRNA pairs was investigated after indole-3-acetic acid (IAA) treatment. IAA enhanced the abundance of homeobox-leucine-zipper protein 32 (HOX32), laccase 12 (LAC12), myeloblastosis86 (MYB86), and pectin methylesterase inhibitor6 (PMEI6) target transcripts by reducing the expression of Sa-miR166m_2, 408d, 858a, and novel_Sa-miR8 in the first 10 min. A schematic model of miRNA-regulated LR development is proposed for this hemi-parasitic species. This novel genetic information for improving sandalwood root growth and development may allow for the cultivation of fast-growing and high-yielding plantations.
Collapse
Affiliation(s)
- Yuan Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; South China National Botanical Garden, Guangzhou, 510650, China.
| | - Feng Jin
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Xiuju Wu
- College of Life Science, Northeast Agricultural University, Harbin, 150040, China.
| | | | - Yuping Xiong
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; South China National Botanical Garden, Guangzhou, 510650, China.
| | - Xinhua Zhang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; South China National Botanical Garden, Guangzhou, 510650, China.
| | - Guohua Ma
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; South China National Botanical Garden, Guangzhou, 510650, China.
| |
Collapse
|
15
|
Fang D, Zhang W, Ye Z, Hu F, Cheng X, Cao J. The plant specific SHORT INTERNODES/STYLISH (SHI/STY) proteins: Structure and functions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:685-695. [PMID: 36565613 DOI: 10.1016/j.plaphy.2022.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 12/02/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
Plant specific SHORT INTERNODES/STYLISH (SHI/STY) protein is a transcription factor involved in the formation and development of early lateral organs in plants. However, research on the SHI/STY protein family is not focused enough. In this article, we review recent studies on SHI/STY genes and explore the evolution and structure of SHI/STY. The biological functions of SHI/STYs are discussed in detail in this review, and the application of each biological function to modern agriculture is discussed. All SHI/STY proteins contain typical conserved RING-like zinc finger domain and IGGH domain. SHI/STYs are involved in the formation and development of lateral root, stem extension, leaf morphogenesis, and root nodule development. They are also involved in the regulation of pistil and stamen development and flowering time. At the same time, the regulation of some GA, JA, and auxin signals also involves these family proteins. For each aspect, unanswered or poorly understood questions were identified to help define future research areas. This review will provide a basis for further functional study of this gene family.
Collapse
Affiliation(s)
- Da Fang
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Weimeng Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Ziyi Ye
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Fei Hu
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xiuzhu Cheng
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jun Cao
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
| |
Collapse
|
16
|
Clark NM, Hurgobin B, Kelley DR, Lewsey MG, Walley JW. A Practical Guide to Inferring Multi-Omics Networks in Plant Systems. Methods Mol Biol 2023; 2698:233-257. [PMID: 37682479 DOI: 10.1007/978-1-0716-3354-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
The inference of gene regulatory networks can reveal molecular connections underlying biological processes and improve our understanding of complex biological phenomena in plants. Many previous network studies have inferred networks using only one type of omics data, such as transcriptomics. However, given more recent work applying multi-omics integration in plant biology, such as combining (phospho)proteomics with transcriptomics, it may be advantageous to integrate multiple omics data types into a comprehensive network prediction. Here, we describe a state-of-the-art approach for integrating multi-omics data with gene regulatory network inference to describe signaling pathways and uncover novel regulators. We detail how to download and process transcriptomics and (phospho)proteomics data for network inference, using an example dataset from the plant hormone signaling field. We provide a step-by-step protocol for inference, visualization, and analysis of an integrative multi-omics network using currently available methods. This chapter serves as an accessible guide for novice and intermediate bioinformaticians to analyze their own datasets and reanalyze published work.
Collapse
Affiliation(s)
- Natalie M Clark
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Bhavna Hurgobin
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, Bundoora, VIC, Australia
- La Trobe Institute for Sustainable Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia
| | - Dior R Kelley
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Mathew G Lewsey
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, Bundoora, VIC, Australia
- La Trobe Institute for Sustainable Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia
- Australian Research Council Centre of Excellence in Plants for Space, AgriBio Building, La Trobe University, Bundoora, VIC, Australia
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| |
Collapse
|
17
|
Santos Teixeira J, van den Berg T, ten Tusscher K. Complementary roles for auxin and auxin signalling revealed by reverse engineering lateral root stable prebranch site formation. Development 2022; 149:279332. [PMID: 36314783 PMCID: PMC9793420 DOI: 10.1242/dev.200927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/24/2022] [Indexed: 11/22/2022]
Abstract
Priming is the process through which periodic elevations in auxin signalling prepattern future sites for lateral root formation, called prebranch sites. Thus far, the extent to which elevations in auxin concentration and/or auxin signalling are required for priming and prebranch site formation has remained a matter of debate. Recently, we discovered a reflux-and-growth mechanism for priming generating periodic elevations in auxin concentration that subsequently dissipate. Here, we reverse engineer a mechanism for prebranch site formation that translates these transient elevations into a persistent increase in auxin signalling, resolving the prior debate into a two-step process of auxin concentration-mediated initial signal and auxin signalling capacity-mediated memorization. A crucial aspect of the prebranch site formation mechanism is its activation in response to time-integrated rather than instantaneous auxin signalling. The proposed mechanism is demonstrated to be consistent with prebranch site auxin signalling dynamics, lateral inhibition, and symmetry-breaking mechanisms and perturbations in auxin homeostasis.
Collapse
Affiliation(s)
- Joana Santos Teixeira
- Computational Developmental Biology Group, Faculty of Science, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Thea van den Berg
- Computational Developmental Biology Group, Faculty of Science, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Kirsten ten Tusscher
- Computational Developmental Biology Group, Faculty of Science, Utrecht University, Utrecht 3584 CH, The Netherlands,Author for correspondence ()
| |
Collapse
|
18
|
An integrated transcriptome mapping the regulatory network of coding and long non-coding RNAs provides a genomics resource in chickpea. Commun Biol 2022; 5:1106. [PMID: 36261617 PMCID: PMC9581958 DOI: 10.1038/s42003-022-04083-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 10/07/2022] [Indexed: 11/11/2022] Open
Abstract
Large-scale transcriptome analysis can provide a systems-level understanding of biological processes. To accelerate functional genomic studies in chickpea, we perform a comprehensive transcriptome analysis to generate full-length transcriptome and expression atlas of protein-coding genes (PCGs) and long non-coding RNAs (lncRNAs) from 32 different tissues/organs via deep sequencing. The high-depth RNA-seq dataset reveal expression dynamics and tissue-specificity along with associated biological functions of PCGs and lncRNAs during development. The coexpression network analysis reveal modules associated with a particular tissue or a set of related tissues. The components of transcriptional regulatory networks (TRNs), including transcription factors, their cognate cis-regulatory motifs, and target PCGs/lncRNAs that determine developmental programs of different tissues/organs, are identified. Several candidate tissue-specific and abiotic stress-responsive transcripts associated with quantitative trait loci that determine important agronomic traits are also identified. These results provide an important resource to advance functional/translational genomic and genetic studies during chickpea development and environmental conditions. A full-length transcriptome and expression atlas of protein-coding genes and long non-coding RNAs is generated in chickpea. Components of transcriptional regulatory networks and candidate tissue-specific transcripts associated with quantitative trait loci are identified.
Collapse
|
19
|
Wu C, Wang X, Zhen W, Nie Y, Li Y, Yuan P, Liu Q, Guo S, Shen Z, Zheng B, Hu Z. SICKLE modulates lateral root development by promoting degradation of lariat intronic RNA. PLANT PHYSIOLOGY 2022; 190:548-561. [PMID: 35788403 PMCID: PMC9434198 DOI: 10.1093/plphys/kiac301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Plant lateral roots (LRs) play vital roles in anchorage and uptake of water and nutrients. Here, we reveal that degradation of lariat intronic RNAs (lariRNAs) modulated by SICKLE (SIC) is required for LR development in Arabidopsis (Arabidopsis thaliana). Loss of SIC results in hyper-accumulation of lariRNAs and restricts the outgrowth of LR primordia, thereby reducing the number of emerged LRs. Decreasing accumulation of lariRNAs by over-expressing RNA debranching enzyme 1 (DBR1), a rate-limiting enzyme of lariRNA decay, restored LR defects in SIC-deficient plants. Mechanistically, SIC interacts with DBR1 and facilitates its nuclear accumulation, which is achieved through two functionally redundant regions (SIC1-244 and SIC252-319) for nuclear localization. Of the remaining amino acids in this region, six (SIC245-251) comprise a DBR1-interacting region while two (SICM246 and SICW251) are essential for DBR1-SIC interaction. Reducing lariRNAs restored microRNA (miRNA) levels and LR development in lariRNA hyper-accumulating plants, suggesting that these well-known regulators of LR development mainly function downstream of lariRNAs. Taken together, we propose that SIC acts as an enhancer of DBR1 nuclear accumulation by driving nuclear localization through direct interaction, thereby promoting lariRNA decay to fine-tune miRNA biogenesis and modulating LR development.
Collapse
Affiliation(s)
- Chengyun Wu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
- Sanya Institute of Henan University, Sanya 572025, China
| | - Xiaoqing Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Weibo Zhen
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yaqing Nie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Penglai Yuan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qiaoqiao Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Siyi Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | | |
Collapse
|
20
|
Wang H, Pak S, Yang J, Wu Y, Li W, Feng H, Yang J, Wei H, Li C. Two high hierarchical regulators, PuMYB40 and PuWRKY75, control the low phosphorus driven adventitious root formation in Populus ussuriensis. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1561-1577. [PMID: 35514032 PMCID: PMC9342623 DOI: 10.1111/pbi.13833] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 04/11/2022] [Accepted: 04/28/2022] [Indexed: 05/20/2023]
Abstract
Adventitious rooting is an essential biological process in the vegetative propagation of economically important horticultural and forest tree species. It enables utilization of the elite genotypes in breeding programmes and production. Promotion of adventitious root (AR) formation has been associated with starvation of inorganic phosphate and some factors involved in low phosphorus (LP) signalling. However, the regulatory mechanism underlying LP-mediated AR formation remains largely elusive. We established an efficient experimental system that guaranteed AR formation through short-term LP treatment in Populus ussuriensis. We then generated a time-course RNA-seq data set to recognize key regulatory genes and regulatory cascades positively regulating AR formation through data analysis and gene network construction, which were followed by experimental validation and characterization. We constructed a multilayered hierarchical gene regulatory network, from which PuMYB40, a typical R2R3-type MYB transcription factor (TF), and its interactive partner, PuWRKY75, as well as their direct targets, PuLRP1 and PuERF003, were identified to function upstream of the known adventitious rooting genes. These regulatory genes were functionally characterized and proved their roles in promoting AR formation in P. ussuriensis. In conclusion, our study unveiled a new hierarchical regulatory network that promoted AR formation in P. ussuriensis, which was activated by short-term LP stimulus and primarily governed by PuMYB40 and PuWRKY75.
Collapse
Affiliation(s)
- Hanzeng Wang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
- College of AgricultureJilin Agricultural Science and Technology UniversityJilinChina
| | - Solme Pak
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Jia Yang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Ye Wu
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Wenlong Li
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - He Feng
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Jingli Yang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Hairong Wei
- College of Forest Resources and Environmental ScienceMichigan Technological UniversityHoughtonMIUSA
| | - Chenghao Li
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| |
Collapse
|
21
|
Chen W, Chen Y, Siddique KH, Li S. Root penetration ability and plant growth in agroecosystems. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 183:160-168. [PMID: 35605464 DOI: 10.1016/j.plaphy.2022.04.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
Root penetration ability is critical for plant growth and development. When roots encounter soil impedance, hormones are activated that affect cells and tissues, leading to changes in root morphology and configuration that often increase root penetration ability. Factors, such as root system architecture, root anatomic traits, rhizosphere exudation and root-induced phytohormones, influencing root penetration ability and how they affect plant performance under soil impedance were summarized. Root penetration ability affects plant capturing water and nutrients, and thus determines plant performance and productivity in adverse environments. Great efforts have been made in searching for the underlying mechanisms of root penetration ability, and tools have been developed for phenotyping variability in root penetration ability. Therefore, with the continued development of agroecosystems based on the advocated low input costs and controlled tillage, crops or genotypes of a crop species with stronger root penetration ability may have the potential for developing new varieties with enhanced adaptation and grain yield under mechanical impedance in soil.
Collapse
Affiliation(s)
- Wenqian Chen
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, 712100, China; College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Yinglong Chen
- The UWA Institute of Agriculture, And School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6155, Australia
| | - Kadambot Hm Siddique
- The UWA Institute of Agriculture, And School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6155, Australia
| | - Shiqing Li
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, 712100, China; College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| |
Collapse
|
22
|
Bowles AMC, Paps J, Bechtold U. Water-related innovations in land plants evolved by different patterns of gene cooption and novelty. THE NEW PHYTOLOGIST 2022; 235:732-742. [PMID: 35048381 PMCID: PMC9303528 DOI: 10.1111/nph.17981] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/25/2021] [Indexed: 05/26/2023]
Abstract
The origin of land plants and their descendants was marked by the evolution of key adaptations to life in terrestrial environments such as roots, vascular tissue and stomata. Though these innovations are well characterized, the evolution of the genetic toolkit underlying their development and function is poorly understood. We analysed molecular data from 532 species to investigate the evolutionary origin and diversification of genes involved in the development and regulation of these adaptations. We show that novel genes in the first land plants led to the single origin of stomata, but the stomatal closure of seed plants resulted from later gene expansions. By contrast, the major mechanism leading to the origin of vascular tissue was cooption of genes that emerged in the first land plants, enabling continuous water transport throughout the ancestral vascular plant. In turn, new key genes in the ancestors of plants with true leaves and seed plants led to the emergence of roots and lateral roots. The analysis highlights the different modes of evolution that enabled plants to conquer land, suggesting that gene expansion and cooption are the most common mechanisms of biological innovation in plant evolutionary history.
Collapse
Affiliation(s)
- Alexander M. C. Bowles
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
- School of Geographical SciencesUniversity of BristolUniversity RoadBristolBS8 1RLUK
| | - Jordi Paps
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
- School of Biological SciencesUniversity of Bristol24 Tyndall AvenueBristolBS8 1TQUK
| | - Ulrike Bechtold
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
- Present address:
Department of BiosciencesDurham UniversitySouth RoadDurhamDH1 3LEUK
| |
Collapse
|
23
|
Li S, Li Q, Tian X, Mu L, Ji M, Wang X, Li N, Liu F, Shu J, Crawford NM, Wang Y. PHB3 regulates lateral root primordia formation via NO-mediated degradation of AUXIN/INDOLE-3-ACETIC ACID proteins. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4034-4045. [PMID: 35303089 DOI: 10.1093/jxb/erac115] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/16/2022] [Indexed: 05/21/2023]
Abstract
We have previously shown that Arabidopsis thaliana Prohibitin 3 (PHB3) controls auxin-stimulated lateral root (LR) formation; however, the underlying molecular mechanism is unknown. Here, we demonstrate that PHB3 regulates lateral root (LR) development mainly through influencing lateral root primordia (LRP) initiation, via affecting nitric oxide (NO) accumulation. The reduced LRP in phb3 mutant was largely rescued by treatment with a NO donor. The decreased NO accumulation in phb3 caused a lower expression of GATA TRANSCRIPTION FACTOR 23 (GATA23) and LATERAL ORGAN BOUNDARIES DOMAIN 16 (LBD16) through inhibiting the degradation of INDOLE-3-ACETIC ACID INDUCIBLE 14/28 (IAA14/28). Overexpression of either GATA23 or LBD16 in phb3 mutant background recovered the reduced density of LRP. These results indicate that PHB3 regulates LRP initiation via NO-mediated auxin signalling, by modulating the degradation of IAA14/28.
Collapse
Affiliation(s)
- Shuna Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Qingqing Li
- College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China
| | - Xiao Tian
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Lijun Mu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Meiling Ji
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Xiaoping Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Na Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Fei Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Jing Shu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
- College of Agriculture Science and Technology, Shandong Agriculture and Engineering University, Jinan Shandong, China
| | - Nigel M Crawford
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California, USA
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| |
Collapse
|
24
|
Ibarra-Laclette E, Venancio-Rodríguez CA, Vásquez-Aguilar AA, Alonso-Sánchez AG, Pérez-Torres CA, Villafán E, Ramírez-Barahona S, Galicia S, Sosa V, Rebollar EA, Lara C, González-Rodríguez A, Díaz-Fleisher F, Ornelas JF. Transcriptional Basis for Haustorium Formation and Host Establishment in Hemiparasitic Psittacanthus schiedeanus Mistletoes. Front Genet 2022; 13:929490. [PMID: 35769994 PMCID: PMC9235361 DOI: 10.3389/fgene.2022.929490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/20/2022] [Indexed: 11/13/2022] Open
Abstract
The mistletoe Psittacanthus schiedeanus, a keystone species in interaction networks between plants, pollinators, and seed dispersers, infects a wide range of native and non-native tree species of commercial interest. Here, using RNA-seq methodology we assembled the whole circularized quadripartite structure of P. schiedeanus chloroplast genome and described changes in the gene expression of the nuclear genomes across time of experimentally inoculated seeds. Of the 140,467 assembled and annotated uniGenes, 2,000 were identified as differentially expressed (DEGs) and were classified in six distinct clusters according to their expression profiles. DEGs were also classified in enriched functional categories related to synthesis, signaling, homoeostasis, and response to auxin and jasmonic acid. Since many orthologs are involved in lateral or adventitious root formation in other plant species, we propose that in P. schiedeanus (and perhaps in other rootless mistletoe species), these genes participate in haustorium formation by complex regulatory networks here described. Lastly, and according to the structural similarities of P. schiedeanus enzymes with those that are involved in host cell wall degradation in fungi, we suggest that a similar enzymatic arsenal is secreted extracellularly and used by mistletoes species to easily parasitize and break through tissues of the host.
Collapse
Affiliation(s)
- Enrique Ibarra-Laclette
- Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
- *Correspondence: Enrique Ibarra-Laclette, ; Juan Francisco Ornelas,
| | | | | | | | - Claudia-Anahí Pérez-Torres
- Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
- Investigador por Mexico-CONACyT en el Instituto de Ecología A.C. (INECOL), Xalapa, Mexico
| | - Emanuel Villafán
- Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Santiago Ramírez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de Mexico (UNAM), Ciudad de Mexico, Mexico
| | - Sonia Galicia
- Instituto de Ecología A.C. (INECOL), Red de Biología Evolutiva, Xalapa, Mexico
| | - Victoria Sosa
- Instituto de Ecología A.C. (INECOL), Red de Biología Evolutiva, Xalapa, Mexico
| | - Eria A. Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, Mexico
| | - Carlos Lara
- Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Antonio González-Rodríguez
- Laboratorio de Genética de la Conservación, Instituto de Investigaciones en Ecosistemas y Sustentabilidad (IIES), UNAM, Morelia, Mexico
| | | | - Juan Francisco Ornelas
- Instituto de Ecología A.C. (INECOL), Red de Biología Evolutiva, Xalapa, Mexico
- *Correspondence: Enrique Ibarra-Laclette, ; Juan Francisco Ornelas,
| |
Collapse
|
25
|
Rutten J, van den Berg T, Tusscher KT. Modeling Auxin Signaling in Roots: Auxin Computations. Cold Spring Harb Perspect Biol 2022; 14:a040089. [PMID: 34001532 PMCID: PMC8805645 DOI: 10.1101/cshperspect.a040089] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Auxin signaling and patterning is an inherently complex process, involving polarized auxin transport, metabolism, and signaling, its effect on developmental zones, as well as growth rates, and the feedback between all these different aspects. This complexity has led to an important role for computational modeling in unraveling the multifactorial roles of auxin in plant developmental and adaptive processes. Here we discuss the basic ingredients of auxin signaling and patterning models for root development as well as a series of key modeling studies in this area. These modeling studies have helped elucidate how plants use auxin signaling to compute the size of their root meristem, the direction in which to grow, and when and where to form lateral roots. Importantly, these models highlight how auxin, through patterning of and collaborating with other factors, can fulfill all these roles simultaneously.
Collapse
Affiliation(s)
- Jaap Rutten
- Computational Developmental Biology Group, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Thea van den Berg
- Computational Developmental Biology Group, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Kirsten Ten Tusscher
- Computational Developmental Biology Group, Utrecht University, Utrecht 3584 CH, The Netherlands
| |
Collapse
|
26
|
Li H, Gao MY, Mo CH, Wong MH, Chen XW, Wang JJ. Potential use of arbuscular mycorrhizal fungi for simultaneous mitigation of arsenic and cadmium accumulation in rice. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:50-67. [PMID: 34610119 DOI: 10.1093/jxb/erab444] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
Rice polluted by metal(loid)s, especially arsenic (As) and cadmium (Cd), imposes serious health risks. Numerous studies have demonstrated that the obligate plant symbionts arbuscular mycorrhizal fungi (AMF) can reduce As and Cd concentrations in rice. The behaviours of metal(loid)s in the soil-rice-AMF system are of significant interest for scientists in the fields of plant biology, microbiology, agriculture, and environmental science. We review the mechanisms of As and Cd accumulation in rice with and without the involvement of AMF. In the context of the soil-rice-AMF system, we assess and discuss the role of AMF in affecting soil ion mobility, chemical forms, transport pathways (including the symplast and apoplast), and genotype variation. A potential strategy for AMF application in rice fields is considered, followed by future research directions to improve theoretical understanding and encourage field application.
Collapse
Affiliation(s)
- Hui Li
- Guangdong Provincial Research Centre for Environment Pollution Control and Remediation Materials, Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Meng Ying Gao
- Guangdong Provincial Research Centre for Environment Pollution Control and Remediation Materials, Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Ce Hui Mo
- Guangdong Provincial Research Centre for Environment Pollution Control and Remediation Materials, Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Ming Hung Wong
- Guangdong Provincial Research Centre for Environment Pollution Control and Remediation Materials, Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
- Consortium on Health, Environment, Education and Research (CHEER), The Education University of Hong Kong, Tai Po, Hong Kong, China
| | - Xun Wen Chen
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jun-Jian Wang
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| |
Collapse
|
27
|
Zhang M, Wang F, Wang X, Feng J, Yi Q, Zhu S, Zhao X. Mining key genes related to root morphogenesis through genome-wide identification and expression analysis of RR gene family in citrus. FRONTIERS IN PLANT SCIENCE 2022; 13:1068961. [PMID: 36483961 PMCID: PMC9725114 DOI: 10.3389/fpls.2022.1068961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/07/2022] [Indexed: 05/21/2023]
Abstract
Morphogenesis of root is a vital factor to determine the root system architecture. Cytokinin response regulators (RRs) are the key transcription factors in cytokinin signaling, which play important roles in regulating the root morphogenesis. In this study, 29 RR proteins, including 21 RRs and 8 pseudo RRs, were identified from the genome of citrus, and termed as CcRR1-21 and CcPRR1-8, respectively. Phylogenetic analysis revealed that the 29 CcRRs could be classified into four types according to their representative domains. Analysis of cis-elements of CcRRs indicated that they were possibly involved in the regulation of growth and abiotic stress resistance in citrus. Within the type A and type B CcRRs, CcRR4, CcRR5, CcRR6 and CcRR16 highly expressed in roots and leaves, and dramatically responded to the treatments of hormones and abiotic stresses. CcRR2, CcRR10, CcRR14 and CcRR19 also highly expressed in roots under different treatments. Characteristic analysis revealed that the above 8 CcRRs significantly and differentially expressed in the three zones of root, suggesting their functional differences in regulating root growth and development. Further investigation of the 3 highly and differentially expressed CcRRs, CcRR5, CcRR10 and CcRR14, in 9 citrus rootstocks showed that the expression of CcRR5, CcRR10 and CcRR14 was significantly correlated to the length of primary root, the number of lateral roots, and both primary root and the number of lateral roots, respectively. Results of this study indicated that CcRRs were involved in regulating the growth and development of the root in citrus with different functions among the members.
Collapse
Affiliation(s)
- Manman Zhang
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
- National Citrus Engineering Research Center, Chongqing, China
| | - Fusheng Wang
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
- National Citrus Engineering Research Center, Chongqing, China
| | - Xiaoli Wang
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
- National Citrus Engineering Research Center, Chongqing, China
| | - Jipeng Feng
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
- National Citrus Engineering Research Center, Chongqing, China
| | - Qian Yi
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
- National Citrus Engineering Research Center, Chongqing, China
| | - Shiping Zhu
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
- National Citrus Engineering Research Center, Chongqing, China
- *Correspondence: Shiping Zhu, ; Xiaochun Zhao,
| | - Xiaochun Zhao
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
- National Citrus Engineering Research Center, Chongqing, China
- *Correspondence: Shiping Zhu, ; Xiaochun Zhao,
| |
Collapse
|
28
|
Yi C, Wang X, Chen Q, Callahan DL, Fournier-Level A, Whelan J, Jost R. Diverse phosphate and auxin transport loci distinguish phosphate tolerant from sensitive Arabidopsis accessions. PLANT PHYSIOLOGY 2021; 187:2656-2673. [PMID: 34636851 PMCID: PMC8644285 DOI: 10.1093/plphys/kiab441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/18/2021] [Indexed: 05/11/2023]
Abstract
Phosphorus (P) is an essential element for plant growth often limiting agroecosystems. To identify genetic determinants of performance under variable phosphate (Pi) supply, we conducted genome-wide association studies on five highly predictive Pi starvation response traits in 200 Arabidopsis (Arabidopsis thaliana) accessions. Pi concentration in Pi-limited organs had the strongest, and primary root length had the weakest genetic component. Of 70 trait-associated candidate genes, 17 responded to Pi withdrawal. The PHOSPHATE TRANSPORTER1 gene cluster on chromosome 5 comprises PHT1;1, PHT1;2, and PHT1;3 with known impact on P status. A second locus featured uncharacterized endomembrane-associated auxin efflux carrier encoding PIN-LIKES7 (PILS7) which was more strongly suppressed in Pi-limited roots of Pi-starvation sensitive accessions. In the Col-0 background, Pi uptake and organ growth were impaired in both Pi-limited pht1;1 and two pils7 T-DNA insertion mutants, while Pi -limited pht1;2 had higher biomass and pht1;3 was indistinguishable from wild-type. Copy number variation at the PHT1 locus with loss of the PHT1;3 gene and smaller scale deletions in PHT1;1 and PHT1;2 predicted to alter both protein structure and function suggest diversification of PHT1 is a key driver for adaptation to P limitation. Haplogroup analysis revealed a phosphorylation site in the protein encoded by the PILS7 allele from stress-sensitive accessions as well as additional auxin-responsive elements in the promoter of the "stress tolerant" allele. The former allele's inability to complement the pils7-1 mutant in the Col-0 background implies the presence of a kinase signaling loop controlling PILS7 activity in accessions from P-rich environments, while survival in P-poor environments requires fine-tuning of stress-responsive root auxin signaling.
Collapse
Affiliation(s)
- Changyu Yi
- Department of Animal, Plant and Soil Sciences and La Trobe Institute for Agriculture and Food (LIAF), ARC Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora VIC 3086, Australia
| | - Xinchao Wang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Zhejiang 31008, China
| | - Qian Chen
- Department of Animal, Plant and Soil Sciences and La Trobe Institute for Agriculture and Food (LIAF), ARC Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora VIC 3086, Australia
| | - Damien L Callahan
- Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University (Burwood Campus), Burwood VIC 3125, Australia
| | | | - James Whelan
- Department of Animal, Plant and Soil Sciences and La Trobe Institute for Agriculture and Food (LIAF), ARC Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora VIC 3086, Australia
| | - Ricarda Jost
- Department of Animal, Plant and Soil Sciences and La Trobe Institute for Agriculture and Food (LIAF), ARC Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora VIC 3086, Australia
- Author for communication:
| |
Collapse
|
29
|
Guzmán-Báez GA, Trejo-Téllez LI, Ramírez-Olvera SM, Salinas-Ruíz J, Bello-Bello JJ, Alcántar-González G, Hidalgo-Contreras JV, Gómez-Merino FC. Silver Nanoparticles Increase Nitrogen, Phosphorus, and Potassium Concentrations in Leaves and Stimulate Root Length and Number of Roots in Tomato Seedlings in a Hormetic Manner. Dose Response 2021; 19:15593258211044576. [PMID: 34840539 PMCID: PMC8619790 DOI: 10.1177/15593258211044576] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022] Open
Abstract
Background Silver nanoparticles (AgNPs) display unique biological activities and may serve as novel biostimulators. Nonetheless, their biostimulant effects on germination, early growth, and major nutrient concentrations (N, P, and K) in tomato (Solanum lycopersicum) have been little explored. Methods Tomato seeds of the Vengador and Rio Grande cultivars were germinated on filter paper inside plastic containers in the presence of 0, 5, 10, and 20 mg/L AgNPs. Germination parameters were recorded daily, while early growth traits of seedlings were determined 20 days after applying the treatments (dat). To determine nutrient concentrations in leaves, a hydroponic experiment was established, adding AgNPs to the nutrient solution. Thirty-day-old plants were established in the hydroponic system and kept there for 7 days, and subsequently, leaves were harvested and nutrient concentrations were determined. Results The AgNPs applied did not affect germination parameters, whereas their application stimulated length and number of roots in a hormetic manner. In 37-day-old plants, low AgNP applications increased the concentrations of N, P, and K in leaves. Conclusion As novel biostimulants, AgNPs promoted root development, especially when applied at 5 mg/L. Furthermore, they increased N, P, and K concentration in leaves, which is advantageous for seedling performance during the early developmental stages.
Collapse
Affiliation(s)
| | | | | | - Josafhat Salinas-Ruíz
- College of Postgraduates in Agricultural Sciences Campus Córdoba, Amatlán de Los Reyes, Veracruz, Mexico
| | - Jericó J Bello-Bello
- CONACYT-College of Postgraduates in Agricultural Sciences Campus Córdoba, Amatlán de Los Reyes, Veracruz, Mexico
| | | | | | - Fernando C Gómez-Merino
- College of Postgraduates in Agricultural Sciences Campus Córdoba, Amatlán de Los Reyes, Veracruz, Mexico
| |
Collapse
|
30
|
Xie X, Wang Y, Datla R, Ren M. Auxin and Target of Rapamycin Spatiotemporally Regulate Root Organogenesis. Int J Mol Sci 2021; 22:ijms222111357. [PMID: 34768785 PMCID: PMC8583787 DOI: 10.3390/ijms222111357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/20/2021] [Indexed: 12/17/2022] Open
Abstract
The programs associated with embryonic roots (ERs), primary roots (PRs), lateral roots (LRs), and adventitious roots (ARs) play crucial roles in the growth and development of roots in plants. The root functions are involved in diverse processes such as water and nutrient absorption and their utilization, the storage of photosynthetic products, and stress tolerance. Hormones and signaling pathways play regulatory roles during root development. Among these, auxin is the most important hormone regulating root development. The target of rapamycin (TOR) signaling pathway has also been shown to play a key role in root developmental programs. In this article, the milestones and influential progress of studying crosstalk between auxin and TOR during the development of ERs, PRs, LRs and ARs, as well as their functional implications in root morphogenesis, development, and architecture, are systematically summarized and discussed.
Collapse
Affiliation(s)
- Xiulan Xie
- Labarotary of Space Biology, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610213, China; (X.X.); (Y.W.)
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Science of Zhengzhou University, Zhengzhou 450000, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Ying Wang
- Labarotary of Space Biology, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610213, China; (X.X.); (Y.W.)
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Science of Zhengzhou University, Zhengzhou 450000, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Raju Datla
- Global Institute for Food Security in Saskatoon, University of Saskatchewan, Saskatoon, SK S7N 0W9, Canada
- Correspondence: (R.D.); (M.R.)
| | - Maozhi Ren
- Labarotary of Space Biology, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610213, China; (X.X.); (Y.W.)
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Science of Zhengzhou University, Zhengzhou 450000, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- Correspondence: (R.D.); (M.R.)
| |
Collapse
|
31
|
Saxena A, Bi WL, Shukla MR, Cannings S, Bennett B, Saxena PK. Micropropagation and Cryopreservation of Yukon Draba ( Draba yukonensis), a Special Concern Plant Species Endemic to Yukon Territory, Canada. PLANTS 2021; 10:plants10102093. [PMID: 34685902 DOI: 10.3390/plants10102093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 09/26/2021] [Accepted: 09/28/2021] [Indexed: 11/16/2022]
Abstract
Yukon Draba (Draba yukonensis) is a small, short-lived perennial mustard species that is endemic to southwestern Yukon in Canada. This plant has been categorized as a species of Special Concern. It faces the threat of habitat loss due to natural and man-made causes and a population that is unevenly distributed to a few large and several small subpopulations in the area. It will therefore be judicious to undertake investigations on the conservation of this species to save it from further deterioration which may lead to its extinction. In this study, a protocol was developed for in vitro propagation and cryopreservation of Yukon Draba. The micropropagation protocol was optimized using shoot tips which enabled clonal propagation and in vitro storage of the species. Shoots grew best in the medium containing MS basal salts and had the highest multiplication with the addition of 2 µM 6-benzylaminopurine or 5 µM Kinetin with 3% sucrose. The addition of 10 µM Indole Butyric Acid (IBA) produced the highest number of adventitious roots on the shoots and the longest root length was observed at 2 µM IBA. The rooted plantlets were transferred to greenhouse and the highest survival (87.5%) was observed for the plantlets treated with a lower concentration of IBA (2 µM). Cryopreservation protocol was developed using the droplet-vitrification method for in vitro shoot tips. Two-week-old shoots had the highest survival and regrowth following exposure to plant vitrification solution 3 (PVS3) for 30 min, prior to direct immersion of the droplets into the liquid nitrogen. The optimized protocols for the micropropagation and cryopreservation may be useful for the long-term germplasm conservation and reintroduction of this species in its natural habitat.
Collapse
Affiliation(s)
- Akansha Saxena
- Gosling Research Institute for Plant Preservation, Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Wen-Lu Bi
- Gosling Research Institute for Plant Preservation, Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Mukund R Shukla
- Gosling Research Institute for Plant Preservation, Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Syd Cannings
- Environment and Climate Change Canada, 91780 Alaska Highway, 1st Floor, Whitehorse, YK Y1A 5X7, Canada
| | - Bruce Bennett
- B.A. Bennett Herbarium (BABY), 33 Chinook Lane, Whitehorse, YT Y1A 5Y2, Canada
| | - Praveen K Saxena
- Gosling Research Institute for Plant Preservation, Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada
| |
Collapse
|
32
|
Li J, Zhang H, Zhu J, Shen Y, Zeng N, Liu S, Wang H, Wang J, Zhan X. Role of miR164 in the growth of wheat new adventitious roots exposed to phenanthrene. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 284:117204. [PMID: 33910135 DOI: 10.1016/j.envpol.2021.117204] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/31/2021] [Accepted: 04/17/2021] [Indexed: 06/12/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs), ubiquitous organic pollutants in the environment, can accumulate in humans via the food chain and then harm human health. MiRNAs (microRNAs), a kind of non-coding small RNAs with a length of 18-30 nucleotides, regulate plant growth and development and respond to environmental stress. In this study, it is demonstrated that miR164 can regulate root growth and adventitious root generation of wheat under phenanthrene exposure by targeting NAC (NAM/ATAF/CUC) transcription factor. We observed that phenanthrene treatment accelerated the senescence and death of wheat roots, and stimulated the occurrence of new roots. However, it is difficult to compensate for the loss caused by old root senescence and death, due to the slower growth of new roots under phenanthrene exposure. Phenanthrene accumulation in wheat roots caused to generate a lot of reactive oxygen species, and enhanced lipoxygenase activity and malonaldehyde concentration, meaning that lipid peroxidation is the main reason for root damage. MiR164 was up-regulated by phenanthrene, enhancing the silence of NAC1, weakening the association with auxin signal, and inhibiting the occurrence of adventitious roots. Phenanthrene also affected the expression of CDK (the coding gene of cyclin-dependent kinase) and CDC2 (a gene regulating cell division cycle), the key genes in the cell cycle of pericycle cells, thereby affecting the occurrence and growth of lateral roots. In addition, NAM (a gene regulating no apical meristem) and NAC23 may also be related to the root growth and development in wheat exposed to phenanthrene. These results provide not only theoretical basis for understanding the molecular mechanism of crop response to PAHs accumulation, but also knowledge support for improving phytoremediation of soil or water contaminated by PAHs.
Collapse
Affiliation(s)
- Jinfeng Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, People's Republic of China; Institute of Botany, Jiangsu Province and Chinese Academy Sciences, Nanjing, 210014, China
| | - Huihui Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, People's Republic of China
| | - Jiahui Zhu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, People's Republic of China; Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, 01003, United States
| | - Yu Shen
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, People's Republic of China; Department of Analytical Chemistry, The Connecticut Agricultural Experiment Station, New Haven, CT, 06504, United States
| | - Nengde Zeng
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, People's Republic of China
| | - Shiqi Liu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, People's Republic of China
| | - Huiqian Wang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, People's Republic of China
| | - Jia Wang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, People's Republic of China
| | - Xinhua Zhan
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, People's Republic of China.
| |
Collapse
|
33
|
Environmental and Cultivation Factors Affect the Morphology, Architecture and Performance of Root Systems in Soilless Grown Plants. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7080243] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Soilless culture systems are currently one of the fastest-growing sectors in horticulture. The plant roots are confined into a specific rootzone and are exposed to environmental changes and cultivation factors. The recent scientific evidence regarding the effects of several environmental and cultivation factors on the morphology, architecture, and performance of the root system of plants grown in SCS are the objectives of this study. The effect of root restriction, nutrient solution, irrigation frequency, rootzone temperature, oxygenation, vapour pressure deficit, lighting, rootzone pH, root exudates, CO2, and beneficiary microorganisms on the functionality and performance of the root system are discussed. Overall, the main results of this review demonstrate that researchers have carried out great efforts in innovation to optimize SCS water and nutrients supply, proper temperature, and oxygen levels at the rootzone and effective plant–beneficiary microorganisms, while contributing to plant yields. Finally, this review analyses the new trends based on emerging technologies and various tools that might be exploited in a smart agriculture approach to improve root management in soilless cropping while procuring a deeper understanding of plant root–shoot communication.
Collapse
|
34
|
Growth of Basil (Ocimum basilicum) in Aeroponics, DRF, and Raft Systems with Effluents of African Catfish (Clarias gariepinus) in Decoupled Aquaponics (s.s.). AGRIENGINEERING 2021. [DOI: 10.3390/agriengineering3030036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Basil (Ocimum basilicum) was cultivated in three hydroponic subsystems (i) a modified commercial aeroponics, (ii) a dynamic root floating (DRF) system, and (iii) a floating raft system in a decoupled aquaponic system in Northern Germany, Mecklenburg–Western Pomerania. For plant nutrition, aquaculture process water from intensive rearing of African catfish (Clarias gariepinus) was used without fertilizer. After 39 days, 16 plant growth parameters were compared, with aeroponics performing significantly better in 11 parameters compared with the DRF, and better compared with the raft in 13 parameters. The economically important leaf wet and dry weight was over 40% higher in aeroponics (28.53 ± 8.74 g; 4.26 ± 1.23 g), but similar in the DRF (20.19 ± 6.57 g; 2.83 ± 0.90 g) and raft (20.35 ± 7.14 g; 2.84 ± 1.04 g). The roots in the DRF grew shorter and thicker; however, this resulted in a higher root dry weight in aeroponics (1.08 ± 0.38 g) compared with the DRF (0.82 ± 0.36 g) and raft (0.67 ± 0.27 g). With optimal fertilizer and system improvement, aquaponic aeroponics (s.s.) could become a productive and sustainable large-scale food production system in the future. Due to its simple construction, the raft is ideal for domestic or semi-commercial use and can be used in areas where water is neither scarce nor expensive. The DRF system is particularly suitable for basil cultivation under hot tropical conditions.
Collapse
|
35
|
Geng H, Wang M, Gong J, Xu Y, Ma S. An Arabidopsis expression predictor enables inference of transcriptional regulators for gene modules. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:597-612. [PMID: 33974299 DOI: 10.1111/tpj.15315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/08/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
The regulation of gene expression by transcription factors (TFs) has been studied for a long time, but no model that can accurately predict transcriptome profiles based on TF activities currently exists. Here, we developed a computational approach, named EXPLICIT (Expression Prediction via Log-linear Combination of Transcription Factors), to construct a universal predictor for Arabidopsis to predict the expression of 29 182 non-TF genes using 1678 TFs. When applied to RNA-Seq samples from diverse tissues, EXPLICIT generated accurate predicted transcriptomes correlating well with actual expression, with an average correlation coefficient of 0.986. After recapitulating the quantitative relationships between TFs and their target genes, EXPLICIT enabled downstream inference of TF regulators for genes and gene modules functioning in diverse plant pathways, including those involved in suberin, flavonoid, glucosinolate metabolism, lateral root, xylem, secondary cell wall development or endoplasmic reticulum stress response. Our approach showed a better ability to recover the correct TF regulators when compared with existing plant tools, and provides an innovative way to study transcriptional regulation.
Collapse
Affiliation(s)
- Haiying Geng
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Meng Wang
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Jiazhen Gong
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Yupu Xu
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Shisong Ma
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
- School of Data Science, University of Science and Technology of China, Hefei, China
| |
Collapse
|
36
|
Wang Y, Sun H, Wang H, Yang X, Xu Y, Yang Z, Xu C, Li P. Integrating transcriptome, co-expression and QTL-seq analysis reveals that primary root growth in maize is regulated via flavonoid biosynthesis and auxin signal transduction. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4773-4795. [PMID: 33909071 DOI: 10.1093/jxb/erab177] [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: 08/01/2020] [Accepted: 04/24/2021] [Indexed: 05/28/2023]
Abstract
The primary root is critical for early seedling growth and survival. To understand the molecular mechanisms governing primary root development, we performed a dynamic transcriptome analysis of two maize (Zea mays) inbred lines with contrasting primary root length at nine time points over a 12-day period. A total of 18 702 genes were differentially expressed between two lines or different time points. Gene enrichment, phytohormone content determination, and metabolomics analysis showed that auxin biosynthesis and signal transduction, as well as the phenylpropanoid and flavonoid biosynthesis pathways, were associated with root development. Co-expression network analysis revealed that eight modules were associated with lines/stages, as well as primary or lateral root length. In root-related modules, flavonoid metabolism accompanied by auxin biosynthesis and signal transduction constituted a complex gene regulatory network during primary root development. Two candidate genes (rootless concerning crown and seminal roots, rtcs and Zm00001d012781) involved in auxin signaling and flavonoid biosynthesis were identified by co-expression network analysis, QTL-seq and functional annotation. These results increase our understanding of the regulatory network controlling the development of primary and lateral root length, and provide a valuable genetic resource for improvement of root performance in maize.
Collapse
Affiliation(s)
- Yunyun Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Hui Sun
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Houmiao Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Xiaoyi Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Yang Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Zefeng Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, China
| | - Chenwu Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, China
| | - Pengcheng Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| |
Collapse
|
37
|
Chapman JM, Muday GK. Flavonols modulate lateral root emergence by scavenging reactive oxygen species in Arabidopsis thaliana. J Biol Chem 2021; 296:100222. [PMID: 33839683 PMCID: PMC7948594 DOI: 10.1074/jbc.ra120.014543] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 12/19/2020] [Accepted: 12/21/2020] [Indexed: 11/20/2022] Open
Abstract
Flavonoids are a class of specialized metabolites with subclasses including flavonols and anthocyanins, which have unique properties as antioxidants. Flavonoids modulate plant development, but whether and how they impact lateral root development is unclear. We examined potential roles for flavonols in this process using Arabidopsis thaliana mutants with defects in genes encoding key enzymes in flavonoid biosynthesis. We observed the tt4 and fls1 mutants, which produce no flavonols, have increased lateral root emergence. The tt4 root phenotype was reversed by genetic and chemical complementation. To more specifically define the flavonoids involved, we tested an array of flavonoid biosynthetic mutants, eliminating roles for anthocyanins and the flavonols quercetin and isorhamnetin in modulating lateral root development. Instead, two tt7 mutant alleles, with defects in a branchpoint enzyme blocking quercetin biosynthesis, formed reduced numbers of lateral roots and tt7-2 had elevated levels of kaempferol. Using a flavonol-specific dye, we observed that in the tt7-2 mutant, kaempferol accumulated within lateral root primordia at higher levels than wild-type. These data are consistent with kaempferol, or downstream derivatives, acting as a negative regulator of lateral root emergence. We examined ROS accumulation using ROS-responsive probes and found reduced fluorescence of a superoxide-selective probe within the primordia of tt7-2 compared with wild-type, but not in the tt4 mutant, consistent with opposite effects of these mutants on lateral root emergence. These results support a model in which increased level of kaempferol in the lateral root primordia of tt7-2 reduces superoxide concentration and ROS-stimulated lateral root emergence.
Collapse
Affiliation(s)
- Jordan M Chapman
- Biology Department, Wake Forest University, Winston Salem, North Carolina, USA
| | - Gloria K Muday
- Biology Department, Wake Forest University, Winston Salem, North Carolina, USA.
| |
Collapse
|
38
|
Singh S, Singh UB, Trivdi M, Malviya D, Sahu PK, Roy M, Sharma PK, Singh HV, Manna MC, Saxena AK. Restructuring the Cellular Responses: Connecting Microbial Intervention With Ecological Fitness and Adaptiveness to the Maize ( Zea mays L.) Grown in Saline-Sodic Soil. Front Microbiol 2021; 11:568325. [PMID: 33643224 PMCID: PMC7907600 DOI: 10.3389/fmicb.2020.568325] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 12/24/2020] [Indexed: 11/13/2022] Open
Abstract
Salt stress hampers plant growth and development. It is now becoming one of the most important threats to agricultural productivity. Rhizosphere microorganisms play key roles in modulating cellular responses and enable plant tolerant to salt stress, but the detailed mechanisms of how this occurs need in-depth investigation. The present study elucidated that the microbe-mediated restructuring of the cellular responses leads to ecological fitness and adaptiveness to the maize (Zea mays L.) grown in saline-sodic soil. In the present study, effects of seed biopriming with B. safensis MF-01, B. altitudinis MF-15, and B. velezensis MF-08 singly and in consortium on different growth parameters were recorded. Soil biochemical and enzymatic analyses were performed. The activity and gene expression of High-Affinity K+ Transporter (ZmHKT-1), Sodium/Hydrogen exchanger 1 (zmNHX1), and antioxidant enzymes (ZmAPX1.2, ZmBADH-1, ZmCAT, ZmMPK5, ZmMPK7, and ZmCPK11) were studied. The expression of genes related to lateral root development (ZmHO-1, ZmGSL-1, and ZmGSL-3) and root architecture were also carried out. Seeds bioprimed with consortium of all three strains have been shown to confer increased seed germination (23.34-26.31%) and vigor indices (vigor index I: 38.71-53.68% and vigor index II: 74.11-82.43%) as compared to untreated control plant grown in saline-sodic soil at 30 days of sowing. Results indicated that plants treated with consortium of three strains induced early production of adventitious roots (tips: 4889.29, forks: 7951.57, and crossings: 2296.45) in maize compared to plants primed with single strains and untreated control (tips: 2019.25, forks: 3021.45, and crossings: 388.36), which was further confirmed by assessing the transcript level of ZmHO-1 (7.20 folds), ZmGSL-1 (4.50 folds), and ZmGSL-3 (12.00 folds) genes using the qPCR approach. The uptake and translocation of Na+, K+, and Ca2+ significantly varied in the plants treated with bioagents alone or in consortium. qRT-PCR analysis also revealed that the ZmHKT-1 and zmNHX1 expression levels varied significantly in the maize root upon inoculation and showed a 6- to 11-fold increase in the plants bioprimed with all the three strains in combination. Further, the activity and gene expression levels of antioxidant enzymes were significantly higher in the leaves of maize subjected seed biopriming with bioagents individually or in combination (3.50- to 12.00-fold). Our research indicated that ZmHKT-1 and zmNHX1 expression could effectively enhance salt tolerance by maintaining an optimal Na+/K+ balance and increasing the antioxidant activity that keeps reactive oxygen species at a low accumulation level. Interestingly, up-regulation of ZmHKT-1, NHX1, ZmHO-1, ZmGSL-1, and ZmGSL-3 and genes encoding antioxidants regulates the cellular responses that could effectively enhance the adaptiveness and ultimately leads to better plant growth and grain production in the maize crop grown in saline-sodic soil.
Collapse
Affiliation(s)
- Shailendra Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, India
| | - Udai B. Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, India
| | - Mala Trivdi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
| | - Deepti Malviya
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, India
| | - Pramod K. Sahu
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, India
| | - Manish Roy
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, India
| | - Pawan K. Sharma
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, India
| | - Harsh V. Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, India
| | - M. C. Manna
- Soil Biology Division, ICAR-Indian Institute of Soil Science, Bhopal, India
| | - Anil K. Saxena
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, India
| |
Collapse
|
39
|
Gandullo J, Ahmad S, Darwish E, Karlova R, Testerink C. Phenotyping Tomato Root Developmental Plasticity in Response to Salinity in Soil Rhizotrons. PLANT PHENOMICS (WASHINGTON, D.C.) 2021; 2021:2760532. [PMID: 33575670 PMCID: PMC7869940 DOI: 10.34133/2021/2760532] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/25/2020] [Indexed: 05/23/2023]
Abstract
Plants have developed multiple strategies to respond to salt stress. In order to identify new traits related to salt tolerance, with potential breeding application, the research focus has recently been shifted to include root system architecture (RSA) and root plasticity. Using a simple but effective root phenotyping system containing soil (rhizotrons), RSA of several tomato cultivars and their response to salinity was investigated. We observed a high level of root plasticity of tomato seedlings under salt stress. The general root architecture was substantially modified in response to salt, especially with respect to position of the lateral roots in the soil. At the soil surface, where salt accumulates, lateral root emergence was most strongly inhibited. Within the set of tomato cultivars, H1015 was the most tolerant to salinity in both developmental stages studied. A significant correlation between several root traits and aboveground growth parameters was observed, highlighting a possible role for regulation of both ion content and root architecture in salt stress resilience.
Collapse
Affiliation(s)
- Jacinto Gandullo
- Section of Plant Physiology and Plant Cell Biology, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
- Departamento de Biología Vegetal y Ecología, Área de Fisiología Vegetal, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Safarina Ahmad
- Section of Plant Physiology and Plant Cell Biology, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - Essam Darwish
- Section of Plant Physiology and Plant Cell Biology, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
- Plant Physiology Section, Agricultural Botany Department, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Rumyana Karlova
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, 6708PB Wageningen, Netherlands
| | - Christa Testerink
- Section of Plant Physiology and Plant Cell Biology, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, 6708PB Wageningen, Netherlands
| |
Collapse
|
40
|
Wang J, Sun W, Kong X, Zhao C, Li J, Chen Y, Gao Z, Zuo K. The peptidyl-prolyl isomerases FKBP15-1 and FKBP15-2 negatively affect lateral root development by repressing the vacuolar invertase VIN2 in Arabidopsis. PLANTA 2020; 252:52. [PMID: 32945964 DOI: 10.1007/s00425-020-03459-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 09/11/2020] [Indexed: 06/11/2023]
Abstract
The peptidyl-prolyl isomerases FKBP15-1 and FKBP15-2 negatively modulate lateral root development by repressing vacuolar invertase VIN2 activity. Lateral root (LR) architecture greatly affects the efficiency of nutrient absorption and the anchorage of plants. Although the internal phytohormone regulatory mechanisms that control LR development are well known, how external nutrients influence lateral root development remains elusive. Here, we characterized the function of two FK506-binding proteins, namely, FKBP15-1 and FKBP15-2, in Arabidopsis. FKBP15-1/15-2 genes were expressed prominently in the vascular bundles of the root basal meristem region, and the FKBP15-1/15-2 proteins were localized to the endoplasmic reticulum of the cells. Using IP-MS, Co-IP, and BiFC assays, we demonstrated that FKBP15-1 and FKBP15-2 interacted with vacuolar invertase 2 (VIN2). Compared to Col-0 and the single mutants, the fkbp15-1fkbp15-2 double mutant had more LRs, and presented higher sucrose catalytic activity. Moreover, genetic analysis showed genetic epistasis of VIN2 over FKBP15-1/FKBP15-2 in controlling LR development. Our results indicate that FKBP15-1 and FKBP15-2 participate in the control of LR number by inhibiting the catalytic activity of VIN2. Owing to the conserved peptidylprolyl cis-trans isomerase activity of FKBP family proteins, our results provide a clue for further analysis of the interplay between lateral root development and protein modification by FKBPs.
Collapse
Affiliation(s)
- Jun Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenjie Sun
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiuzhen Kong
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunyan Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jianfu Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yun Chen
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhengyin Gao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Kaijing Zuo
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| |
Collapse
|
41
|
Xuan W, De Gernier H, Beeckman T. The dynamic nature and regulation of the root clock. Development 2020; 147:147/3/dev181446. [DOI: 10.1242/dev.181446] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
ABSTRACT
Plants explore the soil by continuously expanding their root system, a process that depends on the production of lateral roots (LRs). Sites where LRs can be produced are specified in the primary root axis through a pre-patterning mechanism, determined by a biological clock that is coordinated by temporal signals and positional cues. This ‘root clock’ generates an oscillatory signal that is translated into a developmental cue to specify a set of founder cells for LR formation. In this Review, we summarize recent findings that shed light on the mechanisms underlying the oscillatory signal and discuss how a periodic signal contributes to the conversion of founder cells into LR primordia. We also provide an overview of the phases of the root clock that may be influenced by endogenous factors, such as the plant hormone auxin, and by exogenous environmental cues. Finally, we discuss additional aspects of the root-branching process that act independently of the root clock.
Collapse
Affiliation(s)
- Wei Xuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Hugues De Gernier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052 Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052 Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
| |
Collapse
|
42
|
He Y, Meng X. MAPK Signaling: Emerging Roles in Lateral Root Formation. TRENDS IN PLANT SCIENCE 2020; 25:126-129. [PMID: 31848035 DOI: 10.1016/j.tplants.2019.11.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 06/10/2023]
Abstract
Lateral root (LR) formation is a multistep developmental process in which auxin and peptide hormones play essential roles. Recent studies in arabidopsis by Huang et al. and Zhu et al. have revealed that the mitogen-activated protein kinase (MAPK) cascade MKK4/MKK5-MPK3/MPK6 functions in both a noncanonical auxin signaling pathway and the IDA peptide signaling pathway to regulate LR morphogenesis and emergence, respectively.
Collapse
Affiliation(s)
- Yunxia He
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiangzong Meng
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
| |
Collapse
|
43
|
Ramos RS, Casati P, Spampinato CP, Falcone Ferreyra ML. Ribosomal Protein RPL10A Contributes to Early Plant Development and Abscisic Acid-Dependent Responses in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:582353. [PMID: 33250910 PMCID: PMC7674962 DOI: 10.3389/fpls.2020.582353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 10/01/2020] [Indexed: 05/17/2023]
Abstract
Plant ribosomal proteins play universal roles in translation, although they are also involved in developmental processes and hormone signaling pathways. Among Arabidopsis RPL10 family members, RPL10A exhibits the highest expression during germination and early development, suggesting that RPL10A is the main contributor to these processes. In this work, we first analyzed RPL10A expression pattern in Arabidopsis thaliana using transgenic RPL10Apro:GUS plants. The gene exhibits a ubiquitous expression pattern throughout the plant, but it is most strongly expressed in undifferentiated tissues. Interestingly, gene expression was also detected in stomatal cells. We then examined protein function during seedling establishment and abscisic acid (ABA) response. Heterozygous rpl10A mutant plants show decreased ABA-sensitivity during seed germination, are impaired in early seedling and root development, and exhibit reduced ABA-inhibition of stomatal aperture under light conditions. Overexpression of RPL10A does not affect the germination and seedling growth, but RPL10A-overexpressing lines are more sensitive to ABA during early plant development and exhibit higher stomatal closure under light condition both with and without ABA treatment than wild type plants. Interestingly, RPL10A expression is induced by ABA. Together, we conclude that RPL10A could act as a positive regulator for ABA-dependent responses in Arabidopsis plants.
Collapse
|
44
|
Fromm H. Root Plasticity in the Pursuit of Water. PLANTS (BASEL, SWITZERLAND) 2019; 8:E236. [PMID: 31336579 PMCID: PMC6681320 DOI: 10.3390/plants8070236] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/19/2019] [Accepted: 07/19/2019] [Indexed: 01/22/2023]
Abstract
One of the greatest challenges of terrestrial vegetation is to acquire water through soil-grown roots. Owing to the scarcity of high-quality water in the soil and the environment's spatial heterogeneity and temporal variability, ranging from extreme flooding to drought, roots have evolutionarily acquired tremendous plasticity regarding their geometric arrangement of individual roots and their three-dimensional organization within the soil. Water deficiency has also become an increasing threat to agriculture and dryland ecosystems due to climate change. As a result, roots have become important targets for genetic selection and modification in an effort to improve crop resilience under water-limiting conditions. This review addresses root plasticity from different angles: Their structures and geometry in response to the environment, potential genetic control of root traits suitable for water-limiting conditions, and contemporary and future studies of the principles underlying root plasticity post-Darwin's 'root-brain' hypothesis. Our increasing knowledge of different disciplines of plant sciences and agriculture should contribute to a sustainable management of natural and agricultural ecosystems for the future of mankind.
Collapse
Affiliation(s)
- Hillel Fromm
- School of Plant Sciences and Food Security, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
| |
Collapse
|