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Wu B, Li Y, Li J, Xie Z, Luan M, Gao C, Shi Y, Chen S. Genome-Wide Analysis of Alternative Splicing and Non-Coding RNAs Reveal Complicated Transcriptional Regulation in Cannabis sativa L. Int J Mol Sci 2021; 22:ijms222111989. [PMID: 34769433 PMCID: PMC8584933 DOI: 10.3390/ijms222111989] [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: 09/29/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 12/26/2022] Open
Abstract
It is of significance to mine the structural genes related to the biosynthetic pathway of fatty acid (FA) and cellulose as well as explore the regulatory mechanism of alternative splicing (AS), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in the biosynthesis of cannabinoids, FA and cellulose, which would enhance the knowledge of gene expression and regulation at post-transcriptional level in Cannabis sativa L. In this study, transcriptome, small RNA and degradome libraries of hemp 'Yunma No.1' were established, and comprehensive analysis was performed. As a result, a total of 154, 32 and 331 transcripts encoding key enzymes involved in the biosynthesis of cannabinoids, FA and cellulose were predicted, respectively, among which AS occurred in 368 transcripts. Moreover, 183 conserved miRNAs, 380 C. sativa-specific miRNAs and 7783 lncRNAs were predicted. Among them, 70 miRNAs and 17 lncRNAs potentially targeted 13 and 17 transcripts, respectively, encoding key enzymes or transporters involved in the biosynthesis of cannabinoids, cellulose or FA. Finally, the crosstalk between AS and miRNAs or lncRNAs involved in cannabinoids and cellulose was also predicted. In summary, all these results provided insights into the complicated network of gene expression and regulation in C. sativa.
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Affiliation(s)
- Bin Wu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (B.W.); (Y.L.); (J.L.); (Z.X.)
| | - Yanni Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (B.W.); (Y.L.); (J.L.); (Z.X.)
| | - Jishuang Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (B.W.); (Y.L.); (J.L.); (Z.X.)
| | - Zhenzhen Xie
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (B.W.); (Y.L.); (J.L.); (Z.X.)
| | - Mingbao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (M.L.); (C.G.)
| | - Chunsheng Gao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (M.L.); (C.G.)
| | - Yuhua Shi
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China;
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China;
- Correspondence:
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Riemer E, Qiu D, Laha D, Harmel RK, Gaugler P, Gaugler V, Frei M, Hajirezaei MR, Laha NP, Krusenbaum L, Schneider R, Saiardi A, Fiedler D, Jessen HJ, Schaaf G, Giehl RFH. ITPK1 is an InsP 6/ADP phosphotransferase that controls phosphate signaling in Arabidopsis. MOLECULAR PLANT 2021; 14:1864-1880. [PMID: 34274522 PMCID: PMC8573591 DOI: 10.1016/j.molp.2021.07.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/28/2021] [Accepted: 07/13/2021] [Indexed: 05/20/2023]
Abstract
In plants, phosphate (Pi) homeostasis is regulated by the interaction of PHR transcription factors with stand-alone SPX proteins, which act as sensors for inositol pyrophosphates. In this study, we combined different methods to obtain a comprehensive picture of how inositol (pyro)phosphate metabolism is regulated by Pi and dependent on the inositol phosphate kinase ITPK1. We found that inositol pyrophosphates are more responsive to Pi than lower inositol phosphates, a response conserved across kingdoms. Using the capillary electrophoresis electrospray ionization mass spectrometry (CE-ESI-MS) we could separate different InsP7 isomers in Arabidopsis and rice, and identify 4/6-InsP7 and a PP-InsP4 isomer hitherto not reported in plants. We found that the inositol pyrophosphates 1/3-InsP7, 5-InsP7, and InsP8 increase several fold in shoots after Pi resupply and that tissue-specific accumulation of inositol pyrophosphates relies on ITPK1 activities and MRP5-dependent InsP6 compartmentalization. Notably, ITPK1 is critical for Pi-dependent 5-InsP7 and InsP8 synthesis in planta and its activity regulates Pi starvation responses in a PHR-dependent manner. Furthermore, we demonstrated that ITPK1-mediated conversion of InsP6 to 5-InsP7 requires high ATP concentrations and that Arabidopsis ITPK1 has an ADP phosphotransferase activity to dephosphorylate specifically 5-InsP7 under low ATP. Collectively, our study provides new insights into Pi-dependent changes in nutritional and energetic states with the synthesis of regulatory inositol pyrophosphates.
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Affiliation(s)
- Esther Riemer
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Danye Qiu
- Department of Chemistry and Pharmacy and CIBSS-Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Debabrata Laha
- Medical Research Council Laboratory for Molecular Cell Biology (MRC-LMCB), University College London, London WC1E 6BT, UK; Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka 560 012, India
| | - Robert K Harmel
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany; Department of Chemistry, Humboldt Universität zu Berlin, 12489 Berlin, Germany
| | - Philipp Gaugler
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Verena Gaugler
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Michael Frei
- Institute of Agronomy and Crop Physiology, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Mohammad-Reza Hajirezaei
- Department of Physiology & Cell Biology, Leibniz-Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Nargis Parvin Laha
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Lukas Krusenbaum
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Robin Schneider
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Adolfo Saiardi
- Medical Research Council Laboratory for Molecular Cell Biology (MRC-LMCB), University College London, London WC1E 6BT, UK
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany; Department of Chemistry, Humboldt Universität zu Berlin, 12489 Berlin, Germany
| | - Henning J Jessen
- Department of Chemistry and Pharmacy and CIBSS-Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Gabriel Schaaf
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany.
| | - Ricardo F H Giehl
- Department of Physiology & Cell Biology, Leibniz-Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany.
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Noncoding-RNA-Mediated Regulation in Response to Macronutrient Stress in Plants. Int J Mol Sci 2021; 22:ijms222011205. [PMID: 34681864 PMCID: PMC8539900 DOI: 10.3390/ijms222011205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/13/2021] [Accepted: 10/16/2021] [Indexed: 01/09/2023] Open
Abstract
Macronutrient elements including nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), and sulfur (S) are required in relatively large and steady amounts for plant growth and development. Deficient or excessive supply of macronutrients from external environments may trigger a series of plant responses at phenotypic and molecular levels during the entire life cycle. Among the intertwined molecular networks underlying plant responses to macronutrient stress, noncoding RNAs (ncRNAs), mainly microRNAs (miRNAs) and long ncRNAs (lncRNAs), may serve as pivotal regulators for the coordination between nutrient supply and plant demand, while the responsive ncRNA-target module and the interactive mechanism vary among elements and species. Towards a comprehensive identification and functional characterization of nutrient-responsive ncRNAs and their downstream molecules, high-throughput sequencing has produced massive omics data for comparative expression profiling as a first step. In this review, we highlight the recent findings of ncRNA-mediated regulation in response to macronutrient stress, with special emphasis on the large-scale sequencing efforts for screening out candidate nutrient-responsive ncRNAs in plants, and discuss potential improvements in theoretical study to provide better guidance for crop breeding practices.
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Affiliation(s)
- Christopher A Brosnan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Queensland, Australia.
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Queensland, Australia.
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Abstract
Nutrients are vital to life through intertwined sensing, signaling, and metabolic processes. Emerging research focuses on how distinct nutrient signaling networks integrate and coordinate gene expression, metabolism, growth, and survival. We review the multifaceted roles of sugars, nitrate, and phosphate as essential plant nutrients in controlling complex molecular and cellular mechanisms of dynamic signaling networks. Key advances in central sugar and energy signaling mechanisms mediated by the evolutionarily conserved master regulators HEXOKINASE1 (HXK1), TARGET OF RAPAMYCIN (TOR), and SNF1-RELATED PROTEIN KINASE1 (SNRK1) are discussed. Significant progress in primary nitrate sensing, calcium signaling, transcriptome analysis, and root-shoot communication to shape plant biomass and architecture are elaborated. Discoveries on intracellular and extracellular phosphate signaling and the intimate connections with nitrate and sugar signaling are examined. This review highlights the dynamic nutrient, energy, growth, and stress signaling networks that orchestrate systemwide transcriptional, translational, and metabolic reprogramming, modulate growth and developmental programs, and respond to environmental cues. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Lei Li
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA; ,
| | - Kun-Hsiang Liu
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA; , .,State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, and Institute of Future Agriculture, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China
| | - Jen Sheen
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA; ,
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Deng Z, Wu H, Jin T, Cai T, Jiang M, Wang M, Liang D. A Sequential Three-Phase Pathway Constitutes Tracheary Element Connection in the Arabidopsis/ Nicotiana Interfamilial Grafts. FRONTIERS IN PLANT SCIENCE 2021; 12:664342. [PMID: 34290723 PMCID: PMC8287886 DOI: 10.3389/fpls.2021.664342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/31/2021] [Indexed: 06/06/2023]
Abstract
Scion-rootstock union formation is a critical step toward the functional assemblage of heterogeneous plants. Interfamilial scion-rootstock interaction often results in graft incompatibility during the assemblage process, and the underlying mechanisms are largely unknown. In this study, we reported that tracheary element (TE) remodeling, including TE segmentation and deformation, rather than de novo formation from callus or adjacent tissues, took place at the early stage of grafting interface between Arabidopsis thaliana and Nicotiana benthamiana (At/Nb). Following cellular deposits, the short TEs from both partners were overlapping, dependent on the homogeneity of contacting TEs, with each other. Without overlapping, the TEs at the interface would grow laterally, and the TEs above and below the interface would undergo self-fusion to form insulating spiraling bundles. Finally, the overlapping TEs constituted a continuous network through alignment. Our results provide a definitive framework for the critical process of TE behavior in the At/Nb distant grafts, including (1) segmentation and/or deformation, (2) matching, overlapping, and cellular deposits, and (3) aligning or spiraling. These insights might guide us in the future into constructing more compatible distant grafts from the perspective of TE homogeneity.
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Affiliation(s)
- Zhuying Deng
- Hubei Collaborative Innovation Center for Grain Industry, School of Agriculture, Yangtze University, Jingzhou, China
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
| | - Huiyan Wu
- Hubei Collaborative Innovation Center for Grain Industry, School of Agriculture, Yangtze University, Jingzhou, China
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
| | - Tianlin Jin
- Hubei Collaborative Innovation Center for Grain Industry, School of Agriculture, Yangtze University, Jingzhou, China
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
| | - Tingting Cai
- Hubei Collaborative Innovation Center for Grain Industry, School of Agriculture, Yangtze University, Jingzhou, China
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
| | - Mengting Jiang
- Hubei Collaborative Innovation Center for Grain Industry, School of Agriculture, Yangtze University, Jingzhou, China
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
| | - Mi Wang
- Hubei Collaborative Innovation Center for Grain Industry, School of Agriculture, Yangtze University, Jingzhou, China
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
| | - Dacheng Liang
- Hubei Collaborative Innovation Center for Grain Industry, School of Agriculture, Yangtze University, Jingzhou, China
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
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Kondhare KR, Patil NS, Banerjee AK. A historical overview of long-distance signalling in plants. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4218-4236. [PMID: 33682884 DOI: 10.1093/jxb/erab048] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Be it a small herb or a large tree, intra- and intercellular communication and long-distance signalling between distant organs are crucial for every aspect of plant development. The vascular system, comprising xylem and phloem, acts as a major conduit for the transmission of long-distance signals in plants. In addition to expanding our knowledge of vascular development, numerous reports in the past two decades revealed that selective populations of RNAs, proteins, and phytohormones function as mobile signals. Many of these signals were shown to regulate diverse physiological processes, such as flowering, leaf and root development, nutrient acquisition, crop yield, and biotic/abiotic stress responses. In this review, we summarize the significant discoveries made in the past 25 years, with emphasis on key mobile signalling molecules (mRNAs, proteins including RNA-binding proteins, and small RNAs) that have revolutionized our understanding of how plants integrate various intrinsic and external cues in orchestrating growth and development. Additionally, we provide detailed insights on the emerging molecular mechanisms that might control the selective trafficking and delivery of phloem-mobile RNAs to target tissues. We also highlight the cross-kingdom movement of mobile signals during plant-parasite relationships. Considering the dynamic functions of these signals, their implications in crop improvement are also discussed.
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Affiliation(s)
- Kirtikumar R Kondhare
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL) Pune, Maharashtra, India
| | - Nikita S Patil
- Biology Division, Indian Institute of Science Education and Research (IISER) Pune, Maharashtra, India
| | - Anjan K Banerjee
- Biology Division, Indian Institute of Science Education and Research (IISER) Pune, Maharashtra, India
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Ding J, Liu L, Wang C, Shi L, Xu F, Cai H. High level of zinc triggers phosphorus starvation by inhibiting root-to-shoot translocation and preferential distribution of phosphorus in rice plants. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 277:116778. [PMID: 33639599 DOI: 10.1016/j.envpol.2021.116778] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 05/22/2023]
Abstract
Since the urbanization and industrialization are wildly spread in recent decades, the concentration of Zn in soil has increased in various regions. Although the interactions between P and Zn has long been recognized, the effect of high level of Zn on P uptake, translocation and distribution in rice and its molecular mechanism are not fully understood. In this study, we conducted both hydroponic culture and field trial with different combined applications of P and Zn to analyze the rice growth and yield, the uptake, translocation and distribution of P and Zn, as well as the P- and Zn-related gene expression levels. Our results showed that high level of Zn decreased the rice biomass and yield production, and inhibited the root-to-shoot translocation and distribution of P into new leaves by down-regulating P transporter genes OsPT2 and OsPT8 in shoot, which was controlled by OsPHR2-OsmiR399-OsPHO2 module. High Zn supply triggered P starvation signal in root, thereafter increased the activities of both root-endogenous and -secreted acid phosphatase to release more Pi, and induced the expression OsPT2 and OsPT8 to uptake more P for plant growth. On the other hand, high level of P significantly decreased the Zn concentrations in both root and shoot, and the root uptake ability of Zn through altering the expression levels of OsZIPs, which were further confirmed by the P high-accumulated mutant osnla1-2 and OsPHR2-OE transgenic plant. Taken together, we revealed the physiological and molecular mechanisms of P-Zn interactions, and proposed a working model of the cross-talk between P and Zn in rice plants. Our results also indicated that appropriate application of P fertilizer is an effective strategy to reduce rice uptake of excessive Zn when grown in Zn-contaminated soil.
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Affiliation(s)
- Jingli Ding
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lu Liu
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chuang Wang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei Shi
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China; National Key Laboratory of Crop Genetics and Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fangsen Xu
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China; National Key Laboratory of Crop Genetics and Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hongmei Cai
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China.
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The interplay of phloem-mobile signals in plant development and stress response. Biosci Rep 2021; 40:226464. [PMID: 32955092 PMCID: PMC7538631 DOI: 10.1042/bsr20193329] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 01/28/2023] Open
Abstract
Plants integrate a variety of biotic and abiotic factors for optimal growth in their given environment. While some of these responses are local, others occur distally. Hence, communication of signals perceived in one organ to a second, distal part of the plant and the coordinated developmental response require an intricate signaling system. To do so, plants developed a bipartite vascular system that mediates the uptake of water, minerals, and nutrients from the soil; transports high-energy compounds and building blocks; and traffics essential developmental and stress signals. One component of the plant vasculature is the phloem. The development of highly sensitive mass spectrometry and molecular methods in the last decades has enabled us to explore the full complexity of the phloem content. As a result, our view of the phloem has evolved from a simple transport path of photoassimilates to a major highway for pathogens, hormones and developmental signals. Understanding phloem transport is essential to comprehend the coordination of environmental inputs with plant development and, thus, ensure food security. This review discusses recent developments in its role in long-distance signaling and highlights the role of some of the signaling molecules. What emerges is an image of signaling paths that do not just involve single molecules but rather, quite frequently an interplay of several distinct molecular classes, many of which appear to be transported and acting in concert.
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Sega P, Kruszka K, Bielewicz D, Karlowski W, Nuc P, Szweykowska-Kulinska Z, Pacak A. Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses. BMC Genomics 2021; 22:165. [PMID: 33750301 PMCID: PMC7941915 DOI: 10.1186/s12864-021-07481-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 02/25/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Small RNAs (sRNAs) are 20-30 nt regulatory elements which are responsible for plant development regulation and participate in many plant stress responses. Insufficient inorganic phosphate (Pi) concentration triggers plant responses to balance the internal Pi level. RESULTS In this study, we describe Pi-starvation-responsive small RNAs and transcriptome changes in barley (Hordeum vulgare L.) using Next-Generation Sequencing (NGS) RNA-Seq data derived from three different types of NGS libraries: (i) small RNAs, (ii) degraded RNAs, and (iii) functional mRNAs. We find that differentially and significantly expressed miRNAs (DEMs, Bonferroni adjusted p-value < 0.05) are represented by 15 molecules in shoot and 13 in root; mainly various miR399 and miR827 isomiRs. The remaining small RNAs (i.e., those without perfect match to reference sequences deposited in miRBase) are considered as differentially expressed other sRNAs (DESs, p-value Bonferroni correction < 0.05). In roots, a more abundant and diverse set of other sRNAs (DESs, 1796 unique sequences, 0.13% from the average of the unique small RNA expressed under low-Pi) contributes more to the compensation of low-Pi stress than that in shoots (DESs, 199 unique sequences, 0.01%). More than 80% of differentially expressed other sRNAs are up-regulated in both organs. Additionally, in barley shoots, up-regulation of small RNAs is accompanied by strong induction of two nucleases (S1/P1 endonuclease and 3'-5' exonuclease). This suggests that most small RNAs may be generated upon nucleolytic cleavage to increase the internal Pi pool. Transcriptomic profiling of Pi-starved barley shoots identifies 98 differentially expressed genes (DEGs). A majority of the DEGs possess characteristic Pi-responsive cis-regulatory elements (P1BS and/or PHO element), located mostly in the proximal promoter regions. GO analysis shows that the discovered DEGs primarily alter plant defense, plant stress response, nutrient mobilization, or pathways involved in the gathering and recycling of phosphorus from organic pools. CONCLUSIONS Our results provide comprehensive data to demonstrate complex responses at the RNA level in barley to maintain Pi homeostasis and indicate that barley adapts to Pi-starvation through elicitation of RNA degradation. Novel P-responsive genes were selected as putative candidates to overcome low-Pi stress in barley plants.
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Affiliation(s)
- Pawel Sega
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Katarzyna Kruszka
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Dawid Bielewicz
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
- Center for Advanced Technology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 10, 61-614, Poznań, Poland
| | - Wojciech Karlowski
- Department of Computational Biology, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Przemyslaw Nuc
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Andrzej Pacak
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
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61
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Dissanayaka DMSB, Ghahremani M, Siebers M, Wasaki J, Plaxton WC. Recent insights into the metabolic adaptations of phosphorus-deprived plants. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:199-223. [PMID: 33211873 DOI: 10.1093/jxb/eraa482] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 10/13/2020] [Indexed: 06/11/2023]
Abstract
Inorganic phosphate (Pi) is an essential macronutrient required for many fundamental processes in plants, including photosynthesis and respiration, as well as nucleic acid, protein, and membrane phospholipid synthesis. The huge use of Pi-containing fertilizers in agriculture demonstrates that the soluble Pi levels of most soils are suboptimal for crop growth. This review explores recent advances concerning the understanding of adaptive metabolic processes that plants have evolved to alleviate the negative impact of nutritional Pi deficiency. Plant Pi starvation responses arise from complex signaling pathways that integrate altered gene expression with post-transcriptional and post-translational mechanisms. The resultant remodeling of the transcriptome, proteome, and metabolome enhances the efficiency of root Pi acquisition from the soil, as well as the use of assimilated Pi throughout the plant. We emphasize how the up-regulation of high-affinity Pi transporters and intra- and extracellular Pi scavenging and recycling enzymes, organic acid anion efflux, membrane remodeling, and the remarkable flexibility of plant metabolism and bioenergetics contribute to the survival of Pi-deficient plants. This research field is enabling the development of a broad range of innovative and promising strategies for engineering phosphorus-efficient crops. Such cultivars are urgently needed to reduce inputs of unsustainable and non-renewable Pi fertilizers for maximum agronomic benefit and long-term global food security and ecosystem preservation.
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Affiliation(s)
- D M S B Dissanayaka
- Department of Crop Science, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
- Graduate School of Biosphere Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Japan
| | - Mina Ghahremani
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Meike Siebers
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg, Cologne, Germany
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Jun Wasaki
- Graduate School of Biosphere Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Japan
| | - William C Plaxton
- Department of Biology, Queen's University, Kingston, Ontario, Canada
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Takehisa H, Sato Y. Transcriptome-based approaches for clarification of nutritional responses and improvement of crop production. BREEDING SCIENCE 2021; 71:76-88. [PMID: 33762878 PMCID: PMC7973498 DOI: 10.1270/jsbbs.20098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/01/2020] [Indexed: 06/12/2023]
Abstract
Genome-wide transcriptome profiling is a powerful tool for identifying key genes and pathways involved in plant development and physiological processes. This review summarizes studies that have used transcriptome profiling mainly in rice to focus on responses to macronutrients such as nitrogen, phosphorus and potassium, and spatio-temporal root profiling in relation to the regulation of root system architecture as well as nutrient uptake and transport. We also discuss strategies based on meta- and co-expression analyses with different attributed transcriptome data, which can be used for investigating the regulatory mechanisms and dynamics of nutritional responses and adaptation, and speculate on further advances in transcriptome profiling that could have potential application to crop breeding and cultivation.
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Affiliation(s)
- Hinako Takehisa
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yutaka Sato
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
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Parreira JR, Cappuccio M, Balestrazzi A, Fevereiro P, Araújo SDS. MicroRNAs expression dynamics reveal post-transcriptional mechanisms regulating seed development in Phaseolus vulgaris L. HORTICULTURE RESEARCH 2021; 8:18. [PMID: 33436559 PMCID: PMC7804330 DOI: 10.1038/s41438-020-00448-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/24/2020] [Accepted: 11/27/2020] [Indexed: 05/04/2023]
Abstract
The knowledge on post-transcriptional regulation mechanisms implicated in seed development (SD) is still limited, particularly in one of the most consumed grain legumes, Phaseolus vulgaris L. We explore for the first time the miRNA expression dynamics in P. vulgaris developing seeds. Seventy-two known and 39 new miRNAs were found expressed in P. vulgaris developing seeds. Most of the miRNAs identified were more abundant at 10 and 40 days after anthesis, suggesting that late embryogenesis/early filling and desiccation were SD stages in which miRNA action is more pronounced. Degradome analysis and target prediction identified targets for 77 expressed miRNAs. While several known miRNAs were predicted to target HD-ZIP, ARF, SPL, and NF-Y transcription factors families, most of the predicted targets for new miRNAs encode for functional proteins. MiRNAs-targets expression profiles evidenced that these miRNAs could tune distinct seed developmental stages. MiRNAs more accumulated at early SD stages were implicated in regulating the end of embryogenesis, postponing the seed maturation program, storage compound synthesis and allocation. MiRNAs more accumulated at late SD stages could be implicated in seed quiescence, desiccation tolerance, and longevity with still uncovered roles in germination. The miRNAs herein described represent novel P. vulgaris resources with potential application in future biotechnological approaches to modulate the expression of genes implicated in legume seed traits with impact in horticultural production systems.
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Affiliation(s)
- José Ricardo Parreira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal
| | - Michela Cappuccio
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Alma Balestrazzi
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Pedro Fevereiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal
- InnovPlantProtect Collaborative Laboratory, Estrada de Gil Vaz, 7351-901, Elvas, Portugal
| | - Susana de Sousa Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
- Association BLC3-Technology and Innovation Campus, Centre Bio R&D Unit, Rua Nossa Senhora da Conceição 2, Lagares da Beira, 3405-155, Oliveira do Hospital, Portugal.
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MicroRNA-Mediated Responses to Cadmium Stress in Arabidopsis thaliana. PLANTS 2021; 10:plants10010130. [PMID: 33435199 PMCID: PMC7827075 DOI: 10.3390/plants10010130] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 01/30/2023]
Abstract
In recent decades, the presence of cadmium (Cd) in the environment has increased significantly due to anthropogenic activities. Cd is taken up from the soil by plant roots for its subsequent translocation to shoots. However, Cd is a non-essential heavy metal and is therefore toxic to plants when it over-accumulates. MicroRNA (miRNA)-directed gene expression regulation is central to the response of a plant to Cd stress. Here, we document the miRNA-directed response of wild-type Arabidopsis thaliana (Arabidopsis) plants and the drb1, drb2 and drb4 mutant lines to Cd stress. Phenotypic and physiological analyses revealed the drb1 mutant to display the highest degree of tolerance to the imposed stress while the drb2 mutant was the most sensitive. RT-qPCR-based molecular profiling of miRNA abundance and miRNA target gene expression revealed DRB1 to be the primary double-stranded RNA binding (DRB) protein required for the production of six of the seven Cd-responsive miRNAs analyzed. However, DRB2, and not DRB1, was determined to be required for miR396 production. RT-qPCR further inferred that transcript cleavage was the RNA silencing mechanism directed by each assessed miRNA to control miRNA target gene expression. Taken together, the results presented here reveal the complexity of the miRNA-directed molecular response of Arabidopsis to Cd stress.
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Li S, Wang X, Xu W, Liu T, Cai C, Chen L, Clark CB, Ma J. Unidirectional movement of small RNAs from shoots to roots in interspecific heterografts. NATURE PLANTS 2021; 7:50-59. [PMID: 33452489 DOI: 10.1038/s41477-020-00829-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 12/07/2020] [Indexed: 05/21/2023]
Abstract
Long-distance RNA movement is important for plant growth and environmental responses; however, the extent to which RNAs move between distant tissues, their relative magnitude and functional importance remain to be elucidated on a genomic scale. Using a soybean (Glycine max)-common bean (Phaseolus vulgaris) grafting system, we identified 100 shoot-root mobile microRNAs and 32 shoot-root mobile phased secondary small interfering RNAs (phasiRNAs), which were predominantly produced in shoots and transported to roots, and, in most cases, accumulated to a level similar to that observed in shoots. Many of these microRNAs or phasiRNAs enabled cleavage of their messenger RNA targets or phasiRNA precursors in roots. In contrast, most mobile-capable mRNAs were transcribed in both shoots and roots, with only small proportions transported to recipient tissues. These findings suggest that the regulatory mechanisms for small RNA movement are different from those for mRNA movement, and that the former is more strictly regulated and, probably, more functionally important than the latter.
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Affiliation(s)
- Shuai Li
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Xutong Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
| | - Wenying Xu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Tong Liu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Chunmei Cai
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Liyang Chen
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
| | | | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN, USA.
- Center for Plant Biology, Purdue University, West Lafayette, IN, USA.
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66
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Wang Y, Chen YF, Wu WH. Potassium and phosphorus transport and signaling in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:34-52. [PMID: 33325114 DOI: 10.1111/jipb.13053] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/10/2020] [Indexed: 05/26/2023]
Abstract
Nitrogen (N), potassium (K), and phosphorus (P) are essential macronutrients for plant growth and development, and their availability affects crop yield. Compared with N, the relatively low availability of K and P in soils limits crop production and thus threatens food security and agricultural sustainability. Improvement of plant nutrient utilization efficiency provides a potential route to overcome the effects of K and P deficiencies. Investigation of the molecular mechanisms underlying how plants sense, absorb, transport, and use K and P is an important prerequisite to improve crop nutrient utilization efficiency. In this review, we summarize current understanding of K and P transport and signaling in plants, mainly taking Arabidopsis thaliana and rice (Oryza sativa) as examples. We also discuss the mechanisms coordinating transport of N and K, as well as P and N.
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Affiliation(s)
- Yi Wang
- State Key Laboratory of Plant Physiology and Biochemistry (SKLPPB), College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yi-Fang Chen
- State Key Laboratory of Plant Physiology and Biochemistry (SKLPPB), College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Wei-Hua Wu
- State Key Laboratory of Plant Physiology and Biochemistry (SKLPPB), College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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Sanan-Mishra N, Abdul Kader Jailani A, Mandal B, Mukherjee SK. Secondary siRNAs in Plants: Biosynthesis, Various Functions, and Applications in Virology. FRONTIERS IN PLANT SCIENCE 2021; 12:610283. [PMID: 33737942 PMCID: PMC7960677 DOI: 10.3389/fpls.2021.610283] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/18/2021] [Indexed: 05/13/2023]
Abstract
The major components of RNA silencing include both transitive and systemic small RNAs, which are technically called secondary sRNAs. Double-stranded RNAs trigger systemic silencing pathways to negatively regulate gene expression. The secondary siRNAs generated as a result of transitive silencing also play a substantial role in gene silencing especially in antiviral defense. In this review, we first describe the discovery and pathways of transitivity with emphasis on RNA-dependent RNA polymerases followed by description on the short range and systemic spread of silencing. We also provide an in-depth view on the various size classes of secondary siRNAs and their different roles in RNA silencing including their categorization based on their biogenesis. The other regulatory roles of secondary siRNAs in transgene silencing, virus-induced gene silencing, transitivity, and trans-species transfer have also been detailed. The possible implications and applications of systemic silencing and the different gene silencing tools developed are also described. The details on mobility and roles of secondary siRNAs derived from viral genome in plant defense against the respective viruses are presented. This entails the description of other compatible plant-virus interactions and the corresponding small RNAs that determine recovery from disease symptoms, exclusion of viruses from shoot meristems, and natural resistance. The last section presents an overview on the usefulness of RNA silencing for management of viral infections in crop plants.
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Affiliation(s)
- Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - A. Abdul Kader Jailani
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Advanced Center for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Bikash Mandal
- Advanced Center for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Sunil K. Mukherjee
- Advanced Center for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Sunil K. Mukherjee,
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Hou G, Dong Y, Zhu F, Zhao Q, Li T, Dou D, Ma X, Wu L, Ku L, Chen Y. MicroRNA transcriptomic analysis of the sixth leaf of maize (Zea mays L.) revealed a regulatory mechanism of jointing stage heterosis. BMC PLANT BIOLOGY 2020; 20:541. [PMID: 33256592 PMCID: PMC7708177 DOI: 10.1186/s12870-020-02751-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 11/22/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Zhengdan 958 (Zheng 58 × Chang 7-2), a commercial hybrid that is produced in a large area in China, is the result of the successful use of the heterotic pattern of Reid × Tang-SPT. The jointing stage of maize is the key period from vegetative to reproductive growth, which determines development at later stages and heterosis to a certain degree. MicroRNAs (miRNAs) play vital roles in the regulation of plant development, but how they function in the sixth leaf at the six-leaf (V6) stage to influence jointing stage heterosis is still unclear. RESULT Our objective was to study miRNAs in four hybrid combinations developed in accordance with the Reid × Tang-SPT pattern, Zhengdan 958, Anyu 5 (Ye 478 × Chang 7-2), Ye 478 × Huangzaosi, Zheng 58 × Huangzaosi, and their parental inbred lines to explore the mechanism related to heterosis. A total of 234 miRNAs were identified in the sixth leaf at the V6 stage, and 85 miRNAs were differentially expressed between the hybrid combinations and their parental inbred lines. Most of the differentially expressed miRNAs were non-additively expressed, which indicates that miRNAs may participate in heterosis at the jointing stage. miR164, miR1432 and miR528 families were repressed in the four hybrid combinations, and some miRNAs, such as miR156, miR399, and miR395 families, exhibited different expression trends in different hybrid combinations, which may result in varying effects on the heterosis regulatory mechanism. CONCLUSIONS The potential targets of the identified miRNAs are related to photosynthesis, the response to plant hormones, and nutrient use. Different hybrid combinations employ different mature miRNAs of the same miRNA family and exhibit different expression trends that may result in enhanced or repressed gene expression to regulate heterosis. Taken together, our results reveal a miRNA-mediated network that plays a key role in jointing stage heterosis via posttranscriptional regulation.
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Affiliation(s)
- Gege Hou
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Yahui Dong
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Fangfang Zhu
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Qiannan Zhao
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Tianyi Li
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Dandan Dou
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Xingli Ma
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Liancheng Wu
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Lixia Ku
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Yanhui Chen
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China.
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MIR2111-5 locus and shoot-accumulated mature miR2111 systemically enhance nodulation depending on HAR1 in Lotus japonicus. Nat Commun 2020; 11:5192. [PMID: 33060582 PMCID: PMC7562733 DOI: 10.1038/s41467-020-19037-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 09/17/2020] [Indexed: 11/09/2022] Open
Abstract
Legumes utilize a shoot-mediated signaling system to maintain a mutualistic relationship with nitrogen-fixing bacteria in root nodules. In Lotus japonicus, shoot-to-root transfer of microRNA miR2111 that targets TOO MUCH LOVE, a nodulation suppressor in roots, has been proposed to explain the mechanism underlying nodulation control from shoots. However, the role of shoot-accumulating miR2111s for the systemic regulation of nodulation was not clearly shown. Here, we find L. japonicus has seven miR2111 loci, including those mapped through RNA-seq. MIR2111-5 expression in leaves is the highest among miR2111 loci and repressed after rhizobial infection depending on a shoot-acting HYPERNODULATION ABERRANT ROOT FORMATION1 (HAR1) receptor. MIR2111-5 knockout mutants show significantly decreased nodule numbers and miR2111 levels. Furthermore, grafting experiments using transformants demonstrate scions with altered miR2111 levels influence nodule numbers in rootstocks in a dose-dependent manner. Therefore, miR2111 accumulation in leaves through MIR2111-5 expression is required for HAR1-dependent systemic optimization of nodule number.
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Tolstyko EA, Lezzhov AA, Morozov SY, Solovyev AG. Phloem transport of structured RNAs: A widening repertoire of trafficking signals and protein factors. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 299:110602. [PMID: 32900440 DOI: 10.1016/j.plantsci.2020.110602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/20/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
The conducting sieve tubes of the phloem consist of sieve elements (SEs), which are enucleate cells incapable of transcription and translation. Nevertheless, SEs contain a large variety of RNAs, and long-distance RNA trafficking via the phloem has been documented. The phloem transport of certain RNAs, as well as the further unloading of these RNAs at target tissues, is essential for plant individual development and responses to environmental cues. The translocation of such RNAs via the phloem is believed to be directed by RNA structural elements serving as phloem transport signals (PTSs), which are recognized by proteins that direct the PTS-containing RNAs into the phloem translocation pathway. The ability of phloem transport has been reported for several classes of structured RNAs including viroids, genuine tRNAs, mRNAs with tRNA sequences embedded into mRNA untranslated regions, tRNA-like structures in the genomic RNAs of plant viruses, and micro-RNA (miRNA) precursors (pri-miRNA). Here, three distinct types of such RNAs are discussed, along with the proteins that may specifically interact with these structures in the phloem. Three-dimensional (3D) motifs, which are characteristic of imperfect RNA duplexes, are discussed as elements of phloem-mobile structured RNAs specifically recognized by proteins involved in phloem transport, thus serving as PTSs.
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Affiliation(s)
- Eugeny A Tolstyko
- Department of Virology, Biological Faculty, Moscow State University, Moscow, 119234, Russia
| | - Alexander A Lezzhov
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, 119991, Russia
| | - Sergey Y Morozov
- Department of Virology, Biological Faculty, Moscow State University, Moscow, 119234, Russia; Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119992, Russia
| | - Andrey G Solovyev
- Department of Virology, Biological Faculty, Moscow State University, Moscow, 119234, Russia; Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119992, Russia; Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow, 119991, Russia.
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Zhong Y, Pan X, Wang R, Xu J, Guo J, Yang T, Zhao J, Nadeem F, Liu X, Shan H, Xu Y, Li X. ZmCCD10a Encodes a Distinct Type of Carotenoid Cleavage Dioxygenase and Enhances Plant Tolerance to Low Phosphate. PLANT PHYSIOLOGY 2020; 184:374-392. [PMID: 32586893 PMCID: PMC7479897 DOI: 10.1104/pp.20.00378] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/03/2020] [Indexed: 05/21/2023]
Abstract
Carotenoid cleavage dioxygenases (CCDs) drive carotenoid catabolism to produce various apocarotenoids and immediate derivatives with particular developmental, ecological, and agricultural importance. How CCD genes evolved with species diversification and the resulting functional novelties in cereal crops have remained largely elusive. We constructed a unified four-clade phylogenetic tree of CCDs, revealing a previously unanchored basal clade CCD10 CCD10 underwent highly dynamic duplication or loss events, even in the grass family. Different from cleavage sites of CCD8 and ZAXINONE SYNTHASE (ZAS), maize (Zea mays) ZmCCD10a cleaved differentially structured carotenoids at 5, 6 (5', 6') and 9, 10 (9', 10') positions, generating C8 (6-methyl-5-hepten-2-one) and C13 (geranylacetone, α-ionone, and β-ionone) apocarotenoids in Escherichia coli Localized in plastids, ZmCCD10a cleaved neoxanthin, violaxanthin, antheraxathin, lutein, zeaxanthin, and β-carotene in planta, corroborating functional divergence of ZmCCD10a and ZAS. ZmCCD10a expression was dramatically stimulated in maize and teosinte (Z. mays ssp. parviglumis, Z. mays ssp. huehuetenangensis, Zea luxurians, and Zea diploperennis) roots by phosphate (Pi) limitation. ZmCCD10a silencing favored phosphorus retention in the root and reduced phosphorus and biomass accumulation in the shoot under low Pi. Overexpression of ZmCCD10a in Arabidopsis (Arabidopsis thaliana) enhanced plant tolerance to Pi limitation by preferential phosphorus allocation to the shoot. Thus, ZmCCD10a encodes a unique CCD facilitating plant tolerance to Pi limitation. Additionally, ZmCCD10a silencing and overexpression led to coherent alterations in expression of PHOSPHATE STARVATION RESPONSE REGULATOR 1 (PHR1) and Pi transporters, and cis-regulation of ZmCCD10a expression by ZmPHR1;1 and ZmPHR1;2 implies a probable ZmCCD10a-involved regulatory pathway that adjusts Pi allocation.
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Affiliation(s)
- Yanting Zhong
- Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, MOE, Beijing 100193, China
| | - Xiaoying Pan
- Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, MOE, Beijing 100193, China
- Guangdong Provincial Key Laboratory of Crop Genetic and Improvement, Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Ruifeng Wang
- Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, MOE, Beijing 100193, China
| | - Jiuliang Xu
- Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, MOE, Beijing 100193, China
| | - Jingyu Guo
- Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, MOE, Beijing 100193, China
| | - Tingxue Yang
- Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, MOE, Beijing 100193, China
| | - Jianyu Zhao
- Department of Vegetable Sciences, China Agricultural University, Beijing 100193, China
| | - Faisal Nadeem
- Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, MOE, Beijing 100193, China
| | - Xiaoting Liu
- Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, MOE, Beijing 100193, China
| | - Hongyan Shan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Yanjun Xu
- Department of Applied Chemistry, China Agricultural University, Beijing 100193, China
| | - Xuexian Li
- Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, MOE, Beijing 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
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Gautier AT, Cochetel N, Merlin I, Hevin C, Lauvergeat V, Vivin P, Mollier A, Ollat N, Cookson SJ. Scion genotypes exert long distance control over rootstock transcriptome responses to low phosphate in grafted grapevine. BMC PLANT BIOLOGY 2020; 20:367. [PMID: 32746781 PMCID: PMC7398338 DOI: 10.1186/s12870-020-02578-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/26/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND Grafting is widely used in horticulture and rootstocks are known to modify scion growth and adaptation to soil conditions. However, the role of scion genotype in regulating rootstock development and functioning has remained largely unexplored. In this study, reciprocal grafts of two grapevine genotypes were produced as well as the corresponding homo-graft controls. These plants were subjected to a low phosphate (LP) treatment and transcriptome profiling by RNA sequencing was done on root samples collected 27 h after the onset of the LP treatment. RESULTS A set of transcripts responsive to the LP treatment in all scion/rootstock combinations was identified. Gene expression patterns associated with genetic variation in response to LP were identified by comparing the response of the two homo-grafts. In addition, the scion was shown to modify root transcriptome responses to LP in a rootstock dependent manner. A weighted gene co-expression network analysis identified modules of correlated genes; the analysis of the association of these modules with the phosphate treatment, and the scion and rootstock genotype identified potential hub genes. CONCLUSIONS This study provides insights into the response of grafted grapevine to phosphate supply and identifies potential shoot-to-root signals that could vary between different grapevine genotypes.
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Affiliation(s)
- Antoine T Gautier
- EGFV, Bordeaux Sciences Agro, INRAE, Univ. Bordeaux, ISVV, 33882, Villenave d'Ornon, France
- Crop Production and Biostimulation Laboratory, Université Libre de Bruxelles, Campus Plaine, B-1050, Brussels, Belgium
| | - Noé Cochetel
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Isabelle Merlin
- EGFV, Bordeaux Sciences Agro, INRAE, Univ. Bordeaux, ISVV, 33882, Villenave d'Ornon, France
| | - Cyril Hevin
- EGFV, Bordeaux Sciences Agro, INRAE, Univ. Bordeaux, ISVV, 33882, Villenave d'Ornon, France
| | - Virginie Lauvergeat
- EGFV, Bordeaux Sciences Agro, INRAE, Univ. Bordeaux, ISVV, 33882, Villenave d'Ornon, France
| | - Philippe Vivin
- EGFV, Bordeaux Sciences Agro, INRAE, Univ. Bordeaux, ISVV, 33882, Villenave d'Ornon, France
| | - Alain Mollier
- ISPA, Bordeaux Sciences Agro, INRAE, 33140, Villenave d'Ornon, France
| | - Nathalie Ollat
- EGFV, Bordeaux Sciences Agro, INRAE, Univ. Bordeaux, ISVV, 33882, Villenave d'Ornon, France
| | - Sarah J Cookson
- EGFV, Bordeaux Sciences Agro, INRAE, Univ. Bordeaux, ISVV, 33882, Villenave d'Ornon, France.
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Xu L, Wang F, Li R, Deng M, Fu M, Teng H, Yi K. OsCYCP4s coordinate phosphate starvation signaling with cell cycle progression in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:1017-1033. [PMID: 31697021 DOI: 10.1111/jipb.12885] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 11/04/2019] [Indexed: 06/10/2023]
Abstract
Phosphate starvation leads to a strong reduction in shoot growth and yield in crops. The reduced shoot growth is caused by extensive gene expression reprogramming triggered by phosphate deficiency, which is not itself a direct consequence of low levels of shoot phosphorus. However, how phosphate starvation inhibits shoot growth in rice is still unclear. In this study, we determined the role of OsCYCP4s in the regulation of shoot growth in response to phosphate starvation in rice. We demonstrate that the expression levels of OsCYCP4s, except OsCYCP4;3, were induced by phosphate starvation. Overexpression of the phosphate starvation induced OsCYCP4s could compete with the other cyclins for the binding with cyclin-dependent kinases, therefore suppressing growth by reducing cell proliferation. The phosphate starvation induced growth inhibition in the loss-of-function mutants cycp4;1, cycp4;2, and cycp4;4 is partially compromised. Furthermore, the expression of some phosphate starvation inducible genes is negatively modulated by these cyclins, which indicates that these OsCYCP4s may also be involved in phosphate starvation signaling. We conclude that phosphate starvation induced OsCYCP4s might coordinate phosphate starvation signaling and cell cycle progression under phosphate starvation stress.
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Affiliation(s)
- Lei Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fang Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Ruili Li
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Minjuan Deng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Meilan Fu
- The Semi-arid Agriculture Engineering & Technology Research Center of P. R. China, Shijiazhuang, 050000, China
| | - Huiying Teng
- The Semi-arid Agriculture Engineering & Technology Research Center of P. R. China, Shijiazhuang, 050000, China
| | - Keke Yi
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Blein T, Balzergue C, Roulé T, Gabriel M, Scalisi L, François T, Sorin C, Christ A, Godon C, Delannoy E, Martin-Magniette ML, Nussaume L, Hartmann C, Gautheret D, Desnos T, Crespi M. Landscape of the Noncoding Transcriptome Response of Two Arabidopsis Ecotypes to Phosphate Starvation. PLANT PHYSIOLOGY 2020; 183:1058-1072. [PMID: 32404413 PMCID: PMC7333710 DOI: 10.1104/pp.20.00446] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 04/30/2020] [Indexed: 05/22/2023]
Abstract
Root architecture varies widely between species; it even varies between ecotypes of the same species, despite strong conservation of the coding portion of their genomes. By contrast, noncoding RNAs evolve rapidly between ecotypes and may control their differential responses to the environment, since several long noncoding RNAs (lncRNAs) are known to quantitatively regulate gene expression. Roots from ecotypes Columbia and Landsberg erecta of Arabidopsis (Arabidopsis thaliana) respond differently to phosphate starvation. Here, we compared transcriptomes (mRNAs, lncRNAs, and small RNAs) of root tips from these two ecotypes during early phosphate starvation. We identified thousands of lncRNAs that were largely conserved at the DNA level in these ecotypes. In contrast to coding genes, many lncRNAs were specifically transcribed in one ecotype and/or differentially expressed between ecotypes independent of phosphate availability. We further characterized these ecotype-related lncRNAs and studied their link with small interfering RNAs. Our analysis identified 675 lncRNAs differentially expressed between the two ecotypes, including antisense RNAs targeting key regulators of root-growth responses. Misregulation of several lincRNAs showed that at least two ecotype-related lncRNAs regulate primary root growth in ecotype Columbia. RNA-sequencing analysis following deregulation of lncRNA NPC48 revealed a potential link with root growth and transport functions. This exploration of the noncoding transcriptome identified ecotype-specific lncRNA-mediated regulation in root apexes. The noncoding genome may harbor further mechanisms involved in ecotype adaptation of roots to different soil environments.
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Affiliation(s)
- Thomas Blein
- Institute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay, Université de Paris, 91405 Orsay, France
| | - Coline Balzergue
- Aix Marseille University, Commisariat à l'Énergie Atomique, Centre Nationale de la Recherche, Bioscience and Biotechnology Institute of Aix-Marseilles, Unité Mixte de Recherche 7265 Signalisation pour l'Adaptation des Végétaux à leur Environnement (UMR7265 SAVE), 13108 Saint Paul-Lez-Durance, France
| | - Thomas Roulé
- Institute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay, Université de Paris, 91405 Orsay, France
| | - Marc Gabriel
- Institute for Integrative Biology of the Cell, Commisariat à l'Énergie Atomique, Centre Nationale de la Recherche, Université Paris Sud, 91198 Gif sur Yvette, France
| | - Laetitia Scalisi
- Institute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay, Université de Paris, 91405 Orsay, France
| | - Tracy François
- Institute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay, Université de Paris, 91405 Orsay, France
| | - Céline Sorin
- Institute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay, Université de Paris, 91405 Orsay, France
| | - Aurélie Christ
- Institute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay, Université de Paris, 91405 Orsay, France
| | - Christian Godon
- Aix Marseille University, Commisariat à l'Énergie Atomique, Centre Nationale de la Recherche, Bioscience and Biotechnology Institute of Aix-Marseilles, Unité Mixte de Recherche 7265 Signalisation pour l'Adaptation des Végétaux à leur Environnement (UMR7265 SAVE), 13108 Saint Paul-Lez-Durance, France
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay, Université de Paris, 91405 Orsay, France
| | - Marie-Laure Martin-Magniette
- Institute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay, Université de Paris, 91405 Orsay, France
- Unité Mixte de Recherche MIA-Paris (UMR MIA-Paris), AgroParisTech, Institut National de la Recherche Agronomique, Université Paris-Saclay, 75005 Paris, France
| | - Laurent Nussaume
- Aix Marseille University, Commisariat à l'Énergie Atomique, Centre Nationale de la Recherche, Bioscience and Biotechnology Institute of Aix-Marseilles, Unité Mixte de Recherche 7265 Signalisation pour l'Adaptation des Végétaux à leur Environnement (UMR7265 SAVE), 13108 Saint Paul-Lez-Durance, France
| | - Caroline Hartmann
- Institute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay, Université de Paris, 91405 Orsay, France
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell, Commisariat à l'Énergie Atomique, Centre Nationale de la Recherche, Université Paris Sud, 91198 Gif sur Yvette, France
| | - Thierry Desnos
- Aix Marseille University, Commisariat à l'Énergie Atomique, Centre Nationale de la Recherche, Bioscience and Biotechnology Institute of Aix-Marseilles, Unité Mixte de Recherche 7265 Signalisation pour l'Adaptation des Végétaux à leur Environnement (UMR7265 SAVE), 13108 Saint Paul-Lez-Durance, France
| | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay, Université de Paris, 91405 Orsay, France
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75
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Gamir J, Torres-Vera R, Rial C, Berrio E, de Souza Campos PM, Varela RM, Macías FA, Pozo MJ, Flors V, López-Ráez JA. Exogenous strigolactones impact metabolic profiles and phosphate starvation signalling in roots. PLANT, CELL & ENVIRONMENT 2020; 43:1655-1668. [PMID: 32222984 DOI: 10.1111/pce.13760] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 05/25/2023]
Abstract
Strigolactones (SLs) are important ex-planta signalling molecules in the rhizosphere, promoting the association with beneficial microorganisms, but also affecting plant interactions with harmful organisms. They are also plant hormones in-planta, acting as modulators of plant responses under nutrient-deficient conditions, mainly phosphate (Pi) starvation. In the present work, we investigate the potential role of SLs as regulators of early Pi starvation signalling in plants. A short-term pulse of the synthetic SL analogue 2'-epi-GR24 promoted SL accumulation and the expression of Pi starvation markers in tomato and wheat under Pi deprivation. 2'-epi-GR24 application also increased SL production and the expression of Pi starvation markers under normal Pi conditions, being its effect dependent on the endogenous SL levels. Remarkably, 2'-epi-GR24 also impacted the root metabolic profile under these conditions, promoting the levels of metabolites associated to plant responses to Pi limitation, thus partially mimicking the pattern observed under Pi deprivation. The results suggest an endogenous role for SLs as Pi starvation signals. In agreement with this idea, SL-deficient plants were less sensitive to this stress. Based on the results, we propose that SLs may act as early modulators of plant responses to P starvation.
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Affiliation(s)
- Jordi Gamir
- Group of Mycorrhizas, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
- Biochemistry and Plant Biotechnology Laboratory, Department CAMN, Universitat Jaume I, Castellón, Spain
| | - Rocío Torres-Vera
- Group of Mycorrhizas, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
| | - Carlos Rial
- Allelopathy Group, Department of Organic Chemistry, Institute of Biomolecules (INBIO), Campus de Excelencia Internacional (CeiA3), School of Science, University of Cádiz, Cádiz, Spain
| | - Estefanía Berrio
- Group of Mycorrhizas, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
| | - Pedro M de Souza Campos
- Group of Mycorrhizas, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
- Centro de Investigación en Micorrizas y Sustentabilidad Agroambiental (CIMYSA-UFRO), Universidad de La Frontera, Temuco, Chile
| | - Rosa M Varela
- Allelopathy Group, Department of Organic Chemistry, Institute of Biomolecules (INBIO), Campus de Excelencia Internacional (CeiA3), School of Science, University of Cádiz, Cádiz, Spain
| | - Francisco A Macías
- Allelopathy Group, Department of Organic Chemistry, Institute of Biomolecules (INBIO), Campus de Excelencia Internacional (CeiA3), School of Science, University of Cádiz, Cádiz, Spain
| | - María J Pozo
- Group of Mycorrhizas, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
| | - Victor Flors
- Biochemistry and Plant Biotechnology Laboratory, Department CAMN, Universitat Jaume I, Castellón, Spain
| | - Juan A López-Ráez
- Group of Mycorrhizas, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
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76
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Peng Z, Tian J, Luo R, Kang Y, Lu Y, Hu Y, Liu N, Zhang J, Cheng H, Niu S, Zhang J, Yao Y. MiR399d and epigenetic modification comodulate anthocyanin accumulation in Malus leaves suffering from phosphorus deficiency. PLANT, CELL & ENVIRONMENT 2020; 43:1148-1159. [PMID: 31833568 DOI: 10.1111/pce.13697] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/17/2019] [Accepted: 12/03/2019] [Indexed: 05/14/2023]
Abstract
Inorganic phosphorus (Pi) deficiency induces anthocyanin accumulation in the leaves of some plant species; however, the molecular mechanisms underlying this phenomenon have not been well characterized. Here, we showed that microRNA399d (miR399d), high-affinity Pi transporter McPHT1;4, and McMYB10 are strongly induced in Malus leaves suffering from Pi deficiency. By culturing explants of transiently transformed plants in MS medium under conditions of Pi sufficiency and Pi deficiency, miR399d and McPHT1;4 were shown to play essential roles in the response to Pi deficiency and to play positive roles in the regulation of anthocyanin biosynthesis. Silencing of McHDA6 expression and treatment with the inhibitor trichostatin A suggested that the low expression of McHDA6 simultaneously reduced the transcription of McMET1 and decreased the methylation level of the McMYB10 promoter; however, the expression of McMYB10 and anthocyanin content were increased. Bimolecular fluorescence complementation and yeast two-hybrid assays revealed that McHDA6 binds directly to McMET1 through its BAH2 and DNMT1-RFD domains. Based on the results of our study, we propose a mechanism for the molecular regulation of anthocyanin biosynthesis, namely, the miR399d and epigenetic modification comodulation model, to explain the phenomenon in which leaves turn red under conditions of Pi deficiency.
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Affiliation(s)
- Zhen Peng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Ji Tian
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Rongli Luo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Yanhui Kang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Yanfen Lu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Yujing Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Na Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Hao Cheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Shuqing Niu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Yuncong Yao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
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77
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Sunitha S, Rock CD. CRISPR/Cas9-mediated targeted mutagenesis of TAS4 and MYBA7 loci in grapevine rootstock 101-14. Transgenic Res 2020; 29:355-367. [PMID: 32328868 PMCID: PMC7283210 DOI: 10.1007/s11248-020-00196-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 02/21/2020] [Indexed: 02/07/2023]
Abstract
Pierce’s disease (PD) of grapevine (Vitis vinifera) is caused by the bacterium Xylella fastidiosa and is vectored by xylem sap-sucking insects, whereas Grapevine Red Blotch Virus (GRBV) causes Red Blotch Disease and is transmitted in the laboratory by alfalfa leafhopper Spissistilus festinus. The significance of anthocyanin accumulations in distinct tissues of grapevine by these pathogens is unknown, but vector feeding preferences and olfactory cues from host anthocyanins may be important for these disease etiologies. Phosphate, sugar, and UV light are known to regulate anthocyanin accumulation via miR828 and Trans-Acting Small-interfering locus4 (TAS4), specifically in grape by production of phased TAS4a/b/c small-interfering RNAs that are differentially expressed and target MYBA5/6/7 transcription factor transcripts for post-transcriptional slicing and antisense-mediated silencing. To generate materials that can critically test these genes’ functions in PD and GRBV disease symptoms, we produced transgenic grape plants targeting TAS4b and MYBA7 using CRISPR/Cas9 technology. We obtained five MYBA7 lines all with bi-allelic editing events and no off-targets detected at genomic loci with homology to the guide sequence. We obtained two independent edited TAS4b lines; one bi-allelic, the other heterozygous while both had fortuitous evidences of bi-allelic TAS4a off-target editing events at the paralogous locus. No visible anthocyanin accumulation phenotypes were observed in regenerated plants, possibly due to the presence of genetically redundant TAS4c and MYBA5/6 loci or absence of inductive environmental stress conditions. The editing events encompass single base insertions and di/trinucleotide deletions of Vvi-TAS4a/b and Vvi-MYBA7 at expected positions 3 nt upstream from the guideRNA proximal adjacent motifs NGG. We also identified evidences of homologous recombinations of TAS4a with TAS4b at the TAS4a off-target in one of the TAS4b lines, resulting in a chimeric locus with a bi-allelic polymorphism, supporting independent recombination events in transgenic plants associated with apparent high Cas9 activities. The lack of obvious visible pigment phenotypes in edited plants precluded pathogen challenge tests of the role of anthocyanins in host PD and GRBV resistance/tolerance mechanisms. Nonetheless, we demonstrate successful genome-editing of non-coding RNA and MYB transcription factor loci which can serve future characterizations of the functions of TAS4a/b/c and MYBA7 in developmental, physiological, and environmental biotic/abiotic stress response pathways important for value-added nutraceutical synthesis and pathogen responses of winegrape.
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Affiliation(s)
- Sukumaran Sunitha
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409-3131, USA
| | - Christopher D Rock
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409-3131, USA.
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78
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Oldroyd GED, Leyser O. A plant's diet, surviving in a variable nutrient environment. Science 2020; 368:368/6486/eaba0196. [PMID: 32241923 DOI: 10.1126/science.aba0196] [Citation(s) in RCA: 169] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/14/2020] [Indexed: 12/19/2022]
Abstract
As primary producers, plants rely on a large aboveground surface area to collect carbon dioxide and sunlight and a large underground surface area to collect the water and mineral nutrients needed to support their growth and development. Accessibility of the essential nutrients nitrogen (N) and phosphorus (P) in the soil is affected by many factors that create a variable spatiotemporal landscape of their availability both at the local and global scale. Plants optimize uptake of the N and P available through modifications to their growth and development and engagement with microorganisms that facilitate their capture. The sensing of these nutrients, as well as the perception of overall nutrient status, shapes the plant's response to its nutrient environment, coordinating its development with microbial engagement to optimize N and P capture and regulate overall plant growth.
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Affiliation(s)
- Giles E D Oldroyd
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK. .,Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge CB3 0LE, UK
| | - Ottoline Leyser
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
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79
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Yan Y, Ham BK, Chong YH, Yeh SD, Lucas WJ. A Plant SMALL RNA-BINDING PROTEIN 1 Family Mediates Cell-to-Cell Trafficking of RNAi Signals. MOLECULAR PLANT 2020; 13:321-335. [PMID: 31812689 DOI: 10.1016/j.molp.2019.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/30/2019] [Accepted: 12/02/2019] [Indexed: 05/20/2023]
Abstract
In plants, RNA interference (RNAi) plays a pivotal role in growth and development, and responses to environmental inputs, including pathogen attack. The intercellular and systemic trafficking of small interfering RNA (siRNA)/microRNA (miRNA) is a central component in this regulatory pathway. Currently, little is known with regards to the molecular agents involved in the movement of these si/miRNAs. To address this situation, we employed a biochemical approach to identify and characterize a conserved SMALL RNA-BINDING PROTEIN 1 (SRBP1) family that mediates non-cell-autonomous small RNA (sRNA) trafficking. In Arabidopsis, AtSRBP1 is a glycine-rich (GR) RNA-binding protein, also known as AtGRP7, which we show binds single-stranded siRNA. A viral vector, Zucchini yellow mosaic virus (ZYMV), was employed to functionally characterized the AtSRBP1-4 (AtGRP7/2/4/8) RNA recognition motif and GR domains. Cellular-based studies revealed the GR domain as being necessary and sufficient for SRBP1 cell-to-cell movement. Taken together, our findings provide a foundation for future research into the mechanism and function of mobile sRNA signaling agents in plants.
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Affiliation(s)
- Yan Yan
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Byung-Kook Ham
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Yee Hang Chong
- Department of Plant Pathology, National Chung-Hsing University, Taichung
| | - Shyi-Dong Yeh
- Department of Plant Pathology, National Chung-Hsing University, Taichung
| | - William J Lucas
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA.
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80
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Ramachandran SR, Mueth NA, Zheng P, Hulbert SH. Analysis of miRNAs in Two Wheat Cultivars Infected With Puccinia striiformis f. sp. tritici. FRONTIERS IN PLANT SCIENCE 2020; 10:1574. [PMID: 31998329 PMCID: PMC6965360 DOI: 10.3389/fpls.2019.01574] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/11/2019] [Indexed: 05/27/2023]
Abstract
MicroRNAs are small RNAs that regulate gene expression in eukaryotes. In this study, we analyzed the small RNA profiles of two cultivars that exhibit different reactions to stripe rust infection: one susceptible, the other partially resistant. Using small RNA libraries prepared from the two wheat cultivars infected with stripe rust fungus (Puccinia striiformis f. sp. tritici), we identified 182 previously known miRNAs, 91 variants of known miRNAs, and 163 candidate novel wheat miRNAs. Known miRNA loci were usually copied in all three wheat sub-genomes, whereas novel miRNA loci were often specific to a single sub-genome. DESeq2 analysis of differentially expressed microRNAs revealed 23 miRNAs that exhibit cultivar-specific differences. TA078/miR399b showed cultivar-specific differential regulation in response to infection. Using different target prediction algorithms, 145 miRNAs were predicted to target wheat genes, while 69 miRNAs were predicted to target fungal genes. We also confirmed reciprocal expression of TA078/miR399b and tae-miR9664 and their target genes in different treatments, providing evidence for miRNA-mediated regulation during infection. Both known and novel miRNAs were predicted to target fungal genes, suggesting trans-kingdom regulation of gene expression. Overall, this study contributes to the current repository of wheat miRNAs and provides novel information on the yet-uncharacterized roles for miRNAs in the wheat-stripe rust pathosystem.
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Affiliation(s)
| | - Nicholas A. Mueth
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Ping Zheng
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Scot H. Hulbert
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
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81
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Abstract
The coordination of cell fate decisions within complex multicellular structures rests on intercellular communication. To generate ordered patterns, cells need to know their relative positions within the growing structure. This is commonly achieved via the production and perception of mobile signaling molecules. In animal systems, such positional signals often act as morphogens and subdivide a field of cells into domains of discrete cell identities using a threshold-based readout of their mobility gradient. Reflecting the independent origin of multicellularity, plants evolved distinct signaling mechanisms to drive cell fate decisions. Many of the basic principles underlying developmental patterning are, however, shared between animals and plants, including the use of signaling gradients to provide positional information. In plant development, small RNAs can act as mobile instructive signals, and similar to classical morphogens in animals, employ a threshold-based readout of their mobility gradient to generate precisely defined cell fate boundaries. Given the distinctive nature of peptide morphogens and small RNAs, how might mechanisms underlying the function of traditionally morphogens be adapted to create morphogen-like behavior using small RNAs? In this review, we highlight the contributions of mobile small RNAs to pattern formation in plants and summarize recent studies that have advanced our understanding regarding the formation, stability, and interpretation of small RNA gradients.
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Affiliation(s)
- Simon Klesen
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Kristine Hill
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
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Tolstyko E, Lezzhov A, Solovyev A. Identification of miRNA precursors in the phloem of Cucurbita maxima. PeerJ 2019; 7:e8269. [PMID: 31844599 PMCID: PMC6911342 DOI: 10.7717/peerj.8269] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 11/22/2019] [Indexed: 01/14/2023] Open
Abstract
Plant development and responses to environmental cues largely depend on mobile signals including microRNAs (miRNAs) required for post-transcriptional silencing of specific genes. Short-range cell-to-cell transport of miRNA in developing tissues and organs is involved in transferring positional information essential for determining cell fate. Among other RNA species, miRNAs are found in the phloem sap. Long-distance transport of miRNA via the phloem takes a part in regulation of physiological responses to changing environmental conditions. As shown for regulation of inorganic phosphorus and sulfate homeostasis, mature miRNAs rather than miRNAs precursors are transported in the phloem as signaling molecules. Here, a bioinformatics analysis of transcriptomic data for Cucurbita maxima phloem exudate RNAs was carried out to elucidate whether miRNA precursors could also be present in the phloem. We demonstrated that the phloem transcriptome contained a subset of C. maxima pri-miRNAs that differed from a subset of pri-miRNA sequences abundant in a leaf transcriptome. Differential accumulation of pri-miRNA was confirmed by PCR analysis of C. maxima phloem exudate and leaf RNA samples. Therefore, the presented data indicate that a number of C. maxima pri-miRNAs are selectively recruited to the phloem translocation pathway. This conclusion was validated by inter-species grafting experiments, in which C. maxima pri-miR319a was found to be transported across the graft union via the phloem, confirming the presence of pri-miR319a in sieve elements and showing that phloem miRNA precursors could play a role in long-distance signaling in plants.
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Affiliation(s)
- Eugeny Tolstyko
- Department of Virology, Moscow State University, Moscow, Russia
| | - Alexander Lezzhov
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
| | - Andrey Solovyev
- Department of Virology, Moscow State University, Moscow, Russia.,Belozersky Institute, Moscow State University, Moscow, Russia.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
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83
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Wang T, Xing J, Liu Z, Zheng M, Yao Y, Hu Z, Peng H, Xin M, Zhou D, Ni Z. Histone acetyltransferase GCN5-mediated regulation of long non-coding RNA At4 contributes to phosphate starvation response in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6337-6348. [PMID: 31401648 PMCID: PMC6859718 DOI: 10.1093/jxb/erz359] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/19/2019] [Indexed: 05/04/2023]
Abstract
Phosphate availability is becoming a limiting environmental factor that inhibits plant growth and development. Here, we demonstrated that mutation of the histone acetyltransferase GCN5 impaired phosphate starvation responses (PSRs) in Arabidopsis. Transcriptome analysis revealed that 888 GCN5-regulated candidate genes were potentially involved in responding to phosphate starvation. ChIP assay indicated that four genes, including a long non-coding RNA (lncRNA) At4, are direct targets of GCN5 in PSR regulation. In addition, GCN5-mediated H3K9/14 acetylation of At4 determined dynamic At4 expression. Consistent with the function of At4 in phosphate distribution, mutation of GCN5 impaired phosphate accumulation between shoots and roots under phosphate deficiency condition, whereas constitutive expression of At4 in gcn5 mutants partially restored phosphate relocation. Further evidence proved that GCN5 regulation of At4 influenced the miRNA miR399 and its target PHO2 mRNA level. Taken together, we propose that GCN5-mediated histone acetylation plays a crucial role in PSR regulation via the At4-miR399-PHO2 pathway and provides a new epigenetic mechanism for the regulation of lncRNA in plants.
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Affiliation(s)
- Tianya Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Haidian District, Beijing, China
| | - Jiewen Xing
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Haidian District, Beijing, China
| | - Zhenshan Liu
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Haidian District, Beijing, China
| | - Mei Zheng
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Haidian District, Beijing, China
| | - Yingyin Yao
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Haidian District, Beijing, China
| | - Zhaorong Hu
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Haidian District, Beijing, China
| | - Huiru Peng
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Haidian District, Beijing, China
| | - Mingming Xin
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Haidian District, Beijing, China
| | - Daoxiu Zhou
- Institut of Plant Science Paris-Saclay, Université Paris sud, Orsay, France
| | - Zhongfu Ni
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Haidian District, Beijing, China
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84
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de Souza Campos PM, Cornejo P, Rial C, Borie F, Varela RM, Seguel A, López-Ráez JA. Phosphate acquisition efficiency in wheat is related to root:shoot ratio, strigolactone levels, and PHO2 regulation. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5631-5642. [PMID: 31359044 PMCID: PMC6812720 DOI: 10.1093/jxb/erz349] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 07/18/2019] [Indexed: 05/17/2023]
Abstract
Inorganic phosphorus (Pi) fertilizers are expected to become scarce in the near future; so, breeding for improved Pi acquisition-related root traits would decrease the need for fertilizer application. This work aimed to decipher the physiological and molecular mechanisms underlying the differences between two commercial wheat cultivars (Crac and Tukan) with contrasting Pi acquisition efficiencies (PAE). For that, four independent experiments with different growth conditions were conducted. When grown under non-limiting Pi conditions, both cultivars performed similarly. Crac was less affected by Pi starvation than Tukan, presenting higher biomass production, and an enhanced root development, root:shoot ratio, and root efficiency for Pi uptake under this condition. Higher PAE in Crac correlated with enhanced expression of the Pi transporter genes TaPht1;2 and TaPht1;10. Crac also presented a faster and higher modulation of the IPS1-miR399-PHO2 pathway upon Pi starvation. Interestingly, Crac showed increased levels of strigolactones, suggesting a direct relationship between this phytohormone and plant P responses. Based on these findings, we propose that higher PAE of the cultivar Crac is associated with an improved P signalling through a fine-tuning modulation of PHO2 activity, which seems to be regulated by strigolactones. This knowledge will help to develop new strategies for improved plant performance under P stress conditions.
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Affiliation(s)
- Pedro M de Souza Campos
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- Centro de Investigación en Micorrizas y Sustentabilidad Agroambiental (CIMYSA-UFRO), Universidad de La Frontera, Temuco, Chile
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Temuco, Chile
| | - Pablo Cornejo
- Centro de Investigación en Micorrizas y Sustentabilidad Agroambiental (CIMYSA-UFRO), Universidad de La Frontera, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Temuco, Chile
| | - Carlos Rial
- Allelopathy Group, Department of Organic Chemistry, Institute of Biomolecules (INBIO), Campus de Excelencia Internacional (ceiA3), School of Science, University of Cadiz, Spain
| | - Fernando Borie
- Centro de Investigación en Micorrizas y Sustentabilidad Agroambiental (CIMYSA-UFRO), Universidad de La Frontera, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Temuco, Chile
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad Católica de Temuco, Temuco, Chile, Spain
| | - Rosa M Varela
- Allelopathy Group, Department of Organic Chemistry, Institute of Biomolecules (INBIO), Campus de Excelencia Internacional (ceiA3), School of Science, University of Cadiz, Spain
| | - Alex Seguel
- Centro de Investigación en Micorrizas y Sustentabilidad Agroambiental (CIMYSA-UFRO), Universidad de La Frontera, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Temuco, Chile
| | - Juan Antonio López-Ráez
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
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85
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Xie X, Hu W, Fan X, Chen H, Tang M. Interactions Between Phosphorus, Zinc, and Iron Homeostasis in Nonmycorrhizal and Mycorrhizal Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:1172. [PMID: 31616454 PMCID: PMC6775243 DOI: 10.3389/fpls.2019.01172] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 08/27/2019] [Indexed: 05/16/2023]
Abstract
Phosphorus (P), zinc (Zn), and iron (Fe) are three essential elements for plant survival, and severe deficiencies in these nutrients lead to growth retardation and crop yield reduction. This review synthesizes recent progress on how plants coordinate the acquisition and signaling of Pi, Zn, and Fe from surrounding environments and which genes are involved in these Pi-Zn-Fe interactions with the aim of better understanding of the cross-talk between these macronutrient and micronutrient homeostasis in plants. In addition, identification of genes important for interactions between Pi, Zn, and/or Fe transport and signaling is a useful target for breeders for improvement in plant nutrient acquisition. Furthermore, to understand these processes in arbuscular mycorrhizal plants, the preliminary examination of interactions between Pi, Zn, and Fe homeostasis in some relevant crop species has been performed at the physiological level and is summarized in this article. In conclusion, the development of integrative study of cross-talks between Pi, Zn, and Fe signaling pathway in mycorrhizal plants will be essential for sustainable agriculture all around the world.
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Affiliation(s)
- Xianan Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources (South China Agricultural University), Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Wentao Hu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources (South China Agricultural University), Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xiaoning Fan
- Department of Plant Pathology, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Hui Chen
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources (South China Agricultural University), Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Ming Tang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources (South China Agricultural University), Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
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86
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Small RNA Mobility: Spread of RNA Silencing Effectors and its Effect on Developmental Processes and Stress Adaptation in Plants. Int J Mol Sci 2019; 20:ijms20174306. [PMID: 31484348 PMCID: PMC6747330 DOI: 10.3390/ijms20174306] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/28/2019] [Accepted: 08/30/2019] [Indexed: 01/22/2023] Open
Abstract
Plants are exposed every day to multiple environmental cues, and tight transcriptome reprogramming is necessary to control the balance between responses to stress and processes of plant growth. In this context, the silencing phenomena mediated by small RNAs can drive transcriptional and epigenetic regulatory modifications, in turn shaping plant development and adaptation to the surrounding environment. Mounting experimental evidence has recently pointed to small noncoding RNAs as fundamental players in molecular signalling cascades activated upon exposure to abiotic and biotic stresses. Although, in the last decade, studies on stress responsive small RNAs increased significantly in many plant species, the physiological responses triggered by these molecules in the presence of environmental stresses need to be further explored. It is noteworthy that small RNAs can move either cell-to-cell or systemically, thus acting as mobile silencing effectors within the plant. This aspect has great importance when physiological changes, as well as epigenetic regulatory marks, are inspected in light of plant environmental adaptation. In this review, we provide an overview of the categories of mobile small RNAs in plants, particularly focusing on the biological implications of non-cell autonomous RNA silencing in the stress adaptive response and epigenetic modifications.
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87
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Valentinuzzi F, Venuti S, Pii Y, Marroni F, Cesco S, Hartmann F, Mimmo T, Morgante M, Pinton R, Tomasi N, Zanin L. Common and specific responses to iron and phosphorus deficiencies in roots of apple tree (Malus × domestica). PLANT MOLECULAR BIOLOGY 2019; 101:129-148. [PMID: 31267256 DOI: 10.1007/s11103-019-00896-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 06/24/2019] [Indexed: 05/22/2023]
Abstract
Iron and phosphorus are abundant elements in soils but poorly available for plant nutrition. The availability of these two nutrients represents a major constraint for fruit tree cultivation such as apple (Malus × domestica) leading very often to a decrease of fruit productivity and quality worsening. Aim of this study was to characterize common and specific features of plant response to Fe and P deficiencies by ionomic, transcriptomic and exudation profiling of apple roots. Under P deficiency, the root release of oxalate and flavonoids increased. Genes encoding for transcription factors and transporters involved in the synthesis and release of root exudates were upregulated by P-deficient roots, as well as those directly related to P acquisition. In Fe-deficiency, plants showed an over-accumulation of P, Zn, Cu and Mn and induced the transcription of those genes involved in the mechanisms for the release of Fe-chelating compounds and Fe mobilization inside the plants. The intriguing modulation in roots of some transcription factors, might indicate that, in this condition, Fe homeostasis is regulated by a FIT-independent pathway. In the present work common and specific features of apple response to Fe and P deficiency has been reported. In particular, data indicate similar modulation of a. 230 genes, suggesting the occurrence of a crosstalk between the two nutritional responses involving the transcriptional regulation, shikimate pathway, and the root release of exudates.
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Affiliation(s)
- Fabio Valentinuzzi
- Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100, Bolzano, Italy
| | - Silvia Venuti
- Dipartimento di Scienze Agroambientali, Alimentari e Animali, University of Udine, via delle Scienze 206, 33100, Udine, Italy
| | - Youry Pii
- Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100, Bolzano, Italy
| | - Fabio Marroni
- Dipartimento di Scienze Agroambientali, Alimentari e Animali, University of Udine, via delle Scienze 206, 33100, Udine, Italy
| | - Stefano Cesco
- Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100, Bolzano, Italy
| | - Felix Hartmann
- Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100, Bolzano, Italy
| | - Tanja Mimmo
- Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100, Bolzano, Italy
| | - Michele Morgante
- Dipartimento di Scienze Agroambientali, Alimentari e Animali, University of Udine, via delle Scienze 206, 33100, Udine, Italy
| | - Roberto Pinton
- Dipartimento di Scienze Agroambientali, Alimentari e Animali, University of Udine, via delle Scienze 206, 33100, Udine, Italy
| | - Nicola Tomasi
- Dipartimento di Scienze Agroambientali, Alimentari e Animali, University of Udine, via delle Scienze 206, 33100, Udine, Italy.
| | - Laura Zanin
- Dipartimento di Scienze Agroambientali, Alimentari e Animali, University of Udine, via delle Scienze 206, 33100, Udine, Italy
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88
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Matsui A, Nakaminami K, Seki M. Biological Function of Changes in RNA Metabolism in Plant Adaptation to Abiotic Stress. PLANT & CELL PHYSIOLOGY 2019; 60:1897-1905. [PMID: 31093678 DOI: 10.1093/pcp/pcz068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/08/2019] [Indexed: 05/28/2023]
Abstract
Plant growth and productivity are greatly impacted by environmental stresses. Therefore, plants have evolved various sophisticated mechanisms for adaptation to nonoptimal environments. Recent studies using RNA metabolism-related mutants have revealed that RNA processing, RNA decay and RNA stability play an important role in regulating gene expression at a post-transcriptional level in response to abiotic stresses. Studies indicate that RNA metabolism is a unified network, and modification of stress adaptation-related transcripts at multiple steps of RNA metabolism is necessary to control abiotic stress-related gene expression. Recent studies have also demonstrated the important role of noncoding RNAs (ncRNAs) in regulating abiotic stress-related gene expression and revealed their involvement in various biological functions through their regulation of DNA methylation, DNA structural modifications, histone modifications and RNA-RNA interactions. ncRNAs regulate mRNA transcription and their synthesis is affected by mRNA processing and degradation. In the present review, recent findings pertaining to the role of the metabolic regulation of mRNAs and ncRNAs in abiotic stress adaptation are summarized and discussed.
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Affiliation(s)
- Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, Japan
| | - Kentaro Nakaminami
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, Japan
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89
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Gaut BS, Miller AJ, Seymour DK. Living with Two Genomes: Grafting and Its Implications for Plant Genome-to-Genome Interactions, Phenotypic Variation, and Evolution. Annu Rev Genet 2019; 53:195-215. [PMID: 31424971 DOI: 10.1146/annurev-genet-112618-043545] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Plant genomes interact when genetically distinct individuals join, or are joined, together. Individuals can fuse in three contexts: artificial grafts, natural grafts, and host-parasite interactions. Artificial grafts have been studied for decades and are important platforms for studying the movement of RNA, DNA, and protein. Yet several mysteries about artificial grafts remain, including the factors that contribute to graft incompatibility, the prevalence of genetic and epigenetic modifications caused by exchanges between graft partners, and the long-term effects of these modifications on phenotype. Host-parasite interactions also lead to the exchange of materials, and RNA exchange actively contributes to an ongoing arms race between parasite virulence and host resistance. Little is known about natural grafts except that they can be frequent and may provide opportunities for evolutionary innovation through genome exchange. In this review, we survey our current understanding about these three mechanisms of contact, the genomic interactions that result, and the potential evolutionary implications.
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Affiliation(s)
- Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA;
| | - Allison J Miller
- Department of Biology, Saint Louis University, Saint Louis, Missouri 63103, USA.,Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Danelle K Seymour
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA
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90
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Wacker-Fester K, Uptmoor R, Pfahler V, Dehmer KJ, Bachmann-Pfabe S, Kavka M. Genotype-Specific Differences in Phosphorus Efficiency of Potato ( Solanum tuberosum L.). FRONTIERS IN PLANT SCIENCE 2019; 10:1029. [PMID: 31475025 PMCID: PMC6706458 DOI: 10.3389/fpls.2019.01029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/23/2019] [Indexed: 05/25/2023]
Abstract
Potato is considered to have a low phosphorus (P) efficiency compared to other crops. Therefore, P fertilization requirements are high. New cultivars with improved P efficiency may contribute to save limited mineral P sources and to reduce eutrophication of surface water bodies. The present study aims to characterize the P efficiency of different potato genotypes and to identify mechanisms that improve P efficiency in cultivated potato. A diversity set of 32 potato accessions was used to assess their P efficiency. From this set, five cultivars were selected and two pot experiments with different P-fertilization strategies including a non-fertilized control were conducted to estimate effects of P deficiency on general agronomic and P related traits, root development, phosphatase activity and micro RNA 399 (miR399) expression. Significant differences between the 32 genotypes were found for P utilization efficiency (PUtE). P acquisition efficiency (PAE) as P content in low P in relation to P content in high P was positively correlated to relative biomass production while PUtE was not. Selected genotypes displayed a strong relation between total root length and P content. Root phosphatase activity and miR399 expression increased under P deficiency. However, tuber yields of four cultivars, grown on a soil with suboptimal content of plant available P, were not significantly affected in comparison to yields of well-fertilized plots. We conclude from the present study that PUtE and PAE are important traits when selecting for plants requiring less fertilizer inputs but PAE might be more important for cropping on deficient soils. A large root system might be the most important trait for P acquisition on such soils and therefore in breeding for P efficient crops. Lowering P fertilizer inputs might not necessarily reduce tuber yields.
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Affiliation(s)
| | - Ralf Uptmoor
- Department of Agronomy, University of Rostock, Rostock, Germany
| | - Verena Pfahler
- Department of Agronomy, University of Rostock, Rostock, Germany
| | - Klaus J. Dehmer
- Genebank Department, Satellite Collections North, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gross Luesewitz, Germany
| | - Silvia Bachmann-Pfabe
- Genebank Department, Satellite Collections North, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gross Luesewitz, Germany
| | - Mareike Kavka
- Department of Agronomy, University of Rostock, Rostock, Germany
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91
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Yu Y, Zhang Y, Chen X, Chen Y. Plant Noncoding RNAs: Hidden Players in Development and Stress Responses. Annu Rev Cell Dev Biol 2019; 35:407-431. [PMID: 31403819 DOI: 10.1146/annurev-cellbio-100818-125218] [Citation(s) in RCA: 194] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A large and significant portion of eukaryotic transcriptomes consists of noncoding RNAs (ncRNAs) that have minimal or no protein-coding capacity but are functional. Diverse ncRNAs, including both small RNAs and long ncRNAs (lncRNAs), play essential regulatory roles in almost all biological processes by modulating gene expression at the transcriptional and posttranscriptional levels. In this review, we summarize the current knowledge of plant small RNAs and lncRNAs, with a focus on their biogenesis, modes of action, local and systemic movement, and functions at the nexus of plant development and environmental responses. The complex connections among small RNAs, lncRNAs, and small peptides in plants are also discussed, along with the challenges of identifying and investigating new classes of ncRNAs.
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Affiliation(s)
- Yu Yu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Yuchan Zhang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
| | - Xuemei Chen
- Department of Botany and Plant Sciences and Institute of Integrative Genome Biology, University of California, Riverside, California 92521, USA;
| | - Yueqin Chen
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
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92
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Long L, Ma X, Ye L, Zeng J, Chen G, Zhang G. Root plasticity and Pi recycling within plants contribute to low-P tolerance in Tibetan wild barley. BMC PLANT BIOLOGY 2019; 19:341. [PMID: 31382871 PMCID: PMC6683381 DOI: 10.1186/s12870-019-1949-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 07/29/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND Barley is a low phosphorus (P) demand cereal crop. Tibetan wild barley, as a progenitor of cultivated barley, has revealed outstanding ability of tolerance to low-P stress. However, the underlying mechanisms of low-P adaption and the relevant genetic controlling are still unclear. RESULTS We identified low-P tolerant barley lines in a doubled-haploid (DH) population derived from an elite Tibetan wild barley accession and a high-yield cultivar. The tolerant lines revealed greater root plasticity in the terms of lateral root length, compared to low-P sensitive lines, in response to low-P stress. By integrating the QTLs associated with root length and root transcriptomic profiling, candidate genes encoding isoflavone reductase, nitrate reductase, nitrate transporter and transcriptional factor MYB were identified. The differentially expressed genes (DEGs) involved the growth of lateral root, Pi transport within cells as well as from roots to shoots contributed to the differences between low-P tolerant line L138 and low-P sensitive lines L73 in their ability of P acquisition and utilization. CONCLUSIONS The plasticity of root system is an important trait for barley to tolerate low-P stress. The low-P tolerance in the elite DH line derived from a cross of Tibetan wild barley and cultivated barley is characterized by enhanced growth of lateral root and Pi recycling within plants under low-P stress.
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Affiliation(s)
- Lizhi Long
- Department of Agronomy, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058 China
| | - Xinyi Ma
- Department of Agronomy, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058 China
| | - Lingzhen Ye
- Department of Agronomy, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058 China
| | - Jianbin Zeng
- Department of Agronomy, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058 China
| | - Guang Chen
- Department of Agronomy, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058 China
| | - Guoping Zhang
- Department of Agronomy, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058 China
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93
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Lezzhov AA, Atabekova AK, Tolstyko EA, Lazareva EA, Solovyev AG. RNA phloem transport mediated by pre-miRNA and viral tRNA-like structures. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 284:99-107. [PMID: 31084885 DOI: 10.1016/j.plantsci.2019.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 06/09/2023]
Abstract
Phloem-mobile mRNAs are assumed to contain sequence elements directing RNA to the phloem translocation pathway. One of such elements is represented by tRNA sequences embedded in untranslated regions of many mRNAs, including those proved to be mobile. Genomic RNAs of a number of plant viruses possess a 3'-terminal tRNA-like structures (TLSs) only distantly related to genuine tRNAs, but nevertheless aminoacylated and capable of interaction with some tRNA-binding proteins. Here, we elaborated an experimental system for analysis of RNA phloem transport based on an engineered RNA of Potato virus X capable of replication, but not encapsidation and movement in plants. The TLSs of Brome mosaic virus, Tobacco mosaic virus and Turnip yellow mosaic virus were demonstrated to enable the phloem transport of foreign RNA. A miRNA precursor, pre-miR390b, was also found to render RNA competent for the phloem transport. In line with this, sequences of miRNA precursors were identified in a Cucurbita maxima phloem transcriptome, supporting the hypothesis that, at least in some cases, miRNA phloem signaling can involve miRNA precursors. Collectively, the data presented here suggest that RNA molecules can be directed into the phloem translocation pathway by structured RNA elements such as those of viral TLSs and miRNA precursors.
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Affiliation(s)
- Alexander A Lezzhov
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow 119991, Russia
| | - Anastasia K Atabekova
- Department of Virology, Biological Faculty, Moscow State University, Moscow 119234, Russia
| | - Eugeny A Tolstyko
- Department of Virology, Biological Faculty, Moscow State University, Moscow 119234, Russia
| | - Ekaterina A Lazareva
- Department of Virology, Biological Faculty, Moscow State University, Moscow 119234, Russia
| | - Andrey G Solovyev
- Department of Virology, Biological Faculty, Moscow State University, Moscow 119234, Russia; Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russia; Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow 119991, Russia.
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94
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Chevalier F, Cuyas L, Jouhet J, Gros VR, Chiarenza S, Secco D, Whelan J, Seddiki K, Block MA, Nussaume L, Marechal E. Interplay between Jasmonic Acid, Phosphate Signaling and the Regulation of Glycerolipid Homeostasis in Arabidopsis. PLANT & CELL PHYSIOLOGY 2019; 60:1260-1273. [PMID: 30753691 DOI: 10.1093/pcp/pcz027] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/29/2019] [Indexed: 05/25/2023]
Abstract
Jasmonic acid (JA) biosynthesis and signaling are activated in Arabidopsis cultivated in phosphate (Pi) deprived conditions. This activation occurs mainly in photosynthetic tissues and is less important in roots. In leaves, the enhanced biosynthesis of JA coincides with membrane glycerolipid remodeling triggered by the lack of Pi. We addressed the possible role of JA on the dynamics and magnitude of glycerolipid remodeling in response to Pi deprivation and resupply. Based on combined analyses of gene expression, JA biosynthesis and glycerolipid remodeling in wild-type Arabidopsis and in the coi1-16 mutant, JA signaling seems important in the determination of the basal levels of phosphatidylcholine, phosphatidic acid (PA), monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol. JA impact on MGDG steady state level and fluctuations seem contradictory. In the coi1-16 mutant, the steady state level of MGDG is higher, possibly due to a higher level of PA in the mutant, activating MGD1, and to an increased expression of MGD3. These results support a possible impact of JA in limiting the overall content of this lipid. Concerning lipid variations, upon Pi deprivation, JA seems rather associated with a specific MGDG increase. Following Pi resupply, whereas the expression of glycerolipid remodeling genes returns to basal level, JA biosynthesis and signaling genes are still upregulated, likely due to a JA-induced positive feedback remaining active. Distinct impacts on enzymes synthesizing MGDG, that is, downregulating MGD3, possibly activating MGD1 expression and limiting the activation of MGD1 via PA, might allow JA playing a role in a sophisticated fine tuning of galactolipid variations.
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Affiliation(s)
- Florian Chevalier
- Laboratoire de Physiologie Cellulaire et V�g�tale, Unit� mixe de recherche 5168 CNRS, CEA, INRA, Universit� Grenoble Alpes, IRIG, CEA Grenoble, 17, rue des Martyrs, Grenoble, France
| | - Laura Cuyas
- Laboratoire de Biologie V�g�tale et Microbiologie Environnementale, Unit� mixte de recherche 7265 CNRS, CEA, Universit� Aix-Marseille, Institut de Biosciences et Biotechnologies d'Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, France
- Centre Mondial de l'Innovation, Groupe Roullier, 18 avenue Franklin Roosevelt, Saint-Malo, France
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire et V�g�tale, Unit� mixe de recherche 5168 CNRS, CEA, INRA, Universit� Grenoble Alpes, IRIG, CEA Grenoble, 17, rue des Martyrs, Grenoble, France
| | - Valï Rie Gros
- Laboratoire de Physiologie Cellulaire et V�g�tale, Unit� mixe de recherche 5168 CNRS, CEA, INRA, Universit� Grenoble Alpes, IRIG, CEA Grenoble, 17, rue des Martyrs, Grenoble, France
| | - Serge Chiarenza
- Laboratoire de Biologie V�g�tale et Microbiologie Environnementale, Unit� mixte de recherche 7265 CNRS, CEA, Universit� Aix-Marseille, Institut de Biosciences et Biotechnologies d'Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, France
| | - David Secco
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Khawla Seddiki
- Laboratoire de Physiologie Cellulaire et V�g�tale, Unit� mixe de recherche 5168 CNRS, CEA, INRA, Universit� Grenoble Alpes, IRIG, CEA Grenoble, 17, rue des Martyrs, Grenoble, France
| | - Maryse A Block
- Laboratoire de Physiologie Cellulaire et V�g�tale, Unit� mixe de recherche 5168 CNRS, CEA, INRA, Universit� Grenoble Alpes, IRIG, CEA Grenoble, 17, rue des Martyrs, Grenoble, France
| | - Laurent Nussaume
- Laboratoire de Biologie V�g�tale et Microbiologie Environnementale, Unit� mixte de recherche 7265 CNRS, CEA, Universit� Aix-Marseille, Institut de Biosciences et Biotechnologies d'Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, France
| | - Eric Marechal
- Laboratoire de Physiologie Cellulaire et V�g�tale, Unit� mixe de recherche 5168 CNRS, CEA, INRA, Universit� Grenoble Alpes, IRIG, CEA Grenoble, 17, rue des Martyrs, Grenoble, France
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95
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Pegler JL, Oultram JMJ, Grof CPL, Eamens AL. DRB1, DRB2 and DRB4 Are Required for Appropriate Regulation of the microRNA399/ PHOSPHATE2 Expression Module in Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2019; 8:E124. [PMID: 31086001 PMCID: PMC6571617 DOI: 10.3390/plants8050124] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/03/2019] [Accepted: 05/09/2019] [Indexed: 01/10/2023]
Abstract
Adequate phosphorous (P) is essential to plant cells to ensure normal plant growth and development. Therefore, plants employ elegant mechanisms to regulate P abundance across their developmentally distinct tissues. One such mechanism is PHOSPHATE2 (PHO2)-directed ubiquitin-mediated degradation of a cohort of phosphate (PO4) transporters. PHO2 is itself under tight regulation by the PO4 responsive microRNA (miRNA), miR399. The DOUBLE-STRANDED RNA BINDING (DRB) proteins, DRB1, DRB2 and DRB4, have each been assigned a specific functional role in the Arabidopsis thaliana (Arabidopsis) miRNA pathway. Here, we assessed the requirement of DRB1, DRB2 and DRB4 to regulate the miR399/PHO2 expression module under PO4 starvations conditions. Via the phenotypic and molecular assessment of the knockout mutant plant lines, drb1, drb2 and drb4, we show here that; (1) DRB1 and DRB2 are required to maintain P homeostasis in Arabidopsis shoot and root tissues; (2) DRB1 is the primary DRB required for miR399 production; (3) DRB2 and DRB4 play secondary roles in regulating miR399 production, and; (4) miR399 appears to direct expression regulation of the PHO2 transcript via both an mRNA cleavage and translational repression mode of RNA silencing. Together, the hierarchical contribution of DRB1, DRB2 and DRB4 demonstrated here to be required for the appropriate regulation of the miR399/PHO2 expression module identifies the extreme importance of P homeostasis maintenance in Arabidopsis to ensure that numerous vital cellular processes are maintained across Arabidopsis tissues under a changing cellular environment.
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Affiliation(s)
- Joseph L Pegler
- Centre for Plant Science, School of Environmental and Life Sciences, Faculty of Science, University of Newcastle, Callaghan 2308, New South Wales, Australia.
| | - Jackson M J Oultram
- Centre for Plant Science, School of Environmental and Life Sciences, Faculty of Science, University of Newcastle, Callaghan 2308, New South Wales, Australia.
| | - Christopher P L Grof
- Centre for Plant Science, School of Environmental and Life Sciences, Faculty of Science, University of Newcastle, Callaghan 2308, New South Wales, Australia.
| | - Andrew L Eamens
- Centre for Plant Science, School of Environmental and Life Sciences, Faculty of Science, University of Newcastle, Callaghan 2308, New South Wales, Australia.
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96
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Song X, Li Y, Cao X, Qi Y. MicroRNAs and Their Regulatory Roles in Plant-Environment Interactions. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:489-525. [PMID: 30848930 DOI: 10.1146/annurev-arplant-050718-100334] [Citation(s) in RCA: 366] [Impact Index Per Article: 73.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
MicroRNAs (miRNAs) are 20-24 nucleotide noncoding RNAs abundant in plants and animals. The biogenesis of plant miRNAs involves transcription of miRNA genes, processing of primary miRNA transcripts by DICER-LIKE proteins into mature miRNAs, and loading of mature miRNAs into ARGONAUTE proteins to form miRNA-induced silencing complex (miRISC). By targeting complementary sequences, miRISC negatively regulates gene expression, thereby coordinating plant development and plant-environment interactions. In this review, we present and discuss recent updates on the mechanisms and regulation of miRNA biogenesis, miRISC assembly and actions as well as the regulatory roles of miRNAs in plant developmental plasticity, abiotic/biotic responses, and symbiotic/parasitic interactions. Finally, we suggest future directions for plant miRNA research.
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Affiliation(s)
- Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China;
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China;
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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97
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Zhang Z, Zheng Y, Ham BK, Zhang S, Fei Z, Lucas WJ. Plant lncRNAs are enriched in and move systemically through the phloem in response to phosphate deficiency. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:492-508. [PMID: 30171742 DOI: 10.1111/jipb.12715] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/29/2018] [Indexed: 05/08/2023]
Abstract
In response to phosphate (Pi) deficiency, it has been shown that micro-RNAs (miRNAs) and mRNAs are transported through the phloem for delivery to sink tissues. Growing evidence also indicates that long non-coding RNAs (lncRNAs) are critical regulators of Pi homeostasis in plants. However, whether lncRNAs are present in and move through the phloem, in response to Pi deficiency, remains to be established. Here, using cucumber as a model plant, we show that lncRNAs are enriched in the phloem translocation stream and respond, systemically, to an imposed Pi-stress. A well-known lncRNA, IPS1, the target mimic (TM) of miRNA399, accumulates to a high level in the phloem, but is not responsive to early Pi deficiency. An additional 24 miRNA TMs were also detected in the phloem translocation stream; among them miRNA171 TMs and miR166 TMs were induced in response to an imposed Pi stress. Grafting studies identified 22 lncRNAs which move systemically into developing leaves and root tips. A CU-rich PTB motif was further identified in these mobile lncRNAs. Our findings revealed that lncRNAs respond to Pi deficiency, non-cell-autonomously, and may act as systemic signaling agents to coordinate early Pi deficiency signaling, at the whole-plant level.
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Affiliation(s)
- Zhaoliang Zhang
- State Key Laboratory of Tea Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Yi Zheng
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Byung-Kook Ham
- Global Institute for Food Security, Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Shupei Zhang
- State Key Laboratory of Tea Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - William J Lucas
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, USA
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98
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The Role of UV-B light on Small RNA Activity During Grapevine Berry Development. G3-GENES GENOMES GENETICS 2019; 9:769-787. [PMID: 30647106 PMCID: PMC6404619 DOI: 10.1534/g3.118.200805] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
We explored the effects of ultraviolet B radiation (UV-B) on the developmental dynamics of microRNAs and phased small-interfering-RNA (phasi-RNAs)-producing loci by sequencing small RNAs in vegetative and reproductive organs of grapevine (Vitis vinifera L.). In particular, we tested different UV-B conditions in in vitro-grown plantlets (high-fluence exposition) and in berries from field-grown (radiation filtering) and greenhouse-grown (low- and high-fluence expositions) adult plants throughout fruit development and ripening. The functional significance of the observed UV-coordinated miRNA responses was supported by degradome evidences of ARGONAUTE (AGO)-programmed slicing of mRNAs. Co-expression patterns of the up-regulated miRNAs miR156, miR482, miR530, and miR828 with cognate target gene expressions in response to high-fluence UV-B was tested by q-RT-PCR. The observed UV-response relationships were also interrogated against two published UV-stress and developmental transcriptome datasets. Together, the dynamics observed between miRNAs and targets suggest that changes in target abundance are mediated transcriptionally and, in some cases, modulated post-transcriptionally by miRNAs. Despite the major changes in target abundance are being controlled primarily by those developmental effects that are similar between treatments, we show evidence for novel miRNA-regulatory networks in grape. A model is proposed where high-fluence UV-B increases miR168 and miR530 that target ARGONAUTE 1 (AGO1) and a Plus-3 domain mRNA, respectively, while decreasing miR403 that targets AGO2, thereby coordinating post-transcriptional gene silencing activities by different AGOs. Up-regulation of miR3627/4376 could facilitate anthocyanin accumulation by antagonizing a calcium effector, whereas miR395 and miR399, induced by micronutrient deficiencies known to trigger anthocyanin accumulation, respond positively to UV-B radiation. Finally, increases in the abundance of an anthocyanin-regulatory MYB-bHLH-WD40 complex elucidated in Arabidopsis, mediated by UV-B-induced changes in miR156/miR535, could contribute to the observed up-regulation of miR828. In turn, miR828 would regulate the AtMYB113-ortologues MYBA5, A6 and A7 (and thereby anthocyanins) via a widely conserved and previously validated auto-regulatory loop involving miR828 and phasi TAS4abc RNAs.
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99
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Wang W, Galili G. Tuning the Orchestra: miRNAs in Plant Immunity. TRENDS IN PLANT SCIENCE 2019; 24:189-191. [PMID: 30732937 DOI: 10.1016/j.tplants.2019.01.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/21/2019] [Indexed: 05/04/2023]
Abstract
miRNAs act as negative modulators of target genes and play key roles in post-transcriptional gene regulation through sequence-specific mRNA cleavage and translational inhibition. Two recent reports highlight the orchestrated role of miRNA2111 and miRNA172b in plant innate immunity [1,2] (Science 2018;362:233-236; Plant Cell 2018;30:2779-2794).
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Affiliation(s)
- Wenyi Wang
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, 76100 Israel.
| | - Gad Galili
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, 76100 Israel
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100
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Takehisa H, Sato Y. Transcriptome monitoring visualizes growth stage-dependent nutrient status dynamics in rice under field conditions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:1048-1060. [PMID: 30481387 DOI: 10.1111/tpj.14176] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 11/09/2018] [Accepted: 11/16/2018] [Indexed: 05/24/2023]
Abstract
Crop plants undergo morpho-physiological changes throughout the growth process in response to both the internal and the external environment, and that eventually determine the yield. The system-level adjustment of the morpho-physiological changes has remained largely unclear, however, especially in field conditions. Here, we reveal changes in nutrient status associated with tiller development and soil conditions based on the leaf transcriptome profile of rice (Oryza sativa) throughout the entire period of growth. We performed gene co-expression network analysis and identified three gene sets as indicators for monitoring the internal nitrogen and phosphorus status. Expression profiling reveals that the phosphorus starvation response is expressed during the tillering stage and is then switched off with the transition to nitrogen deficiency. Coincident with phosphorus status dynamics, the level of phosphate in the leaf is demonstrated to be low during the tillering stage and subsequently increases drastically. The phosphorus dynamics are genetically validated by analysing mutants with a defect in phosphorus homeostasis. Notably, we show that nitrogen limitation directly suppresses the phosphorus starvation response. Finally, the phosphorus starvation response is demonstrated to be activated in soil with a high phosphate retention capacity, without the visible phenotypes associated with phosphorus starvation. Our results reveal a growth stage- and soil condition-dependent reaction that requires phosphorus, which is expressed to promote the phosphorus uptake required for developing tillers and is directly adjusted by nitrogen status. A molecular framework for elucidating nutrient status dynamics under field conditions would provide insights into improving crop productivity.
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Affiliation(s)
- Hinako Takehisa
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Yutaka Sato
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
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