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Kok Z, Kuo YW, Soh ZT, Huang HC, Tseng BS, Hsieh HC, Tsai WA, Jeng ST, Chen SP, Lin JS. Regulatory roles of microRNA163 in responses to stresses in Arabidopsis. PHYSIOLOGIA PLANTARUM 2023; 175:e14053. [PMID: 37882263 DOI: 10.1111/ppl.14053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/07/2023] [Accepted: 10/09/2023] [Indexed: 10/27/2023]
Abstract
MicroRNAs (miRNAs) are small regulatory RNAs that participate in various biological processes by silencing target genes. In Arabidopsis, microRNA163 (miR163) was found to be involved in seed germination, root development, and biotic resistance. However, the regulatory roles of miR163 remain unclear. In the current study, the mir163 mutant was investigated to comprehensively understand and characterize its functions in Arabidopsis. RNA-sequencing and Gene Ontology enrichment analyses revealed that miR163 might be involved in "response to stimulus" and "metabolic process". Interestingly, "response to stress", including heat, cold, and oxidative stress, was enriched under the subcategory of "response to stimulus". We observed that miR163 and PXMT were repressed and induced under heat stress, respectively. Furthermore, the study detected significant differences in seed germination rate, hypocotyl length, and survival rate, indicating a variation in the thermotolerance between WT and mir163 mutant. The results revealed that the mir163 mutant had a lesser degree of germination inhibition by heat treatment than WT. In addition, the mir163 mutant showed a better survival rate and longer hypocotyl length under heat treatment than the WT. The metabolomes of WT and mir163 mutant were further analyzed. The contents of benzene derivatives and flavonoids were affected by miR163, which could enhance plants' defense abilities. In conclusion, miR163/targets regulated the expression of stress-responsive genes and the accumulation of defense-related metabolites to alter stress tolerance.
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Affiliation(s)
- Zhenyuan Kok
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Yun-Wei Kuo
- Department of Agronomy, National Chung Hsing University, Taichung, Taiwan
| | - Zhi Thong Soh
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Hao-Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Bo-Shun Tseng
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Hung-Cheng Hsieh
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Wei-An Tsai
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Shih-Tong Jeng
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Shi-Peng Chen
- Department of Horticulture and Biotechnology, Chinese Culture University, Taipei, Taiwan
| | - Jeng-Shane Lin
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Advanced Plant and Food Crop Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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Saputra TI, Maryanto SD, Tanjung ZA, Utomo C, Liwang T. Identification of microRNAs involved in the Phosphate starvation response in Oil Palm (Elaeis guineensis Jacq.). Mol Biol Rep 2023:10.1007/s11033-023-08484-4. [PMID: 37171552 DOI: 10.1007/s11033-023-08484-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 04/25/2023] [Indexed: 05/13/2023]
Abstract
BACKGROUND Plant microRNA, often known as miRNA, is a novel form of gene expression regulator that is known to play a significant role in phosphate starvation. The identification of microRNAs involved in the response to phosphate starvation in oil palms is beneficial for breeding programs. METHOD The main nursery stage seedlings of two oil palm progenies were treated with three different fertiliser namely: complete fertiliser with urea, P2O5, K2O, and MgO based on the standard procedure as a control (C); fertiliser with urea, K2O, MgO without P2O5 (P0); and no fertiliser (F0) for 24 weeks. A total of six oil palm roots were subjected to RNA isolation, followed by miRNA sequencing using the Illumina HiSeq 4000 platform, and all reads were computationally analysed. RESULTS In total, 119 potential miRNAs related to 5,891 genes were identified. The P-specific miRNAs were assumed based on the miRNAs that identified without P fertilizer treatment, resulted of twenty miRNA sequences in the treatment comparison of (C vs P0) vs (C vs F0). Those 20 miRNA sequences were grouped into 9 families, namely EgmiR319; EgmiR399; EgmiR396; EgmiR172; EgmiR156; EgmiR157; miR5648; miR5645; and EgmiRNA_unidentified. Two miRNAs were selected for RT-qPCR validation, namely EgMir399 and EgMir172. Their expression pattern was similar with the RNA sequencing results and shown opposite expression pattern with their target genes, UBC E2 24 and APETALA2, respectively. CONCLUSIONS The nine micro RNA families was identified in oil palm root tissue at phosphate starvation.
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Affiliation(s)
- Tengku Imam Saputra
- Genomic and Transcriptomic Section, Department of Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia.
| | - Sigit Dwi Maryanto
- Genomic and Transcriptomic Section, Department of Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia
| | - Zulfikar Achmad Tanjung
- Bioinformatics Section, Department of Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia
| | - Condro Utomo
- Department of Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia
| | - Tony Liwang
- Division of Plant Production and Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia
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Paries M, Gutjahr C. The good, the bad, and the phosphate: regulation of beneficial and detrimental plant-microbe interactions by the plant phosphate status. THE NEW PHYTOLOGIST 2023. [PMID: 37145847 DOI: 10.1111/nph.18933] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/21/2023] [Indexed: 05/06/2023]
Abstract
Phosphate (Pi ) is indispensable for life on this planet. However, for sessile land plants it is poorly accessible. Therefore, plants have developed a variety of strategies for enhanced acquisition and recycling of Pi . The mechanisms to cope with Pi limitation as well as direct uptake of Pi from the substrate via the root epidermis are regulated by a conserved Pi starvation response (PSR) system based on a family of key transcription factors (TFs) and their inhibitors. Furthermore, plants obtain Pi indirectly through symbiosis with mycorrhiza fungi, which employ their extensive hyphal network to drastically increase the soil volume that can be explored by plants for Pi . Besides mycorrhizal symbiosis, there is also a variety of other interactions with epiphytic, endophytic, and rhizospheric microbes that can indirectly or directly influence plant Pi uptake. It was recently discovered that the PSR pathway is involved in the regulation of genes that promote formation and maintenance of AM symbiosis. Furthermore, the PSR system influences plant immunity and can also be a target of microbial manipulation. It is known for decades that the nutritional status of plants influences the outcome of plant-microbe interactions. The first molecular explanations for these observations are now emerging.
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Affiliation(s)
- Michael Paries
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, Freising, 85354, Germany
| | - Caroline Gutjahr
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, Freising, 85354, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
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Begum Y. Regulatory role of microRNAs (miRNAs) in the recent development of abiotic stress tolerance of plants. Gene 2022; 821:146283. [PMID: 35143944 DOI: 10.1016/j.gene.2022.146283] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/12/2022] [Accepted: 02/03/2022] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) are a distinct groups of single-stranded non-coding, tiny regulatory RNAs approximately 20-24 nucleotides in length. miRNAs negatively influence gene expression at the post-transcriptional level and have evolved considerably in the development of abiotic stress tolerance in a number of model plants and economically important crop species. The present review aims to deliver the information on miRNA-mediated regulation of the expression of major genes or Transcription Factors (TFs), as well as genetic and regulatory pathways. Also, the information on adaptive mechanisms involved in plant abiotic stress responses, prediction, and validation of targets, computational tools, and databases available for plant miRNAs, specifically focus on their exploration for engineering abiotic stress tolerance in plants. The regulatory function of miRNAs in plant growth, development, and abiotic stresses consider in this review, which uses high-throughput sequencing (HTS) technologies to generate large-scale libraries of small RNAs (sRNAs) for conventional screening of known and novel abiotic stress-responsive miRNAs adds complexity to regulatory networks in plants. The discoveries of miRNA-mediated tolerance to multiple abiotic stresses, including salinity, drought, cold, heat stress, nutritional deficiency, UV-radiation, oxidative stress, hypoxia, and heavy metal toxicity, are highlighted and discussed in this review.
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Affiliation(s)
- Yasmin Begum
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, APC Road, Kolkata 700009, West Bengal, India; Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-III), University of Calcutta, JD-2, Sector III, Salt Lake, Kolkata 700106, West Bengal, India.
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Paz-Ares J, Puga MI, Rojas-Triana M, Martinez-Hevia I, Diaz S, Poza-Carrión C, Miñambres M, Leyva A. Plant adaptation to low phosphorus availability: Core signaling, crosstalks, and applied implications. MOLECULAR PLANT 2022; 15:104-124. [PMID: 34954444 DOI: 10.1016/j.molp.2021.12.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/11/2021] [Accepted: 12/20/2021] [Indexed: 05/25/2023]
Abstract
Phosphorus (P) is an essential nutrient for plant growth and reproduction. Plants preferentially absorb P as orthophosphate (Pi), an ion that displays low solubility and that is readily fixed in the soil, making P limitation a condition common to many soils and Pi fertilization an inefficient practice. To cope with Pi limitation, plants have evolved a series of developmental and physiological responses, collectively known as the Pi starvation rescue system (PSR), aimed to improve Pi acquisition and use efficiency (PUE) and protect from Pi-starvation-induced stress. Intensive research has been carried out during the last 20 years to unravel the mechanisms underlying the control of the PSR in plants. Here we review the results of this research effort that have led to the identification and characterization of several core Pi starvation signaling components, including sensors, transcription factors, microRNAs (miRNAs) and miRNA inhibitors, kinases, phosphatases, and components of the proteostasis machinery. We also refer to recent results revealing the existence of intricate signaling interplays between Pi and other nutrients and antagonists, N, Fe, Zn, and As, that have changed the initial single-nutrient-centric view to a more integrated view of nutrient homeostasis. Finally, we discuss advances toward improving PUE and future research priorities.
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Affiliation(s)
- Javier Paz-Ares
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain.
| | - Maria Isabel Puga
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Monica Rojas-Triana
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Iris Martinez-Hevia
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Sergio Diaz
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Cesar Poza-Carrión
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Miguel Miñambres
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Antonio Leyva
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain
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Dełeńko K, Nuc P, Kubiak D, Bielewicz D, Dolata J, Niedojadło K, Górka S, Jarmołowski A, Szweykowska-Kulińska Z, Niedojadło J. MicroRNA biogenesis and activity in plant cell dedifferentiation stimulated by cell wall removal. BMC PLANT BIOLOGY 2022; 22:9. [PMID: 34979922 PMCID: PMC8722089 DOI: 10.1186/s12870-021-03323-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/05/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Despite the frequent use of protoplast-to-plant system in in vitro cultures of plants, the molecular mechanisms regulating the first and most limiting stages of this process, i.e., protoplast dedifferentiation and the first divisions leading to the formation of a microcallus, have not been elucidated. RESULTS In this study, we investigated the function of miRNAs in the dedifferentiation of A. thaliana mesophyll cells in a process stimulated by the enzymatic removal of the cell wall. Leaf cells, protoplasts and CDPs (cells derived from protoplasts) cultured for 24, 72 and 120 h (first cell division). In protoplasts, a strong decrease in the amount of AGO1 in both the nucleus and the cytoplasm, as well as dicing bodies (DBs), which are considered to be sites of miRNA biogenesis, was shown. However during CDPs division, the amounts of AGO1 and DBs strongly increased. MicroRNA transcriptome studies demonstrated that lower amount of differentially expressed miRNAs are present in protoplasts than in CDPs cultured for 120 h. Then analysis of differentially expressed miRNAs, selected pri-miRNA and mRNA targets were performed. CONCLUSION This result indicates that miRNA function is not a major regulation of gene expression in the initial but in later steps of dedifferentiation during CDPs divisions. miRNAs participate in organogenesis, oxidative stress, nutrient deficiencies and cell cycle regulation in protoplasts and CDPs. The important role played by miRNAs in the process of dedifferentiation of mesophyll cells was confirmed by the increased mortality and reduced cell division of CDPs derived from mutants with defective miRNA biogenesis and miR319b expression.
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Affiliation(s)
- Konrad Dełeńko
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100, Torun, Poland
| | - Przemysław Nuc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Dawid Kubiak
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100, Torun, Poland
| | - Dawid Bielewicz
- Center for Advanced Technology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 10, 61-614, Poznań, Poland
| | - Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Katarzyna Niedojadło
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
| | - Sylwia Górka
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100, Torun, Poland
| | - Artur Jarmołowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Zofia Szweykowska-Kulińska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Janusz Niedojadło
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland.
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100, Torun, Poland.
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Fasani E, DalCorso G, Zorzi G, Vitulo N, Furini A. Comparative analysis identifies micro-RNA associated with nutrient homeostasis, development and stress response in Arabidopsis thaliana upon high Zn and metal hyperaccumulator Arabidopsis halleri. PHYSIOLOGIA PLANTARUM 2021; 173:920-934. [PMID: 34171137 PMCID: PMC8597110 DOI: 10.1111/ppl.13488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/21/2021] [Indexed: 05/05/2023]
Abstract
miRNAs have been found to be key players in mineral homeostasis, both in the control of nutrient balance and in the response to toxic trace elements. However, the effect of Zn excess on miRNAs has not been elucidated; moreover, no data are present regarding miRNAs in hyperaccumulator species, where metal homeostasis is tightly regulated. Therefore, expression levels of mature miRNAs were measured by RNA-Seq in Zn-sensitive Arabidopsis thaliana grown in control conditions and upon high Zn, in soil and in Zn-hyperaccumulator Arabidopsis halleri grown in control conditions. Differential expression of notable miRNAs and their targets was confirmed by real-time RT-PCR. The comparison in A. thaliana revealed a small subset modulated upon Zn treatment that is associated with stress response and nutrient homeostasis. On the other hand, a more consistent group of miRNAs was differentially expressed in A. halleri compared with A. thaliana, reflecting inherent differences in nutritional requirements and response to stresses and plant growth and development. Overall, these results confirm the involvement of miRNAs in Zn homeostasis and support the hypothesis of distinct regulatory pathways in hyperaccumulator species.
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Affiliation(s)
- Elisa Fasani
- Department of BiotechnologyUniversity of VeronaVeronaItaly
| | | | - Gianluca Zorzi
- Department of BiotechnologyUniversity of VeronaVeronaItaly
| | - Nicola Vitulo
- Department of BiotechnologyUniversity of VeronaVeronaItaly
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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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Mehdi SMM, Krishnamoorthy S, Szczesniak MW, Ludwików A. Identification of Novel miRNAs and Their Target Genes in the Response to Abscisic Acid in Arabidopsis. Int J Mol Sci 2021; 22:7153. [PMID: 34281207 PMCID: PMC8268864 DOI: 10.3390/ijms22137153] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 12/12/2022] Open
Abstract
miRNAs are involved in various biological processes, including adaptive responses to abiotic stress. To understand the role of miRNAs in the response to ABA, ABA-responsive miRNAs were identified by small RNA sequencing in wild-type Arabidopsis, as well as in abi1td, mkkk17, and mkkk18 mutants. We identified 10 novel miRNAs in WT after ABA treatment, while in abi1td, mkkk17, and mkkk18 mutants, three, seven, and nine known miRNAs, respectively, were differentially expressed after ABA treatment. One novel miRNA (miRn-8) was differentially expressed in the mkkk17 mutant. Potential target genes of the miRNA panel were identified using psRNATarget. Sequencing results were validated by quantitative RT-PCR of several known and novel miRNAs in all genotypes. Of the predicted targets of novel miRNAs, seven target genes of six novel miRNAs were further validated by 5' RLM-RACE. Gene ontology analyses showed the potential target genes of ABA-responsive known and novel miRNAs to be involved in diverse cellular processes in plants, including development and stomatal movement. These outcomes suggest that a number of the identified miRNAs have crucial roles in plant responses to environmental stress, as well as in plant development, and might have common regulatory roles in the core ABA signaling pathway.
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Affiliation(s)
- Syed Muhammad Muntazir Mehdi
- Laboratory of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (S.M.M.M.); (S.K.)
| | - Sivakumar Krishnamoorthy
- Laboratory of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (S.M.M.M.); (S.K.)
| | - Michal Wojciech Szczesniak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland;
| | - Agnieszka Ludwików
- Laboratory of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (S.M.M.M.); (S.K.)
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Huen A, Bally J, Smith P. Identification and characterisation of microRNAs and their target genes in phosphate-starved Nicotiana benthamiana by small RNA deep sequencing and 5'RACE analysis. BMC Genomics 2018; 19:940. [PMID: 30558535 PMCID: PMC6296076 DOI: 10.1186/s12864-018-5258-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 11/16/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Phosphorus is an important macronutrient that is severely lacking in soils. In plants, specific microRNAs (miRNAs) essential for nutrient management and the regulation of stress responses are responsible for the control of many phosphate starvation responses. Further understanding of conserved and species-specific microRNA species has potential implications for the development of crops tolerant to soils with low phosphate. RESULTS This study identified and characterised phosphate starvation-responsive miRNAs in the native Australian tobacco Nicotiana benthamiana. Small RNA libraries were constructed and sequenced from phosphate-starved plant leaves, stems and roots. Twenty-four conserved miRNA families and 36 species-specific miRNAs were identified. The majority of highly phosphate starvation-responsive miRNAs were highly conserved, comprising of members from the miR399, miR827, and miR2111 families. In addition, two miRNA-star species were identified to be phosphate starvation-responsive. A total of seven miRNA targets were confirmed using RLM-5'RACE to be cleaved by five miRNA families, including two confirmed cleavage targets for Nbe-miR399 species, one for Nbe-miR2111, and two for Nbe-miR398. A number of N. benthamiana-specific features for conserved miRNAs were identified, including species-specific miRNA targets predicted or confirmed for miR399, miR827, and miR398. CONCLUSIONS Our results give an insight into the phosphate starvation-responsive miRNAs of Nicotiana benthamiana, and indicate that the phosphate starvation response pathways in N. benthamiana contain both highly conserved and species-specific components.
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Affiliation(s)
- Amanda Huen
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Julia Bally
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, QLD, Brisbane, 4000, Australia
| | - Penelope Smith
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, 3086, Australia.
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Cardoso TCDS, Alves TC, Caneschi CM, Santana DDRG, Fernandes-Brum CN, Reis GLD, Daude MM, Ribeiro THC, Gómez MMD, Lima AA, Gomes LAA, Gomes MDS, Gandolfi PE, Amaral LRD, Chalfun-Júnior A, Maluf WR, de Souza Gomes M. New insights into tomato microRNAs. Sci Rep 2018; 8:16069. [PMID: 30375421 PMCID: PMC6207730 DOI: 10.1038/s41598-018-34202-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/12/2018] [Indexed: 12/21/2022] Open
Abstract
Cultivated tomato, Solanum lycopersicum, is one of the most common fruits in the global food industry. Together with the wild tomato Solanum pennellii, it is widely used for developing better cultivars. MicroRNAs affect mRNA regulation, inhibiting its translation and/or promoting its degradation. Important proteins involved in these processes are ARGONAUTE and DICER. This study aimed to identify and characterize the genes involved in the miRNA processing pathway, miRNA molecules and target genes in both species. We validated the presence of pathway genes and miRNA in different NGS libraries and 6 miRNA families using quantitative RT-PCR. We identified 71 putative proteins in S. lycopersicum and 108 in S. pennellii likely involved in small RNAs processing. Of these, 29 and 32 participate in miRNA processing pathways, respectively. We identified 343 mature miRNAs, 226 pre-miRNAs in 87 families, including 192 miRNAs, which were not previously identified, belonging to 38 new families in S. lycopersicum. In S. pennellii, we found 388 mature miRNAs and 234 pre-miRNAs contained in 85 families. All miRNAs found in S. pennellii were unpublished, being identified for the first time in our study. Furthermore, we identified 2471 and 3462 different miRNA target in S. lycopersicum and S. pennellii, respectively.
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Affiliation(s)
- Thaís Cunha de Sousa Cardoso
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Tamires Caixeta Alves
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Carolina Milagres Caneschi
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Douglas Dos Reis Gomes Santana
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | | | - Gabriel Lasmar Dos Reis
- Department of Agriculture, Federal University of Lavras (UFLA), Lavras, 37 - 37200-000, Brazil
| | - Matheus Martins Daude
- Laboratory of Molecular Analysis, Federal University of Tocantins (UFT), Gurupi, 77402-970, Brazil
| | | | - Miguel Maurício Díaz Gómez
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - André Almeida Lima
- Laboratory of Plant Molecular Physiology, Federal University of Lavras (UFLA), Lavras, 3037 - 37200-000, Brazil
| | | | - Marcos de Souza Gomes
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Peterson Elizandro Gandolfi
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Laurence Rodrigues do Amaral
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Antonio Chalfun-Júnior
- Laboratory of Plant Molecular Physiology, Federal University of Lavras (UFLA), Lavras, 3037 - 37200-000, Brazil
| | - Wilson Roberto Maluf
- Department of Agriculture, Federal University of Lavras (UFLA), Lavras, 37 - 37200-000, Brazil
| | - Matheus de Souza Gomes
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil.
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Wang Z, Zheng Z, Song L, Liu D. Functional Characterization of Arabidopsis PHL4 in Plant Response to Phosphate Starvation. FRONTIERS IN PLANT SCIENCE 2018; 9:1432. [PMID: 30327661 PMCID: PMC6174329 DOI: 10.3389/fpls.2018.01432] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/10/2018] [Indexed: 05/09/2023]
Abstract
Plants have evolved an array of adaptive responses to cope with phosphate (Pi) starvation. These responses are mainly controlled at the transcriptional level. In Arabidopsis, PHR1, a member of the MYB-CC transcription factor family, is a key component of the central regulatory system controlling plant transcriptional responses to Pi starvation. Its homologs in the MYB-CC family, PHL1 (PHR1-LIKE 1), PHL2, and perhaps also PHL3, act redundantly with PHR1 to regulate plant Pi starvation responses. The functions of PHR1's closest homolog in this family, PHL4, however, have not been characterized due to the lack of its null mutant. In this work, we generated two phl4 null mutants using the CRISPR/Cas9 technique and investigated the functions of PHL4 in plant responses to Pi starvation. The results indicated that the major developmental, physiological, and molecular responses of the phl4 mutants to Pi starvation did not significantly differ from those of the wild type. By comparing the phenotypes of the phr1 single mutant and phr1phl1 and phr1phl4 double mutants, we found that PHL4 also acts redundantly with PHR1 to regulate plant Pi responses, but that its effects are weaker than those of PHL1. We also found that the overexpression of PHL4 suppresses plant development under both Pi-sufficient and -deficient conditions. Taken together, the results indicate that PHL4 has only a minor role in the regulation of plant responses to Pi starvation and is a negative regulator of plant development.
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13
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Wang F, Deng M, Xu J, Zhu X, Mao C. Molecular mechanisms of phosphate transport and signaling in higher plants. Semin Cell Dev Biol 2017. [PMID: 28648582 DOI: 10.1016/j.semcdb.2017.06.013] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Phosphorus (P) is an essential macronutrient for plant growth and development. To adapt to low inorganic-phosphate (Pi) environments, plants have evolved complex mechanisms and pathways that regulate the acquisition and remobilization of Pi and maintain P homeostasis. These mechanisms are regulated by complex gene regulatory networks through the functions of Pi transporters (PTs) and Pi starvation-induced (PSI) genes. This review summarizes recent progress in determining the molecular regulatory mechanisms of phosphate transporters and the Pi signaling network in the dicot Arabidopsis (Arabidopsis thaliana) and the monocot rice (Oryza sativa L.). Recent advances in this field provide a reference for understanding plant Pi signaling and specific mechanisms that mediate plant adaptation to environments with limited Pi availability. We propose potential biotechnological applications of known genes to develop plant cultivars with improved Pi uptake and use efficiency.
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Affiliation(s)
- Fei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Meiju Deng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jiming Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xinlu Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Chuanzao Mao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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14
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Araceli O, Alfredo C, Javier M, Luis H. A phosphate starvation-driven bidirectional promoter as a potential tool for crop improvement and in vitro plant biotechnology. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:558-567. [PMID: 27775858 PMCID: PMC5398999 DOI: 10.1111/pbi.12653] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/11/2016] [Accepted: 10/20/2016] [Indexed: 05/27/2023]
Abstract
Phosphate (Pi)-deficient soils are a major limitant factor for crop production in many regions of the world. Despite that plants have innovated several developmental and biochemical strategies to deal with this stress, there are still massive extensions of land which combine several abiotic stresses, including phosphate starvation, that limit their use for plant growth and food production. In several plant species, a genetic programme underlies the biochemical and developmental responses of the organism to cope with low phosphate (Pi) availability. Both protein- and miRNA-coding genes involved in the adaptative response are transcriptionally activated upon Pi starvation. Several of the responsive genes have been identified as transcriptional targets of PHR1, a transcription factor that binds a conserved cis-element called PHR1-binding site (P1BS). Our group has previously described and characterized a minimal genetic arrangement that includes two P1BS elements, as a phosphate-responsive enhancer (EZ2). Here, we report the engineering and successful use of a phosphate-dependent bidirectional promoter, which has been designed and constructed based on the palindromic sequences of the two P1BS elements present in EZ2. This bidirectional promoter has a potential use in both plant in vitro approaches and in the generation of improved crops adapted to Pi starvation and other abiotic stresses.
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Affiliation(s)
- Oropeza‐Aburto Araceli
- Metabolic Engineering LaboratoryUnidad de Genómica Avanzada – LANGEBIO CINVESTAVIrapuatoGuanajuatoMexico
| | - Cruz‐Ramírez Alfredo
- Molecular and Developmental Complexity LaboratoryUnidad de Genómica Avanzada – LANGEBIO CINVESTAVIrapuatoGuanajuatoMexico
| | - Mora‐Macías Javier
- Metabolic Engineering LaboratoryUnidad de Genómica Avanzada – LANGEBIO CINVESTAVIrapuatoGuanajuatoMexico
| | - Herrera‐Estrella Luis
- Metabolic Engineering LaboratoryUnidad de Genómica Avanzada – LANGEBIO CINVESTAVIrapuatoGuanajuatoMexico
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15
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Abstract
The plant vascular system plays a central role in coordinating physiological and developmental events through delivery of both essential nutrients and long-distance signaling agents. The enucleate phloem sieve tube system of the angiosperms contains a broad spectrum of RNA species. Grafting and transcriptomics studies have indicated that several thousand mRNAs move long distances from source organs to meristematic sink tissues. Ribonucleoprotein complexes play a pivotal role as stable RNA-delivery systems for systemic translocation of cargo RNA. In this review, we assess recent progress in the characterization of phloem and plasmodesmal transport as an integrated local and systemic communication network. We discuss the roles of phloem-mobile small RNAs in epigenetic events, including meristem development and genome stability, and the delivery of mRNAs to specific tissues in response to environmental inputs. A large body of evidence now supports a model in which phloem-mobile RNAs act as critical components of gene regulatory networks involved in plant growth, defense, and crop yield at the whole-plant level.
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Affiliation(s)
- Byung-Kook Ham
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California 95616; ,
| | - William J Lucas
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California 95616; ,
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16
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Kumar S, Verma S, Trivedi PK. Involvement of Small RNAs in Phosphorus and Sulfur Sensing, Signaling and Stress: Current Update. FRONTIERS IN PLANT SCIENCE 2017; 8:285. [PMID: 28344582 PMCID: PMC5344913 DOI: 10.3389/fpls.2017.00285] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 02/16/2017] [Indexed: 05/14/2023]
Abstract
Plants require several essential mineral nutrients for their growth and development. These nutrients are required to maintain physiological processes and structural integrity in plants. The root architecture has evolved to absorb nutrients from soil and transport them to other parts of the plant. Nutrient deficiency affects several physiological and biological processes in plants and leads to reduction in crop productivity and yield. To compensate this adversity, plants have developed adaptive mechanisms to enhance the acquisition, conservation, and mobilization of these nutrients under deficient or adverse conditions. In addition, plants have evolved an intricate nexus of complex signaling cascades, which help in nutrient sensing and uptake as well as to maintain nutrient homeostasis. In recent years, small non-coding RNAs such as micro RNAs (miRNAs) and endogenous small interfering RNAs have emerged as important component in regulating plant stress responses. A set of these small RNAs (sRNAs) have been implicated in regulating various processes involved in nutrient uptake, assimilation, and deficiency. In response to phosphorus (P) and sulphur (S) deficiencies, role of sRNAs, miR395 and miR399, have been identified to be instrumental; however, many more miRNAs might be involved in regulating the plant response to these nutrient stresses. These sRNAs modulate expression of target genes in response to P and S deficiencies and regulate their uptake and utilization for proper growth and development of the plant. This review summarizes the current understanding of uptake, sensing, and signaling of P and S and highlights the regulatory role of sRNAs in adaptive responses to these nutrient stresses in plants.
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Affiliation(s)
- Smita Kumar
- Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
- Centre of Bio-Medical ResearchSanjay Gandhi Post-Graduate Institute of Medical Sciences Lucknow, India
- *Correspondence: Prabodh K. Trivedi, ; Smita Kumar,
| | - Saurabh Verma
- Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar UniversityLucknow, India
| | - Prabodh K. Trivedi
- Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
- *Correspondence: Prabodh K. Trivedi, ; Smita Kumar,
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17
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Cabrera J, Barcala M, García A, Rio-Machín A, Medina C, Jaubert-Possamai S, Favery B, Maizel A, Ruiz-Ferrer V, Fenoll C, Escobar C. Differentially expressed small RNAs in Arabidopsis galls formed by Meloidogyne javanica: a functional role for miR390 and its TAS3-derived tasiRNAs. THE NEW PHYTOLOGIST 2016; 209:1625-40. [PMID: 26542733 DOI: 10.1111/nph.13735] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/25/2015] [Indexed: 05/20/2023]
Abstract
Root-knot nematodes (RKNs) induce inside the vascular cylinder the giant cells (GCs) embedded in the galls. The distinctive gene repression in early-developing GCs could be facilitated by small RNAs (sRNA) such as miRNAs, and/or epigenetic mechanisms mediated by 24nt-sRNAs, rasiRNAs and 21-22nt-sRNAs. Therefore, the sRNA-population together with the role of the miR390/TAS3/ARFs module were studied during early gall/GC formation. Three sRNA libraries from 3-d-post-inoculation (dpi) galls induced by Meloidogyne javanica in Arabidopsis and three from uninfected root segments were sequenced following Illumina-Solexa technology. pMIR390a::GUS and pTAS3::GUS lines were assayed for nematode-dependent promoter activation. A sensor line indicative of TAS3-derived tasiRNAs binding to the ARF3 sequence (pARF3:ARF3-GUS) together with a tasiRNA-resistant ARF3 line (pARF3:ARF3m-GUS) were used for functional analysis. The sRNA population showed significant differences between galls and controls, with high validation rate and correspondence with their target expression: 21-nt sRNAs corresponding mainly to miRNAs were downregulated, whilst 24-nt-sRNAs from the rasiRNA family were mostly upregulated in galls. The promoters of MIR390a and TAS3, active in galls, and the pARF3:ARF3-GUS line, indicated a role of TAS3-derived-tasiRNAs in galls. The regulatory module miR390/TAS3 is necessary for proper gall formation possibly through auxin-responsive factors, and the abundance of 24-nt sRNAs (mostly rasiRNAs) constitutes a gall hallmark.
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Affiliation(s)
- Javier Cabrera
- Universidad de Castilla-La Mancha, Facultad de Ciencias Ambientales y Bioquímica, Avda. Carlos III, s/n 45071, Toledo, Spain
| | - Marta Barcala
- Universidad de Castilla-La Mancha, Facultad de Ciencias Ambientales y Bioquímica, Avda. Carlos III, s/n 45071, Toledo, Spain
| | - Alejandra García
- Universidad de Castilla-La Mancha, Facultad de Ciencias Ambientales y Bioquímica, Avda. Carlos III, s/n 45071, Toledo, Spain
| | - Ana Rio-Machín
- Molecular Cytogenetics Group, Human Cancer Genetics Programme, Centro Nacional Investigaciones Oncológicas (CNIO), C/Melchor Fernández Almagro, 3, 28029 , Madrid, Spain
| | - Clémence Medina
- INRA, Université Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Stephanie Jaubert-Possamai
- INRA, Université Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Bruno Favery
- INRA, Université Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Alexis Maizel
- Centre for Organismal Studies University of Heidelberg, Im Neuenheimer Feld, 230-69120, Heidelberg, Germany
| | - Virginia Ruiz-Ferrer
- Centro de Investigaciones Biológicas, CSIC, Av. Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Carmen Fenoll
- Universidad de Castilla-La Mancha, Facultad de Ciencias Ambientales y Bioquímica, Avda. Carlos III, s/n 45071, Toledo, Spain
| | - Carolina Escobar
- Universidad de Castilla-La Mancha, Facultad de Ciencias Ambientales y Bioquímica, Avda. Carlos III, s/n 45071, Toledo, Spain
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18
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Shriram V, Kumar V, Devarumath RM, Khare TS, Wani SH. MicroRNAs As Potential Targets for Abiotic Stress Tolerance in Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:817. [PMID: 27379117 PMCID: PMC4906921 DOI: 10.3389/fpls.2016.00817] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/25/2016] [Indexed: 05/19/2023]
Abstract
The microRNAs (miRNAs) are small (20-24 nt) sized, non-coding, single stranded riboregulator RNAs abundant in higher organisms. Recent findings have established that plants assign miRNAs as critical post-transcriptional regulators of gene expression in sequence-specific manner to respond to numerous abiotic stresses they face during their growth cycle. These small RNAs regulate gene expression via translational inhibition. Usually, stress induced miRNAs downregulate their target mRNAs, whereas, their downregulation leads to accumulation and function of positive regulators. In the past decade, investigations were mainly aimed to identify plant miRNAs, responsive to individual or multiple environmental factors, profiling their expression patterns and recognizing their roles in stress responses and tolerance. Altered expressions of miRNAs implicated in plant growth and development have been reported in several plant species subjected to abiotic stress conditions such as drought, salinity, extreme temperatures, nutrient deprivation, and heavy metals. These findings indicate that miRNAs may hold the key as potential targets for genetic manipulations to engineer abiotic stress tolerance in crop plants. This review is aimed to provide recent updates on plant miRNAs, their biogenesis and functions, target prediction and identification, computational tools and databases available for plant miRNAs, and their roles in abiotic stress-responses and adaptive mechanisms in major crop plants. Besides, the recent case studies for overexpressing the selected miRNAs for miRNA-mediated enhanced abiotic stress tolerance of transgenic plants have been discussed.
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Affiliation(s)
- Varsha Shriram
- Department of Botany, Prof. Ramkrishna More Arts, Commerce and Science College, Savitribai Phule Pune UniversityPune, India
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune UniversityPune, India
- *Correspondence: Vinay Kumar
| | - Rachayya M. Devarumath
- Molecular Biology and Genetic Engineering Section, Vasantdada Sugar InstitutePune, India
| | - Tushar S. Khare
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune UniversityPune, India
| | - Shabir H. Wani
- Division of Genetics and Plant Breeding, Faculty of Agriculture WADURA, Sher-e-Kashmir University of Agricultural Sciences and TechnologyKashmir, India
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19
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Chen CC, Fu SF, Norikazu M, Yang YW, Liu YJ, Ikeo K, Gojobori T, Huang HJ. Comparative miRNAs analysis of Two contrasting broccoli inbred lines with divergent head-forming capacity under temperature stress. BMC Genomics 2015; 16:1026. [PMID: 26625945 PMCID: PMC4667509 DOI: 10.1186/s12864-015-2201-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 11/11/2015] [Indexed: 11/10/2022] Open
Abstract
Background MicroRNAs (miRNAs) play a vital role in growth, development, and stress response at the post-transcriptional level. Broccoli (Brassica oleracea L. var italic) is an important vegetable crop, and the yield and quality of broccoli are decreased by heat stress. The broccoli inbred lines that are capable of producing head at high temperature in summer are unique varieties in Taiwan. However, knowledge of miRNAomes during the broccoli head formation under heat stress is limited. Methods In this study, molecular characterization of two nearly isogenic lines with contrasting head-forming capacity was investigated. Head-forming capacity was better for heat-tolerant (HT) than heat-sensitive (HS) broccoli under heat stress. Results By deep sequencing and computational analysis, 20 known miRNAs showed significant differential expression between HT and HS genotypes. According to the criteria for annotation of new miRNAs, 24 novel miRNA sequences with differential expression between the two genotypes were identified. To gain insight into functional significance, 213 unique potential targets of these 44 differentially expressed miRNAs were predicted. These targets were implicated in shoot apical development, phase change, response to temperature stimulus, hormone and energy metabolism. The head-forming capacity of the unique HT line was related to autonomous regulation of Bo-FT genes and less expression level of heat shock protein genes as compared to HS. For the genotypic comparison, a set of miRNAs and their targets had consistent expression patterns in various HT genotypes. Conclusions This large-scale characterization of broccoli miRNAs and their potential targets is to unravel the regulatory roles of miRNAs underlying heat-tolerant head-forming capacity. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2201-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chi-Chien Chen
- Department of Life Sciences, National Cheng Kung University, No. 1 University Road, East Dist, Tainan, 701, Taiwan.
| | - Shih-Feng Fu
- Department of Biology, National Chunghua University of Education, No.1, Jin-De Road, Changhua, 500, Taiwan.
| | - Monma Norikazu
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata, Mishima, Shizuoka, 411-8540, Japan.
| | - Yau-Wen Yang
- Kale Biotech. Co, No.68-1, Chongde 16th St., East Dist, Tainan, 701, Taiwan.
| | - Yu-Ju Liu
- Department of Life Sciences, National Cheng Kung University, No. 1 University Road, East Dist, Tainan, 701, Taiwan.
| | - Kazuho Ikeo
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata, Mishima, Shizuoka, 411-8540, Japan.
| | - Takashi Gojobori
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata, Mishima, Shizuoka, 411-8540, Japan.
| | - Hao-Jen Huang
- Department of Life Sciences, National Cheng Kung University, No. 1 University Road, East Dist, Tainan, 701, Taiwan.
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20
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Nguyen GN, Rothstein SJ, Spangenberg G, Kant S. Role of microRNAs involved in plant response to nitrogen and phosphorous limiting conditions. FRONTIERS IN PLANT SCIENCE 2015; 6:629. [PMID: 26322069 PMCID: PMC4534779 DOI: 10.3389/fpls.2015.00629] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/30/2015] [Indexed: 05/22/2023]
Abstract
Plant microRNAs (miRNAs) are a class of small non-coding RNAs which target and regulate the expression of genes involved in several growth, development, and metabolism processes. Recent researches have shown involvement of miRNAs in the regulation of uptake and utilization of nitrogen (N) and phosphorus (P) and more importantly for plant adaptation to N and P limitation conditions by modifications in plant growth, phenology, and architecture and production of secondary metabolites. Developing strategies that allow for the higher efficiency of using both N and P fertilizers in crop production is important for economic and environmental benefits. Improved crop varieties with better adaptation to N and P limiting conditions could be a key approach to achieve this effectively. Furthermore, understanding on the interactions between N and P uptake and use and their regulation is important for the maintenance of nutrient homeostasis in plants. This review describes the possible functions of different miRNAs and their cross-talk relevant to the plant adaptive responses to N and P limiting conditions. In addition, a comprehensive understanding of these processes at molecular level and importance of biological adaptation for improved N and P use efficiency is discussed.
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Affiliation(s)
- Giao N. Nguyen
- Biosciences Research, Department of Economic DevelopmentHorsham, VIC, Australia
| | - Steven J. Rothstein
- Department of Molecular and Cellular Biology, College of Biological Science, University of GuelphGuelph, ON, Canada
| | - German Spangenberg
- Biosciences Research, Department of Economic Development, AgriBio, Centre for AgriBioscienceBundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe UniversityBundoora, VIC, Australia
| | - Surya Kant
- Biosciences Research, Department of Economic DevelopmentHorsham, VIC, Australia
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21
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Paul S, Datta SK, Datta K. miRNA regulation of nutrient homeostasis in plants. FRONTIERS IN PLANT SCIENCE 2015; 6:232. [PMID: 25914709 PMCID: PMC4392614 DOI: 10.3389/fpls.2015.00232] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/23/2015] [Indexed: 05/02/2023]
Abstract
Small RNAs including micro RNAs (miRNA) play an indispensable role in cell signaling mechanisms. Generally, miRNAs that are 20-24 nucleotides long bind to specific complementary transcripts, attenuating gene expression at the post-transcriptional level or via translational inhibition. In plants, miRNAs have emerged as the principal regulator of various stress responses, including low nutrient availability. It has been reported that miRNAs are vital for maintaining nutrient homeostasis in plants by regulating the expression of transporters that are involved in nutrient uptake and mobilization. The present review highlights the role of various miRNAs in several macro- or micronutrient deficiencies in plants. Understanding the regulation of different transporters by miRNAs will aid in elucidating the underlying molecular signal transduction mechanisms during nutritional stress. Recent findings regarding nutrient related-miRNAs and their gene regulation machinery may delineate a novel platform for improving the nutritional status of cereal grains or crop biofortification programs in the future.
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Affiliation(s)
| | | | - Karabi Datta
- Translational Research Laboratory of Transgenic Rice, Department of Botany, University of CalcuttaKolkata, India
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22
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Qu B, He X, Wang J, Zhao Y, Teng W, Shao A, Zhao X, Ma W, Wang J, Li B, Li Z, Tong Y. A wheat CCAAT box-binding transcription factor increases the grain yield of wheat with less fertilizer input. PLANT PHYSIOLOGY 2015; 167:411-23. [PMID: 25489021 PMCID: PMC4326744 DOI: 10.1104/pp.114.246959] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 12/04/2014] [Indexed: 05/18/2023]
Abstract
Increasing fertilizer consumption has led to low fertilizer use efficiency and environmental problems. Identifying nutrient-efficient genes will facilitate the breeding of crops with improved fertilizer use efficiency. This research performed a genome-wide sequence analysis of the A (NFYA), B (NFYB), and C (NFYC) subunits of Nuclear Factor Y (NF-Y) in wheat (Triticum aestivum) and further investigated their responses to nitrogen and phosphorus availability in wheat seedlings. Sequence mining together with gene cloning identified 18 NFYAs, 34 NFYBs, and 28 NFYCs. The expression of most NFYAs positively responded to low nitrogen and phosphorus availability. In contrast, microRNA169 negatively responded to low nitrogen and phosphorus availability and degraded NFYAs. Overexpressing TaNFYA-B1, a low-nitrogen- and low-phosphorus-inducible NFYA transcript factor on chromosome 6B, significantly increased both nitrogen and phosphorus uptake and grain yield under differing nitrogen and phosphorus supply levels in a field experiment. The increased nitrogen and phosphorus uptake may have resulted from the fact that that overexpressing TaNFYA-B1 stimulated root development and up-regulated the expression of both nitrate and phosphate transporters in roots. Our results suggest that TaNFYA-B1 plays essential roles in root development and in nitrogen and phosphorus usage in wheat. Furthermore, our results provide new knowledge and valuable gene resources that should be useful in efforts to breed crops targeting high yield with less fertilizer input.
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Affiliation(s)
- Baoyuan Qu
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xue He
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Wang
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanyan Zhao
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wan Teng
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - An Shao
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xueqiang Zhao
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenying Ma
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Junyi Wang
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Li
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhensheng Li
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yiping Tong
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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Kulcheski FR, Côrrea R, Gomes IA, de Lima JC, Margis R. NPK macronutrients and microRNA homeostasis. FRONTIERS IN PLANT SCIENCE 2015; 6:451. [PMID: 26136763 PMCID: PMC4468412 DOI: 10.3389/fpls.2015.00451] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 06/02/2015] [Indexed: 05/02/2023]
Abstract
Macronutrients are essential elements for plant growth and development. In natural, non-cultivated systems, the availability of macronutrients is not a limiting factor of growth, due to fast recycling mechanisms. However, their availability might be an issue in modern agricultural practices, since soil has been frequently over exploited. From a crop management perspective, the nitrogen (N), phosphorus (P), and potassium (K) are three important limiting factors and therefore frequently added as fertilizers. NPK are among the nutrients that have been reported to alter post-embryonic root developmental processes and consequently, impairs crop yield. To cope with nutrients scarcity, plants have evolved several mechanisms involved in metabolic, physiological, and developmental adaptations. In this scenario, microRNAs (miRNAs) have emerged as additional key regulators of nutrients uptake and assimilation. Some studies have demonstrated the intrinsic relation between miRNAs and their targets, and how they can modulate plants to deal with the NPK availability. In this review, we focus on miRNAs and their regulation of targets involved in NPK metabolism. In general, NPK starvation is related with miRNAs that are involved in root-architectural changes and uptake activity modulation. We further show that several miRNAs were discovered to be involved in plant-microbe symbiosis during N and P uptake, and in this way we present a global view of some studies that were conducted in the last years. The integration of current knowledge about miRNA-NPK signaling may help future studies to focus in good candidates genes for the development of important tools for plant nutritional breeding.
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Affiliation(s)
- Franceli R. Kulcheski
- Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto AlegreBrazil
| | - Régis Côrrea
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de JaneiroBrazil
| | - Igor A. Gomes
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de JaneiroBrazil
| | - Júlio C. de Lima
- Laboratório de Genética Molecular, Instituto de Ciências Biológicas, Universidade de Passo Fundo, Passo FundoBrazil
| | - Rogerio Margis
- Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto AlegreBrazil
- *Correspondence: Rogerio Margis, Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, Setor IV, Prédio 43431, Sala 213, Porto Alegre, RS, CEP, Brazil
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Liu TY, Lin WY, Huang TK, Chiou TJ. MicroRNA-mediated surveillance of phosphate transporters on the move. TRENDS IN PLANT SCIENCE 2014; 19:647-55. [PMID: 25001521 DOI: 10.1016/j.tplants.2014.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/29/2014] [Accepted: 06/06/2014] [Indexed: 05/06/2023]
Abstract
Phosphate (Pi), which is indispensable for the structural and metabolic needs of plants, is acquired and translocated by Pi transporters. Deciphering the regulatory network of Pi signaling and homeostasis that involves the control of Pi transporters trafficking to, and their activity at, the plasma membrane provides insight into how plants adapt to environmental changes in Pi availability. Here, we review recent studies that revealed the involvement of microRNA399-PHOSPHATE 2 (PHO2) and microR827-NITROGEN LIMITATION ADAPTATION (NLA) modules in mediating the ubiquitination and degradation of PHOSPHATE TRANSPORTER 1 (PHT1) and/or PHOSPHATE 1 (PHO1). These discoveries show that miRNAs are an effective way for plants to monitor the turnover of Pi transporters in the membrane system by modulating the functioning of the membrane-associated ubiquitin machinery.
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Affiliation(s)
- Tzu-Yin Liu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Wei-Yi Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Teng-Kuei Huang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan; Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan; Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung 402, Taiwan
| | - Tzyy-Jen Chiou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan; Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan; Biotechnology Center, National Chung-Hsing University, Taichung 402, Taiwan.
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25
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Stauffer E, Maizel A. Post-transcriptional regulation in root development. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:679-96. [PMID: 24827552 DOI: 10.1002/wrna.1239] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 03/20/2014] [Accepted: 03/26/2014] [Indexed: 11/08/2022]
Abstract
Plants constantly adapt their root system to the changing environmental conditions. This developmental plasticity is underpinned by changes in the profile of the mRNA expressed. Here we review how post-transcriptional modulation of gene expression control root development and growth. In particular we focus on the role of small RNA-mediated post-transcriptional regulation processes. Small RNAs play an important role in fine tuning gene expression during root formation and patterning, development of lateral organs and symbiosis, nutrient homeostasis, and other stress-related responses. We also highlight the impact of alternative splicing on root development and the establishment of symbiotic structures as well as the emerging role of long noncoding RNAs in root physiology.
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Affiliation(s)
- Eva Stauffer
- Center for Organismal Studies, University of Heidelberg, Heidelberg, Germany
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Zhang Z, Liao H, Lucas WJ. Molecular mechanisms underlying phosphate sensing, signaling, and adaptation in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:192-220. [PMID: 24417933 DOI: 10.1111/jipb.12163] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 01/06/2014] [Indexed: 05/18/2023]
Abstract
As an essential plant macronutrient, the low availability of phosphorus (P) in most soils imposes serious limitation on crop production. Plants have evolved complex responsive and adaptive mechanisms for acquisition, remobilization and recycling of phosphate (Pi) to maintain P homeostasis. Spatio-temporal molecular, physiological, and biochemical Pi deficiency responses developed by plants are the consequence of local and systemic sensing and signaling pathways. Pi deficiency is sensed locally by the root system where hormones serve as important signaling components in terms of developmental reprogramming, leading to changes in root system architecture. Root-to-shoot and shoot-to-root signals, delivered through the xylem and phloem, respectively, involving Pi itself, hormones, miRNAs, mRNAs, and sucrose, serve to coordinate Pi deficiency responses at the whole-plant level. A combination of chromatin remodeling, transcriptional and posttranslational events contribute to globally regulating a wide range of Pi deficiency responses. In this review, recent advances are evaluated in terms of progress toward developing a comprehensive understanding of the molecular events underlying control over P homeostasis. Application of this knowledge, in terms of developing crop plants having enhanced attributes for P use efficiency, is discussed from the perspective of agricultural sustainability in the face of diminishing global P supplies.
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Affiliation(s)
- Zhaoliang Zhang
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, 95616, USA
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Smith AP. Systemic Signaling in the Maintenance of Phosphate Homeostasis. LONG-DISTANCE SYSTEMIC SIGNALING AND COMMUNICATION IN PLANTS 2013. [DOI: 10.1007/978-3-642-36470-9_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Marín-González E, Suárez-López P. "And yet it moves": cell-to-cell and long-distance signaling by plant microRNAs. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 196:18-30. [PMID: 23017896 DOI: 10.1016/j.plantsci.2012.07.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 07/17/2012] [Accepted: 07/21/2012] [Indexed: 05/07/2023]
Abstract
MicroRNAs (miRNAs) are key regulators of numerous genes in many eukaryotes. Some plant miRNAs are involved in developmental and physiological processes that require intercellular or inter-organ signaling. Movement of other small RNAs within plants has been established. Recent findings also demonstrate intercellular signaling by miRNAs and strongly support that a subset of these regulatory molecules move from one cell to another or over long distances. Phloem exudates contain diverse miRNAs and at least two of them, involved in responses to nutrient availability, are transmitted through grafts, indicating long-distance movement. Two miRNAs that regulate developmental processes are present in cells outside their domains of expression. Several results strongly support that one of them moves from cell to cell. Research on a mutant affected in plasmodesmata trafficking indicates that these intercellular channels are required for transmission of miRNA activity to adjacent cells. Moreover, ARGONAUTE proteins might be involved in the regulation of miRNA trafficking. Hypothesis on the features and mechanisms that may determine miRNA mobility are presented. Future challenges include identifying other mobile miRNAs; demonstrating that miRNA movement is required for non-cell autonomous action; and characterizing the mechanisms of translocation and genetic pathways that regulate miRNA movement.
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Affiliation(s)
- Esther Marín-González
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra-Cerdanyola del Vallès, 08193 Barcelona, Spain
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29
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Luo QJ, Mittal A, Jia F, Rock CD. An autoregulatory feedback loop involving PAP1 and TAS4 in response to sugars in Arabidopsis. PLANT MOLECULAR BIOLOGY 2012; 80:117-29. [PMID: 21533841 PMCID: PMC3272322 DOI: 10.1007/s11103-011-9778-9] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Accepted: 04/12/2011] [Indexed: 05/18/2023]
Abstract
miR828 in Arabidopsis triggers the cleavage of Trans-Acting SiRNA Gene 4 (TAS4) transcripts and production of small interfering RNAs (ta-siRNAs). One siRNA, TAS4-siRNA81(-), targets a set of MYB transcription factors including PAP1, PAP2, and MYB113 which regulate the anthocyanin biosynthesis pathway. Interestingly, miR828 also targets MYB113, suggesting a close relationship between these MYBs, miR828, and TAS4, but their evolutionary origins are unknown. We found that PAP1, PAP2, and TAS4 expression is induced specifically by exogenous treatment with sucrose and glucose in seedlings. The induction is attenuated in abscisic acid (ABA) pathway mutants, especially in abi3-1 and abi5-1 for PAP1 or PAP2, while no such effect is observed for TAS4. PAP1 is under regulation by TAS4, demonstrated by the accumulation of PAP1 transcripts and anthocyanin in ta-siRNA biogenesis pathway mutants. TAS4-siR81(-) expression is induced by physiological concentrations of Suc and Glc and in pap1-D, an activation-tagged line, indicating a feedback regulatory loop exists between PAP1 and TAS4. Bioinformatic analysis revealed MIR828 homologues in dicots and gymnosperms, but only in one basal monocot, whereas TAS4 is only found in dicots. Consistent with this observation, PAP1, PAP2, and MYB113 dicot paralogs show peptide and nucleotide footprints for the TAS4-siR81(-) binding site, providing evidence for purifying selection in contrast to monocots. Extended sequence similarities between MIR828, MYBs, and TAS4 support an inverted duplication model for the evolution of MIR828 from an ancestral gymnosperm MYB gene and subsequent formation of TAS4 by duplication of the miR828* arm. We obtained evidence by modified 5'-RACE for a MYB mRNA cleavage product guided by miR828 in Pinus resinosa. Taken together, our results suggest that regulation of anthocyanin biosynthesis by TAS4 and miR828 in higher plants is evolutionarily significant and consistent with the evolution of TAS4 since the dicot-monocot divergence.
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31
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Jeong DH, Park S, Zhai J, Gurazada SGR, De Paoli E, Meyers BC, Green PJ. Massive analysis of rice small RNAs: mechanistic implications of regulated microRNAs and variants for differential target RNA cleavage. THE PLANT CELL 2011; 23:4185-207. [PMID: 22158467 PMCID: PMC3269859 DOI: 10.1105/tpc.111.089045] [Citation(s) in RCA: 221] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Small RNAs have a variety of important roles in plant development, stress responses, and other processes. They exert their influence by guiding mRNA cleavage, translational repression, and chromatin modification. To identify previously unknown rice (Oryza sativa) microRNAs (miRNAs) and those regulated by environmental stress, 62 small RNA libraries were constructed from rice plants and used for deep sequencing with Illumina technology. The libraries represent several tissues from control plants and plants subjected to different environmental stress treatments. More than 94 million genome-matched reads were obtained, resulting in more than 16 million distinct small RNA sequences. This allowed an evaluation of ~400 annotated miRNAs with current criteria and the finding that among these, ~150 had small interfering RNA-like characteristics. Seventy-six new miRNAs were found, and miRNAs regulated in response to water stress, nutrient stress, or temperature stress were identified. Among the new examples of miRNA regulation were members of the same miRNA family that were differentially regulated in different organs and had distinct sequences Some of these distinct family members result in differential target cleavage and provide new insight about how an agriculturally important rice phenotype could be regulated in the panicle. This high-resolution analysis of rice miRNAs should be relevant to plant miRNAs in general, particularly in the Poaceae.
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32
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Khan GA, Declerck M, Sorin C, Hartmann C, Crespi M, Lelandais-Brière C. MicroRNAs as regulators of root development and architecture. PLANT MOLECULAR BIOLOGY 2011; 77:47-58. [PMID: 21607657 DOI: 10.1007/s11103-011-9793-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Accepted: 05/09/2011] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators of growth and development in both plants and animals. In plants, roots play essential roles in their anchorage to the soil as well as in nutrient and water uptake. In this review, we present recent advances made in the identification of miRNAs involved in embryonic root development, radial patterning, vascular tissue differentiation and formation of lateral organs (i.e., lateral and adventitious roots and symbiotic nitrogen-fixing nodules in legumes). Certain mi/siRNAs target members of the Auxin Response Factors family involved in auxin homeostasis and signalling and participate in complex regulatory loops at several crucial stages of root development. Other miRNAs target and restrict the action of various transcription factors that control root-related processes in several species. Finally, because abiotic stresses, which include nutrient or water deficiencies, generally modulate root growth and branching, we summarise the action of certain miRNAs in response to these stresses that may be involved in the adaptation of the root system architecture to the soil environment.
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Affiliation(s)
- Ghazanfar A Khan
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique (C.N.R.S.), 91198 Gif-sur-Yvette Cedex, France
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Hammond JP, White PJ. Sugar signaling in root responses to low phosphorus availability. PLANT PHYSIOLOGY 2011; 156:1033-40. [PMID: 21487049 PMCID: PMC3135921 DOI: 10.1104/pp.111.175380] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 04/10/2011] [Indexed: 05/18/2023]
Affiliation(s)
- John P Hammond
- Division of Plant and Crop Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, United Kingdom.
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34
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Kuo HF, Chiou TJ. The role of microRNAs in phosphorus deficiency signaling. PLANT PHYSIOLOGY 2011; 156:1016-24. [PMID: 21562333 PMCID: PMC3135939 DOI: 10.1104/pp.111.175265] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Accepted: 05/06/2011] [Indexed: 05/18/2023]
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Lundmark M, Nilsson L, K Rner CJ, Nielsen TH. Overexpression of the MYB-related transcription factor GCC7 in Arabidopsis thaliana leads to increased levels of P i and changed P-dependent gene regulation. FUNCTIONAL PLANT BIOLOGY : FPB 2011; 38:151-162. [PMID: 32480871 DOI: 10.1071/fp10081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 11/24/2010] [Indexed: 06/11/2023]
Abstract
A proper concentration and turnover of inorganic phosphate (Pi) is essential to maintain cellular processes. Consequently, plants have mechanisms to control Pi homeostasis and to alleviate Pi limitation. The MYB-related transcription factor, PHR1, is important for gene induction during Pi starvation. PHR1 belongs to a family, characterised by the presence of a GARP- and a coiled coil domain. We propose that this family, with 15 members in Arabidopsis thaliana (L.) Heynh., be termed the GCC-family. In this study, transgenic plants overexpressing one member, GCC7, and a T-DNA knockout mutant, gcc7, are characterised. We find overexpressor plants to accumulate more Pi in shoots, irrespective of the Pi supply. Therefore, GCC7 was characterised in relation to Pi starvation. We conclude that GCC7 is not strictly required for a P-starvation response since the gcc7 mutant responds to Pi limitation. However, overexpression of GCC7 strongly interferes with the P-starvation response, abolishing induction of several P-responsive genes including AT4, IPS1 and several P-transporter genes, whereas GCC7 does not directly interfere with the PHR1 (GCC1) dependent regulation of miR399d. Thus GCC7 influences P-accumulation and P-dependent gene regulation, but GCC7 has a function entirely different from PHR1.
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Affiliation(s)
- Maria Lundmark
- Section for Plant Molecular Biology, VKR centre Pro-Active Plants, Department of Plant Biology and Biotechnology, Faculty of Life Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lena Nilsson
- Section for Plant Molecular Biology, VKR centre Pro-Active Plants, Department of Plant Biology and Biotechnology, Faculty of Life Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Camilla J K Rner
- Section for Plant Molecular Biology, VKR centre Pro-Active Plants, Department of Plant Biology and Biotechnology, Faculty of Life Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tom H Nielsen
- Section for Plant Molecular Biology, VKR centre Pro-Active Plants, Department of Plant Biology and Biotechnology, Faculty of Life Sciences, University of Copenhagen, Copenhagen, Denmark
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36
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Chiou TJ, Lin SI. Signaling network in sensing phosphate availability in plants. ANNUAL REVIEW OF PLANT BIOLOGY 2011; 62:185-206. [PMID: 21370979 DOI: 10.1146/annurev-arplant-042110-103849] [Citation(s) in RCA: 429] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plants acquire phosphorus in the form of phosphate (Pi), the concentration of which is often limited for plant uptake. Plants have developed diverse responses to conserve and remobilize internal Pi and to enhance Pi acquisition to secure them against Pi deficiency. These responses are achieved by the coordination of an elaborate signaling network comprising local and systemic machineries. Recent advances have revealed several important components involved in this network. Pi functions as a signal to report its own availability. miR399 and sugars act as systemic signals to regulate responses occurring in roots. Hormones also play crucial roles in modulating gene expression and in altering root system architecture. Transcription factors function as a hub to perceive the signals and to elicit steady outputs. In this review, we outline the current knowledge on this subject and present hypotheses pertaining to other potential signals and to the organization and coordination of signaling.
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Affiliation(s)
- Tzyy-Jen Chiou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
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