1
|
Li S, Zhao Z, Lu Q, Li M, Dai X, Shan M, Liu Z, Bai MY, Xiang F. miR394 modulates brassinosteroid signaling to regulate hypocotyl elongation in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:645-657. [PMID: 38761364 DOI: 10.1111/tpj.16806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 04/13/2024] [Accepted: 04/30/2024] [Indexed: 05/20/2024]
Abstract
The interplay between microRNAs (miRNAs) and phytohormones allows plants to integrate multiple internal and external signals to optimize their survival of different environmental conditions. Here, we report that miR394 and its target gene LEAF CURLING RESPONSIVENESS (LCR), which are transcriptionally responsive to BR, participate in BR signaling to regulate hypocotyl elongation in Arabidopsis thaliana. Phenotypic analysis of various transgenic and mutant lines revealed that miR394 negatively regulates BR signaling during hypocotyl elongation, whereas LCR positively regulates this process. Genetically, miR394 functions upstream of BRASSINOSTEROID INSENSITIVE2 (BIN2), BRASSINAZOLEs RESISTANT1 (BZR1), and BRI1-EMS-SUPPRESSOR1 (BES1), but interacts with BRASSINOSTEROID INSENSITIVE1 (BRI1) and BRI1 SUPRESSOR PROTEIN (BSU1). RNA-sequencing analysis suggested that miR394 inhibits BR signaling through BIN2, as miR394 regulates a significant number of genes in common with BIN2. Additionally, miR394 increases the accumulation of BIN2 but decreases the accumulation of BZR1 and BES1, which are phosphorylated by BIN2. MiR394 also represses the transcription of PACLOBUTRAZOL RESISTANCE1/5/6 and EXPANSIN8, key genes that regulate hypocotyl elongation and are targets of BZR1/BES1. These findings reveal a new role for a miRNA in BR signaling in Arabidopsis.
Collapse
Affiliation(s)
- Shuo Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, People's Republic of China
| | - Zhongjuan Zhao
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, People's Republic of China
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute of Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250013, China
| | - Qing Lu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, People's Republic of China
| | - Mingru Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, People's Republic of China
| | - Xuehuan Dai
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, People's Republic of China
| | - Mengqi Shan
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, People's Republic of China
| | - Zhenhua Liu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, People's Republic of China
| | - Ming-Yi Bai
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, People's Republic of China
| | - Fengning Xiang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, People's Republic of China
| |
Collapse
|
2
|
Szymonik K, Klimek-Chodacka M, Lukasiewicz A, Macko-Podgórni A, Grzebelus D, Baranski R. Comparative analysis of the carrot miRNAome in response to salt stress. Sci Rep 2023; 13:21506. [PMID: 38057586 PMCID: PMC10700493 DOI: 10.1038/s41598-023-48900-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023] Open
Abstract
Soil salinity adversely affects the yield and quality of crops, including carrot. During salt stress, plant growth and development are impaired by restricted water uptake and ion cytotoxicity, leading to nutrient imbalance and oxidative burst. However, the molecular mechanisms of the carrot plant response to salt stress remain unclear. The occurrence and expression of miRNAs that are potentially involved in the regulation of carrot tolerance to salinity stress were investigated. The results of small RNA sequencing revealed that salt-sensitive (DH1) and salt-tolerant (DLBA) carrot varieties had different miRNA expression profiles. A total of 95 miRNAs were identified, including 71 novel miRNAs, of which 30 and 23 were unique to DH1 and DLBA, respectively. The comparison of NGS and qPCR results allowed identification of two conserved and five novel miRNA involved in carrot response to salt stress, and which differentiated the salt-tolerant and salt-sensitive varieties. Degradome analysis supported by in silico-based predictions and followed by expression analysis of exemplary target genes pointed at genes related to proline, glutathione, and glutamate metabolism pathways as potential miRNA targets involved in salt tolerance, and indicated that the regulation of osmoprotection and antioxidant protection, earlier identified as being more efficient in the tolerant variety, may be controlled by miRNAs. Furthermore, potential miRNA target genes involved in chloroplast protection, signal transduction and the synthesis and modification of cell wall components were indicated in plants growing in saline soil.
Collapse
Affiliation(s)
- Kamil Szymonik
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland.
| | - Magdalena Klimek-Chodacka
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland.
| | - Aneta Lukasiewicz
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland
| | - Alicja Macko-Podgórni
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland
| | - Dariusz Grzebelus
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland
| | - Rafal Baranski
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland.
| |
Collapse
|
3
|
Bakirbas A, Castro-Rodriguez R, Walker EL. The Small RNA Component of Arabidopsis thaliana Phloem Sap and Its Response to Iron Deficiency. PLANTS (BASEL, SWITZERLAND) 2023; 12:2782. [PMID: 37570935 PMCID: PMC10421156 DOI: 10.3390/plants12152782] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 08/13/2023]
Abstract
In order to discover sRNA that might function during iron deficiency stress, RNA was prepared from phloem exudates of Arabidopsis thaliana, and used for RNA-seq. Bioanalyzer results indicate that abundant RNA from phloem is small in size-less than 200 nt. Moreover, typical rRNA bands were not observed. Sequencing of eight independent phloem RNA samples indicated that tRNA-derived fragments, specifically 5' tRFs and 5' tRNA halves, are highly abundant in phloem sap, comprising about 46% of all reads. In addition, a set of miRNAs that are present in phloem sap was defined, and several miRNAs and sRNAs were identified that are differentially expressed during iron deficiency.
Collapse
Affiliation(s)
- Ahmet Bakirbas
- Biology Department and Plant Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA;
| | | | - Elsbeth L. Walker
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
| |
Collapse
|
4
|
Ma Z, Hu L. MicroRNA: A Dynamic Player from Signalling to Abiotic Tolerance in Plants. Int J Mol Sci 2023; 24:11364. [PMID: 37511124 PMCID: PMC10379455 DOI: 10.3390/ijms241411364] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 07/06/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of non-coding single-stranded RNA molecules composed of approximately 20-24 nucleotides in plants. They play an important regulatory role in plant growth and development and as a signal in abiotic tolerance. Some abiotic stresses include drought, salt, cold, high temperature, heavy metals and nutritional elements. miRNAs affect gene expression by manipulating the cleavage, translational expression or DNA methylation of target messenger RNAs (mRNAs). This review describes the current progress in the field considering two aspects: (i) the way miRNAs are produced and regulated and (ii) the way miRNA/target genes are used in plant responses to various abiotic stresses. Studying the molecular mechanism of action of miRNAs' downstream target genes could optimize the genetic manipulation of crop growth and development conditions to provide a more theoretically optimized basis for improving crop production. MicroRNA is a novel signalling mechanism in interplant communication relating to abiotic tolerance.
Collapse
Affiliation(s)
- Ziming Ma
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, 85354 Freising, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Lanjuan Hu
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China
| |
Collapse
|
5
|
Liu W, Ji X, Cao H, Huo C, He L, Peng X, Yang Y, Yang F, Xiong S. Comparative Transcriptome Analysis Reveals the Effect of miR156a Overexpression on Mineral Nutrient Homeostasis in Nicotiana tabacum. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091739. [PMID: 37176797 PMCID: PMC10181358 DOI: 10.3390/plants12091739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/15/2023]
Abstract
Mineral nutrition plays an important role in crop growth, yield and quality. MiR156 is a regulatory hub for growth and development. To date, the understanding of miR156-mediated mineral homeostasis is limited. In this study, we overexpressed Nta-miR156a in the tobacco cultivar TN90 and analyzed the effects of miR156 on mineral element homeostasis in tobacco by comparative transcriptome analysis. The results showed that the overexpression of miR156a caused significant morphological changes in transgenic tobacco. Chlorophyll and three anti-resistance markers, proline, total phenolics, and total flavonoids, were altered due to increased miR156 expression levels. Interestingly, the distribution of Cu, Mn, Zn, and Fe in different tissues of transgenic tobacco was disordered compared with that of the wild type. Comparative transcriptome analysis showed that the overexpression of miR156 resulted in 2656 significantly differentially expressed genes. The expression levels of several metal-transport-related genes, such as NtABC, NtZIP, NtHMA, and NtCAX, were significantly increased or decreased in transgenic tobacco. These results suggest that miR156 plays an essential role in regulating mineral homeostasis. Our study provides a new perspective for the further study of mineral nutrient homeostasis in plants.
Collapse
Affiliation(s)
- Wanhong Liu
- School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing 401331, China
| | - Xue Ji
- School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing 401331, China
| | - Hanping Cao
- School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing 401331, China
| | - Chunsong Huo
- School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing 401331, China
| | - Linshen He
- School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing 401331, China
| | - Xiang Peng
- School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing 401331, China
| | - Ya Yang
- School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing 401331, China
| | - Fang Yang
- School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing 401331, China
| | - Shu Xiong
- Department of Basic Medicine, Chongqing Three Gorges Medical College, Chongqing 404120, China
| |
Collapse
|
6
|
Banerjee S, Roy P, Nandi S, Roy S. Advanced biotechnological strategies towards the development of crops with enhanced micronutrient content. PLANT GROWTH REGULATION 2023; 100:355-371. [PMID: 36686885 PMCID: PMC9845834 DOI: 10.1007/s10725-023-00968-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 01/06/2023] [Indexed: 05/17/2023]
Abstract
Micronutrients are essential mineral elements required for both plant and human development.An integrated system involving soil, climatic conditions, and types of crop plants determines the level of micronutrient acquisition and utilization. Most of the staple food crops consumed globally predominantly include the cereal grains, tubers and roots, respectively and in many cases, particularly in the resource-poor countries they are grown in nutrient-deficient soils. These situations frequently lead to micronutrient deficiency in crops. Moreover, crop plants with micronutrient deficiency also show high level of susceptibility to various abiotic and biotic stress factors. Apart from this, climate change and soil pollution severely affect the accumulation of micronutrients, such as zinc (Zn), iron (Fe), selenium (Se), manganese (Mn), and copper (Cu) in food crops. Therefore, overcoming the issue of micronutrient deficiency in staple crops and to achieve the adequate level of food production with enriched nutrient value is one of the major global challenges at present. Conventional breeding approaches are not adequate to feed the increasing global population with nutrient-rich staple food crops. To address these issues, alongside traditional approaches, genetic modification strategies have been adopted during the past couple of years in order to enhance the transport, production, enrichment and bioavailability of micronutrients in staple crops. Recent advances in agricultural biotechnology and genome editing approaches have shown promising response in the development of micronutrient enriched biofortified crops. This review highlights the current advancement of our knowledge on the possible implications of various biotechnological tools for the enrichment and enhancement of bioavailability of micronutrients in crops.
Collapse
Affiliation(s)
- Samrat Banerjee
- Department of Botany, UGC Centre for Advanced Studies, The University of Burdwan, Golapbag Campus, 713104 Burdwan, West Bengal India
| | - Pinaki Roy
- Department of Botany, UGC Centre for Advanced Studies, The University of Burdwan, Golapbag Campus, 713104 Burdwan, West Bengal India
| | - Shreyashi Nandi
- Department of Botany, UGC Centre for Advanced Studies, The University of Burdwan, Golapbag Campus, 713104 Burdwan, West Bengal India
| | - Sujit Roy
- Department of Botany, UGC Centre for Advanced Studies, The University of Burdwan, Golapbag Campus, 713104 Burdwan, West Bengal India
| |
Collapse
|
7
|
Jamla M, Joshi S, Patil S, Tripathi BN, Kumar V. MicroRNAs modulating nutrient homeostasis: a sustainable approach for developing biofortified crops. PROTOPLASMA 2023; 260:5-19. [PMID: 35657503 DOI: 10.1007/s00709-022-01775-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
During their lifespan, sessile plants have to cope with bioavailability of the suboptimal nutrient concentration and have to constantly sense/evolve the connecting web of signal cascades for efficient nutrient uptake, storage, and translocation for proper growth and metabolism. However, environmental fluctuations and escalating anthropogenic activities are making it a formidable challenge for plants. This is adding to (micro)nutrient-deficient crops and nutritional insecurity. Biofortification is emerging as a sustainable and efficacious approach which can be utilized to combat the micronutrient malnutrition. A biofortified crop has an enriched level of desired nutrients developed using conventional breeding, agronomic practices, or advanced biotechnological tools. Nutrient homeostasis gets hampered under nutrient stress, which involves disturbance in short-distance and long-distance cell-cell/cell-organ communications involving multiple cellular and molecular components. Advanced sequencing platforms coupled with bioinformatics pipelines and databases have suggested the potential roles of tiny signaling molecules and post-transcriptional regulators, the microRNAs (miRNAs) in key plant phenomena including nutrient homeostasis. miRNAs are seen as emerging targets for biotechnology-based biofortification programs. Thus, understanding the mechanistic insights and regulatory role of miRNAs could open new windows for exploring them in developing nutrient-efficient biofortified crops. This review discusses significance and roles of miRNAs in plant nutrition and nutrient homeostasis and how they play key roles in plant responses to nutrient imbalances/deficiencies/toxicities covering major nutrients-nitrogen (N), phosphorus (P), sulfur (S), magnesium (Mg), iron (Fe), and zinc (Zn). A perspective view has been given on developing miRNA-engineered biofortified crops with recent success stories. Current challenges and future strategies have also been discussed.
Collapse
Affiliation(s)
- Monica Jamla
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Shrushti Joshi
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Suraj Patil
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Bhumi Nath Tripathi
- Department of Biotechnology, Indira Gandhi National Tribal University, Amarkantak, 484887, India
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India.
| |
Collapse
|
8
|
Fan K, Sze CC, Li MW, Lam HM. Roles of non-coding RNAs in the hormonal and nutritional regulation in nodulation and nitrogen fixation. FRONTIERS IN PLANT SCIENCE 2022; 13:997037. [PMID: 36330261 PMCID: PMC9623164 DOI: 10.3389/fpls.2022.997037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Symbiotic nitrogen fixation is an important component in the nitrogen cycle and is a potential solution for sustainable agriculture. It is the result of the interactions between the plant host, mostly restricted to legume species, and the rhizobial symbiont. From the first encounter between the host and the symbiont to eventual successful nitrogen fixation, there are delicate processes involved, such as nodule organogenesis, rhizobial infection thread progression, differentiation of the bacteroid, deregulation of the host defense systems, and reallocation of resources. All these processes are tightly regulated at different levels. Recent evidence revealed that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), participate in these processes by controlling the transcription and translation of effector genes. In general, ncRNAs are functional transcripts without translation potential and are important gene regulators. MiRNAs, negative gene regulators, bind to the target mRNAs and repress protein production by causing the cleavage of mRNA and translational silencing. LncRNAs affect the formation of chromosomal loops, DNA methylation, histone modification, and alternative splicing to modulate gene expression. Both lncRNAs and circRNAs could serve as target mimics of miRNA to inhibit miRNA functions. In this review, we summarized and discussed the current understanding of the roles of ncRNAs in legume nodulation and nitrogen fixation in the root nodule, mainly focusing on their regulation of hormone signal transduction, the autoregulation of nodulation (AON) pathway and nutrient homeostasis in nodules. Unraveling the mediation of legume nodulation by ncRNAs will give us new insights into designing higher-performance leguminous crops for sustainable agriculture.
Collapse
|
9
|
Jha R, Yadav HK, Raiya R, Singh RK, Jha UC, Sathee L, Singh P, Thudi M, Singh A, Chaturvedi SK, Tripathi S. Integrated breeding approaches to enhance the nutritional quality of food legumes. FRONTIERS IN PLANT SCIENCE 2022; 13:984700. [PMID: 36161025 PMCID: PMC9490089 DOI: 10.3389/fpls.2022.984700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 07/26/2022] [Indexed: 05/31/2023]
Abstract
Global food security, both in terms of quantity and quality remains as a challenge with the increasing population. In parallel, micronutrient deficiency in the human diet leads to malnutrition and several health-related problems collectively known as "hidden hunger" more prominent in developing countries around the globe. Biofortification is a potential tool to fortify grain legumes with micronutrients to mitigate the food and nutritional security of the ever-increasing population. Anti-nutritional factors like phytates, raffinose (RFO's), oxalates, tannin, etc. have adverse effects on human health upon consumption. Reduction of the anti-nutritional factors or preventing their accumulation offers opportunity for enhancing the intake of legumes in diet besides increasing the bioavailability of micronutrients. Integrated breeding methods are routinely being used to exploit the available genetic variability for micronutrients through modern "omic" technologies such as genomics, transcriptomics, ionomics, and metabolomics for developing biofortified grain legumes. Molecular mechanism of Fe/Zn uptake, phytate, and raffinose family oligosaccharides (RFOs) biosynthesis pathways have been elucidated. Transgenic, microRNAs and genome editing tools hold great promise for designing nutrient-dense and anti-nutrient-free grain legumes. In this review, we present the recent efforts toward manipulation of genes/QTLs regulating biofortification and Anti-nutrient accumulation in legumes using genetics-, genomics-, microRNA-, and genome editing-based approaches. We also discuss the success stories in legumes enrichment and recent advances in development of low Anti-nutrient lines. We hope that these emerging tools and techniques will expedite the efforts to develop micronutrient dense legume crop varieties devoid of Anti-nutritional factors that will serve to address the challenges like malnutrition and hidden hunger.
Collapse
Affiliation(s)
- Rintu Jha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Hemant Kumar Yadav
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rahul Raiya
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rajesh Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Uday Chand Jha
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India
| | - Lekshmy Sathee
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Prashant Singh
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Mahendar Thudi
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Samastipur, India
- Shandong Academy of Agricultural Sciences, Jinan, China
- Center for Crop Health, University of Southern Queensland, Toowmba, QLD, Australia
| | - Anshuman Singh
- College of Agriculture, Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh, India
| | - Sushil Kumar Chaturvedi
- College of Agriculture, Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh, India
| | - Shailesh Tripathi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| |
Collapse
|
10
|
Zhu H, Wang J, Jiang D, Hong Y, Xu J, Zheng S, Yang J, Chen W. The miR157-SPL-CNR module acts upstream of bHLH101 to negatively regulate iron deficiency responses in tomato. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1059-1075. [PMID: 35297168 DOI: 10.1111/jipb.13251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/14/2022] [Indexed: 05/23/2023]
Abstract
Iron (Fe) homeostasis is critical for plant growth, development, and stress responses. Fe levels are tightly controlled by intricate regulatory networks in which transcription factors (TFs) play a central role. A series of basic helix-loop-helix (bHLH) TFs have been shown to contribute to Fe homeostasis, but the regulatory layers beyond bHLH TFs remain largely unclear. Here, we demonstrate that the SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL) TF SlSPL-CNR negatively regulates Fe-deficiency responses in tomato (Solanum lycopersicum) roots. Fe deficiency rapidly repressed the expression of SlSPL-CNR, and Fe deficiency responses were intensified in two clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9-generated SlSPL-CNR knock-out lines compared to the wild-type. Comparative transcriptome analysis identified 47 Fe deficiency-responsive genes the expression of which is negatively regulated by SlSPL-CNR, one of which, SlbHLH101, helps regulate Fe uptake genes. SlSPL-CNR localizes the nucleus and interacts with the GTAC and BOX 4 (ATTAAT) motifs in the SlbHLH101 promoter to repress its expression. Inhibition of SlSPL-CNR expression in response to Fe deficiency was well correlated with the expression of the microRNA SlymiR157. SlymiR157-overexpressing tomato lines displayed enhanced Fe deficiency responses, as did SlSPL-CNR loss-of-function mutants. We propose that the SlymiR157-SlSPL-CNR module represents a novel pathway that acts upstream of SlbHLH101 to regulate Fe homeostasis in tomato roots.
Collapse
Affiliation(s)
- Huihui Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jiayi Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dan Jiang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Jiming Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shaojian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jianli Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Weiwei Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| |
Collapse
|
11
|
Perea-García A, Puig S, Peñarrubia L. The role of post-transcriptional modulators of metalloproteins in response to metal deficiencies. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1735-1750. [PMID: 34849747 DOI: 10.1093/jxb/erab521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Copper and iron proteins have a wide range of functions in living organisms. Metal assembly into metalloproteins is a complex process, where mismetalation is detrimental and energy consuming to cells. Under metal deficiency, metal distribution is expected to reach a metalation ranking, prioritizing essential versus dispensable metalloproteins, while avoiding interference with other metals and protecting metal-sensitive processes. In this review, we propose that post-transcriptional modulators of metalloprotein mRNA (ModMeR) are good candidates in metal prioritization under metal-limited conditions. ModMeR target high quota or redundant metalloproteins and, by adjusting their synthesis, ModMeR act as internal metal distribution valves. Inappropriate metalation of ModMeR targets could compete with metal delivery to essential metalloproteins and interfere with metal-sensitive processes, such as chloroplastic photosynthesis and mitochondrial respiration. Regulation of ModMeR targets could increase or decrease the metal flow through interconnected pathways in cellular metal distribution, helping to achieve adequate differential metal requirements. Here, we describe and compare ModMeR that function in response to copper and iron deficiencies. Specifically, we describe copper-miRNAs from Arabidopsis thaliana and diverse iron ModMeR from yeast, mammals, and bacteria under copper and iron deficiencies, as well as the influence of oxidative stress. Putative functions derived from their role as ModMeR are also discussed.
Collapse
Affiliation(s)
- Ana Perea-García
- Departament de Bioquímica i Biologia Molecular and Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, Burjassot, Valencia, Spain
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Sergi Puig
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Lola Peñarrubia
- Departament de Bioquímica i Biologia Molecular and Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, Burjassot, Valencia, Spain
| |
Collapse
|
12
|
MicroRNA Mediated Plant Responses to Nutrient Stress. Int J Mol Sci 2022; 23:ijms23052562. [PMID: 35269700 PMCID: PMC8910084 DOI: 10.3390/ijms23052562] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 01/18/2023] Open
Abstract
To complete their life cycles, plants require several minerals that are found in soil. Plant growth and development can be affected by nutrient shortages or high nutrient availability. Several adaptations and evolutionary changes have enabled plants to cope with inappropriate growth conditions and low or high nutrient levels. MicroRNAs (miRNAs) have been recognized for transcript cleavage and translational reduction, and can be used for post-transcriptional regulation. Aside from regulating plant growth and development, miRNAs play a crucial role in regulating plant’s adaptations to adverse environmental conditions. Additionally, miRNAs are involved in plants’ sensory functions, nutrient uptake, long-distance root transport, and physiological functions related to nutrients. It may be possible to develop crops that can be cultivated in soils that are either deficient in nutrients or have extreme nutrient supplies by understanding how plant miRNAs are associated with nutrient stress. In this review, an overview is presented regarding recent advances in the understanding of plants’ responses to nitrogen, phosphorus, potassium, sulfur, copper, iron, boron, magnesium, manganese, zinc, and calcium deficiencies via miRNA regulation. We conclude with future research directions emphasizing the modification of crops for improving future food security.
Collapse
|
13
|
Pagano L, Rossi R, Paesano L, Marmiroli N, Marmiroli M. miRNA regulation and stress adaptation in plants. ENVIRONMENTAL AND EXPERIMENTAL BOTANY 2021. [PMID: 0 DOI: 10.1016/j.envexpbot.2020.104369] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
|
14
|
Jin LF, Yarra R, Yin XX, Liu YZ, Cao HX. Identification and function prediction of iron-deficiency-responsive microRNAs in citrus leaves. 3 Biotech 2021; 11:121. [PMID: 33628708 PMCID: PMC7873142 DOI: 10.1007/s13205-021-02669-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/28/2021] [Indexed: 01/15/2023] Open
Abstract
Iron is a critical micronutrient for growth and development of plants and its deficiency limiting the crop productivity. MicroRNAs (miRNAs) play vital roles in adaptation of plants to various nutrient deficiencies. However, the role of miRNAs and their target genes related to Fe-deficiency is limited. In this study, we identified Fe-deficiency-responsive miRNAs from citrus. In Fe-deficiency conditions, about 50 and 31 miRNAs were up-regulated and down-regulated, respectively. The differently expressed miRNAs might play critical roles in contributing the Fe-deficiency tolerance in citrus plants. The miRNAs-mediated Fe-deficiency tolerance in citrus plants might related to the enhanced stress tolerance by decreased expression of miR172; regulation of S homeostasis by decreased expression of miR395; inhibition of plant growth by increased expression of miR319 and miR477; regulation of Cu homeostasis as well as activation of Cu/Zn superoxide dismutase activity due to decreased expression of miR398 and miR408 and regulation of lignin accumulation by decreased expression of miR397 and miR408. The identified miRNAs in present study laid a foundation to understand the Fe-deficiency adaptive mechanisms in citrus plants. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02669-z.
Collapse
Affiliation(s)
- Long-Fei Jin
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, 571339 Hainan China
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Rajesh Yarra
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, 571339 Hainan China
| | - Xin-Xing Yin
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, 571339 Hainan China
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Yong-Zhong Liu
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Hong-Xing Cao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, 571339 Hainan China
| |
Collapse
|
15
|
Lin Y, Chen Y, Zeng Y, Zhang S, Zhang Z, Chen Y, Gong J, Lai Z. Molecular characterization of miRNA genes and their expression in Dimocarpus longan Lour. PLANTA 2021; 253:41. [PMID: 33475870 DOI: 10.1007/s00425-021-03564-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 01/02/2021] [Indexed: 06/12/2023]
Abstract
A genome-wide analysis of longan miRNA genes was conducted, and full-length pri-miRNA transcripts were cloned. Bioinformatics and expression analyses contributed to the functional characterization of longan miRNA genes. MicroRNAs are important for the post-transcriptional regulation of target genes. However, little is known about the transcription and regulation of miRNA genes in longan (Dimocarpus longan Lour.). In this study, 80 miRNA precursors (pre-miRNA) were predicted, and their secondary structure, size, conservation, and diversity were analyzed. Furthermore, the full-length cDNA sequences of 13 longan primary miRNAs (pri-miRNAs) were amplified by RLM-RACE and SMART-RACE and analyzed, which revealed that longan pri-miRNA transcripts have multiple transcription start sites (TSSs) and the downstream pre-miRNAs are polymorphic. Accordingly, the longan pri-miRNAs and protein-encoding genes may have similar transcriptional specificities. An analysis of the longan miRNA gene promoter elements indicated that the three most abundant cis-acting elements were light-responsive, stress-responsive, and hormone-responsive elements. A quantitative real-time PCR assay elucidated the potential spatial and temporal expression patterns of longan pre-miRNAs during the early stages of somatic embryogenesis (SE) and in different longan organs/tissues. This is the first report regarding the molecular characterization of miRNA genes and their expression profiles in longan. The generated data may serve as a foundation for future research aimed at clarifying the longan miRNA gene functions.
Collapse
Affiliation(s)
- Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yan Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Youjing Zeng
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Shuting Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - YuKun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jiawei Gong
- Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| |
Collapse
|
16
|
Comparative Transcriptome Analysis of Iron and Zinc Deficiency in Maize ( Zea mays L.). PLANTS 2020; 9:plants9121812. [PMID: 33371388 PMCID: PMC7767415 DOI: 10.3390/plants9121812] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 11/30/2020] [Accepted: 11/30/2020] [Indexed: 11/17/2022]
Abstract
Globally, one-third of the population is affected by iron (Fe) and zinc (Zn) deficiency, which is severe in developing and underdeveloped countries where cereal-based diets predominate. The genetic biofortification approach is the most sustainable and one of the cost-effective ways to address Fe and Zn malnutrition. Maize is a major source of nutrition in sub-Saharan Africa, South Asia and Latin America. Understanding systems’ biology and the identification of genes involved in Fe and Zn homeostasis facilitate the development of Fe- and Zn-enriched maize. We conducted a genome-wide transcriptome assay in maize inbred SKV616, under –Zn, –Fe and –Fe–Zn stresses. The results revealed the differential expression of several genes related to the mugineic acid pathway, metal transporters, photosynthesis, phytohormone and carbohydrate metabolism. We report here Fe and Zn deficiency-mediated changes in the transcriptome, root length, stomatal conductance, transpiration rate and reduced rate of photosynthesis. Furthermore, the presence of multiple regulatory elements and/or the co-factor nature of Fe and Zn in enzymes indicate their association with the differential expression and opposite regulation of several key gene(s). The differentially expressed candidate genes in the present investigation would help in breeding for Fe and Zn efficient and kernel Fe- and Zn-rich maize cultivars through gene editing, transgenics and molecular breeding.
Collapse
|
17
|
Tang C, Han R, Zhou Z, Yang Y, Zhu M, Xu T, Wang A, Li Z, Dong T. Identification of candidate miRNAs related in storage root development of sweet potato by high throughput sequencing. JOURNAL OF PLANT PHYSIOLOGY 2020; 251:153224. [PMID: 32634748 DOI: 10.1016/j.jplph.2020.153224] [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: 02/11/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 05/16/2023]
Abstract
Sweet potato (Ipomoea batatas L.) is a food consumed worldwide, an industrial raw material and new energy crop. The storage root is the most economical part of the crop. However, the mechanism of storage root initiation and development is still unclear. In this study, conserved and novel miRNAs during storage root development were identified by high-throughput sequencing technology by constructing small RNA libraries from sweet potato fibrous roots (F) and storage roots at four different developmental stages (storage roots with different diameters: 1 cm, D1; 3 cm, D3; 5 cm, D5 and 10 cm, D10). A total of 61 known miRNAs and 471 novel miRNAs were identified. In addition, 145 differentially expressed miRNAs were identified in the F library compared with the four storage root libraries, with 30 known miRNAs and 115 novel miRNAs. Moreover, the targets of the differentially expressed miRNAs were predicted and their network was further investigated by GO analysis using our previous transcriptome data. The GO analysis revealed that antioxidant activity and binding process were the most enriched terms of the target genes. The secondary structure and expression of six candidate miRNAs including three conserved miRNAs and three novel miRNAs were investigated and their predicted targets were validated by qRT-PCR. The results showed that the expression levels of the miRNAs were all consistent with the sequencing data. Most of the miRNAs and their corresponding targets had obvious negative correlations. This study contributed to elucidating the potential miRNA mediated regulatory mechanism of storage root development in sweet potato. The specific differentially expressed miRNAs in sweet potato storage roots can be used to breed high-yield sweet potatoes and other tuberous root crops.
Collapse
Affiliation(s)
- Cheng Tang
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Rongpeng Han
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Zhengkun Zhou
- College of Health Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Yiyu Yang
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Mingku Zhu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Tao Xu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Aimin Wang
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Zongyun Li
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Tingting Dong
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| |
Collapse
|
18
|
Gupta OP, Pandey V, Saini R, Narwal S, Malik VK, Khandale T, Ram S, Singh GP. Identifying transcripts associated with efficient transport and accumulation of Fe and Zn in hexaploid wheat (T. aestivum L.). J Biotechnol 2020; 316:46-55. [PMID: 32305628 DOI: 10.1016/j.jbiotec.2020.03.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/06/2020] [Accepted: 03/28/2020] [Indexed: 11/26/2022]
Abstract
Wheat (T. aestivum L.) is the second most important staple food crop consumed in the form of various end-use products across the world. However, it contains lower concentrations of Fe and Zn leading to micronutrient deficiency in human beings where wheat is the sole diet. Therefore, increasing grain Fe/Zn content in wheat has become priority in wheat breeding programmes across the world. Understanding the molecular mechanism of Fe/Zn transport and accumulation in grains is required to expedite the breeding process. For this purpose, whole seedling transcriptome analysis was conducted in four wheat genotypes (CRP 1660, Sonora 64, Vinata, : high, and DBW17: low) differing in grain Fe/Zn content under controlled and Fe/Zn deficient conditions. Twenty eight key transcripts involved in phytosiderophore biosynthesis, Fe/Zn uptake and transport were identified. Expression analysis of 12 of the transcripts using qPCR was conducted in seedling stage and flag leaf which exhibited greater differential accumulation in CRP 1660 followed by Vinata, Sonora 64 and DBW 17 in both flag leaf and seedling. However, there was significantly higher differential accumulation of the transcripts in flag leaf as compared to seedling. In CRP 1660, transcripts pertaining to phytosiderophore biosynthesis like DMAS1-B, NRAMP2 and NAAT2-D showed greater accumulation. Additionally, corresponding miRNAs were also identified for these 28 transcripts. The findings will help in better understanding of molecular basis of Fe/Zn transport and accumulation in grain and subsequent utilization in breeding to improve Fe/Zn content in wheat grain.
Collapse
Affiliation(s)
- Om Prakash Gupta
- Division of Quality and Basic Sciences, ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, 132001, Haryana, India.
| | - Vanita Pandey
- Division of Quality and Basic Sciences, ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, 132001, Haryana, India.
| | - Ritu Saini
- Division of Quality and Basic Sciences, ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, 132001, Haryana, India.
| | - Sneh Narwal
- Division of Quality and Basic Sciences, ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, 132001, Haryana, India.
| | - Vipin Kumar Malik
- Division of Quality and Basic Sciences, ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, 132001, Haryana, India.
| | - Tushar Khandale
- Division of Quality and Basic Sciences, ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, 132001, Haryana, India.
| | - Sewa Ram
- Division of Quality and Basic Sciences, ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, 132001, Haryana, India.
| | - Gyanendra Pratap Singh
- Director, ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, 132001, Haryana, India.
| |
Collapse
|
19
|
|
20
|
Sánchez-Sanuy F, Peris-Peris C, Tomiyama S, Okada K, Hsing YI, San Segundo B, Campo S. Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus. BMC PLANT BIOLOGY 2019; 19:563. [PMID: 31852430 PMCID: PMC6921540 DOI: 10.1186/s12870-019-2156-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 11/21/2019] [Indexed: 05/14/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the post-transcriptional level in eukaryotes. In rice, MIR7695 expression is regulated by infection with the rice blast fungus Magnaporthe oryzae with subsequent down-regulation of an alternatively spliced transcript of natural resistance-associated macrophage protein 6 (OsNramp6). NRAMP6 functions as an iron transporter in rice. RESULTS Rice plants grown under high iron supply showed blast resistance, which supports that iron is a factor in controlling blast resistance. During pathogen infection, iron accumulated in the vicinity of M. oryzae appressoria, the sites of pathogen entry, and in cells surrounding infected regions of the rice leaf. Activation-tagged MIR7695 rice plants (MIR7695-Ac) exhibited enhanced iron accumulation and resistance to M. oryzae infection. RNA-seq analysis revealed that blast resistance in MIR7695-Ac plants was associated with strong induction of defense-related genes, including pathogenesis-related and diterpenoid biosynthetic genes. Levels of phytoalexins during pathogen infection were higher in MIR7695-Ac than wild-type plants. Early phytoalexin biosynthetic genes, OsCPS2 and OsCPS4, were also highly upregulated in wild-type rice plants grown under high iron supply. CONCLUSIONS Our data support a positive role of miR7695 in regulating rice immunity that further underpin links between defense and iron signaling in rice. These findings provides a basis to better understand regulatory mechanisms involved in rice immunity in which miR7695 participates which has a great potential for the development of strategies to improve blast resistance in rice.
Collapse
Affiliation(s)
- Ferran Sánchez-Sanuy
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| | - Cristina Peris-Peris
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| | - Shiho Tomiyama
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Kazunori Okada
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Yue-Ie Hsing
- Institute of Plant and Microrbial Biology, Academia Sinica, Taipei, Taiwan
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Sonia Campo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| |
Collapse
|
21
|
Grewal RK, Saraf S, Deb A, Kundu S. Differentially Expressed MicroRNAs Link Cellular Physiology to Phenotypic Changes in Rice Under Stress Conditions. PLANT & CELL PHYSIOLOGY 2018; 59:2143-2154. [PMID: 30010993 DOI: 10.1093/pcp/pcy136] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Indexed: 06/08/2023]
Abstract
Plant microRNAs (miRNAs) and their target genes have important functional roles in nutrition deficiency and stress response. However, the underlying mechanisms relating relative expression of miRNAs and target mRNAs to morphological adjustments are not well defined. By combining miRNA expression profiles, corresponding target genes and transcription factors that bind to computationally identified over-represented cis-regulatory elements (CREs) common in miRNAs and target gene promoters, we implement a strategy that identifies a set of differentially expressed regulatory interactions which, in turn, relate underlying cellular mechanisms to some of the phenotypic changes observed. Integration of experimentally reported individual interactions with identified regulatory interactions explains how (i) during mineral deficiency osa-miR167 inhibits shoot growth but activates adventitious root growth by influencing free auxin content; (ii) during sulfur deficiency osa-miR394 is involved in adventitious root growth inhibition, sulfur and iron homeostasis, and auxin-mediated regulation of sulfur homeostasis; (iii) osa-miR399 contributes to cross-talk between cytokinin and phosphorus deficiency signaling; and (iv) a feed-forward loop involving the osa-miR166, trihelix and HD-ZIP III transcription factors may regulate leaf senescence during drought. This strategy not only identifies various regulatory interactions connecting phenotypic changes with cellular or molecular events triggered by stress, but also provides a framework to deepen our understanding of stress cellular physiology.
Collapse
Affiliation(s)
- Rumdeep K Grewal
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
- Department of Botany, Bhairab Ganguly College, Kolkata, India
| | - Shradha Saraf
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Arindam Deb
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Sudip Kundu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| |
Collapse
|
22
|
Kakar KU, Nawaz Z, Cui Z, Cao P, Jin J, Shu Q, Ren X. Evolutionary and expression analysis of CAMTA gene family in Nicotiana tabacum yielded insights into their origin, expansion and stress responses. Sci Rep 2018; 8:10322. [PMID: 29985386 PMCID: PMC6037683 DOI: 10.1038/s41598-018-28148-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 06/18/2018] [Indexed: 02/06/2023] Open
Abstract
Calmodulin-binding transcription activators (CAMTAs) represent the novel gene family of transcriptional regulators, which play important biological functions. Though, the first ever plant CAMTA gene was evidenced in Nicotiana tabacum in 2002. But, the systematic identification, origin and function of this gene family has not been performed due to the lack of reference genome information until now. Here, we identified 29 CAMTA genes in four Nicotiana species, including thirteen NtabCAMTAs, six NsylCAMTAs, and five NtomCAMTAs and NbenCAMTAs. These CAMTA families were classified into five phylogenetic groups (I-V), among which, the group-IV CAMTAs probably emerged the earliest. The NtabCAMTA family genes have diverse structures, and are randomly localized on five chromosomes and scaffolds. N. tabacum acquired 11 copies of homolog CAMATA genes from the parental genomes of N. tomentosiformis and N. sylvestris, followed by expansion through polyploidization and duplication. The NtabCAMTA genes were differentially expressed in different plant parts, and showed sensitivity towards different abiotic and biotic stresses. Co-expression network analysis revealed that some NtabCAMTA subunits interact with each other, and co-expressed. The current study is the first report presenting a comprehensive overview of Nicotiana CAMTA families, and opens a new avenue for the improvement of the cultivated tobacco.
Collapse
Affiliation(s)
- Kaleem U Kakar
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, 550081, China
- State Key Laboratory of Rice Biology, Institution of Crop Science, Zhejiang University, Hangzhou, 310058, China
- Department of Microbiology, Faculty of Life Sciences & Informatics, Balochistan University of Information Technology, Engineering, and Management Sciences, Quetta, 87300, Pakistan
| | - Zarqa Nawaz
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, 550081, China
| | - Zhouqi Cui
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experimental Station, New haven, CT, 06511, USA
- Department of Biological Sciences, University of Wisconsin, Milwaukee, WI, 53211, USA
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Jingjing Jin
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Qingyao Shu
- State Key Laboratory of Rice Biology, Institution of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Xueliang Ren
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, 550081, China.
| |
Collapse
|
23
|
Locato V, Cimini S, De Gara L. ROS and redox balance as multifaceted players of cross-tolerance: epigenetic and retrograde control of gene expression. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3373-3391. [PMID: 29722828 DOI: 10.1093/jxb/ery168] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 04/27/2018] [Indexed: 05/07/2023]
Abstract
Retrograde pathways occurring between chloroplasts, mitochondria, and the nucleus involve oxidative and antioxidative signals that, working in a synergistic or antagonistic mode, control the expression of specific patterns of genes following stress perception. Increasing evidence also underlines the relevance of mitochondrion-chloroplast-nucleus crosstalk in modulating the whole cellular redox metabolism by a controlled and integrated flux of information. Plants can maintain the acquired tolerance by a stress memory, also operating at the transgenerational level, via epigenetic and miRNA-based mechanisms controlling gene expression. Data discussed in this review strengthen the idea that ROS, redox signals, and shifts in cellular redox balance permeate the signalling network leading to cross-tolerance. The identification of specific ROS/antioxidative signatures leading a plant to different fates under stress is pivotal for identifying strategies to monitor and increase plant fitness in a changing environment. This review provides an update of the plant redox signalling network implicated in stress responses, in particular in cross-tolerance acquisition. The interplay between reactive oxygen species (ROS), ROS-derived signals, and antioxidative pathways is also discussed in terms of plant acclimation to stress in the short and long term.
Collapse
Affiliation(s)
- Vittoria Locato
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University, Rome, Italy
| | - Sara Cimini
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University, Rome, Italy
| | - Laura De Gara
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University, Rome, Italy
| |
Collapse
|
24
|
Tian X, Song L, Wang Y, Jin W, Tong F, Wu F. miR394 Acts as a Negative Regulator of Arabidopsis Resistance to B. cinerea Infection by Targeting LCR. FRONTIERS IN PLANT SCIENCE 2018; 9:903. [PMID: 30018624 PMCID: PMC6037856 DOI: 10.3389/fpls.2018.00903] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/07/2018] [Indexed: 05/11/2023]
Abstract
Gray mold of tomato is caused by the pathogen Botrytis cinerea. MicroRNAs play a crucial role in the biotic and abiotic stress responses of plants and regulate their targets by gene silencing. miR394 is an ancient and conserved miRNA in plants, and it participates in the regulation of plant development and stress responses. In our previous study, miR394 was found to respond to B. cinerea infection in tomato, but the roles and regulatory mechanisms of miR394 in B. cinerea-infected tomato remain unclear. miR394 was down-regulated in tomato in response to B. cinerea infection, showing an expression pattern opposite to the previous finding that miR394 was up-regulated in tomato cv. Jinpeng 1 infected by B. cinerea. We obtained transgenic Arabidopsis overexpressing miR394, which resulted in low expression levels of its target LEAF CURLING RESPONSIVENESS (LCR). Leaf lesion size and trypan blue staining showed that miR394 overexpression led to increased sensitivity of transgenic Arabidopsis to B. cinerea compared to wild type. We also detected changes in the expression levels of stress-related miRNAs, including miR159, miR156, miR168, and miR172. In the transgenic plants, it indicated potential cross talk between these miRNAs and miR394, except for miR159. miR394 also enhanced the expression of ARGONAUTE 1 (AGO1), DSRNA-BINDING PROTEIN 4 (DRB4) and the RNA-binding protein gene DAWDLE (DDL), which are involved in the pathways of miRNA biosynthesis and regulation, suggesting that miR394 overexpression has a feedback effect on these genes. Our data indicate that overexpression of miR394 in Arabidopsis increased the susceptibility of plants to B. cinerea by affecting the expression of its target gene LCR along with a number of key genes involved in plant miRNA metabolism (AGO1). Thus, miR394 is a negative regulator of Arabidopsis resistance to B. cinerea infection by targeting LCR.
Collapse
Affiliation(s)
| | | | | | - Weibo Jin
- *Correspondence: Weibo Jin, Fudan Tong, Fangli Wu,
| | - Fudan Tong
- *Correspondence: Weibo Jin, Fudan Tong, Fangli Wu,
| | - Fangli Wu
- *Correspondence: Weibo Jin, Fudan Tong, Fangli Wu,
| |
Collapse
|
25
|
|
26
|
|
27
|
Li J, Yue L, Shen Y, Sheng Y, Zhan X, Xu G, Xing B. Phenanthrene-responsive microRNAs and their targets in wheat roots. CHEMOSPHERE 2017; 186:588-598. [PMID: 28818587 DOI: 10.1016/j.chemosphere.2017.08.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/14/2017] [Accepted: 08/06/2017] [Indexed: 05/07/2023]
Abstract
MicroRNAs (miRNAs) play key roles in plant growth, development and responses to abiotic stress. Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental pollutants. However, it is yet unknown how miRNAs work during PAH uptake by plant roots. Thus, in this study we ascertain phenanthrene (a model PAH)-responsive miRNAs using small RNA high-throughput deep sequencing and their target genes in wheat roots. We identified 108 conserved and non-conserved miRNA members belonging to 82 miRNA families and found 11 differentially expressed miRNAs, among which four miRNAs (miR156, miR164, miR171a and miR9678-3p) were up-regulated and the other seven miRNAs (miR398, miR531, miR1121, miR5048-5p, miR9653b, miR9773 and miR9778) were down-regulated. ABC-transporter-related Gene CA704421 and CA697226 did not respond to phenanthrene exposure. miR156 and miR164 might regulate directly the growth and development of wheat roots by targeting SPL and NAC, respectively. miR398 and miR1121 could regulate oxidative reactions to respond to phenanthrene stress. Additionally, miR9773 might involve phenanthrene metabolism through acting on CYP450. Therefore, it is concluded that phenanthrene triggers variation in miRNA expression, which is associated with uptake of and response to phenanthrene. These findings are of significance for further understanding miRNA regulation mechanisms on PAH uptake, and providing guidance for screening of resistant cultivars in crop production and phytoremediation of PAH-contaminated soils or water at genetic level.
Collapse
Affiliation(s)
- Jinfeng Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, People's Republic of China
| | - Le Yue
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, People's Republic of China; Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, United States
| | - Yu Shen
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, People's Republic of China; Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, United States
| | - Yu Sheng
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, People's Republic of China
| | - Xinhua Zhan
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, People's Republic of China.
| | - Guohua Xu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, People's Republic of China
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, United States.
| |
Collapse
|
28
|
Alptekin B, Langridge P, Budak H. Abiotic stress miRNomes in the Triticeae. Funct Integr Genomics 2017; 17:145-170. [PMID: 27665284 PMCID: PMC5383695 DOI: 10.1007/s10142-016-0525-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/02/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022]
Abstract
The continued growth in world population necessitates increases in both the quantity and quality of agricultural production. Triticeae members, particularly wheat and barley, make an important contribution to world food reserves by providing rich sources of carbohydrate and protein. These crops are grown over diverse production environments that are characterized by a range of environmental or abiotic stresses. Abiotic stresses such as drought, heat, salinity, or nutrient deficiencies and toxicities cause large yield losses resulting in economic and environmental damage. The negative effects of abiotic stresses have increased at an alarming rate in recent years and are predicted to further deteriorate due to climate change, land degradation, and declining water supply. New technologies have provided an important tool with great potential for improving crop tolerance to the abiotic stresses: microRNAs (miRNAs). miRNAs are small regulators of gene expression that act on many different molecular and biochemical processes such as development, environmental adaptation, and stress tolerance. miRNAs can act at both the transcriptional and post-transcriptional levels, although post-transcriptional regulation is the most common in plants where miRNAs can inhibit the translation of their mRNA targets via complementary binding and cleavage. To date, expression of several miRNA families such as miR156, miR159, and miR398 has been detected as responsive to environmental conditions to regulate stress-associated molecular mechanisms individually and/or together with their various miRNA partners. Manipulation of these miRNAs and their targets may pave the way to improve crop performance under several abiotic stresses. Here, we summarize the current status of our knowledge on abiotic stress-associated miRNAs in members of the Triticeae tribe, specifically in wheat and barley, and the miRNA-based regulatory mechanisms triggered by stress conditions. Exploration of further miRNA families together with their functions under stress will improve our knowledge and provide opportunities to enhance plant performance to help us meet global food demand.
Collapse
Affiliation(s)
- Burcu Alptekin
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Peter Langridge
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, Australia
| | - Hikmet Budak
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA.
| |
Collapse
|
29
|
Noman A, Aqeel M. miRNA-based heavy metal homeostasis and plant growth. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:10068-10082. [PMID: 28229383 DOI: 10.1007/s11356-017-8593-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 02/07/2017] [Indexed: 05/27/2023]
Abstract
Plants have been naturally gifted with mechanisms to adjust under very high or low nutrient concentrations. Heavy metal toxicity is considered as a major growth and yield-limiting factor for plants. This stress includes essential as well as non-essential metals. MicroRNAs (miRNAs) are known for mediating post-transcriptional regulation by cleaving transcripts or translational inhibition. It is commonly agreed that an extensive understanding of plant miRNAs will significantly help in the induction of tolerance against environmental stresses. With the introduction of the latest technology like next generation sequencing (NGS), a growing figure of miRNAs has been productively recognized in several plants for their diverse roles. These miRNAs are well-known modulators of plant responses to heavy metal (HM) stress. Data regarding metal-responsive miRNAs point out the vital role of plant miRNAs in supplementing metal detoxification by means of transcription factors (TF) or gene regulation. Acting as systemic signals, miRNAs also synchronize different physiological processes for plant responses to metal toxicities. In contrast to practicing techniques, using miRNA is a greatly helpful, pragmatic, and feasible approach. The earlier findings point towards miRNAs as a prospective target to engineer heavy metal tolerance in plants. Therefore, there is a need to augment our knowledge about the orchestrated functions of miRNAs during HM stress. We reviewed the deterministic significance of plant miRNAs in heavy metal tolerance and their role in mediating plant responses to HM toxicities. This review also summarized the topical developments by identification and validation of different metal stress-responsive miRNAs.
Collapse
Affiliation(s)
- Ali Noman
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, People's Republic of China.
| | - Muhammad Aqeel
- School of Life Sciences, Lanzhou University, Lanzhou, People's Republic of China
| |
Collapse
|
30
|
Genome-wide analysis of miRNAs and Tasi-RNAs in Zea mays in response to phosphate deficiency. Funct Integr Genomics 2017; 17:335-351. [PMID: 28070736 DOI: 10.1007/s10142-016-0538-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 11/28/2016] [Accepted: 12/05/2016] [Indexed: 12/12/2022]
Abstract
Globally important cereal crop maize provides important nutritions and starch in dietary foods. Low phosphate (LPi) availability in the soil frequently limits the maize quality and yield across the world. Small non-coding RNAs (Snc-RNAs) play crucial roles in growth and adaptation of plants to the environment. Snc-RNAs like microRNAs (miRs) and trans-acting small interfering RNAs (Tasi-Rs) play important functions in posttranscriptional regulation of gene expression, which controls plant development, reproduction, and biotic/abiotic stress responses. In order to identify the miR and Tasi-R alterations in leaf and root of maize in response to sufficient phosphate and LPi at 3LS and 4LS, the snc-RNA population libraries for 0th, 1st, 2nd, 4th, and 8th day were constructed. These libraries were used for genome-wide alignment and RNA-fold analysis for possible prediction of potential miRs and Tasi-Rs. This study reported 174 known and conserved differentially expressed miRs of 27 miR families of maize plant. In addition, leaf and root specific potential novel miRs representing 155 new families were also discovered. Differentially expressed conserved as well as novel miR functions in root and leaf during early stage of Pi starvation were extensively discussed. Leaf and root specific miRs as well as common miRs with their target genes, participating in different biological, cellular, and metabolic processes were explored. Further, four miR390-directed Tasi-Rs which belong to TAS3 gene family along with other orthologs of Tasi-Rs were also identified. Finally, the study provides an insight into the composite regulatory mechanism of miRs in maize in response to Pi deficiency.
Collapse
|
31
|
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.
Collapse
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,
| |
Collapse
|
32
|
Nie Z, Ren Z, Wang L, Su S, Wei X, Zhang X, Wu L, Liu D, Tang H, Liu H, Zhang S, Gao S. Genome-wide identification of microRNAs responding to early stages of phosphate deficiency in maize. PHYSIOLOGIA PLANTARUM 2016; 157:161-74. [PMID: 26572939 DOI: 10.1111/ppl.12409] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 10/03/2015] [Accepted: 10/08/2015] [Indexed: 05/18/2023]
Abstract
Phosphorus (P) is an essential element involved in numerous biochemical reactions. In plants, stress responses, such as the expression of microRNAs (miRNAs), are induced to help them adapt to low phosphate (Pi) concentrations. In this study, deep sequencing was performed using the roots and leaves of maize seedlings grown under low Pi concentrations to identify miRNAs that are differentially expressed during the early stages of Pi deficiency. Eight small RNA libraries were constructed, and 159 known miRNAs representing 32 miRNA families and 10 novel miRNAs. Members of the miR396 family were extremely abundant. Further, 28 Pi-responsive miRNAs were identified (27 known and 1 novel) of which 8 and 7 were significantly expressed exclusively in leaf and root tissues, respectively. The analysis of Pi-responsive miRNAs target genes suggested that most target genes functioning as transcription factors were involved in root and leaf development. The expression profiles of selected Pi-responsive miRNAs and target genes were confirmed by quantitative real-time polymerase chain reaction (qRT-PCR). Moreover, we discuss the significance of the differences in expression patterns of these miRNAs during the early and later stages of Pi starvation. This study provides useful information concerning the role of miRNAs in response to Pi starvation and will further our understanding of the mechanisms governing Pi homeostasis in maize.
Collapse
Affiliation(s)
- Zhi Nie
- Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhiyong Ren
- Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Libo Wang
- Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shunzong Su
- Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xuan Wei
- Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiao Zhang
- Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ling Wu
- Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Dan Liu
- Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Haitao Tang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Hailan Liu
- Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Suzhi Zhang
- Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shibin Gao
- Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| |
Collapse
|
33
|
Ma CL, Qi YP, Liang WW, Yang LT, Lu YB, Guo P, Ye X, Chen LS. MicroRNA Regulatory Mechanisms on Citrus sinensis leaves to Magnesium-Deficiency. FRONTIERS IN PLANT SCIENCE 2016; 7:201. [PMID: 26973661 PMCID: PMC4778066 DOI: 10.3389/fpls.2016.00201] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 02/05/2016] [Indexed: 05/06/2023]
Abstract
Magnesium (Mg)-deficiency, which affects crop productivity and quality, widespreadly exists in many agricultural crops, including citrus. However, very limited data are available on Mg-deficiency-responsive microRNAs (miRNAs) in higher plants. Using Illumina sequencing, we isolated 75 (73 known and 2 novel) up- and 71 (64 known and 7 novel) down-regulated miRNAs from Mg-deficient Citrus sinensis leaves. In addition to the remarkable metabolic flexibility as indicated by the great alteration of miRNA expression, the adaptive responses of leaf miRNAs to Mg-deficiency might also involve the following several aspects: (a) up-regulating stress-related genes by down-regulating miR164, miR7812, miR5742, miR3946, and miR5158; (b) enhancing cell transport due to decreased expression of miR3946 and miR5158 and increased expression of miR395, miR1077, miR1160, and miR8019; (c) activating lipid metabolism-related genes by repressing miR158, miR5256, and miR3946; (d) inducing cell wall-related gene expansin 8A by repressing miR779; and (e) down-regulating the expression of genes involved in the maintenance of S, K and Cu by up-regulating miR395 and miR6426. To conclude, we isolated some new known miRNAs (i.e., miR7812, miR8019, miR6218, miR1533, miR6426, miR5256, miR5742, miR5561, miR5158, and miR5818) responsive to nutrient deficiencies and found some candidate miRNAs that might contribute to Mg-deficiency tolerance. Therefore, our results not only provide novel information about the responses of plant to Mg-deficiency, but also are useful for obtaining the key miRNAs for plant Mg-deficiency tolerance.
Collapse
Affiliation(s)
- Cui-Lan Ma
- Institute of Plant Nutritional Physiology and Molecular Biology, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Life Science, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Yi-Ping Qi
- Institute of Materia Medica, Fujian Academy of Medical SciencesFuzhou, China
| | - Wei-Wei Liang
- Institute of Plant Nutritional Physiology and Molecular Biology, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Resource and Environmental Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Lin-Tong Yang
- Institute of Plant Nutritional Physiology and Molecular Biology, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Resource and Environmental Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Yi-Bin Lu
- Institute of Plant Nutritional Physiology and Molecular Biology, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Resource and Environmental Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Peng Guo
- Institute of Plant Nutritional Physiology and Molecular Biology, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Resource and Environmental Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Xin Ye
- Institute of Plant Nutritional Physiology and Molecular Biology, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Resource and Environmental Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Li-Song Chen
- Institute of Plant Nutritional Physiology and Molecular Biology, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Resource and Environmental Science, Fujian Agriculture and Forestry UniversityFuzhou, China
- The Higher Educational Key Laboratory of Fujian Province for Soil Ecosystem Health and Regulation, Fujian Agriculture and Forestry UniversityFuzhou, China
- Fujian Key Laboratory for Plant Molecular and Cell Biology, Fujian Agriculture and Forestry UniversityFuzhou, China
| |
Collapse
|
34
|
Lu YB, Qi YP, Yang LT, Guo P, Li Y, Chen LS. Boron-deficiency-responsive microRNAs and their targets in Citrus sinensis leaves. BMC PLANT BIOLOGY 2015; 15:271. [PMID: 26538180 PMCID: PMC4634795 DOI: 10.1186/s12870-015-0642-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 10/08/2015] [Indexed: 05/22/2023]
Abstract
BACKGROUND MicroRNAs play important roles in the adaptive responses of plants to nutrient deficiencies. Most research, however, has focused on nitrogen (N), phosphorus (P), sulfur (S), copper (Cu) and iron (Fe) deficiencies, limited data are available on the differential expression of miRNAs and their target genes in response to deficiencies of other nutrient elements. In this study, we identified the known and novel miRNAs as well as the boron (B)-deficiency-responsive miRNAs from citrus leaves in order to obtain the potential miRNAs related to the tolerance of citrus to B-deficiency. METHODS Seedlings of 'Xuegan' [Citrus sinensis (L.) Osbeck] were supplied every other day with B-deficient (0 μM H3BO3) or -sufficient (10 μM H3BO3) nutrient solution for 15 weeks. Thereafter, we sequenced two small RNA libraries from B-deficient and -sufficient (control) citrus leaves, respectively, using Illumina sequencing. RESULTS Ninety one (83 known and 8 novel) up- and 81 (75 known and 6 novel) down-regulated miRNAs were isolated from B-deficient leaves. The great alteration of miRNA expression might contribute to the tolerance of citrus to B-deficiency. The adaptive responses of miRNAs to B-deficiency might related to several aspects: (a) attenuation of plant growth and development by repressing auxin signaling due to decreased TIR1 level and ARF-mediated gene expression by altering the expression of miR393, miR160 and miR3946; (b) maintaining leaf phenotype and enhancing the stress tolerance by up-regulating NACs targeted by miR159, miR782, miR3946 and miR7539; (c) activation of the stress responses and antioxidant system through down-regulating the expression of miR164, miR6260, miR5929, miR6214, miR3946 and miR3446; (d) decreasing the expression of major facilitator superfamily protein genes targeted by miR5037, thus lowering B export from plants. Also, B-deficiency-induced down-regulation of miR408 might play a role in plant tolerance to B-deficiency by regulating Cu homeostasis and enhancing superoxide dismutase activity. CONCLUSIONS Our study reveals some novel responses of citrus to B-deficiency, which increase our understanding of the adaptive mechanisms of citrus to B-deficiency at the miRNA (post-transcriptional) level.
Collapse
Affiliation(s)
- Yi-Bin Lu
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yi-Ping Qi
- Institute of Materia Medica, Fujian Academy of Medical Sciences, Fuzhou, 350001, China.
| | - Lin-Tong Yang
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Peng Guo
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Yan Li
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Li-Song Chen
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- The Higher Educational Key Laboratory of Fujian Province for Soil Ecosystem Health and Regulation, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Fujian Key Laboratory for Plant Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
35
|
Neto LB, Arenhart RA, de Oliveira LFV, de Lima JC, Bodanese-Zanettini MH, Margis R, Margis-Pinheiro M. ASR5 is involved in the regulation of miRNA expression in rice. PLANT CELL REPORTS 2015; 34:1899-1907. [PMID: 26183952 DOI: 10.1007/s00299-015-1836-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 06/25/2015] [Accepted: 06/30/2015] [Indexed: 06/04/2023]
Abstract
The work describes an ASR knockdown transcriptomic analysis by deep sequencing of rice root seedlings and the transactivation of ASR cis-acting elements in the upstream region of a MIR gene. MicroRNAs are key regulators of gene expression that guide post-transcriptional control of plant development and responses to environmental stresses. ASR (ABA, Stress and Ripening) proteins are plant-specific transcription factors with key roles in different biological processes. In rice, ASR proteins have been suggested to participate in the regulation of stress response genes. This work describes the transcriptomic analysis by deep sequencing two libraries, comparing miRNA abundance from the roots of transgenic ASR5 knockdown rice seedlings with that of the roots of wild-type non-transformed rice seedlings. Members of 59 miRNA families were detected, and 276 mature miRNAs were identified. Our analysis detected 112 miRNAs that were differentially expressed between the two libraries. A predicted inverse correlation between miR167abc and its target gene (LOC_Os07g29820) was confirmed using RT-qPCR. Protoplast transactivation assays showed that ASR5 is able to recognize binding sites upstream of the MIR167a gene and drive its expression in vivo. Together, our data establish a comparative study of miRNAome profiles and is the first study to suggest the involvement of ASR proteins in miRNA gene regulation.
Collapse
Affiliation(s)
- Lauro Bücker Neto
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, prédio 43312, Porto Alegre, RS, 91501-970, Brazil.
| | - Rafael Augusto Arenhart
- Centro Nacional de Pesquisa de Uva e Vinho, Empresa Brasileira de Pesquisa Agropecuária, Rua Livramento 515, Bento Gonçalves, RS, 95700-000, Brazil.
| | - Luiz Felipe Valter de Oliveira
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, prédio 43431, Porto Alegre, RS, 91501-970, Brazil.
| | - Júlio Cesar de Lima
- Universidade de Passo Fundo, Laboratório de Genética Molecular, BR285, Passo Fundo, RS, 99052-900, Brazil.
| | - Maria Helena Bodanese-Zanettini
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, prédio 43312, Porto Alegre, RS, 91501-970, Brazil.
| | - Rogerio Margis
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, prédio 43431, Porto Alegre, RS, 91501-970, Brazil.
| | - Márcia Margis-Pinheiro
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, prédio 43312, Porto Alegre, RS, 91501-970, Brazil.
| |
Collapse
|
36
|
Aung B, Gruber MY, Hannoufa A. The MicroRNA156 system: A tool in plant biotechnology. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2015. [DOI: 10.1016/j.bcab.2015.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
37
|
Swapna KS, Salim N, Chandra R, Puthur JT. Structural changes in response to bioaccumulation of iron and mercury in Chromolaena odorata (L.) King & Robins. ENVIRONMENTAL MONITORING AND ASSESSMENT 2015; 187:551. [PMID: 26239568 DOI: 10.1007/s10661-015-4732-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 07/07/2015] [Indexed: 06/04/2023]
Abstract
A comparative study was designed to elucidate the effect of iron and mercury on the morphological and anatomical changes as well as bioaccumulation potential in Chromolaena odorata. Plants were grown in half-strength Hoagland nutrient medium artificially contaminated with known quantities of HgCl2 (15 μM) and FeCl3 (1000 μM). Bioaccumulation of Hg and Fe was maximum in the root, and comparatively reduced bioaccumulation was recorded in the stem and leaves. Microscopic studies on morphology and anatomy revealed development of trichomes and lenticels on the stem and modified trichomes on leaves. Localized deposits of stained masses in various internal parts of the root, stem and leaf also were observed. Differential adaptation/strategy of C. odorata to attain tolerance towards Hg and Fe and phytoremediation potential of the plant is discussed.
Collapse
Affiliation(s)
- K S Swapna
- Plant Physiology and Biochemistry Division, Department of Botany, University of Calicut, C.U. Campus P.O., Kerala, 673635, India
| | | | | | | |
Collapse
|
38
|
Mai HJ, Lindermayr C, von Toerne C, Fink-Straube C, Durner J, Bauer P. Iron and FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR-dependent regulation of proteins and genes in Arabidopsis thaliana
roots. Proteomics 2015; 15:3030-47. [DOI: 10.1002/pmic.201400351] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 03/10/2015] [Accepted: 04/30/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Hans-Jörg Mai
- Institute of Botany; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Christian Lindermayr
- Helmholtz Zentrum München (GmbH); German Research Center for Environmental Health; Institute of Biochemical Plant Pathology (BIOP); Neuherberg Germany
| | - Christine von Toerne
- Research Unit Protein Science; Helmholtz Zentrum München (GmbH); German Research Center for Environmental Health; Neuherberg Germany
| | | | - Jörg Durner
- Helmholtz Zentrum München (GmbH); German Research Center for Environmental Health; Institute of Biochemical Plant Pathology (BIOP); Neuherberg Germany
| | - Petra Bauer
- Institute of Botany; Heinrich Heine University Düsseldorf; Düsseldorf Germany
- CEPLAS Cluster of Excellence on Plant Sciences; Heinrich Heine Universität Düsseldorf; Düsseldorf Germany
| |
Collapse
|
39
|
Jung IL, Ryu M, Cho SK, Shah P, Lee JH, Bae H, Kim IG, Yang SW. Cesium Toxicity Alters MicroRNA Processing and AGO1 Expressions in Arabidopsis thaliana. PLoS One 2015; 10:e0125514. [PMID: 25946015 PMCID: PMC4422737 DOI: 10.1371/journal.pone.0125514] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/13/2015] [Indexed: 01/21/2023] Open
Abstract
MicroRNAs (miRNAs) are short RNA fragments that play important roles in controlled gene silencing, thus regulating many biological processes in plants. Recent studies have indicated that plants modulate miRNAs to sustain their survival in response to a variety of environmental stimuli, such as biotic stresses, cold, drought, nutritional starvation, and toxic heavy metals. Cesium and radio-cesium contaminations have arisen as serious problems that both impede plant growth and enter the food chain through contaminated plants. Many studies have been performed to define plant responses against cesium intoxication. However, the complete profile of miRNAs in plants during cesium intoxication has not been established. Here we show the differential expression of the miRNAs that are mostly down-regulated during cesium intoxication. Furthermore, we found that cesium toxicity disrupts both the processing of pri-miRNAs and AGONOUTE 1 (AGO1)-mediated gene silencing. AGO 1 seems to be especially destabilized by cesium toxicity, possibly through a proteolytic regulatory pathway. Our study presents a comprehensive profile of cesium-responsive miRNAs, which is distinct from that of potassium, and suggests two possible mechanisms underlying the cesium toxicity on miRNA metabolism.
Collapse
Affiliation(s)
- Il Lae Jung
- Department of Radiation Biology, Environmental Radiation Research Group, Korea Atomic Energy Research Institute, Daejeon, 305–353, Republic of Korea
| | - Moonyoung Ryu
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg, Copenhagen, Denmark
| | - Seok Keun Cho
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg, Copenhagen, Denmark
| | - Pratik Shah
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg, Copenhagen, Denmark
| | - Ju Hye Lee
- Department of Radiation Biology, Environmental Radiation Research Group, Korea Atomic Energy Research Institute, Daejeon, 305–353, Republic of Korea
| | - Hansol Bae
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg, Copenhagen, Denmark
| | - In Gyu Kim
- Department of Radiation Biology, Environmental Radiation Research Group, Korea Atomic Energy Research Institute, Daejeon, 305–353, Republic of Korea
| | - Seong Wook Yang
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg, Copenhagen, Denmark
| |
Collapse
|
40
|
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.
Collapse
Affiliation(s)
| | | | - Karabi Datta
- Translational Research Laboratory of Transgenic Rice, Department of Botany, University of CalcuttaKolkata, India
| |
Collapse
|
41
|
Zhang B. MicroRNA: a new target for improving plant tolerance to abiotic stress. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1749-61. [PMID: 25697792 PMCID: PMC4669559 DOI: 10.1093/jxb/erv013] [Citation(s) in RCA: 284] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 12/14/2014] [Accepted: 12/17/2014] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are an extensive class of endogenous, small RNA molecules that sit at the heart of regulating gene expression in multiple developmental and signalling pathways. Recent studies have shown that abiotic stresses induce aberrant expression of many miRNAs, thus suggesting that miRNAs may be a new target for genetically improving plant tolerance to certain stresses. These studies have also shown that miRNAs respond to environmental stresses in a miRNA-, stress-, tissue-, and genotype-dependent manner. During abiotic stress, miRNAs function by regulating target genes within the miRNA-target gene network and by controlling signalling pathways and root development. Generally speaking, stress-induced miRNAs lead to down-regulation of negative regulators of stress tolerance whereas stress-inhibited miRNAs allow the accumulation and function of positive regulators. Currently, the majority of miRNA-based studies have focused on the identification of miRNAs that are responsive to different stress conditions and analysing their expression profile changes during these treatments. This has predominately been accomplished using deep sequencing technologies and other expression analyses, such as quantitative real-time PCR. In the future, more function and expression studies will be necessary in order to elucidate the common miRNA-mediated regulatory mechanisms that underlie tolerance to different abiotic stresses. The use of artificial miRNAs, as well as overexpression and knockout/down of both miRNAs and their targets, will be the best techniques for determining the specific roles of individual miRNAs in response to environmental stresses.
Collapse
Affiliation(s)
- Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| |
Collapse
|
42
|
Ferdous J, Hussain SS, Shi BJ. Role of microRNAs in plant drought tolerance. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:293-305. [PMID: 25583362 PMCID: PMC6680329 DOI: 10.1111/pbi.12318] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Revised: 11/27/2014] [Accepted: 11/29/2014] [Indexed: 05/19/2023]
Abstract
Drought is a normal and recurring climate feature in most parts of the world and plays a major role in limiting crop productivity. However, plants have their own defence systems to cope with adverse climatic conditions. One of these defence mechanisms is the reprogramming of gene expression by microRNAs (miRNAs). miRNAs are small noncoding RNAs of approximately 22 nucleotides length, which have emerged as important regulators of genes at post-transcriptional levels in a range of organisms. Some miRNAs are functionally conserved across plant species and are regulated by drought stress. These properties suggest that miRNA-based genetic modifications have the potential to enhance drought tolerance in cereal crops. This review summarizes the current understanding of the regulatory mechanisms of plant miRNAs, involvement of plant miRNAs in drought stress responses in barley (Hordeum vulgare L.), wheat (Triticum spp.) and other plant species, and the involvement of miRNAs in plant-adaptive mechanisms under drought stress. Potential strategies and directions for future miRNA research and the utilization of miRNAs in the improvement of cereal crops for drought tolerance are also discussed.
Collapse
Affiliation(s)
- Jannatul Ferdous
- Australian Centre for Plant Functional Genomics, The University of Adelaide, Urrbrae, SA, Australia
| | | | | |
Collapse
|
43
|
Jin W, Wu F. Characterization of miRNAs associated with Botrytis cinerea infection of tomato leaves. BMC PLANT BIOLOGY 2015; 15:1. [PMID: 25592487 PMCID: PMC4311480 DOI: 10.1186/s12870-014-0410-4] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 12/30/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Botrytis cinerea Pers. Fr. is an important pathogen causing stem rot in tomatoes grown indoors for extended periods. MicroRNAs (miRNAs) have been reported as gene expression regulators related to several stress responses and B. cinerea infection in tomato. However, the function of miRNAs in the resistance to B. cinerea remains unclear. RESULTS The miRNA expression patterns in tomato in response to B. cinerea stress were investigated by high-throughput sequencing. In total, 143 known miRNAs and seven novel miRNAs were identified and their corresponding expression was detected in mock- and B. cinerea-inoculated leaves. Among those, one novel and 57 known miRNAs were differentially expressed in B. cinerea-infected leaves, and 8 of these were further confirmed by quantitative reverse-transcription PCR (qRT-PCR). Moreover, five of these eight differentially expressed miRNAs could hit 10 coding sequences (CDSs) via CleaveLand pipeline and psRNAtarget program. In addition, qRT-PCR revealed that four targets were negatively correlated with their corresponding miRNAs (miR319, miR394, and miRn1). CONCLUSION Results of sRNA high-throughput sequencing revealed that the upregulation of miRNAs may be implicated in the mechanism by which tomato respond to B. cinerea stress. Analysis of the expression profiles of B. cinerea-responsive miRNAs and their targets strongly suggested that miR319, miR394, and miRn1 may be involved in the tomato leaves' response to B. cinerea infection.
Collapse
Affiliation(s)
- Weibo Jin
- College of Life Science, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China.
| | - Fangli Wu
- College of Life Science, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China.
| |
Collapse
|
44
|
Feng H, Wang B, Zhang Q, Fu Y, Huang L, Wang X, Kang Z. Exploration of microRNAs and their targets engaging in the resistance interaction between wheat and stripe rust. FRONTIERS IN PLANT SCIENCE 2015; 6:469. [PMID: 26175740 PMCID: PMC4485317 DOI: 10.3389/fpls.2015.00469] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 06/12/2015] [Indexed: 05/02/2023]
Abstract
Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat worldwide. miRNAs are important regulators, they play very central roles in plant organ development, vegetable phase change and defense responses. In this study, two miRNA libraries from wheat cultivar Xingzi 9104 (XZ) challenged with the avirulent Pst race CYR32 and sterile water were constructed, respectively. A total of 596 miRNA candidates were obtained. 420 wheat-specific candidate miRNAs were screened in adult plants challenged with Pst using microarray-based analyses. We analyzed the abundance of candidate miRNAs, and the levels of a subset of candidate miRNAs were determined by quantitative real time PCR (qRT-PCR). The qRT-PCR results indicated that some miRNAs were involved in the incompatible interaction between wheat and Pst. In addition, we identified some miRNAs differentially expressed in different leaves. Additionally, the target genes of wheat miRNAs were confirmed by using degradome sequencing technology. Most of the annotated target genes are related to signal transduction, energy metabolism, and other functions. We selected some target genes for relative expression analysis using qRT-PCR, and found that RabGAP/TBC domain-containing protein, zinc finger protein and Cysteine-rich receptor-like protein kinase 41 may play important role in the incompatible interaction between XZ and CYR32. Intriguingly, miRNAs and target gene seem to form a complicated regulation network that regulates the wheat-Pst interaction. Our data provide the foundation for evaluating the important regulatory roles of miRNAs in the wheat-Pst interaction.
Collapse
Affiliation(s)
- Hao Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Bing Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Qiong Zhang
- College of Life Sciences, Northwest A&F UniversityYangling, China
| | - Yanping Fu
- College of Life Sciences, Northwest A&F UniversityYangling, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China
- *Correspondence: Zhensheng Kang and Xiaojie Wang, State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3#, Yangling, Shaanxi 712100, China ;
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China
- *Correspondence: Zhensheng Kang and Xiaojie Wang, State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3#, Yangling, Shaanxi 712100, China ;
| |
Collapse
|
45
|
Li H, Wang L, Yang ZM. Co-expression analysis reveals a group of genes potentially involved in regulation of plant response to iron-deficiency. Gene 2014; 554:16-24. [PMID: 25300251 DOI: 10.1016/j.gene.2014.10.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 10/01/2014] [Accepted: 10/03/2014] [Indexed: 10/24/2022]
Abstract
Iron (Fe) is an essential element for plant growth and development. Iron deficiency results in abnormal metabolisms from respiration to photosynthesis. Exploration of Fe-deficient responsive genes and their networks is critically important to understand molecular mechanisms leading to the plant adaptation to soil Fe-limitation. Co-expression genes are a cluster of genes that have a similar expression pattern to execute relatively biological functions at a stage of development or under a certain environmental condition. They may share a common regulatory mechanism. In this study, we investigated Fe-starved-related co-expression genes from Arabidopsis. From the biological process GO annotation of TAIR (The Arabidopsis Information Resource), 180 iron-deficient responsive genes were detected. Using ATTED-II database, we generated six gene co-expression networks. Among these, two modules of PYE and IRT1 were successfully constructed. There are 30 co-expression genes that are incorporated in the two modules (12 in PYE-module and 18 in IRT1-module). Sixteen of the co-expression genes were well characterized. The remaining genes (14) are poorly or not functionally identified with iron stress. Validation of the 14 genes using real-time PCR showed differential expression under iron-deficiency. Most of the co-expression genes (23/30) could be validated in pye and fit mutant plants with iron-deficiency. We further identified iron-responsive cis-elements upstream of the co-expression genes and found that 22 out of 30 genes contain the iron-responsive motif IDE1. Furthermore, some auxin and ethylene-responsive elements were detected in the promoters of the co-expression genes. These results suggest that some of the genes can be also involved in iron stress response through the phytohormone-responsive pathways.
Collapse
Affiliation(s)
- Hua Li
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China; Department of Plant Science, College of Life Science, Henan Agricultural University, Henan 450002, China
| | - Lei Wang
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhi Min Yang
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
46
|
Lu YB, Yang LT, Qi YP, Li Y, Li Z, Chen YB, Huang ZR, Chen LS. Identification of boron-deficiency-responsive microRNAs in Citrus sinensis roots by Illumina sequencing. BMC PLANT BIOLOGY 2014; 14:123. [PMID: 24885979 PMCID: PMC4041134 DOI: 10.1186/1471-2229-14-123] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 04/30/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Boron (B)-deficiency is a widespread problem in many crops, including Citrus. MicroRNAs (miRNAs) play important roles in nutrient deficiencies. However, little is known on B-deficiency-responsive miRNAs in plants. In this study, we first identified miRNAs and their expression pattern in B-deficient Citrus sinensis roots by Illumina sequencing in order to identify miRNAs that might be involved in the tolerance of plants to B-deficiency. RESULTS We isolated 52 (40 known and 12 novel) up-regulated and 82 (72 known and 10 novel) down-regulated miRNAs from B-deficient roots, demonstrating remarkable metabolic flexibility of roots, which might contribute to the tolerance of plants to B-deficiency. A model for the possible roles of miRNAs in the tolerance of roots to B-deficiency was proposed. miRNAs might regulate the adaptations of roots to B-deficiency through following several aspects: (a) inactivating reactive oxygen species (ROS) signaling and scavenging through up-regulating miR474 and down-regulating miR782 and miR843; (b) increasing lateral root number by lowering miR5023 expression and maintaining a certain phenotype favorable for B-deficiency-tolerance by increasing miR394 expression; (c) enhancing cell transport by decreasing the transcripts of miR830, miR5266 and miR3465; (d) improving osmoprotection (miR474) and regulating other metabolic reactions (miR5023 and miR821). Other miRNAs such as miR472 and miR2118 in roots increased in response to B-deficiency, thus decreasing the expression of their target genes, which are involved in disease resistance, and hence, the disease resistance of roots. CONCLUSIONS Our work demonstrates the possible roles of miRNAs and related mechanisms in the response of plant roots to B-deficiency.
Collapse
Affiliation(s)
- Yi-Bin Lu
- College of Resources and Environmental Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lin-Tong Yang
- College of Resources and Environmental Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yi-Ping Qi
- Institute of Materia Medica, Fujian Academy of Medical Sciences, Fuzhou 350001, China
| | - Yan Li
- College of Resources and Environmental Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhong Li
- College of Resources and Environmental Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yan-Bin Chen
- College of Resources and Environmental Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zeng-Rong Huang
- College of Resources and Environmental Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Li-Song Chen
- College of Resources and Environmental Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Key Laboratory for Plant Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| |
Collapse
|
47
|
Matsuoka K, Furukawa J, Bidadi H, Asahina M, Yamaguchi S, Satoh S. Gibberellin-Induced Expression of Fe Uptake-Related Genes in Arabidopsis. ACTA ACUST UNITED AC 2013; 55:87-98. [DOI: 10.1093/pcp/pct160] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
48
|
Song JB, Gao S, Sun D, Li H, Shu XX, Yang ZM. miR394 and LCR are involved in Arabidopsis salt and drought stress responses in an abscisic acid-dependent manner. BMC PLANT BIOLOGY 2013; 13:210. [PMID: 24330668 PMCID: PMC3870963 DOI: 10.1186/1471-2229-13-210] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 12/05/2013] [Indexed: 05/19/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are a class of short, endogenous non-coding small RNAs that have ability to base pair with their target mRNAs to induce their degradation in plants. miR394a/b are conserved small RNAs and its target gene LCR (LEAF CURLING RESPONSIVENESS) encodes an F-box protein (SKP1-Cullin/CDC53-F-box) but whether miR394a/b and its target gene LCR are involved in regulation of plant response to abscisic acid (ABA) and abiotic stresses is unknown. RESULTS Mature miR394 and precursor miR394a/b are shown to be slightly induced by ABA. By contrast, LCR expression is depressed by ABA. Analysis of LCR and its promoter (pLCR::GUS) revealed that LCR is expressed at all development stages. MIR394a/b over-expression (35S::MIR394a/b) and lcr (LCR loss of function) mutant plants are hypersensitive to salt stress, but LCR over-expressing (35S::m5LCR) plants display the salt-tolerant phenotype. Both 35S::MIR394a/b and lcr plants are highly tolerant to severe drought stress compared with wild-type, but 35S::m5LCR plants are susceptible to water deficiency. Over-expression of MIR394a/b led to ABA hypersensitivity and ABA-associated phenotypes, whereas 35S::m5LCR plants show ABA resistance phenotypes. Moreover, 35S::MIR394a/b plants accumulated higher levels of ABA-induced hydrogen peroxide and superoxide anion radicals than wild-type and 35S::m5LCR plants. Expressions of ABA- and stress-responsive genes, ABI3, ABI4, ABI5, ABF3, and ABF4 are up-regulated in MIR394a/b over-expressing plants but down-regulated in 35S::m5LCR plants. Over-expression of MIR394a in abi4-1 or abi5-1 background resulted in loss of ABA-sensitivity in 35S::MIR394a plants. CONCLUSIONS The silencing of LCR mRNA by miR394 is essential to maintain a certain phenotype favorable for the adaptive response to abiotic stresses. The contrasting phenotypes of salt and drought responses may be mediated by a functional balance between miR394 and LCR. If the balance is perturbed in case of the abiotic stress, an identical phenotype related to the stress response occurs, resulting in either ABA sensitive or insensitive response. Thus, miR394-regulated LCR abundance may allow plants to fine-tune their responses to ABA and abiotic stress.
Collapse
Affiliation(s)
- Jian Bo Song
- Weigang No. 1, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuai Gao
- Weigang No. 1, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Di Sun
- Weigang No. 1, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Hua Li
- Weigang No. 1, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Xia Xia Shu
- Weigang No. 1, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhi Min Yang
- Weigang No. 1, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
49
|
Santos CS, Silva AI, Serrão I, Carvalho AL, Vasconcelos MW. Transcriptomic analysis of iron deficiency related genes in the legumes. Food Res Int 2013. [DOI: 10.1016/j.foodres.2013.06.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
50
|
Zhou M, Luo H. MicroRNA-mediated gene regulation: potential applications for plant genetic engineering. PLANT MOLECULAR BIOLOGY 2013; 83:59-75. [PMID: 23771582 DOI: 10.1007/s11103-013-0089-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 06/05/2013] [Indexed: 05/19/2023]
Abstract
Food security is one of the most important issues challenging the world today. Any strategies to solve this problem must include increasing crop yields and quality. MicroRNA-based genetic modification technology (miRNA-based GM tech) can be one of the most promising solutions that contribute to agricultural productivity directly by developing superior crop cultivars with enhanced biotic and abiotic stress tolerance and increased biomass yields. Indirectly, the technology may increase usage of marginal soils and decrease pesticide use, among other benefits. This review highlights the most recent progress of transgenic studies utilizing various miRNAs and their targets for plant trait modifications, and analyzes the potential of miRNA-mediated gene regulation for use in crop improvement. Strategies for manipulating miRNAs and their targets in transgenic plants including constitutive, stress-induced, or tissue-specific expression of miRNAs or their targets, RNA interference, expressing miRNA-resistant target genes, artificial target mimic and artificial miRNAs were discussed. We also discussed potential risks of utilizing miRNA-based GM tech. In general, miRNAs and their targets not only provide an invaluable source of novel transgenes, but also inspire the development of several new GM strategies, allowing advances in breeding novel crop cultivars with agronomically useful characteristics.
Collapse
MESH Headings
- Adaptation, Biological
- Crops, Agricultural/genetics
- Crops, Agricultural/immunology
- Crops, Agricultural/metabolism
- Disease Resistance
- Food Supply
- Food, Genetically Modified
- Gene Expression Regulation, Plant
- Genes, Plant
- Genetic Engineering/methods
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/immunology
- Plants, Genetically Modified/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Risk Factors
- Transgenes
Collapse
Affiliation(s)
- Man Zhou
- Department of Genetics and Biochemistry, Clemson University, 110 Biosystems Research Complex, Clemson, SC, 29634, USA
| | | |
Collapse
|