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Kaur G, Jain S, Bhushan S, Das N, Sharma M, Sharma D. Role of microRNAs and their putative mechanism in regulating potato (Solanum tuberosum L.) life cycle and response to various environmental stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108334. [PMID: 38219424 DOI: 10.1016/j.plaphy.2024.108334] [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: 02/26/2023] [Revised: 10/31/2023] [Accepted: 01/02/2024] [Indexed: 01/16/2024]
Abstract
The exponentially increasing population and the demand for food is inextricably linked. This has shifted global attention to improving crop plant traits to meet global food demands. Potato (Solanum tuberosum L.) is a major non-grain food crop that is grown all over the world. Currently, some of the major global potato research work focuses on the significance of microRNAs (miRNAs) in potato. miRNAs are a type of non-coding RNAs that regulate the gene expression of their target mRNA genes by cleavage and/or their translational inhibition. This suggests an essential role of miRNAs in a multitude of plant biological processes, including maintenance of genome integrity, plant growth, development and maturation, and initiation of responses to various stress conditions. Therefore, engineering miRNAs to generate stress-resistant varieties of potato may result in high yield and improved nutritional qualities. In this review, we discuss the potato miRNAs specifically known to play an essential role in the various stages of the potato life cycle, conferring stress-resistant characteristics, and modifying gene expression. This review highlights the significance of the miRNA machinery in plants, especially potato, encouraging further research into engineering miRNAs to boost crop yields and tolerance towards stress.
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Affiliation(s)
- Gurpreet Kaur
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, 147004, Punjab, India
| | - Sahil Jain
- Department of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Sakshi Bhushan
- Department of Botany, Central University of Jammu, Jammu and Kashmir (UT), India
| | - Niranjan Das
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, 147004, Punjab, India
| | - Munish Sharma
- Department of Plant Science, Central University of Himachal Pradesh, Shahpur Parisar, Kangra, Himachal Pradesh, India.
| | - Deepak Sharma
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada.
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Zhong C, Smith NA, Zhang D, Gou X, Greaves IK, Millar AA, Walsh TK, Shan W, Wang MB. G-U base-paired hpRNA confers potent inhibition of small RNA function in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1206-1222. [PMID: 38038953 DOI: 10.1111/tpj.16555] [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: 07/24/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
MicroRNA (miRNA) target mimicry technologies, utilizing naturally occurring miRNA decoy molecules, represent a potent tool for analyzing miRNA function. In this study, we present a highly efficient small RNA (sRNA) target mimicry design based on G-U base-paired hairpin RNA (hpG:U), which allows for the simultaneous targeting of multiple sRNAs. The hpG:U constructs consistently generate high amounts of intact, polyadenylated stem-loop (SL) RNA outside the nuclei, in contrast to traditional hairpin RNA designs with canonical base pairing (hpWT), which were predominantly processed resulting in a loop. By incorporating a 460-bp G-U base-paired double-stranded stem and a 312-576 nt loop carrying multiple miRNA target mimicry sites (GUMIC), the hpG:U construct displayed effective repression of three Arabidopsis miRNAs, namely miR165/166, miR157, and miR160, both individually and in combination. Additionally, a GUMIC construct targeting a prominent cluster of siRNAs derived from cucumber mosaic virus (CMV) Y-satellite RNA (Y-Sat) effectively inhibited Y-Sat siRNA-directed silencing of the chlorophyll biosynthetic gene CHLI, thereby reducing the yellowing symptoms in infected Nicotiana plants. Therefore, the G-U base-paired hpRNA, characterized by differential processing compared to traditional hpRNA, acts as an efficient decoy for both miRNAs and siRNAs. This technology holds great potential for sRNA functional analysis and the management of sRNA-mediated diseases.
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Affiliation(s)
- Chengcheng Zhong
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
- Stake Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Neil A Smith
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
| | - Daai Zhang
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
| | - Xiuhong Gou
- Stake Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ian K Greaves
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
| | - Anthony A Millar
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, 2601, ACT, Australia
| | - Tom K Walsh
- CSIRO Environment, Canberra, 2601, ACT, Australia
| | - Weixing Shan
- Stake Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ming-Bo Wang
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
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Wong GY, Millar AA. Target Landscape of Conserved Plant MicroRNAs and the Complexities of Their Ancient MicroRNA-Binding Sites. PLANT & CELL PHYSIOLOGY 2023; 64:604-621. [PMID: 36943747 DOI: 10.1093/pcp/pcad019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/02/2023] [Accepted: 03/19/2023] [Indexed: 06/16/2023]
Abstract
In plants, microRNA (miRNA)-target interactions (MTIs) require high complementarity, a feature from which bioinformatic programs have predicted numerous and diverse targets for any given miRNA, promoting the idea of complex miRNA networks. Opposing this is a hypothesis of constrained miRNA specificity, in which functional MTIs are restricted to the few targets whose required expression output is compatible with the expression of the miRNA. To explore these opposing views, the bioinformatic pipeline Targets Ranked Using Experimental Evidence was applied to strongly conserved miRNAs to identity their high-evidence (HE) targets across species. For each miRNA family, HE targets predominantly consisted of homologs from one conserved target gene family (primary family). These primary families corresponded to the known canonical miRNA-target families, validating the approach. Very few additional HE target families were identified (secondary family), and if so, they were likely functionally related to the primary family. Many primary target families contained highly conserved nucleotide sequences flanking their miRNA-binding sites that were enriched in HE homologs across species. A number of these flanking sequences are predicted to form conserved RNA secondary structures that preferentially base pair with the miRNA-binding site, implying that these sites are highly structured. Our findings support a target landscape view that is dominated by the conserved primary target families, with a minority of either secondary target families or non-conserved targets. This is consistent with the constrained hypothesis of functional miRNA specificity, which potentially in part is being facilitated by features beyond complementarity.
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Affiliation(s)
- Gigi Y Wong
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Anthony A Millar
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
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Othman SMIS, Mustaffa AF, Che-Othman MH, Samad AFA, Goh HH, Zainal Z, Ismail I. Overview of Repressive miRNA Regulation by Short Tandem Target Mimic (STTM): Applications and Impact on Plant Biology. PLANTS (BASEL, SWITZERLAND) 2023; 12:669. [PMID: 36771753 PMCID: PMC9918958 DOI: 10.3390/plants12030669] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The application of miRNA mimic technology for silencing mature miRNA began in 2007. This technique originated from the discovery of the INDUCED BY PHOSPHATE STARVATION 1 (IPS1) gene, which was found to be a competitive mimic that prevents the cleavage of the targeted mRNA by miRNA inhibition at the post-transcriptional level. To date, various studies have been conducted to understand the molecular mimic mechanism and to improve the efficiency of this technology. As a result, several mimic tools have been developed: target mimicry (TM), short tandem target mimic (STTM), and molecular sponges (SPs). STTM is the most-developed tool due to its stability and effectiveness in decoying miRNA. This review discusses the application of STTM technology on the loss-of-function studies of miRNA and members from diverse plant species. A modified STTM approach for studying the function of miRNA with spatial-temporal expression under the control of specific promoters is further explored. STTM technology will enhance our understanding of the miRNA activity in plant-tissue-specific development and stress responses for applications in improving plant traits via miRNA regulation.
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Affiliation(s)
- Syed Muhammad Iqbal Syed Othman
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Arif Faisal Mustaffa
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - M. Hafiz Che-Othman
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Abdul Fatah A. Samad
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai, Johor Bahru 81310, Johor, Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Zamri Zainal
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Ismanizan Ismail
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
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Genome-Wide Analysis of miR159 Gene Family and Predicted Target Genes Associated with Environmental Stress in Dendrobium officinale: A Bioinformatics Study. Genes (Basel) 2022; 13:genes13071221. [PMID: 35886004 PMCID: PMC9320484 DOI: 10.3390/genes13071221] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/27/2022] [Accepted: 07/06/2022] [Indexed: 11/26/2022] Open
Abstract
Dendrobium officinale (D. officinale) is a widely used traditional Chinese medicine with high economic value. MicroR159 (miR159) is an ancient and conserved microRNA (miRNA) family in land plants, playing roles in the progress of growth and development, as well as the stress response. In order to find out functions of miR159 in D. officinale, multiple bioinformatic approaches were employed and 10 MIR159 genes were found, localizing on seven chromosomes and an unanchored segment of the D. officinale genome. All of the precursor sequences of Dof-miR159 could form a stable stem-loop structure. The phylogenetic analysis revealed that the MIR159 genes of D. officinale were divided into five clades. Furthermore, the conservation analysis suggested that the 2 to 20 nt region of miR159 mature sequences were highly conserved among family members. The promoter analysis of MIR159s showed that the majority of the predicted cis-elements were related to environmental stress or hormones. In total, five classes of genes were predicted to be the target genes of Dof-miR159s, including GAMYB transcription factors, which had been confirmed in many other land plants. The expression patterns of predicted target genes revealed their potential roles in the growth and development of D. officinale, as well as in cold and drought stress responses. In conclusion, our results illustrated the stress-related miR159-targeted genes in D. officinale, which could provide candidate genes for resistance breeding in the future.
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Huang L, Luo J, Song N, Gao W, Zhu L, Yao W. CRISPR/Cas9-Mediated Knockout of miR-130b Affects Mono- and Polyunsaturated Fatty Acid Content via PPARG-PGC1α Axis in Goat Mammary Epithelial Cells. Int J Mol Sci 2022; 23:3640. [PMID: 35409000 PMCID: PMC8998713 DOI: 10.3390/ijms23073640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/09/2022] [Accepted: 03/24/2022] [Indexed: 02/01/2023] Open
Abstract
MicroRNA (miRNA)-130b, as a regulator of lipid metabolism in adipose and mammary gland tissues, is actively involved in lipogenesis, but its endogenous role in fatty acid synthesis remains unclear. Here, we aimed to explore the function and underlying mechanism of miR-130b in fatty acid synthesis using the CRISPR/Cas9 system in primary goat mammary epithelial cells (GMEC). A single clone with deletion of 43 nucleotides showed a significant decrease in miR-130b-5p and miR-130b-3p abundances and an increase of target genes PGC1α and PPARG. In addition, knockout of miR-130b promoted triacylglycerol (TAG) and cholesterol accumulation, and decreased the proportion of monounsaturated fatty acids (MUFA) C16:1, C18:1 and polyunsaturated fatty acids (PUFA) C18:2, C20:3, C20:4, C20:5, C22:6. Similarly, the abundance of fatty acid synthesis genes ACACA and FASN and transcription regulators SREBP1c and SREBP2 was elevated. Subsequently, interference with PPARG instead of PGC1α in knockout cells restored the effect of miR-130b knockout, suggesting that PPARG is responsible for miR-130b regulating fatty acid synthesis. Moreover, disrupting PPARG inhibits PGC1α transcription and translation. These results reveal that miR-130b directly targets the PPARG-PGC1α axis, to inhibit fatty acid synthesis in GMEC. In conclusion, miR-130b could be a potential molecular regulator for improving the beneficial fatty acids content in goat milk.
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Affiliation(s)
| | - Jun Luo
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (L.H.); (N.S.); (W.G.); (L.Z.); (W.Y.)
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Patil S, Joshi S, Jamla M, Zhou X, Taherzadeh MJ, Suprasanna P, Kumar V. MicroRNA-mediated bioengineering for climate-resilience in crops. Bioengineered 2021; 12:10430-10456. [PMID: 34747296 PMCID: PMC8815627 DOI: 10.1080/21655979.2021.1997244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 12/24/2022] Open
Abstract
Global projections on the climate change and the dynamic environmental perturbations indicate severe impacts on food security in general, and crop yield, vigor and the quality of produce in particular. Sessile plants respond to environmental challenges such as salt, drought, temperature, heavy metals at transcriptional and/or post-transcriptional levels through the stress-regulated network of pathways including transcription factors, proteins and the small non-coding endogenous RNAs. Amongs these, the miRNAs have gained unprecedented attention in recent years as key regulators for modulating gene expression in plants under stress. Hence, tailoring of miRNAs and their target pathways presents a promising strategy for developing multiple stress-tolerant crops. Plant stress tolerance has been successfully achieved through the over expression of microRNAs such as Os-miR408, Hv-miR82 for drought tolerance; OsmiR535A and artificial DST miRNA for salinity tolerance; and OsmiR535 and miR156 for combined drought and salt stress. Examples of miR408 overexpression also showed improved efficiency of irradiation utilization and carbon dioxide fixation in crop plants. Through this review, we present the current understanding about plant miRNAs, their roles in plant growth and stress-responses, the modern toolbox for identification, characterization and validation of miRNAs and their target genes including in silico tools, machine learning and artificial intelligence. Various approaches for up-regulation or knock-out of miRNAs have been discussed. The main emphasis has been given to the exploration of miRNAs for development of bioengineered climate-smart crops that can withstand changing climates and stressful environments, including combination of stresses, with very less or no yield penalties.
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Affiliation(s)
- Suraj Patil
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Pune, India
| | - Shrushti Joshi
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Pune, India
| | - Monica Jamla
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Pune, India
| | - Xianrong Zhou
- School of Life Science and Biotechnology, Yangtze Normal University, Ch-ongqing, China
| | | | - Penna Suprasanna
- Bhabha Atomic Research Centre, Homi Bhabha National Institute, Mumbai, India
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Pune, India
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Lin Y, Zhu Y, Cui Y, Chen R, Chen Z, Li G, Fan M, Chen J, Li Y, Guo X, Zheng X, Chen L, Wang F. Derepression of specific miRNA-target genes in rice using CRISPR/Cas9. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7067-7077. [PMID: 34283216 PMCID: PMC8547147 DOI: 10.1093/jxb/erab336] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 07/20/2021] [Indexed: 05/20/2023]
Abstract
MicroRNAs (miRNAs) target specific mRNA molecules based on sequence complementarity for their degradation or repression of translation, thereby regulating various developmental and physiological processes in eukaryotic organisms. Expressing the target mimicry (MIM) and short tandem target mimicry (STTM) can block endogenous activity of mature miRNAs and eliminate the inhibition of their target genes, resulting in phenotypic changes due to higher expression of the target genes. Here, we report a strategy to achieve derepression of interested miRNA-target genes through CRISPR/Cas9-based generation of in-frame mutants within the miRNA-complementary sequence of the target gene. We show that two rice genes, OsGRF4 (GROWTH REGULATING FACTOR 4) and OsGRF8 carrying in-frame mutants with disruption of the miR396 recognition sites, escape from miR396-mediated post-transcriptional silencing, resulting in enlarged grain size and increase in brown planthopper (BPH) resistance, in their respective transgenic rice lines. These results demonstrate that CRISPR/Cas9-mediated disruption of miRNA target sites can be effectively employed to precisely derepress particular target genes of functional importance for trait improvement in plants.
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Affiliation(s)
- Yarong Lin
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fuzhou, China
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yiwang Zhu
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fuzhou, China
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yuchao Cui
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Rui Chen
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fuzhou, China
| | - Zaijie Chen
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fuzhou, China
| | - Gang Li
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fuzhou, China
| | - Meiying Fan
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fuzhou, China
| | - Jianmin Chen
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fuzhou, China
| | - Yan Li
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xinrui Guo
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fuzhou, China
| | - Xijun Zheng
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Liang Chen
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
- Correspondence: or
| | - Feng Wang
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fuzhou, China
- Correspondence: or
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Zhou Q, Shi J, Li Z, Zhang S, Zhang S, Zhang J, Bao M, Liu G. miR156/157 Targets SPLs to Regulate Flowering Transition, Plant Architecture and Flower Organ Size in Petunia. PLANT & CELL PHYSIOLOGY 2021; 62:839-857. [PMID: 33768247 DOI: 10.1093/pcp/pcab041] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/19/2021] [Indexed: 05/15/2023]
Abstract
miR156/157 plays multiple pivotal roles during plant growth and development. In this study, we identified 11 miR156- and 5 miR157-encoding loci from the genome of Petunia axillaris and Petunia inflata, designated as PaMIR0156/157s and PiMIR0156/157s, respectively. Real-time quantitative reverse transcription PCR (qRT-PCR) analysis indicated that PhmiR156/157 was expressed predominantly in cotyledons, germinating seeds, flower buds, young fruits and seedlings. PhmiR156/157 levels declined in shoot apical buds and leaves of petunia before flowering as the plant ages; moreover, the temporal expression patterns of most miR156/157-targeted PhSPLs were complementary to that of PhmiR156/157. Ectopic expression of PhMIR0157a in Arabidopsis and petunia resulted in delayed flowering, dwarf plant stature, increased branches and reduced organ size. However, PhMIR0156f-overexpressing Arabidopsis and petunia plants showed only delayed flowering. In addition, downregulation of PhmiR156/157 level by overexpressing STTM156/157 led to taller plants with less branches, longer internodes and precocious flowering. qRT-PCR analysis indicated that PhmiR156/157 modulates these traits mainly by downregulating their PhSPL targets and subsequently decreasing the expression of flowering regulatory genes. Our results demonstrate that the PhmiR156/157-PhSPL module has conserved but also divergent functions in growth and development, which will help us decipher the genetic basis for the improvement of flower transition, plant architecture and organ development in petunia.
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Affiliation(s)
- Qin Zhou
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiewei Shi
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhineng Li
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education; College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Sisi Zhang
- Wuhan Institute of Landscape Architecture, Peace Avenue No. 1240, Wuhan 430081, China
| | - Shuting Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiaqi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Guofeng Liu
- Department of Botany, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, China
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Šečić E, Kogel KH, Ladera-Carmona MJ. Biotic stress-associated microRNA families in plants. JOURNAL OF PLANT PHYSIOLOGY 2021; 263:153451. [PMID: 34119743 DOI: 10.1016/j.jplph.2021.153451] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 06/12/2023]
Abstract
Plants and animals utilize various regulatory mechanisms for control of gene expression during development in different tissues and cell types. About 30 years ago, a new mechanism of gene regulation, termed RNA interference (RNAi), was discovered and proved revolutionary for the mechanistic understanding of gene regulation. Noncoding RNAs, including short, 21-24 nucleotide (nt) long microRNAs (miRNAs), endogenously-generated from MIR genes, are key components of RNAi processes, by post-transcriptionally controlling transcripts with antisense complementarity through either translational repression or mRNA degradation. Since their discovery, important roles in regulation of ontogenetic development, cell differentiation, proliferation, and apoptosis in eukaryotes have been elucidated. In plants, miRNAs are known regulatory elements of basic endogenous functions and responses to the environmental stimuli. While the role of miRNAs in regulation of nutrient uptake, circadian clock and general response to abiotic stress is already well understood, a comprehensive understanding of their immune-regulatory roles in response to various biotic stress factors has not yet been achieved. This review summarizes the current understanding of the function of miRNAs and their targets in plants during interaction with microbial pathogens and symbionts. Additionally, we provide a consensus conclusion regarding the typical induction or repression response of conserved miRNA families to pathogenic and beneficial fungi, bacteria, and oomycetes, as well as an outlook of agronomic application of miRNAs in plants. Further investigation of plant miRNAs responsive to microbes, aided with novel sequencing and bioinformatics approaches for discovery and prediction in non-model organisms holds great potential for development of new forms of plant protection.
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Affiliation(s)
- Ena Šečić
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26, D-35392, Giessen, Germany.
| | - Karl-Heinz Kogel
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26, D-35392, Giessen, Germany.
| | - Maria Jose Ladera-Carmona
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26, D-35392, Giessen, Germany.
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Hong Y, Meng J, He X, Zhang Y, Liu Y, Zhang C, Qi H, Luan Y. Editing miR482b and miR482c Simultaneously by CRISPR/Cas9 Enhanced Tomato Resistance to Phytophthora infestans. PHYTOPATHOLOGY 2021; 111:1008-1016. [PMID: 33258411 DOI: 10.1094/phyto-08-20-0360-r] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Late blight, caused by Phytophthora infestans, is severely damaging to the global tomato industry. Micro-RNAs (miRNAs) have been widely demonstrated to play vital roles in plant resistance by repressing their target genes. Recently, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) method has been continuously improved and extensively applied to edit plant genomes. However, editing multiplex miRNAs by CRISPR/Cas9 in tomato has not been studied yet. We knocked out miR482b and miR482c simultaneously in tomato through the multiplex CRISPR/Cas9 system. Two transgenic plants with silenced miR482b and miR482c simultaneously and one transgenic line with silenced miR482b alone were obtained. Compared with wild-type plants, the disease symptoms of three transgenic plants upon infection were reduced, accompanied by increased expression of their common target nucleotide binding site-leucine-rich repeat genes and decreased levels of reactive oxygen species. Furthermore, silencing miR482b and miR482c simultaneously was more resistant than silencing miR482b alone in tomato. More importantly, we found that knocking out miR482b and miR482c can elicit expression perturbation of other miRNAs, suggesting cross-regulation between miRNAs. Our study demonstrated that editing miR482b and miR482c simultaneously with CRISPR/Cas9 is an efficient strategy for generating pathogen-resistant tomatoes, and cross-regulation between miRNAs may reveal the novel mechanism in tomato-P. infestans interactions.
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Affiliation(s)
- Yuhui Hong
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiaoli He
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Yuanyuan Zhang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Yarong Liu
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Chengwei Zhang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100000, China
| | - Hongyan Qi
- College of Horticulture, Shenyang Agricultural University/Key Laboratory of Protected Horticulture, Ministry of Education/Northern National & Local Joint Engineering Research Center of Horticultural Facilities Design and Application Technology (Liaoning), Shenyang 110866, China
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
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12
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Chaudhary S, Grover A, Sharma PC. MicroRNAs: Potential Targets for Developing Stress-Tolerant Crops. Life (Basel) 2021; 11:life11040289. [PMID: 33800690 PMCID: PMC8066829 DOI: 10.3390/life11040289] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/24/2022] Open
Abstract
Crop yield is challenged every year worldwide by changing climatic conditions. The forecasted climatic scenario urgently demands stress-tolerant crop varieties to feed the ever-increasing global population. Molecular breeding and genetic engineering approaches have been frequently exploited for developing crops with desired agronomic traits. Recently, microRNAs (miRNAs) have emerged as powerful molecules, which potentially serve as expression markers during stress conditions. The miRNAs are small non-coding endogenous RNAs, usually 20-24 nucleotides long, which mediate post-transcriptional gene silencing and fine-tune the regulation of many abiotic- and biotic-stress responsive genes in plants. The miRNAs usually function by specifically pairing with the target mRNAs, inducing their cleavage or repressing their translation. This review focuses on the exploration of the functional role of miRNAs in regulating plant responses to abiotic and biotic stresses. Moreover, a methodology is also discussed to mine stress-responsive miRNAs from the enormous amount of transcriptome data available in the public domain generated using next-generation sequencing (NGS). Considering the functional role of miRNAs in mediating stress responses, these molecules may be explored as novel targets for engineering stress-tolerant crop varieties.
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Affiliation(s)
- Saurabh Chaudhary
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
- Correspondence: (S.C.); (P.C.S.)
| | - Atul Grover
- Defence Institute of Bio-Energy Research, Defence Research and Development Organisation (DRDO), Haldwani 263139, India;
| | - Prakash Chand Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi 110078, India
- Correspondence: (S.C.); (P.C.S.)
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Chen J, Teotia S, Lan T, Tang G. MicroRNA Techniques: Valuable Tools for Agronomic Trait Analyses and Breeding in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:744357. [PMID: 34616418 PMCID: PMC8489592 DOI: 10.3389/fpls.2021.744357] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/16/2021] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) are a class of small noncoding RNAs that regulate gene expression at the post-transcriptional level. Extensive studies have revealed that miRNAs have critical functions in plant growth, development, and stress responses and may provide valuable genetic resources for plant breeding research. We herein reviewed the development, mechanisms, and characteristics of miRNA techniques while highlighting widely used approaches, namely, the short tandem target mimic (STTM) approach. We described STTM-based advances in plant science, especially in the model crop rice, and introduced the CRISPR-based transgene-free crop breeding. Finally, we discussed the challenges and unique opportunities related to combining STTM and CRISPR technology for crop improvement and agriculture.
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Affiliation(s)
- Jiwei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Sachin Teotia
- Department of Biotechnology, Sharda University, Greater Noida, India
| | - Ting Lan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
- *Correspondence: Ting Lan,
| | - Guiliang Tang
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI, United States
- Guiliang Tang,
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14
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Chung PJ, Chung H, Oh N, Choi J, Bang SW, Jung SE, Jung H, Shim JS, Kim JK. Efficiency of Recombinant CRISPR/rCas9-Mediated miRNA Gene Editing in Rice. Int J Mol Sci 2020; 21:ijms21249606. [PMID: 33339449 PMCID: PMC7766165 DOI: 10.3390/ijms21249606] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/30/2022] Open
Abstract
Drought is one of the major environmental stresses adversely affecting crop productivity worldwide. Precise characterization of genes involved in drought response is necessary to develop new crop varieties with enhanced drought tolerance. Previously, we identified 66 drought-induced miRNAs in rice plants. For the further functional investigation of the miRNAs, we applied recombinant codon-optimized Cas9 (rCas9) for rice with single-guide RNAs specifically targeting mature miRNA sequences or sites required for the biogenesis of mature miRNA. A total of 458 T0 transgenic plants were analyzed to determine the frequency and type of mutations induced by CRISPR/rCas9 on 13 independent target miRNAs. The average mutation frequency for 13 genes targeted by single guide RNAs (sgRNAs) in T0 generation was 59.4%, including mono-allelic (8.54%), bi-allelic (11.1%), and hetero-allelic combination (39.7%) mutations. The mutation frequency showed a positive correlation with Tm temperature of sgRNAs. For base insertion, one base insertion (99%) was predominantly detected in transgenic plants. Similarly, one base deletion accounted for the highest percentage, but there was also a significant percentage of cases in which more than one base was deleted. The deletion of more than two bases in OsmiR171f and OsmiR818b significantly reduced the level of corresponding mature miRNAs. Further functional analysis using CRISPR/Cas9-mediated mutagenesis confirmed that OsmiR818b is involved in drought response in rice plants. Overall, this study suggests that the CRISPR/rCas9 system is a powerful tool for loss-of-function analysis of miRNA in rice.
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Affiliation(s)
- Pil Joong Chung
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science & Technology, Seoul National University, Pyeongchang 25354, Korea; (P.J.C.); (H.C.); (N.O.); (J.C.); (S.W.B.); (S.E.J.); (H.J.)
- Temasek Life Science Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Hoyong Chung
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science & Technology, Seoul National University, Pyeongchang 25354, Korea; (P.J.C.); (H.C.); (N.O.); (J.C.); (S.W.B.); (S.E.J.); (H.J.)
- 3BIGS, Suwon 16506, Korea
| | - Nuri Oh
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science & Technology, Seoul National University, Pyeongchang 25354, Korea; (P.J.C.); (H.C.); (N.O.); (J.C.); (S.W.B.); (S.E.J.); (H.J.)
- College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Joohee Choi
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science & Technology, Seoul National University, Pyeongchang 25354, Korea; (P.J.C.); (H.C.); (N.O.); (J.C.); (S.W.B.); (S.E.J.); (H.J.)
- Novel food Division, National Institute of Food and Drug Safety Evaluation, Cheongju 28159, Korea
| | - Seung Woon Bang
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science & Technology, Seoul National University, Pyeongchang 25354, Korea; (P.J.C.); (H.C.); (N.O.); (J.C.); (S.W.B.); (S.E.J.); (H.J.)
| | - Se Eun Jung
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science & Technology, Seoul National University, Pyeongchang 25354, Korea; (P.J.C.); (H.C.); (N.O.); (J.C.); (S.W.B.); (S.E.J.); (H.J.)
| | - Harin Jung
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science & Technology, Seoul National University, Pyeongchang 25354, Korea; (P.J.C.); (H.C.); (N.O.); (J.C.); (S.W.B.); (S.E.J.); (H.J.)
- NUS Synthetic Biology for Clinical and Technological Innovation, Department of Biochemistry, Yong Loo Lin, School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Jae Sung Shim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
- Correspondence: (J.S.S.); (J.-K.K.); Tel.: +82-62-530-0507 (J.S.S.); +82-33-339-5826 (J.-K.K.)
| | - Ju-Kon Kim
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science & Technology, Seoul National University, Pyeongchang 25354, Korea; (P.J.C.); (H.C.); (N.O.); (J.C.); (S.W.B.); (S.E.J.); (H.J.)
- Correspondence: (J.S.S.); (J.-K.K.); Tel.: +82-62-530-0507 (J.S.S.); +82-33-339-5826 (J.-K.K.)
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15
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Zhou X, Cui J, Meng J, Luan Y. Interactions and links among the noncoding RNAs in plants under stresses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3235-3248. [PMID: 33025081 DOI: 10.1007/s00122-020-03690-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 09/16/2020] [Indexed: 05/11/2023]
Abstract
The complex interplay among sRNAs, lncRNAs and circRNAs has been implicated in plants under biotic and abiotic stresses. Here, we review current advances in our understanding of ncRNA interactions and links, which have considerable potential for improving the agronomic traits and the environmental adaptability of plants. Plants can respond to biotic or abiotic stresses. To cope with various conditions, numerous intricate molecular regulatory mechanisms have evolved in plants. Noncoding RNAs (ncRNAs) can be divided into small noncoding RNAs (sRNAs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs). Emerging evidence has demonstrated that interplay among the ncRNAs acts as a novel layer in the regulatory mechanisms, which has attracted substantial interest. Links between sRNAs can affect plant immune responses and development in synergistic or antagonistic manners. Additionally, multiple interactions between lncRNAs and sRNAs are involved in crop breeding, disease resistance and high tolerance to environmental stresses. Here, we summarize current knowledge of the interactions and links among the ncRNAs in plant responses to stresses and the methods for identifying ncRNA interactions. Furthermore, challenges and prospects for further progress in elucidating ncRNA interactions and links are highlighted.
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Affiliation(s)
- Xiaoxu Zhou
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Jun Cui
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.
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16
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Wójcik AM. Research Tools for the Functional Genomics of Plant miRNAs During Zygotic and Somatic Embryogenesis. Int J Mol Sci 2020; 21:E4969. [PMID: 32674459 PMCID: PMC7420248 DOI: 10.3390/ijms21144969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022] Open
Abstract
During early plant embryogenesis, some of the most fundamental decisions on fate and identity are taken making it a fascinating process to study. It is no surprise that higher plant embryogenesis was intensively analysed during the last century, while somatic embryogenesis is probably the most studied regeneration model. Encoded by the MIRNA, short, single-stranded, non-coding miRNAs, are commonly present in all Eukaryotic genomes and are involved in the regulation of the gene expression during the essential developmental processes such as plant morphogenesis, hormone signaling, and developmental phase transition. During the last few years dedicated to miRNAs, analytical methods and tools have been developed, which have afforded new opportunities in functional analyses of plant miRNAs, including (i) databases for in silico analysis; (ii) miRNAs detection and expression approaches; (iii) reporter and sensor lines for a spatio-temporal analysis of the miRNA-target interactions; (iv) in situ hybridisation protocols; (v) artificial miRNAs; (vi) MIM and STTM lines to inhibit miRNA activity, and (vii) the target genes resistant to miRNA. Here, we attempted to summarise the toolbox for functional analysis of miRNAs during plant embryogenesis. In addition to characterising the described tools/methods, examples of the applications have been presented.
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Affiliation(s)
- Anna Maria Wójcik
- University of Silesia in Katowice, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland
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17
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Basso MF, Arraes FBM, Grossi-de-Sa M, Moreira VJV, Alves-Ferreira M, Grossi-de-Sa MF. Insights Into Genetic and Molecular Elements for Transgenic Crop Development. FRONTIERS IN PLANT SCIENCE 2020; 11:509. [PMID: 32499796 PMCID: PMC7243915 DOI: 10.3389/fpls.2020.00509] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 04/03/2020] [Indexed: 05/21/2023]
Abstract
Climate change and the exploration of new areas of cultivation have impacted the yields of several economically important crops worldwide. Both conventional plant breeding based on planned crosses between parents with specific traits and genetic engineering to develop new biotechnological tools (NBTs) have allowed the development of elite cultivars with new features of agronomic interest. The use of these NBTs in the search for agricultural solutions has gained prominence in recent years due to their rapid generation of elite cultivars that meet the needs of crop producers, and the efficiency of these NBTs is closely related to the optimization or best use of their elements. Currently, several genetic engineering techniques are used in synthetic biotechnology to successfully improve desirable traits or remove undesirable traits in crops. However, the features, drawbacks, and advantages of each technique are still not well understood, and thus, these methods have not been fully exploited. Here, we provide a brief overview of the plant genetic engineering platforms that have been used for proof of concept and agronomic trait improvement, review the major elements and processes of synthetic biotechnology, and, finally, present the major NBTs used to improve agronomic traits in socioeconomically important crops.
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Affiliation(s)
| | - Fabrício Barbosa Monteiro Arraes
- Plant Biotechnology, Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
- Department of Molecular Biology and Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Maíra Grossi-de-Sa
- Plant Biotechnology, Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - Valdeir Junio Vaz Moreira
- Plant Biotechnology, Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
- Department of Molecular Biology and Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Maria Fatima Grossi-de-Sa
- Plant Biotechnology, Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
- Department of Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília, Brazil
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18
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López-Márquez D, Del-Espino Á, Bejarano ER, Beuzón CR, Ruiz-Albert J. Protocol: low cost fast and efficient generation of molecular tools for small RNA analysis. PLANT METHODS 2020; 16:41. [PMID: 32206081 PMCID: PMC7082952 DOI: 10.1186/s13007-020-00581-w] [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: 10/24/2019] [Accepted: 03/04/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Small RNAs are sequence-dependent negative regulators of gene expression involved in many relevant plant processes such as development, genome stability, or stress response. Functional characterization of sRNAs in plants typically relies on the modification of the steady state levels of these molecules. State-of-the-art strategies to reduce plant sRNA levels include molecular tools such as Target Mimics (MIMs or TMs), Short Tandem Target Mimic (STTMs), or molecular SPONGES (SPs). Construction of these tools routinely involve many different molecular biology techniques, steps, and reagents rendering such processes expensive, time consuming, and difficult to implement, particularly high-throughput approaches. RESULTS We have developed a vector and a cloning strategy that significantly reduces the number of steps required for the generation of MIMs against any given small RNA (sRNA). Our pGREEN-based binary expression vector (pGREEN-DLM100) contains the IPS1 gene from A. thaliana bisected by a ccdB cassette that is itself flanked by restriction sites for a type IIS endonuclease. Using a single digestion plus a sticky-end ligation step, the ccdB cassette that functions as a negative (counter) selection system is replaced by a pair of 28 nt self-annealing primers that provide specificity against the selected target miRNA/siRNA. The method considerably reduces the number of steps and the time required to generate the construct, minimizes the errors derived from long-range PCRs, bypasses bottlenecks derived from subcloning steps, and eliminates the need for any additional cloning technics and reagents, overall saving time and reagents. CONCLUSIONS Our streamlined system guarantees a low cost, fast and efficient cloning process that it can be easily implemented into high-throughput strategies, since the same digested plasmid can be used for any given sRNA. We believe this method represents a significant technical improvement on state-of-the-art methods to facilitate the characterization of functional aspects of sRNA biology.
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Affiliation(s)
- Diego López-Márquez
- Dpto. Biología Celular, Genética y Fisiología, Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos, Málaga, 29071 Spain
| | - Ángel Del-Espino
- Dpto. Biología Celular, Genética y Fisiología, Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos, Málaga, 29071 Spain
| | - Eduardo R. Bejarano
- Dpto. Biología Celular, Genética y Fisiología, Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos, Málaga, 29071 Spain
| | - Carmen R. Beuzón
- Dpto. Biología Celular, Genética y Fisiología, Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos, Málaga, 29071 Spain
| | - Javier Ruiz-Albert
- Dpto. Biología Celular, Genética y Fisiología, Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos, Málaga, 29071 Spain
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Peng X, Ma X, Lu S, Li Z. A Versatile Plant Rhabdovirus-Based Vector for Gene Silencing, miRNA Expression and Depletion, and Antibody Production. FRONTIERS IN PLANT SCIENCE 2020; 11:627880. [PMID: 33510764 PMCID: PMC7835261 DOI: 10.3389/fpls.2020.627880] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 12/16/2020] [Indexed: 05/12/2023]
Abstract
Plant virus vectors are ideal tools for delivery of genetic cargo into host cells for functional genomics studies and protein overexpression. Although a vast number of plant virus vectors have been developed for different purposes, the utility of a particular virus vector is generally limited. Here, we report a multipurpose plant rhabdovirus-based vector system suitable for a wide range of applications in Nicotiana benthamiana. We engineered sonchus yellow net rhabdovirus (SYNV)-based gene silencing vectors through expressing a sense, antisense, or double-stranded RNAs of target genes. Robust target gene silencing was also achieved with an SYNV vector expressing a designed artificial microRNA. In addition, ectopic expression of a short tandem target mimic RNA using the SYNV vector led to a significant depletion of the target miR165/166 and caused abnormal leaf development. More importantly, SYNV was able to harbor two expression cassettes that permitted simultaneous RNA silencing and overexpression of large reporter gene. This dual capacity vector also enabled systemic expression of a whole-molecule monoclonal antibody consisting of light and heavy chains. These results highlight the utility of the SYNV vector system in gene function studies and agricultural biotechnology and provide a technical template for developing similar vectors of other economically important plant rhabdoviruses.
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Affiliation(s)
- Xingxing Peng
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiaonan Ma
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Shuting Lu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhenghe Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou, China
- *Correspondence: Zhenghe Li,
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20
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Basso MF, Ferreira PCG, Kobayashi AK, Harmon FG, Nepomuceno AL, Molinari HBC, Grossi‐de‐Sa MF. MicroRNAs and new biotechnological tools for its modulation and improving stress tolerance in plants. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1482-1500. [PMID: 30947398 PMCID: PMC6662102 DOI: 10.1111/pbi.13116] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/22/2019] [Accepted: 03/17/2019] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) modulate the abundance and spatial-temporal accumulation of target mRNAs and indirectly regulate several plant processes. Transcriptional regulation of the genes encoding miRNAs (MIR genes) can be activated by numerous transcription factors, which themselves are regulated by other miRNAs. Fine-tuning of MIR genes or miRNAs is a powerful biotechnological strategy to improve tolerance to abiotic or biotic stresses in crops of economic importance. Current approaches for miRNA fine-tuning are based on the down- or up-regulation of MIR gene transcription and the use of genetic engineering tools to manipulate the final concentration of these miRNAs in the cytoplasm. Transgenesis, cisgenesis, intragenesis, artificial MIR genes, endogenous and artificial target mimicry, MIR genes editing using Meganucleases, ZNF proteins, TALENs and CRISPR/Cas9 or CRISPR/Cpf1, CRISPR/dCas9 or dCpf1, CRISPR13a, topical delivery of miRNAs and epigenetic memory have been successfully explored to MIR gene or miRNA modulation and improve agronomic traits in several model or crop plants. However, advantages and drawbacks of each of these new biotechnological tools (NBTs) are still not well understood. In this review, we provide a brief overview of the biogenesis and role of miRNAs in response to abiotic or biotic stresses, we present critically the main NBTs used for the manipulation of MIR genes and miRNAs, we show current efforts and findings with the MIR genes and miRNAs modulation in plants, and we summarize the advantages and drawbacks of these NBTs and provide some alternatives to overcome. Finally, challenges and future perspectives to miRNA modulating in important crops are also discussed.
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Affiliation(s)
| | | | | | - Frank G. Harmon
- Plant Gene Expression CenterUSDA‐ARSAlbanyCAUSA
- Department of Plant and Microbial BiologyUC BerkeleyBerkeleyCAUSA
| | | | | | - Maria Fatima Grossi‐de‐Sa
- Embrapa Genetic Resources and BiotechnologyBrasíliaDFBrazil
- Post‐Graduation Program in Genomic Sciences and BiotechnologyCatholic University of BrasíliaBrasíliaDFBrazil
- Post‐Graduation Program in BiotechnologyPotiguar University (UNP)NatalRNBrazil
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21
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Millar AA, Lohe A, Wong G. Biology and Function of miR159 in Plants. PLANTS 2019; 8:plants8080255. [PMID: 31366066 PMCID: PMC6724108 DOI: 10.3390/plants8080255] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/18/2019] [Accepted: 07/23/2019] [Indexed: 12/26/2022]
Abstract
MicroR159 (miR159) is ancient, being present in the majority of land plants where it targets a class of regulatory genes called GAMYB or GAMYB-like via highly conserved miR159-binding sites. These GAMYB genes encode R2R3 MYB domain transcription factors that transduce the gibberellin (GA) signal in the seed aleurone and the anther tapetum. Here, GAMYB plays a conserved role in promoting the programmed cell death of these tissues, where miR159 function appears weak. By contrast, GAMYB is not involved in GA-signaling in vegetative tissues, but rather its expression is deleterious, leading to the inhibition of growth and development. Here, the major function of miR159 is to mediate strong silencing of GAMYB to enable normal growth. Highlighting this requirement of strong silencing are conserved RNA secondary structures associated with the miR159-binding site in GAMYB mRNA that promotes miR159-mediated repression. Although the miR159-GAMYB pathway in vegetative tissues has been implicated in a number of different functions, presently no conserved role for this pathway has emerged. We will review the current knowledge of the different proposed functions of miR159, and how this ancient pathway has been used as a model to help form our understanding of miRNA biology in plants.
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Affiliation(s)
- Anthony A Millar
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia.
| | - Allan Lohe
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
| | - Gigi Wong
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
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Paschoal AR, Lozada-Chávez I, Domingues DS, Stadler PF. ceRNAs in plants: computational approaches and associated challenges for target mimic research. Brief Bioinform 2019; 19:1273-1289. [PMID: 28575144 DOI: 10.1093/bib/bbx058] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 04/27/2017] [Indexed: 11/13/2022] Open
Abstract
The competing endogenous RNA hypothesis has gained increasing attention as a potential global regulatory mechanism of microRNAs (miRNAs), and as a powerful tool to predict the function of many noncoding RNAs, including miRNAs themselves. Most studies have been focused on animals, although target mimic (TMs) discovery as well as important computational and experimental advances has been developed in plants over the past decade. Thus, our contribution summarizes recent progresses in computational approaches for research of miRNA:TM interactions. We divided this article in three main contributions. First, a general overview of research on TMs in plants is presented with practical descriptions of the available literature, tools, data, databases and computational reports. Second, we describe a common protocol for the computational and experimental analyses of TM. Third, we provide a bioinformatics approach for the prediction of TM motifs potentially cross-targeting both members within the same or from different miRNA families, based on the identification of consensus miRNA-binding sites from known TMs across sequenced genomes, transcriptomes and known miRNAs. This computational approach is promising because, in contrast to animals, miRNA families in plants are large with identical or similar members, several of which are also highly conserved. From the three consensus TM motifs found with our approach: MIM166, MIM171 and MIM159/319, the last one has found strong support on the recent experimental work by Reichel and Millar [Specificity of plant microRNA TMs: cross-targeting of mir159 and mir319. J Plant Physiol 2015;180:45-8]. Finally, we stress the discussion on the major computational and associated experimental challenges that have to be faced in future ceRNA studies.
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Affiliation(s)
| | - Irma Lozada-Chávez
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Germany
| | - Douglas Silva Domingues
- Department of Botany, Institute of Biosciences, S~ao Paulo State University (UNESP) in Rio Claro, Brazil
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23
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Farhat S, Jain N, Singh N, Sreevathsa R, Dash PK, Rai R, Yadav S, Kumar P, Sarkar AK, Jain A, Singh NK, Rai V. CRISPR-Cas9 directed genome engineering for enhancing salt stress tolerance in rice. Semin Cell Dev Biol 2019; 96:91-99. [PMID: 31075379 DOI: 10.1016/j.semcdb.2019.05.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 05/04/2019] [Accepted: 05/06/2019] [Indexed: 12/20/2022]
Abstract
Crop productivity in rice is harshly limited due to high concentration of salt in the soil. To understand the intricacies of the mechanism it is important to unravel the key pathways operating inside the plant cell. Emerging state-of-the art technologies have provided the tools to discover the key components inside the plant cell for salt tolerance. Among the molecular entities, transcription factors and/or other important components of sensing and signaling cascades have been the attractive targets and the role of NHX and SOS1 transporters amply described. Not only marker assisted programs but also transgenic approaches by using reverse genetic strategies (knockout or knockdown) or overexpression have been extensively used to engineer rice crop. CRISPR/Cas is an attractive paradigm and provides the feasibility for manipulating several genes simultaneously. Here, in this review we highlight some of the molecular entities that could be potentially targeted for generating rice amenable to sustain growth under high salinity conditions by employing CRISPR/Cas. We also try to address key questions for rice salt stress tolerance other than what is already known.
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Affiliation(s)
- Sufia Farhat
- National Institute for Plant Biotechnology, IARI, PUSA Campus, New Delhi 110012, India.
| | - Neha Jain
- National Institute for Plant Biotechnology, IARI, PUSA Campus, New Delhi 110012, India.
| | - Nisha Singh
- National Institute for Plant Biotechnology, IARI, PUSA Campus, New Delhi 110012, India.
| | - Rohini Sreevathsa
- National Institute for Plant Biotechnology, IARI, PUSA Campus, New Delhi 110012, India.
| | - Prasanta K Dash
- National Institute for Plant Biotechnology, IARI, PUSA Campus, New Delhi 110012, India.
| | - Rhitu Rai
- National Institute for Plant Biotechnology, IARI, PUSA Campus, New Delhi 110012, India.
| | - Sandeep Yadav
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Pramod Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Ananda K Sarkar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Ajay Jain
- Department of Biotechnology, Amity University, Jaipur, India.
| | - Nagendra K Singh
- National Institute for Plant Biotechnology, IARI, PUSA Campus, New Delhi 110012, India.
| | - Vandna Rai
- National Institute for Plant Biotechnology, IARI, PUSA Campus, New Delhi 110012, India.
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24
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Jiao Y, Wang J, Deng R, Yu X, Wang X. AcMNPV-miR-3 is a miRNA encoded by Autographa californica nucleopolyhedrovirus and regulates the viral infection by targeting ac101. Virus Res 2019; 267:49-58. [PMID: 31077766 DOI: 10.1016/j.virusres.2019.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 05/04/2019] [Accepted: 05/07/2019] [Indexed: 01/04/2023]
Abstract
MicroRNAs (miRNAs), which are small noncoding RNAs found in plants, animals, and many viruses, regulate various biological processes. Our group has previously reported the first miRNA encoded by Autographa californica multiple Nucleopolyhedrovirus (AcMNPV), AcMNPV-miR-1, which regulates the expression of three viral genes. This study characterizes another miRNA encoded by AcMNPV, AcMNPV-miR-3. This miRNA is located on the opposite strand of the viral gene ac101 coding sequence in the AcMNPV genome, and it can be detected at 6 h post-infection and accumulated to a peak around 12 h post-infection in AcMNPV infected Sf9 cells. Five viral genes (ac101, ac23, ac25, ac86, and ac98) were verified to be regulated by AcMNPV-miR-3. Ac101 was markedly down-regulated by AcMNPV-miR-3 that may be via a siRNA-like cleavage mode. Administrating excessive AcMNPV-miR-3 resulted in decreased production of infectious budded virions (BV) and accelerated the formation of occlusion-derived virions (ODV). These results suggest that AcMNPV-miR-3 may play a regulatory role in BV and ODV production.
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Affiliation(s)
- Yingzhen Jiao
- School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jinwen Wang
- School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Riqiang Deng
- School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Xinghua Yu
- School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Xunzhang Wang
- School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, China.
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25
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Karlik E, Ari S, Gozukirmizi N. LncRNAs: genetic and epigenetic effects in plants. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1581085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Elif Karlik
- Department of Biotechnology Institute of Graduate Studies in Science and Engineering, Istanbul University, Istanbul, Turkey
- Department of Molecular Biology and Genetics Faculty of Science, Istinye University, Istanbul, Turkey
| | - Sule Ari
- Department of Molecular Biology and Genetics Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Nermin Gozukirmizi
- Department of Molecular Biology and Genetics Faculty of Science, Istanbul University, Istanbul, Turkey
- Department of Molecular Biology and Genetics Faculty of Science, Istinye University, Istanbul, Turkey
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26
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Arora S, Pandey DK, Chaudhary B. Target-mimicry based diminution of miRNA167 reinforced flowering-time phenotypes in tobacco via spatial-transcriptional biases of flowering-associated miRNAs. Gene 2019; 682:67-80. [PMID: 30292869 DOI: 10.1016/j.gene.2018.10.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 08/29/2018] [Accepted: 10/04/2018] [Indexed: 11/24/2022]
Abstract
Evolutionarily conserved microRNAs such as miR156, miR159, miR167 and miR172 tightly regulate the extensive array of gene expression during flowering in plants, through instant and long-term alterations in the expression of their target genes. Here we employed a novel target-mimicry approach for the diminution of auxin signalling regulator miRNA167 by developing mimic-transgenic lines in tobacco, to investigate the transcriptional biases of flowering-associated miRNAs in apical and floral meristematic tissues and their phenotypic implications. Recorded morpho-alterations such as uneven flowering-time phenotypes, anomalous floral organ formation, and large variations in the seed forming characteristics permitted us to determine the consequence of the extent of miR167 expression diminution accompanying the transcriptional biases of interrelated miRNAs. We demonstrate that percent diminution of miR167 gene expression is proportionally associated with both early and late flowering-time phenotypes in mimic lines. Also, the associated miRNAs, miR156, miR159, and miR172 showed >90% transcriptional diminution in at least 'early-flowering' miR167 mimic lines. On contrary, low percentages of their respective diminution were recorded in 'late-flowering' lines. Evidently, the misexpression of miR156, miR159, and miR172 led to the over-expression of their respective target genes SPL9, AtMYB33-like and AP2 genes in mimic lines which resulted in assorted phenotypes. We describe the scope of spatial regulation of these microRNAs in floral bud tissues of mimic lines which showed negative- or very low (<25%) misexpression levels in early/late-flowering lines highlighting their roles in the acquisition of flowering mechanism. To our knowledge, this study represents the first characterization of transcriptional biases of flowering associated miRNAs in miR167-mimic lines and certainly augments our understanding of the importance of microRNA-mediated regulation of flowering in plants.
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Affiliation(s)
- Sakshi Arora
- School of Biotechnology, Gautam Buddha University, Greater Noida 201310 U.P., India
| | - Dhananjay K Pandey
- School of Biotechnology, Gautam Buddha University, Greater Noida 201310 U.P., India
| | - Bhupendra Chaudhary
- School of Biotechnology, Gautam Buddha University, Greater Noida 201310 U.P., India.
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27
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Armenta-Medina A, Gillmor CS. An Introduction to Methods for Discovery and Functional Analysis of MicroRNAs in Plants. Methods Mol Biol 2019; 1932:1-14. [PMID: 30701488 DOI: 10.1007/978-1-4939-9042-9_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
MicroRNAs play important roles in posttranscriptional regulation of plant development, metabolism, and abiotic stress responses. The recent generation of massive amounts of small RNA sequence data, along with development of bioinformatic tools to identify miRNAs and their mRNA targets, has led to an explosion of newly identified putative miRNAs in plants. Genome editing techniques like CRISPR-Cas9 will allow us to study the biological role of these potential novel miRNAs by efficiently targeting both the miRNA and its mRNA target. In this chapter, we review bioinformatic tools and experimental methods for the identification and functional characterization of miRNAs and their target mRNAs in plants.
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Affiliation(s)
- Alma Armenta-Medina
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - C Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico.
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28
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Wong G, Millar AA. The Use of MicroRNA Decoy Technologies to Inhibit miRNA Function in Arabidopsis. Methods Mol Biol 2019; 1932:227-238. [PMID: 30701504 DOI: 10.1007/978-1-4939-9042-9_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The study of gene function is best achieved through the generation of loss-of-function mutants. However, for many plant microRNAs (miRNAs), this has proven challenging, as they often belong to sequence-related families, which are encoded by multiple genes that are functionally redundant. To overcome this issue, transgenic methods have been developed that express miRNA decoys, which can sequester and inhibit families of sequence-related miRNAs. This includes miRNA MIMICs, SHORT TANDEM TARGET MIMICs, and miRNA SPONGEs. Here, we describe the methods to generate transgenic Arabidopsis that express these miRNA decoys in order to determine miRNA function.
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Affiliation(s)
- Gigi Wong
- Research School of Biology, Plant Science Division, Australian National University, Canberra, ACT, Australia
| | - Anthony A Millar
- Research School of Biology, Plant Science Division, Australian National University, Canberra, ACT, Australia.
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29
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Abstract
BACKGROUND MicroRNAs (miRNAs) are small noncoding RNAs that play important roles in plant development and stress responses. Loss-of-function analysis of miRNA genes has been traditionally challenging due to lack of appropriate knockout tools. In this chapter, we describe a method of using CRISPR-Cas9 for knocking out microRNA genes in rice by Agrobacterium-mediated transformation. We also demonstrate single-strand conformation polymorphism (SSCP) as an effective genotyping method for screening CRISPR-Cas9-induced mutations.
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30
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Zhang Y, Zhang Q, Hao L, Wang S, Wang S, Zhang W, Xu C, Yu Y, Li T. A novel miRNA negatively regulates resistance to Glomerella leaf spot by suppressing expression of an NBS gene in apple. HORTICULTURE RESEARCH 2019; 6:93. [PMID: 31645951 PMCID: PMC6804642 DOI: 10.1038/s41438-019-0175-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/13/2019] [Accepted: 06/15/2019] [Indexed: 05/07/2023]
Abstract
Glomerella leaf spot (GLS) of apple (Malus×domestica Borkh.), caused by Glomerella cingulata, is an emerging fungal epidemic threatening the apple industry. Little is known about the molecular mechanism underlying resistance to this devastating fungus. In this study, high-throughput sequencing technology was used to identify microRNAs (miRNAs) involved in GLS resistance in apple. We focused on miRNAs that target genes related to disease and found that expression of a novel miRNA, Md-miRln20, was higher in susceptible apple varieties than in resistant ones. Furthermore, its target gene Md-TN1-GLS exhibited the opposite expression pattern, which suggested that the expression levels of Md-miRln20 and its target gene are closely related to apple resistance to GLS. Furthermore, downregulation of Md-miRln20 in susceptible apple leaves resulted in upregulation of Md-TN1-GLS and reduced the disease incidence. Conversely, overexpression of Md-miRln20 in resistant apple leaves suppressed Md-TN1-GLS expression, with increased disease incidence. We demonstrated that Md-miRln20 negatively regulates resistance to GLS by suppressing Md-TN1-GLS expression and showed, for the first time, a crucial role for miRNA in response to GLS in apple.
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Affiliation(s)
- Yi Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Qiulei Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Li Hao
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Shengnan Wang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Shengyuan Wang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Wenna Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Chaoran Xu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Yunfei Yu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Tianzhong Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
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31
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Felden B, Gilot D. Modulation of Bacterial sRNAs Activity by Epigenetic Modifications: Inputs from the Eukaryotic miRNAs. Genes (Basel) 2018; 10:genes10010022. [PMID: 30602712 PMCID: PMC6356536 DOI: 10.3390/genes10010022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 12/18/2018] [Accepted: 12/21/2018] [Indexed: 12/14/2022] Open
Abstract
Trans-encoded bacterial regulatory RNAs (sRNAs) are functional analogues of eukaryotic microRNAs (miRNAs). These RNA classes act by base-pairing complementarity with their RNA targets to modulate gene expression (transcription, half-life and/or translation). Based on base-pairing, algorithms predict binding and the impact of small RNAs on targeted-RNAs expression and fate. However, other actors are involved such as RNA binding proteins and epigenetic modifications of the targeted and small RNAs. Post-transcriptional base modifications are widespread in all living organisms where they lower undesired RNA folds through conformation adjustments and influence RNA pairing and stability, especially if remodeling their ends. In bacteria, sRNAs possess RNA modifications either internally (methylation, pseudouridinylation) or at their ends. Nicotinamide adenine dinucleotide were detected at 5′-ends, and polyadenylation can occur at 3′-ends. Eukaryotic miRNAs possess N6-methyladenosine (m6A), A editing into I, and non-templated addition of uridines at their 3′-ends. Biological functions and enzymes involved in those sRNA and micro RNA epigenetic modifications, when known, are presented and challenged.
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Affiliation(s)
- Brice Felden
- University of Rennes 1, Inserm, BRM (Bacterial Regulatory RNAs and Medicine), UMR_S 1230, F-35043 Rennes, France.
| | - David Gilot
- CNRS UMR 6290, IGDR, University of Rennes 1, F-35043 Rennes, France.
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32
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Peng T, Qiao M, Liu H, Teotia S, Zhang Z, Zhao Y, Wang B, Zhao D, Shi L, Zhang C, Le B, Rogers K, Gunasekara C, Duan H, Gu Y, Tian L, Nie J, Qi J, Meng F, Huang L, Chen Q, Wang Z, Tang J, Tang X, Lan T, Chen X, Wei H, Zhao Q, Tang G. A Resource for Inactivation of MicroRNAs Using Short Tandem Target Mimic Technology in Model and Crop Plants. MOLECULAR PLANT 2018; 11:1400-1417. [PMID: 30243763 DOI: 10.1016/j.molp.2018.09.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 08/01/2018] [Accepted: 09/06/2018] [Indexed: 05/04/2023]
Abstract
microRNAs (miRNAs) are endogenous small non-coding RNAs that bind to mRNAs and target them for cleavage and/or translational repression, leading to gene silencing. We previously developed short tandem target mimic (STTM) technology to deactivate endogenous miRNAs in Arabidopsis. Here, we created hundreds of STTMs that target both conserved and species-specific miRNAs in Arabidopsis, tomato, rice, and maize, providing a resource for the functional interrogation of miRNAs. We not only revealed the functions of several miRNAs in plant development, but also demonstrated that tissue-specific inactivation of a few miRNAs in rice leads to an increase in grain size without adversely affecting overall plant growth and development. RNA-seq and small RNA-seq analyses of STTM156/157 and STTM165/166 transgenic plants revealed the roles of these miRNAs in plant hormone biosynthesis and activation, secondary metabolism, and ion-channel activity-associated electrophysiology, demonstrating that STTM technology is an effective approach for studying miRNA functions. To facilitate the study and application of STTM transgenic plants and to provide a useful platform for storing and sharing of information about miRNA-regulated gene networks, we have established an online Genome Browser (https://blossom.ffr.mtu.edu/designindex2.php) to display the transcriptomic and miRNAomic changes in STTM-induced miRNA knockdown plants.
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Affiliation(s)
- Ting Peng
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Mengmeng Qiao
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Haiping Liu
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Sachin Teotia
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Zhanhui Zhang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Yafan Zhao
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China
| | - Bobo Wang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China
| | - Dongjie Zhao
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Lina Shi
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Cui Zhang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Brandon Le
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Kestrel Rogers
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Chathura Gunasekara
- School of Forest Resources and Environmental Science, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Haitang Duan
- Department of Computer Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Yiyou Gu
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Lei Tian
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Jinfu Nie
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, China; Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jian Qi
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, China
| | - Fanrong Meng
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Lan Huang
- College of Information and Electrical Engineering, China Agricultural University, Beijing 100083, China
| | - Qinghui Chen
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA; Department of Kinesiology and Integrative Physiology, Life Science and Technology Instituted, Michigan Technological University, Houghton, MI 49931, USA
| | - Zhenlin Wang
- Department of Computer Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Jinshan Tang
- School of Technology, Michigan Technological University, Houghton, MI 49931, USA
| | - Xiaoqing Tang
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Ting Lan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA; Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China.
| | - Hairong Wei
- School of Forest Resources and Environmental Science, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, P.R. China.
| | - Quanzhi Zhao
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China.
| | - Guiliang Tang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA; Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China; Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, China.
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33
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Devi K, Dey KK, Singh S, Mishra SK, Modi MK, Sen P. Identification and validation of plant miRNA from NGS data—an experimental approach. Brief Funct Genomics 2018; 18:13-22. [DOI: 10.1093/bfgp/ely034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 09/17/2018] [Accepted: 10/02/2018] [Indexed: 12/18/2022] Open
Affiliation(s)
- Kamalakshi Devi
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | - Kuntal Kumar Dey
- Distributed Information Centre, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | - Sanjay Singh
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | | | - Mahendra Kumar Modi
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
- Distributed Information Centre, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | - Priyabrata Sen
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
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34
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35
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Wong G, Alonso‐Peral M, Li B, Li J, Millar AA. MicroRNA MIMIC binding sites: Minor flanking nucleotide alterations can strongly impact MIMIC silencing efficacy in Arabidopsis. PLANT DIRECT 2018; 2:e00088. [PMID: 31245688 PMCID: PMC6508833 DOI: 10.1002/pld3.88] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/19/2018] [Accepted: 09/25/2018] [Indexed: 05/12/2023]
Abstract
In plants, microRNA (miRNA) target MIMICs (MIMs) have been widely used to inhibit miRNA function. They are based on the Arabidopsis INSENSITIVE TO PHOSPATE STARVATION 1 (IPS1) gene that corresponds to a non-coding RNA containing a miR399 binding site that can be modified to sequester and inhibit any miRNA of interest. However, the efficacy of miRNA inhibition of these different MIMs can vary greatly. Using MIMs that have strong efficacy (MIM159) and poor efficacy (MIM165), we investigate the underlying cause of this variation. Firstly, sequence alignments of IPS1 homologs from the Brassicaceae identified a highly conserved sequence immediately downstream of the miRNA binding site. Mutating this sequence in the context of the MIM159 attenuates its strong efficacy. This conserved flanking region contains a predicted stem-loop structure that is also predicted to be present in most modified MIMs that appear to have a strong efficacy, but not in MIM165 that has a poor efficacy. Restoring this predicted stem-loop in MIM165 via mutation of only three or five nucleotides within the conserved flanking region resulted in MIM165 variants that have very strong efficacies of miRNA inhibition. However, specifically mutating this predicted stem-loop in the MIM159 context failed to significantly reduce efficacy, and additional mutations to restore this predicted stem-loop weakened efficacy further. Although this shows there is no simple correlation between this predicted stem-loop and efficacy, these results add to the growing evidence that the sequence context of miRNA binding sites is important, and that minor nucleotide substitutions to flanking sequences of miRNA binding sites can strongly enhance or attenuate the miRNA-target interaction.
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Affiliation(s)
- Gigi Wong
- Division of Plant ScienceResearch School of BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Maria Alonso‐Peral
- Division of Plant ScienceResearch School of BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Bingjun Li
- Division of Plant ScienceResearch School of BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Junyan Li
- Division of Plant ScienceResearch School of BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Anthony A. Millar
- Division of Plant ScienceResearch School of BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
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36
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Borah P, Das A, Milner MJ, Ali A, Bentley AR, Pandey R. Long Non-Coding RNAs as Endogenous Target Mimics and Exploration of Their Role in Low Nutrient Stress Tolerance in Plants. Genes (Basel) 2018; 9:E459. [PMID: 30223541 PMCID: PMC6162444 DOI: 10.3390/genes9090459] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/05/2018] [Accepted: 09/07/2018] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNA (lncRNA) research in plants has recently gained momentum taking cues from studies in animals systems. The availability of next-generation sequencing has enabled genome-wide identification of lncRNA in several plant species. Some lncRNAs are inhibitors of microRNA expression and have a function known as target mimicry with the sequestered transcript known as an endogenous target mimic (eTM). The lncRNAs identified to date show diverse mechanisms of gene regulation, most of which remain poorly understood. In this review, we discuss the role of identified putative lncRNAs that may act as eTMs for nutrient-responsive microRNAs (miRNAs) in plants. If functionally validated, these putative lncRNAs would enhance current understanding of the role of lncRNAs in nutrient homeostasis in plants.
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Affiliation(s)
- Priyanka Borah
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110 012, India.
- Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Antara Das
- ICAR-National Research Centre on Plant Biotechnology, New Delhi 110012, India.
| | - Matthew J Milner
- The John Bingham Laboratory, National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge CB30LE, UK.
| | - Arif Ali
- Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Alison R Bentley
- The John Bingham Laboratory, National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge CB30LE, UK.
| | - Renu Pandey
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110 012, India.
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Lou S, Sun T, Li H, Hu Z. Mechanisms of microRNA-mediated gene regulation in unicellular model alga Chlamydomonas reinhardtii. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:244. [PMID: 30202439 PMCID: PMC6129010 DOI: 10.1186/s13068-018-1249-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/31/2018] [Indexed: 05/30/2023]
Abstract
MicroRNAs are a class of endogenous non-coding RNAs that play a vital role in post-transcriptional gene regulation in eukaryotic cells. In plants and animals, miRNAs are implicated in diverse roles ranging from immunity against viral infections, developmental pathways, molecular pathology of cancer and regulation of protein expression. However, the role of miRNAs in the unicellular model green alga Chlamydomonas reinhardtii remains unclear. The mode of action of miRNA-induced gene silencing in C. reinhardtii is very similar to that of higher eukaryotes, in terms of the activation of the RNA-induced silencing complex and mRNA targeting. Certain studies indicate that destabilization of mRNAs and mRNA turnover could be the major possible functions of miRNAs in eukaryotic algae. Here, we summarize recent findings that have advanced our understanding of miRNA regulatory mechanisms in C. reinhardtii.
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Affiliation(s)
- Sulin Lou
- Guangdong Key Laboratory of Plant Epigenetics, Guangdong Engineering Research Center for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Key Laboratory of Optoeletronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoeletronic Engineering, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Ting Sun
- Guangdong Key Laboratory of Plant Epigenetics, Guangdong Engineering Research Center for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Key Laboratory of Optoeletronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoeletronic Engineering, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Hui Li
- Guangdong Key Laboratory of Plant Epigenetics, Guangdong Engineering Research Center for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Zhangli Hu
- Guangdong Key Laboratory of Plant Epigenetics, Guangdong Engineering Research Center for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
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Zhang B, Unver T. A critical and speculative review on microRNA technology in crop improvement: Current challenges and future directions. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 274:193-200. [PMID: 30080603 DOI: 10.1016/j.plantsci.2018.05.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 05/21/2018] [Accepted: 05/26/2018] [Indexed: 05/24/2023]
Abstract
MicroRNAs (miRNAs) lie at the center of gene regulation and, as such, have become novel targets for crop improvement including the enhancement of crop quality and yields as well as responses to environmental stresses. There are several major issues related to miRNA technology including the functional analysis of miRNAs and their nomenclature. In this critical and speculative review, we recommend several directions for future plant miRNA research and perspectives. Research on miRNA needs to be extended from merely descriptive studies to functional studies. More genetic tools, such as genome editing, should be developed for miRNA functional study. Obtaining transgenic plants is a bottleneck for plant miRNA functional studies and, hence, more reliable transformation methods need to be developed. We also propose a new terminology approach for miRNA nomenclature. The current miRNA nomenclature is confusing and has mislead much research. Here we suggest to name a miRNA as miR#-5p or -3p, and to name their opposite strand as miR#*-3p or -5p. The advantages of the new nomenclature is that it covers information on the history, relationship, family, and location of an individual miRNA. It recognizes both traditional and new discovery.
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Affiliation(s)
- Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA.
| | - Turgay Unver
- International Biomedicine and Genome Institute (iBG-izmir), Dokuz Eylül University, Balcova 35340 Izmir, Turkey
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Rosa C, Kuo YW, Wuriyanghan H, Falk BW. RNA Interference Mechanisms and Applications in Plant Pathology. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:581-610. [PMID: 29979927 DOI: 10.1146/annurev-phyto-080417-050044] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The origin of RNA interference (RNAi), the cell sentinel system widely shared among eukaryotes that recognizes RNAs and specifically degrades or prevents their translation in cells, is suggested to predate the last eukaryote common ancestor ( 138 ). Of particular relevance to plant pathology is that in plants, but also in some fungi, insects, and lower eukaryotes, RNAi is a primary and effective antiviral defense, and recent studies have revealed that small RNAs (sRNAs) involved in RNAi play important roles in other plant diseases, including those caused by cellular plant pathogens. Because of this, and because RNAi can be manipulated to interfere with the expression of endogenous genes in an intra- or interspecific manner, RNAi has been used as a tool in studies of gene function but also for plant protection. Here, we review the discovery of RNAi, canonical mechanisms, experimental and translational applications, and new RNA-based technologies of importance to plant pathology.
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Affiliation(s)
- Cristina Rosa
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Yen-Wen Kuo
- Department of Plant Pathology, University of California, Davis, California 95616, USA;
| | - Hada Wuriyanghan
- School of Life Sciences, University of Inner Mongolia, Hohhot, Inner Mongolia 010021, China
| | - Bryce W Falk
- Department of Plant Pathology, University of California, Davis, California 95616, USA;
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Pan J, Huang D, Guo Z, Kuang Z, Zhang H, Xie X, Ma Z, Gao S, Lerdau MT, Chu C, Li L. Overexpression of microRNA408 enhances photosynthesis, growth, and seed yield in diverse plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:323-340. [PMID: 29330900 DOI: 10.1111/jipb.12634] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 01/10/2018] [Indexed: 05/21/2023]
Abstract
The ability of a plant to produce grain, fruit, or forage depends ultimately on photosynthesis. There have been few attempts, however, to study microRNAs, which are a class of endogenous small RNAs post-transcriptionally programming gene expression, in relation to photosynthetic traits. We focused on miR408, one of the most conserved plant miRNAs, and overexpressed it in parallel in Arabidopsis, tobacco, and rice. The transgenic plants all exhibited increased copper content in the chloroplast, elevated abundance of plastocyanin, and an induction of photosynthetic genes. By means of gas exchange and optical spectroscopy analyses, we showed that higher expression of miR408 leads to enhanced photosynthesis through improving efficiency of irradiation utilization and the capacity for carbon dioxide fixation. Consequently, miR408 hyper-accumulating plants exhibited higher rate of vegetative growth. An enlargement of seed size was also observed in all three species overproducing miR408. Moreover, we conducted a 2-year-two-location field trial and observed miR408 overexpression in rice significantly increased yield, which was primarily attributed to an elevation in grain weight. Taken together, these results demonstrate that miR408 is a positive regulator of photosynthesis and that its genetic engineering is a promising route for enhancing photosynthetic performance and yield in diverse plants.
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Affiliation(s)
- Jiawei Pan
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Dahui Huang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Zhonglong Guo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Zheng Kuang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - He Zhang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Xinyu Xie
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Zengfeng Ma
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Shaopei Gao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Manuel T Lerdau
- Department of Environmental Sciences, University of Virginia, Charlottesville, VA 22903, USA
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
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41
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Cho J. Transposon-Derived Non-coding RNAs and Their Function in Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:600. [PMID: 29774045 PMCID: PMC5943564 DOI: 10.3389/fpls.2018.00600] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/16/2018] [Indexed: 05/03/2023]
Abstract
Transposable elements (TEs) are often regarded as harmful genomic factors and indeed they are strongly suppressed by the epigenetic silencing mechanisms. On the other hand, the mobilization of TEs brings about variability of genome and transcriptome which are essential in the survival and evolution of the host species. The vast majority of such controlling TEs influence the neighboring genes in cis by either promoting or repressing the transcriptional activities. Although TEs are highly repetitive in the genomes and transcribed in specific stress conditions or developmental stages, the trans-acting regulatory roles of TE-derived RNAs have been rarely studied. It was only recently that TEs were investigated for their regulatory roles as a form of RNA. Particularly in plants, TEs are ample source of small RNAs such as small interfering (si) RNAs and micro (mi) RNAs. Those TE-derived small RNAs have potentials to affect non-TE transcripts by sequence complementarity, thereby generating novel gene regulatory networks including stress resistance and hybridization barrier. Apart from the small RNAs, a number of long non-coding RNAs (lncRNAs) are originated from TEs in plants. For example, a retrotransposon-derived lncRNA expressed in rice root acts as a decoy RNA or miRNA target mimic which negatively controls miRNA171. The post-transcriptional suppression of miRNA171 in roots ensures the stabilization of the target transcripts encoding SCARECROW-LIKE transcription factors, the key regulators of root development. In this review article, the recent discoveries of the regulatory roles of TE-derived RNAs in plants will be highlighted.
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42
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A non-coding function of TYRP1 mRNA promotes melanoma growth. Nat Cell Biol 2017; 19:1348-1357. [PMID: 28991221 DOI: 10.1038/ncb3623] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 09/06/2017] [Indexed: 02/07/2023]
Abstract
Competition among RNAs to bind miRNA is proposed to influence biological systems. However, the role of this competition in disease onset is unclear. Here, we report that TYRP1 mRNA, in addition to encoding tyrosinase-related protein 1 (TYRP1), indirectly promotes cell proliferation by sequestering miR-16 on non-canonical miRNA response elements. Consequently, the sequestered miR-16 is no longer able to repress its mRNA targets, such as RAB17, which is involved in melanoma cell proliferation and tumour growth. Restoration of miR-16 tumour-suppressor function can be achieved in vitro by silencing TYRP1 or increasing miR-16 expression. Importantly, TYRP1-dependent miR-16 sequestration can also be overcome in vivo by using small oligonucleotides that mask miR-16-binding sites on TYRP1 mRNA. Together, our findings assign a pathogenic non-coding function to TYRP1 mRNA and highlight miRNA displacement as a promising targeted therapeutic approach for melanoma.
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Abstract
Small RNAs, including microRNAs (miRNAs), are abundant in plants and play key roles in controlling plant development and physiology. miRNAs regulate the expression of the target genes involved in key plant processes. Due to functional redundancy among miRNA family members in plants, an ideal approach to silence the expression of all members simultaneously, for their functional characterization, is desirable. Target mimic (TM) was the first approach to achieve this goal. Short tandem target mimic (STTM) is a potent approach complementing TM for silencing miRNAs in plants. STTMs have been successfully used in dicots to block miRNA functions. Here, we describe in detail the protocol for designing STTM construct to block miRNA functions in rice. Such approach can be applied to silence miRNAs in other monocots as well.
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Affiliation(s)
- Sachin Teotia
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, 49931, USA
| | - Dabing Zhang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guiliang Tang
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, 49931, USA.
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Zhou J, Deng K, Cheng Y, Zhong Z, Tian L, Tang X, Tang A, Zheng X, Zhang T, Qi Y, Zhang Y. CRISPR-Cas9 Based Genome Editing Reveals New Insights into MicroRNA Function and Regulation in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:1598. [PMID: 28955376 PMCID: PMC5602353 DOI: 10.3389/fpls.2017.01598] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 08/31/2017] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that play important roles in plant development and stress responses. Loss-of-function analysis of miRNA genes has been traditionally challenging due to lack of appropriate knockout tools. In this study, single miRNA genes (OsMIR408 and OsMIR528) and miRNA gene families (miR815a/b/c and miR820a/b/c) in rice were targeted by CRISPR-Cas9. We showed single strand conformation polymorphism (SSCP) is a more reliable method than restriction fragment length polymorphism (RFLP) for identifying CRISPR-Cas9 generated mutants. Frequencies of targeted mutagenesis among regenerated T0 lines ranged from 48 to 89% at all tested miRNA target sites. In the case of miRNA528, three independent guide RNAs (gRNAs) all generated biallelic mutations among confirmed mutant lines. When targeted by two gRNAs, miRNA genes were readily to be deleted at a frequency up to 60% in T0 rice lines. Thus, we demonstrate CRISPR-Cas9 is an effective tool for knocking out plant miRNAs. Single-base pair (bp) insertion/deletion mutations (indels) in mature miRNA regions can lead to the generation of functionally redundant miRNAs. Large deletions at either the mature miRNA or the complementary miRNA* were found to readily abolish miRNA function. Utilizing mutants of OsMIR408 and OsMIR528, we find that knocking out a single miRNA can result in expression profile changes of many other seemingly unrelated miRNAs. In a case study on OsMIR528, we reveal it is a positive regulator in salt stress. Our work not only provides empirical guidelines on targeting miRNAs with CRISPR-Cas9, but also brings new insights into miRNA function and complex cross-regulation in rice.
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Affiliation(s)
- Jianping Zhou
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of ChinaChengdu, China
| | - Kejun Deng
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of ChinaChengdu, China
| | - Yan Cheng
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of ChinaChengdu, China
| | - Zhaohui Zhong
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of ChinaChengdu, China
| | - Li Tian
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of ChinaChengdu, China
| | - Xu Tang
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of ChinaChengdu, China
| | - Aiting Tang
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of ChinaChengdu, China
| | - Xuelian Zheng
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of ChinaChengdu, China
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou UniversityYangzhou, China
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of MarylandCollege Park, MD, United States
- Institute for Bioscience and Biotechnology Research, University of MarylandRockville, MD, United States
- *Correspondence: Yiping Qi
| | - Yong Zhang
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of ChinaChengdu, China
- Yong Zhang
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Teotia S, Tang G. Silencing of Stress-Regulated miRNAs in Plants by Short Tandem Target Mimic (STTM) Approach. Methods Mol Biol 2017; 1631:337-348. [PMID: 28735409 DOI: 10.1007/978-1-4939-7136-7_22] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In plants, microRNAs (miRNAs) regulate more than hundred target genes comprising largely transcription factors that control growth and development as well as stress responses. However, the exact functions of miRNA families could not be deciphered because each miRNA family has multiple loci in the genome, thus are functionally redundant. Therefore, an ideal approach to study the function of a miRNA family is to silence the expression of all members simultaneously, which is a daunting task. However, this can be partly overcome by Target Mimic (TM) approach that can knockdown an entire miRNA family. STTM is a modification of TM approach and complements it. STTMs have been successfully used in monocots and dicots to block miRNA functions. miR159 has been shown to be differentially regulated by various abiotic stresses including ABA in various plant species. Here, we describe in detail the protocol for designing STTM construct to block miR159 functions in Arabidopsis, with the potential to apply this technique on a number of other stress-regulated miRNAs in plants.
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Affiliation(s)
- Sachin Teotia
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201312, India
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Dr, Houghton, MI, 49931, USA
| | - Guiliang Tang
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Dr, Houghton, MI, 49931, USA.
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Zhang Q, Li Y, Zhang Y, Wu C, Wang S, Hao L, Wang S, Li T. Md-miR156ab and Md-miR395 Target WRKY Transcription Factors to Influence Apple Resistance to Leaf Spot Disease. FRONTIERS IN PLANT SCIENCE 2017; 8:526. [PMID: 28469624 PMCID: PMC5395612 DOI: 10.3389/fpls.2017.00526] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/24/2017] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are key regulators of gene expression that post-transcriptionally regulate transcription factors involved in plant physiological activities. Little is known about the effects of miRNAs in disease resistance in apple (Malus×domestica). We globally profiled miRNAs in the apple cultivar Golden Delicious (GD) infected or not with the apple leaf spot fungus Alternaria alternaria f. sp. mali (ALT1), and identified 58 miRNAs that exhibited more than a 2-fold upregulation upon ALT1 infection. We identified a pair of miRNAs that target protein-coding genes involved in the defense response against fungal pathogens; Md-miR156ab targets a novel WRKY transcription factor, MdWRKYN1, which harbors a TIR and a WRKY domain. Md-miR395 targets another transcription factor, MdWRKY26, which contains two WRKY domains. Real-time PCR analysis showed that Md-miR156ab and Md-miR395 levels increased, while MdWRKYN1 and MdWRKY26 expression decreased in ALT1-inoculated GD leaves; furthermore, the overexpression of Md-miR156ab and Md-miR395 resulted in a significant reduction in MdWRKYN1 and MdWRKY26 expression. To investigate whether these miRNAs and their targets play a crucial role in plant defense, we overexpressed MdWRKYN1 or knocked down Md-miR156ab activity, which in both cases enhanced the disease resistance of the plants by upregulating the expression of the WRKY-regulated pathogenesis-related (PR) protein-encoding genes MdPR3-1, MdPR3-2, MdPR4, MdPR5, MdPR10-1, and MdPR10-2. In a similar analysis, we overexpressed MdWRKY26 or suppressed Md-miR395 activity, and found that many PR protein-encoding genes were also regulated by MdWRKY26. In GD, ALT-induced Md-miR156ab and Md-miR395 suppress MdWRKYN1 and MdWRKY26 expression, thereby decreasing the expression of some PR genes, and resulting in susceptibility to ALT1.
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47
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Zhang Q, Li Y, Zhang Y, Wu C, Wang S, Hao L, Wang S, Li T. Md-miR156ab and Md-miR395 Target WRKY Transcription Factors to Influence Apple Resistance to Leaf Spot Disease. FRONTIERS IN PLANT SCIENCE 2017; 8:526. [PMID: 28469624 DOI: 10.3389/fpls.2017.0052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/24/2017] [Indexed: 05/23/2023]
Abstract
MicroRNAs (miRNAs) are key regulators of gene expression that post-transcriptionally regulate transcription factors involved in plant physiological activities. Little is known about the effects of miRNAs in disease resistance in apple (Malus×domestica). We globally profiled miRNAs in the apple cultivar Golden Delicious (GD) infected or not with the apple leaf spot fungus Alternaria alternaria f. sp. mali (ALT1), and identified 58 miRNAs that exhibited more than a 2-fold upregulation upon ALT1 infection. We identified a pair of miRNAs that target protein-coding genes involved in the defense response against fungal pathogens; Md-miR156ab targets a novel WRKY transcription factor, MdWRKYN1, which harbors a TIR and a WRKY domain. Md-miR395 targets another transcription factor, MdWRKY26, which contains two WRKY domains. Real-time PCR analysis showed that Md-miR156ab and Md-miR395 levels increased, while MdWRKYN1 and MdWRKY26 expression decreased in ALT1-inoculated GD leaves; furthermore, the overexpression of Md-miR156ab and Md-miR395 resulted in a significant reduction in MdWRKYN1 and MdWRKY26 expression. To investigate whether these miRNAs and their targets play a crucial role in plant defense, we overexpressed MdWRKYN1 or knocked down Md-miR156ab activity, which in both cases enhanced the disease resistance of the plants by upregulating the expression of the WRKY-regulated pathogenesis-related (PR) protein-encoding genes MdPR3-1, MdPR3-2, MdPR4, MdPR5, MdPR10-1, and MdPR10-2. In a similar analysis, we overexpressed MdWRKY26 or suppressed Md-miR395 activity, and found that many PR protein-encoding genes were also regulated by MdWRKY26. In GD, ALT-induced Md-miR156ab and Md-miR395 suppress MdWRKYN1 and MdWRKY26 expression, thereby decreasing the expression of some PR genes, and resulting in susceptibility to ALT1.
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Affiliation(s)
- Qiulei Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural UniversityBeijing, China
| | - Yang Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural UniversityBeijing, China
| | - Yi Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural UniversityBeijing, China
| | - Chuanbao Wu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural UniversityBeijing, China
| | - Shengnan Wang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural UniversityBeijing, China
| | - Li Hao
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural UniversityBeijing, China
| | - Shengyuan Wang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural UniversityBeijing, China
| | - Tianzhong Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural UniversityBeijing, China
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48
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Migault M, Donnou-Fournet E, Galibert MD, Gilot D. Definition and identification of small RNA sponges: Focus on miRNA sequestration. Methods 2016; 117:35-47. [PMID: 27876678 DOI: 10.1016/j.ymeth.2016.11.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/18/2016] [Indexed: 02/09/2023] Open
Abstract
Targeting RNAs appears as an important opportunity to modulate biological processes. Here, we overviewed critical parameters implied in RNAs competition to bind small RNAs. These competitions influence small RNA availability and thereby gene expression and cell fate. We focused on the ability of RNAs to sequester small RNA, mainly the microRNAs (miRNAs) and proposed experimental workflows to demonstrate the existence and activity of RNA-sponge. From this basic science, we detailed tailored oligonucleotides, developed to challenge the binding of small RNA. In vitro and in vivo, these tailored oligonucleotides efficiently restore small RNA activity by preventing their sequestration on RNA-sponges.
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Affiliation(s)
- Mélodie Migault
- Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6290, Institut de Génétique et Développement de Rennes, France; Université de Rennes 1, Rennes, France; Cancer Research Association (ARC) Labelled Team, France
| | - Emmanuelle Donnou-Fournet
- Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6290, Institut de Génétique et Développement de Rennes, France; Université de Rennes 1, Rennes, France; Cancer Research Association (ARC) Labelled Team, France
| | - Marie-Dominique Galibert
- Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6290, Institut de Génétique et Développement de Rennes, France; Université de Rennes 1, Rennes, France; Cancer Research Association (ARC) Labelled Team, France; Department of Medical Genomic, Rennes University Hospital, Rennes, France.
| | - David Gilot
- Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6290, Institut de Génétique et Développement de Rennes, France; Université de Rennes 1, Rennes, France; Cancer Research Association (ARC) Labelled Team, France.
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49
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Zhao J, Liu Q, Hu P, Jia Q, Liu N, Yin K, Cheng Y, Yan F, Chen J, Liu Y. An efficient Potato virus X -based microRNA silencing in Nicotiana benthamiana. Sci Rep 2016; 6:20573. [PMID: 26837708 PMCID: PMC4738334 DOI: 10.1038/srep20573] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 01/06/2016] [Indexed: 01/25/2023] Open
Abstract
Plant microRNAs (miRNAs) play pivotal roles in many biological processes. Although many miRNAs have been identified in various plant species, the functions of these miRNAs remain largely unknown due to the shortage of effective genetic tools to block their functional activity. Recently, miRNA target mimic (TM) technologies have been applied to perturb the activity of specific endogenous miRNA or miRNA families. We previously reported that Tobacco rattle virus (TRV)-based TM expression can successfully mediate virus-based miRNA silencing/suppression (VbMS) in plants. In this study, we show the Potato virus X (PVX)-based TM expression causes strong miRNA silencing in Nicotiana benthamiana. The PVX-based expression of short tandem target mimic (STTMs) against miR165/166 and 159 caused the corresponding phenotype in all infected plants. Thus, a PVX-based VbMS is a powerful method to study miRNA function and may be useful for high-throughput investigation of miRNA function in N. benthamiana.
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Affiliation(s)
- Jinping Zhao
- Center for Plant Biology, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
- The State Key Laboratory Breeding Base for Sustainable control of Pest and Disease, Hangzhou, 310021, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Qingtao Liu
- Center for Plant Biology, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Pu Hu
- Center for Plant Biology, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qi Jia
- Center for Plant Biology, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Na Liu
- Center for Plant Biology, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Kangquan Yin
- Center for Plant Biology, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ye Cheng
- The State Key Laboratory Breeding Base for Sustainable control of Pest and Disease, Hangzhou, 310021, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Fei Yan
- The State Key Laboratory Breeding Base for Sustainable control of Pest and Disease, Hangzhou, 310021, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jianping Chen
- The State Key Laboratory Breeding Base for Sustainable control of Pest and Disease, Hangzhou, 310021, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yule Liu
- Center for Plant Biology, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
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50
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Teotia S, Singh D, Tang X, Tang G. Essential RNA-Based Technologies and Their Applications in Plant Functional Genomics. Trends Biotechnol 2016; 34:106-123. [PMID: 26774589 DOI: 10.1016/j.tibtech.2015.12.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/19/2015] [Accepted: 12/07/2015] [Indexed: 12/20/2022]
Abstract
Genome sequencing has not only extended our understanding of the blueprints of many plant species but has also revealed the secrets of coding and non-coding genes. We present here a brief introduction to and personal account of key RNA-based technologies, as well as their development and applications for functional genomics of plant coding and non-coding genes, with a focus on short tandem target mimics (STTMs), artificial microRNAs (amiRNAs), and CRISPR/Cas9. In addition, their use in multiplex technologies for the functional dissection of gene networks is discussed.
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Affiliation(s)
- Sachin Teotia
- Provincial State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China; School of Biotechnology, Gautam Buddha University, Greater Noida, UP 201312, India; Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA
| | - Deepali Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, UP 201312, India; Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA
| | - Xiaoqing Tang
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA
| | - Guiliang Tang
- Provincial State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA.
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