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Zhang Z, Yang T, Li N, Tang G, Tang J. MicroRNA166: Old Players and New Insights into Crop Agronomic Traits Improvement. Genes (Basel) 2024; 15:944. [PMID: 39062723 PMCID: PMC11276106 DOI: 10.3390/genes15070944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/14/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
MicroRNA (miRNA), a type of non-coding RNA, is crucial for controlling gene expression. Among the various miRNA families, miR166 stands out as a highly conserved group found in both model and crop plants. It plays a key role in regulating a wide range of developmental and environmental responses. In this review, we explore the diverse sequences of MIR166s in major crops and discuss the important regulatory functions of miR166 in plant growth and stress responses. Additionally, we summarize how miR166 interacts with other miRNAs and highlight the potential for enhancing agronomic traits by manipulating the expression of miR166 and its targeted HD-ZIP III genes.
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Affiliation(s)
- Zhanhui Zhang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China;
| | - Tianxiao Yang
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA;
| | - Na Li
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China;
| | - Guiliang Tang
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA;
| | - Jihua Tang
- The Shennong Laboratory, Zhengzhou 450002, China
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2
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Wang H, Yu R, Zhu Q, Tian Z, Li F. A highly sensitive biotin-based probe for small RNA northern blot and its application in dissecting miRNA function in pepper. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:263-276. [PMID: 38078656 DOI: 10.1111/tpj.16585] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/26/2023] [Accepted: 12/01/2023] [Indexed: 04/02/2024]
Abstract
Small RNAs play important roles in regulation of plant development and response to various stresses. Northern blot is an important technique in small RNA research. Isotope- and biotin- (or digoxigenin) labeled probes are frequently used in small RNA northern blot. However, isotope-based probe is limited by strict environmental regulation and availability in many places in the world while biotin-based probe is usually suffered from low sensitivity. In this study, we developed a T4 DNA polymerase-based method for incorporation of a cluster of 33 biotin-labeled C in small RNA probe (T4BC33 probe). T4BC33 probe reaches similar sensitivity as 32P-labeled probe in dot blot and small RNA northern blot experiments. Addition of locked nucleic acids in T4BC33 probe further enhanced its sensitivity in detecting low-abundance miRNAs. With newly developed northern blot method, expression of miR6027 and miR6149 family members was validated. Northern blot analysis also confirmed the successful application of virus-based miRNA silencing in pepper, knocking down accumulation of Can-miR6027a and Can-miR6149L. Importantly, further analysis showed that knocking-down Can-miR6027a led to upregulation of a nucleotide binding-leucine rich repeat domain protein coding gene (CaRLb1) and increased immunity against Phytophthora capsici in pepper leaves. Our study provided a highly sensitive and convenient method for sRNA research and identified new targets for genetic improvement of pepper immunity against P. capsici.
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Affiliation(s)
- Hongzheng Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ruimin Yu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiangqiang Zhu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhendong Tian
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Feng Li
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, 430070, China
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3
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Wu J, Zhang Y, Li F, Zhang X, Ye J, Wei T, Li Z, Tao X, Cui F, Wang X, Zhang L, Yan F, Li S, Liu Y, Li D, Zhou X, Li Y. Plant virology in the 21st century in China: Recent advances and future directions. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:579-622. [PMID: 37924266 DOI: 10.1111/jipb.13580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/02/2023] [Indexed: 11/06/2023]
Abstract
Plant viruses are a group of intracellular pathogens that persistently threaten global food security. Significant advances in plant virology have been achieved by Chinese scientists over the last 20 years, including basic research and technologies for preventing and controlling plant viral diseases. Here, we review these milestones and advances, including the identification of new crop-infecting viruses, dissection of pathogenic mechanisms of multiple viruses, examination of multilayered interactions among viruses, their host plants, and virus-transmitting arthropod vectors, and in-depth interrogation of plant-encoded resistance and susceptibility determinants. Notably, various plant virus-based vectors have also been successfully developed for gene function studies and target gene expression in plants. We also recommend future plant virology studies in China.
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Affiliation(s)
- Jianguo Wu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongliang Zhang
- State Key Laboratory of Plant Environmental Resilience and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Fangfang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Ye
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Taiyun Wei
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhenghe Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xiaorong Tao
- Department of Plant Pathology, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Cui
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianbing Wang
- State Key Laboratory of Plant Environmental Resilience and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Lili Zhang
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Shifang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Dawei Li
- State Key Laboratory of Plant Environmental Resilience and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yi Li
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
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4
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Singh V, Lone RA, Kumar V, Mohanty CS. Reducing the biosynthesis of condensed tannin in winged bean ( Psophocarpus tetragonolobus (L.) DC.) by virus-induced gene silencing of anthocyanidin synthase (ANS) gene. 3 Biotech 2023; 13:16. [PMID: 36561838 PMCID: PMC9763518 DOI: 10.1007/s13205-022-03435-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
The Underutilized legume-winged bean (Psophocarpus tetragonolobus (L.) DC.) and its various parts are infested with condensed tannin (CT) or proanthocyanidin (PA). CT has anti-nutritional effect as it adversely affects the digestion of proteins, minerals and vitamin among ruminants and humans. It is also responsible for low protein digestibility and decreased amino acid availability. One of the probable reasons of underutilization of P. tetragonolobus is due to its infestation with CT. Histochemical staining of various tissues of P. tetragonolobus with dimethylcinnmaldehyde (DMACA) developed a deep-blue colour indicating the presence of polyphenolic condensed tannin. Structural monomeric unit catechin and epi-catechin were reported to be responsible for biosynthesis of CT in P. tetragonolobus. The enzyme anthocyanidin synthase (ANS) and its corresponding transcripts were identified and phylogenetically mapped. The transcript was subjected to virus-induced gene silencing (VIGS) through agro-infiltration in P. tetragonolobus for reducing the CT-content. The WbANS-VIGS induced P. tetragonolobus resulted in four-fold decrease of CT as compared to the control P. tetragonolobus. A decrease of 73% of CT level was reported in VIGS silenced Wb-ANS line of P. tetragonolobus. This study resulted and confirmed that, the silencing of (ANS) gene in P. tetragonolobus has a regulatory effect on the condensed tannin biosynthesis. This study will pave way for further manipulation of ANS enzyme for reducing the biosynthesis of the anti-nutrient CT. Reducing the CT content will make this underutilized legume more acceptable. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03435-5.
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Affiliation(s)
- Vinayak Singh
- Plant Genetic Resources and Improvement Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 Uttar Pradesh India
- Department of Biology, Western University, London, Ontario Canada
| | - Rayees Ahmad Lone
- Plant Genetic Resources and Improvement Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 Uttar Pradesh India
- Academy of Scientific and Innovative Research, Ghaziabad, 201002 India
| | - Verandra Kumar
- Plant Genetic Resources and Improvement Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 Uttar Pradesh India
| | - Chandra Sekhar Mohanty
- Plant Genetic Resources and Improvement Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 Uttar Pradesh India
- Academy of Scientific and Innovative Research, Ghaziabad, 201002 India
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5
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Guo G, Li MJ, Lai JL, Du ZY, Liao QS. Development of tobacco rattle virus-based platform for dual heterologous gene expression and CRISPR/Cas reagent delivery. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111491. [PMID: 36216296 DOI: 10.1016/j.plantsci.2022.111491] [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: 06/26/2022] [Revised: 09/29/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
A large number of viral delivery systems have been developed for characterizing functional genes and producing heterologous recombinant proteins in plants, and but most of them are unable to co-express two fusion-free foreign proteins in the whole plant for extended periods of time. In this study, we modified tobacco rattle virus (TRV) as a TRVe dual delivery vector, using the strategy of gene substitution. The reconstructed TRVe had the capability to simultaneously produce two fusion-free foreign proteins at the whole level of Nicotiana benthamiana, and maintained the genetic stability for the insert of double foreign genes. Moreover, TRVe allowed systemic expression of two foreign proteins with the total lengths up to ∼900 aa residues. In addition, Cas12a protein and crRNA were delivered by the TRVe expression system for site-directed editing of genomic DNA in N. benthamiana 16c line constitutively expressing green fluorescent protein (GFP). Taker together, the TRV-based delivery system will be a simple and powerful means to rapidly co-express two non-fused foreign proteins at the whole level and facilitate functional genomics studies in plants.
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Affiliation(s)
- Ge Guo
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Meng-Jiao Li
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Jia-Liang Lai
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Zhi-You Du
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Qian-Sheng Liao
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China.
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6
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Shi G, Wang S, Wang P, Zhan J, Tang Y, Zhao G, Li F, Ge X, Wu J. Cotton miR393-TIR1 Module Regulates Plant Defense Against Verticillium dahliae via Auxin Perception and Signaling. FRONTIERS IN PLANT SCIENCE 2022; 13:888703. [PMID: 35592575 PMCID: PMC9111529 DOI: 10.3389/fpls.2022.888703] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 03/24/2022] [Indexed: 06/15/2023]
Abstract
Plant auxin is essential in plant growth and development. However, the molecular mechanisms of auxin involvement in plant immunity are unclear. Here, we addressed the function of the cotton (Gossypium hirsutum) miR393-TIR1 module in plant defense against Verticillium dahliae infection via auxin perception and signaling. GhTIR1 was directedly cleaved by ghr-miR393 according to mRNA degradome data, 5'-RACE analysis, and a GUS reporter assay. Ghr-miR393 knockdown significantly increased plant susceptibility to V. dahliae compared to the control, while ghr-miR393 overexpression and GhTIR1 knockdown significantly increased plant resistance. External indole-3-acetic acid (IAA) application significantly enhanced susceptibility to V. dahliae in ghr-miR393 knockdown and control plants compared to mock treatment, and only slightly increased susceptibility in overexpressing ghr-miR393 and GhTIR1-silenced plants. Application of external PEO-IAA (an auxin antagonist) had a contrary trend with IAA application. Based on yeast two-hybrid and bimolecular fluorescence complementation assays, GhTIR1 interacted with GhIAA14 in the nucleus, and GhIAA14 knockdown reduced plant resistance to V. dahliae infection. The results suggested that the ghr-miR393-GhTIR1 module regulates plant defense via auxin perception and signaling. Additionally, simultaneous knockdown of GhTIR1 and GhICS1 significantly increased plant susceptibility to V. dahliae compared to the control, indicating that salicylic acid (SA) accumulation is vital for the ghr-miR393-GhTIR1 module to regulates plant resistance. Transcriptome data also demonstrated that GhTIR1 knockdown significantly downregulated expression of auxin-related genes and upregulated expression of SA-related genes. Overall, the ghr-miR393-GhTIR1 module participates in plant response to V. dahliae infection via IAA perception and signaling partially depending on the SA defense pathway.
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Affiliation(s)
- Gege Shi
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Saisai Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Peng Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jingjing Zhan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Ye Tang
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ge Zhao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaoyang Ge
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jiahe Wu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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7
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Chen X, Luo H, Zhang J, Ma Y, Li K, Xiong F, Yang Y, Yang J, Lan P, Wei T, Xu Y, Chen H, Li F. Synergism Among the Four Tobacco Bushy Top Disease Casual Agents in Symptom Induction and Aphid Transmission. Front Microbiol 2022; 13:846857. [PMID: 35444628 PMCID: PMC9014100 DOI: 10.3389/fmicb.2022.846857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Tobacco bushy top disease (TBTD), caused by multiple pathogens including tobacco bushy top virus (TBTV), tobacco vein distorting virus (TVDV), TBTV satellite RNA (TBTVsatRNA), and TVDV-associated RNA (TVDVaRNA), is a destructive disease in tobacco fields. To date, how these causal agents are co-transmitted by aphid vectors in field and their roles in disease symptom induction remain largely unknown, due mainly to the lack of purified causal agents. In this study, we have constructed four full-length infectious clones, representing the Yunnan Kunming isolates of TVDV, TBTV, TBTVsatRNA, and TVDVaRNA (TVDV-YK, TBTV-YK, TBTVsatRNA-YK, and TVDVaRNA-YK), respectively. Co-inoculation of these four causal agents to tobacco K326 plants caused typical TBTD symptoms, including smaller leaves, necrosis, and plant stunting. In addition, inoculation of tobacco K326 plants with TBTV alone caused necrosis in systemic leaves by 7 dpi. Tobacco K326 and Nicotiana benthamiana plants infected by single virus or multiple viruses showed very different disease symptoms at various dpi. RT-PCR results indicated that co-infection of TVDVaRNA-YK could increase TVDV-YK or TBTV-YK accumulation in N. benthamiana plants, suggesting that TVDVaRNA-YK can facilitate TVDV-YK and TBTV-YK replication and/or movement in the infected plants. Aphid transmission assays showed that the successful transmission of TBTV-YK, TBTVsatRNA-YK, and TVDVaRNA-YK by Myzus persicae depended on the presence of TVDV-YK, while the presence of TBTVsatRNA-YK increased the aphid transmission efficiency of TBTV and TVDV. We consider that these four new infectious clones will allow us to further dissect the roles of these four causal agents in TBTD induction as well as aphid transmission.
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Affiliation(s)
- Xiaojiao Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Hengming Luo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Jingyi Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Yan Ma
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Kehua Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Feng Xiong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Yahui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Jiazhen Yang
- Key Laboratory of Agricultural Biotechnology of Yunnan Province, Institute of Biotechnology and Germplasm Resources, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Pingxiu Lan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Taiyun Wei
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yi Xu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Hairu Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Fan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
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8
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Zhao J, Rios CG, Xu J, Ahmad I, Song J. Development of a Ligation-Independent Cloning-Based Dual Vector System for RNA Interference in Plants. Methods Mol Biol 2022; 2408:283-292. [PMID: 35325429 DOI: 10.1007/978-1-0716-1875-2_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
RNA interference (RNAi) is an evolutionarily conserved post-transcriptional gene silencing mechanism that responds to double-stranded RNA (dsRNA) by sequence-specific downregulation of target genes. The dsRNA-mediated RNAi technology has become one of the most widely used and powerful tools for functional genomic studies in diverse organisms. However, its application has been limited due to the technical difficulty of making RNAi constructs caused by the inverted repeat structure that is required for the formation of hairpin RNA. Here, we present a ligation-independent cloning-based dual vector-mediated RNAi system for silencing specific genes in plants. This approach is simple, efficient, and cost-effective and can be readily adapted to other binary vectors for functional analysis of target genes and the development of sustainable disease and pest control strategies in a broad range of plant species.
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Affiliation(s)
- Jinping Zhao
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, USA
| | - Carlos Garcia Rios
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, USA
| | - Jingjing Xu
- Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ijaz Ahmad
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, USA
| | - Junqi Song
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, USA.
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, USA.
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9
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Chu L, He X, Shu W, Wang L, Tang F. Knockdown of miR393 Promotes the Growth and Biomass Production in Poplar. FRONTIERS IN PLANT SCIENCE 2021; 12:714907. [PMID: 34335671 PMCID: PMC8317616 DOI: 10.3389/fpls.2021.714907] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Short tandem target mimic (STTM), which is composed of two short sequences mimicking small RNA target sites, separated by a linker of optimal size, can block the functions of all members in a miRNA family. microRNA393 (miR393), which is one of the conserved miRNA families in plants, can regulate plant root growth, leaf development, plant architecture, and stress resistance. In order to verify the role of miR393 in the secondary growth of trees, we created its STTM transgenic poplar lines (STTM393). The expression of miR393 in STTM393 lines was reduced by over 10 times compared with the control plants. STTM393 lines showed promoted growth with about 20% higher, 15% thicker, and 2-4 more internodes than the control plants after 3 months of growth. The cross-section of the stems showed that STTM393 lines had wider phloem, xylem, and more cambium cell layers than control plants, and the lignin content in STTM393 lines was also higher as revealed by staining and chemical determination. Based on the transcriptome analysis, the genes related to the auxin signaling pathway, cell cyclin, cell expansion, and lignin synthesis had higher expression in STTM393 lines than that in control plants. The higher expression levels of FBL family members suggested that the auxin signaling pathway was strengthened in STTM393 lines to promote plant growth. Therefore, the knockdown of miR393 using the STTM approach provides a way to improve poplar growth and biomass production.
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Affiliation(s)
- Liwei Chu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xuejiao He
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Wenbo Shu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Lijuan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Fang Tang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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10
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Fang L, Wei XY, Liu LZ, Zhou LX, Tian YP, Geng C, Li XD. A tobacco ringspot virus-based vector system for gene and microRNA function studies in cucurbits. PLANT PHYSIOLOGY 2021; 186:853-864. [PMID: 33764466 PMCID: PMC8195500 DOI: 10.1093/plphys/kiab146] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/11/2021] [Indexed: 06/01/2023]
Abstract
Cucurbits are economically important crops worldwide. The genomic data of many cucurbits are now available. However, functional analyses of cucurbit genes and noncoding RNAs have been impeded because genetic transformation is difficult for many cucurbitaceous plants. Here, we developed a set of tobacco ringspot virus (TRSV)-based vectors for gene and microRNA (miRNA) function studies in cucurbits. A TRSV-based expression vector could simultaneously express GREEN FLUORESCENT PROTEIN (GFP) and heterologous viral suppressors of RNA silencing in TRSV-infected plants, while a TRSV-based gene silencing vector could knock down endogenous genes exemplified by PHYTOENE DESATURASE (PDS) in Cucumis melo, Citrullus lanatus, Cucumis sativus, and Nicotiana benthamiana plants. We also developed a TRSV-based miRNA silencing vector to dissect the functions of endogenous miRNAs. Four representative miRNAs, namely, miR159, miR166, miR172, and miR319, from different cucurbits were inserted into the TRSV vector using a short tandem target mimic strategy and induced characteristic phenotypes in TRSV-miRNA-infected plants. This TRSV-based vector system will facilitate functional genomic studies in cucurbits.
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Affiliation(s)
- Le Fang
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Xin-Yu Wei
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Ling-Zhi Liu
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Ling-Xi Zhou
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Yan-Ping Tian
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Chao Geng
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Xiang-Dong Li
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
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11
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Wei T, Tang Y, Jia P, Zeng Y, Wang B, Wu P, Quan Y, Chen A, Li Y, Wu J. A Cotton Lignin Biosynthesis Gene, GhLAC4, Fine-Tuned by ghr-miR397 Modulates Plant Resistance Against Verticillium dahliae. FRONTIERS IN PLANT SCIENCE 2021; 12:743795. [PMID: 34868127 PMCID: PMC8636836 DOI: 10.3389/fpls.2021.743795] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/25/2021] [Indexed: 05/16/2023]
Abstract
Plant lignin is a component of the cell wall, and plays important roles in the transport potential of water and mineral nutrition and plant defence against biotic stresses. Therefore, it is necessary to identify lignin biosynthesis-related genes and dissect their functions and underlying mechanisms. Here, we characterised a cotton LAC, GhLAC4, which participates in lignin biosynthesis and plant resistance against Verticillium dahliae. According to degradome sequencing and GUS reporter analysis, ghr-miR397 was identified to directedly cleave the GhLAC4 transcript through base complementary. GhLAC4 knockdown and ghr-miR397 overexpression significantly reduced basal lignin content compared to the control, whereas ghr-miR397 silencing significantly increased basal lignin levels. Based on staining patterns and GC/MS analysis, GhLAC4 acted in G-lignin biosynthesis. Under V. dahliae infection, we found that G-lignin content in ghr-miR397-knockdowned plants significantly increased, compared to these plants under the mock treatment, while G-lignin contents in GhLAC4-silenced plants and ghr-miR397-overexpressed plants treated with pathogen were comparable with these plants treated with mock, indicating that GhLAC4 participates in defence-induced G-lignin biosynthesis in the cell wall. Knockdown of ghr-miR397 in plants inoculated with V. dahliae promoted lignin accumulation and increased plant resistance. The overexpression of ghr-miR397 and knockdown of GhLAC4 reduced lignin content and showed higher susceptibility of plants to the fungal infection compared to the control. The extract-free stems of ghr-miR397-knockdowned plants lost significantly less weight when treated with commercial cellulase and V. dahliae secretion compared to the control, while the stems of ghr-miR397-overexpressed and GhLAC4-silenced plants showed significantly higher loss of weight. These results suggest that lignin protects plant cell walls from degradation mediated by cellulase or fungal secretions. In summary, the ghr-miR397-GhLAC4 module regulates both basal lignin and defence-induced lignin biosynthesis and increases plant resistance against infection by V. dahliae.
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Affiliation(s)
- Taiping Wei
- School of Resources and Environmental Engineering, Anhui University, Hefei, China
- State Key Laboratory of Plant Genomic, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ye Tang
- State Key Laboratory of Plant Genomic, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Pei Jia
- State Key Laboratory of Plant Genomic, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yanming Zeng
- State Key Laboratory of Plant Genomic, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Bingting Wang
- State Key Laboratory of Plant Genomic, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Pan Wu
- State Key Laboratory of Plant Genomic, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yonggang Quan
- The Key Laboratory for the Creation of Cotton Varieties in the Northwest, Ministry of Agriculture, Join Hope Seeds Co. Ltd., Changji, China
| | - Aimin Chen
- The Key Laboratory for the Creation of Cotton Varieties in the Northwest, Ministry of Agriculture, Join Hope Seeds Co. Ltd., Changji, China
| | - Yucheng Li
- School of Resources and Environmental Engineering, Anhui University, Hefei, China
- *Correspondence: Yucheng Li,
| | - Jiahe Wu
- School of Resources and Environmental Engineering, Anhui University, Hefei, China
- State Key Laboratory of Plant Genomic, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Jiahe Wu,
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12
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Yuan C, Li H, Qin C, Zhang X, Chen Q, Zhang P, Xu X, He M, Zhang X, Tör M, Xue D, Wang H, Jackson S, He Y, Liu Y, Shi N, Hong Y. Foxtail mosaic virus-induced flowering assays in monocot crops. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3012-3023. [PMID: 32061090 DOI: 10.1093/jxb/eraa080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 02/11/2020] [Indexed: 05/04/2023]
Abstract
Virus-induced flowering (VIF) exploits RNA or DNA viruses to express flowering time genes to induce flowering in plants. Such plant virus-based tools have recently attracted widespread attention for their fundamental and applied uses in flowering physiology and in accelerating breeding in dicotyledonous crops and woody fruit-trees. We now extend this technology to a monocot grass and a cereal crop. Using a Foxtail mosaic virus (FoMV)-based VIF system, dubbed FoMViF, we showed that expression of florigenic Flowering Locus T (FT) genes can promote early flowering and spikelet development in proso millet, a C4 grass species with potential as a nutritional food and biofuel resource, and in non-vernalized C3 wheat, a major food crop worldwide. Floral and spikelet/grain induction in the two monocot plants was caused by the virally expressed untagged or FLAG-tagged FT orthologs, and the florigenic activity of rice Hd3a was more pronounced than its dicotyledonous counterparts in proso millet. The FoMViF system is easy to use and its efficacy to induce flowering and early spikelet/grain production is high. In addition to proso millet and wheat, we envisage that FoMViF will be also applicable to many economically important monocotyledonous food and biofuel crops.
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Affiliation(s)
- Chen Yuan
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Hongmei Li
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Cheng Qin
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xian Zhang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Qianqian Chen
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Pengcheng Zhang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xiaorui Xu
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Meiling He
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xinlian Zhang
- Department of Family Medicine and Public Health, Division of Biostatistics & Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Mahmut Tör
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, School of Science and the Environment, University of Worcester, Worcester, UK
| | - Dawei Xue
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Huizhong Wang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Stephen Jackson
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry, UK
| | - Yuehui He
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yule Liu
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Nongnong Shi
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, School of Science and the Environment, University of Worcester, Worcester, UK
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry, UK
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13
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Hu G, Hao M, Wang L, Liu J, Zhang Z, Tang Y, Peng Q, Yang Z, Wu J. The Cotton miR477- CBP60A Module Participates in Plant Defense Against Verticillium dahlia. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:624-636. [PMID: 31868566 DOI: 10.1094/mpmi-10-19-0302-r] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Previous reports have shown that, when Verticillium dahliae localizes at the root surface, many microRNAs (miRNAs) were identified at the early induction stage. Here, we constructed two groups from two timepoints of small RNA (sRNA) in cotton root responses to V. dahliae at the later induction stage, pathogen localizing in the interior of root tissue. We identified 71 known and 378 novel miRNAs from six libraries of the pathogen-induced and the control sRNAs. Combined with degradome and sRNA sequencing, 178 corresponding miRNA target genes were identified, in which 40 target genes from differentially expressed miRNAs were primarily associated with oxidation-reduction and stress responses. More importantly, we characterized the cotton miR477-CBP60A module in the later response of the plant to V. dahliae infection. A β-glucuronidase fusion reporter and cleavage site analysis showed that ghr-miR477 directly cleaved the messenger RNA of GhCBP60A in the posttranscriptional process. The ghr-miR477-silencing decreased plant resistance to this fungus, while the knockdown of GhCBP60A increased plant resistance, which regulated GhICS1 expression to determine salicylic acid level. Our data documented that numerous later-inducible miRNAs in the plant response to V. dahliae, suggesting that these miRNAs play important roles in plant resistance to vascular disease.
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Affiliation(s)
- Guang Hu
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, China
| | - Mengyan Hao
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Le Wang
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianfen Liu
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhennan Zhang
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ye Tang
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qingzhong Peng
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, China
| | - Zuoren Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China
| | - Jiahe Wu
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, China
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14
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Hu G, Lei Y, Liu J, Hao M, Zhang Z, Tang Y, Chen A, Wu J. The ghr-miR164 and GhNAC100 modulate cotton plant resistance against Verticillium dahlia. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 293:110438. [PMID: 32081275 DOI: 10.1101/440826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/23/2020] [Accepted: 02/05/2020] [Indexed: 05/28/2023]
Abstract
MicroRNAs (miRNAs) participate in plant development and defence through post-transcriptional regulation of the target genes. However, few miRNAs were reported to regulate cotton plant disease resistance. Here, we characterized the cotton miR164-NAC100 module in the later induction stage response of the plant to Verticillium dahliae infection. The results of GUS fusing reporter and transcript identity showed that ghr-miR164 can directly cleave the mRNA of GhNAC100 in the post-transcriptional process. The ghr-miR164 positively regulated the cotton plant resistance to V. dahliae according to analyses of its over-expression and knockdown. In link with results, the knockdown of GhNAC100 increased the plant resistance to V. dahliae. Based on LUC reporter, expression analyses and yeast one-hybrid (Y1H) assays, GhNAC100 bound to the CGTA-box of GhPR3 promoter and repressed its expression, negatively regulating plant disease resistance. These results showed that the ghr-miR164 and GhNAC100 module fine-tunes plant defence through the post-transcriptional regulation, which documented that miRNAs play important roles in plant resistance to vascular disease.
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Affiliation(s)
- Guang Hu
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450001, Zhengzhou, China
| | - Yu Lei
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jianfen Liu
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mengyan Hao
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhennan Zhang
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ye Tang
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Aiming Chen
- The Key Laboratory for the Creation of Cotton Varieties in the Northwest, Ministry of Agriculture, Join Hope Seeds CO. Ltd, Changji, Xinjiang, 831100, China
| | - Jiahe Wu
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450001, Zhengzhou, China.
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15
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Du J, Wu R, Liu Z, Sun M, Ghanem H, Li M, Wu G, Qing L. Suppression of nbe-miR1919c-5p Expression in Nicotiana benthamiana Enhances Tobacco Curly Shoot Virus and Its Betasatellite Co-Infection. Viruses 2020; 12:E392. [PMID: 32244650 PMCID: PMC7232422 DOI: 10.3390/v12040392] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/27/2020] [Accepted: 03/28/2020] [Indexed: 12/29/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding but functional RNA molecules of 21-25 nucleotides in length. MiRNAs play significant regulatory roles in diverse plant biological processes. In order to decipher the relationship between nbe-miR1919c-5p and the accumulations of tobacco curly shoot virus (TbCSV) and its betasatellite (TbCSB) DNAs, as well as viral symptom development, we investigated the function of nbe-miR1919c-5p during TbCSV and TbCSB co-infection in plants using a PVX-and a TRV-based short tandem target mimic (STTM) technology. Suppression of nbe-miR1919c-5p expression using these two technologies enhanced TbCSV and TbCSB co-infection-induced leaf curling symptoms in Nicotiana benthamiana plants. Furthermore, suppression of nbe-miR1919c-5p expression enhanced TbCSV and TbCSB DNA accumulations in the infected plants. Our results can advance our knowledge on the nbe-miR1919c-5p function during TbCSV and TbCSB co-infection.
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Affiliation(s)
| | | | | | | | | | | | - Gentu Wu
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing 400716, China; (J.D.); (R.W.); (Z.L.); (M.S.); (H.G.); (M.L.)
| | - Ling Qing
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing 400716, China; (J.D.); (R.W.); (Z.L.); (M.S.); (H.G.); (M.L.)
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16
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Hu G, Lei Y, Liu J, Hao M, Zhang Z, Tang Y, Chen A, Wu J. The ghr-miR164 and GhNAC100 modulate cotton plant resistance against Verticillium dahlia. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 293:110438. [PMID: 32081275 DOI: 10.1016/j.plantsci.2020.110438] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/23/2020] [Accepted: 02/05/2020] [Indexed: 05/15/2023]
Abstract
MicroRNAs (miRNAs) participate in plant development and defence through post-transcriptional regulation of the target genes. However, few miRNAs were reported to regulate cotton plant disease resistance. Here, we characterized the cotton miR164-NAC100 module in the later induction stage response of the plant to Verticillium dahliae infection. The results of GUS fusing reporter and transcript identity showed that ghr-miR164 can directly cleave the mRNA of GhNAC100 in the post-transcriptional process. The ghr-miR164 positively regulated the cotton plant resistance to V. dahliae according to analyses of its over-expression and knockdown. In link with results, the knockdown of GhNAC100 increased the plant resistance to V. dahliae. Based on LUC reporter, expression analyses and yeast one-hybrid (Y1H) assays, GhNAC100 bound to the CGTA-box of GhPR3 promoter and repressed its expression, negatively regulating plant disease resistance. These results showed that the ghr-miR164 and GhNAC100 module fine-tunes plant defence through the post-transcriptional regulation, which documented that miRNAs play important roles in plant resistance to vascular disease.
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Affiliation(s)
- Guang Hu
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450001, Zhengzhou, China
| | - Yu Lei
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jianfen Liu
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mengyan Hao
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhennan Zhang
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ye Tang
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Aiming Chen
- The Key Laboratory for the Creation of Cotton Varieties in the Northwest, Ministry of Agriculture, Join Hope Seeds CO. Ltd, Changji, Xinjiang, 831100, China
| | - Jiahe Wu
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450001, Zhengzhou, China.
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17
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Zhao J, Jiang H, Wang G, Wang Z, Dong J, Song J. Virus-Induced Gene Silencing in Diploid and Tetraploid Potato Species. Methods Mol Biol 2020; 2172:39-50. [PMID: 32557360 DOI: 10.1007/978-1-0716-0751-0_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Potato is the world's fourth largest food crop and a vegetatively propagated model polyploid plant. To facilitate genomic studies in potato, here we describe detailed protocols to silence genes in both diploid potato Solanum bulbocastanum and tetraploid potato cultivars such as Maris Bard, Arran Pilot, Ancilla, and Serrana using tobacco rattle virus (TRV)- or potato virus X (PVX)-induced gene silencing (VIGS) system, respectively. The established VIGS system represents an efficient and powerful approach for functional analysis of genes involved in growth, development, metabolism, and responses to biotic and abiotic stresses in potato.
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Affiliation(s)
- Jinping Zhao
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, USA
| | - Haolang Jiang
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, USA
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guanyu Wang
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Mycotoxin and Molecular Plant Pathology Laboratory, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Jingao Dong
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Mycotoxin and Molecular Plant Pathology Laboratory, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Junqi Song
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, USA.
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, USA.
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18
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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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19
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Technologies to Address Plant microRNA Functions. CONCEPTS AND STRATEGIES IN PLANT SCIENCES 2020. [DOI: 10.1007/978-3-030-35772-6_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Bao S, Owens RA, Sun Q, Song H, Liu Y, Eamens AL, Feng H, Tian H, Wang MB, Zhang R. Silencing of transcription factor encoding gene StTCP23 by small RNAs derived from the virulence modulating region of potato spindle tuber viroid is associated with symptom development in potato. PLoS Pathog 2019; 15:e1008110. [PMID: 31790500 PMCID: PMC6907872 DOI: 10.1371/journal.ppat.1008110] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 12/12/2019] [Accepted: 09/25/2019] [Indexed: 11/18/2022] Open
Abstract
Viroids are small, non-protein-coding RNAs which can induce disease symptoms in a variety of plant species. Potato (Solanum tuberosum L.) is the natural host of Potato spindle tuber viroid (PSTVd) where infection results in stunting, distortion of leaves and tubers and yield loss. Replication of PSTVd is accompanied by the accumulation of viroid-derived small RNAs (sRNAs) proposed to play a central role in disease symptom development. Here we report that PSTVd sRNAs direct RNA silencing in potato against StTCP23, a member of the TCP (teosinte branched1/Cycloidea/Proliferating cell factor) transcription factor family genes that play an important role in plant growth and development as well as hormonal regulation, especially in responses to gibberellic acid (GA). The StTCP23 transcript has 21-nucleotide sequence complementarity in its 3ʹ untranslated region with the virulence-modulating region (VMR) of PSTVd strain RG1, and was downregulated in PSTVd-infected potato plants. Analysis using 3ʹ RNA ligase-mediated rapid amplification of cDNA ends (3ʹ RLM RACE) confirmed cleavage of StTCP23 transcript at the expected sites within the complementarity with VMR-derived sRNAs. Expression of these VMR sRNA sequences as artificial miRNAs (amiRNAs) in transgenic potato plants resulted in phenotypes reminiscent of PSTVd-RG1-infected plants. Furthermore, the severity of the phenotypes displayed was correlated with the level of amiRNA accumulation and the degree of amiRNA-directed down-regulation of StTCP23. In addition, virus-induced gene silencing (VIGS) of StTCP23 in potato also resulted in PSTVd-like phenotypes. Consistent with the function of TCP family genes, amiRNA lines in which StTCP23 expression was silenced showed a decrease in GA levels as well as alterations to the expression of GA biosynthesis and signaling genes previously implicated in tuber development. Application of GA to the amiRNA plants minimized the PSTVd-like phenotypes. Taken together, our results indicate that sRNAs derived from the VMR of PSTVd-RG1 direct silencing of StTCP23 expression, thereby disrupting the signaling pathways regulating GA metabolism and leading to plant stunting and formation of small and spindle-shaped tubers. Potato spindle tuber viroid (PSTVd) is a small RNA pathogen that causes severe pandemic diseases in potato. How this non-protein-coding RNA induces disease symptom development in potato is unknown, thereby hindering the development of effective control measures. Here we report the first evidence that PSTVd disease is caused by the silencing of StTCP23, a potato transcription factor encoding gene, by PSTVd-derived small-interfering RNA (siRNAs). Specifically, we demonstrate that 3ʹ untranslated region (UTR) region of StTCP23 mRNA contains a 21-nt sequence that is complementary to the virulence-modulating region (VMR) of PSTVd. Furthermore, we show that StTCP23 expression is repressed in PSTVd-infected potato, and this repression is accompanied by StTCP23 transcript cleavage within the identified region of complementary. In planta expression of VMR sequences as 21-nt artificial microRNAs (amiRNAs) or infection of potato plants with a virus-induced gene silencing vector containing a portion the StTCP23 coding sequence, results in reduced StTCP23 transcript abundance and the expression of PSTVd-like disease symptoms. Consistent with the predicted functional role of StTCP23 in regulating the gibberellic acid (GA) biosynthesis and signaling pathways, GA levels were reduced both in PSTVd-infected and amiRNA-expressing plants. Our results provide compelling evidence that StTCP23 positively regulates potato sprouting and tuber development via a GA-related mechanism, and that the disease symptoms that develop upon PSTVd infection result from silencing of StTCP23 by VMR-derived siRNAs.
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Affiliation(s)
- Sarina Bao
- School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Robert A. Owens
- Molecular Plant Pathology Laboratory, USDA/ARS, Beltsville, Maryland, United States of America
| | - Qinghua Sun
- School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Hui Song
- School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yanan Liu
- School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Andrew Leigh Eamens
- Centre for Plant Science, School of Environmental and Life Sciences, Faculty of Science, University of Newcastle, Australia
| | - Hao Feng
- School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Hongzhi Tian
- School of Life Sciences, Inner Mongolia University, Hohhot, China
| | | | - Ruofang Zhang
- School of Life Sciences, Inner Mongolia University, Hohhot, China
- * E-mail:
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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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Wu G, Hu Q, Du J, Li K, Sun M, Jing C, Li M, Li J, Qing L. Molecular characterization of virus-derived small RNAs in Nicotiana benthamiana plants infected with tobacco curly shoot virus and its β satellite. Virus Res 2019; 265:10-19. [PMID: 30831178 DOI: 10.1016/j.virusres.2019.02.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 02/25/2019] [Accepted: 02/28/2019] [Indexed: 10/27/2022]
Abstract
Tobacco curly shoot virus (TbCSV) is a monopartite DNA virus of the genus Begomovirus, which causes leaf curl symptoms in tobacco and tomato. The β satellite of TbCSV (TbCSB induces more severe symptoms and enhanced virus accumulation when co-infects the host plants with TbCSV. Small interfering RNAs derived from virus(vsiRNAs) induce disease symptoms and promote virus invasion by target and guide the degradation of host transcripts The vsiRNAs derived from TbCSV and TbCSV + TbCSB remained to be explored to elucidate the molecular mechanism of symptoms development in plants. In the present work, two libraries of small RNA from TbCSV-infected and TbCSV + TbCSB-infected N. benthamiana plants were constructed and the vsiRNAs in both samples shared the same characteristics. The size of the vsiRNAs ranged from 18 to 30 nucleotides (nt), with most of them being 21 or 22 nt, which accounted for 29.11% and 23.22% in TbCSV plants and 29.39% and 21.82% in TbCSV + TbCSV plants, respectively. The vsiRNAs with A/U bias at the first site were abundant in both the TbCSV-treated and TbCSV + TbCSB-treated plants. It is discovered that the vsiRNAs continuously, but heterogeneously, distributed through bothe the TbCSV and TbCSB sequences. And the distribution profiles were similar in both the treatments such as mainly in the overlapping region of the AC2/AC3 coding sequences. The host transcripts targeted by vsiRNAs were predicted, and the targeted genes were found to be involved in varied biological processes. It is indicated that the presence of TbCSB does not significantly affect the production of vsiRNAs from TbCSV in plants, the distribution hotsopt of TbCSV vsiRNAs could be useful in designing effective targets for TbCSV resistance exploiting RNA interference.
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Affiliation(s)
- Gentu Wu
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, 400716, China.
| | - Qiao Hu
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, 400716, China.
| | - Jiang Du
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, 400716, China.
| | - Ke Li
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, 400716, China.
| | - Miao Sun
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, 400716, China.
| | - Chenchen Jing
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, 400716, China.
| | - Mingjun Li
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, 400716, China.
| | - Junmin Li
- Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
| | - Ling Qing
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, 400716, China.
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Miao Y, Xu L, He X, Zhang L, Shaban M, Zhang X, Zhu L. Suppression of tryptophan synthase activates cotton immunity by triggering cell death via promoting SA synthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:329-345. [PMID: 30604574 DOI: 10.1111/tpj.14222] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 02/11/2019] [Accepted: 12/17/2018] [Indexed: 05/14/2023]
Abstract
Primary metabolism plays an important role in plant growth and development, however the relationship between primary metabolism and the adaptive immune response is largely unknown. Here, we employed RNA interference (RNAi), virus-induced gene silencing (VIGS) technology, phytohormone profiling, genetic studies, and transcriptome and metabolome analysis to investigate the function of the tryptophan synthesis pathway in the resistance of cotton to V. dahliae. We found that knock-down of GbTSA1 (Tryptophan Synthase α) and GbTSB1 (tryptophan synthase β) induced a spontaneous cell death phenotype in a salicylic acid (SA)-dependent manner and enhanced resistance to V. dahliae in cotton plants. Metabolome analysis showed that indole and indolic metabolites were highly accumulated in GbTSA1- or GbTSB1-silenced plants. Transcriptomic analysis showed that exogenous indole promotes the expression levels of genes involved in SA synthesis and the defense response. Similarly, indole application strongly enhanced cotton resistance to V. dahliae. These results suggested that metabolic intermediates in the Trp synthesis pathway may be a signal to activate SA synthesis. These results also provided a strategy to elicit plant defense responses by the application of indole.
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Affiliation(s)
- Yuhuan Miao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Lian Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xin He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Lin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Muhammad Shaban
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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Chen L, Meng J, He XL, Zhang M, Luan YS. Solanum lycopersicum microRNA1916 targets multiple target genes and negatively regulates the immune response in tomato. PLANT, CELL & ENVIRONMENT 2019; 42:1393-1407. [PMID: 30362126 DOI: 10.1111/pce.13468] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/17/2018] [Accepted: 10/18/2018] [Indexed: 06/08/2023]
Abstract
MicroRNA1916 (miR1916) is one of the nonconserved miRNAs that respond to various stresses in plants, but little has been known at present about its mechanisms in biotic stresses. In this study, the expression of Solanum lycopersicum (sly)-miR1916 in tomato was found to be down-regulated after infection with Phytophthora infestans or Botrytis cinerea. Tomato plants that overexpressed sly-miR1916 displayed significant enhancement in susceptibility to P. infestans and B. cinerea infection, as well as increased tendency to produce reactive oxygen species. Silencing of sly-miR1916 by short tandem target mimic and artificial microRNA strategies caused the tomato plants to become more tolerant to adverse conditions. In addition, lower sly-miR1916 expression could up-regulate the expression of strictosidine synthase (STR-2), UDP-glycosyltransferases (UGTs), late blight resistance protein homolog R1B-16, disease resistance protein RPP13-like, and MYB transcription factor (MYB12), which ultimately resulted in the accumulation of α-tomatine and anthocyanins via STR-2, UGT, and MYB12. Furthermore, ectopic expression of sly-miR1916/STR-2 significantly changed the tolerance of tobacco to B. cinerea. Taken together, the results demonstrated that sly-miR1916 might regulate the expression of STR-2, UGT, and MYB12 in tomato plant, conferring sensitivity to biotic stress via modulating α-tomatine and anthocyanins.
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Affiliation(s)
- Lei Chen
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Xiao Li He
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Min Zhang
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Yu Shi Luan
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, 116024, China
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25
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Liu X, Liu S, Wang R, Chen X, Fan Z, Wu B, Zhou T. Analyses of MiRNA Functions in Maize Using a Newly Developed ZMBJ-CMV-2b N81-STTM Vector. FRONTIERS IN PLANT SCIENCE 2019; 10:1277. [PMID: 31681375 PMCID: PMC6811604 DOI: 10.3389/fpls.2019.01277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/12/2019] [Indexed: 05/21/2023]
Abstract
Endogenous microRNAs (miRNAs) play pivotal roles in plant development and responses to various biotic or abiotic stresses. Up to now, more than 500 maize miRNAs have been identified. However, functions of these identified miRNAs remained largely unknown due mainly to the lack of rapid and reliable tools. We previously reported a cucumber mosaic virus strain ZMBJ (ZMBJ-CMV)-based gene silencing vector for rapid and efficient gene function studies in maize lines with agronomical importance. Because ZMBJ-CMV induces very mild disease symptoms but strong gene silencing in maize, we decided to further modify this vector to suppress miRNA expressions in maize. The newly developed ZMBJ-CMV-2bN81-STTM vector expresses a short tandem target mimic (STTM) containing two target-mimic sequences separated by a short spacer sequence. Our results showed that ZMBJ-CMV-2bN81-STTM can be used to investigate miRNA function in Nicotiana benthamiana and maize seedlings. The ZMBJ-CMV-2bN81-STTM-based downregulation of Nbe-miR165/166 or Nbe-miR159 induced specific and strong miRNA-sequestering phenotypes, and increased the expressions of their predicted target genes. For maize, the ZMBJ-CMV-2bN81-STTM based downregulation of zma-miR167 or zma-miR482 caused a decrease of lateral roots growth and a plant stunting phenotypes, respectively. In both cases, the target genes of zma-miR167- or zma-miR482 were increased significantly. Thus, we consider ZMBJ-CMV based VbMS system as a useful tool for high-throughput investigations of miRNA functions in maize.
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Affiliation(s)
- Xuedong Liu
- State Key Laboratory for Agro-Biotechnology and Key Laboratory for Pest Monitoring and Green Management-Ministry of Agriculture and Rural Affairs, Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Sijia Liu
- State Key Laboratory for Agro-Biotechnology and Key Laboratory for Pest Monitoring and Green Management-Ministry of Agriculture and Rural Affairs, Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Rong Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xi Chen
- State Key Laboratory for Agro-Biotechnology and Key Laboratory for Pest Monitoring and Green Management-Ministry of Agriculture and Rural Affairs, Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Zaifeng Fan
- State Key Laboratory for Agro-Biotechnology and Key Laboratory for Pest Monitoring and Green Management-Ministry of Agriculture and Rural Affairs, Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Boming Wu
- State Key Laboratory for Agro-Biotechnology and Key Laboratory for Pest Monitoring and Green Management-Ministry of Agriculture and Rural Affairs, Department of Plant Pathology, China Agricultural University, Beijing, China
- *Correspondence: Boming Wu, ; Tao Zhou,
| | - Tao Zhou
- State Key Laboratory for Agro-Biotechnology and Key Laboratory for Pest Monitoring and Green Management-Ministry of Agriculture and Rural Affairs, Department of Plant Pathology, China Agricultural University, Beijing, China
- *Correspondence: Boming Wu, ; Tao Zhou,
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26
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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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27
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Agarwal AV, Singh D, Dhar YV, Michael R, Gupta P, Chandra D, Trivedi PK. Virus-Induced Silencing of Key Genes Leads to Differential Impact on Withanolide Biosynthesis in the Medicinal Plant, Withania somnifera. PLANT & CELL PHYSIOLOGY 2018; 59:262-274. [PMID: 29165715 DOI: 10.1093/pcp/pcx179] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 11/13/2017] [Indexed: 05/20/2023]
Abstract
Withanolides are a collection of naturally occurring, pharmacologically active, secondary metabolites synthesized in the medicinally important plant, Withania somnifera. These bioactive molecules are C28-steroidal lactone triterpenoids and their synthesis is proposed to take place via the mevalonate (MVA) and 2-C-methyl-d-erythritol-4-phosphate (MEP) pathways through the sterol pathway using 24-methylene cholesterol as substrate flux. Although the phytochemical profiles as well as pharmaceutical activities of Withania extracts have been well studied, limited genomic information and difficult genetic transformation have been a major bottleneck towards understanding the participation of specific genes in withanolide biosynthesis. In this study, we used the Tobacco rattle virus (TRV)-mediated virus-induced gene silencing (VIGS) approach to study the participation of key genes from MVA, MEP and triterpenoid biosynthesis for their involvement in withanolide biosynthesis. TRV-infected W. somnifera plants displayed unique phenotypic characteristics and differential accumulation of total Chl as well as carotenoid content for each silenced gene suggesting a reduction in overall isoprenoid synthesis. Comprehensive expression analysis of putative genes of withanolide biosynthesis revealed transcriptional modulations conferring the presence of complex regulatory mechanisms leading to withanolide biosynthesis. In addition, silencing of genes exhibited modulated total and specific withanolide accumulation at different levels as compared with control plants. Comparative analysis also suggests a major role for the MVA pathway as compared with the MEP pathway in providing substrate flux for withanolide biosynthesis. These results demonstrate that transcriptional regulation of selected Withania genes of the triterpenoid biosynthetic pathway critically affects withanolide biosynthesis, providing new horizons to explore this process further, in planta.
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Affiliation(s)
- Aditya Vikram Agarwal
- Council of Scientific and Industrial Research, National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India
- Department of Biochemistry, University of Lucknow, Lucknow 226007, India
| | - Deeksha Singh
- Council of Scientific and Industrial Research, National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India
- Academy of Scientific and Innovative Research (AcSIR) Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | - Yogeshwar Vikram Dhar
- Council of Scientific and Industrial Research, National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India
- Academy of Scientific and Innovative Research (AcSIR) Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | - Rahul Michael
- Council of Scientific and Industrial Research, National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India
- Academy of Scientific and Innovative Research (AcSIR) Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | - Parul Gupta
- Council of Scientific and Industrial Research, National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India
| | - Deepak Chandra
- Department of Biochemistry, University of Lucknow, Lucknow 226007, India
| | - Prabodh Kumar Trivedi
- Council of Scientific and Industrial Research, National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India
- Academy of Scientific and Innovative Research (AcSIR) Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
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Yang J, Zhang TY, Liao QS, He L, Li J, Zhang HM, Chen X, Li J, Yang J, Li JB, Chen JP. Chinese Wheat Mosaic Virus-Induced Gene Silencing in Monocots and Dicots at Low Temperature. FRONTIERS IN PLANT SCIENCE 2018; 9:1627. [PMID: 30487803 PMCID: PMC6247046 DOI: 10.3389/fpls.2018.01627] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/18/2018] [Indexed: 05/21/2023]
Abstract
Virus-induced gene silencing (VIGS) is an important tool for functional genomics studies in plants. With this method, it is possible to target most endogenous genes and downregulate the messenger RNA (mRNA) in a sequence-specific manner. Chinese wheat mosaic virus (CWMV) has a bipartite, single-strand positive RNA genome, and can infect both wheat and Nicotiana benthamiana, and the optimal temperature for systemic infection in plants is 17°C. To assess the potential of the virus as a vector for gene silencing at low temperature, a fragment of the N. benthamiana or wheat phytoene desaturase (PDS) gene was expressed from a modified CWMV RNA2 clone and the resulting photo bleaching in infected plants was used as a reporter for silencing. Downregulation of PDS mRNA was also measured by quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR). In experiments using fragments of PDS ranging from 500 to 1500 nucleotides, insert length influenced the stability and the efficiency of VIGS. The CWMV induced silencing system was also used to suppress miR165/166 and miR3134a through expression of miRNA target mimics. The relative expression levels of mature miR165/166 and miR3134a decreased whereas the transcript levels of their target genes increased. Interestingly, we also found the CWMV-induced silencing system was more efficient compare with the vector based on Barley stripe mosaic virus (BSMV) or Foxtail mosaic virus (FoMV) in wheat or the vector based on TRV in N. benthamiana at 17°C. In summary, the CWMV vector is effective in silencing endogenous genes and miRNAs at 17°C, thereby providing a powerful tool for gene function analysis in both N. benthamiana and wheat at low temperature.
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Affiliation(s)
- Jian Yang
- Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Tian-Ye Zhang
- Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Qian-Sheng Liao
- College of Life Science, Zhejiang SCI-Tech University, Hangzhou, China
| | - Long He
- Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Juang Li
- Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Heng-Mu Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Plant Protection and Biotechnology, Ministry of Agriculture, Beijing, China
- Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Heng-Mu Zhang, Jian-Ping Chen,
| | - Xuan Chen
- Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jing Li
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Plant Protection and Biotechnology, Ministry of Agriculture, Beijing, China
- Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jin Yang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Plant Protection and Biotechnology, Ministry of Agriculture, Beijing, China
- Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jin-Bang Li
- Nanyang Academy of Agricultural Sciences, Nanyang, China
| | - Jian-Ping Chen
- Institute of Plant Virology, Ningbo University, Ningbo, China
- *Correspondence: Heng-Mu Zhang, Jian-Ping Chen,
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Lang PLM, Christie MD, Dogan ES, Schwab R, Hagmann J, van de Weyer AL, Scacchi E, Weigel D. A Role for the F-Box Protein HAWAIIAN SKIRT in Plant microRNA Function. PLANT PHYSIOLOGY 2018; 176:730-741. [PMID: 29114080 PMCID: PMC5761791 DOI: 10.1104/pp.17.01313] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 11/06/2017] [Indexed: 05/02/2023]
Abstract
As regulators of gene expression in multicellular organisms, microRNAs (miRNAs) are crucial for growth and development. Although a plethora of factors involved in their biogenesis and action in Arabidopsis (Arabidopsis thaliana) has been described, these processes and their fine-tuning are not fully understood. Here, we used plants expressing an artificial miRNA target mimic (MIM) to screen for negative regulators of miR156. We identified a new mutant allele of the F-box gene HAWAIIAN SKIRT (HWS; At3G61590), hws-5, as a suppressor of the MIM156-induced developmental and molecular phenotypes. In hws plants, levels of some endogenous miRNAs are increased and their mRNA targets decreased. Plants constitutively expressing full-length HWS-but not a truncated version lacking the F-box domain-display morphological and molecular phenotypes resembling those of mutants defective in miRNA biogenesis and activity. In combination with such mutants, hws loses its delayed floral organ abscission ("skirt") phenotype, suggesting epistasis. Also, the hws transcriptome profile partially resembles those of well-known miRNA mutants hyl1-2, se-3, and ago1-27, pointing to a role in a common pathway. We thus propose HWS as a novel, F-box dependent factor involved in miRNA function.
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Affiliation(s)
| | | | - Ezgi S Dogan
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Rebecca Schwab
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jörg Hagmann
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | - Emanuele Scacchi
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
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30
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Ali S, Ahmad Nasir I, Rafiq M, Javed Butt S, Ihsan F, Qayyum Rao A, Husnain T. Sugarcane Mosaic Virus-Based Gene Silencing in Nicotiana benthamiana. IRANIAN JOURNAL OF BIOTECHNOLOGY 2017; 15:260-267. [PMID: 29845078 PMCID: PMC5903913 DOI: 10.15171/ijb.1536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 02/14/2017] [Accepted: 07/27/2017] [Indexed: 06/08/2023]
Abstract
Background: Potyvirus-based virus-induced gene silencing (VIGS) is used for knocking down the expression of a target gene in numerous plant species. Sugarcane mosaic virus (SCMV) is a monopartite, positive single strand RNA virus. Objectives: pBINTRA6 vector was modifi ed by inserting a gene segment of SCMV in place of Tobacco rattle virus (TRV) genome part 1 (TRV1 or RNA1) and the two nonstructural proteins of TRV2(RNA2). Materials and Methods: SCMV construct was inoculated into 3-4 weeks Nicotiana benthamiana plant leaves either by using a needleless syringe or applying pricking with a toothpick. Results: The construct (SCMV-RNA2) successfully induced post-transcriptional gene silencing (PTGS) of the target genes GFP and ChlI through agroinoculation proving that SCMV is a substitute of the RNA1, which plays a pivotal role in the systemic gene silencing. 2-3-weeks of post inoculation, target genes' silencing was observed in the newly developed noninoculated leaves. Conclusions: The newly developed construct expresses the knocked down of the endogenous as well as exogenous genes and only four weeks are required for the transient expression of the gene silencing based on SCMV-VIGS system.
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Affiliation(s)
- Sajed Ali
- Department of Biotechnology, School of Sciences, University of Management and Technology, Sialkot Campus, Sialkot, Pakistan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Idrees Ahmad Nasir
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Rafiq
- Institute of Clinical Psychology, University of Management and Technology, Lahore, Pakistan
| | - Shahid Javed Butt
- Department of Biotechnology, School of Sciences, University of Management and Technology, Sialkot Campus, Sialkot, Pakistan
| | - Farooq Ihsan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Abdul Qayyum Rao
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Tayyab Husnain
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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32
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Tang L, Chen HY, Hao NB, Tang B, Guo H, Yong X, Dong H, Yang SM. microRNA inhibitors: Natural and artificial sequestration of microRNA. Cancer Lett 2017; 407:139-147. [PMID: 28602827 DOI: 10.1016/j.canlet.2017.05.025] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 05/16/2017] [Accepted: 05/31/2017] [Indexed: 12/14/2022]
Abstract
MicroRNA (miRNAs) is post-transcriptional regulator of mRNA. However, the prevalence and activity of miRNA are regulated by other regulators. miRNA inhibitors are natural or artificial RNA transcripts that sequestrate miRNAs and decrease or even eliminate miRNA activity. Competing endogenous RNAs (ceRNAs) are natural and intracellular miRNA inhibitors that compete to bind to shared miRNA recognition elements (MREs) to decrease microRNA availability and relieve the repression of target RNAs. In recent years, studies have revealed that ceRNA crosstalk is involved in many pathophysiological processes and adds a new dimension to miRNA regulation. Artificial miRNA inhibitors are RNA transcripts that are synthesized via chemical and genetic methods. Artificial miRNA inhibitors can be used in miRNA loss-of-function research and gene therapies for certain diseases. In this review, we summarize the recent advances in the two different types of miRNA inhibitors.
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Affiliation(s)
- Li Tang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Hong-Yan Chen
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Ning-Bo Hao
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Bo Tang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Hong Guo
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Xin Yong
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Hui Dong
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Shi-Ming Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
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33
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Qin C, Chen W, Shen J, Cheng L, Akande F, Zhang K, Yuan C, Li C, Zhang P, Shi N, Cheng Q, Liu Y, Jackson S, Hong Y. A Virus-Induced Assay for Functional Dissection and Analysis of Monocot and Dicot Flowering Time Genes. PLANT PHYSIOLOGY 2017; 174:875-885. [PMID: 28400493 PMCID: PMC5462034 DOI: 10.1104/pp.17.00392] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 04/07/2017] [Indexed: 05/20/2023]
Abstract
Virus-induced flowering (VIF) uses virus vectors to express Flowering Locus T (FT) to induce flowering in plants. This approach has recently attracted wide interest for its practical applications in accelerating breeding in crops and woody fruit trees. However, the insight into VIF and its potential as a powerful tool for dissecting florigenic proteins remained to be elucidated. Here, we describe the mechanism and further applications of Potato virus X (PVX)-based VIF in the short-day Nicotiana tabacum cultivar Maryland Mammoth. Ectopic delivery of Arabidopsis (Arabidopsis thaliana) AtFT by PVX/AtFT did not induce the expression of the endogenous FT ortholog NtFT4; however, it was sufficient to trigger flowering in Maryland Mammoth plants grown under noninductive long-day conditions. Infected tobacco plants developed no systemic symptoms, and the PVX-based VIF did not cause transgenerational flowering. We showed that the PVX-based VIF is a much more rapid method to examine the impacts of single amino acid mutations on AtFT for floral induction than making individual transgenic Arabidopsis lines for each mutation. We also used the PVX-based VIF to demonstrate that adding a His- or FLAG-tag to the N or C terminus of AtFT could affect its florigenic activity and that this system can be applied to assay the function of FT genes from heterologous species, including tomato (Solanum lycopersicum) SFT and rice (Oryza sativa) Hd3a Thus, the PVX-based VIF represents a simple and efficient system to identify individual amino acids that are essential for FT-mediated floral induction and to test the ability of mono- and dicotyledonous FT genes and FT fusion proteins to induce flowering.
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Affiliation(s)
- Cheng Qin
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Weiwei Chen
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Jiajia Shen
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Linming Cheng
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Femi Akande
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Ke Zhang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Chen Yuan
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Chunyang Li
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Pengcheng Zhang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Nongnong Shi
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Qi Cheng
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Yule Liu
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Stephen Jackson
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.);
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.);
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
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Jian C, Han R, Chi Q, Wang S, Ma M, Liu X, Zhao H. Virus-Based MicroRNA Silencing and Overexpressing in Common Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2017; 8:500. [PMID: 28443107 PMCID: PMC5385339 DOI: 10.3389/fpls.2017.00500] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/22/2017] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs that arise from large RNA precursors with a stem-loop structure and play important roles in plant development and responses to environmental stress. Although a hundred and nineteen wheat miRNAs have been identified and registered in the miRBase (Release 21.0, June, 2014; http://www.mirbase.org), the functional characterization of these miRNAs in wheat growth and development is lagging due to lack of effective techniques to investigate endogenous miRNA functions in wheat. Here we report barley stripe mosaic virus(BSMV)-based miRNA overexpression and silence systems that can be applied to study miRNA functions in wheat. By utilizing the BSMV system, we successfully knocked down endogenous miR156 and miR166 levels and over-expressed endogenous miR156 and artificial miRNA against phytoene desaturase gene PDS (amiR-PDS) in wheat. amiR-PDS expression caused a great reduction in endogenous mRNA abundance of PDS gene in wheat plant, leading to leaf obviously photobleaching. miR156 silencing led to a great increase in the mRNA level of its target gene SPL2, resulting in a leaf-curl phenotype in wheat seedlings. In contrast, overexpression of miR156 led to a significant reduction in the mRNA level of SPL2 in wheat seedlings, resulting in serious delay of the vegetative phase transitions as well as booting and flowering in wheat. These confirmed that miR156 regulates wheat development and booting time through SPL genes. In summary, the BSMV-based miRNA overexpression and silence systems have extraordinary potential not only for functional study of protein-encoding genes but also for miRNA genes in wheat.
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Affiliation(s)
- Chao Jian
- College of Life Sciences, Northwest A&F University, YanglingChina
| | - Ran Han
- Crop Research Institute, Shandong Academy of Agricultural SciencesJinan, China
| | - Qing Chi
- College of Life Sciences, Northwest A&F University, YanglingChina
| | - Shijuan Wang
- College of Life Sciences, Northwest A&F University, YanglingChina
| | - Meng Ma
- College of Life Sciences, Northwest A&F University, YanglingChina
| | - Xiangli Liu
- College of Life Sciences, Northwest A&F University, YanglingChina
| | - Huixian Zhao
- College of Life Sciences, Northwest A&F University, YanglingChina
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F UniversityYangling, China
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35
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Wang C, Wang G, Zhang C, Zhu P, Dai H, Yu N, He Z, Xu L, Wang E. OsCERK1-Mediated Chitin Perception and Immune Signaling Requires Receptor-like Cytoplasmic Kinase 185 to Activate an MAPK Cascade in Rice. MOLECULAR PLANT 2017; 10:619-633. [PMID: 28111288 DOI: 10.1016/j.molp.2017.01.006] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 01/02/2017] [Accepted: 01/10/2017] [Indexed: 05/06/2023]
Abstract
Conserved pathogen-associated molecular patterns (PAMPs), such as chitin, are perceived by pattern recognition receptors (PRRs) located at the host cell surface and trigger rapid activation of mitogen-activated protein kinase (MAPK) cascades, which are required for plant resistance to pathogens. However, the direct links from PAMP perception to MAPK activation in plants remain largely unknown. In this study, we found that the PRR-associated receptor-like cytoplasmic kinase Oryza sativa RLCK185 transmits immune signaling from the PAMP receptor OsCERK1 to an MAPK signaling cascade through interaction with an MAPK kinase kinase, OsMAPKKKε, which is the initial kinase of the MAPK cascade. OsRLCK185 interacts with and phosphorylates the C-terminal regulatory domain of OsMAPKKKε. Coexpression of phosphomimetic OsRLCK185 and OsMAPKKKε activates MAPK3/6 phosphorylation in Nicotiana benthamiana leaves. Moreover, OsMAPKKKε interacts with and phosphorylates OsMKK4, a key MAPK kinase that transduces the chitin signal. Overexpression of OsMAPKKKε increases chitin-induced MAPK3/6 activation, whereas OsMAPKKKε knockdown compromises chitin-induced MAPK3/6 activation and resistance to rice blast fungus. Taken together, our results suggest the existence of a phospho-signaling pathway from cell surface chitin perception to intracellular activation of an MAPK cascade in rice.
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Affiliation(s)
- Chao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Gang Wang
- Department of Biology, East China Normal University, Shanghai 200241, China; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chi Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Pinkuan Zhu
- Department of Biology, East China Normal University, Shanghai 200241, China
| | - Huiling Dai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Nan Yu
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ling Xu
- Department of Biology, East China Normal University, Shanghai 200241, China.
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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Ju Z, Cao D, Gao C, Zuo J, Zhai B, Li S, Zhu H, Fu D, Luo Y, Zhu B. A Viral Satellite DNA Vector (TYLCCNV) for Functional Analysis of miRNAs and siRNAs in Plants. PLANT PHYSIOLOGY 2017; 173:1940-1952. [PMID: 28228536 PMCID: PMC5373046 DOI: 10.1104/pp.16.01489] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 02/19/2017] [Indexed: 05/11/2023]
Abstract
With experimental and bioinformatical methods, numerous small RNAs, including microRNAs (miRNAs) and short interfering RNAs (siRNAs), have been found in plants, and they play vital roles in various biological regulation processes. However, most of these small RNAs remain to be functionally characterized. Until now, only several viral vectors were developed to overexpress miRNAs with limited application in plants. In this study, we report a new small RNA overexpression system via viral satellite DNA associated with Tomato yellow leaf curl China virus (TYLCCNV) vector, which could highly overexpress not only artificial and endogenous miRNAs but also endogenous siRNAs in Nicotiana benthamiana First, we constructed basic TYLCCNV-amiRPDS(319L) vector with widely used AtMIR319a backbone, but the expected photobleaching phenotype was very weak. Second, through comparing the effect of backbones (AtMIR319a, AtMIR390a, and SlMIR159) on specificity and significance of generating small RNAs, the AtMIR390a backbone was optimally selected to construct the small RNA overexpression system. Third, through sRNA-Seq and Degradome-Seq, the small RNAs from AtMIR390a backbone in TYLCCNV-amiRPDS(390) vector were confirmed to highly overexpress amiRPDS and specifically silence targeted PDS gene. Using this system, rapid functional analysis of endogenous miRNAs and siRNAs was carried out, including miR156 and athTAS3a 5'D8(+). Meanwhile, through designing corresponding artificial miRNAs, this system could also significantly silence targeted endogenous genes and show specific phenotypes, including PDS, Su, and PCNA These results demonstrated that this small RNA overexpression system could contribute to investigating not only the function of endogenous small RNAs, but also the functional genes in plants.
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Affiliation(s)
- Zheng Ju
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China (Z.J., D.C., Ba.Z., S.L., H.Z., D.F., Y.L., Be.Z.)
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, China (C.G.); and
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China (J.Z.)
| | - Dongyan Cao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China (Z.J., D.C., Ba.Z., S.L., H.Z., D.F., Y.L., Be.Z.)
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, China (C.G.); and
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China (J.Z.)
| | - Chao Gao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China (Z.J., D.C., Ba.Z., S.L., H.Z., D.F., Y.L., Be.Z.)
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, China (C.G.); and
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China (J.Z.)
| | - Jinhua Zuo
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China (Z.J., D.C., Ba.Z., S.L., H.Z., D.F., Y.L., Be.Z.)
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, China (C.G.); and
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China (J.Z.)
| | - Baiqiang Zhai
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China (Z.J., D.C., Ba.Z., S.L., H.Z., D.F., Y.L., Be.Z.)
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, China (C.G.); and
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China (J.Z.)
| | - Shan Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China (Z.J., D.C., Ba.Z., S.L., H.Z., D.F., Y.L., Be.Z.)
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, China (C.G.); and
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China (J.Z.)
| | - Hongliang Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China (Z.J., D.C., Ba.Z., S.L., H.Z., D.F., Y.L., Be.Z.)
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, China (C.G.); and
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China (J.Z.)
| | - Daqi Fu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China (Z.J., D.C., Ba.Z., S.L., H.Z., D.F., Y.L., Be.Z.)
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, China (C.G.); and
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China (J.Z.)
| | - Yunbo Luo
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China (Z.J., D.C., Ba.Z., S.L., H.Z., D.F., Y.L., Be.Z.)
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, China (C.G.); and
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China (J.Z.)
| | - Benzhong Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China (Z.J., D.C., Ba.Z., S.L., H.Z., D.F., Y.L., Be.Z.);
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, China (C.G.); and
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China (J.Z.)
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37
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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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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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Liu H, Able AJ, Able JA. SMARTER De-Stressed Cereal Breeding. TRENDS IN PLANT SCIENCE 2016; 21:909-925. [PMID: 27514453 DOI: 10.1016/j.tplants.2016.07.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/30/2016] [Accepted: 07/05/2016] [Indexed: 05/06/2023]
Abstract
In cereal breeding programs, improved yield potential and stability are ultimate goals when developing new varieties. To facilitate achieving these goals, reproductive success under stressful growing conditions is of the highest priority. In recent times, small RNA (sRNA)-mediated pathways have been associated with the regulation of genes involved in stress adaptation and reproduction in both model plants and several cereals. Reproductive and physiological traits such as flowering time, reproductive branching, and root architecture can be manipulated by sRNA regulatory modules. We review sRNA-mediated pathways that could be exploited to expand crop diversity with adaptive traits and, in particular, the development of high-yielding stress-tolerant cereals: SMARTER cereal breeding through 'Small RNA-Mediated Adaptation of Reproductive Targets in Epigenetic Regulation'.
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Affiliation(s)
- Haipei Liu
- School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, PMB 1, Glen Osmond, South Australia 5064, Australia
| | - Amanda J Able
- School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, PMB 1, Glen Osmond, South Australia 5064, Australia
| | - Jason A Able
- School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, PMB 1, Glen Osmond, South Australia 5064, Australia.
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Jia Q, Liu N, Xie K, Dai Y, Han S, Zhao X, Qian L, Wang Y, Zhao J, Gorovits R, Xie D, Hong Y, Liu Y. CLCuMuB βC1 Subverts Ubiquitination by Interacting with NbSKP1s to Enhance Geminivirus Infection in Nicotiana benthamiana. PLoS Pathog 2016; 12:e1005668. [PMID: 27315204 PMCID: PMC4912122 DOI: 10.1371/journal.ppat.1005668] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 05/10/2016] [Indexed: 11/21/2022] Open
Abstract
Viruses interfere with and usurp host machinery and circumvent defense responses to create a suitable cellular environment for successful infection. This is usually achieved through interactions between viral proteins and host factors. Geminiviruses are a group of plant-infecting DNA viruses, of which some contain a betasatellite, known as DNAβ. Here, we report that Cotton leaf curl Multan virus (CLCuMuV) uses its sole satellite-encoded protein βC1 to regulate the plant ubiquitination pathway for effective infection. We found that CLCuMu betasatellite (CLCuMuB) βC1 interacts with NbSKP1, and interrupts the interaction of NbSKP1s with NbCUL1. Silencing of either NbSKP1s or NbCUL1 enhances the accumulation of CLCuMuV genomic DNA and results in severe disease symptoms in plants. βC1 impairs the integrity of SCFCOI1 and the stabilization of GAI, a substrate of the SCFSYL1 to hinder responses to jasmonates (JA) and gibberellins (GA). Moreover, JA treatment reduces viral accumulation and symptoms. These results suggest that CLCuMuB βC1 inhibits the ubiquitination function of SCF E3 ligases through interacting with NbSKP1s to enhance CLCuMuV infection and symptom induction in plants.
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Affiliation(s)
- Qi Jia
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Na Liu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ke Xie
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yanwan Dai
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Shaojie Han
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xijuan Zhao
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Lichao Qian
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yunjing Wang
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jinping Zhao
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Rena Gorovits
- Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Daoxin Xie
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
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41
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Singh G, Tiwari M, Singh SP, Singh S, Trivedi PK, Misra P. Silencing of sterol glycosyltransferases modulates the withanolide biosynthesis and leads to compromised basal immunity of Withania somnifera. Sci Rep 2016; 6:25562. [PMID: 27146059 PMCID: PMC4857139 DOI: 10.1038/srep25562] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 03/22/2016] [Indexed: 11/10/2022] Open
Abstract
Sterol glycosyltransferases (SGTs) catalyse transfer of glycon moiety to sterols and their related compounds to produce diverse glyco-conjugates or steryl glycosides with different biological and pharmacological activities. Functional studies of SGTs from Withania somnifera indicated their role in abiotic stresses but details about role under biotic stress are still unknown. Here, we have elucidated the function of SGTs by silencing SGTL1, SGTL2 and SGTL4 in Withania somnifera. Down-regulation of SGTs by artificial miRNAs led to the enhanced accumulation of withanolide A, withaferin A, sitosterol, stigmasterol and decreased content of withanoside V in Virus Induced Gene Silencing (VIGS) lines. This was further correlated with increased expression of WsHMGR, WsDXR, WsFPPS, WsCYP710A1, WsSTE1 and WsDWF5 genes, involved in withanolide biosynthesis. These variations of withanolide concentrations in silenced lines resulted in pathogen susceptibility as compared to control plants. The infection of Alternaria alternata causes increased salicylic acid, callose deposition, superoxide dismutase and H2O2 in aMIR-VIGS lines. The expression of biotic stress related genes, namely, WsPR1, WsDFS, WsSPI and WsPR10 were also enhanced in aMIR-VIGS lines in time dependent manner. Taken together, our observations revealed that a positive feedback regulation of withanolide biosynthesis occurred by silencing of SGTLs which resulted in reduced biotic tolerance.
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Affiliation(s)
- Gaurav Singh
- Council of Scientific and Industrial Research-National Botanical Research Institute, Rana Pratap Marg, Lucknow-226001, Uttar Pradesh, India.,Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Manish Tiwari
- Council of Scientific and Industrial Research-National Botanical Research Institute, Rana Pratap Marg, Lucknow-226001, Uttar Pradesh, India
| | - Surendra Pratap Singh
- Council of Scientific and Industrial Research-National Botanical Research Institute, Rana Pratap Marg, Lucknow-226001, Uttar Pradesh, India
| | - Surendra Singh
- Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Prabodh Kumar Trivedi
- Council of Scientific and Industrial Research-National Botanical Research Institute, Rana Pratap Marg, Lucknow-226001, Uttar Pradesh, India
| | - Pratibha Misra
- Council of Scientific and Industrial Research-National Botanical Research Institute, Rana Pratap Marg, Lucknow-226001, Uttar Pradesh, India
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42
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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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43
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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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44
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45
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Butler NM, Baltes NJ, Voytas DF, Douches DS. Geminivirus-Mediated Genome Editing in Potato (Solanum tuberosum L.) Using Sequence-Specific Nucleases. FRONTIERS IN PLANT SCIENCE 2016; 7:1045. [PMID: 27493650 PMCID: PMC4955380 DOI: 10.3389/fpls.2016.01045] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 07/04/2016] [Indexed: 05/17/2023]
Abstract
Genome editing using sequence-specific nucleases (SSNs) is rapidly being developed for genetic engineering in crop species. The utilization of zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/CRISPR-associated systems (CRISPR/Cas) for inducing double-strand breaks facilitates targeting of virtually any sequence for modification. Targeted mutagenesis via non-homologous end-joining (NHEJ) has been demonstrated extensively as being the preferred DNA repair pathway in plants. However, gene targeting via homologous recombination (HR) remains more elusive but could be a powerful tool for directed DNA repair. To overcome barriers associated with gene targeting, a geminivirus replicon (GVR) was used to deliver SSNs targeting the potato ACETOLACTATE SYNTHASE1 (ALS1) gene and repair templates designed to incorporate herbicide-inhibiting point mutations within the ALS1 locus. Transformed events modified with GVRs held point mutations that were capable of supporting a reduced herbicide susceptibility phenotype, while events transformed with conventional T-DNAs held no detectable mutations and were similar to wild-type. Regeneration of transformed events improved detection of point mutations that supported a stronger reduced herbicide susceptibility phenotype. These results demonstrate the use of geminiviruses for delivering genome editing reagents in plant species, and a novel approach to gene targeting in a vegetatively propagated species.
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Affiliation(s)
- Nathaniel M. Butler
- Department of Plant, Soils and Microbial Sciences, Michigan State University, East LansingMI, USA
| | - Nicholas J. Baltes
- Department of Genetics, Cell Biology and Development and Center for Genome Engineering, University of Minnesota, MinneapolisMN, USA
| | - Daniel F. Voytas
- Department of Genetics, Cell Biology and Development and Center for Genome Engineering, University of Minnesota, MinneapolisMN, USA
| | - David S. Douches
- Department of Plant, Soils and Microbial Sciences, Michigan State University, East LansingMI, USA
- *Correspondence: David S. Douches,
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46
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Liao Q, Tu Y, Carr JP, Du Z. An improved cucumber mosaic virus-based vector for efficient decoying of plant microRNAs. Sci Rep 2015; 5:13178. [PMID: 26278008 PMCID: PMC4538387 DOI: 10.1038/srep13178] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 07/08/2015] [Indexed: 12/05/2022] Open
Abstract
We previously devised a cucumber mosaic virus (CMV)-based vector system carrying microRNA target mimic sequences for analysis of microRNA function in Arabidopsis thaliana. We describe an improved version in which target mimic cloning is achieved by annealing two partly-overlapping complementary DNA oligonucleotides for insertion into an infectious clone of CMV RNA3 (LS strain) fused to the cauliflower mosaic virus-derived 35S promoter. LS-CMV variants carrying mimic sequences were generated by co-infiltrating plants with Agrobacterium tumefaciens cells harboring engineered RNA3 with cells carrying RNA1 and RNA2 infectious clones. The utility of using agroinfection to deliver LS-CMV-derived microRNA target mimic sequences was demonstrated using a miR165/166 target mimic and three solanaceous hosts: Nicotiana benthamiana, tobacco (N. tabacum), and tomato (Solanum lycopersicum). In all three hosts the miR165/166 target mimic induced marked changes in developmental phenotype. Inhibition of miRNA accumulation and increased target mRNA (HD-ZIP III) accumulation was demonstrated in tomato. Thus, a CMV-derived target mimic delivered via agroinfection is a simple, cheap and powerful means of launching virus-based miRNA mimics and is likely to be useful for high-throughput investigation of miRNA function in a wide range of plants.
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Affiliation(s)
- Qiansheng Liao
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Yifei Tu
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - John P. Carr
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Zhiyou Du
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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Reichel M, Millar AA. Specificity of plant microRNA target MIMICs: Cross-targeting of miR159 and miR319. JOURNAL OF PLANT PHYSIOLOGY 2015; 180:45-48. [PMID: 25899728 DOI: 10.1016/j.jplph.2015.03.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 03/11/2015] [Accepted: 03/12/2015] [Indexed: 06/04/2023]
Abstract
Plant microRNA (miRNA) target MIMICs (MIMs) are non-coding RNA transcripts that can inhibit endogenous miRNAs, as they contain a miRNA binding site that forms a three nucleotide (nt) mismatch loop opposite the miRNA cleavage site upon miRNA binding. This loop renders the MIMs non-cleavable, presumably leading to sequestration of the miRNA and thus enabling the endogenous targets to be deregulated. Arabidopsis miR319 and miR159 are two closely related but distinct miRNA families, as they are functionally specific for two different sets of targets, TCP and MYB genes, respectively. Being offset by one nt, MIM319 and MIM159 should have specificity to their respective miRNA families. However, MIM319 and MIM159 plants appear indistinguishable, having highly similar developmental defects reminiscent of a loss-of-function mir159 mutant. In both MIM319 and MIM159 plants, miR159 and miR319 levels are reduced, and correspondingly, both MYB and TCP mRNA levels are elevated, implying that these MIMs are inhibiting both miR159 and miR319. These data demonstrate that MIMs are able to inhibit closely related miRNAs, including those with cleavage sites not opposite the three nt loop. This highlights that MIMs can have unintended off-target effects and that their use should include corresponding molecular analysis to investigate their impact on closely related miRNAs.
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Affiliation(s)
- Marlene Reichel
- Plant Science Division, Research School of Biology, Australian National University, 2601 ACT, Australia
| | - Anthony A Millar
- Plant Science Division, Research School of Biology, Australian National University, 2601 ACT, Australia.
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Jiao J, Wang Y, Selvaraj JN, Xing F, Liu Y. Barley Stripe Mosaic Virus (BSMV) Induced MicroRNA Silencing in Common Wheat (Triticum aestivum L.). PLoS One 2015; 10:e0126621. [PMID: 25955840 PMCID: PMC4425524 DOI: 10.1371/journal.pone.0126621] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 04/03/2015] [Indexed: 01/14/2023] Open
Abstract
MicroRNAs (miRNAs) play important roles in growth, development, and response to environmental changes in plants. Based on the whole-genome shotgun sequencing strategy, more and more wheat miRNAs have been annotated. Now, there is a need for an effective technology to analyse endogenous miRNAs function in wheat. We report here that the modified barley stripe mosaic virus (BSMV)-induced miRNAs silencing system can be utilized to silence miRNAs in wheat. BSMV-based miRNA silencing system is performed through BSMV-based expression of miRNA target mimics to suppress miR159a and miR3134a. The relative expression levels of mature miR159a and miR3134a decrease with increasing transcript levels of their target genes in wheat plants. In summary, the developed approach is effective in silencing endogenous miRNAs, thereby providing a powerful tool for biological function analyses of miRNA molecules in common wheat.
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Affiliation(s)
- Jian Jiao
- Institute of Agro-Products Processing Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing, P.R. China
| | - Yichun Wang
- Institute of Agro-Products Processing Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing, P.R. China
| | - Jonathan Nimal Selvaraj
- Institute of Agro-Products Processing Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing, P.R. China
| | - Fuguo Xing
- Institute of Agro-Products Processing Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing, P.R. China
| | - Yang Liu
- Institute of Agro-Products Processing Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing, P.R. China
- * E-mail:
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Krenek P, Samajova O, Luptovciak I, Doskocilova A, Komis G, Samaj J. Transient plant transformation mediated by Agrobacterium tumefaciens: Principles, methods and applications. Biotechnol Adv 2015; 33:1024-42. [PMID: 25819757 DOI: 10.1016/j.biotechadv.2015.03.012] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 03/05/2015] [Accepted: 03/19/2015] [Indexed: 12/20/2022]
Abstract
Agrobacterium tumefaciens is widely used as a versatile tool for development of stably transformed model plants and crops. However, the development of Agrobacterium based transient plant transformation methods attracted substantial attention in recent years. Transient transformation methods offer several applications advancing stable transformations such as rapid and scalable recombinant protein production and in planta functional genomics studies. Herein, we highlight Agrobacterium and plant genetics factors affecting transfer of T-DNA from Agrobacterium into the plant cell nucleus and subsequent transient transgene expression. We also review recent methods concerning Agrobacterium mediated transient transformation of model plants and crops and outline key physical, physiological and genetic factors leading to their successful establishment. Of interest are especially Agrobacterium based reverse genetics studies in economically important crops relying on use of RNA interference (RNAi) or virus-induced gene silencing (VIGS) technology. The applications of Agrobacterium based transient plant transformation technology in biotech industry are presented in thorough detail. These involve production of recombinant proteins (plantibodies, vaccines and therapeutics) and effectoromics-assisted breeding of late blight resistance in potato. In addition, we also discuss biotechnological potential of recombinant GFP technology and present own examples of successful Agrobacterium mediated transient plant transformations.
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Affiliation(s)
- Pavel Krenek
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic.
| | - Olga Samajova
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic.
| | - Ivan Luptovciak
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic.
| | - Anna Doskocilova
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic.
| | - George Komis
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic.
| | - Jozef Samaj
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic.
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50
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Shapiro JA. Epigenetic control of mobile DNA as an interface between experience and genome change. Front Genet 2014; 5:87. [PMID: 24795749 PMCID: PMC4007016 DOI: 10.3389/fgene.2014.00087] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/01/2014] [Indexed: 12/29/2022] Open
Abstract
Mobile DNA in the genome is subject to RNA-targeted epigenetic control. This control regulates the activity of transposons, retrotransposons and genomic proviruses. Many different life history experiences alter the activities of mobile DNA and the expression of genetic loci regulated by nearby insertions. The same experiences induce alterations in epigenetic formatting and lead to trans-generational modifications of genome expression and stability. These observations lead to the hypothesis that epigenetic formatting directed by non-coding RNA provides a molecular interface between life history events and genome alteration.
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Affiliation(s)
- James A. Shapiro
- Department of Biochemistry and Molecular Biology, University of ChicagoChicago, IL, USA
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