1
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Kumar S, Sharma N, Sopory SK, Sanan-Mishra N. miRNAs and genes as molecular regulators of rice grain morphology and yield. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108363. [PMID: 38281341 DOI: 10.1016/j.plaphy.2024.108363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/07/2023] [Accepted: 01/10/2024] [Indexed: 01/30/2024]
Abstract
Rice is one of the most consumed crops worldwide and the genetic and molecular basis of its grain yield attributes are well understood. Various studies have identified different yield-related parameters in rice that are regulated by the microRNAs (miRNAs). MiRNAs are endogenous small non-coding RNAs that silence gene expression during or after transcription. They control a variety of biological or genetic activities in plants including growth, development and response to stress. In this review, we have summarized the available information on the genetic control of panicle architecture and grain yield (number and morphology) in rice. The miRNA nodes that are associated with their regulation are also described while focussing on the central role of miR156-SPL node to highlight the co-regulation of two master regulators that determine the fate of panicle development. Since abiotic stresses are known to negatively affect yield, the impact of abiotic stress induced alterations on the levels of these miRNAs are also discussed to highlight the potential of miRNAs for regulating crop yields.
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Affiliation(s)
- Sudhir Kumar
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
| | - Neha Sharma
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
| | - Sudhir K Sopory
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
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2
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Berbati M, Kaldis A, Voloudakis A. Efficient artificial microRNA-mediated resistance against zucchini yellow mosaic virus in zucchini via agroinfiltration. J Virol Methods 2023; 321:114805. [PMID: 37673287 DOI: 10.1016/j.jviromet.2023.114805] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/09/2023] [Accepted: 08/31/2023] [Indexed: 09/08/2023]
Abstract
Zucchini yellow mosaic virus (ZYMV) infects cucurbits causing yellow mosaic in leaves, malformations in fruits, and degradation of the product quality. RNA interference (RNAi) is a cellular mechanism in eukaryotes and it is exploited to protect them against viruses. The artificial micro RNA (amiRNA) mediated approach was employed to develop resistance against ZYMV. Four amiRNAs, amiZYMV_HC-115s and amiZYMV_HC-1162s (sense), amiZYMV_HC-182as and amiZYMV_HC-196as (antisense), were computationally designed and introduced into the AtMIR390a backbone. At four days post agroinfiltration (dpa) of zucchini cotyledons the corresponding pre- and the mature amiRNAs were identified in local tissue. Upon ZYMV inoculation of zucchini, ZYMV titer was significantly lower where amiZYMV_HCs were applied in relation to control starting at two days post inoculation (dpi). Control zucchini plants exhibited symptoms at 5-8 dpi, whereas the amiZYMV_HC-treated zucchini had symptoms at 14 dpi; at 21 dpi treated zucchini exhibited a 16 %, 19 %, 32 %, and 42.5 % protection, respectively. For luffa, we observed a lower protection (0 %, 17 %, 22.5 %, and 31 % at 21 dpi). Nicotiana benthamiana DCL4 knock-down mutants were infected by ZYMV, whereas when the amiZYMV_HC-196as was agroinfiltrated ZYMV was not detected by RT-PCR. These results indicate that amiRNA-mediated resistance could be applied against ZYMV in zucchini.
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Affiliation(s)
- Margarita Berbati
- Laboratory of Plant Breeding and Biometry, Faculty of Crop Science, Agricultural University of Athens, Athens 11855, Greece
| | - Athanasios Kaldis
- Laboratory of Plant Breeding and Biometry, Faculty of Crop Science, Agricultural University of Athens, Athens 11855, Greece
| | - Andreas Voloudakis
- Laboratory of Plant Breeding and Biometry, Faculty of Crop Science, Agricultural University of Athens, Athens 11855, Greece.
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3
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Akbarimotlagh M, Azizi A, Shams-Bakhsh M, Jafari M, Ghasemzadeh A, Palukaitis P. Critical points for the design and application of RNA silencing constructs for plant virus resistance. Adv Virus Res 2023; 115:159-203. [PMID: 37173065 DOI: 10.1016/bs.aivir.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Control of plant virus diseases is a big challenge in agriculture as is resistance in plant lines to infection by viruses. Recent progress using advanced technologies has provided fast and durable alternatives. One of the most promising techniques against plant viruses that is cost-effective and environmentally safe is RNA silencing or RNA interference (RNAi), a technology that could be used alone or along with other control methods. To achieve the goals of fast and durable resistance, the expressed and target RNAs have been examined in many studies, with regard to the variability in silencing efficiency, which is regulated by various factors such as target sequences, target accessibility, RNA secondary structures, sequence variation in matching positions, and other intrinsic characteristics of various small RNAs. Developing a comprehensive and applicable toolbox for the prediction and construction of RNAi helps researchers to achieve the acceptable performance level of silencing elements. Although the attainment of complete prediction of RNAi robustness is not possible, as it also depends on the cellular genetic background and the nature of the target sequences, some important critical points have been discerned. Thus, the efficiency and robustness of RNA silencing against viruses can be improved by considering the various parameters of the target sequence and the construct design. In this review, we provide a comprehensive treatise regarding past, present and future prospective developments toward designing and applying RNAi constructs for resistance to plant viruses.
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Affiliation(s)
- Masoud Akbarimotlagh
- Plant Pathology Department, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran, Iran
| | - Abdolbaset Azizi
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran.
| | - Masoud Shams-Bakhsh
- Plant Pathology Department, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran, Iran
| | - Majid Jafari
- Department of Plant Protection, Higher Education Complex of Saravan, Saravan, Iran
| | - Aysan Ghasemzadeh
- Plant Pathology Department, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran, Iran
| | - Peter Palukaitis
- Department of Horticulture Sciences, Seoul Women's University, Seoul, Republic of Korea.
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4
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Liu F, Zhang P, Li J, Zhang T, Xie L, Gong C. miR2119, a Novel Transcriptional Regulator, Plays a Positive Role in Woody Plant Drought Tolerance by Mediating the Degradation of the CkBI-1 Gene Associated with Apoptosis. Int J Mol Sci 2022; 23:6306. [PMID: 35682985 PMCID: PMC9181555 DOI: 10.3390/ijms23116306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/02/2022] [Accepted: 06/02/2022] [Indexed: 02/04/2023] Open
Abstract
Caragana korshinskii, an important vegetation restoration species with economic and ecological benefits in the arid region of northwest China, is characterized by significant drought tolerance. However, the underlying molecular mechanisms by which miRNAs confer this trait in C. korshinskii are unclear. Here, we investigate the effect of CkmiR2119 on drought tolerance and identified its target gene, CkBI-1. A negative correlation of CkmiR2119 and CkBI-1 in both stems and leaves in a drought gradient treatment followed by target gene validation suggest that CkmiR2119 might negatively regulate CkBI-1. Consistently, a decrease in the expression of the CkBI-1 gene was observed after both transient transformation and stable transformation of CkamiR2119 in tobacco (Nicotiana tabacum). Moreover, the physiological analysis of CkamiR2119 and CkBI-1 transgenic plants further indicate that CkmiR2119 can enhance the drought tolerance of C. korshinskii in two aspects: (i) downregulating CkBI-1 expression to accelerate vessel maturation in stems; (ii) contributing to a higher level of CkBI-1 in mesophyll cells to inhibit programmed cell death (PCD). This work reveals that CkmiR2119 can increase plants' drought tolerance by downregulating the expression of CkBI-1, providing a theoretical basis to improve plants' ability to withstand stress tolerance by manipulating miRNAs.
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Affiliation(s)
- Furong Liu
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (F.L.); (P.Z.); (T.Z.); (L.X.)
| | - Puzhi Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (F.L.); (P.Z.); (T.Z.); (L.X.)
| | - Jiayang Li
- College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China;
| | - Tianxin Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (F.L.); (P.Z.); (T.Z.); (L.X.)
| | - Lifang Xie
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (F.L.); (P.Z.); (T.Z.); (L.X.)
| | - Chunmei Gong
- College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China;
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5
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Rani V, Sengar RS. Biogenesis and Mechanisms of miRNA-Mediated Gene Regulation. Biotechnol Bioeng 2022; 119:685-692. [PMID: 34979040 DOI: 10.1002/bit.28029] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 10/19/2021] [Accepted: 12/21/2021] [Indexed: 11/07/2022]
Abstract
Endogenous RNAs that control post-transcriptional gene expression are microRNAs (miRNAs). These small regulatory molecules play a crucial role in certain biological processes and their expression is often strictly regulated. They are small 21-24 nucleotide molecules that act as major regulators of gene expression at the post-transcriptional level. One of the mechanisms by which miRNAs control the gene expression is to interact the interaction of the seeds with the 3'-end and more seldom the 5'-end of mRNA transcribed by the target genes. miRNAs have been identified as important cytoplasmic regulators of gene expression. miRNAs function as post-transcriptional regulators of their messenger RNA (mRNA) targets by mRNA degradation and/or translational repression. It is becoming evident, however, that miRNAs have nuclear functions as well. About the cell type, the physiological state of the body, and various external factors, the following explanation will summarize the complex multilevel regulation of miRNA expression. A better understanding of the molecular mechanisms controlling miRNA expression will provide clarification of the variations in the expression of protein-coding genes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Varsha Rani
- Dept. Of Agricultural biotechnology, Sardar Vallabhbhai Patel university of agriculture and technology, Meerut, 250110
| | - R S Sengar
- Dept. Of Agricultural biotechnology, Sardar Vallabhbhai Patel university of agriculture and technology, Meerut, 250110
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Patil S, Joshi S, Jamla M, Zhou X, Taherzadeh MJ, Suprasanna P, Kumar V. MicroRNA-mediated bioengineering for climate-resilience in crops. Bioengineered 2021; 12:10430-10456. [PMID: 34747296 PMCID: PMC8815627 DOI: 10.1080/21655979.2021.1997244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 12/24/2022] Open
Abstract
Global projections on the climate change and the dynamic environmental perturbations indicate severe impacts on food security in general, and crop yield, vigor and the quality of produce in particular. Sessile plants respond to environmental challenges such as salt, drought, temperature, heavy metals at transcriptional and/or post-transcriptional levels through the stress-regulated network of pathways including transcription factors, proteins and the small non-coding endogenous RNAs. Amongs these, the miRNAs have gained unprecedented attention in recent years as key regulators for modulating gene expression in plants under stress. Hence, tailoring of miRNAs and their target pathways presents a promising strategy for developing multiple stress-tolerant crops. Plant stress tolerance has been successfully achieved through the over expression of microRNAs such as Os-miR408, Hv-miR82 for drought tolerance; OsmiR535A and artificial DST miRNA for salinity tolerance; and OsmiR535 and miR156 for combined drought and salt stress. Examples of miR408 overexpression also showed improved efficiency of irradiation utilization and carbon dioxide fixation in crop plants. Through this review, we present the current understanding about plant miRNAs, their roles in plant growth and stress-responses, the modern toolbox for identification, characterization and validation of miRNAs and their target genes including in silico tools, machine learning and artificial intelligence. Various approaches for up-regulation or knock-out of miRNAs have been discussed. The main emphasis has been given to the exploration of miRNAs for development of bioengineered climate-smart crops that can withstand changing climates and stressful environments, including combination of stresses, with very less or no yield penalties.
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Affiliation(s)
- Suraj Patil
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Pune, India
| | - Shrushti Joshi
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Pune, India
| | - Monica Jamla
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Pune, India
| | - Xianrong Zhou
- School of Life Science and Biotechnology, Yangtze Normal University, Ch-ongqing, China
| | | | - Penna Suprasanna
- Bhabha Atomic Research Centre, Homi Bhabha National Institute, Mumbai, India
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Pune, India
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Jia M, He J, Bai W, Lin Q, Deng J, Li W, Bai J, Fu D, Ma Y, Ren J, Xiong S. Cross-kingdom regulation by dietary plant miRNAs: an evidence-based review with recent updates. Food Funct 2021; 12:9549-9562. [PMID: 34664582 DOI: 10.1039/d1fo01156a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
As non-coding RNA molecules, microRNAs (miRNAs) are widely known for their critical role in gene regulation. Recent studies have shown that plant miRNAs obtained through dietary oral administration can survive in the gastrointestinal (GI) tract, enter the circulatory system and regulate endogenous mRNAs. Diet-derived plant miRNAs have 2'-O-methylated modified 3'ends and high cytosine and guanine (GC) content, as well as exosomal packaging, which gives them high stability even in the harsh environment of the digestive system and circulatory system. The latest evidence shows that dietary plant miRNAs can not only be absorbed in the intestine, but also be absorbed and packaged by gastric epithelial cells and then secreted into the circulatory system. Alternatively, these biologically active plant-derived miRNAs may also affect the health of the host by affecting the function of the microbiome, while not need to be taken into the host's circulatory system and transferred to remote tissues. This cross-kingdom regulation of miRNAs gives us hope for exploring their therapeutic potential and as dietary supplements. However, doubts have also been raised about the cross-border regulation of miRNAs, suggesting that technical flaws in the experiments may have led to this hypothesis. In this article, we summarize the visibility of dietary plant miRNAs in the development of human health and recent research data on their use in therapeutics. The regulation of plant miRNAs across kingdoms is a novel concept. Continued efforts in this area will broaden our understanding of the biological role of plant miRNAs and will open the way for the development of new approaches to prevent or treat human diseases.
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Affiliation(s)
- MingXi Jia
- National Engineering Laboratory for Deep Process of Rice and Byproducts, Hunan Province Key Laboratory of Edible forestry Resources Safety and Processing Utilization, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China. .,College of Light Industry and Food Sciences, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, China
| | - JinTao He
- National Engineering Laboratory for Deep Process of Rice and Byproducts, Hunan Province Key Laboratory of Edible forestry Resources Safety and Processing Utilization, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.
| | - WeiDong Bai
- College of Light Industry and Food Sciences, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, China
| | - QinLu Lin
- National Engineering Laboratory for Deep Process of Rice and Byproducts, Hunan Province Key Laboratory of Edible forestry Resources Safety and Processing Utilization, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.
| | - Jing Deng
- National Engineering Laboratory for Deep Process of Rice and Byproducts, Hunan Province Key Laboratory of Edible forestry Resources Safety and Processing Utilization, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.
| | - Wen Li
- National Engineering Laboratory for Deep Process of Rice and Byproducts, Hunan Province Key Laboratory of Edible forestry Resources Safety and Processing Utilization, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.
| | - Jie Bai
- National Engineering Laboratory for Deep Process of Rice and Byproducts, Hunan Province Key Laboratory of Edible forestry Resources Safety and Processing Utilization, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.
| | - Da Fu
- National Engineering Laboratory for Deep Process of Rice and Byproducts, Hunan Province Key Laboratory of Edible forestry Resources Safety and Processing Utilization, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China. .,Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - YuShui Ma
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - JiaLi Ren
- National Engineering Laboratory for Deep Process of Rice and Byproducts, Hunan Province Key Laboratory of Edible forestry Resources Safety and Processing Utilization, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.
| | - ShouYao Xiong
- College of Mathematics and Statistics, Changsha University of Science and Technology, Changsha 410114, China
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Wen N, Chen J, Chen G, Du L, Chen H, Li Y, Peng Y, Yang X, Han L. The overexpression of insect endogenous microRNA in transgenic rice inhibits the pupation of Chilo suppressalis and Cnaphalocrocis medinalis. PEST MANAGEMENT SCIENCE 2021; 77:3990-3999. [PMID: 33890699 DOI: 10.1002/ps.6422] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/11/2021] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Chilo suppressalis and Cnaphalocrocis medinalis are destructive rice pests co-occurring in major rice-growing areas in China. RNA interference (RNAi)-based insect-resistant genetically engineered (IRGE) crops provide a promising approach for pest management by suppressing gene expression or translation. A microRNA (miRNA)-mediated IRGE rice line expressing endogenous Chilo suppressalis miRNA Csu-novel-260, showing significant resistance against Chilo suppressalis, provides an attractive control strategy for Chilo suppressalis by suppressing the expression of the disembodied (dib) gene expression. However, whether this transgenic line also shows the resistance against Cnaphalocrocis medinalis remains unknown. RESULTS A spatiotemporal expression analysis of Csu-novel-260 in the transgenic rice line was performed by quantitative reverse transcription polymerase chain reaction (qRT-PCR) to determine the paddy field pest exposure dose. In diet feeding assays, a chemically synthesized Csu-novel-260 agomir at 200 fmol g-1 significantly inhibited Chilo suppressalis pupation. However, larval development, survival and pupal weight were not significantly affected. Additionally, the transgenic line significantly affected Cnaphalocrocis medinalis pupation but not larval survival. The qRT-PCR showed that Csdib and Cmdib expression levels were significantly suppressed when the two pests fed on the transgenic line. Additionally, the transgenic line significantly decreased Cry1C-resistant and Cry1C-susceptible Chilo suppressalis larval survival in detached rice tissue feeding assays, indicating that Cry1C-resistant Chilo suppressalis was not cross-resistant to Csu-novel-260 expressed in miRNA-mediated IRGE rice. CONCLUSION Our study demonstrated that miRNA-mediated IRGE rice significantly inhibited Chilo suppressalis and Cnaphalocrocis medinalis pupation. The results provide a new viewpoint for the application of RNAi-based plants and the inspiration for environmental risk assessment.
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Affiliation(s)
- Ning Wen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junjie Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Geng Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixiao Du
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hao Chen
- Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yunhe Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yufa Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaowei Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lanzhi Han
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Chen J, Wang H, Yang X, Chen G, Du L, Chen H, Li Y, Peng Y, Han L. Consumption of miRNA-Mediated Insect-Resistant Transgenic Rice Pollen Does Not Harm Apis mellifera Adults. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:4234-4242. [PMID: 33818077 DOI: 10.1021/acs.jafc.1c00585] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
RNAi-based insect-resistant genetically engineered (IRGE) crops represent a promising approach for pest management by suppressing gene expressions or translation. A developed microRNA-mediated IRGE rice line expressing endogenous Chilo suppressalis Csu-novel-260 shows significant resistance to target pests. The nontarget insect Apis mellifera is an important pollinator used as a surrogate species for the ecological risk assessment of IRGE plants. To simulate a worst-case scenario, the full-length C. suppressalis and A. mellifera disembodied (dib) cDNAs were cloned. The dib 3'-untranslated regions shared 58.06% nucleotide sequence similarity between C. suppressalis and A. mellifera. No potential Csu-novel-260 binding site in Amdib was detected through the bioinformatics analysis. A dietary RNAi toxicity assay of the impacts of ingested Csu-novel-260 on A. mellifera adults showed that the survival rates of RNAi-treated A. mellifera did not significantly differ from those in the blank control (CK) and negative control (NC) treatments. The Csu-novel-260 uptake by A. mellifera peaked at 8 days postfeeding and then gradually decreased. The Amdib expression was not affected by the RNAi assay days or treatments. These results suggest that A. mellifera adults are not susceptible to high doses of Csu-novel-260 in the dietary RNAi assay and that the impact of miRNA-mediated IRGE plants on A. mellifera is negligible.
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Affiliation(s)
- Junjie Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huilin Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaowei Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Geng Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lixiao Du
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hao Chen
- Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yunhe Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yufa Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lanzhi Han
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Chaudhary S, Grover A, Sharma PC. MicroRNAs: Potential Targets for Developing Stress-Tolerant Crops. Life (Basel) 2021; 11:life11040289. [PMID: 33800690 PMCID: PMC8066829 DOI: 10.3390/life11040289] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/24/2022] Open
Abstract
Crop yield is challenged every year worldwide by changing climatic conditions. The forecasted climatic scenario urgently demands stress-tolerant crop varieties to feed the ever-increasing global population. Molecular breeding and genetic engineering approaches have been frequently exploited for developing crops with desired agronomic traits. Recently, microRNAs (miRNAs) have emerged as powerful molecules, which potentially serve as expression markers during stress conditions. The miRNAs are small non-coding endogenous RNAs, usually 20-24 nucleotides long, which mediate post-transcriptional gene silencing and fine-tune the regulation of many abiotic- and biotic-stress responsive genes in plants. The miRNAs usually function by specifically pairing with the target mRNAs, inducing their cleavage or repressing their translation. This review focuses on the exploration of the functional role of miRNAs in regulating plant responses to abiotic and biotic stresses. Moreover, a methodology is also discussed to mine stress-responsive miRNAs from the enormous amount of transcriptome data available in the public domain generated using next-generation sequencing (NGS). Considering the functional role of miRNAs in mediating stress responses, these molecules may be explored as novel targets for engineering stress-tolerant crop varieties.
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Affiliation(s)
- Saurabh Chaudhary
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
- Correspondence: (S.C.); (P.C.S.)
| | - Atul Grover
- Defence Institute of Bio-Energy Research, Defence Research and Development Organisation (DRDO), Haldwani 263139, India;
| | - Prakash Chand Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi 110078, India
- Correspondence: (S.C.); (P.C.S.)
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11
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Gaafar YZA, Ziebell H. Novel targets for engineering Physostegia chlorotic mottle and tomato brown rugose fruit virus-resistant tomatoes: in silico prediction of tomato microRNA targets. PeerJ 2020; 8:e10096. [PMID: 33194382 PMCID: PMC7597636 DOI: 10.7717/peerj.10096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/14/2020] [Indexed: 11/20/2022] Open
Abstract
Background Physostegia chlorotic mottle virus (PhCMoV; genus: Alphanucleorhabdovirus, family: Rhabdoviridae) and tomato brown rugose fruit virus (ToBRFV; genus: Tobamovirus, family: Virgaviridae) are newly emerging plant viruses that have a dramatic effect on tomato production. Among various known virus-control strategies, RNAi-mediated defence has shown the potential to protect plants against various pathogens including viral infections. Micro(mi)RNAs play a major role in RNAi-mediated defence. Methods Using in silico analyses, we investigated the possibility of tomato-encoded miRNAs (TomiRNA) to target PhCMoV and ToBRFV genomes using five different algorithms, i.e., miRanda, RNAhybrid, RNA22, Tapirhybrid and psRNATarget. Results The results revealed that 14 loci on PhCMoV and 10 loci on ToBRFV can be targeted by the TomiRNAs based on the prediction of at least three algorithms. Interestingly, one TomiRNA, miR6026, can target open reading frames from both viruses, i.e., the phosphoprotein encoding gene of PhCMoV, and the two replicase components of ToBRFV. There are currently no commercially available PhCMoV- or ToBRFV-resistant tomato varieties, therefore the predicted data provide useful information for the development of PhCMoV- and ToBFRV-resistant tomato plants.
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Affiliation(s)
- Yahya Zakaria Abdou Gaafar
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) -Federal Research Centre for Cultivated Plants, Braunschweig, Lower Saxony, Germany
| | - Heiko Ziebell
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) -Federal Research Centre for Cultivated Plants, Braunschweig, Lower Saxony, Germany
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12
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Yogindran S, Rajam MV. Host-derived artificial miRNA-mediated silencing of ecdysone receptor gene provides enhanced resistance to Helicoverpa armigera in tomato. Genomics 2020; 113:736-747. [PMID: 33058987 DOI: 10.1016/j.ygeno.2020.10.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/12/2020] [Accepted: 10/08/2020] [Indexed: 01/18/2023]
Abstract
Helicoverpa armigera causes huge crop losses due to its polyphagous nature. The present study demonstrates the use of artificial microRNA (amiRNA) mediated gene silencing approach to generate insect resistant tomato plants. Ecdysone receptor (HaEcR) gene of the target pest, H. armigera, which is involved in the regulation of all developmental stages of the insect life cycle, was silenced by sequence-specific amiRNA (amiRNA-HaEcR). Continuous feeding on detached tomato leaves expressing the amiRNA-319a-HaEcR resulted in reduced target gene transcripts and affected the overall growth and survival of H. armigera. Not only the target gene was down-regulated but, the feeding also affected the expression of down-stream genes involved in the ecdysone signaling pathway. The resistant trait was also observed in T1 generation of tomato transgenic lines. These results further established the role of EcR as a master regulator in insect development and effectiveness of amiRNA technology for efficient control of H. armigera.
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Affiliation(s)
- Sneha Yogindran
- Department of Genetics, University of Delhi South Campus, Benito Juarez Marg, New Delhi 110021, India
| | - Manchikatla Venkat Rajam
- Department of Genetics, University of Delhi South Campus, Benito Juarez Marg, New Delhi 110021, India.
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13
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Liang C, Hao J, Li J, Baker B, Luo L. Artificial microRNA-mediated resistance to cucumber green mottle mosaic virus in Nicotiana benthamiana. PLANTA 2019; 250:1591-1601. [PMID: 31388829 DOI: 10.1007/s00425-019-03252-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
MAIN CONCLUSION We describe a Nicotiana benthamiana system for rapid identification of artificial microRNA (amiRNA) to control cucumber green mottle mosaic virus (CGMMV) disease. Although artificial miRNA technology has been used to control other viral diseases, it has not been applied to reduce severe cucumber green mottle mosaic virus (CGMMV) disease and crop loss in the economically important cucurbits. We used our system to identify three amiRNAs targeting CGMMV RNA (amiR1-CP, amiR4-MP and amiR6-Rep) and show that their expression reduces CGMMV replication and disease in virus-infected plants. This work streamlines the process of generating amiRNA virus-resistant crops and can be broadly applied to identify active antiviral amiRNAs against a broad spectrum of viruses to control disease in diverse crops.
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Affiliation(s)
- Chaoqiong Liang
- College of Plant Protection/Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, 100193, China
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Jianjun Hao
- School of Food and Agriculture, The University of Maine, Orono, ME, 04469, USA
| | - Jianqiang Li
- College of Plant Protection/Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, 100193, China
| | - Barbara Baker
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720, USA.
- United States Department of Agriculture, Plant Gene Expression Center, Agricultural Research Service, Albany, CA, 94710, USA.
| | - Laixin Luo
- College of Plant Protection/Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, 100193, China.
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14
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Sabzehzari M, Naghavi MR. Phyto-miRNAs-based regulation of metabolites biosynthesis in medicinal plants. Gene 2019; 682:13-24. [PMID: 30267812 DOI: 10.1016/j.gene.2018.09.049] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/20/2018] [Accepted: 09/25/2018] [Indexed: 12/20/2022]
Abstract
Medicinal plants, are known to produce a wide range of plant secondary metabolites (PSMs) applied as insecticides, drugs, dyes and toxins in agriculture, medicine, industry and bio-warfare plus bio-terrorism, respectively. However, production of PSMs is usually in small quantities, so we need to find novel ways to increase both quantity and quality of them. Fortunately, biotechnology suggests several options through which secondary metabolism in plants can be engineered in innovative ways to: 1) over-produce the useful metabolites, 2) down-produce the toxic metabolites, 3) produce the new metabolites. Among the ways, RNA interference (RNAi) technology which involves gene-specific regulation by small non-coding RNAs (sncRNAs) have been recently emerged as a promising tool for plant biotechnologist, not only to decipher the function of plant genes, but also for development of the plants with improved and novel traits through manipulation of both desirable and undesirable genes. Among sncRNAs, miRNAs have been recorded various regulatory roles in plants such as development, signal transduction, response to environmental stresses, metabolism. Certainly, the use of miRNAs in metabolic engineering requires identification of miRNAs involved in metabolites biosynthesis, understanding of the biosynthetic pathways, as well as the identification of key points of the pathways in which the miRNAs have their own effect. Thus, we firstly consider these three issues on metabolic engineering of medicinal plants. Our review shows, application of miRNAs can open a novel perspective to metabolic engineering of medicinal plants.
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Affiliation(s)
- M Sabzehzari
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Iran
| | - M R Naghavi
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Iran.
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15
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Tyagi S, Mazumdar PA, Mayee P, Shivaraj SM, Anand S, Singh A, Madhurantakam C, Sharma P, Das S, Kumar A, Singh A. Natural variation in Brassica FT homeologs influences multiple agronomic traits including flowering time, silique shape, oil profile, stomatal morphology and plant height in B. juncea. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:251-266. [PMID: 30466591 DOI: 10.1016/j.plantsci.2018.09.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/17/2018] [Accepted: 09/21/2018] [Indexed: 06/09/2023]
Abstract
Natural structural variants of regulatory proteins causing quantitative phenotypic consequences have not been reported in plants. Herein, we show that 28 natural structural variants of FT homeologs, isolated from 6 species of Brassica, differ with respect to amino-acid substitutions in regions critical for interactions with FD and represent two evolutionarily distinct categories. Analysis of structural models of selected candidates from Brassica juncea (BjuFT_AAMF1) and Brassica napus (BnaFT_CCLF) predicted stronger binding between BjuFT and Arabidopsis thaliana FD. Over-expression of BjuFT and BnaFT in wild type and ft-10 mutant backgrounds of Arabidopsis validated higher potency of BjuFT in triggering floral transition. Analysis of gain-of-function and artificial miRNA mediated silenced lines of B. juncea implicated Brassica FT in multiple agronomic traits beyond flowering, consistent with a pleiotropic effect. Several dependent and independent traits such as lateral branching, silique shape, seed size, oil-profile, stomatal morphology and plant height were found altered in mutant lines. Enhanced FT levels caused early flowering, which in turn was positively correlated to a higher proportion of desirable fatty acids (PUFA). However, higher FT levels also resulted in altered silique shape and reduced seed size, suggesting trait trade-offs. Modulation of FT levels for achieving optimal balance of trait values and parsing pair-wise interactions among a reportoire of regulatory protein homeologs in polyploid genomes are indeed future areas of crop research.
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Affiliation(s)
- Shikha Tyagi
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India
| | | | - Pratiksha Mayee
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India; Department of Research, Ankur Seeds Pvt. Ltd., 27, Nagpur, Maharashtra, 440018, India
| | - S M Shivaraj
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India; Departement de Phytologie, Université Laval, Quebec City, Quebec, G1V 0A6, Canada
| | - Saurabh Anand
- Department of Botany, University of Delhi, New Delhi, 110007, India
| | - Anupama Singh
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India
| | - Chaithanya Madhurantakam
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India
| | - Prateek Sharma
- Department of Energy and Environment, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India
| | - Sandip Das
- Department of Botany, University of Delhi, New Delhi, 110007, India
| | - Arun Kumar
- National Phytotron Facility, IARI, New Delhi, 110012, India
| | - Anandita Singh
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India.
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16
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Minutolo A, Potestà M, Gismondi A, Pirrò S, Cirilli M, Gattabria F, Galgani A, Sessa L, Mattei M, Canini A, Muleo R, Colizzi V, Montesano C. Olea europaea small RNA with functional homology to human miR34a in cross-kingdom interaction of anti-tumoral response. Sci Rep 2018; 8:12413. [PMID: 30120339 PMCID: PMC6098056 DOI: 10.1038/s41598-018-30718-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 08/02/2018] [Indexed: 12/19/2022] Open
Abstract
Functional foods include compounds with nutritional and health properties. The human diet could play a stronger role in cancer prevention. Only a few studies have described the presence of plant small RNA, in humans who were fed with plant foods, which demonstrated the ability of these molecules to modulate consumer's genes and evidenced the existence of a plant-animal regulation. Through in silico prediction, Olea europaea small RNAs (sRs), which had been previously reported as miRNAs, were identified, each with functional homology to hsa-miR34a. According to this initial funding, we investigated the ability of oeu-sRs to regulate tumorigenesis in human cells. The transfection of these synthetic oeu-sRs reduced the protein expression of hsa-miR34a mRNA targets, increased apoptosis and decreased proliferation in different tumor cells; by contrast, no effect was observed in PBMCs from healthy donors. The introduction of oeu-small RNA in hsa-miR34a-deficient tumor cells restores its function, whereas cells with normal expression of endogenous hsa-miR34a remained unaffected. The natural oeu-small RNAs that were extracted from O. europaea drupes induce the same effects as synthetic sRs. Careful research on the small RNA sequences executed for mapping and annotation in the genome of O. europaea var. Sylvestris and var. Farga led to the hypothesis that RNA fragments with functional homology to human miRNAs could be generated from the degradation of regions of RNA transcripts. These results indicate the possibility of developing novel natural non-toxic drugs that contain active plant-derived tumor-suppressing small RNA with functional homology to hsa-miRNAs and that can support antineoplastic strategies.
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Affiliation(s)
| | - Marina Potestà
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Angelo Gismondi
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Stefano Pirrò
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
- Mir-Nat s.r.l, Rome, Italy
| | - Marco Cirilli
- Department of Agricultural and Forestry, Science, University of Tuscia, Viterbo, Italy
| | - Fabiano Gattabria
- Department of Agricultural and Forestry, Science, University of Tuscia, Viterbo, Italy
| | - Andrea Galgani
- Mir-Nat s.r.l, Rome, Italy
- Interdepartmental Center for Animal Technology, University of Rome "Tor Vergata", Rome, Italy
| | - Libera Sessa
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Maurizio Mattei
- Interdepartmental Center for Animal Technology, University of Rome "Tor Vergata", Rome, Italy
| | - Antonella Canini
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Rosario Muleo
- Department of Agricultural and Forestry, Science, University of Tuscia, Viterbo, Italy
| | - Vittorio Colizzi
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
- Mir-Nat s.r.l, Rome, Italy
| | - Carla Montesano
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy.
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17
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Yue X, Lin S, Yu Y, Huang L, Cao J. The putative pectin methylesterase gene, BcMF23a, is required for microspore development and pollen tube growth in Brassica campestris. PLANT CELL REPORTS 2018; 37:1003-1009. [PMID: 29644403 DOI: 10.1007/s00299-018-2285-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 03/28/2018] [Indexed: 05/24/2023]
Abstract
BcMF23a contributes to pollen wall development via influencing intine construction, which, in turn, influences pollen tube growth. Pollen wall, the morphological out face of pollen, surrounds male gametophyte and plays an important role in plant reproduction. Pectin methylesterases (PMEs) are involved in pollen wall construction by de-esterifying pectin of the intine. In this study, the function of a putative pectin methylesterase gene, Brassica campestris Male Fertility 23a (BcMF23a), was investigated. Knockdown of BcMF23a by artificial microRNA (amiRNA) technology resulted in abnormal pollen intine formation outside of the germinal furrows at the binucleate stage. At the trinucleate stage, 20.69% of pollen possessed the degradation of nuclei, cytoplasm and the intine, resulting in shrunken pollen, whereas the remaining 75.86% were wall-disrupted with degrading cytoplasm and broken exine inside the germinal furrows. In addition, pollen abortion in transgenic plants caused germination percentage reduction by 19% in vitro and pollen tube growth disruption in natural stigma in vivo. Taken together, BcMF23a is involved in pollen development and pollen tube growth, possibly via participating in intine construction. This study may contribute towards understanding the function of pollen-specific PMEs and the molecular regulatory network of pollen wall development.
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Affiliation(s)
- Xiaoyan Yue
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
| | - Sue Lin
- Institute of Life Sciences, Wenzhou University, Wenzhou, 325000, China
| | - Youjian Yu
- College of Agriculture and Food Science, Zhejiang A & F University, Lin'an, 311300, Zhejiang, China
| | - Li Huang
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
| | - Jiashu Cao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China.
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18
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Wang Y, Zhang J, Cui W, Guan C, Mao W, Zhang Z. Improvement in Fruit Quality by Overexpressing miR399a in Woodland Strawberry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:7361-7370. [PMID: 28783952 DOI: 10.1021/acs.jafc.7b01687] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Fruit quality is an important trait in strawberry and is determined by many factors. The soluble solid content in strawberry fruits is positively related to the phosphorus content. MicroRNA399 (miR399) is involved in the regulation of phosphate (Pi) homeostasis. However, the effect of miR399 on strawberry quality remains unknown. In this study, miR399a-overexpressing transgenic woodland strawberries (Fragaria vesca) were obtained via an Agrobacterium-mediated transformation. The phosphorus (P) content was 1.1-fold to 2.1-fold higher in the leaves and fruits of the miR399a-overexpressing plants than in the wild type (WT). However, the P content in the miR399a-overexpressing plants was decreased by 25% to 45% in the roots. The primary root length of the transgenic lines in both the high-Pi and low-Pi media was shorter than that of the WT. Interestingly, the transgenic lines in pots under Pi-sufficient conditions grew better than the WT, and the fruit quality, including the contents of fructose and glucose and soluble solid, was significantly higher in the transgenic lines than in the WT. The overexpression of miR399a in strawberry can be used to improve the parameters involved in fruit quality and provides information regarding breeding nutrient-improved strawberry.
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Affiliation(s)
- Yan Wang
- College of Horticulture, Shenyang Agricultural University , Shenyang 110866, China
| | - Junxiang Zhang
- College of Horticulture, Shenyang Agricultural University , Shenyang 110866, China
| | - Weixu Cui
- College of Horticulture, Shenyang Agricultural University , Shenyang 110866, China
| | - Chunyue Guan
- College of Horticulture, Shenyang Agricultural University , Shenyang 110866, China
| | - Wenjuan Mao
- College of Horticulture, Shenyang Agricultural University , Shenyang 110866, China
| | - Zhihong Zhang
- College of Horticulture, Shenyang Agricultural University , Shenyang 110866, China
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19
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Dhakate P, Tyagi S, Singh A, Singh A. Functional characterization of a novel Brassica LEAFY homolog from Indian mustard: Expression pattern and gain-of-function studies. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 258:29-44. [PMID: 28330561 DOI: 10.1016/j.plantsci.2017.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 01/13/2017] [Accepted: 02/10/2017] [Indexed: 06/06/2023]
Abstract
LEAFY plays a central role in regulation of flowering time and floral meristem identity in plants. Unfortunately, LFY function remains uncharacterized in agronomicaly important Brassicas. Herein, we illustrate fine-mapping of expression domains of LFY in 15 cultivars of 6 Brassica species and describe gain-of-function phenotypes in Arabidopsis and Brassica. We depict early flowering and altered fatty-acid composition in transgenic seed. The cDNA encoding BjuLFY (417aa) shared only 85% identity with reported homolog of B.juncea implying distinctness. Quantitative RT-PCR based coarse expression mapping of BjuLFY in tissue samples representing 3 time points at specific days after sowing (DAS), pre-flowering (30 DAS), flowering (75 DAS) and post-flowering (110 DAS), depicted an intense pulse of BjuLFY expression restricted to primary floral buds (75 DAS) which subsided in secondary floral buds (110 DAS); expression in root samples was also recorded implying neo-functionalization. Fine-mapping of expression during flowering confirmed tightly regulated LFY expression during early stages of bud development in 15 cultivars of 6 Brassica species implying functional conservation. Ectopic expression of BjuLFY in A. thaliana and B. juncea caused floral meristem defects and precocious flowering. B. juncea transgenics (T1) over-expressing BjuLFY flowered 20days earlier produced normal flowers. GC-MS analysis of mature seed from Brassica transgenics showed an altered fatty-acid profile suggestive of seed maturation occurring at lower temperatures vis-à-vis control. Our findings implicate BjuLFY as a regulator of flowering in B. juncea and suggest its application in developing climate resilient crops.
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Affiliation(s)
- Priyanka Dhakate
- Department of Biotechnology, TERI University, 10 Institutional Area, Vasant Kunj, Delhi 110070, India
| | - Shikha Tyagi
- Department of Biotechnology, TERI University, 10 Institutional Area, Vasant Kunj, Delhi 110070, India
| | - Anupama Singh
- Department of Biotechnology, TERI University, 10 Institutional Area, Vasant Kunj, Delhi 110070, India
| | - Anandita Singh
- Department of Biotechnology, TERI University, 10 Institutional Area, Vasant Kunj, Delhi 110070, India.
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20
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Yang K, Sablok G, Qiao G, Nie Q, Wen X. isomiR2Function: An Integrated Workflow for Identifying MicroRNA Variants in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:322. [PMID: 28377776 PMCID: PMC5359237 DOI: 10.3389/fpls.2017.00322] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 02/22/2017] [Indexed: 05/28/2023]
Abstract
In plants, post transcriptional regulation by non-coding RNAs (ncRNAs), in particular miRNAs (19-24 nt) has been involved in modulating the transcriptional landscape in developmental, biotic and abiotic interactions. In past few years, considerable focus has been leveraged on delineating and deciphering the role of miRNAs and their canonical isomiRs in plants. However, proper classification and accurate prediction of plant isomiRs taking into account the relative features by which we define isomiRs, such as templated or non-templated is still lacking. In the present research, we present isomiR2Function, a standalone easily deployable tool that allows for the robust and high-throughput discovery of templated and non-templated isomiRs. Additionally, isomiR2Function allows for identification of differentially expressed isomiRs and in parallel target prediction based on both transcripts or PARE-Seq either using Targetfinder or Cleaveland. isomiR2Function allows for the functional enrichment of the detected targets using TopGO package. Benchmarking of isomiR2Function revealed highly accurate prediction and classification of isomiRs as compared to the previously developed isomiR prediction tools. Additionally, the downstream implementation of additional features allows isomiR2Function to be classified as a single standalone tool for isomiR profiling from discovery to functional roles. All in all, isomiR2Function allows the streamline processing of the miRNA-seq for the identification and characterization of isomiRs with minimal efforts. isomiR2Function can be accessed through: https://github.com/347033139/isomiR2Function.
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Affiliation(s)
- Kun Yang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region – Ministry of Education, Institute of Agro-bioengineering, Guizhou UniversityGuiyang, China
- College of Life Sciences, Guizhou UniversityGuiyang, China
| | - Gaurav Sablok
- Climate Change Cluster (C3), University of Technology SydneySydney, NSW, Australia
| | - Guang Qiao
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region – Ministry of Education, Institute of Agro-bioengineering, Guizhou UniversityGuiyang, China
- College of Life Sciences, Guizhou UniversityGuiyang, China
| | - Qiong Nie
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region – Ministry of Education, Institute of Agro-bioengineering, Guizhou UniversityGuiyang, China
- College of Life Sciences, Guizhou UniversityGuiyang, China
| | - Xiaopeng Wen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region – Ministry of Education, Institute of Agro-bioengineering, Guizhou UniversityGuiyang, China
- College of Life Sciences, Guizhou UniversityGuiyang, China
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21
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Branham SE, Wright SJ, Reba A, Linder CR. Genome-Wide Association Study of Arabidopsis thaliana Identifies Determinants of Natural Variation in Seed Oil Composition. J Hered 2016; 107:248-56. [PMID: 26704140 PMCID: PMC4885229 DOI: 10.1093/jhered/esv100] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 11/24/2015] [Indexed: 01/14/2023] Open
Abstract
The renewable source of highly reduced carbon provided by plant triacylglycerols (TAGs) fills an ever increasing demand for food, biodiesel, and industrial chemicals. Each of these uses requires different compositions of fatty acid proportions in seed oils. Identifying the genes responsible for variation in seed oil composition in nature provides targets for bioengineering fatty acid proportions optimized for various industrial and nutrition goals. Here, we characterized the seed oil composition of 391 world-wide, wild accessions of Arabidopsis thaliana, and performed a genome-wide association study (GWAS) of the 9 major fatty acids in the seed oil and 4 composite measures of the fatty acids. Four to 19 regions of interest were associated with the seed oil composition traits. Thirty-four of the genes in these regions are involved in lipid metabolism or transport, with 14 specific to fatty acid synthesis or breakdown. Eight of the genes encode transcription factors. We have identified genes significantly associated with variation in fatty acid proportions that can be used as a resource across the Brassicaceae. Two-thirds of the regions identified contain candidate genes that have never been implicated in lipid metabolism and represent potential new targets for bioengineering.
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Affiliation(s)
- Sandra E Branham
- From the US Vegetable Laboratory, Agricultural Research Service, United States Department of Agriculture, Charleston, SC 29414 (Branham); Department of Biology, Washington University, St. Louis, MO 63130 (Wright); Integrative Biology Department, University of Texas at Austin, Austin, TX 78712 (Branham, Reba, and Linder).
| | - Sara J Wright
- From the US Vegetable Laboratory, Agricultural Research Service, United States Department of Agriculture, Charleston, SC 29414 (Branham); Department of Biology, Washington University, St. Louis, MO 63130 (Wright); Integrative Biology Department, University of Texas at Austin, Austin, TX 78712 (Branham, Reba, and Linder)
| | - Aaron Reba
- From the US Vegetable Laboratory, Agricultural Research Service, United States Department of Agriculture, Charleston, SC 29414 (Branham); Department of Biology, Washington University, St. Louis, MO 63130 (Wright); Integrative Biology Department, University of Texas at Austin, Austin, TX 78712 (Branham, Reba, and Linder)
| | - C Randal Linder
- From the US Vegetable Laboratory, Agricultural Research Service, United States Department of Agriculture, Charleston, SC 29414 (Branham); Department of Biology, Washington University, St. Louis, MO 63130 (Wright); Integrative Biology Department, University of Texas at Austin, Austin, TX 78712 (Branham, Reba, and Linder)
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22
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Calloni R, Bonatto D. Scaffolds for Artificial miRNA Expression in Animal Cells. Hum Gene Ther Methods 2015; 26:162-74. [PMID: 26406928 DOI: 10.1089/hgtb.2015.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Artificial miRNAs (amiRNAs) are molecules that have been developed to promote gene silencing in a similar manner to naturally occurring miRNAs. amiRNAs are generally constructed by replacing the mature miRNA sequence in the pre-miRNA stem-loop with a sequence targeting a gene of interest. These molecules offer an interesting alternative to silencing approaches that are based on shRNAs and siRNAs because they present the same efficiency as these options and are less cytotoxic. amiRNAs have mostly been applied to gene knockdown in plants; they have been examined to a lesser extent in animal cells. Therefore, this article reviews the amiRNAs that have been developed for animal cells and focuses on the miRNA scaffolds that can already be applied to construct the artificial counterparts, as well as on the different approaches that have been described to promote amiRNA expression and silencing efficiency. Furthermore, the availability of amiRNA libraries and other tools that can be used to design and construct these molecules is briefly discussed, along with an overview of the therapeutic applications for which amiRNAs have already been evaluated.
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Affiliation(s)
- Raquel Calloni
- Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul, and Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul , Porto Alegre, Brazil
| | - Diego Bonatto
- Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul, and Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul , Porto Alegre, Brazil
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A novel chemopreventive strategy based on therapeutic microRNAs produced in plants. Cell Res 2015; 25:521-4. [PMID: 25721325 PMCID: PMC4387556 DOI: 10.1038/cr.2015.25] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Sablok G, Srivastva AK, Suprasanna P, Baev V, Ralph PJ. isomiRs: Increasing Evidences of isomiRs Complexity in Plant Stress Functional Biology. FRONTIERS IN PLANT SCIENCE 2015; 6:949. [PMID: 26617614 PMCID: PMC4639611 DOI: 10.3389/fpls.2015.00949] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 10/17/2015] [Indexed: 05/11/2023]
Affiliation(s)
- Gaurav Sablok
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology SydneySydney, NSW, Australia
- *Correspondence: Gaurav Sablok
| | - Ashish K. Srivastva
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research CentreMumbai, India
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research CentreMumbai, India
| | - Vesselin Baev
- Department of Plant Physiology and Molecular Biology, University of PlovdivPlovdiv, Bulgaria
| | - Peter J. Ralph
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology SydneySydney, NSW, Australia
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Yu S, Pilot G. Testing the efficiency of plant artificial microRNAs by transient expression in Nicotiana benthamiana reveals additional action at the translational level. FRONTIERS IN PLANT SCIENCE 2014; 5:622. [PMID: 25477887 PMCID: PMC4237044 DOI: 10.3389/fpls.2014.00622] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 10/21/2014] [Indexed: 05/21/2023]
Abstract
Artificial microRNAs (amiRNAs) have become an important tool to assess gene functions due to their high efficiency and specificity to decrease target gene expression. Based on the observed degree of complementarity between microRNAs (miRNAs) and their targets, it was widely accepted that plant miRNAs act at the mRNA stability level, while the animal miRNAs act at the translational level. Contrary to these canonical dogmas, recent evidence suggests that both plant and animal miRNAs act at both levels. Nevertheless, it is still impossible to predict the effect of an artificial miRNA on the stability or translation of the target mRNA in plants. Consequently, identifying and discarding inefficient amiRNAs prior to stable plant transformation would help getting suppressed mutants faster and at reduced cost. We designed and tested a method using transient expression of amiRNAs and the corresponding target genes in Nicotiana benthamiana leaves to test the efficacy of amiRNAs for suppression of the target protein accumulation. The ability of the amiRNAs to suppress the target gene expression in N. benthamiana was then compared to that in stably transformed Arabidopsis. It was found that the efficacy of 16 amiRNAs, targeting a total of four genes, varied greatly. The effects of amiRNAs on target mRNA accumulation did not always correlate with target protein accumulation or the corresponding phenotypes, while a similar trend of the silencing efficacy of amiRNAs could be observed between N. benthamiana and stably transformed Arabidopsis. Our results showed that, similar to endogenous plant miRNAs, plant amiRNAs could act at the translational level, a property needed to be taken into account when testing the efficacy of individual amiRNAs. Preliminary tests in N. benthamiana can help determine which amiRNA would be the most likely to suppress target gene expression in stably transformed plants.
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Affiliation(s)
| | - Guillaume Pilot
- Department of Plant Pathology Physiology and Weed Science, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
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Patel AK, Shah RK, Patel UA, Tripathi AK, Joshi CG. Goat activin receptor type IIB knockdown by muscle specific promoter driven artificial microRNAs. J Biotechnol 2014; 187:87-97. [PMID: 25107506 DOI: 10.1016/j.jbiotec.2014.07.450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 07/20/2014] [Accepted: 07/25/2014] [Indexed: 01/30/2023]
Abstract
Activin receptor type IIB (ACVR2B) is a transmembrane receptor which mediates signaling of TGF beta superfamily ligands known to function in regulation of muscle mass, embryonic development and reproduction. ACVR2B antagonism has shown to enhance the muscle growth in several disease and transgenic models. Here, we show ACVR2B knockdown by RNA interference using muscle creatine kinase (MCK) promoter driven artificial microRNAs (amiRNAs). Among the various promoter elements tested, the ∼1.26 kb MCK promoter region showed maximum transcriptional activity in goat myoblasts cells. We observed up to 20% silencing in non-myogenic 293T cells and up to 32% silencing in myogenic goat myoblasts by MCK directed amiRNAs by transient transfection. Goat myoblasts stably integrated with MCK directed amiRNAs showed merely 8% silencing in proliferating myoblasts which was increased to 34% upon induction of differentiation at transcript level whereas up to 57% silencing at protein level. Knockdown of ACVR2B by 5'-UTR derived amiRNAs resulted in decreased SMAD2/3 signaling, increased expression of myogenic regulatory factors (MRFs) and enhanced proliferation and differentiation of myoblasts. Unexpectedly, knockdown of ACVR2B by 3'-UTR derived amiRNAs resulted in increased SMAD2/3 signaling, reduced expression of MRFs and suppression of myogenesis. Our study offers muscle specific knockdown of ACVR2B as a potential strategy to enhance muscle mass in the farm animal species.
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Affiliation(s)
- Amrutlal K Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388001, India
| | - Ravi K Shah
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388001, India
| | - Utsav A Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388001, India
| | - Ajai K Tripathi
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388001, India.
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Tiwari M, Sharma D, Trivedi PK. Artificial microRNA mediated gene silencing in plants: progress and perspectives. PLANT MOLECULAR BIOLOGY 2014; 86:1-18. [PMID: 25022825 DOI: 10.1007/s11103-014-0224-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 07/05/2014] [Indexed: 05/24/2023]
Abstract
Homology based gene silencing has emerged as a convenient approach for repressing expression of genes in order to study their functions. For this purpose, several antisense or small interfering RNA based gene silencing techniques have been frequently employed in plant research. Artificial microRNAs (amiRNAs) mediated gene silencing represents one of such techniques which can utilize as a potential tool in functional genomics. Similar to microRNAs, amiRNAs are single-stranded, approximately 21 nt long, and designed by replacing the mature miRNA sequences of duplex within pre-miRNAs. These amiRNAs are processed via small RNA biogenesis and silencing machinery and deregulate target expression. Holding to various refinements, amiRNA technology offers several advantages over other gene silencing methods. This is a powerful and robust tool, and could be applied to unravel new insight of metabolic pathways and gene functions across the various disciplines as well as in translating observations for improving favourable traits in plants. This review highlights general background of small RNAs, improvements made in RNAi based gene silencing, implications of amiRNA in gene silencing, and describes future themes for improving value of this technology in plant science.
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Affiliation(s)
- Manish Tiwari
- Council of Scientific and Industrial Research-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
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Patel AK, Shah RK, Parikh IK, Joshi CG. Goat activin receptor type IIB knockdown by artificial microRNAs in vitro. Appl Biochem Biotechnol 2014; 174:424-36. [PMID: 25080379 DOI: 10.1007/s12010-014-1071-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 07/21/2014] [Indexed: 10/25/2022]
Abstract
Activin receptor type IIB (ACVR2B) has been known to negatively regulate the muscle growth through mediating the action of transforming growth factor beta superfamily ligands. Recently, the artificial microRNAs (amiRNAs) which are processed by endogenous miRNA processing machinery have been proposed as promising approach for efficient gene knockdown. We evaluated amiRNAs targeting goat ACVR2B in HEK293T and goat myoblasts cells. The amiRNAs were designed based on the miR-155 backbone and cloned in 5'- and 3'-UTR of GFP reporter gene under the CMV promoter. Although both 5'- and 3'-UTR-amiRNAs vectors showed efficient synthesis of GFP transcripts, amiRNAs in 5'-UTR drastically affected GFP protein synthesis in transfected goat myoblast cells. Among the four amiRNAs targeting ACVR2B derived from either 5'- or 3'-UTR, ami318 showed highest silencing efficiency against exogenously co-expressed ACVR2B in both 293T and goat myoblast cells whereas ami204 showed highest silencing efficiency against endogenous ACVR2B in goat myoblasts cells. The 3'-UTR-derived amiRNA exerted higher knockdown efficiency against endogenous ACVR2B at transcript level whereas 5'-UTR-derived amiRNAs exerted higher knockdown efficiency at protein level. The expression of ACVR2B showed positive correlation with the expression of MYOD (r = 0.744; p = 0.009) and MYOG (r = 0.959; p = 0.000) in the amiRNA-transfected myoblasts. Although both 5'- and 3'-UTR-amiRNA vectors led to substantial induction of interferon response, the magnitude of the response was found to be higher with the 3'-UTR-amiRNA vectors.
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Affiliation(s)
- Amrutlal K Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, 388001, Gujarat, India
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Chi M, Bhagwat B, Lane WD, Tang G, Su Y, Sun R, Oomah BD, Wiersma PA, Xiang Y. Reduced polyphenol oxidase gene expression and enzymatic browning in potato (Solanum tuberosum L.) with artificial microRNAs. BMC PLANT BIOLOGY 2014; 14:62. [PMID: 24618103 PMCID: PMC4007649 DOI: 10.1186/1471-2229-14-62] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Accepted: 03/04/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Polyphenol oxidase (PPO), often encoded by a multi-gene family, causes oxidative browning, a significant problem in many food products. Low-browning potatoes were produced previously through suppression of PPO gene expression, but the contribution of individual PPO gene isoform to the oxidative browning process was unknown. Here we investigated the contributions of different PPO genes to total PPO protein activity, and the correlations between PPO protein level, PPO activity and tuber tissue browning potential by suppression of all previously characterized potato PPO genes, both individually and in combination using artificial microRNAs (amiRNAs) technology. RESULTS Survey of the potato genome database revealed 9 PPO-like gene models, named StuPPO1 to StuPPO9 in this report. StuPPO1, StuPPO2, StuPPO3 and StuPPO4 are allelic to the characterized POTP1/P2, POT32, POT33 and POT72, respectively. Fewer ESTs were found to support the transcriptions of StuPPO5 to StuPPO8. StuPPO9 related ESTs were expressed at significant higher levels in pathogen-infected potato tissues. A series of browning phenotypes were obtained by suppressing StuPPO1 to StuPPO4 genes alone and in combination. Down-regulation of one or several of the PPO genes did not usually cause up-regulation of the other PPO genes in the transgenic potato tubers, but resulted in reduced PPO protein levels. The different PPO genes did not contribute equally to the total PPO protein content in the tuber tissues, with StuPPO2 accounting for ~ 55% as the major contributor, followed by StuPPO1, ~ 25-30% and StuPPO3 and StuPPO4 together with less than 15%. Strongly positive correlations between PPO protein level, PPO activity and browning potential were demonstrated in our analysis. Low PPO activity and low-browning potatoes were produced by simultaneous down-regulation of StuPPO2 to StuPPO4, but the greatest reduction occurred when StuPPO1 to StuPPO4 were all suppressed. CONCLUSION StuPPO1 to StuPPO4 genes contributed to browning reactions in tuber tissues but their effect was not equal. Different PPO genes may be regulated independently reflecting their diversified functions. Our results show that amiRNAs can be used to suppress closely related members of highly conserved multi-gene family. This approach also suggests a new strategy for breeding low-browning crops using small DNA inserts.
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Affiliation(s)
- Ming Chi
- College of Forestry, Northwest A & F University, Yangling, Shaanxi, China
- Agriculture and Agri-Food Canada, Pacific Agri-Food Research Centre, Summerland, British Columbia V0H 1Z0, Canada
| | - Basdeo Bhagwat
- Agriculture and Agri-Food Canada, Pacific Agri-Food Research Centre, Summerland, British Columbia V0H 1Z0, Canada
| | - W David Lane
- Agriculture and Agri-Food Canada, Pacific Agri-Food Research Centre, Summerland, British Columbia V0H 1Z0, Canada
| | - Guiliang Tang
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA
| | - Yinquan Su
- College of Forestry, Northwest A & F University, Yangling, Shaanxi, China
| | - Runcang Sun
- College of Forestry, Northwest A & F University, Yangling, Shaanxi, China
| | - B Dave Oomah
- Agriculture and Agri-Food Canada, Pacific Agri-Food Research Centre, Summerland, British Columbia V0H 1Z0, Canada
| | - Paul A Wiersma
- Agriculture and Agri-Food Canada, Pacific Agri-Food Research Centre, Summerland, British Columbia V0H 1Z0, Canada
| | - Yu Xiang
- Agriculture and Agri-Food Canada, Pacific Agri-Food Research Centre, Summerland, British Columbia V0H 1Z0, Canada
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Non-coding RNAs in crop genetic modification: considerations and predictable environmental risk assessments (ERA). Mol Biotechnol 2014; 55:87-100. [PMID: 23381873 DOI: 10.1007/s12033-013-9648-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Of late non-coding RNAs (ncRNAs)-mediated gene silencing is an influential tool deliberately deployed to negatively regulate the expression of targeted genes. In addition to the widely employed small interfering RNA (siRNA)-mediated gene silencing approach, other variants like artificial miRNA (amiRNA), miRNA mimics, and artificial transacting siRNAs (tasiRNAs) are being explored and successfully deployed in developing non-coding RNA-based genetically modified plants. The ncRNA-based gene manipulations are typified with mobile nature of silencing signals, interference from viral genome-derived suppressor proteins, and an obligation for meticulous computational analysis to prevaricate any inadvertent effects. In a broad sense, risk assessment inquiries for genetically modified plants based on the expression of ncRNAs are competently addressed by the environmental risk assessment (ERA) models, currently in vogue, designed for the first generation transgenic plants which are based on the expression of heterologous proteins. Nevertheless, transgenic plants functioning on the foundation of ncRNAs warrant due attention with respect to their unique attributes like off-target or non-target gene silencing effects, small RNAs (sRNAs) persistence, food and feed safety assessments, problems in detection and tracking of sRNAs in food, impact of ncRNAs in plant protection measures, effect of mutations etc. The role of recent developments in sequencing techniques like next generation sequencing (NGS) and the ERA paradigm of the different countries in vogue are also discussed in the context of ncRNA-based gene manipulations.
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Braidwood L, Breuer C, Sugimoto K. My body is a cage: mechanisms and modulation of plant cell growth. THE NEW PHYTOLOGIST 2014; 201:388-402. [PMID: 24033322 DOI: 10.1111/nph.12473] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 08/01/2013] [Indexed: 05/19/2023]
Abstract
388 I. 388 II. 389 III. 389 IV. 390 V. 391 VI. 393 VII. 394 VIII. 398 399 References 399 SUMMARY: The wall surrounding plant cells provides protection from abiotic and biotic stresses, and support through the action of turgor pressure. However, the presence of this strong elastic wall also prevents cell movement and resists cell growth. This growth can be likened to extending a house from the inside, using extremely high pressures to push out the walls. Plants must increase cell volume in order to explore their environment, acquire nutrients and reproduce. Cell wall material must stretch and flow in a controlled manner and, concomitantly, new cell wall material must be deposited at the correct rate and site to prevent wall and cell rupture. In this review, we examine biomechanics, cell wall structure and growth regulatory networks to provide a 'big picture' of plant cell growth.
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Affiliation(s)
- Luke Braidwood
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Christian Breuer
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
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Zhou M, Luo H. MicroRNA-mediated gene regulation: potential applications for plant genetic engineering. PLANT MOLECULAR BIOLOGY 2013; 83:59-75. [PMID: 23771582 DOI: 10.1007/s11103-013-0089-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 06/05/2013] [Indexed: 05/19/2023]
Abstract
Food security is one of the most important issues challenging the world today. Any strategies to solve this problem must include increasing crop yields and quality. MicroRNA-based genetic modification technology (miRNA-based GM tech) can be one of the most promising solutions that contribute to agricultural productivity directly by developing superior crop cultivars with enhanced biotic and abiotic stress tolerance and increased biomass yields. Indirectly, the technology may increase usage of marginal soils and decrease pesticide use, among other benefits. This review highlights the most recent progress of transgenic studies utilizing various miRNAs and their targets for plant trait modifications, and analyzes the potential of miRNA-mediated gene regulation for use in crop improvement. Strategies for manipulating miRNAs and their targets in transgenic plants including constitutive, stress-induced, or tissue-specific expression of miRNAs or their targets, RNA interference, expressing miRNA-resistant target genes, artificial target mimic and artificial miRNAs were discussed. We also discussed potential risks of utilizing miRNA-based GM tech. In general, miRNAs and their targets not only provide an invaluable source of novel transgenes, but also inspire the development of several new GM strategies, allowing advances in breeding novel crop cultivars with agronomically useful characteristics.
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MESH Headings
- Adaptation, Biological
- Crops, Agricultural/genetics
- Crops, Agricultural/immunology
- Crops, Agricultural/metabolism
- Disease Resistance
- Food Supply
- Food, Genetically Modified
- Gene Expression Regulation, Plant
- Genes, Plant
- Genetic Engineering/methods
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/immunology
- Plants, Genetically Modified/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Risk Factors
- Transgenes
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Affiliation(s)
- Man Zhou
- Department of Genetics and Biochemistry, Clemson University, 110 Biosystems Research Complex, Clemson, SC, 29634, USA
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Zhou J, Yu F, Chen B, Wang X, Yang Y, Cheng Y, Yan C, Chen J. Universal vectors for constructing artificial microRNAs in plants. Biotechnol Lett 2013; 35:1127-33. [PMID: 23568377 DOI: 10.1007/s10529-013-1197-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Accepted: 02/26/2013] [Indexed: 11/30/2022]
Abstract
Universal amiRNA vectors (pUAs) for constructing plant amiRNAs in Arabidopsis and rice have been developed. By using type IIg restriction enzyme, BaeI, a single amiRNA construct can be produced using only one PCR and one ligation reaction. Thus, only one pair of primers is required for each amiRNA vector and these can be designed to be compatible with existing or newly developed methods. Because the BaeI recognition sequence is completely digested, there is no modification to the miRNA backbone, therefore avoids the risk of sequence changes that may affect downstream analysis. Based on these vectors, specific amiRNA constructs were created and verified. With optimized parameters, 38-45% colonies for each amiRNA construct contain insertions with the expected orientation, and approximately 80% of these colonies have the correct sequences.
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Affiliation(s)
- Jie Zhou
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, MOA Key Laboratory for Plant Protection and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, People's Republic of China
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Belide S, Petrie JR, Shrestha P, Singh SP. Modification of Seed Oil Composition in Arabidopsis by Artificial microRNA-Mediated Gene Silencing. FRONTIERS IN PLANT SCIENCE 2012; 3:168. [PMID: 22866055 PMCID: PMC3408671 DOI: 10.3389/fpls.2012.00168] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 07/07/2012] [Indexed: 05/03/2023]
Abstract
Various post transcriptional gene silencing strategies have been developed and exploited to study gene function or engineer disease resistance. The recently developed artificial microRNA strategy is an alternative method of effectively silencing target genes. The Δ12-desaturase (FAD2), Fatty acid elongase (FAE1), and Fatty acyl-ACP thioesterase B (FATB) were targeted with amiR159b-based constructs in Arabidopsisthaliana to evaluate changes in oil composition when expressed with the seed-specific Brassica napus truncated napin (FP1) promoter. Fatty acid profiles from transgenic homozygous seeds reveal that the targeted genes were silenced. The down-regulation of the AtFAD-2 gene substantially increased oleic acid from the normal levels of ∼15% to as high as 63.3 and reduced total PUFA content (18:2(Δ9,12) + 18:3(Δ9,12,15) + 20:2(Δ11,14) + 20:3(Δ11,14,17)) from 46.8 to 4.8%. Δ12-desaturase activity was reduced to levels as low as those in the null fad-2-1 and fad-2-2 mutants. Silencing of the FAE1 gene resulted in the reduction of eicosenoic acid (20:1(Δ11)) to 1.9 from 15.4% and silencing of FATB resulted in the reduction of palmitic acid (16:0) to 4.4% from 8.0%. Reduction in FATB activity is comparable with a FATB knock-out mutant. These results demonstrate for the first time amiR159b constructs targeted against three endogenous seed-expressed genes are clearly able to down-regulate and generate genotypic changes that are inherited stably over three generations.
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Affiliation(s)
- Srinivas Belide
- Food Futures National Research Flagship, CSIRO Plant IndustryCanberra, ACT, Australia
- Department of Biotechnology, Sreenidhi Institute of Science and TechnologyHyderabad, Andhra Pradesh, India
| | | | - Pushkar Shrestha
- Food Futures National Research Flagship, CSIRO Plant IndustryCanberra, ACT, Australia
| | - Surinder Pal Singh
- Food Futures National Research Flagship, CSIRO Plant IndustryCanberra, ACT, Australia
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Thiebaut F, Grativol C, Carnavale-Bottino M, Rojas CA, Tanurdzic M, Farinelli L, Martienssen RA, Hemerly AS, Ferreira PCG. Computational identification and analysis of novel sugarcane microRNAs. BMC Genomics 2012; 13:290. [PMID: 22747909 PMCID: PMC3464620 DOI: 10.1186/1471-2164-13-290] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 05/02/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND MicroRNA-regulation of gene expression plays a key role in the development and response to biotic and abiotic stresses. Deep sequencing analyses accelerate the process of small RNA discovery in many plants and expand our understanding of miRNA-regulated processes. We therefore undertook small RNA sequencing of sugarcane miRNAs in order to understand their complexity and to explore their role in sugarcane biology. RESULTS A bioinformatics search was carried out to discover novel miRNAs that can be regulated in sugarcane plants submitted to drought and salt stresses, and under pathogen infection. By means of the presence of miRNA precursors in the related sorghum genome, we identified 623 candidates of new mature miRNAs in sugarcane. Of these, 44 were classified as high confidence miRNAs. The biological function of the new miRNAs candidates was assessed by analyzing their putative targets. The set of bona fide sugarcane miRNA includes those likely targeting serine/threonine kinases, Myb and zinc finger proteins. Additionally, a MADS-box transcription factor and an RPP2B protein, which act in development and disease resistant processes, could be regulated by cleavage (21-nt-species) and DNA methylation (24-nt-species), respectively. CONCLUSIONS A large scale investigation of sRNA in sugarcane using a computational approach has identified a substantial number of new miRNAs and provides detailed genotype-tissue-culture miRNA expression profiles. Comparative analysis between monocots was valuable to clarify aspects about conservation of miRNA and their targets in a plant whose genome has not yet been sequenced. Our findings contribute to knowledge of miRNA roles in regulatory pathways in the complex, polyploidy sugarcane genome.
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Affiliation(s)
- Flávia Thiebaut
- Laboratorio de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Simón-Mateo C, García JA. Antiviral strategies in plants based on RNA silencing. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:722-31. [PMID: 21652000 DOI: 10.1016/j.bbagrm.2011.05.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Revised: 05/17/2011] [Accepted: 05/18/2011] [Indexed: 01/25/2023]
Abstract
One of the challenges being faced in the twenty-first century is the biological control of plant viral infections. Among the different strategies to combat virus infections, those based on pathogen-derived resistance (PDR) are probably the most powerful approaches to confer virus resistance in plants. The application of the PDR concept not only revealed the existence of a previously unknown sequence-specific RNA-degradation mechanism in plants, but has also helped to design antiviral strategies to engineer viral resistant plants in the last 25 years. In this article, we review the different platforms related to RNA silencing that have been developed during this time to obtain plants resistant to viruses and illustrate examples of current applications of RNA silencing to protect crop plants against viral diseases of agronomic relevance. This article is part of a Special Issue entitled: MicroRNAs in viral gene regulation.
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