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Jha N, Mangukia N, Patel MP, Bhavsar M, Gadhavi H, Rawal RM, Patel SK. Exploring the MiRnome of Carica papaya: A cross kingdom approach. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Li C, Wang M, Qiu X, Zhou H, Lu S. Noncoding RNAs in Medicinal Plants and their Regulatory Roles in Bioactive Compound Production. Curr Pharm Biotechnol 2021; 22:341-359. [PMID: 32469697 DOI: 10.2174/1389201021666200529101942] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/14/2020] [Accepted: 03/30/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Noncoding RNAs (ncRNAs), such as microRNAs (miRNAs), small interfering RNAs (siRNAs) and long noncoding RNAs (lncRNAs), play significant regulatory roles in plant development and secondary metabolism and are involved in plant response to biotic and abiotic stresses. They have been intensively studied in model systems and crops for approximately two decades and massive amount of information have been obtained. However, for medicinal plants, ncRNAs, particularly their regulatory roles in bioactive compound biosynthesis, are just emerging as a hot research field. OBJECTIVE This review aims to summarize current knowledge on herbal ncRNAs and their regulatory roles in bioactive compound production. RESULTS So far, scientists have identified thousands of miRNA candidates from over 50 medicinal plant species and 11794 lncRNAs from Salvia miltiorrhiza, Panax ginseng, and Digitalis purpurea. Among them, more than 30 miRNAs and five lncRNAs have been predicted to regulate bioactive compound production. CONCLUSION The regulation may achieve through various regulatory modules and pathways, such as the miR397-LAC module, the miR12112-PPO module, the miR156-SPL module, the miR828-MYB module, the miR858-MYB module, and other siRNA and lncRNA regulatory pathways. Further functional analysis of herbal ncRNAs will provide useful information for quality and quantity improvement of medicinal plants.
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Affiliation(s)
- Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Meizhen Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Xiaoxiao Qiu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Hong Zhou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
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Patel M, Mangukia N, Jha N, Gadhavi H, Shah K, Patel S, Mankad A, Pandya H, Rawal R. Computational identification of miRNA and their cross kingdom targets from expressed sequence tags of Ocimum basilicum. Mol Biol Rep 2019; 46:2979-2995. [PMID: 31066002 DOI: 10.1007/s11033-019-04759-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 03/12/2019] [Indexed: 12/26/2022]
Abstract
MicroRNAs (miRNAs) are conserved small non coding RNAs, which are typically 22-24 nucleotides long and play an important role in post transcription regulation andin various biological processes in both animals and plants. Ocimum basilicum is an important medicinal plant having different bioactive compounds eugenol and essential oils that possess numerous therapeutic properties. However, only a few miRNAs of Ocimum basilicum and its function have been studied till date. The present study focusses on the identification of miRNA from expressed sequenced tags by carrying out computational approaches based on the homology search method. A total of 10 potential miRNAs with 8 different families were predicted in O.basilicum. Furthermore, the psRNA target server was used to predict cross kingdom target genes on human transcriptome for identification ofpotential miRNAs. Eight miRNA families were found to modulate the 87 human target genes which were associated with RAS/MAPK signalling cascade, cardiomyopathy, HIV, breast cancer, lung cancer, Alzheimer's diseases and several neurological disorders. Moreover, O.basilicum miRNAs regulate the key human target genes having significance in various diseases and important biological networks with 10 hub nodes interactions. Thus this study gives the pave for further studies to explore the potential of miRNA mediated cross kingdom regulation and treatment of various diseases including cancer.
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Affiliation(s)
- Maulikkumar Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Naman Mangukia
- Department of Botany, Bioinformatics and Climate Change Impacts Management School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Neha Jha
- Department of Botany, Bioinformatics and Climate Change Impacts Management School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Harshida Gadhavi
- Department of Botany, Bioinformatics and Climate Change Impacts Management School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Kanisha Shah
- Department of Life Sciences, Food Science and Nutrition, School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Saumya Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Archana Mankad
- Department of Botany, Bioinformatics and Climate Change Impacts Management School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Himanshu Pandya
- Department of Botany, Bioinformatics and Climate Change Impacts Management School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Rakesh Rawal
- Department of Life Sciences, Food Science and Nutrition, School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India.
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An approach to identify the novel miRNA encoded from H. Annuus EST sequences. GENOMICS DATA 2015; 6:139-44. [PMID: 26697356 PMCID: PMC4664742 DOI: 10.1016/j.gdata.2015.09.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/06/2015] [Indexed: 01/15/2023]
Abstract
MicroRNAs are a newly discovered class of non-protein small RNAs with 22-24 nucleotides. They play multiple roles in biological processes including development, cell proliferation, apoptosis, stress responses and many other cell functions. In this research, several approaches were combined to make a computational prediction of potential miRNAs and their targets in Helianthus annuus (H. annuus). The already available information of the plant miRNAs present in miRBase v21 was used against expressed sequence tags (ESTs). A total of three miRNAs were detected from which one potential novel miRNA was identified following a range of strict filtering criteria. The target prediction was carried out for these three miRNAs having various targets. These targets were functionally annotated and GO terms were assigned. To study the conserved nature of the miRNAs, predicted phylogenetic analysis was carried out. These findings will significantly provide the broader picture for understanding the functions in H. annuus.
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New insights of medicinal plant therapeutic activity-The miRNA transfer. Biomed Pharmacother 2015; 74:228-32. [PMID: 26349990 DOI: 10.1016/j.biopha.2015.08.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 08/04/2015] [Indexed: 01/21/2023] Open
Abstract
MicroRNA (miRNA) has become the spotlight of the biomedical research around the world and is considered to be a major post-transcriptional gene regulator. This small, endogenous RNA (21-25 nucleotides long) plays an important role by targeting specific mRNAs in plants, animals and humans. Herbal medicine has been used for thousands of years, however little is known about its molecular mechanism of action. Since the discovery of plant miRNA in human tissue and sera after ingestion, the connection between the two kingdoms is presented under a new perspective. Forward pharmacology, such as miRNA therapeutics could be the next best step toward identifying novel therapeutic options involving medicinal plants. Besides reporting the latest findings regarding the cross-kingdom transfer of miRNA and its therapeutic application, this review can inform further investigations that could lead to a modern definition of herbal medicine.
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Li X, Hou Y, Zhang L, Zhang W, Quan C, Cui Y, Bian S. Computational identification of conserved microRNAs and their targets from expression sequence tags of blueberry (Vaccinium corybosum). PLANT SIGNALING & BEHAVIOR 2014; 9:e29462. [PMID: 25763692 PMCID: PMC4203583 DOI: 10.4161/psb.29462] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/03/2014] [Accepted: 06/04/2014] [Indexed: 05/21/2023]
Abstract
MicroRNAs (miRNAs) are a class of endogenous, approximately 21nt in length, non-coding RNA, which mediate the expression of target genes primarily at post-transcriptional levels. miRNAs play critical roles in almost all plant cellular and metabolic processes. Although numerous miRNAs have been identified in the plant kingdom, the miRNAs in blueberry, which is an economically important small fruit crop, still remain totally unknown. In this study, we reported a computational identification of miRNAs and their targets in blueberry. By conducting an EST-based comparative genomics approach, 9 potential vco-miRNAs were discovered from 22,402 blueberry ESTs according to a series of filtering criteria, designated as vco-miR156-5p, vco-miR156-3p, vco-miR1436, vco-miR1522, vco-miR4495, vco-miR5120, vco-miR5658, vco-miR5783, and vco-miR5986. Based on sequence complementarity between miRNA and its target transcript, 34 target ESTs from blueberry and 70 targets from other species were identified for the vco-miRNAs. The targets were found to be involved in transcription, RNA splicing and binding, DNA duplication, signal transduction, transport and trafficking, stress response, as well as synthesis and metabolic process. These findings will greatly contribute to future research in regard to functions and regulatory mechanisms of blueberry miRNAs.
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Affiliation(s)
- Xuyan Li
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
| | - Yanming Hou
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
| | - Li Zhang
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
| | - Wenhao Zhang
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
| | - Chen Quan
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
| | - Yuhai Cui
- Agriculture and Agri-Food Canada; Southern Crop Protection and Food Research Centre; London, ON Canada
- Department of Biology; Western University; London, ON Canada
| | - Shaomin Bian
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
- Correspondence to: Shaomin Bian,
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Vishwakarma NP, Jadeja VJ. Identification of miRNA encoded by Jatropha curcas from EST and GSS. PLANT SIGNALING & BEHAVIOR 2013; 8:e23152. [PMID: 23299511 PMCID: PMC3657014 DOI: 10.4161/psb.23152] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 12/06/2012] [Indexed: 05/30/2023]
Abstract
miRNAs are endogenous approx 22 nucleotide RNA which mediates transcriptional or Post-transcriptional gene regulation and play a critical role in diverse aspects of plant development. miRNA identification in wet lab have various constraints, it is time consuming and expensive. It also faces the limitation of identifying miRNAs expressed at specific time and/or at special conditions. Due to the nature of strong conservation of miRNA in plant species, the use of comparative genomics approach for expressed sequence tags (ESTs), Genome Survey Sequence (GSS) and structural feature criteria filter has paved the way toward the identification of conserved miRNAs from the plant species whose genomes are not yet available in public domain. To identify the novel miRNA from Jatropha curcas, a total of 46862 EST sequences and 1569 GSS were searched for homology to previously known viridiplantae 2502 mature miRNA. After predicting the RNA secondary structure, 24 new potential miRNA were identified in J. curcas. Using the newly identified miRNA sequences, a total of 78 potential target genes were identified for 3 miRNA families. Most of the miRNA targeted genes were predicted to encode transcription factors that regulate cell growth and development, signaling, and metabolism. These findings considerably broaden the scope of understanding the functions of miRNA in J. curcas.
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Affiliation(s)
| | - Vasant J. Jadeja
- Department of Microbiology; Shree M. & N. Virani Science College; Rajkot, Gujarat, India
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