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Wei G, Xu M, Shi X, Wang Y, Shi Y, Wang J, Feng L. Integrative analysis of miRNA profile and degradome reveals post-transcription regulation involved in fragrance formation of Rosa rugosa. Int J Biol Macromol 2024; 279:135266. [PMID: 39244114 DOI: 10.1016/j.ijbiomac.2024.135266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2024] [Revised: 08/30/2024] [Accepted: 08/31/2024] [Indexed: 09/09/2024]
Abstract
Rosa rugosa is renowned for its fragrant essential oils (EOs) including the primary volatile compounds such as terpenes (geraniol and citronellol) and 2-phenylethanol. While the role of miRNAs in plant secondary metabolism has been explored, their involvement in EOs metabolism remains largely unknown. Sequencing of the petals of R. rugosa identified 383 conserved miRNAs and 625 novel miRNAs including 53 miRNAs differentially expressed in a strong fragrance variety R. rugosa 'White Purple Branch'. Degradome sequencing predicted 1969 targets enriched in GO terms involved in the negative regulation of macromolecule metabolic process. Furthermore, 122 targets of differentially expressed miRNAs were enriched in phenylalanine metabolism and other KEGG pathways. A post-transcriptional regulation network of 52 miRNAs and 70 miRNA-transcription factor modules target terpene and 2-phenylethanol biosynthesis pathways. Six interactions including miR535f-RrHMGR, NOV146-RrNUDX1, miR166l-RrHY5 and miR156c-RrSPL2 were validated using RNA ligase-mediated RACE. Sequence alignment revealed that the NOV146-RrNUDX1 was conserved in the Rosa genus. Moreover, weaker silencing of RrNUDX1 by NOV146 contributed to the stronger fragrance of R. rugosa. These findings offer a comprehensive understanding of the post-transcriptional regulation involved in essential oil biosynthesis and identify candidate miRNAs for further genetic improvement of EO yields in R. rugosa.
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Affiliation(s)
- Guo Wei
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Mengmeng Xu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Xinwei Shi
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Yue Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Yuqing Shi
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Jianwen Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China.
| | - Liguo Feng
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China.
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2
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Saifi M, Ashrafi K, Qamar F, Abdin MZ. Regulatory trends in engineering bioactive-phytocompounds. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112167. [PMID: 38925476 DOI: 10.1016/j.plantsci.2024.112167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 06/12/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024]
Abstract
The secondary plant metabolites are of enormous importance because of their extensive medicinal, nutraceutical, and industrial applications. In plants, these secondary metabolites are often found in extremely small amounts, therefore, following the discovery of any prospective metabolite, the main constraining element is the ability to generate enough material for use in both industrial and therapeutic settings. In order to satisfy the rising demand for value-added metabolites, researchers prefer to use different molecular approaches for scalable and sustainable production of these phytocompounds. Here, we discuss the emerging regulatory trends in engineering these bioactive-phytocompounds and provide recommendation on successful employment of these state-of-the-art technologies for translation of these academic researches into novel process and products.
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Affiliation(s)
- Monica Saifi
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India
| | - Kudsiya Ashrafi
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India
| | - Firdaus Qamar
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India
| | - M Z Abdin
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India.
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3
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Ramprosand S, Govinden-Soulange J, Ranghoo-Sanmukhiya VM, Sanan-Mishra N. miRNA, phytometabolites and disease: Connecting the dots. Phytother Res 2024. [PMID: 39072874 DOI: 10.1002/ptr.8287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/30/2024]
Abstract
miRNAs are tiny noncoding ribonucleotides that function as critical regulators of gene-expression in eukaryotes. A single miRNA may be involved in the regulation of several target mRNAs forming complex cellular networks to regulate diverse aspects of development in an organism. The deregulation of miRNAs has been associated with several human diseases. Therefore, miRNA-based therapeutics is gaining interest in the pharmaceutical industry as the next-generation drugs for the cure of many diseases. Medicinal plants have also been used for the treatment of several human diseases and their curative potential is attributed to their reserve in bioactive metabolites. A role for miRNAs as regulators of the phytometabolic pathways in plants has emerged in the recent past. Experimental studies have also indicated the potential of plant encoded secondary phytometabolites to act as cross-regulators of mammalian miRNAs and transcripts to regulate human diseases (like cancer). The evidence for this cross-kingdom gene regulation through miRNA has gathered considerable enthusiasm in the scientific field, even though there are on-going debates regarding the reproducibility and the effectiveness of these findings. In this review, we provide information to connect the medicinal and gene regulatory properties of secondary phytometabolites, their regulation by miRNAs in plants and their effects on human miRNAs for regulating downstream metabolic or pathological processes. While further extensive research initiatives and good clinical evidence are required to prove or disapprove these findings, understanding of these regulations will have important implications in the potential use of synthetic or artificial miRNAs as effective alternatives for providing health benefits.
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Affiliation(s)
- Srutee Ramprosand
- Faculty of Agriculture, University of Mauritius, Réduit, Mauritius
- 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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4
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Su Y, Fang J, Zeeshan Ul Haq M, Yang W, Yu J, Yang D, Liu Y, Wu Y. Genome-Wide Identification and Expression Analysis of the Casparian Strip Membrane Domain Protein-like Gene Family in Peanut ( Arachis hypogea L.) Revealed Its Crucial Role in Growth and Multiple Stress Tolerance. PLANTS (BASEL, SWITZERLAND) 2024; 13:2077. [PMID: 39124195 PMCID: PMC11313903 DOI: 10.3390/plants13152077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 07/20/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024]
Abstract
Casparian strip membrane domain proteins (CASPs), regulating the formation of Casparian strips in plants, serve crucial functions in facilitating plant growth, development, and resilience to abiotic stress. However, little research has focused on the characteristics and functions of AhCASPs in cultivated peanuts. In this study, the genome-wide identification and expression analysis of the AhCASPs gene family was performed using bioinformatics and transcriptome data. Results showed that a total of 80 AhCASPs members on 20 chromosomes were identified and divided into three subclusters, which mainly localized to the cell membrane. Ka/Ks analysis revealed that most of the genes underwent purifying selection. Analysis of cis elements suggested the possible involvement of AhCASPs in hormonal and stress responses, including GA, MeJA, IAA, ABA, drought, and low temperature. Moreover, 20 different miRNAs for 37 different AhCASPs genes were identified by the psRNATarget service. Likewise, transcriptional analysis revealed key AhCASPs responding to various stresses, hormonal processing, and tissue types, including 33 genes in low temperature and drought stress and 41 genes in tissue-specific expression. These results provide an important theoretical basis for the functions of AhCASPs in growth, development, and multiple stress resistance in cultivated peanuts.
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Affiliation(s)
- Yating Su
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Jieyun Fang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Muhammad Zeeshan Ul Haq
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Wanli Yang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Jing Yu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Dongmei Yang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Ya Liu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Hainan University, Haikou 570228, China
| | - Yougen Wu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
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Deng K, Li Z, Huang T, Huang J. Noncoding RNAs in regulation of plant secondary metabolism. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108718. [PMID: 38733939 DOI: 10.1016/j.plaphy.2024.108718] [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: 05/10/2023] [Revised: 05/04/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
Plant secondary metabolites (PSMs) are a large class of structurally diverse molecules, mainly consisting of terpenoids, phenolic compounds, and nitrogen-containing compounds, which play active roles in plant development and stress responses. The biosynthetic processes of PSMs are governed by a sophisticated regulatory network at multiple levels. Noncoding RNAs (ncRNAs) such as microRNAs (miRNAs), long ncRNAs (lncRNAs), and circular RNAs (circRNAs) may serve as post-transcriptional regulators for plant secondary metabolism through acting on genes encoding either transcription factors or participating enzymes in relevant metabolic pathways. High-throughput sequencing technologies have facilitated the large-scale identifications of ncRNAs potentially involved in plant secondary metabolism in model plant species as well as certain species with enriched production of specific types of PSMs. Moreover, a series of miRNA-target modules have been functionally characterized to be responsible for regulating PSM biosynthesis and accumulation in plants under abiotic or biotic stresses. In this review, we will provide an overview of current findings on the ncRNA-mediated regulation of plant secondary metabolism with special attention to its participation in plant stress responses, and discuss possible issues to be addressed in future fundamental research and breeding practice.
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Affiliation(s)
- Keyin Deng
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, China
| | - Ziwei Li
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, China
| | - Tengbo Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, China
| | - Jianzi Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, China.
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Kasprzak-Drozd K, Niziński P, Hawrył A, Gancarz M, Hawrył D, Oliwa W, Pałka M, Markowska J, Oniszczuk A. Potential of Curcumin in the Management of Skin Diseases. Int J Mol Sci 2024; 25:3617. [PMID: 38612433 PMCID: PMC11012053 DOI: 10.3390/ijms25073617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Curcumin is a polyphenolic molecule derived from the rhizoma of Curcuma longa L. This compound has been used for centuries due to its anti-inflammatory, antioxidant, and antimicrobial properties. These make it ideal for preventing and treating skin inflammation, premature skin ageing, psoriasis, and acne. Additionally, it exhibits antiviral, antimutagenic, and antifungal effects. Curcumin provides protection against skin damage caused by prolonged exposure to UVB radiation. It reduces wound healing times and improves collagen deposition. Moreover, it increases fibroblast and vascular density in wounds. This review summarizes the available information on the therapeutic effect of curcumin in treating skin diseases. The results suggest that curcumin may be an inexpensive, well-tolerated, and effective agent for treating skin diseases. However, larger clinical trials are needed to confirm these observations due to limitations in its in vivo use, such as low bioavailability after oral administration and metabolism.
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Affiliation(s)
- Kamila Kasprzak-Drozd
- Department of Inorganic Chemistry, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland; (K.K.-D.); (A.H.)
| | - Przemysław Niziński
- Department of Pharmacology, Medical University of Lublin, Radziwiłłowska 11, 20-080 Lublin, Poland;
| | - Anna Hawrył
- Department of Inorganic Chemistry, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland; (K.K.-D.); (A.H.)
| | - Marek Gancarz
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland;
- Faculty of Production and Power Engineering, University of Agriculture in Krakow, Balicka 116B, 30-149 Krakow, Poland
| | | | - Weronika Oliwa
- Science Circle of the Department of Inorganic Chemistry, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland; (W.O.); (M.P.); (J.M.)
| | - Magdalena Pałka
- Science Circle of the Department of Inorganic Chemistry, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland; (W.O.); (M.P.); (J.M.)
| | - Julia Markowska
- Science Circle of the Department of Inorganic Chemistry, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland; (W.O.); (M.P.); (J.M.)
| | - Anna Oniszczuk
- Department of Inorganic Chemistry, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland; (K.K.-D.); (A.H.)
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7
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Li H, Guo Z, Xu M, Zhao J, Xu D. Molecular mechanism of miRNA mediated biosynthesis of secondary metabolites in medicinal plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108524. [PMID: 38518432 DOI: 10.1016/j.plaphy.2024.108524] [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: 01/27/2024] [Revised: 02/28/2024] [Accepted: 03/10/2024] [Indexed: 03/24/2024]
Abstract
Plant secondary metabolites are important raw materials for the pharmaceutical industry, and their biosynthetic processes are subject to diverse and precise regulation by miRNA. The identification of miRNA molecules in medicinal plants and exploration of their mechanisms not only contribute to a deeper understanding of the molecular genetic mechanisms of plant growth, development and resistance to stress, but also provide a theoretical basis for elucidating the pharmacological effects of authentic medicinal materials and constructing bioreactors for the synthesis of medicinal secondary metabolite components. This paper summarizes the research reports on the discovery of miRNA in medicinal plants and their regulatory mechanisms on the synthesis of secondary metabolites by searching the relevant literature in public databases. It summarizes the currently discovered miRNA and their functions in medicinal plants, and summarizes the molecular mechanisms regulating the synthesis and degradation of secondary metabolites. Furthermore, it provides a prospect for the research and development of medicinal plant miRNA. The compiled information contributes to a comprehensive understanding of the research progress on miRNA in medicinal plants and provides a reference for the industrial development of related secondary metabolite biosynthesis.
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Affiliation(s)
- Hongwei Li
- Department of Cell Biology, Zunyi Medical University, No.6 Xuefuxi Road, Xinpu District, Zunyi City, Guizhou Province, 563099, China
| | - Ziyi Guo
- Department of Cell Biology, Zunyi Medical University, No.6 Xuefuxi Road, Xinpu District, Zunyi City, Guizhou Province, 563099, China
| | - Mengwei Xu
- Department of Cell Biology, Zunyi Medical University, No.6 Xuefuxi Road, Xinpu District, Zunyi City, Guizhou Province, 563099, China
| | - Juanjuan Zhao
- Department of Immunology, Zunyi Medical University, No.6 Xuefuxi Road, Xinpu District, Zunyi City, Guizhou Province, 563099, China.
| | - Delin Xu
- Department of Cell Biology, Zunyi Medical University, No.6 Xuefuxi Road, Xinpu District, Zunyi City, Guizhou Province, 563099, China; Department of Medical Instrumental Analysis, Zunyi Medical University, No.6 Xuefuxi Road, Xinpu District, Zunyi City, Guizhou Province, 563099, China.
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8
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Kang K, Gao W, Cui Y, Xiao M, An L, Wu J. Curcumin Changed the Number, Particle Size, and miRNA Profile of Serum Exosomes in Roman Laying Hens under Heat Stress. Genes (Basel) 2024; 15:217. [PMID: 38397207 PMCID: PMC10887567 DOI: 10.3390/genes15020217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Exosomes have the ability to transport RNA/miRNAs and possess immune modulatory functions. Heat stress, a significant limiting factor in the poultry industry, can induce oxidative stress and suppress the immune responses of laying hens. In this study, we investigated the expression profiles of serum exosomes and their miRNAs in Roman laying hens who were fed a diet with either 0 or 200 mg/kg curcumin under heat stress conditions. The numbers of exosomes were significantly higher in both the HC (heat stress) and HT (heat stress with 200 mg/kg curcumin) groups compared to the NC (control) group and NT (control with 200 mg/kg curcumin) group (p < 0.05). Additionally, we observed that the most prevalent particle diameters were 68.75 nm, 68.25 nm, 54.25 nm, and 60.25 nm in the NC, NT, HC, and HT groups, respectively. From our sRNA library analysis, we identified a total of 863 unique miRNAs; among them, we screened out for subsequent bioinformatics analysis a total of 328 gga-miRNAs(chicken miRNA from the miRbase database). The KEGG pathways that are associated with target genes which are regulated by differentially expressed miRNAs across all four groups at a p-value < 0.01 included oxidative phosphorylation, protein export, cysteine and methionine metabolism, fatty acid degradation, ubiquitin-mediated proteolysis, and cardiac muscle contraction. The above findings suggest that curcumin could mitigate heat-induced effects on laying hens by altering the miRNA expression profiles of serum exosomes along with related regulatory pathways.
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Affiliation(s)
| | | | | | | | | | - Jiang Wu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (K.K.)
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9
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Guo Y, Qi Y, Feng Y, Yang Y, Xue L, El-Kassaby YA, Wang G, Fu F. Inferring the Regulatory Network of miRNAs on Terpene Trilactone Biosynthesis Affected by Environmental Conditions. Int J Mol Sci 2023; 24:17002. [PMID: 38069325 PMCID: PMC10707241 DOI: 10.3390/ijms242317002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
As a medicinal tree species, ginkgo (Ginkgo biloba L.) and terpene trilactones (TTLs) extracted from its leaves are the main pharmacologic activity constituents and important economic indicators of its value. The accumulation of TTLs is known to be affected by environmental stress, while the regulatory mechanism of environmental response mediated by microRNAs (miRNAs) at the post-transcriptional levels remains unclear. Here, we focused on grafted ginkgo grown in northwestern, southwestern, and eastern-central China and integrally analyzed RNA-seq and small RNA-seq high-throughput sequencing data as well as metabolomics data from leaf samples of ginkgo clones grown in natural environments. The content of bilobalide was highest among detected TTLs, and there was more than a twofold variation in the accumulation of bilobalide between growth conditions. Meanwhile, transcriptome analysis found significant differences in the expression of 19 TTL-related genes among ginkgo leaves from different environments. Small RNA sequencing and analysis showed that 62 of the 521 miRNAs identified were differentially expressed among different samples, especially the expression of miRN50, miR169h/i, and miR169e was susceptible to environmental changes. Further, we found that transcription factors (ERF, MYB, C3H, HD-ZIP, HSF, and NAC) and miRNAs (miR319e/f, miRN2, miRN54, miR157, miR185, and miRN188) could activate or inhibit the expression of TTL-related genes to participate in the regulation of terpene trilactones biosynthesis in ginkgo leaves by weighted gene co-regulatory network analysis. Our findings provide new insights into the understanding of the regulatory mechanism of TTL biosynthesis but also lay the foundation for ginkgo leaves' medicinal value improvement under global change.
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Affiliation(s)
- Ying Guo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.Q.); (Y.F.)
| | - Yongli Qi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.Q.); (Y.F.)
| | - Yangfan Feng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.Q.); (Y.F.)
| | - Yuting Yang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.Q.); (Y.F.)
| | - Liangjiao Xue
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.Q.); (Y.F.)
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
| | - Guibin Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.Q.); (Y.F.)
| | - Fangfang Fu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.Q.); (Y.F.)
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10
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Kumar D, Ramkumar MK, Dutta B, Kumar A, Pandey R, Jain PK, Gaikwad K, Mishra DC, Chaturvedi KK, Rai A, Solanke AU, Sevanthi AM. Integration of miRNA dynamics and drought tolerant QTLs in rice reveals the role of miR2919 in drought stress response. BMC Genomics 2023; 24:526. [PMID: 37674140 PMCID: PMC10481553 DOI: 10.1186/s12864-023-09609-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 08/20/2023] [Indexed: 09/08/2023] Open
Abstract
To combat drought stress in rice, a major threat to global food security, three major quantitative trait loci for 'yield under drought stress' (qDTYs) were successfully exploited in the last decade. However, their molecular basis still remains unknown. To understand the role of secondary regulation by miRNA in drought stress response and their relation, if any, with the three qDTYs, the miRNA dynamics under drought stress was studied at booting stage in two drought tolerant (Sahbaghi Dhan and Vandana) and one drought sensitive (IR 20) cultivars. In total, 53 known and 40 novel differentially expressed (DE) miRNAs were identified. The primary drought responsive miRNAs were Osa-MIR2919, Osa-MIR3979, Osa-MIR159f, Osa-MIR156k, Osa-MIR528, Osa-MIR530, Osa-MIR2091, Osa-MIR531a, Osa-MIR531b as well as three novel ones. Sixty-one target genes that corresponded to 11 known and 4 novel DE miRNAs were found to be co-localized with the three qDTYs, out of the 1746 target genes identified. We could validate miRNA-mRNA expression under drought for nine known and three novel miRNAs in eight different rice genotypes showing varying degree of tolerance. From our study, Osa-MIR2919, Osa-MIR3979, Osa-MIR528, Osa-MIR2091-5p and Chr01_11911S14Astr and their target genes LOC_Os01g72000, LOC_Os01g66890, LOC_Os01g57990, LOC_Os01g56780, LOC_Os01g72834, LOC_Os01g61880 and LOC_Os01g72780 were identified as the most promising candidates for drought tolerance at booting stage. Of these, Osa-MIR2919 with 19 target genes in the qDTYs is being reported for the first time. It acts as a negative regulator of drought stress tolerance by modulating the cytokinin and brassinosteroid signalling pathway.
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Affiliation(s)
- Deepesh Kumar
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- PG School, Indian Agricultural Research Institute, Pusa Campus New Delhi, New Delhi, 110012, India
| | - M K Ramkumar
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Bipratip Dutta
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- PG School, Indian Agricultural Research Institute, Pusa Campus New Delhi, New Delhi, 110012, India
| | - Ajay Kumar
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Rakesh Pandey
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Pradeep Kumar Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Dwijesh C Mishra
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - K K Chaturvedi
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
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11
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Das P, Chandra T, Negi A, Jaiswal S, Iquebal MA, Rai A, Kumar D. A comprehensive review on genomic resources in medicinally and industrially important major spices for future breeding programs: Status, utility and challenges. Curr Res Food Sci 2023; 7:100579. [PMID: 37701635 PMCID: PMC10494321 DOI: 10.1016/j.crfs.2023.100579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/21/2023] [Accepted: 08/26/2023] [Indexed: 09/14/2023] Open
Abstract
In the global market, spices possess a high-value but low-volume commodities of commerce. The food industry depends largely on spices for taste, flavor, and therapeutic properties in replacement of cheap synthetic ones. The estimated growth rate for spices demand in the world is ∼3.19%. Since spices grow in limited geographical regions, India is one of the leading producer of spices, contributing 25-30 percent of total world trade. Hitherto, there has been no comprehensive review of the genomic resources of industrially important major medicinal spices to overcome major impediments in varietal improvement and management. This review focuses on currently available genomic resources of 24 commercially significant spices, namely, Ajwain, Allspice, Asafoetida, Black pepper, Cardamom large, Cardamom small, Celery, Chillies, Cinnamon, Clove, Coriander, Cumin, Curry leaf, Dill seed, Fennel, Fenugreek, Garlic, Ginger, Mint, Nutmeg, Saffron, Tamarind, Turmeric and Vanilla. The advent of low-cost sequencing machines has contributed immensely to the voluminous data generation of these spices, cracking the complex genomic architecture, marker discovery, and understanding comparative and functional genomics. This review of spice genomics resources concludes the perspective and way forward to provide footprints by uncovering genome assemblies, sequencing and re-sequencing projects, transcriptome-based studies, non-coding RNA-mediated regulation, organelles-based resources, developed molecular markers, web resources, databases and AI-directed resources in candidate spices for enhanced breeding potential in them. Further, their integration with molecular breeding could be of immense use in formulating a strategy to protect and expand the production of the spices due to increased global demand.
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Affiliation(s)
- Parinita Das
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Tilak Chandra
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ankita Negi
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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12
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MicroRNAs in Medicinal Plants. Int J Mol Sci 2022; 23:ijms231810477. [PMID: 36142389 PMCID: PMC9500639 DOI: 10.3390/ijms231810477] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Medicinal plant microRNAs (miRNAs) are an endogenous class of small RNA central to the posttranscriptional regulation of gene expression. Biosynthetic research has shown that the mature miRNAs in medicinal plants can be produced from either the standard messenger RNA splicing mechanism or the pre-ribosomal RNA splicing process. The medicinal plant miRNA function is separated into two levels: (1) the cross-kingdom level, which is the regulation of disease-related genes in animal cells by oral intake, and (2) the intra-kingdom level, which is the participation of metabolism, development, and stress adaptation in homologous or heterologous plants. Increasing research continues to enrich the biosynthesis and function of medicinal plant miRNAs. In this review, peer-reviewed papers on medicinal plant miRNAs published on the Web of Science were discussed, covering a total of 78 species. The feasibility of the emerging role of medicinal plant miRNAs in regulating animal gene function was critically evaluated. Staged progress in intra-kingdom miRNA research has only been found in a few medicinal plants, which may be mainly inhibited by their long growth cycle, high demand for growth environment, immature genetic transformation, and difficult RNA extraction. The present review clarifies the research significance, opportunities, and challenges of medicinal plant miRNAs in drug development and agricultural production. The discussion of the latest results furthers the understanding of medicinal plant miRNAs and helps the rational design of the corresponding miRNA/target genes functional modules.
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13
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Research progress about microRNAs involved in plant secondary metabolism. Int J Biol Macromol 2022; 216:820-829. [DOI: 10.1016/j.ijbiomac.2022.07.224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 11/18/2022]
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14
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Yue J, Liu Z, Zhao C, Zhao J, Zheng Y, Zhang H, Tan C, Zhang Z, Xue L, Lei J. Comparative Transcriptome Analysis Uncovers the Regulatory Roles of MicroRNAs Involved in Petal Color Change of Pink-Flowered Strawberry. FRONTIERS IN PLANT SCIENCE 2022; 13:854508. [PMID: 35422831 PMCID: PMC9002178 DOI: 10.3389/fpls.2022.854508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
The pink-flowered strawberry is popular in China due to its high ornamental value. In the present study, sRNAome, transcriptome, and degradome sequencing were performed to understand the functions of microRNAs (miRNAs) and their target genes during flower development in pink-flowered strawberry. Nine small RNA libraries and a mixed degradome library from flower petals at different developmental stages were constructed and sequenced. A total of 739 known miRNAs and 964 novel miRNAs were identified via small RNA sequencing, and 639 miRNAs were identified to cleave 2,816 target genes based on the degradome data. Additionally, 317 differentially expressed miRNAs among the various stages of flower development were identified, which regulated 2,134 differentially expressed target genes. These target genes were significantly enriched in the transcriptional regulation, phenylpropanoid biosynthesis, and plant hormone signal transduction pathways. Furthermore, integrated microRNAomic and transcriptomic analyses suggested that 98 miRNAs targeted several transcription factors, including MYBs (26), bHLHs (12), NACs (14), and SPLs (19), related to anthocyanin accumulation. In addition, 27 differentially expressed miRNAs might affect anthocyanin biosynthesis by regulating 23 targets involved in the hormone signal transduction pathway. The quantitative real-time PCR (qRT-PCR) analysis confirmed the expression changes of 21 miRNA-target pairs. Furthermore, the transient expression of candidate miRNAs was performed in the pink-flowered strawberry cultivar "Fenyun" at the bud stage. Introduction of FamiR156a, FamiR396e, and FamiR858_R-2 in the "Fenyun" increased flower color intensity, while transient expression of FamiR828a decreased flower color intensity. Overall, the present study uncovers the regulatory functions of microRNAs, including anthocyanin biosynthesis, hormone signaling, and regulation factors during flower development and coloration in pink-flowered strawberry. This work expands the knowledge of miRNAs affecting coloration in strawberry and provides rich resources for future functional studies.
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Affiliation(s)
- Jingyu Yue
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zhixiang Liu
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China
| | - Can Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Jun Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Yang Zheng
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Hongwei Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Changhua Tan
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zhentang Zhang
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China
| | - Li Xue
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Jiajun Lei
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
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15
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Yang K, Han H, Li Y, Ye J, Xu F. Significance of miRNA in enhancement of flavonoid biosynthesis. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:217-226. [PMID: 34806280 DOI: 10.1111/plb.13361] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 10/15/2021] [Indexed: 05/20/2023]
Abstract
Flavonoid metabolism shows very strong plasticity in plant development and coping with the changing environment. Flavonoid biosynthesis is regulated by many metabolic pathways, including transcriptional regulation, post-transcriptional control, post-translational regulationand epigenetic regulation. miRNA is a form of endogenous noncoding single-strand small molecule RNA that primarily regulates the expression of target genes horizontally after transcription through splicing and translational suppression. It also plays an important role in regulating plant growth and development, secondary metabolism and biotic and abiotic stress. miRNA can regulate the formation of flavonoids by acting on structural genes or indirectly by using an MBW transcription complex comprising MYB-bHLH-WD40. This study summarizes the biosynthesis and mechanisms of miRNA, and provides a summary of the mechanisms of miRNAs involved in production of flavonoids, in order to elucidate the biosynthesis pathway and complex regulatory network of plant flavonoids. We aim to provide new insights into improving the content of flavonoid active ingredients in plants.
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Affiliation(s)
- K Yang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - H Han
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - Y Li
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - J Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - F Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
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16
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Xing H, Li Y, Ren Y, Zhao Y, Wu X, Li HL. Genome-wide investigation of microRNAs and expression profiles during rhizome development in ginger (Zingiber officinale Roscoe). BMC Genomics 2022; 23:49. [PMID: 35021996 PMCID: PMC8756691 DOI: 10.1186/s12864-021-08273-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 12/20/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are endogenous, non-coding small functional RNAs that govern the post-transcriptional regulatory system of gene expression and control the growth and development of plants. Ginger is an herb that is well-known for its flavor and medicinal properties. The genes involved in ginger rhizome development and secondary metabolism have been discovered, but the genome-wide identification of miRNAs and their overall expression profiles and targets during ginger rhizome development are largely unknown. In this study, we used BGISEQ-500 technology to perform genome-wide identification of miRNAs from the leaf, stem, root, flower, and rhizome of ginger during three development stages. RESULTS In total, 104 novel miRNAs and 160 conserved miRNAs in 28 miRNA families were identified. A total of 181 putative target genes for novel miRNAs and 2772 putative target genes for conserved miRNAs were predicted. Transcriptional factors were the most abundant target genes of miRNAs, and 17, 9, 8, 4, 13, 8, 3 conserved miRNAs and 5, 7, 4, 5, 5, 15, 9 novel miRNAs showed significant tissue-specific expression patterns in leaf, stem, root, flower, and rhizome. Additionally, 53 miRNAs were regarded as rhizome development-associated miRNAs, which mostly participate in metabolism, signal transduction, transport, and catabolism, suggesting that these miRNAs and their target genes play important roles in the rhizome development of ginger. Twelve candidate miRNA target genes were selected, and then, their credibility was confirmed using qRT-PCR. As the result of qRT-PCR analysis, the expression of 12 candidate target genes showed an opposite pattern after comparison with their miRNAs. The rhizome development system of ginger was observed to be governed by miR156, miR319, miR171a_2, miR164, and miR529, which modulated the expression of the SPL, MYB, GRF, SCL, and NAC genes, respectively. CONCLUSION This is a deep genome-wide investigation of miRNA and identification of miRNAs involved in rhizome development in ginger. We identified 52 rhizome-related miRNAs and 392 target genes, and this provides an important basis for understanding the molecular mechanisms of the miRNA target genes that mediate rhizome development in ginger.
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Affiliation(s)
- Haitao Xing
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, 402168, China
| | - Yuan Li
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China.
| | - Yun Ren
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, 402168, China
| | - Ying Zhao
- Research Center for Terrestrial Biodiversity of the South China Sea, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, Hainan, China
| | - Xiaoli Wu
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China
| | - Hong-Lei Li
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China.
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, 402168, China.
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17
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Hossain R, Quispe C, Saikat ASM, Jain D, Habib A, Janmeda P, Islam MT, Radha, Daştan SD, Kumar M, Butnariu M, Cho WC, Sharifi-Rad J, Kipchakbayeva A, Calina D. Biosynthesis of Secondary Metabolites Based on the Regulation of MicroRNAs. BIOMED RESEARCH INTERNATIONAL 2022; 2022:9349897. [PMID: 35281611 PMCID: PMC8916866 DOI: 10.1155/2022/9349897] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 02/07/2022] [Indexed: 12/12/2022]
Abstract
MicroRNA (miRNA), a noncoding ribonucleic acid, is considered to be important for the progression of gene expression in plants and animals by rupture or translational repression of targeted mRNAs. Many types of miRNA regulate plant metabolism, growth, and response to biotic and abiotic factors. miRNA characterization helps to expose its function in regulating the process of post-transcriptional genetic regulation. There are a lot of factors associated with miRNA function, but the function of miRNA in the organic synthesis of by-products by natural products is not yet fully elucidated. The current review is aimed at observing and characterizing miRNAs and identifying those involved in the functioning of the biosynthesis of secondary metabolites in plants, with their use in controlled manipulation.
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Affiliation(s)
- Rajib Hossain
- 1Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Cristina Quispe
- 2Facultad de Ciencias de la Salud, Universidad Arturo Prat, Avda. Arturo Prat 2120, Iquique 1110939, Chile
| | - Abu Saim Mohammad Saikat
- 3Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Divya Jain
- 4Department of Bioscience and Biotechnology, Banasthali Vidyapith, Rajasthan, India
| | - Arslan Habib
- 5Lab of Infectious and Molecular Immunology, School of Life Sciences, Fudan University, Shanghai, China
| | - Pracheta Janmeda
- 4Department of Bioscience and Biotechnology, Banasthali Vidyapith, Rajasthan, India
| | - Muhammad Torequl Islam
- 1Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Radha
- 6School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan 173229, India
| | - Sevgi Durna Daştan
- 7Department of Biology, Faculty of Science, Sivas Cumhuriyet University, Sivas 58140, Turkey
- 8Beekeeping Development Application and Research Center, Sivas Cumhuriyet University, Sivas 58140, Turkey
| | - Manoj Kumar
- 9Chemical and Biochemical Processing Division, ICAR-Central Institute for Research on Cotton Technology, Mumbai 400019, India
| | - Monica Butnariu
- 10Banat's University of Agricultural Sciences and Veterinary Medicine “King Michael I of Romania” from Timisoara, Timisoara, Romania
| | - William C. Cho
- 11Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | | | - Aliya Kipchakbayeva
- 13Faculty of Chemistry and Chemical Technology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Daniela Calina
- 14Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, Craiova 200349, Romania
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18
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Ding Y, Mao Y, Cen Y, Hu L, Su Y, Ma X, Long L, Hu H, Hao C, Luo J. Small RNA sequencing reveals various microRNAs involved in piperine biosynthesis in black pepper (Piper nigrum L.). BMC Genomics 2021; 22:838. [PMID: 34794378 PMCID: PMC8603596 DOI: 10.1186/s12864-021-08154-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 11/03/2021] [Indexed: 11/29/2022] Open
Abstract
Background Black pepper (Piper nigrum L.), an important and long-cultivated spice crop, is native to South India and grown in the tropics. Piperine is the main pungent and bioactive alkaloid in the berries of black pepper, but the molecular mechanism for piperine biosynthesis has not been determined. MicroRNAs (miRNAs), which are classical endogenous noncoding small RNAs, play important roles in regulating secondary metabolism in many species, but less is known regarding black pepper or piperine biosynthesis. Results To dissect the functions of miRNAs in secondary metabolism especially in piperine biosynthesis, 110 known miRNAs, 18 novel miRNAs and 1007 individual targets were identified from different tissues of black pepper by small RNA sequencing. qRT-PCR and 5′-RLM-RACE experiments were conducted to validate the reliability of the sequencing data and predicted targets. We found 3 miRNAs along with their targets including miR166-4CL, miR396-PER and miR397-CCR modules that are involved in piperine biosynthesis. Conclusion MiRNA regulation of secondary metabolism is a common phenomenon in plants. Our study revealed new miRNAs that regulate piperine biosynthesis, which are special alkaloids in the piper genus, and they might be useful for future piperine genetic improvement of black pepper. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08154-4.
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Affiliation(s)
- Yuanhao Ding
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Yuyuan Mao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Yi Cen
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, School of Tropical Crops, Hainan University, Haikou, 570228, China.,Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, Hainan, China
| | - Lisong Hu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, Hainan, China.,Ministry of Agriculture Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Wanning, 571533, Hainan, China
| | - Yuefeng Su
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, School of Tropical Crops, Hainan University, Haikou, 570228, China.,Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, Hainan, China
| | - Xuemin Ma
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Lu Long
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, 475004, Henan, China
| | - Haiyan Hu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, School of Tropical Crops, Hainan University, Haikou, 570228, China.
| | - Chaoyun Hao
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, Hainan, China. .,Ministry of Agriculture Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Wanning, 571533, Hainan, China. .,Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, 571533, Hainan, China.
| | - Jie Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, School of Tropical Crops, Hainan University, Haikou, 570228, China.
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Chakraborty A, Mahajan S, Jaiswal SK, Sharma VK. Genome sequencing of turmeric provides evolutionary insights into its medicinal properties. Commun Biol 2021; 4:1193. [PMID: 34654884 PMCID: PMC8521574 DOI: 10.1038/s42003-021-02720-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 08/13/2021] [Indexed: 12/28/2022] Open
Abstract
Curcuma longa, or turmeric, is traditionally known for its immense medicinal properties and has diverse therapeutic applications. However, the absence of a reference genome sequence is a limiting factor in understanding the genomic basis of the origin of its medicinal properties. In this study, we present the draft genome sequence of C. longa, belonging to Zingiberaceae plant family, constructed using 10x Genomics linked reads and Oxford Nanopore long reads. For comprehensive gene set prediction and for insights into its gene expression, transcriptome sequencing of leaf tissue was also performed. The draft genome assembly had a size of 1.02 Gbp with ~70% repetitive sequences, and contained 50,401 coding gene sequences. The phylogenetic position of C. longa was resolved through a comprehensive genome-wide analysis including 16 other plant species. Using 5,388 orthogroups, the comparative evolutionary analysis performed across 17 species including C. longa revealed evolution in genes associated with secondary metabolism, plant phytohormones signaling, and various biotic and abiotic stress tolerance responses. These mechanisms are crucial for perennial and rhizomatous plants such as C. longa for defense and environmental stress tolerance via production of secondary metabolites, which are associated with the wide range of medicinal properties in C. longa.
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Affiliation(s)
- Abhisek Chakraborty
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Shruti Mahajan
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Shubham K Jaiswal
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Vineet K Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.
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20
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Akbari A, Sedaghat M, Heshmati J, Tabaeian SP, Dehghani S, Pizarro AB, Rostami Z, Agah S. Molecular mechanisms underlying curcumin-mediated microRNA regulation in carcinogenesis; Focused on gastrointestinal cancers. Biomed Pharmacother 2021; 141:111849. [PMID: 34214729 DOI: 10.1016/j.biopha.2021.111849] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/08/2021] [Accepted: 06/24/2021] [Indexed: 02/07/2023] Open
Abstract
Curcumin is a bioactive ingredient found in the Rhizomes of Curcuma longa. Curcumin is well known for its chemopreventive and anti-cancer properties. Recent findings have demonstrated several pharmacological and biological impacts of curcumin, related to the control and the management of gastrointestinal cancers. Mechanistically, curcumin exerts its biological impacts via antioxidant and anti-inflammatory effects through the interaction with various transcription factors and signaling molecules. Moreover, epigenetic modulators such as microRNAs (miRNAs) have been revealed as novel targets of curcumin. Curcumin was discovered to regulate the expression of numerous pathogenic miRNAs in gastric, colorectal, esophageal and liver cancers. The present systematic review was performed to identify miRNAs that are modulated by curcumin in gastrointestinal cancers.
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Affiliation(s)
- Abolfazl Akbari
- Colorectal Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Meghdad Sedaghat
- Department of Internal Medicine, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Javad Heshmati
- Songhor Healthcare Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Seidamir Pasha Tabaeian
- Colorectal Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Internal Medicine, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Sadegh Dehghani
- Radiation Sciences Department, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Zahra Rostami
- Department of Genetics, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran.
| | - Shahram Agah
- Colorectal Research Center, Iran University of Medical Sciences, Tehran, Iran.
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21
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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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Waheed S, Anwar M, Saleem MA, Wu J, Tayyab M, Hu Z. The Critical Role of Small RNAs in Regulating Plant Innate Immunity. Biomolecules 2021; 11:biom11020184. [PMID: 33572741 PMCID: PMC7912340 DOI: 10.3390/biom11020184] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/14/2021] [Accepted: 01/14/2021] [Indexed: 12/12/2022] Open
Abstract
Plants, due to their sessile nature, have an innate immune system that helps them to defend against different pathogen infections. The defense response of plants is composed of a highly regulated and complex molecular network, involving the extensive reprogramming of gene expression during the presence of pathogenic molecular signatures. Plants attain proper defense against pathogens through the transcriptional regulation of genes encoding defense regulatory proteins and hormone signaling pathways. Small RNAs are emerging as versatile regulators of plant development and act in different tiers of plant immunity, including pathogen-triggered immunity (PTI) and effector-triggered immunity (ETI). The versatile regulatory functions of small RNAs in plant growth and development and response to biotic and abiotic stresses have been widely studied in recent years. However, available information regarding the contribution of small RNAs in plant immunity against pathogens is more limited. This review article will focus on the role of small RNAs in innate immunity in plants.
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Affiliation(s)
- Saquib Waheed
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Muhammad Anwar
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
- Correspondence: (M.A.); (Z.H.)
| | - Muhammad Asif Saleem
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan 60800, Pakistan;
| | - Jinsong Wu
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518060, China;
| | - Muhammad Tayyab
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Forestry University, Fuzhou 350002, China;
| | - Zhangli Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518060, China;
- Correspondence: (M.A.); (Z.H.)
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23
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Li Y, Kong D, Fu Y, Sussman MR, Wu H. The effect of developmental and environmental factors on secondary metabolites in medicinal plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 148:80-89. [PMID: 31951944 DOI: 10.1016/j.plaphy.2020.01.006] [Citation(s) in RCA: 357] [Impact Index Per Article: 89.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 12/12/2019] [Accepted: 01/04/2020] [Indexed: 05/25/2023]
Abstract
Secondary metabolites (SMs) of medicinal plants are the material basis of their clinically curative effects. They are also important indicators for evaluating the quality of medicinal materials. However, the synthesis and accumulation of SMs are very complex, which are affected by many factors including internal developmental genetic circuits (regulated gene, enzyme) and by external environment factors (light, temperature, water, salinity, etc.). Currently, lots of literatures focused on the effect of environmental factors on the synthesis and accumulation of SMs of medicinal plants, the effect of the developmental growth and genetic factors on the synthesis and accumulation of SMs still lack systematic classification and summary. Here, we have given the review base on our previous works on the morphological development of medicinal plants and their secondary metabolites, and systematically outlined the literature reports how different environmental factors affected the synthesis and accumulation of SMs. The results of our reviews can know how developmental and environmental factors qualitatively and quantitatively influence SMs of medicinal plants and how these can be integrated as tools to quality control, as well as on the improvement of clinical curative effects by altering their genomes, and/or growth conditions.
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Affiliation(s)
- Yanqun Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China; Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, 510642, China; Guangdong Technology Research Center for Traditional Chinese Veterinary Medicine and Natural Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Dexin Kong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Ying Fu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, 510642, China
| | - Michael R Sussman
- Biotechnology Center, University of Wisconsin, Madison, WI, 53706, USA
| | - Hong Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China; Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, 510642, China; Guangdong Technology Research Center for Traditional Chinese Veterinary Medicine and Natural Medicine, South China Agricultural University, Guangzhou, 510642, China.
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24
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Gadhavi H, Patel M, Mangukia N, Shah K, Bhadresha K, Patel SK, Rawal RM, Pandya HA. Transcriptome-wide miRNA identification of Bacopa monnieri: a cross-kingdom approach. PLANT SIGNALING & BEHAVIOR 2020; 15:1699265. [PMID: 31797719 PMCID: PMC7012157 DOI: 10.1080/15592324.2019.1699265] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Bacopa monnieri known as 'Brahmi' is a well-known medicinal plant belonging to Scrophulariaceae family for its nootropic properties. To the best of our knowledge, no characterization data is available on the potential role of micro RNAs (miRNAs) from this plant till date. We present here the first report of computational characterizations of miRNAs from B. monnieri. Owing to the high conservation of miRNAs in nature, new and potential miRNAs can be identified in plants using in silico techniques. Using the plant miRNA sequences present in the miRBase repository, a total of 12 miRNAs were identified from B. monnieri which pertained to 11 miRNA families from the shoot and root transcriptome data. Furthermore, gene ontology analysis of the identified 68 human target genes exhibited significance in various biological processes. These human target genes were associated with signaling pathways like NF-kB and MAPK with TRAF2, CBX1, IL1B, ITGA4 and ITGB1BP1 as the top five hub nodes. This cross-kingdom study provides initial insights about the potential of miRNA-mediated cross-kingdom regulation and unravels the essential target genes of human with implications in numerous human diseases including cancer.
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Affiliation(s)
- Harshida Gadhavi
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, India
| | - Maulikkumar Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, India
| | - Naman Mangukia
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, India
| | - Kanisha Shah
- Department of Life Sciences, Food Science and Nutrition, School of Sciences, Gujarat University, Ahmedabad, India
| | - Kinjal Bhadresha
- Department of Life Sciences, Food Science and Nutrition, School of Sciences, Gujarat University, Ahmedabad, India
| | - Saumya K. Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, India
| | - Rakesh M. Rawal
- Department of Life Sciences, Food Science and Nutrition, School of Sciences, Gujarat University, Ahmedabad, India
| | - Himanshu A. Pandya
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, India
- CONTACT Himanshu A. Pandya Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
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25
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Bouwmeester H, Schuurink RC, Bleeker PM, Schiestl F. The role of volatiles in plant communication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:892-907. [PMID: 31410886 PMCID: PMC6899487 DOI: 10.1111/tpj.14496] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 05/31/2019] [Accepted: 06/17/2019] [Indexed: 05/08/2023]
Abstract
Volatiles mediate the interaction of plants with pollinators, herbivores and their natural enemies, other plants and micro-organisms. With increasing knowledge about these interactions the underlying mechanisms turn out to be increasingly complex. The mechanisms of biosynthesis and perception of volatiles are slowly being uncovered. The increasing scientific knowledge can be used to design and apply volatile-based agricultural strategies.
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Affiliation(s)
- Harro Bouwmeester
- University of AmsterdamSwammerdam Institute for Life SciencesGreen Life Science research clusterScience Park 9041098 XHAmsterdamThe Netherlands
| | - Robert C. Schuurink
- University of AmsterdamSwammerdam Institute for Life SciencesGreen Life Science research clusterScience Park 9041098 XHAmsterdamThe Netherlands
| | - Petra M. Bleeker
- University of AmsterdamSwammerdam Institute for Life SciencesGreen Life Science research clusterScience Park 9041098 XHAmsterdamThe Netherlands
| | - Florian Schiestl
- Department of Systematic and Evolutionary BotanyUniversity of ZürichZollikerstrasse 107CH‐8008ZürichSwitzerland
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26
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Pirrò S, Matic I, Guidi A, Zanella L, Gismondi A, Cicconi R, Bernardini R, Colizzi V, Canini A, Mattei M, Galgani A. Identification of microRNAs and relative target genes in Moringa oleifera leaf and callus. Sci Rep 2019; 9:15145. [PMID: 31641153 PMCID: PMC6805943 DOI: 10.1038/s41598-019-51100-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 09/20/2019] [Indexed: 01/30/2023] Open
Abstract
MicroRNAs, a class of small, non-coding RNAs, play important roles in plant growth, development and stress response by negatively regulating gene expression. Moringa oleifera Lam. plant has many medical and nutritional uses; however, little attention has been dedicated to its potential for the bio production of active compounds. In this study, 431 conserved and 392 novel microRNA families were identified and 9 novel small RNA libraries constructed from leaf, and cold stress treated callus, using high-throughput sequencing technology. Based on the M. oleifera genome, the microRNA repertoire of the seed was re-evaluated. qRT-PCR analysis confirmed the expression pattern of 11 conserved microRNAs in all groups. MicroRNA159 was found to be the most abundant conserved microRNA in leaf and callus, while microRNA393 was most abundantly expressed in the seed. The majority of predicted microRNA target genes were transcriptional factors involved in plant reproduction, growth/development and abiotic/biotic stress response. In conclusion, this is the first comprehensive analysis of microRNAs in M. oleifera leaf and callus which represents an important addition to the existing M. oleifera seed microRNA database and allows for possible exploitation of plant microRNAs induced with abiotic stress, as a tool for bio-enrichment with pharmacologically important phytochemicals.
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Affiliation(s)
- Stefano Pirrò
- Mir-Nat s.r.l., Rome, 00133, Italy
- Bioinformatics Unit, Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University London, London, EC1M 6BQ, UK
| | - Ivana Matic
- Mir-Nat s.r.l., Rome, 00133, Italy
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | | | - Letizia Zanella
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Angelo Gismondi
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | | | | | - Vittorio Colizzi
- Mir-Nat s.r.l., Rome, 00133, Italy
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Antonella Canini
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | | | - Andrea Galgani
- Mir-Nat s.r.l., Rome, 00133, Italy.
- CIMETA, University of Rome Tor Vergata, Rome, Italy.
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27
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Narnoliya LK, Kaushal G, Singh SP. Long noncoding RNAs and miRNAs regulating terpene and tartaric acid biosynthesis in rose-scented geranium. FEBS Lett 2019; 593:2235-2249. [PMID: 31210363 DOI: 10.1002/1873-3468.13493] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This study aimed to explore the noncoding RNAs, which have emerged as key regulatory molecules in biological processes, in rose-scented geranium. We analyzed RNA-seq data revealing 26 784 long noncoding RNAs (lncRNAs) and 871 miRNAs in rose-scented geranium. A total of 466 lncRNAs were annotated using different plant lncRNA public databases. Furthermore, 372 lncRNAs and 99 miRNAs were detected that target terpene and tartarate biosynthetic pathways. An interactome, comprising of lncRNAs, miRNAs, and mRNAs, was constructed that represents a noncoding RNA regulatory network of the target mRNAs. Real-time quantitative PCR expression validation was done for selected lncRNAs involved in the regulation of terpene and tartaric acid pathways. This study provides the first insights into the regulatory functioning of noncoding RNAs in rose-scented geranium.
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Affiliation(s)
| | - Girija Kaushal
- Center of Innovative and Applied Bioprocessing, S.A.S. Nagar, Mohali, India
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing, S.A.S. Nagar, Mohali, India
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28
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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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