1
|
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.
Collapse
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.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Gajurel G, Hasan R, Medina-Bolivar F. Water-deficit stress induces prenylated stilbenoid production and affects biomass in peanut hairy roots: Exploring the role of stilbenoid prenyltransferase downregulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108596. [PMID: 38579541 DOI: 10.1016/j.plaphy.2024.108596] [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: 02/13/2024] [Revised: 03/22/2024] [Accepted: 04/01/2024] [Indexed: 04/07/2024]
Abstract
The peanut plant is one of the most economically important crops around the world. Abiotic stress, such as drought, causes over five hundred million dollars in losses in peanut production per year. Peanuts are known to produce prenylated stilbenoids to counteract biotic stress. However, their role in abiotic stress tolerance has not been elucidated. To address this issue, hairy roots with the capacity to produce prenylated stilbenoids were established. An RNA-interference (RNAi) molecular construct targeting the stilbenoid-specific prenyltransferase AhR4DT-1 was designed and expressed via Agrobacterium rhizogenes-mediated transformation in hairy roots of peanut cultivar Georgia Green. Two transgenic hairy roots with the RNAi molecular construct were established, and the downregulation of AhR4DT-1 was validated using reverse transcriptase quantitative PCR. To determine the efficacy of the RNAi-approach in modifying the levels of prenylated stilbenoids, the hairy roots were co-treated with methyl jasmonate, hydrogen peroxide, cyclodextrin, and magnesium chloride to induce the production of stilbenoids and then the stilbenoids were analyzed in extracts of the culture medium. Highly reduced levels of prenylated stilbenoids were observed in the RNAi hairy roots. Furthermore, the hairy roots were evaluated in a polyethylene glycol (PEG) assay to assess the role of prenylated stilbenoids on water-deficit stress. Upon PEG treatment, stilbenoids were induced and secreted into the culture medium of RNAi and wild-type hairy roots. Additionally, the biomass of the RNAi hairy roots decreased by a higher amount as compared to the wild-type hairy roots suggesting that prenylated stilbenoids might play a role against water-deficit stress.
Collapse
Affiliation(s)
- Gaurav Gajurel
- Arkansas Bioscience Institute, Arkansas State University, Jonesboro, AR, 72401, USA; Molecular Biosciences Graduate Program, Arkansas State University, Jonesboro, AR, 72401, USA
| | - Rokib Hasan
- Arkansas Bioscience Institute, Arkansas State University, Jonesboro, AR, 72401, USA; Molecular Biosciences Graduate Program, Arkansas State University, Jonesboro, AR, 72401, USA
| | - Fabricio Medina-Bolivar
- Arkansas Bioscience Institute, Arkansas State University, Jonesboro, AR, 72401, USA; Department of Biological Sciences, Arkansas State University, Jonesboro, AR, 72401, USA.
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Madhuvanthi CK, Muthulakshmi E, Ghosh Dasgupta M. Integrated mRNA and small RNA sequencing reveals post-transcriptional regulation of the sesquiterpene pathway in Santalum album L. (Indian sandalwood). 3 Biotech 2023; 13:387. [PMID: 37942052 PMCID: PMC10628100 DOI: 10.1007/s13205-023-03816-4] [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: 07/11/2023] [Accepted: 10/15/2023] [Indexed: 11/10/2023] Open
Abstract
Key message In sandalwood, negative pattern of regulation by miRNAs was documented in key genes from the sesquiterpene pathway, with cytochrome P450 reductase showing maximum miRNA targets, followed by sesquisabianene synthase 1. Abstract A comprehensive knowledge of the molecular regulation of sesquiterpene biosynthetic pathway through transcriptomic studies is well established in Santalum album (Indian Sandalwood). However, the post-transcriptional regulation of the genes regulating the pathway is still elusive in this genus. In the present study, an integrated analysis of wood transcriptome and small RNA datasets was conducted to investigate the role of miRNAs in regulating the expression of transcripts involved in santalol production mediated by the sesquiterpene biosynthesis pathway. A total of 24,237 transcripts were annotated from the wood transcriptome, and 45 transcripts were mapped to the sesquiterpenoid pathway. Small RNA data analysis identified 257 conserved miRNAs belonging to 50 families and 7 novel putative miRNAs. Sa-miR156, Sa-miR396, Sa-miR166, and Sa-miR319 had the most number of members among the miRNA families. An integrated analysis predicted 69 miRNA members belonging to 12 families that targeted 12 transcripts from the sesquiterpene pathway, with a maximum of 24 miRNAs regulating cytochrome P450 reductase, followed by sesquisabianene synthase 1, which was targeted by 23 miRNAs. Validation of miRNA-mRNA interaction by qRT-PCR revealed a negative pattern of regulation in six miRNA-mRNA target pairs across wood tissues sourced from four genotypes. The present study provides the first crucial insight into the post-transcriptional regulation of the sesquiterpene pathway genes in the genus Santalum and opens up a new perspective in metabolite engineering for enhanced essential oil production in sandalwood. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03816-4.
Collapse
Affiliation(s)
- Chandramouli K. Madhuvanthi
- Division of Plant Biotechnology and Cytogenetics, ICFRE-Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu 641002 India
| | - Eswaran Muthulakshmi
- Division of Plant Biotechnology and Cytogenetics, ICFRE-Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu 641002 India
| | - Modhumita Ghosh Dasgupta
- Division of Plant Biotechnology and Cytogenetics, ICFRE-Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu 641002 India
| |
Collapse
|
7
|
Zhao Y, Liu G, Yang F, Liang Y, Gao Q, Xiang C, Li X, Yang R, Zhang G, Jiang H, Yu L, Yang S. Multilayered regulation of secondary metabolism in medicinal plants. MOLECULAR HORTICULTURE 2023; 3:11. [PMID: 37789448 PMCID: PMC10514987 DOI: 10.1186/s43897-023-00059-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/27/2023] [Indexed: 10/05/2023]
Abstract
Medicinal plants represent a huge reservoir of secondary metabolites (SMs), substances with significant pharmaceutical and industrial potential. However, obtaining secondary metabolites remains a challenge due to their low-yield accumulation in medicinal plants; moreover, these secondary metabolites are produced through tightly coordinated pathways involving many spatiotemporally and environmentally regulated steps. The first regulatory layer involves a complex network of transcription factors; a second, more recently discovered layer of complexity in the regulation of SMs is epigenetic modification, such as DNA methylation, histone modification and small RNA-based mechanisms, which can jointly or separately influence secondary metabolites by regulating gene expression. Here, we summarize the findings in the fields of genetic and epigenetic regulation with a special emphasis on SMs in medicinal plants, providing a new perspective on the multiple layers of regulation of gene expression.
Collapse
Affiliation(s)
- Yan Zhao
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Guanze Liu
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
| | - Feng Yang
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanli Liang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Qingqing Gao
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Chunfan Xiang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Xia Li
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Run Yang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Guanghui Zhang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Huifeng Jiang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Lei Yu
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, 650214, China.
| | - Shengchao Yang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China.
| |
Collapse
|
8
|
Habán M, Korczyk-Szabó J, Čerteková S, Ražná K. Lavandula Species, Their Bioactive Phytochemicals, and Their Biosynthetic Regulation. Int J Mol Sci 2023; 24:ijms24108831. [PMID: 37240177 DOI: 10.3390/ijms24108831] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/12/2023] [Accepted: 05/14/2023] [Indexed: 05/28/2023] Open
Abstract
Lavandula species are one of the most useful aromatic and medicinal plants and have great economic potential. The phytopharmaceutical contribution of the secondary metabolites of the species is unquestionable. Most recent studies have been focusing on the elucidation of the genetic background of secondary metabolite production in lavender species. Therefore, knowledge of not only genetic but especially epigenetic mechanisms for the regulation of secondary metabolites is necessary for the modification of those biosynthesis processes and the understanding of genotypic differences in the content and compositional variability of these products. The review discusses the genetic diversity of Lavandula species in relation to the geographic area, occurrence, and morphogenetic factors. The role of microRNAs in secondary-metabolites biosynthesis is described.
Collapse
Affiliation(s)
- Miroslav Habán
- Institute of Agronomic Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
- Department of Pharmacognosy and Botany, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, 83232 Bratislava, Slovakia
| | - Joanna Korczyk-Szabó
- Institute of Agronomic Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
| | - Simona Čerteková
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
| | - Katarína Ražná
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
| |
Collapse
|
9
|
Sharma M, Bhushan S, Sharma D, Kaul S, Dhar MK. A Brief Review of Plant Cell Transfection, Gene Transcript Expression, and Genotypic Integration for Enhancing Compound Production. Methods Mol Biol 2023; 2575:153-179. [PMID: 36301475 DOI: 10.1007/978-1-0716-2716-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Plants possess a plethora of important secondary metabolites, which are unique sources of natural pigments, pharmaceutical compounds, food additives, natural pesticides, and other industrial components. The commercial significance of such metabolites/compounds has directed the research toward their production and exploration of methods for enhancement of production. Biotechnological tools are critical in selecting, integrating, multiplying, improving, and analyzing medicinal plants for secondary metabolite production. Out of many techniques that are being explored to enhance secondary metabolite production, "plant cell transfection" is the latest tool to achieve maximum output from the plant source. It is based upon the introduction of foreign DNA into the plant cell relying on physical treatment such as electroporation, cell squeezing, sonoporation, optical transfection nanoparticles, magnetofection, and chemical treatment or biological treatment that depends upon carrier. One of the promising tools that have been exploited is CRISPR-Cas9. Overall, the abovementioned tools focus on the stable transfection of desired gene transcripts. Since the integration and continuous expression of transfected gene of particular trait represents stable transfection of host cell genome, resulting from transfer of required trait to daughter cells ultimately leading to enhanced production of secondary metabolites of interest. This chapter will review a set of biotechnological tools that are candidates for achieving the enhanced bioactive compound production indicated here to be used for drug discovery.
Collapse
Affiliation(s)
- Munish Sharma
- Department of Plant Sciences, Central University of Himachal Pradesh, Shahpur, Kangra, Himachal Pradesh, India.
| | - Sakshi Bhushan
- Department of Botany, Central University of Jammu, Jammu, Jammu and Kashmir, India
| | - Deepak Sharma
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir, India
| | - Sanjana Kaul
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir, India
| | - Manoj K Dhar
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir, India
| |
Collapse
|
10
|
Kavas M, Abdulla MF, Mostafa K, Seçgin Z, Yerlikaya BA, Otur Ç, Gökdemir G, Kurt Kızıldoğan A, Al-Khayri JM, Jain SM. Investigation and Expression Analysis of R2R3-MYBs and Anthocyanin Biosynthesis-Related Genes during Seed Color Development of Common Bean ( Phaseolus vulgaris). PLANTS (BASEL, SWITZERLAND) 2022; 11:3386. [PMID: 36501424 PMCID: PMC9736660 DOI: 10.3390/plants11233386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Anthocyanins are responsible for the coloration of common bean seeds, and their accumulation is positively correlated with the expression level of anthocyanin biosynthetic genes. The MBW (MYB-bHLH-WD40) complex is thought to regulate the expression of these genes, and MYB proteins, which are a key factor in activating anthocyanin pathway genes, have been identified in several plants. This study demonstrated gene structures, chromosomal placements, gene duplications of R2R3-MYBs, miRNAs associated with R2R3-MYBs, and the interaction of these genes with other flavonoid regulatory genes. qRT-PCR was used to investigate the role of specific R2R3-MYBs and flavonoid genes in common bean seed color development. As a result of a comprehensive analysis with the help of in silico tools, we identified 160 R2R3-MYB genes in the common bean genome. We divided these genes into 16 classes on the basis of their intron-exon and motif structures. Except for three, the rest of the common bean R2R3-MYB members were distributed to all chromosomes with different densities, primarily located on chromosomes 3 and 8. We identified a total of 44 duplicated gene pairs dispersed across 11 chromosomes and evolved under purifying selection (Ka/Ks < 1), 19 of which were derived from a whole-genome duplication. Our research uncovered 25 putative repressor PvMYB proteins that contain the EAR motif. Additionally, fifty different cis-regulatory elements regulated by light, stress, and hormone were identified. Within the genome of the common bean, we discovered a total of 36 microRNAs that target a total of 72 R2R3-MYB transcripts. The effect of 16 R2R3-MYB genes and 16 phenylpropanoid pathway genes, selected on the basis of their interaction in the protein-protein interaction map, playing role in the regulation of seed coat color development was evaluated using qRT-PCR in 5 different tissues at different developmental stages. The results revealed that these specific genes have different expression levels during different developmental periods, with higher levels in the pod filling and early pod stages than in the rest of the developmental periods. Furthermore, it was shown that PvTT8 (bHLH), PvTT2 (PvMYB42), PvMYB113, PvTTG1, and PvWD68 genes have effects on the regulation of seed coat color. The findings of this study, which is the first to use whole-genome analysis to identify and characterize the R2R3-MYB genes in common bean, may serve as a reference for future functional research in the legume.
Collapse
Affiliation(s)
- Musa Kavas
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun 55270, Turkey
| | - Mohamed Farah Abdulla
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun 55270, Turkey
| | - Karam Mostafa
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun 55270, Turkey
- The Central Laboratory for Date Palm Research and Development, Agricultural Research Center (ARC), Giza 12619, Egypt
| | - Zafer Seçgin
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun 55270, Turkey
| | - Bayram Ali Yerlikaya
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun 55270, Turkey
| | - Çiğdem Otur
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun 55270, Turkey
| | - Gökhan Gökdemir
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun 55270, Turkey
| | - Aslıhan Kurt Kızıldoğan
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun 55270, Turkey
| | - Jameel Mohammed Al-Khayri
- Department of Plant Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Shri Mohan Jain
- Department of Agricultural Sciences, University of Helsinki, PL-27, 00014 Helsinki, Finland
| |
Collapse
|
11
|
Xue T, Zhao M, Chen J, Chen Y, Zhang C, Li B. Revealing the mechanisms of the bioactive ingredients accumulation in Polygonatum cyrtonema by multiomics analyses. FRONTIERS IN PLANT SCIENCE 2022; 13:1055721. [PMID: 36466239 PMCID: PMC9709641 DOI: 10.3389/fpls.2022.1055721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/28/2022] [Indexed: 06/17/2023]
Abstract
Polygonatum cyrtonema is a medicinal and edible herb rich in polysaccharides, steroidal saponins, and flavonoids that has been widely used as a food, vegetable, and medicine over the years. Although previous studies have preliminarily explored the metabolic and transcriptional regulatory mechanisms of the main secondary metabolites in P. cyrtonema, the complex mechanism of microRNA (miRNA)-mediated posttranscriptional regulation remains unclear. Metabolome analysis showed that iso-ophiopogonanone B, (25S)-pratioside D1, disporopsin, and isodiosgenin-Glc-Glc, which are associated with intermediates in the flavonoids and saponins pathways, were significantly upregulated in the stem and leaf compared with the rhizome, and most saccharides, including arabinose, cellobiose, maltotetraose, and panose, showed the opposite trend, suggesting that they may contribute to the formation and accumulation of the main active ingredients in P. cyrtonema. We found that 4-hydroxymandelonitrile have a relatively good inhibitory effect on α-glucosidase, indicating that it may play a role in hypoglycemic functions. Transcriptome and weighted gene coexpression network analysis (WGCNA) were combined to reveal several candidate genes involved in the accumulation of polysaccharides, saponins, and flavonoids, including PcSQLE, PcCYP71A1, PcSUS, PcFK, and PcMYB102. Integrated analyses of miRNAs and messengerRNAs (mRNAs) showed that novel_miR14, novel_miR49, novel_miR75, and aof_miR164 were negatively correlated with alpha-linolenic acid metabolism and the mitogen activated protein kinase (MAPK) signaling pathway, including PcAOS, PcSPLA2, PcFRK1, and PcDELLA, indicating that these miRNAs may coordinately regulate the biosynthesis of other secondary metabolites in P. cyrtonema. These findings will facilitate in-depth research on the functions of these miRNAs and mRNAs related to the main active substances for pathological and biological regulation, which will be beneficial to provide theoretical guidance for the molecular breeding of P. cyrtonema.
Collapse
Affiliation(s)
- Ting Xue
- Fujian Provincial Key Laboratory for Plant Eco-physiology, State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, College of Geographical Sciences, Fujian Normal University, Fuzhou, China
- College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Miaohua Zhao
- Fujian Provincial Key Laboratory for Plant Eco-physiology, State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, College of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Jing Chen
- College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Youqiang Chen
- College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Chuanhai Zhang
- Fujian Provincial Key Laboratory of Eco-Industrial Green Technology, College of Ecology and Resource Engineering, Wuyi University, Nanping, China
| | - Baoyin Li
- Fujian Provincial Key Laboratory for Plant Eco-physiology, State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, College of Geographical Sciences, Fujian Normal University, Fuzhou, China
| |
Collapse
|
12
|
Jeena GS, Singh N, Shukla RK. An insight into microRNA biogenesis and its regulatory role in plant secondary metabolism. PLANT CELL REPORTS 2022; 41:1651-1671. [PMID: 35579713 DOI: 10.1007/s00299-022-02877-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
The present review highlights the regulatory roles of microRNAs in plant secondary metabolism and focuses on different bioengineering strategies to modulate secondary metabolite content in plants. MicroRNAs (miRNAs) are the class of small endogenous, essential, non-coding RNAs that riboregulate the gene expression involved in various biological processes in most eukaryotes. MiRNAs has emerged as important regulators in plants that function by silencing target genes through cleavage or translational inhibition. These miRNAs plays an important role in a wide range of plant biological and metabolic processes, including plant development and various environmental response controls. Several important plant secondary metabolites like alkaloids, terpenoids, and phenolics are well studied for their function in plant defense against different types of pests and herbivores. Due to the presence of a wide range of biological and pharmaceutical properties of plant secondary metabolites, it is important to study the regulation of their biosynthetic pathways. The contribution of miRNAs in regulating plant secondary metabolism is not well explored. Recent advancements in molecular techniques have improved our knowledge in understanding the molecular function of genes, proteins, enzymes, and small RNAs involved in different steps of secondary metabolic pathways. In the present review, we have discussed the recent progress made on miRNA biogenesis, its regulation, and highlighted the current research developed in the field of identification, analysis, and characterizations of various miRNAs that regulate plant secondary metabolism. We have also discussed how different bioengineering strategies such as artificial miRNA (amiRNA), endogenous target mimicry, and CRISPR/Cas9 could be utilized to enhance the secondary metabolite production in plants.
Collapse
Affiliation(s)
- Gajendra Singh Jeena
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O. CIMAP, Near Kukrail Picnic Spot, Lucknow, 226015, India
| | - Neeti Singh
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O. CIMAP, Near Kukrail Picnic Spot, Lucknow, 226015, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - Rakesh Kumar Shukla
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O. CIMAP, Near Kukrail Picnic Spot, Lucknow, 226015, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India.
| |
Collapse
|
13
|
Ražná K, Harenčár Ľ, Kučka M. The Involvement of microRNAs in Plant Lignan Biosynthesis—Current View. Cells 2022; 11:cells11142151. [PMID: 35883592 PMCID: PMC9323225 DOI: 10.3390/cells11142151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 02/01/2023] Open
Abstract
Lignans, as secondary metabolites synthesized within a phenylpropanoid pathway, play various roles in plants, including their involvement in growth and plant defense processes. The health and nutritional benefits of lignans are unquestionable, and many studies have been devoted to these attributes. Although the regulatory role of miRNAs in the biosynthesis of secondary metabolites has been widely reported, there is no systematic review available on the miRNA-based regulatory mechanism of lignans biosynthesis. However, the genetic background of lignan biosynthesis in plants is well characterized. We attempted to put together a regulatory mosaic based on current knowledge describing miRNA-mediated regulation of genes, enzymes, or transcription factors involved in this biosynthesis process. At the same time, we would like to underline the fact that further research is necessary to improve our understanding of the miRNAs regulating plant lignan biosynthesis by exploitation of current approaches for functional identification of miRNAs.
Collapse
|
14
|
Jiang L, Yue M, Liu Y, Ye Y, Zhang Y, Lin Y, Wang X, Chen Q, Tang H. Alterations of Phenylpropanoid Biosynthesis Lead to the Natural Formation of Pinkish-Skinned and White-Fleshed Strawberry (Fragaria × ananassa). Int J Mol Sci 2022; 23:ijms23137375. [PMID: 35806380 PMCID: PMC9267004 DOI: 10.3390/ijms23137375] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 12/20/2022] Open
Abstract
Anthocyanin content is important for both the external and internal fruit quality of cultivated strawberries, but the mechanism of its accumulation in pinkish-skinned and white-fleshed strawberries is puzzling. Here, we found that the factor determining variation in the flesh color was not the FaMYB10 but the FaC4H in the cultivated strawberry Benihoppe and its white-fleshed mutant Xiaobai. Compared with Benihoppe, there was no significant difference in the coding sequence and expression level of FaMYB10 in Xiaobai’s flesh. Instead, the transcription of FaC4H was dramatically inhibited. The combined analyses of transcriptomics and metabolomics showed that the differential genes and metabolites were significantly enriched in the phenylpropanoid biosynthesis pathway. Furthermore, the transient overexpression of FaC4H greatly restored anthocyanins’ accumulation in Xiaobai’s flesh and did not produce additional pigment species, as in Benihoppe. The transcriptional repression of FaC4H was not directly caused by promoter methylations, lncRNAs, or microRNAs. In addition, the unexpressed FaF3′H, which resulted in the loss of cyanidin 3-O-glucoside in the flesh, was not due to methylation in promoters. Our findings suggested that the repression of FaC4H was responsible for the natural formation of pinkish-skinned and white-fleshed strawberries.
Collapse
Affiliation(s)
- Leiyu Jiang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (L.J.); (M.Y.); (Y.L.); (Y.Y.); (X.W.)
| | - Maolan Yue
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (L.J.); (M.Y.); (Y.L.); (Y.Y.); (X.W.)
| | - Yongqiang Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (L.J.); (M.Y.); (Y.L.); (Y.Y.); (X.W.)
| | - Yuyun Ye
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (L.J.); (M.Y.); (Y.L.); (Y.Y.); (X.W.)
| | - Yunting Zhang
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.Z.); (Y.L.)
| | - Yuanxiu Lin
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.Z.); (Y.L.)
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (L.J.); (M.Y.); (Y.L.); (Y.Y.); (X.W.)
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.Z.); (Y.L.)
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (L.J.); (M.Y.); (Y.L.); (Y.Y.); (X.W.)
- Correspondence: (Q.C.); (H.T.); Tel.: +86-158-9268-5193 (Q.C.); +86-136-0826-4028 (H.T.)
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (L.J.); (M.Y.); (Y.L.); (Y.Y.); (X.W.)
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.Z.); (Y.L.)
- Correspondence: (Q.C.); (H.T.); Tel.: +86-158-9268-5193 (Q.C.); +86-136-0826-4028 (H.T.)
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Zhu WJ, Liu Y, Cao YN, Peng LX, Yan ZY, Zhao G. Insights into Health-Promoting Effects of Plant MicroRNAs: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:14372-14386. [PMID: 34813309 DOI: 10.1021/acs.jafc.1c04737] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Plant-derived microRNAs (miRNAs) play a significant role in human health and are "dark nutrients", as opposed to traditional plant nutrients, as well as important components of food diversification. Studies have revealed that multiple plant-derived miRNA pathways affect human health. First, plant miRNAs regulate plant growth and development and accumulation of metabolites, which alters the food quality and thus indirectly interferes with the health of the host. Moreover, when absorbed in vivo, some miRNAs may target the host cell mRNAs to affect protein expression. In addition, plant miRNAs target and reshape the human gut microbiota (GM), which interferes with the physiology and metabolism of the host. Therefore, miRNAs play a significant role in the cross-kingdom communication of plants, GM, and the host and in maintaining a balance of the three. Future contributions of plant miRNAs can bring new perspectives and opportunities to better understand food nutrition and health care research, which will facilitate the right exploitation of plant resources.
Collapse
Affiliation(s)
- Wen-Jing Zhu
- Key Laboratory of Coarse Cereal Processing of Ministry of Agriculture and Rural Affairs; Sichuan Province Engineering Technology Research Center of Coarse Cereal Industrialization, Chengdu University, Chengdu 610106, People's Republic of China
| | - Yu Liu
- Key Laboratory of Coarse Cereal Processing of Ministry of Agriculture and Rural Affairs; Sichuan Province Engineering Technology Research Center of Coarse Cereal Industrialization, Chengdu University, Chengdu 610106, People's Republic of China
| | - Ya-Nan Cao
- Key Laboratory of Coarse Cereal Processing of Ministry of Agriculture and Rural Affairs; Sichuan Province Engineering Technology Research Center of Coarse Cereal Industrialization, Chengdu University, Chengdu 610106, People's Republic of China
| | - Lian-Xin Peng
- Key Laboratory of Coarse Cereal Processing of Ministry of Agriculture and Rural Affairs; Sichuan Province Engineering Technology Research Center of Coarse Cereal Industrialization, Chengdu University, Chengdu 610106, People's Republic of China
| | - Zhu-Yun Yan
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Gang Zhao
- Key Laboratory of Coarse Cereal Processing of Ministry of Agriculture and Rural Affairs; Sichuan Province Engineering Technology Research Center of Coarse Cereal Industrialization, Chengdu University, Chengdu 610106, People's Republic of China
| |
Collapse
|
18
|
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.
Collapse
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.
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
The Multifunctional Roles of Polyphenols in Plant-Herbivore Interactions. Int J Mol Sci 2021; 22:ijms22031442. [PMID: 33535511 PMCID: PMC7867105 DOI: 10.3390/ijms22031442] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/24/2021] [Accepted: 01/26/2021] [Indexed: 12/26/2022] Open
Abstract
There is no argument to the fact that insect herbivores cause significant losses to plant productivity in both natural and agricultural ecosystems. To counter this continuous onslaught, plants have evolved a suite of direct and indirect, constitutive and induced, chemical and physical defenses, and secondary metabolites are a key group that facilitates these defenses. Polyphenols—widely distributed in flowering plants—are the major group of such biologically active secondary metabolites. Recent advances in analytical chemistry and metabolomics have provided an opportunity to dig deep into extraction and quantification of plant-based natural products with insecticidal/insect deterrent activity, a potential sustainable pest management strategy. However, we currently lack an updated review of their multifunctional roles in insect-plant interactions, especially focusing on their insect deterrent or antifeedant properties. This review focuses on the role of polyphenols in plant-insect interactions and plant defenses including their structure, induction, regulation, and their anti-feeding and toxicity effects. Details on mechanisms underlying these interactions and localization of these compounds are discussed in the context of insect-plant interactions, current findings, and potential avenues for future research in this area.
Collapse
|
21
|
Mohanty P, Ayachit G, Mohanty JN, Pandya H, Mankad AU, Das J. Documentation of conserved and novel miRNAs participated in plant secondary metabolic pathways of sanctified Aegle marmelos. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
22
|
Beedessee G, Kubota T, Arimoto A, Nishitsuji K, Waller RF, Hisata K, Yamasaki S, Satoh N, Kobayashi J, Shoguchi E. Integrated omics unveil the secondary metabolic landscape of a basal dinoflagellate. BMC Biol 2020; 18:139. [PMID: 33050904 PMCID: PMC7557087 DOI: 10.1186/s12915-020-00873-6] [Citation(s) in RCA: 10] [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: 06/02/2020] [Accepted: 09/18/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Some dinoflagellates cause harmful algal blooms, releasing toxic secondary metabolites, to the detriment of marine ecosystems and human health. Our understanding of dinoflagellate toxin biosynthesis has been hampered by their unusually large genomes. To overcome this challenge, for the first time, we sequenced the genome, microRNAs, and mRNA isoforms of a basal dinoflagellate, Amphidinium gibbosum, and employed an integrated omics approach to understand its secondary metabolite biosynthesis. RESULTS We assembled the ~ 6.4-Gb A. gibbosum genome, and by probing decoded dinoflagellate genomes and transcriptomes, we identified the non-ribosomal peptide synthetase adenylation domain as essential for generation of specialized metabolites. Upon starving the cells of phosphate and nitrogen, we observed pronounced shifts in metabolite biosynthesis, suggestive of post-transcriptional regulation by microRNAs. Using Iso-Seq and RNA-seq data, we found that alternative splicing and polycistronic expression generate different transcripts for secondary metabolism. CONCLUSIONS Our genomic findings suggest intricate integration of various metabolic enzymes that function iteratively to synthesize metabolites, providing mechanistic insights into how dinoflagellates synthesize secondary metabolites, depending upon nutrient availability. This study provides insights into toxin production associated with dinoflagellate blooms. The genome of this basal dinoflagellate provides important clues about dinoflagellate evolution and overcomes the large genome size, which has been a challenge previously.
Collapse
Affiliation(s)
- Girish Beedessee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
- Present address: Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.
| | - Takaaki Kubota
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo, 194-8543, Japan
| | - Asuka Arimoto
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
- Marine Biological Laboratory, Graduate School of Integrated Sciences for Life, Hiroshima University, Onomichi, Hiroshima, 722-0073, Japan
| | - Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Shinichi Yamasaki
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Jun'ichi Kobayashi
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| |
Collapse
|
23
|
Azaman SNA, Satharasinghe DA, Tan SW, Nagao N, Yusoff FM, Yeap SK. Identification and Analysis of microRNAs in Chlorella sorokiniana Using High-Throughput Sequencing. Genes (Basel) 2020; 11:genes11101131. [PMID: 32992970 PMCID: PMC7599482 DOI: 10.3390/genes11101131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 08/29/2020] [Accepted: 09/09/2020] [Indexed: 12/24/2022] Open
Abstract
Chlorella is a popular microalga with robust physiological and biochemical characteristics, which can be cultured under various conditions. The exploration of the small RNA content of Chlorella could improve strategies for the enhancement of metabolite production from this microalga. In this study, stress was introduced to the Chlorella sorokiniana culture to produce high-value metabolites such as carotenoids and phenolic content. The small RNA transcriptome of C. sorokiniana was sequenced, focusing on microRNA (miRNA) content. From the analysis, 98 miRNAs were identified in cultures subjected to normal and stress conditions. The functional analysis result showed that the miRNA targets found were most often involved in the biosynthesis of secondary metabolites, followed by protein metabolism, cell cycle, and porphyrin and chlorophyll metabolism. Furthermore, the biosynthesis of secondary metabolites such as carotenoids, terpenoids, and lipids was found mostly in stress conditions. These results may help to improve our understanding of regulatory mechanisms of miRNA in the biological and metabolic process of Chlorella species. It is important and timely to determine the true potential of this microalga species and to support the potential for genetic engineering of microalgae as they receive increasing focus for their development as an alternative source of biofuel, food, and health supplements.
Collapse
Affiliation(s)
- Siti Nor Ani Azaman
- Centre of Foundation Studies for Agricultural Science, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
- Aquatic Animal Health and Therapeutics Laboratory (AquaHealth), Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Dilan Amila Satharasinghe
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine and Animal Science University of Peradeniya, Peradeniya 20400, Sri Lanka;
| | - Sheau Wei Tan
- Laboratory of Vaccine and Biomolecules (VacBio), Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
| | - Norio Nagao
- 102 Naname-go, Shinkamigoto-cho, Minami Matsuura-gun, Nagasaki 857-4214, Japan;
| | - Fatimah M. Yusoff
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia;
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, 43900 Selangor, Malaysia
- Correspondence:
| |
Collapse
|
24
|
Martins TF, Souza PFN, Alves MS, Silva FDA, Arantes MR, Vasconcelos IM, Oliveira JTA. Identification, characterization, and expression analysis of cowpea (Vigna unguiculata [L.] Walp.) miRNAs in response to cowpea severe mosaic virus (CPSMV) challenge. PLANT CELL REPORTS 2020; 39:1061-1078. [PMID: 32388590 DOI: 10.1007/s00299-020-02548-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/04/2020] [Accepted: 04/25/2020] [Indexed: 06/11/2023]
Abstract
Cowpea miRNAs and Argonaute genes showed differential expression patterns in response to CPSMV challenge Several biotic stresses affect cowpea production and yield. CPSMV stands out for causing severe negative impacts on cowpea. Plants have two main induced immune systems. In the basal system (PTI, PAMP-triggered immunity), plants recognize and respond to conserved molecular patterns associated with pathogens (PAMPs). The second type (ETI, Effector-triggered immunity) is induced after plant recognition of specific factors from pathogens. RNA silencing is another important defense mechanism in plants. Our research group has been using biochemical and proteomic approaches to learn which proteins and pathways are involved and could explain why some cowpea genotypes are resistant whereas others are susceptible to CPSMV. This current study was conducted to determine the role of cowpea miRNA in the interaction between a resistant cowpea genotype (BRS-Marataoã) and CPSMV. Previously identified and deposited plant microRNA sequences were used to find out all possible microRNAs in the cowpea genome. This search detected 617 mature microRNAs, which were distributed in 89 microRNA families. Next, 4 out of these 617 miRNAs and their possible target genes that encode the proteins Kat-p80, DEAD-Box, GST, and SPB9, all involved in the defense response of cowpea to CPSMV, had their expression compared between cowpea leaves uninoculated and inoculated with CPSMV. Additionally, the differential expression of genes that encode the Argonaute (AGO) proteins 1, 2, 4, 6, and 10 is reported. In summary, the studied miRNAs and AGO 2 and AGO4 associated genes showed differential expression patterns in response to CPSMV challenge, which indicate their role in cowpea defense.
Collapse
Affiliation(s)
- Thiago F Martins
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE, Brazil
| | - Pedro F N Souza
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE, Brazil
| | - Murilo S Alves
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE, Brazil
| | - Fredy Davi A Silva
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE, Brazil
| | - Mariana R Arantes
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE, Brazil
| | - Ilka M Vasconcelos
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE, Brazil
| | - Jose T A Oliveira
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE, Brazil.
| |
Collapse
|
25
|
Kajal M, Kaushal N, Kaur R, Singh K. Identification of novel microRNAs and their targets in Chlorophytum borivilianum by small RNA and degradome sequencing. Noncoding RNA Res 2020; 4:141-154. [PMID: 32072082 PMCID: PMC7012778 DOI: 10.1016/j.ncrna.2019.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/20/2019] [Accepted: 11/21/2019] [Indexed: 11/04/2022] Open
Abstract
Plant specific miRNAs (Novel miRNAs) are well known to perform distinctive functions in biological processes. Identification of new miRNAs is necessary to understand their gene regulation. Degradome provides an opportunity to explore the miRNA functions by comparing the miRNA population and their degraded products. In the present study, Small RNA sequencing data was used to identify novel miRNAs. Further, degradome sequencing was carried out to identify miRNAs targets in the plant, Chlorophytum borivilianum. The present study supplemented 40 more novel miRNAs correlating degradome data with smallRNAome. Novel miRNAs, complementary to mRNA partial sequences obtained from degradome sequencing were actually targeting the later. A big pool of miRNA was established by using Oryza sativa, Arabidopsis thaliana, Populus trichocarpa, Ricinus communis, and Vitis vinifera genomic data. Targets were identified for novel miRNAs and total 109 targets were predicted. BLAST2GO analysis elaborate about localization of novel miRNAs’ targets and their corresponding KEGG (Kyoto Encyclopedia for Genes and Genomes) pathways. Identified targets were annotated and were found to be involved in significant biological processes like Nitrogen metabolism, Pyruvate metabolism, Citrate cycle (TCA cycle), photosynthesis, and Glycolysis/Gluconeogenesis. The present study provides an overall view of the miRNA regulation in multiple metabolic pathways that are involved in plant growth, pathogen resistance and secondary metabolism of C. borivilianum.
Collapse
Key Words
- AGO, Argonaute
- BLAST, Basic local Alignment Search Tool
- BP, Biological Process
- CC, Cellular Component
- Chlorophytum borivilianum
- Degradome
- FAO, Food and Agriculture Organization of the United Nations
- GO, Gene Ontology
- IL, Interleukin
- Illumina sequencing
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MCF-7, PC3, HCT-116, Types of cell lines
- MEP, 2-C-methyl-Derythritol-4-phosphate pathway
- MF, Molecular Function
- MFEs, Minimum Fold Energies
- MTT, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide
- MVA, Mevalonic Acid Pathway
- RdDM, RNA-directed DNA methylation
- SRA
- SRA, Sequencing Read Archieve
- TNF, Tumor Necrosis Factor
- iNOS, Inducible Nitric Oxide Synthase
- mgmL−1, milligram per millilitre
- microRNAs
- nt, nucleotide
Collapse
Affiliation(s)
- Monika Kajal
- Department of Biotechnology, Panjab University, BMS Block-I, Sector 25, Chandigarh, 160014, India
| | - Nishant Kaushal
- Department of Biotechnology, Panjab University, BMS Block-I, Sector 25, Chandigarh, 160014, India
| | - Ravneet Kaur
- Department of Biotechnology, Panjab University, BMS Block-I, Sector 25, Chandigarh, 160014, India
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, BMS Block-I, Sector 25, Chandigarh, 160014, India
| |
Collapse
|
26
|
Galdino JH, Eguiluz M, Guzman F, Margis R. Novel and Conserved miRNAs Among Brazilian Pine and Other Gymnosperms. Front Genet 2019; 10:222. [PMID: 30984236 PMCID: PMC6448024 DOI: 10.3389/fgene.2019.00222] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/28/2019] [Indexed: 01/01/2023] Open
Abstract
The knowledge about plant miRNAs has increased exponentially, with thousands of miRNAs been reported in different plant taxa using high throughput sequencing technologies and bioinformatic tools. Nevertheless, several groups of plants remain unexplored, and the gap of knowledge about conifer miRNAs is considerable. There is no sequence or functional information available on miRNAs in Araucariaceae. This group is represented in Brazil by only one species, Araucaria angustifolia, an endangered species known as Brazilian pine. In the present study, Brazilian pine has its transcriptome explored with respect to small RNAs, representing the first description in a member of the Araucariaceae family. The screening for conserved miRNAs in Brazilian pine revealed 115 sequences of 30 miRNA families. A total of 106 precursors sequences were predicted. Forty one comprised conserved miRNAs from 16 families, whereas 65 were annotated as novel miRNAs. The comparison of Brazilian pine precursors with sRNA libraries of other five conifer species indicates that 9 out 65 novel miRNAs are conserved among gymnosperms, while 56 seems to be specific for Brazilian pine or restricted to Araucariaceae family. Analysis comparing novel Brazilian pine miRNAs precursors and Araucaria cunninghamii RNA-seq data identified seven orthologs between both species. Mature miRNA identified by bioinformatics predictions were validated using stem-loop RT-qPCR assays. The expression pattern of conserved and novel miRNAs was analyzed in five different tissues of 3-month-old Araucaria seedlings. The present study provides insights about the nature and composition of miRNAs in an Araucariaceae species, with valuable information on miRNAs diversity and conservation in this taxon.
Collapse
Affiliation(s)
- José Henrique Galdino
- Programa de Pós-graduação e Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Maria Eguiluz
- Programa de Pós-graduação e Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Frank Guzman
- Programa de Pós-graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Rogerio Margis
- Programa de Pós-graduação e Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
- Programa de Pós-graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
- Departamento de Biofísica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| |
Collapse
|
27
|
Lin Y, Jiang L, Chen Q, Li Y, Zhang Y, Luo Y, Zhang Y, Sun B, Wang X, Tang H. Comparative Transcriptome Profiling Analysis of Red- and White-Fleshed Strawberry (Fragaria�ananassa) Provides New Insight into the Regulation of the Anthocyanin Pathway. PLANT & CELL PHYSIOLOGY 2018; 59:1844-1859. [PMID: 29800352 DOI: 10.1093/pcp/pcy098] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 05/14/2018] [Indexed: 05/07/2023]
Abstract
Anthocyanins are water-soluble pigments in plants. They confer both economic and healthy profits for humans. To gain a deeper insight into the regulation of anthocyanin biosynthesis in octoploid strawberry (Fragaria�ananassa; Fa), a widely consumed economically important fruit, we performed comparative transcriptomic analysis of red- and white-fleshed strawberry cultivars in two ripening stages. In total, 365,455 non-redundant transcripts were assembled from the RNA sequencing (RNAseq) data. Of this collection, 377 were annotated as putative anthocyanin-related transcripts. Differential expression analysis revealed that 57 anthocyanin biosynthesis transcripts were down-regulated, and 89 transcription factors (TFs) were either down- or up-regulated under anthocyanin deficiency. Additionally, amongst the 50,601 putative long non-coding RNAs (lncRNAs) identified here, 68 lncRNAs were differentially expressed and co-expressed with differentially expressed anthocyanin-related mRNAs; 2,070 co-expressing lncRNA-mRNA pairs were generated. Expression profile analysis revealed that it was the limited expression of FaF3'H (flavonoid 3'-hydroxylase) that blocked the cyanidin 3-glucoside accumulation in the two investigated strawberry cultivars. This was further supported by a transient overexpression experiment with FaMYB10. The down-regulated lncRNAs might participate in anthocyanin regulation by acting as targets for microRNAs (miRNAs). The level of competitive intensity in miRNA and lncRNA for the same mRNA targets was probably lower in the white-fleshed strawberries, which can release the repression effect of the mRNAs in red-fleshed strawberry as a result. This study for the first time presents lncRNAs related to anthocyanins in strawberries, provides new insights into the anthocyanin regulatory network and also lays the foundation for identifying new anthocyanin regulators in strawberry.
Collapse
Affiliation(s)
- Yuanxiu Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Leiyu Jiang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yali Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yunting Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bo Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| |
Collapse
|
28
|
Cao A, Jin J, Li S, Wang J. Integrated analysis of mRNA and miRNA expression profiling in rice backcrossed progenies (BC2F12) with different plant height. PLoS One 2017; 12:e0184106. [PMID: 28859136 PMCID: PMC5578646 DOI: 10.1371/journal.pone.0184106] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 08/17/2017] [Indexed: 11/18/2022] Open
Abstract
Inter-specific hybridization and backcrossing commonly occur in plants. The use of progeny generated from inter-specific hybridization and backcrossing has been developed as a novel model system to explore gene expression divergence. The present study investigated the analysis of gene expression and miRNA regulation in backcrossed introgression lines constructed from cultivated and wild rice. High-throughput sequencing was used to compare gene and miRNA expression profiles in three progeny lines (L1710, L1817 and L1730), with different plant heights resulting from the backcrossing of introgression lines (BC2F12) and their parents (O. sativa and O. longistaminata). A total of 25,387 to 26,139 mRNAs and 379 to 419 miRNAs were obtained in these rice lines. More differentially expressed genes and miRNAs were detected in progeny/O. longistaminata comparison groups than in progeny/O. sativa comparison groups. Approximately 80% of the genes and miRNAs showed expression level dominance to O. sativa, indicating that three progeny lines were closer to the recurrent parent, which might be influenced by their parental genome dosage. Approximately 16% to 64% of the differentially expressed miRNAs possessing coherent target genes were predicted, and many of these miRNAs regulated multiple target genes. Most genes were up-regulated in progeny lines compared with their parents, but down-regulated in the higher plant height line in the comparison groups among the three progeny lines. Moreover, certain genes related to cell walls and plant hormones might play crucial roles in the plant height variations of the three progeny lines. Taken together, these results provided valuable information on the molecular mechanisms of hybrid backcrossing and plant height variations based on the gene and miRNA expression levels in the three progeny lines.
Collapse
Affiliation(s)
- Aqin Cao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jie Jin
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail:
| |
Collapse
|
29
|
Hazra A, Dasgupta N, Sengupta C, Das S. Extrapolative microRNA precursor based SSR mining from tea EST database in respect to agronomic traits. BMC Res Notes 2017; 10:261. [PMID: 28683768 PMCID: PMC5501407 DOI: 10.1186/s13104-017-2577-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/28/2017] [Indexed: 11/10/2022] Open
Abstract
Tea (Camellia sinensis, (L.) Kuntze) is considered as most popular drink across the world and it is widely consumed beverage for its several health-benefit characteristics. These positive traits primarily rely on its regulatory networks of different metabolic pathways. Development of microsatellite markers from the conserved genomic regions are being worthwhile for reviewing the genetic diversity of closely related species or self-pollinated species. Although several SSR markers have been reported, in tea, the trait-specific Simple Sequence Repeat (SSR) markers, leading to be useful in marker assisted breeding technique, are yet to be identified. Micro RNAs are short, non-coding RNA molecules, involved in post transcriptional mode of gene regulation and thus effects on related phenotype. Present study deals with identification of the microsatellite motifs within the reported and predicted miRNA precursors that are effectively followed by designing of primers from SSR flanking regions in order to PCR validation. In addition to the earlier reports, two new miRNAs are predicting here from tea expressed tag sequence database. Furthermore, 18 SSR motifs are found to be in 13 of all 33 predicted miRNAs. Trinucleotide motifs are most abundant among all followed by dinucleotides. Since, miRNA based SSR markers are evidenced to have significant role on genetic fingerprinting study, these outcomes would pave the way in developing novel markers for tagging tea specific agronomic traits as well as substantiating non-conventional breeding program.
Collapse
Affiliation(s)
- Anjan Hazra
- Agricultural and Ecological Research Unit, Indian Statistical Institute, 203, Barrackpore Trunk Road, Kolkata, 700 108, India.,Department of Botany, University of Kalyani, Nadia, Kalyani, 741235, India
| | - Nirjhar Dasgupta
- Agricultural and Ecological Research Unit, Indian Statistical Institute, 203, Barrackpore Trunk Road, Kolkata, 700 108, India
| | - Chandan Sengupta
- Department of Botany, University of Kalyani, Nadia, Kalyani, 741235, India
| | - Sauren Das
- Agricultural and Ecological Research Unit, Indian Statistical Institute, 203, Barrackpore Trunk Road, Kolkata, 700 108, India.
| |
Collapse
|
30
|
Gupta OP, Karkute SG, Banerjee S, Meena NL, Dahuja A. Contemporary Understanding of miRNA-Based Regulation of Secondary Metabolites Biosynthesis in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:374. [PMID: 28424705 PMCID: PMC5372812 DOI: 10.3389/fpls.2017.00374] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/03/2017] [Indexed: 05/20/2023]
Abstract
Plant's secondary metabolites such as flavonoids, terpenoids, and alkaloids etc. are known for their role in the defense against various insects-pests of plants and for medicinal benefits in human. Due to the immense biological importance of these phytochemicals, understanding the regulation of their biosynthetic pathway is crucial. In the recent past, advancement in the molecular technologies has enabled us to better understand the proteins, enzymes, genes, etc. involved in the biosynthetic pathway of the secondary metabolites. miRNAs are magical, tiny, non-coding ribonucleotides that function as critical regulators of gene expression in eukaryotes. Despite the accumulated knowledge of the miRNA-mediated regulation of several processes, the involvement of miRNAs in regulating secondary plant product biosynthesis is still poorly understood. Here, we summarize the recent progress made in the area of identification and characterizations of miRNAs involved in regulating the biosynthesis of secondary metabolites in plants and discuss the future perspectives for designing the viable strategies for their targeted manipulation.
Collapse
Affiliation(s)
- Om P. Gupta
- Division of Quality and Basic Sciences, ICAR-Indian Institute of Wheat and Barley ResearchKarnal, India
- *Correspondence: Om P. Gupta
| | - Suhas G. Karkute
- Division of Vegetable Improvement, ICAR-Indian Institute of Vegetable ResearchVaranasi, India
| | - Sagar Banerjee
- Division of Biochemistry, ICAR-Indian Agricultural Research InstituteNew Delhi, India
| | - Nand L. Meena
- Division of Basic Sciences, ICAR-Indian Institute of Millets ResearchHyderabad, India
| | - Anil Dahuja
- Division of Biochemistry, ICAR-Indian Agricultural Research InstituteNew Delhi, India
| |
Collapse
|
31
|
Hazra S, Bhattacharyya D, Chattopadhyay S. Methyl Jasmonate Regulates Podophyllotoxin Accumulation in Podophyllum hexandrum by Altering the ROS-Responsive Podophyllotoxin Pathway Gene Expression Additionally through the Down Regulation of Few Interfering miRNAs. FRONTIERS IN PLANT SCIENCE 2017; 8:164. [PMID: 28261233 PMCID: PMC5306198 DOI: 10.3389/fpls.2017.00164] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/26/2017] [Indexed: 05/04/2023]
Abstract
Podophylloxin (ptox), primarily obtained from Podophyllum hexandrum, is the precursor for semi-synthetic anticancer drugs viz. etoposide, etopophos, and teniposide. Previous studies established that methyl jasmonate (MeJA) treated cell culture of P. hexandrum accumulate ptox significantly. However, the molecular mechanism of MeJA induced ptox accumulation is yet to be explored. Here, we demonstrate that MeJA induces reactive oxygen species (ROS) production, which stimulates ptox accumulation significantly and up regulates three ROS-responsive ptox biosynthetic genes, namely, PhCAD3, PhCAD4 (cinnamyl alcohol dehydrogenase), and NAC3 by increasing their mRNA stability. Classic uncoupler of oxidative phosphorylation, carbonylcyanide m-chlorophenylhydrazone, as well as H2O2 treatment induced the ROS generation and consequently, enhanced the ptox production. However, when the ROS was inhibited with NADPH oxidase inhibitor diphenylene iodonium and Superoxide dismutase inhibitor diethyldithio-carbamic acid, the ROS inhibiting agent, the ptox production was decreased significantly. We also noted that, MeJA up regulated other ptox biosynthetic pathway genes which are not affected by the MeJA induced ROS. Further, these ROS non-responsive genes were controlled by MeJA through the down regulation of five secondary metabolites biosynthesis specific miRNAs viz. miR172i, miR035, miR1438, miR2275, and miR8291. Finally, this study suggested two possible mechanisms through which MeJA modulates the ptox biosynthesis: primarily by increasing the mRNA stability of ROS-responsive genes and secondly, by the up regulation of ROS non-responsive genes through the down regulation of some ROS non-responsive miRNAs.
Collapse
|