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Li H, Guo Z, Xu M, Zhao J, Xu D. Molecular mechanism of miRNA mediated biosynthesis of secondary metabolites in medicinal plants. Plant Physiol Biochem 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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 02/28/2024] [Accepted: 03/10/2024] [Indexed: 03/24/2024]
Abstract
Plant secondary metabolites are important raw materials for the pharmaceutical industry, and their biosynthetic processes are subject to diverse and precise regulation by miRNA. The identification of miRNA molecules in medicinal plants and exploration of their mechanisms not only contribute to a deeper understanding of the molecular genetic mechanisms of plant growth, development and resistance to stress, but also provide a theoretical basis for elucidating the pharmacological effects of authentic medicinal materials and constructing bioreactors for the synthesis of medicinal secondary metabolite components. This paper summarizes the research reports on the discovery of miRNA in medicinal plants and their regulatory mechanisms on the synthesis of secondary metabolites by searching the relevant literature in public databases. It summarizes the currently discovered miRNA and their functions in medicinal plants, and summarizes the molecular mechanisms regulating the synthesis and degradation of secondary metabolites. Furthermore, it provides a prospect for the research and development of medicinal plant miRNA. The compiled information contributes to a comprehensive understanding of the research progress on miRNA in medicinal plants and provides a reference for the industrial development of related secondary metabolite biosynthesis.
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Affiliation(s)
- Hongwei Li
- Department of Cell Biology, Zunyi Medical University, No.6 Xuefuxi Road, Xinpu District, Zunyi City, Guizhou Province, 563099, China
| | - Ziyi Guo
- Department of Cell Biology, Zunyi Medical University, No.6 Xuefuxi Road, Xinpu District, Zunyi City, Guizhou Province, 563099, China
| | - Mengwei Xu
- Department of Cell Biology, Zunyi Medical University, No.6 Xuefuxi Road, Xinpu District, Zunyi City, Guizhou Province, 563099, China
| | - Juanjuan Zhao
- Department of Immunology, Zunyi Medical University, No.6 Xuefuxi Road, Xinpu District, Zunyi City, Guizhou Province, 563099, China.
| | - Delin Xu
- Department of Cell Biology, Zunyi Medical University, No.6 Xuefuxi Road, Xinpu District, Zunyi City, Guizhou Province, 563099, China; Department of Medical Instrumental Analysis, Zunyi Medical University, No.6 Xuefuxi Road, Xinpu District, Zunyi City, Guizhou Province, 563099, China.
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Lian C, Zhang F, Yang H, Zhang X, Lan J, Zhang B, Liu X, Yang J, Chen S. Multi-omics analysis of small RNA, transcriptome, and degradome to identify putative miRNAs linked to MeJA regulated and oridonin biosynthesis in Isodon rubescens. Int J Biol Macromol 2024; 258:129123. [PMID: 38163496 DOI: 10.1016/j.ijbiomac.2023.129123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/13/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
Isodon rubescens has garnered much attention due to its anti-tumor or anti-cancer properties. However, little is known about the molecular mechanism of oridonin biosynthesis leveraging the regulatory network between small RNAs and mRNAs. In this study, the regulatory networks of miRNAs and targets were examined by combining mRNA, miRNA, and degradome. A total of 348 miRNAs, including 287 known miRNAs and 61 novel miRNAs, were identified. Among them, 51 miRNAs were significantly expressed, and 36 miRNAs responded to MeJA. A total of 3066 target genes were associated with 228 miRNAs via degradome sequencing. Multi-omics analysis demonstrated that 27 miRNA-mRNA pairs were speculated to be involved in MeJA regulation, and 36 miRNA-mRNA pairs were hypothesized to be involved in the genotype-dependence of I. rubescens. Furthermore, 151 and 7 miRNA-mRNA modules were likely engaged in oridonin biosynthesis as identified by psRNATarget and degradome sequencing, respectively. Some miRNA-mRNA modules were confirmed via RT-qPCR. Moreover, miRNAs targeting plant hormone signal transduction pathway genes were identified, such as miR156, miR167, miR393, and PC-3p-19822_242. Collectively, our results demonstrate for the first time that miRNAs are identified in I. rubescens, and laid a solid foundation for further research on the molecular mechanism of oridonin biosynthesis mediated by miRNA.
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Affiliation(s)
- Conglong Lian
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China; Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China
| | - Fei Zhang
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China; Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China
| | - Hao Yang
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China; Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China
| | - Xueyu Zhang
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China; Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China
| | - Jinxu Lan
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China; Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China
| | - Bao Zhang
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China; Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China
| | - Xiuyu Liu
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China; Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China
| | - Jingfan Yang
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China; Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China
| | - Suiqing Chen
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China; Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China.
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Xu P, Li Q, Liang W, Hu Y, Chen R, Lou K, Zhan L, Wu X, Pu J. A tissue-specific profile of miRNAs and their targets related to paeoniaflorin and monoterpenoids biosynthesis in Paeonia lactiflora Pall. by transcriptome, small RNAs and degradome sequencing. PLoS One 2023; 18:e0279992. [PMID: 36701382 PMCID: PMC9879538 DOI: 10.1371/journal.pone.0279992] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 12/19/2022] [Indexed: 01/27/2023] Open
Abstract
Paeonia lactiflora Pall. (Paeonia) has aroused many concerns due to its extensive medicinal value, in which monoterpene glucoside paeoniflorin and its derivatives are the active chemical components. However, little is known in the molecular mechanism of monoterpenoids biosynthesis, and the regulation network between small RNAs and mRNAs in monoterpenoids biosynthesis has not been investigated yet. Herein, we attempted to reveal the tissue-specific regulation network of miRNAs and their targets related to paeoniaflorin and monoterpenoids biosynthesis in Paeonia by combining mRNA and miRNA expression data with degradome analysis. In all, 289 miRNAs and 30177 unigenes were identified, of which nine miRNAs from seven miRNA families including miR396, miR393, miR835, miR1144, miR3638, miR5794 and miR9555 were verified as monoterpenoids biosynthesis-related miRNAs by degradome sequencing. Moreover, the co-expression network analysis showed that four monoterpenoids-regulating TFs, namely AP2, MYBC1, SPL12 and TCP2, were putatively regulated by five miRNAs including miR172, miR828, miR858, miR156 and miR319, respectively. The present study will improve our knowledge of the molecular mechanisms of the paeoniaflorin and monoterpenoids biosynthesis mediated by miRNA to a new level, and provide a valuable resource for further study on Paeonia.
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Affiliation(s)
- Pan Xu
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Quanqing Li
- Department of Pharmacy, Zhejiang Xiaoshan Hospital, Hangzhou, Zhejiang Province, China
| | - Weiqing Liang
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Yijuan Hu
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Rubing Chen
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Kelang Lou
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Lianghui Zhan
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Xiaojun Wu
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Jinbao Pu
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
- * E-mail:
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Wang XD, Xu CY, Zheng YJ, Wu YF, Zhang YT, Zhang T, Xiong ZY, Yang HK, Li J, Fu C, Qiu FY, Dai XY, Liu XL, He XS, Zhou SS, Li SX, Fu T, Xie H, Chen YL, Zhang QQ, Wang HQ, Wang YD, Zhou C, Jiang XM. Chromosome-level genome assembly and resequencing of camphor tree ( Cinnamomum camphora) provides insight into phylogeny and diversification of terpenoid and triglyceride biosynthesis of Cinnamomum. Hortic Res 2022; 9:uhac216. [PMID: 36479586 PMCID: PMC9720445 DOI: 10.1093/hr/uhac216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 09/15/2022] [Indexed: 06/17/2023]
Abstract
Cinnamomum species attract attentions owing to their scents, medicinal properties, and ambiguous relationship in the phylogenetic tree. Here, we report a high-quality genome assembly of Cinnamomum camphora, based on which two whole-genome duplication (WGD) events were detected in the C. camphora genome: one was shared with Magnoliales, and the other was unique to Lauraceae. Phylogenetic analyses illustrated that Lauraceae species formed a compact sister clade to the eudicots. We then performed whole-genome resequencing on 24 Cinnamomum species native to China, and the results showed that the topology of Cinnamomum species was not entirely consistent with morphological classification. The rise and molecular basis of chemodiversity in Cinnamomum were also fascinating issues. In this study, six chemotypes were classified and six main terpenoids were identified as major contributors of chemodiversity in C. camphora by the principal component analysis. Through in vitro assays and subcellular localization analyses, we identified two key terpene synthase (TPS) genes (CcTPS16 and CcTPS54), the products of which were characterized to catalyze the biosynthesis of two uppermost volatiles (i.e. 1,8-cineole and (iso)nerolidol), respectively, and meditate the generation of two chemotypes by transcriptional regulation and compartmentalization. Additionally, the pathway of medium-chain triglyceride (MCT) biosynthesis in Lauraceae was investigated for the first time. Synteny analysis suggested that the divergent synthesis of MCT and long-chain triglyceride (LCT) in Lauraceae kernels was probably controlled by specific medium-chain fatty acyl-ACP thioesterase (FatB), type-B lysophosphatidic acid acyltransferase (type-B LPAAT), and diacylglycerol acyltransferase 2b (DGAT 2b) isoforms during co-evolution with retentions or deletions in the genome.
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Affiliation(s)
| | | | | | | | - Yue-Ting Zhang
- Camphor Engineering and Technology Research Center of National Forestry and Grassland Administration, Jiangxi Academy of Forestry, Nanchang 330032, China
- Jiangxi Provincial Key Lab for Plant Biotechnology, Jiangxi Academy of Forestry, Nanchang 330032, Jiangxi, China
| | - Ting Zhang
- Camphor Engineering and Technology Research Center of National Forestry and Grassland Administration, Jiangxi Academy of Forestry, Nanchang 330032, China
| | - Zhen-Yu Xiong
- Jiangxi Provincial Key Lab for Plant Biotechnology, Jiangxi Academy of Forestry, Nanchang 330032, Jiangxi, China
| | - Hai-Kuan Yang
- Camphor Engineering and Technology Research Center of National Forestry and Grassland Administration, Jiangxi Academy of Forestry, Nanchang 330032, China
| | - Jiang Li
- Camphor Engineering and Technology Research Center of National Forestry and Grassland Administration, Jiangxi Academy of Forestry, Nanchang 330032, China
| | - Chao Fu
- Camphor Engineering and Technology Research Center of National Forestry and Grassland Administration, Jiangxi Academy of Forestry, Nanchang 330032, China
| | - Feng-Ying Qiu
- Camphor Engineering and Technology Research Center of National Forestry and Grassland Administration, Jiangxi Academy of Forestry, Nanchang 330032, China
| | - Xiao-Ying Dai
- Camphor Engineering and Technology Research Center of National Forestry and Grassland Administration, Jiangxi Academy of Forestry, Nanchang 330032, China
| | - Xin-Liang Liu
- Camphor Engineering and Technology Research Center of National Forestry and Grassland Administration, Jiangxi Academy of Forestry, Nanchang 330032, China
| | - Xiao-San He
- Camphor Engineering and Technology Research Center of National Forestry and Grassland Administration, Jiangxi Academy of Forestry, Nanchang 330032, China
| | - Song-Song Zhou
- Camphor Engineering and Technology Research Center of National Forestry and Grassland Administration, Jiangxi Academy of Forestry, Nanchang 330032, China
| | - Sheng-Xing Li
- Camphor Engineering and Technology Research Center of National Forestry and Grassland Administration, Jiangxi Academy of Forestry, Nanchang 330032, China
| | - Tao Fu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Han Xie
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | | | | | - Hong-Qi Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
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Sun M, Xu S, Mei Y, Li J, Gu Y, Zhang W, Wang J. MicroRNAs in Medicinal Plants. Int J Mol Sci 2022; 23:10477. [PMID: 36142389 DOI: 10.3390/ijms231810477] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Medicinal plant microRNAs (miRNAs) are an endogenous class of small RNA central to the posttranscriptional regulation of gene expression. Biosynthetic research has shown that the mature miRNAs in medicinal plants can be produced from either the standard messenger RNA splicing mechanism or the pre-ribosomal RNA splicing process. The medicinal plant miRNA function is separated into two levels: (1) the cross-kingdom level, which is the regulation of disease-related genes in animal cells by oral intake, and (2) the intra-kingdom level, which is the participation of metabolism, development, and stress adaptation in homologous or heterologous plants. Increasing research continues to enrich the biosynthesis and function of medicinal plant miRNAs. In this review, peer-reviewed papers on medicinal plant miRNAs published on the Web of Science were discussed, covering a total of 78 species. The feasibility of the emerging role of medicinal plant miRNAs in regulating animal gene function was critically evaluated. Staged progress in intra-kingdom miRNA research has only been found in a few medicinal plants, which may be mainly inhibited by their long growth cycle, high demand for growth environment, immature genetic transformation, and difficult RNA extraction. The present review clarifies the research significance, opportunities, and challenges of medicinal plant miRNAs in drug development and agricultural production. The discussion of the latest results furthers the understanding of medicinal plant miRNAs and helps the rational design of the corresponding miRNA/target genes functional modules.
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Jeena GS, Singh N, Shukla RK. An insight into microRNA biogenesis and its regulatory role in plant secondary metabolism. Plant Cell Rep 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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Zhang L, Zhang X, Begum N, Xia P, Liu J, Liang Z. Effects of Different Processing Methods Based on Different Drying Conditions on the Active Ingredients of Salvia miltiorrhiza Bunge. Molecules 2022; 27:4860. [PMID: 35956808 PMCID: PMC9369592 DOI: 10.3390/molecules27154860] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 11/18/2022] Open
Abstract
Compared to the traditional processing method, fresh processing can significantly enhance the preservation of biologically active ingredients and reduce processing time. This study evaluated the influences of fresh and traditional processing based on different drying conditions (sun drying, oven drying and shade drying) on the active ingredients in the roots and rhizomes of S. miltiorrhiza. High-performance liquid chromatography (HPLC) was utilized to determine the contents of six active ingredients in the roots and rhizomes of S. miltiorrhiza. The data were analyzed by fingerprint similarity evaluation, hierarchical cluster analysis (HCA) and principal component analysis (PCA). The results suggest that compared to the traditional processing method, the fresh processing method may significantly increase the preservation of biologically active ingredients. Furthermore, the findings demonstrated that among the three drying methods under fresh processing conditions, the shade-drying (21.02–26.38%) method is most beneficial for retaining the active ingredients in the roots and rhizomes of S. miltiorrhiza. Moreover, the fingerprint analysis identified 17 common peaks, and the similarity of fingerprints among samples processed by different methods ranged from 0.989 to 1.000. Collectively, these results suggest novel processing methods that may improve the yield of active ingredients for S. miltiorrhiza and may be implemented for industrial production.
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Majewska M, Kuźma Ł, Szymczyk P. Isolation and Comprehensive in Silico Characterisation of a New 3-Hydroxy-3-Methylglutaryl-Coenzyme A Reductase 4 (HMGR4) Gene Promoter from Salvia miltiorrhiza: Comparative Analyses of Plant HMGR Promoters. Plants 2022; 11:1861. [PMID: 35890495 PMCID: PMC9318348 DOI: 10.3390/plants11141861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/29/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022]
Abstract
Salvia miltiorrhiza synthesises tanshinones with multidirectional therapeutic effects. These compounds have a complex biosynthetic pathway, whose first rate limiting enzyme is 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR). In the present study, a new 1646 bp fragment of the S. miltiorrhiza HMGR4 gene consisting of a promoter, 5′ untranslated region and part of a coding sequence was isolated and characterised in silico using bioinformatics tools. The results indicate the presence of a TATA box, tandem repeat and pyrimidine-rich sequence, and the absence of CpG islands. The sequence was rich in motifs recognised by specific transcription factors sensitive mainly to light, salicylic acid, bacterial infection and auxins; it also demonstrated many binding sites for microRNAs. Moreover, our results suggest that HMGR4 expression is possibly regulated during flowering, embryogenesis, organogenesis and the circadian rhythm. The obtained data were verified by comparison with microarray co-expression results obtained for Arabidopsis thaliana. Alignment of the isolated HMGR4 sequence with other plant HMGRs indicated the presence of many common binding sites for transcription factors, including conserved ones. Our findings provide valuable information for understanding the mechanisms that direct transcription of the S. miltiorrhiza HMGR4 gene.
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Hossain R, Quispe C, Saikat ASM, Jain D, Habib A, Janmeda P, Islam MT, Radha, Daştan SD, Kumar M, Butnariu M, Cho WC, Sharifi-Rad J, Kipchakbayeva A, Calina D. Biosynthesis of Secondary Metabolites Based on the Regulation of MicroRNAs. Biomed Res Int 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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 02/07/2022] [Indexed: 12/12/2022]
Abstract
MicroRNA (miRNA), a noncoding ribonucleic acid, is considered to be important for the progression of gene expression in plants and animals by rupture or translational repression of targeted mRNAs. Many types of miRNA regulate plant metabolism, growth, and response to biotic and abiotic factors. miRNA characterization helps to expose its function in regulating the process of post-transcriptional genetic regulation. There are a lot of factors associated with miRNA function, but the function of miRNA in the organic synthesis of by-products by natural products is not yet fully elucidated. The current review is aimed at observing and characterizing miRNAs and identifying those involved in the functioning of the biosynthesis of secondary metabolites in plants, with their use in controlled manipulation.
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Affiliation(s)
- Rajib Hossain
- 1Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Cristina Quispe
- 2Facultad de Ciencias de la Salud, Universidad Arturo Prat, Avda. Arturo Prat 2120, Iquique 1110939, Chile
| | - Abu Saim Mohammad Saikat
- 3Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Divya Jain
- 4Department of Bioscience and Biotechnology, Banasthali Vidyapith, Rajasthan, India
| | - Arslan Habib
- 5Lab of Infectious and Molecular Immunology, School of Life Sciences, Fudan University, Shanghai, China
| | - Pracheta Janmeda
- 4Department of Bioscience and Biotechnology, Banasthali Vidyapith, Rajasthan, India
| | - Muhammad Torequl Islam
- 1Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Radha
- 6School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan 173229, India
| | - Sevgi Durna Daştan
- 7Department of Biology, Faculty of Science, Sivas Cumhuriyet University, Sivas 58140, Turkey
- 8Beekeeping Development Application and Research Center, Sivas Cumhuriyet University, Sivas 58140, Turkey
| | - Manoj Kumar
- 9Chemical and Biochemical Processing Division, ICAR-Central Institute for Research on Cotton Technology, Mumbai 400019, India
| | - Monica Butnariu
- 10Banat's University of Agricultural Sciences and Veterinary Medicine “King Michael I of Romania” from Timisoara, Timisoara, Romania
| | - William C. Cho
- 11Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | | | - Aliya Kipchakbayeva
- 13Faculty of Chemistry and Chemical Technology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Daniela Calina
- 14Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, Craiova 200349, Romania
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Jiang M, Chen H, Du Q, Wang L, Liu X, Liu C. Genome-Wide Identification of Circular RNAs Potentially Involved in the Biosynthesis of Secondary Metabolites in Salvia miltiorrhiza. Front Genet 2021; 12:645115. [PMID: 34804110 PMCID: PMC8602197 DOI: 10.3389/fgene.2021.645115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 10/13/2021] [Indexed: 11/13/2022] Open
Abstract
Circular RNAs (circRNAs) play various roles in cellular functions. However, no studies have been reported on the potential involvement of circRNAs in the biosynthesis of secondary metabolites in plants. Here, we performed a genome-wide discovery of circRNAs from root, stem and leaf samples of Salvia miltiorrhiza using RNA-Seq. We predicted a total of 2,476 circRNAs with at least two junction reads using circRNA_finder and CIRI, of which 2,096, 151 and 229 were exonic, intronic and intergenic circRNAs, respectively. Sequence similarity analysis showed that 294 out of 2,476 circRNAs were conserved amongst multiple plants. Of the 55 predicted circRNAs, 31 (56%) were validated successfully by PCR and Sanger sequencing using convergent and divergent primer pairs. Alternative circularisation analysis showed that most parental genes produced two circRNAs. Functional enrichment analyses of the parental genes showed that the primary metabolism pathways were significantly enriched, particularly the carbon metabolism. Differential expression analysis showed that the expression profiles of circRNAs were tissue-specific. Co-expression analysis showed 275 circRNAs, and their parental genes had significantly positive correlations. However, 14 had significantly negative correlations. Weighted gene co-expression network analysis showed that nine circRNAs were co-expressed with four modules of protein-coding genes. Next, we found 416 exonic circRNAs with miRNA-binding sites, suggesting possible interactions between circRNAs and miRNAs. Lastly, we found six validated circRNAs, namely, SMscf2473-46693-46978, SMscf3091-29256-29724, SMscf16-111773-112193, SMscf432-13232-13866, SMscf7007-10563-10888 and SMscf1730-1749-2013, which were originated from the genes involved in the biosynthesis of secondary metabolites. Their parental genes were acetyl-CoA C-acetyltransferase 1 (SmAACT1), 1-deoxy-d-xylulose-5-phosphate synthase 2 (SmDXS2), 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 1 (SmHDR1), kaurene synthase-like 2 (SmKSL2), DWF4 and CYP88A3, respectively. In particular, the correlation coefficient of SMscf2473-46693-46978 and SmDXS2 gene was 0.86 (p = 0.003), indicating a potential interaction between this pair of circRNA and its parent gene. Our results provided the first comprehensive catalogue of circRNAs in S. miltiorrhiza and identified one circRNA that might play important roles in the biosynthesis of secondary metabolites.
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Affiliation(s)
- Mei Jiang
- School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China.,Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China.,Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Qing Du
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,Key Laboratory of Plant Resources of Qinghai-Tibet Plateau in Chemical Research, College of Pharmacy, Qinghai Nationalities University, Xining, China
| | - Liqiang Wang
- College of Pharmacy, Heze University, Heze, China
| | - Xinyue Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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11
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Cao L, Lu X, Wang G, Zhang P, Fu J, Wang Z, Wei L, Wang T. Transcriptional regulatory networks in response to drought stress and rewatering in maize (Zea mays L.). Mol Genet Genomics 2021; 296:1203-1219. [PMID: 34601650 DOI: 10.1007/s00438-021-01820-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/31/2021] [Indexed: 11/26/2022]
Abstract
Drought severely affects the growth and development of maize, but there is a certain degree of compensation effect after rewatering. This study intends to elaborate the response mechanism of maize at the physiological and molecular level as well as excavating potential genes with strong drought resistance and recovery ability. Physiological indexes analysis demonstrated that stomata conductance, transpiration rate, photosynthesis rate, antioxidant enzymes, and proline levels in maize were significantly altered in response to drought for 60 and 96 h and rewatering for 3 days. At 60 h, 96 h, and R3d, we detected 3095, 1941, and 5966 differentially expressed genes (DEGs) and 221, 226, and 215 differentially expressed miRNAs. Weighted correlation network analysis (WGCNA) showed that DEGs responded to maize drought and rewatering through participating in photosynthesis, proline metabolism, ABA signaling, and oxidative stress. Joint analysis of DEGs, miRNA, and target genes showed that zma-miR529, miR5072, zma-miR167e, zma-miR167f, zma-miR167j, miR397, and miR6214 were involved to regulate SBPs, MYBs, ARFs, laccases, and antioxidant enzymes, respectively. Hundreds of differentially expressed DNA methylation-related 24-nt siRNA clusters overlap with DEGs, indicating that DNA methylation is involved in responses under drought stress. These results provide new insights into the molecular mechanisms of drought tolerance, and may identify new targets for breeding drought-tolerant maize lines.
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Affiliation(s)
- Liru Cao
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Xiaomin Lu
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Guorui Wang
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Pengyu Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jiaxu Fu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhenhua Wang
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
| | - Li Wei
- National Engineering Research Centre for Wheat, Zhengzhou, 450002, China.
| | - Tongchao Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
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12
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Li C, Wang M, Qiu X, Zhou H, Lu S. Noncoding RNAs in Medicinal Plants and their Regulatory Roles in Bioactive Compound Production. Curr Pharm Biotechnol 2021; 22:341-359. [PMID: 32469697 DOI: 10.2174/1389201021666200529101942] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/14/2020] [Accepted: 03/30/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Noncoding RNAs (ncRNAs), such as microRNAs (miRNAs), small interfering RNAs (siRNAs) and long noncoding RNAs (lncRNAs), play significant regulatory roles in plant development and secondary metabolism and are involved in plant response to biotic and abiotic stresses. They have been intensively studied in model systems and crops for approximately two decades and massive amount of information have been obtained. However, for medicinal plants, ncRNAs, particularly their regulatory roles in bioactive compound biosynthesis, are just emerging as a hot research field. OBJECTIVE This review aims to summarize current knowledge on herbal ncRNAs and their regulatory roles in bioactive compound production. RESULTS So far, scientists have identified thousands of miRNA candidates from over 50 medicinal plant species and 11794 lncRNAs from Salvia miltiorrhiza, Panax ginseng, and Digitalis purpurea. Among them, more than 30 miRNAs and five lncRNAs have been predicted to regulate bioactive compound production. CONCLUSION The regulation may achieve through various regulatory modules and pathways, such as the miR397-LAC module, the miR12112-PPO module, the miR156-SPL module, the miR828-MYB module, the miR858-MYB module, and other siRNA and lncRNA regulatory pathways. Further functional analysis of herbal ncRNAs will provide useful information for quality and quantity improvement of medicinal plants.
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Affiliation(s)
- Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Meizhen Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Xiaoxiao Qiu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Hong Zhou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
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Jiang M, Chen H, Liu J, Du Q, Lu S, Liu C. Genome-wide identification and functional characterization of natural antisense transcripts in Salvia miltiorrhiza. Sci Rep 2021; 11:4769. [PMID: 33637790 PMCID: PMC7910453 DOI: 10.1038/s41598-021-83520-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 01/29/2021] [Indexed: 01/01/2023] Open
Abstract
Salvia miltiorrhiza is one of the most widely used traditional medicines. Natural antisense transcripts (NATs) are a class of long noncoding RNAs that can regulate gene expression. Here, we identified 812 NATs, including 168 cis-NATs and 644 trans-NATs from twelve root, flower, and leaf samples of S. miltiorrhiza using RNA-seq. The expression profiles for 41 of 50 NATs and their sense transcripts (STs) obtained from RNA-Seq were validated using qRT-PCR. The expression profiles of 17 NATs positively correlated with their STs. GO and KEGG pathway analyses mapped the STs for cis-NATs to pathways for biosynthesis of secondary metabolites. We characterized four NATs in detail, including NAT0001, NAT0002, NAT0004, and NAT00023. Their STs are kaurene synthase-like 1 and the homologs of UDP-glucose flavonoid 3-O-glucosyltransferase 6, UDP-glycosyltransferase 90A1, and beta-glucosidase 40, respectively. The first gene is involved in the biosynthesis of bioactive tanshinones, the next two are involved in anthocyanin biosynthesis, whereas the last is involved in phenylpropanoid biosynthesis. Besides, we found seven STs that are potential targets of miRNAs. And we found two miRNAs including miR156a and miR7208, might originate from NATs, NAT0112 and NAT0086. The results suggest that S. miltiorrhiza NATs might interact with STs, produce miRNAs, and be regulated by miRNAs. They potentially play significant regulatory roles in the biosynthesis of bioactive compounds.
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Affiliation(s)
- Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Jingting Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Qing Du
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China.,College of Pharmacy, Key Laboratory of Plant Resources of Qinghai-Tibet Plateau in Chemical Research, Qinghai Nationalities University, Xining, 810007, Qinghai, People's Republic of China
| | - Shanfa Lu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China.
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China.
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14
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You S, He X, Wang M, Mao L, Zhang L. Tanshinone IIA Suppresses Glioma Cell Proliferation, Migration and Invasion Both in vitro and in vivo Partially Through miR-16-5p/Talin-1 (TLN1) Axis. Cancer Manag Res 2020; 12:11309-11320. [PMID: 33192091 PMCID: PMC7654526 DOI: 10.2147/cmar.s256347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 10/01/2020] [Indexed: 01/13/2023] Open
Abstract
Background Tanshinone IIA (TIIA) is one of the active constituents derived from the rhizome of Danshen, a traditional Chinese herbal. Recently, microRNAs (miRNAs) have been suggested to be associated with the anticancer role of TIIA. However, it remains vague of the interaction between miRNAs and TIIA in glioma, a common aggressive brain tumor in humans. Methods Expression of miRNA (miR)-16-5p and talin-1 (TLN1) was detected using reverse transcription-quantitative polymerase chain reaction and Western blotting. Cell proliferation, migration and invasion were assessed with cell viability assay, transwell assay, Western blotting, and xenograft tumor experiment. The target binding between miR-16-5p and TLN1 was confirmed by dual-luciferase reporter assay and RNA pull-down assay. Results TIIA treatment inhibited cell viability, migration and invasion, and decreased Cyclin D1, matrix metalloproteinase (MMP)-9 and Vimentin expression in glioma T98G and A172 cells both in vitro and in vivo. Thus, TIIA induced anti-glioma role, wherein miR-16-5p was upregulated and TLN1 was downregulated. Moreover, silencing miR-16-5p could abate TIIA-mediated suppression on glioma cell proliferation, migration and invasion in vitro and in vivo. TLN1 overexpression also exerted tumor-promoting effect in TIIA-treated T98G and A172 cells. Mechanically, miR-16-5p could regulate TLN1 expression via target binding, and depleting TLN1 could counteract the inhibitory effect of miR-16-5p knockdown on the curative effect of TIIA in T98G and A172 cells. Conclusion TIIA exerted the anti-proliferation, anti-migration and anti-invasion role in glioma cells both in vitro and in vivo partially through regulating miR-16-5p/TLN1 axis.
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Affiliation(s)
- Shihao You
- Department of Neurology, Qingdao Fuwai Cardiovascular Hospital, Qingdao, Shandong, People's Republic of China
| | - Xianghui He
- Department of Emergency, Qingdao Fuwai Cardiovascular Hospital, Qingdao, Shandong, People's Republic of China
| | - Mei Wang
- Department of Neurology, Qingdao Fuwai Cardiovascular Hospital, Qingdao, Shandong, People's Republic of China
| | - Lina Mao
- Department of Neurology, Qingdao Fuwai Cardiovascular Hospital, Qingdao, Shandong, People's Republic of China
| | - Lu Zhang
- Department of Peripheral Vascular Diseases, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, People's Republic of China
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15
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Zheng X, Li H, Chen M, Zhang J, Tan R, Zhao S, Wang Z. smi-miR396b targeted SmGRFs, SmHDT1, and SmMYB37/4 synergistically regulates cell growth and active ingredient accumulation in Salvia miltiorrhiza hairy roots. Plant Cell Rep 2020; 39:1263-1283. [PMID: 32607753 DOI: 10.1007/s00299-020-02562-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/19/2020] [Indexed: 06/11/2023]
Abstract
MIR396b had been cloned and overexpressed in Salvia miltiorrhiza hairy roots. MiR396b targets SmGRFs, SmHDT1, and SmMYB37/4 to regulate cell growth and secondary metabolism in S. miltiorrhiza hairy roots. Danshen (Salvia miltiorrhiza Bunge) is a valuable medicinal herb with two kinds of clinically used natural products, salvianolic acids and tanshinones. miR396 is a conserved microRNA and plays extensive roles in plants. However, it is still unclear how miR396 works in S. miltiorrhiza. In this study, an smi-MIR396b has been cloned from S. miltiorrhiza. Overexpression of miR396b in danshen hairy roots inhibited hairy root growth, reduced salvianolic acid concentration, but enhanced tanshinone accumulation, resulting in the biomass and total salvianolic acids respectively reduced to 55.5 and 72.1% of the control and total tanshinones increased up to 1.91-fold of the control. Applied degradome sequencing, 5'RLM-RACE, and qRT-PCR, 13 targets for miR396b were identified including seven conserved SmGRF1-7 and six novel ones. Comparative transcriptomics and microRNomics analysis together with qRT-PCR results confirmed that miR396b targets SmGRFs, SmHDT1, and SmMYB37/4 to mediate the phytohormone, especially gibberellin signaling pathways and consequentially resulted in the phenotype variation of miR396b-OE hairy roots. Furthermore, miR396b could be activated by methyl jasmonate, abscisic acid, gibberellin, salt, and drought stresses. The findings in this study indicated that smi-miR396b acts as an upstream and central regulator in cell growth and the biosynthesis of tanshinones and salvianolic acids, shedding light on the coordinated regulation of plant growth and biosynthesis of active ingredients in S. miltiorrhiza.
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Affiliation(s)
- Xiaoyu Zheng
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New District, Shanghai, 201203, People's Republic of China
| | - Hang Li
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New District, Shanghai, 201203, People's Republic of China
| | - Min Chen
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New District, Shanghai, 201203, People's Republic of China
| | - Jinjia Zhang
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New District, Shanghai, 201203, People's Republic of China
| | - Ronghui Tan
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New District, Shanghai, 201203, People's Republic of China
| | - Shujuan Zhao
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New District, Shanghai, 201203, People's Republic of China.
| | - Zhengtao Wang
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New District, Shanghai, 201203, People's Republic of China.
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Li C, Li D, Zhou H, Li J, Lu S. Analysis of the laccase gene family and miR397-/miR408-mediated posttranscriptional regulation in Salvia miltiorrhiza. PeerJ 2019; 7:e7605. [PMID: 31528508 PMCID: PMC6717658 DOI: 10.7717/peerj.7605] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 08/02/2019] [Indexed: 01/21/2023] Open
Abstract
Salvia miltiorrhiza is one of the most commonly used traditional Chinese medicine materials. It contains important bioactive phenolic compounds, such as salvianolic acids, flavonoids and anthocyanins. Elucidation of phenolic compound biosynthesis and its regulatory mechanism is of great significance for S. miltiorrhiza quality improvement. Laccases (LACs) are multicopper-containing enzymes potentially involved in the polymerization of phenolic compounds. So far, little has been known about LAC genes in S. miltiorrhiza. Through systematic investigation of the whole genome sequence and transcriptomes of S. miltiorrhiza, we identified 65 full-length SmLAC genes (SmLAC1–SmLAC65). Phylogenetic analysis showed that 62 of the identified SmLACs clustered with LACs from Arabidopsis and Populus trichocarpa in seven clades (C1–C7), whereas the other three fell into one S. miltiorrhiza-specific clade (C8). All of the deduced SmLAC proteins contain four conserved signature sequences and three typical Cu-oxidase domains, and gene structures of most LACs from S. miltiorrhiza, Arabidopsis and P. trichocarpa were highly conserved, however SmLACs encoding C8 proteins showed distinct intron-exon structures. It suggests the conservation and diversity of plant LACs in gene structures. The majority of SmLACs exhibited tissue-specific expression patterns, indicates manifold functions of SmLACs played in S. miltiorrhiza. Analysis of high-throughput small RNA sequences and degradome data and experimental validation using the 5′ RACE method showed that 23 SmLACs were targets of Smi-miR397. Among them, three were also targeted by Smi-miR408. It suggests the significance of miR397 and miR408 in posttranscriptional regulation of SmLAC genes. Our results provide a foundation for further demonstrating the functions of SmLACs in the production of bioactive phenolic compounds in S. miltiorrhiza.
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Affiliation(s)
- Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Dongqiao Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hong Zhou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jiang Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Guo X, Niu J, Cao X. Heterologous Expression of Salvia miltiorrhiza MicroRNA408 Enhances Tolerance to Salt Stress in Nicotiana benthamiana. Int J Mol Sci 2018; 19:E3985. [PMID: 30544912 PMCID: PMC6321395 DOI: 10.3390/ijms19123985] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 12/04/2018] [Accepted: 12/07/2018] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of endogenous small RNAs that regulate the expression of target genes post-transcriptionally; they are known to play major roles in development and responses to abiotic stress. MicroRNA408 (miR408) is a conserved small RNA in plants; it was reported that miR408 genes were involved in abiotic stress in Arabidopsis. However, miR408 in Salvia miltiorrhiza has been rarely investigated. In this study, we cloned Sm-MIR408, the miR408 precursor sequence, and its promoter sequence from S. miltiorrhiza and the role in tolerance to salt stress is described. The effects of salt stress on miR408 expression were studied by using β-glucuronidase (GUS) staining. Our data indicated that transgenic tobacco overexpressing Sm-MIR408 promoted seed germination and reduced the accumulation of reactive oxygen species under salt stress. Transcript levels of antioxidative genes, i.e., NbSOD, NbPOD, and NbCAT, and their enzyme activities increased in salinity-stressed transgenic tobacco plants, suggesting a better antioxidant system to cope the oxidative damage caused by salinity stress. Taken together, these findings indicated that miR408 functions in positive responses to salt tolerance in tobacco.
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Affiliation(s)
- Xiaorong Guo
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shanxi Normal University, Xi'an 710062, China.
| | - Junfeng Niu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shanxi Normal University, Xi'an 710062, China.
| | - Xiaoyan Cao
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shanxi Normal University, Xi'an 710062, China.
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Xu Y, Geng L, Zhao S. Biosynthesis of bioactive ingredients of Salvia miltiorrhiza and advanced biotechnologies for their production. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1532318] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Yingpeng Xu
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Shanghai, P.R. China
| | - Lijun Geng
- The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai, P.R. China
| | - Shujuan Zhao
- Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, P.R. China
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20
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Li J, Li C, Lu S. Systematic analysis of DEMETER-like DNA glycosylase genes shows lineage-specific Smi-miR7972 involved in SmDML1 regulation in Salvia miltiorrhiza. Sci Rep 2018; 8:7143. [PMID: 29739980 PMCID: PMC5940787 DOI: 10.1038/s41598-018-25315-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 04/09/2018] [Indexed: 11/09/2022] Open
Abstract
DEMETER-like DNA glycosylases (DMLs) initiate the base excision repair-dependent DNA demethylation to regulate a wide range of biological processes in plants. Six putative SmDML genes, termed SmDML1-SmDML6, were identified from the genome of S. miltiorrhiza, an emerging model plant for Traditional Chinese Medicine (TCM) studies. Integrated analysis of gene structures, sequence features, conserved domains and motifs, phylogenetic analysis and differential expression showed the conservation and divergence of SmDMLs. SmDML1, SmDML2 and SmDML4 were significantly down-regulated by the treatment of 5Aza-dC, a general DNA methylation inhibitor, suggesting involvement of SmDMLs in genome DNA methylation change. SmDML1 was predicted and experimentally validated to be target of Smi-miR7972. Computational analysis of forty whole genome sequences and almost all of RNA-seq data from Lamiids revealed that MIR7972s were only distributed in some plants of the three orders, including Lamiales, Solanales and Boraginales, and the number of MIR7972 genes varied among species. It suggests that MIR7972 genes underwent expansion and loss during the evolution of some Lamiids species. Phylogenetic analysis of MIR7972s showed closer evolutionary relationships between MIR7972s in Boraginales and Solanales in comparison with Lamiales. These results provide a valuable resource for elucidating DNA demethylation mechanism in S. miltiorrhiza.
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Affiliation(s)
- Jiang 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
| | - 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
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No.151 Malianwa North Road, Haidian District, Beijing, 100193, China.
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Li C, Li D, Li J, Shao F, Lu S. Characterization of the polyphenol oxidase gene family reveals a novel microRNA involved in posttranscriptional regulation of PPOs in Salvia miltiorrhiza. Sci Rep 2017; 7:44622. [PMID: 28304398 PMCID: PMC5356337 DOI: 10.1038/srep44622] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/10/2017] [Indexed: 12/11/2022] Open
Abstract
Salvia miltiorrhiza is a well-known material of traditional Chinese medicine. Understanding the regulatory mechanisms of phenolic acid biosynthesis and metabolism are important for S. miltiorrhiza quality improvement. We report here that S. miltiorrhiza contains 19 polyphenol oxidases (PPOs), forming the largest PPO gene family in plant species to our knowledge. Analysis of gene structures and sequence features revealed the conservation and divergence of SmPPOs. SmPPOs were differentially expressed in plant tissues and eight of them were predominantly expressed in phloem and xylem, indicating that some SmPPOs are functionally redundant, whereas the others are associated with different physiological processes. Expression patterns of eighteen SmPPOs were significantly altered under MeJA treatment, and twelve were yeast extract and Ag+-responsive, suggesting the majority of SmPPOs are stress-responsive. Analysis of high-throughput small RNA sequences and degradome data showed that miR1444-mediated regulation of PPOs existing in P. trichocarpa is absent from S. miltiorrhiza. Instead, a subset of SmPPOs was posttranscriptionally regulated by a novel miRNA, termed Smi-miR12112. It indicates the specificity and significance of miRNA-mediated regulation of PPOs. The results shed light on the regulation of SmPPO expression and suggest the complexity of SmPPO-associated phenolic acid biosynthesis and metabolism.
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Affiliation(s)
- Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Dongqiao 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
| | - Jiang 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
| | - Fenjuan Shao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
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Yang Y, Qiu S, Qian L, Tian Y, Chen Y, Bi L, Chen W. OCF can repress tumor metastasis by inhibiting epithelial-mesenchymal transition involved in PTEN/PI3K/AKT pathway in lung cancer cells. PLoS One 2017; 12:e0174021. [PMID: 28301605 DOI: 10.1371/journal.pone.0174021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 03/02/2017] [Indexed: 01/31/2023] Open
Abstract
A component formula with definite compositions provides a new approach to treat various diseases. Salvia miltiorrhiza and Panax ginseng are widely used in China because of their antitumor properties. In the previous study, the optimizing component formula (OCF), prepared with salvianolic acids, ginsenosides, and ginseng polysaccharides (5, 10, and 5 mg·L−1, respectively) extracted from S. miltiorrhiza and P. ginseng on the basis of IC50 in lung cancer A549 cells and damage minimization on human bronchial epithelial cells in vitro. Currently, we also have demonstrated the inhibitory effect of OCF on A549 cell migration and invasion in vitro. According to Lewis lung cancer cells (LLC) allograft in C57BL/6 mice and A549 xenograft in nude mice experiment, we found that the anti-tumor and anti-metastasis effects of OCF treatment were related to the inhibition of epithelial–mesenchymal transition (EMT). Further studies showed that the inhibitory effect of OCF on EMT was associated with the PTEN/PI3K/AKT pathway. Therefore, all studies revealed that OCF could prevent cancer progression and tumor metastasis by inhibiting EMT involved PTEN/PI3K/AKT signaling pathway in lung cancer cells.
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Wu B, Chen H, Shao J, Zhang H, Wu K, Liu C. Identification of Symmetrical RNA Editing Events in the Mitochondria of Salvia miltiorrhiza by Strand-specific RNA Sequencing. Sci Rep 2017; 7:42250. [PMID: 28186130 DOI: 10.1038/srep42250] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 01/08/2017] [Indexed: 01/08/2023] Open
Abstract
Salvia miltiorrhiza is one of the most widely-used medicinal plants. Here, we systematically analyzed the RNA editing events in its mitochondria. We developed a pipeline using REDItools to predict RNA editing events from stand-specific RNA-Seq data. The predictions were validated using reverse transcription, RT-PCR amplification and Sanger sequencing experiments. Putative sequences motifs were characterized. Comparative analyses were carried out between S. miltiorrhiza, Arabidopsis thaliana and Oryza sativa. We discovered 1123 editing sites, including 225 “C to U” sites in the protein-coding regions. Fourteen of sixteen (87.5%) sites were validated. Three putative DNA motifs were identified around the predicted sites. The nucleotides on both strands at 115 of the 225 sites had undergone RNA editing, which we called symmetrical RNA editing (SRE). Four of six these SRE sites (66.7%) were experimentally confirmed. Re-examination of strand-specific RNA-Seq data from A. thaliana and O. sativa identified 327 and 369 SRE sites respectively. 78, 20 and 13 SRE sites were found to be conserved among A. thaliana, O. sativa and S. miltiorrhiza respectively. This study provides a comprehensive picture of RNA editing events in the mitochondrial genome of S. miltiorrhiza. We identified SREs for the first time, which may represent a universal phenomenon.
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Gupta OP, Karkute SG, Banerjee S, Meena NL, Dahuja A. Contemporary Understanding of miRNA-Based Regulation of Secondary Metabolites Biosynthesis in Plants. Front Plant Sci 2017; 8:374. [PMID: 28424705 PMCID: PMC5372812 DOI: 10.3389/fpls.2017.00374] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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Zhang H, Jin W, Zhu X, Liu L, He Z, Yang S, Liang Z, Yan X, He Y, Liu Y. Identification and Characterization of Salvia miltiorrhizain miRNAs in Response to Replanting Disease. PLoS One 2016; 11:e0159905. [PMID: 27483013 PMCID: PMC4970794 DOI: 10.1371/journal.pone.0159905] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 07/11/2016] [Indexed: 11/25/2022] Open
Abstract
Replanting disease is a major factor limiting the artificial cultivation of the traditional Chinese medicinal herb Salvia miltiorrhiza. At present, little information is available regarding the role of miRNAs in response to replanting disease. In this study, two small RNA libraries obtained from first-year (FPR) and second-year plant (SPR) roots were subjected to a high-throughput sequencing method. Bioinformatics analysis revealed that 110 known and 7 novel miRNAs were annotated in the roots of S. miltiorrhiza. Moreover, 39 known and 2 novel miRNAs were identified and validated for differential expression in FPR compared with SPR. Thirty-one of these miRNAs were further analyzed by qRT-PCR, which revealed that 5 miRNAs negatively regulated the expression levels of 7 target genes involved in root development or stress responses. This study not only provides novel insights into the miRNA content of S. miltiorrhiza in response to replanting disease but also demonstrates that 5 miRNAs may be involved in these responses. Interactions among the differentially expressed miRNAs with their targets may form an important component of the molecular basis of replanting disease in S. miltiorrhiza.
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Affiliation(s)
- Haihua Zhang
- College of Life Sciences, Northwest A & F University, Yangling, 712100, China
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Weibo Jin
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Xiaole Zhu
- College of Life Sciences, Northwest A & F University, Yangling, 712100, China
| | - Lin Liu
- College of Life Sciences, Northwest A & F University, Yangling, 712100, China
| | - Zhigui He
- College of Life Sciences, Northwest A & F University, Yangling, 712100, China
| | - Shushen Yang
- College of Life Sciences, Northwest A & F University, Yangling, 712100, China
| | - Zongsuo Liang
- College of Life Sciences, Northwest A & F University, Yangling, 712100, China
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Xijun Yan
- Tasly R&D Institute, Tasly Holding Group Co. Ltd, Tianjin, 300410, China
| | - Yanfeng He
- Tasly R&D Institute, Tasly Holding Group Co. Ltd, Tianjin, 300410, China
| | - Yan Liu
- Tianjin Tasly Modern TCM Resources Co., Ltd., Tianjin, 300402, China
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26
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Wang Y, Liu J, Wang X, Liu S, Wang G, Zhou J, Yuan Y, Chen T, Jiang C, Zha L, Huang L. Validation of Suitable Reference Genes for Assessing Gene Expression of MicroRNAs in Lonicera japonica. Front Plant Sci 2016; 7:1101. [PMID: 27507983 PMCID: PMC4961011 DOI: 10.3389/fpls.2016.01101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/11/2016] [Indexed: 06/06/2023]
Abstract
MicroRNAs (miRNAs), which play crucial regulatory roles in plant secondary metabolism and responses to the environment, could be developed as promising biomarkers for different varieties and production areas of herbal medicines. However, limited information is available for miRNAs from Lonicera japonica, which is widely used in East Asian countries owing to various pharmaceutically active secondary metabolites. Selection of suitable reference genes for quantification of target miRNA expression through quantitative real-time (qRT)-PCR is important for elucidating the molecular mechanisms of secondary metabolic regulation in different tissues and varieties of L. japonica. For precise normalization of gene expression data in L. japonica, 16 candidate miRNAs were examined in three tissues, as well as 21 cultivated varieties collected from 16 production areas, using GeNorm, NormFinder, and RefFinder algorithms. Our results revealed combination of u534122 and u3868172 as the best reference genes across all samples. Their specificity was confirmed by detecting the cycling threshold (C t) value ranges in different varieties of L. japonica collected from diverse production areas, suggesting the use of these two reference miRNAs is sufficient for accurate transcript normalization with different tissues, varieties, and production areas. To our knowledge, this is the first report on validation of reference miRNAs in honeysuckle (Lonicera spp.). Restuls from this study can further facilitate discovery of functional regulatory miRNAs in different varieties of L. japonica.
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Affiliation(s)
- Yaolong Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Juan Liu
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Xumin Wang
- Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China
| | - Shuang Liu
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Guoliang Wang
- Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China
| | - Junhui Zhou
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Yuan Yuan
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Tiying Chen
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Chao Jiang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Liangping Zha
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
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da Silva AC, Grativol C, Thiebaut F, Hemerly AS, Ferreira PCG. Computational identification and comparative analysis of miRNA precursors in three palm species. Planta 2016; 243:1265-1277. [PMID: 26919984 DOI: 10.1007/s00425-016-2486-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/09/2016] [Indexed: 06/05/2023]
Abstract
In the present study, miRNA precursors in the genomes of three palm species were identified. Analyzes of sequence conservation and biological function of their putative targets contribute to understand the roles of miRNA in palm biology. MicroRNAs are small RNAs of 20-25 nucleotides in length, with important functions in the regulation of gene expression. Recent genome sequencing of the palm species Elaeis guineensis, Elaeis oleifera and Phoenix dactylifera have enabled the discovery of miRNA genes, which can be used as biotechnological tools in palm trees breeding. The goal of this study is the identification of miRNA precursors in the genomes of these species and their possible biological roles suggested by the mature miRNA-based regulation of target genes. Mature miRNA sequences from Arabidopsis thaliana, Oryza sativa, and Zea mays available at the miRBase were used to predict microRNA precursors in the palm genomes. Three hundred and thirty-eight precursors, ranging from 76 to 220 nucleotide (nt) in size and distributed in 33 families were identified. Moreover, we also identified 266 miRNA precursors of Musa acuminata, which are phylogenetically close to palms species. To understand the biological function of palm miRNAs, 374 putative miRNA targets were identified. An enrichment analysis of target-gene function was carried out using the agriGO tool. The results showed that the targets are involved in plant developmental processes, mainly regulating root development. Our findings contribute to increase the knowledge on microRNA roles in palm biology and could help breeding programs of palm trees.
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Affiliation(s)
- Aline Cunha da Silva
- Universidade Federal Rural da Amazonia, Belém, Brazil
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, CCS, Bl.L-29ss, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Clícia Grativol
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Av. Alberto Lamego, 2000, P5-227A, Parque Califórnia, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Flávia Thiebaut
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, CCS, Bl.L-29ss, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Adriana Silva Hemerly
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, CCS, Bl.L-29ss, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Paulo Cavalcanti Gomes Ferreira
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, CCS, Bl.L-29ss, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil.
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Liao P, Hemmerlin A, Bach TJ, Chye ML. The potential of the mevalonate pathway for enhanced isoprenoid production. Biotechnol Adv 2016; 34:697-713. [PMID: 26995109 DOI: 10.1016/j.biotechadv.2016.03.005] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 03/12/2016] [Accepted: 03/14/2016] [Indexed: 01/03/2023]
Abstract
The cytosol-localised mevalonic acid (MVA) pathway delivers the basic isoprene unit isopentenyl diphosphate (IPP). In higher plants, this central metabolic intermediate is also synthesised by the plastid-localised methylerythritol phosphate (MEP) pathway. Both MVA and MEP pathways conspire through exchange of intermediates and regulatory interactions. Products downstream of IPP such as phytosterols, carotenoids, vitamin E, artemisinin, tanshinone and paclitaxel demonstrate antioxidant, cholesterol-reducing, anti-ageing, anticancer, antimalarial, anti-inflammatory and antibacterial activities. Other isoprenoid precursors including isoprene, isoprenol, geraniol, farnesene and farnesol are economically valuable. An update on the MVA pathway and its interaction with the MEP pathway is presented, including the improvement in the production of phytosterols and other isoprenoid derivatives. Such attempts are for instance based on the bioengineering of microbes such as Escherichia coli and Saccharomyces cerevisiae, as well as plants. The function of relevant genes in the MVA pathway that can be utilised in metabolic engineering is reviewed and future perspectives are presented.
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Affiliation(s)
- Pan Liao
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
| | - Andréa Hemmerlin
- Centre National de la Recherche Scientifique, UPR 2357, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 67083 Strasbourg, France.
| | - Thomas J Bach
- Centre National de la Recherche Scientifique, UPR 2357, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 67083 Strasbourg, France.
| | - Mee-Len Chye
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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Shao F, Qiu D, Lu S. Comparative analysis of the Dicer-like gene family reveals loss of miR162 target site in SmDCL1 from Salvia miltiorrhiza. Sci Rep 2015; 5:9891. [PMID: 25970825 DOI: 10.1038/srep09891] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/23/2015] [Indexed: 11/08/2022] Open
Abstract
DCL1, the core component for miRNA biogenesis, is itself regulated by miR162 in Arabidopsis. MiRNA-mediated feedback regulation of AtDCL1 is important to maintain the proper level of DCL1 transcripts. However, it is unknown whether the miRNA-mediated regulation of DCL1 is conserved among plants. We analyzed the SmDCL gene family in Salvia miltiorrhiza, an emerging model plant for Traditional Chinese Medicine (TCM) studies, using a comprehensive approach integrating genome-wide prediction, molecular cloning, gene expression profiling, and posttranscriptional regulation analysis. A total of five SmDCLs were identified. Comparative analysis of SmDCLs and AtDCLs showed an apparent enlargement of SmDCL introns in S. miltiorrhiza. The absence of miR162 in S. miltiorrhiza and the loss of miR162 target site in SmDCL1 were unexpectedly found. Further analysis showed that the miR162 target site was not present in DCL1 from ancient plants and was gained during plant evolution. The gained miR162 target site might be lost in a few modern plants through nucleotide mutations. Our results provide evidence for the gain and loss of miR162 and its target sites in Dicer-like genes during evolution. The data is useful for understanding the evolution of miRNA-mediated feedback regulation of DCLs in plants.
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