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Wang H, Zhao P, He Y, Su Y, Zhou X, Guo H. Transcriptome and miRNAs Profiles Reveal Regulatory Network and Key Regulators of Secondary Xylem Formation in "84K" Poplar. Int J Mol Sci 2023; 24:16438. [PMID: 38003631 PMCID: PMC10671414 DOI: 10.3390/ijms242216438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Secondary xylem produced by stem secondary growth is the main source of tree biomass and possesses great economic and ecological value in papermaking, construction, biofuels, and the global carbon cycle. The secondary xylem formation is a complex developmental process, and the underlying regulatory networks and potential mechanisms are still under exploration. In this study, using hybrid poplar (Populus alba × Populus glandulosa clone 84K) as a model system, we first ascertained three representative stages of stem secondary growth and then investigated the regulatory network of secondary xylem formation by joint analysis of transcriptome and miRNAs. Notably, 7507 differentially expressed genes (DEGs) and 55 differentially expressed miRNAs (DEMs) were identified from stage 1 without initiating secondary growth to stage 2 with just initiating secondary growth, which was much more than those identified from stage 2 to stage 3 with obvious secondary growth. DEGs encoding transcription factors and lignin biosynthetic enzymes and those associated with plant hormones were found to participate in the secondary xylem formation. MiRNA-target analysis revealed that a total of 85 DEMs were predicted to have 2948 putative targets. Among them, PagmiR396d-PagGRFs, PagmiR395c-PagGA2ox1/PagLHW/PagSULTR2/PagPolyubiquitin 1, PagmiR482d-PagLAC4, PagmiR167e-PagbHLH62, and PagmiR167f/g/h-PagbHLH110 modules were involved in the regulating cambial activity and its differentiation into secondary xylem, cell expansion, secondary cell wall deposition, and programmed cell death. Our results give new insights into the regulatory network and mechanism of secondary xylem formation.
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Affiliation(s)
| | | | | | | | | | - Huihong Guo
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing 100083, China; (H.W.); (P.Z.); (Y.H.); (Y.S.); (X.Z.)
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MicroRNAs in Medicinal Plants. Int J Mol Sci 2022; 23:ijms231810477. [PMID: 36142389 PMCID: PMC9500639 DOI: 10.3390/ijms231810477] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Medicinal plant microRNAs (miRNAs) are an endogenous class of small RNA central to the posttranscriptional regulation of gene expression. Biosynthetic research has shown that the mature miRNAs in medicinal plants can be produced from either the standard messenger RNA splicing mechanism or the pre-ribosomal RNA splicing process. The medicinal plant miRNA function is separated into two levels: (1) the cross-kingdom level, which is the regulation of disease-related genes in animal cells by oral intake, and (2) the intra-kingdom level, which is the participation of metabolism, development, and stress adaptation in homologous or heterologous plants. Increasing research continues to enrich the biosynthesis and function of medicinal plant miRNAs. In this review, peer-reviewed papers on medicinal plant miRNAs published on the Web of Science were discussed, covering a total of 78 species. The feasibility of the emerging role of medicinal plant miRNAs in regulating animal gene function was critically evaluated. Staged progress in intra-kingdom miRNA research has only been found in a few medicinal plants, which may be mainly inhibited by their long growth cycle, high demand for growth environment, immature genetic transformation, and difficult RNA extraction. The present review clarifies the research significance, opportunities, and challenges of medicinal plant miRNAs in drug development and agricultural production. The discussion of the latest results furthers the understanding of medicinal plant miRNAs and helps the rational design of the corresponding miRNA/target genes functional modules.
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Xing H, Li Y, Ren Y, Zhao Y, Wu X, Li HL. Genome-wide investigation of microRNAs and expression profiles during rhizome development in ginger (Zingiber officinale Roscoe). BMC Genomics 2022; 23:49. [PMID: 35021996 PMCID: PMC8756691 DOI: 10.1186/s12864-021-08273-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 12/20/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are endogenous, non-coding small functional RNAs that govern the post-transcriptional regulatory system of gene expression and control the growth and development of plants. Ginger is an herb that is well-known for its flavor and medicinal properties. The genes involved in ginger rhizome development and secondary metabolism have been discovered, but the genome-wide identification of miRNAs and their overall expression profiles and targets during ginger rhizome development are largely unknown. In this study, we used BGISEQ-500 technology to perform genome-wide identification of miRNAs from the leaf, stem, root, flower, and rhizome of ginger during three development stages. RESULTS In total, 104 novel miRNAs and 160 conserved miRNAs in 28 miRNA families were identified. A total of 181 putative target genes for novel miRNAs and 2772 putative target genes for conserved miRNAs were predicted. Transcriptional factors were the most abundant target genes of miRNAs, and 17, 9, 8, 4, 13, 8, 3 conserved miRNAs and 5, 7, 4, 5, 5, 15, 9 novel miRNAs showed significant tissue-specific expression patterns in leaf, stem, root, flower, and rhizome. Additionally, 53 miRNAs were regarded as rhizome development-associated miRNAs, which mostly participate in metabolism, signal transduction, transport, and catabolism, suggesting that these miRNAs and their target genes play important roles in the rhizome development of ginger. Twelve candidate miRNA target genes were selected, and then, their credibility was confirmed using qRT-PCR. As the result of qRT-PCR analysis, the expression of 12 candidate target genes showed an opposite pattern after comparison with their miRNAs. The rhizome development system of ginger was observed to be governed by miR156, miR319, miR171a_2, miR164, and miR529, which modulated the expression of the SPL, MYB, GRF, SCL, and NAC genes, respectively. CONCLUSION This is a deep genome-wide investigation of miRNA and identification of miRNAs involved in rhizome development in ginger. We identified 52 rhizome-related miRNAs and 392 target genes, and this provides an important basis for understanding the molecular mechanisms of the miRNA target genes that mediate rhizome development in ginger.
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Affiliation(s)
- Haitao Xing
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, 402168, China
| | - Yuan Li
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China.
| | - Yun Ren
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, 402168, China
| | - Ying Zhao
- Research Center for Terrestrial Biodiversity of the South China Sea, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, Hainan, China
| | - Xiaoli Wu
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China
| | - Hong-Lei Li
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China.
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, 402168, China.
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Qi YS, Xie JB, Xie P, Duan Y, Ling YQ, Gu YL, Piao XL. Uncovering the anti-NSCLC effects and mechanisms of gypenosides by metabolomics and network pharmacology analysis. JOURNAL OF ETHNOPHARMACOLOGY 2021; 281:114506. [PMID: 34371113 DOI: 10.1016/j.jep.2021.114506] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Lung cancer is the chief reason of cancer death worldwide, and non-small cell lung cancer (NSCLC) make up the majority of lung cancers. Gypenosides are the main active constituents from Gynostemma pentaphyllum. Previous studies showed that they were used to remedy many cancers. The effect of gypenosides on NSCLC has never been studied from the perspective of network pharmacology and metabolomics. The mechanism is still not clear and remains to be explored. AIM OF THE STUDY To explore the anti-NSCLC activity and mechanism of gypenosides in A549 cells. MATERIAL/METHODS Gypenosides of G. pentaphyllum were detected by HPLC-MS. The cytotoxicity was detected by MTT assay. The migration, cell cycle and apoptosis of gypenosides were studied by wound healing assay, JC-1 assay and flow cytometry. The mechanism of gypenosides on NSCLC was studied by metabolomics and network pharmacology. Some key proteins and pathways were further confirmed by Western blot. RESULTS Eleven gypenosides were detected by HPLC-MS. Gypenosides could suppress the proliferation of A549 cells, inhibit the migration of A549 cells, induce apoptosis and arrest cell cycle in G0/G1 phase. Metabolomics and network pharmacology approach revealed that gypenosides might affect 17 metabolite related proteins by acting on 9 candidate targets (STAT3, VEGFA, EGFR, MMP9, IL2, TYMS, FGF2, HPSE, LGALS3), thus resulting in the changes of two metabolites (uridine 5'-monophosphate, D-4'-Phosphopantothenate) and two metabolic pathways (pyrimidine metabolism; pantothenate and CoA biosynthesis). Western blotting indicated that gypenosides might inhibit A549 cells through MMP9, STAT3 and TYMS to indirectly affect the pathways of pyrimidine metabolism, pantothenate and CoA biosynthesis. CONCLUSIONS This study revealed that metabolomics combined with network pharmacology was conducive to understand the anti-NSCLC mechanism of gypenosides.
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Affiliation(s)
- Yan-Shuang Qi
- Key Laboratory of Ethnomedicine of Ministry of Education, Center on Translational Neuroscience, School of Pharmacy, Minzu University of China, Beijing, 100081, PR China
| | - Jin-Bo Xie
- Key Laboratory of Ethnomedicine of Ministry of Education, Center on Translational Neuroscience, School of Pharmacy, Minzu University of China, Beijing, 100081, PR China
| | - Peng Xie
- Key Laboratory of Ethnomedicine of Ministry of Education, Center on Translational Neuroscience, School of Pharmacy, Minzu University of China, Beijing, 100081, PR China
| | - Yu Duan
- Key Laboratory of Ethnomedicine of Ministry of Education, Center on Translational Neuroscience, School of Pharmacy, Minzu University of China, Beijing, 100081, PR China
| | - Ya-Qin Ling
- Key Laboratory of Ethnomedicine of Ministry of Education, Center on Translational Neuroscience, School of Pharmacy, Minzu University of China, Beijing, 100081, PR China
| | - Yu-Long Gu
- Key Laboratory of Ethnomedicine of Ministry of Education, Center on Translational Neuroscience, School of Pharmacy, Minzu University of China, Beijing, 100081, PR China
| | - Xiang-Lan Piao
- Key Laboratory of Ethnomedicine of Ministry of Education, Center on Translational Neuroscience, School of Pharmacy, Minzu University of China, Beijing, 100081, PR China.
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Cao H, Zhang X, Ruan Y, Zhang L, Cui Z, Li X, Jia B. miRNA expression profiling and zeatin dynamic changes in a new model system of in vivo indirect regeneration of tomato. PLoS One 2020; 15:e0237690. [PMID: 33332392 PMCID: PMC7745965 DOI: 10.1371/journal.pone.0237690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/27/2020] [Indexed: 01/15/2023] Open
Abstract
Callus formation and adventitious shoot differentiation could be observed on the cut surface of completely decapitated tomato plants. We propose that this process can be used as a model system to investigate the mechanisms that regulate indirect regeneration of higher plants without the addition of exogenous hormones. This study analyzed the patterns of trans-zeatin and miRNA expression during in vivo regeneration of tomato. Analysis of trans-zeatin revealed that the hormone cytokinin played an important role in in vivo regeneration of tomato. Among 183 miRNAs and 1168 predicted target genes sequences identified, 93 miRNAs and 505 potential targets were selected based on differential expression levels for further characterization. Expression patterns of six miRNAs, including sly-miR166, sly-miR167, sly-miR396, sly-miR397, novel 156, and novel 128, were further validated by qRT-PCR. We speculate that sly-miR156, sly-miR160, sly-miR166, and sly-miR397 play major roles in callus formation of tomato during in vivo regeneration by regulating cytokinin, IAA, and laccase levels. Overall, our microRNA sequence and target analyses of callus formation during in vivo regeneration of tomato provide novel insights into the regulation of regeneration in higher plants.
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Affiliation(s)
- Huiying Cao
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, China
| | - Xinyue Zhang
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, China
| | - Yanye Ruan
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, China
- * E-mail: (YR); (LZ)
| | - Lijun Zhang
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, China
- * E-mail: (YR); (LZ)
| | - Zhenhai Cui
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, China
| | - Xuxiao Li
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, China
| | - Bing Jia
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, China
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Ma J, Zhao P, Liu S, Yang Q, Guo H. The Control of Developmental Phase Transitions by microRNAs and Their Targets in Seed Plants. Int J Mol Sci 2020; 21:E1971. [PMID: 32183075 PMCID: PMC7139601 DOI: 10.3390/ijms21061971] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 02/29/2020] [Accepted: 03/12/2020] [Indexed: 12/18/2022] Open
Abstract
Seed plants usually undergo various developmental phase transitions throughout their lifespan, mainly including juvenile-to-adult and vegetative-to-reproductive transitions, as well as developmental transitions within organ/tissue formation. MicroRNAs (miRNAs), as a class of small endogenous non-coding RNAs, are involved in the developmental phase transitions in plants by negatively regulating the expression of their target genes at the post-transcriptional level. In recent years, cumulative evidence has revealed that five miRNAs, miR156, miR159, miR166, miR172, and miR396, are key regulators of developmental phase transitions in plants. In this review, the advanced progress of the five miRNAs and their targets in regulating plant developmental transitions, especially in storage organ formation, are summarized and discussed, combining our own findings with the literature. In general, the functions of the five miRNAs and their targets are relatively conserved, but their functional divergences also emerge to some extent. In addition, potential research directions of miRNAs in regulating plant developmental phase transitions are prospected.
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Affiliation(s)
- Jingyi Ma
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing 100083, China; (J.M.); (P.Z.); (Q.Y.)
| | - Pan Zhao
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing 100083, China; (J.M.); (P.Z.); (Q.Y.)
| | - Shibiao Liu
- College of Biology and Environmental Sciences, Jishou University, Jishou 416000, China;
| | - Qi Yang
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing 100083, China; (J.M.); (P.Z.); (Q.Y.)
| | - Huihong Guo
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing 100083, China; (J.M.); (P.Z.); (Q.Y.)
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