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Molecular Mechanism and Regulation of Secondary Metabolites Biosynthesis in Plants
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Molecular Mechanism and Regulation of Secondary Metabolites Biosynthesis in Plants

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 31 December 2024 | Viewed by 2721

Special Issue Editor

Dr. Deyou Qiu

E-Mail Website
Guest Editor
State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
Interests: plant metabolites; tree breeding; biosynthetic pathway; epigenetics; transcription factor; genome; transcriptome; metabolome; genetic engineering; synthetic biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant secondary metabolites are important sources for pharmaceuticals, food additives, flavors, and other industrial materials. However, compared with plant primary metabolites, the number of studies on plant secondary metabolites has fallen far behind. Recently, with the increase in demand for plant secondary metabolites and the development and application of high-throughput technologies, the research field of plant secondary metabolites has rapidly expanded. Significant progress has been made in finding the biosynthetic pathway of secondary metabolites, key enzymes of the pathway, and regulatory mechanisms of secondary metabolism. This enables the production of secondary metabolites through new technologies such as synthetic biology. Moreover, novel strategies are being applied to this research field. This open access Special Issue of Plants is devoted to publishing original research and review articles on studies of the biosynthesis of secondary metabolites, highlighting recent advances in molecular mechanisms and regulation of the biosynthesis of secondary metabolites in plants, particularly new discoveries and the development and application of novel technologies. This Special Issue aims to provide an accessible collection of research that shares the latest innovative results from the research field of plants to aid further studies on secondary metabolism, plant improvement, and the production of important secondary metabolites.

Topics of this Special Issue include, but are not limited to, the following:

  • Biosynthetic pathways of secondary metabolites;
  • Key genes or enzymes involved in the biosynthesis of secondary metabolites;
  • Epigenetics of plant secondary metabolism;
  • Transcription factors and regulatory networks in plant secondary metabolism;
  • Metabolic engineering and synthetic biology of plant secondary metabolites;
  • Application of high-throughput sequencing technologies;
  • Databases associated with the biosynthesis and regulation of plant secondary metabolites;
  • Novel technologies and strategies for plant secondary metabolism studies;
  • Genomics, epigenomics, transcriptomics, proteomics, and metabolomics of medicinal plants.

Dr. Deyou Qiu
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • secondary metabolites
  • biosynthetic pathway
  • functional characterization of gene and enzyme
  • epigenetic regulation
  • high-throughput sequencing
  • metabolic engineering
  • synthetic biology
  • transcription factor
  • medicinal plants
  • molecular regulatory mechanisms
  • genome editing
  • multi-omics
  • AI

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Published Papers (3 papers)

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16 pages, 3974 KiB  
Article
Transcriptomic Analysis of the Combined Effects of Methyl Jasmonate and Wounding on Flavonoid and Anthraquinone Biosynthesis in Senna tora
by Saemin Chang, Woo-Haeng Lee, Hyo Ju Lee, Tae-Jin Oh, Si-Myung Lee, Jeong Hwan Lee and Sang-Ho Kang
Plants 2024, 13(20), 2944; https://doi.org/10.3390/plants13202944 - 21 Oct 2024
Viewed by 672
Abstract
Jasmonates, including jasmonic acid (JA) and its derivatives such as methyl jasmonate (MeJA) or jasmonly isoleucine (JA-Ile), regulate plant responses to various biotic and abiotic stresses. In this study, we applied exogenous MeJA onto Senna tora leaves subjected to wounding and conducted a [...] Read more.
Jasmonates, including jasmonic acid (JA) and its derivatives such as methyl jasmonate (MeJA) or jasmonly isoleucine (JA-Ile), regulate plant responses to various biotic and abiotic stresses. In this study, we applied exogenous MeJA onto Senna tora leaves subjected to wounding and conducted a transcriptome deep sequencing analysis at 1 (T1), 3 (T3), 6 (T6), and 24 (T24) h after MeJA induction, along with the pretreatment control at 0 h (T0). Out of 18,883 mapped genes, we identified 10,048 differentially expressed genes (DEGs) between the T0 time point and at least one of the four treatment times. We detected the most DEGs at T3, followed by T6, T1, and T24. We observed the upregulation of genes related to JA biosynthesis upon exogenous MeJA application. Similarly, transcript levels of genes related to flavonoid biosynthesis increased after MeJA application and tended to reach their maximum at T6. In agreement, the flavonols kaempferol and quercetin reached their highest accumulation at T24, whereas the levels of the anthraquinones aloe-emodin, emodin, and citreorosein remained constant until T24. This study highlights an increase in flavonoid biosynthesis following both MeJA application and mechanical wounding, whereas no significant influence is observed on anthraquinone biosynthesis. These results provide insights into the distinct regulatory pathways of flavonoid and anthraquinone biosynthesis in response to MeJA and mechanical wounding. Full article
(This article belongs to the Special Issue Molecular Mechanism and Regulation of Secondary Metabolites Biosynthesis in Plants)
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18 pages, 2405 KiB  
Article
Identification of Black Cumin (Nigella sativa) MicroRNAs by Next-Generation Sequencing and Their Implications in Secondary Metabolite Biosynthesis
by Andrea G. Uriostegui-Pena, Almendra Reyes-Calderón, Claudia Gutiérrez-García, Aashish Srivastava, Ashutosh Sharma and Sujay Paul
Plants 2024, 13(19), 2806; https://doi.org/10.3390/plants13192806 - 8 Oct 2024
Viewed by 1113
Abstract
Secondary metabolites are bioactive compounds believed to contribute to the pharmacological properties of plants. MicroRNAs (miRNAs) are small non-coding RNA molecules involved in post-transcriptional regulation and are thought to play an important role in regulating secondary metabolism biosynthesis. Nevertheless, the extent of miRNA [...] Read more.
Secondary metabolites are bioactive compounds believed to contribute to the pharmacological properties of plants. MicroRNAs (miRNAs) are small non-coding RNA molecules involved in post-transcriptional regulation and are thought to play an important role in regulating secondary metabolism biosynthesis. Nevertheless, the extent of miRNA involvement in secondary metabolism remains minimal. Nigella sativa (black cumin/black seed) is a popular medicinal and culinary plant known for its pharmaceutical properties; however, its genomic information is scarce. In this study, next-generation sequencing (NGS) technology was employed to obtain the miRNA profile of N. sativa, and their involvement in secondary metabolite biosynthesis was explored. A total of 25,139,003 unique reads ranging from 16 to 40 nucleotides were attained, out of which 240 conserved and 34 novel miRNAs were identified. Moreover, 6083 potential target genes were recognized in this study. Several conserved and novel black cumin miRNAs were found to target enzymes involved in the terpenoid, diterpenoid, phenylpropanoid, carotenoid, flavonoid, steroid, and ubiquinone biosynthetic pathways, among others, for example, beta-carotene 3-hydroxylase, gibberellin 3 beta-dioxygenase, trimethyltridecatetraene synthase, carboxylic ester hydrolases, acetyl-CoA C-acetyltransferase, isoprene synthase, peroxidase, shikimate O-hydroxycinnamoyltransferase, etc. Furthermore, sequencing data were validated through qPCR by checking the relative expression of eleven randomly selected conserved and novel miRNAs (nsa-miR164d, nsa-miR166a, nsa-miR167b, nsa-miR171a, nsa-miR390b, nsa-miR396, nsa-miR159a, nsa-miRN1, nsa-miRN29, nsa-miRN32, and nsa-miRN34) and their expression patterns were found to be corroborated with the sequencing data. We anticipate that this work will assist in clarifying the implications of miRNAs in plant secondary metabolism and aid in the generation of artificial miRNA-based strategies to overproduce highly valuable secondary metabolites from N. sativa. Full article
(This article belongs to the Special Issue Molecular Mechanism and Regulation of Secondary Metabolites Biosynthesis in Plants)
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15 pages, 7796 KiB  
Article
Light-Regulated Growth, Anatomical, Metabolites Biosynthesis and Transcriptional Changes in Angelica sinensis
by Hongyan Su, Xiuwen Cui, Yan Zhao, Mengfei Li, Jianhe Wei and Paul W. Paré
Plants 2024, 13(19), 2744; https://doi.org/10.3390/plants13192744 - 30 Sep 2024
Viewed by 630
Abstract
Angelica sinensis is an alpine medicinal plant that has been widely used as a general blood tonic and gynecological indications over 2000 years, which depend on the bioactive metabolites (e.g., volatile oils, organic acids, and flavonoids). Although the accumulation of these metabolites is [...] Read more.
Angelica sinensis is an alpine medicinal plant that has been widely used as a general blood tonic and gynecological indications over 2000 years, which depend on the bioactive metabolites (e.g., volatile oils, organic acids, and flavonoids). Although the accumulation of these metabolites is significantly affected by the environmental factors (e.g., altitude, temperature, and sunshine) as found in previous studies, the regulatory mechanism of different lights has not been clearly revealed. Here, growth parameters, contents of bioactive metabolites, and expression levels of related genes were examined when A. sinensis was exposed to different white-light (WL) and UV-B radiation treatments. The results showed that the differences in growth parameters (e.g., plant height, root length, and plant biomass) and leaf tissue characteristics (e.g., leaf thickness, stomatal density and shape, and chloroplast density) were observed under different light treatments. The contents of Z-ligustilide and ferulic acid elevated with the increase of WL (50 to 150 µmol·m2/s) and maximized under the combination of WL-100 and UV-B (107 µW/m2, UV-107) radiation, while the total flavonoids and polysaccharides contents, as well as in vitro antioxidant capacity, elevated with the increasing of WL and UV-B. mRNA transcripts encoding for the biosynthesis of volatile oils, ferulic acid, flavonoids, and polysaccharides were found to be differentially regulated under the different WL and UV-B treatments. These morphological, anatomical, and transcriptional changes are consistent with the elevated bioactive metabolites in A. sinensis under the combination of WL and UV-B. These findings will provide useful references for improving bioactive metabolite production via the cultivation and bioengineering of A. sinensis. Full article
(This article belongs to the Special Issue Molecular Mechanism and Regulation of Secondary Metabolites Biosynthesis in Plants)
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