Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
7.8
5.6
Journals
IJMS
Special Issues
Biological Networks of Specialized Metabolites and Plants
ijms-logo
Submit to IJMS Review for IJMS Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

Biological Networks of Specialized Metabolites and Plants

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (31 May 2021) | Viewed by 15794

Special Issue Editors

Dr. Kengo Morohashi

E-Mail Website
Guest Editor
Department of Biochemistry and Molecular Biology, College of Natural Science, Michigan State University, East Lansing, MI 48824, USA
Interests: systems biology; chemical biology; gene regulatory networks in plants
Dr. Kenji Hashimoto

E-Mail Website
Guest Editor
Department of Applied Biological Science, Tokyo University of Science, Tokyo, Japan
Interests: Environmental stress responses; Morphogenesis; Calcium signaling networks in plants

Special Issue Information

Dear Colleagues,

Plants produce a broad range of specialized metabolites; however, their functions in plants have been ignored. Over the past few decades, reports on the significant roles that specialized metabolites play in biological events have been accumulating. Since there are plenty of specialized metabolites in and around plants, the interactions between specialized metabolites and plants produce complex networks. Elucidation of the biological relevance of such large networks remains a challenge. The recent advances in technology have enabled researchers to obtain "big data" that include biological and chemical information. These interdisciplinary data are anticipated to become a driving force for the study of biological networks.

This Special Issue focuses on networks of metabolites and plants. Authors are invited to submit original research and review papers related to transcriptomics, metabolomics, genomics, and computational approaches. We also welcome papers that comprehensively study the relationship between specialized metabolites and plants.

Dr. Kengo Morohashi
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • specialized metabolite;
  • secondary metabolite;
  • omics approach;
  • transcriptomics;
  • metabolomics;
  • proteomics;
  • genomics;
  • systems biology;
  • chemical biology;
  • network biology.

Published Papers (5 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

21 pages, 42817 KiB  
Article
Genome-Wide Identification of GRAS Gene Family and Their Responses to Abiotic Stress in Medicago sativa
by Han Zhang, Xiqiang Liu, Xuemeng Wang, Ming Sun, Rui Song, Peisheng Mao and Shangang Jia
Int. J. Mol. Sci. 2021, 22(14), 7729; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22147729 - 20 Jul 2021
Cited by 23 | Viewed by 2922
Abstract
Alfalfa (Medicago sativa) is a high-quality legume forage crop worldwide, and alfalfa production is often threatened by abiotic environmental stresses. GRAS proteins are important transcription factors that play a vital role in plant development, as well as in response to environmental [...] Read more.
Alfalfa (Medicago sativa) is a high-quality legume forage crop worldwide, and alfalfa production is often threatened by abiotic environmental stresses. GRAS proteins are important transcription factors that play a vital role in plant development, as well as in response to environmental stress. In this study, the availability of alfalfa genome “Zhongmu No.1” allowed us to identify 51 GRAS family members, i.e., MsGRAS. MsGRAS proteins could be classified into nine subgroups with distinct conserved domains, and tandem and segmental duplications were observed as an expansion strategy of this gene family. In RNA-Seq analysis, 14 MsGRAS genes were not expressed in the leaf or root, 6 GRAS genes in 3 differentially expressed gene clusters were involved in the salinity stress response in the leaf. Moreover, qRT-PCR results confirmed that MsGRAS51 expression was induced under drought stress and hormone treatments (ABA, GA and IAA) but down-regulated in salinity stress. Collectively, our genome-wide characterization, evolutionary, and expression analysis suggested that the MsGRAS proteins might play crucial roles in response to abiotic stresses and hormonal cues in alfalfa. For the breeding of alfalfa, it provided important information on stress resistance and functional studies on MsGRAS and hormone signaling. Full article
(This article belongs to the Special Issue Biological Networks of Specialized Metabolites and Plants)
►▼ Show Figures

Figure 1

17 pages, 2397 KiB  
Article
Regulation of Oxalate Metabolism in Spinach Revealed by RNA-Seq-Based Transcriptomic Analysis
by Vijay Joshi, Arianne Penalosa, Madhumita Joshi and Sierra Rodriguez
Int. J. Mol. Sci. 2021, 22(10), 5294; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22105294 - 18 May 2021
Cited by 9 | Viewed by 3093
Abstract
Although spinach (Spinacia oleracea L.) is considered to be one of the most nutrient-rich leafy vegetables, it is also a potent accumulator of anti-nutritional oxalate. Reducing oxalate content would increase the nutritional value of spinach by enhancing the dietary bioavailability of calcium [...] Read more.
Although spinach (Spinacia oleracea L.) is considered to be one of the most nutrient-rich leafy vegetables, it is also a potent accumulator of anti-nutritional oxalate. Reducing oxalate content would increase the nutritional value of spinach by enhancing the dietary bioavailability of calcium and other minerals. This study aimed to investigate the proposed hypothesis that a complex network of genes associated with intrinsic metabolic and physiological processes regulates oxalate homeostasis in spinach. Transcriptomic (RNA-Seq) analysis of the leaf and root tissues of two spinach genotypes with contrasting oxalate phenotypes was performed under normal physiological conditions. A total of 2308 leaf- and 1686 root-specific differentially expressed genes (DEGs) were identified in the high-oxalate spinach genotype. Gene Ontology (GO) analysis of DEGs identified molecular functions associated with various enzymatic activities, while KEGG pathway analysis revealed enrichment of the metabolic and secondary metabolite pathways. The expression profiles of genes associated with distinct physiological processes suggested that the glyoxylate cycle, ascorbate degradation, and photorespiratory pathway may collectively regulate oxalate in spinach. The data support the idea that isocitrate lyase (ICL), ascorbate catabolism-related genes, and acyl-activating enzyme 3 (AAE3) all play roles in oxalate homeostasis in spinach. The findings from this study provide the foundation for novel insights into oxalate metabolism in spinach. Full article
(This article belongs to the Special Issue Biological Networks of Specialized Metabolites and Plants)
►▼ Show Figures

Figure 1

16 pages, 5126 KiB  
Article
Metabolome and Transcriptome Analyses Reveal the Regulatory Mechanisms of Photosynthesis in Developing Ginkgo biloba Leaves
by Ying Guo, Tongli Wang, Fang-Fang Fu, Yousry A. El-Kassaby and Guibin Wang
Int. J. Mol. Sci. 2021, 22(5), 2601; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22052601 - 05 Mar 2021
Cited by 7 | Viewed by 3322
Abstract
Ginkgo (Ginkgo biloba L.) is a deciduous tree species with high timber, medicinal, ecological, ornamental, and scientific values, and is widely cultivated worldwide. However, for such an important tree species, the regulatory mechanisms involved in the photosynthesis of developing leaves remain largely [...] Read more.
Ginkgo (Ginkgo biloba L.) is a deciduous tree species with high timber, medicinal, ecological, ornamental, and scientific values, and is widely cultivated worldwide. However, for such an important tree species, the regulatory mechanisms involved in the photosynthesis of developing leaves remain largely unknown. Here, we observed variations in light response curves (LRCs) and photosynthetic parameters (photosynthetic capacity (Pnmax) and dark respiration rate (Rd)) of leaves across different developmental stages. We found the divergence in the abundance of compounds (such as 3-phospho-d-glyceroyl phosphate, sedoheptulose-1,7-bisphosphate, and malate) involved in photosynthetic carbon metabolism. Additionally, a co-expression network was constructed to reveal 242 correlations between transcription factors (TFs) and photosynthesis-related genes (p < 0.05, |r| > 0.8). We found that the genes involved in the photosynthetic light reaction pathway were regulated by multiple TFs, such as bHLH, WRKY, ARF, IDD, and TFIIIA. Our analysis allowed the identification of candidate genes that most likely regulate photosynthesis, primary carbon metabolism, and plant development and as such, provide a theoretical basis for improving the photosynthetic capacity and yield of ginkgo trees. Full article
(This article belongs to the Special Issue Biological Networks of Specialized Metabolites and Plants)
►▼ Show Figures

Figure 1

32 pages, 11156 KiB  
Article
Transcriptome Analysis and Identification of Lipid Genes in Physaria lindheimeri, a Genetic Resource for Hydroxy Fatty Acids in Seed Oil
by Grace Q. Chen, Won Nyeong Kim, Kumiko Johnson, Mid-Eum Park, Kyeong-Ryeol Lee and Hyun Uk Kim
Int. J. Mol. Sci. 2021, 22(2), 514; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22020514 - 06 Jan 2021
Cited by 2 | Viewed by 3095
Abstract
Hydroxy fatty acids (HFAs) have numerous industrial applications but are absent in most vegetable oils. Physaria lindheimeri accumulating 85% HFA in its seed oil makes it a valuable resource for engineering oilseed crops for HFA production. To discover lipid genes involved in HFA [...] Read more.
Hydroxy fatty acids (HFAs) have numerous industrial applications but are absent in most vegetable oils. Physaria lindheimeri accumulating 85% HFA in its seed oil makes it a valuable resource for engineering oilseed crops for HFA production. To discover lipid genes involved in HFA synthesis in P. lindheimeri, transcripts from developing seeds at various stages, as well as leaf and flower buds, were sequenced. Ninety-seven percent clean reads from 552,614,582 raw reads were assembled to 129,633 contigs (or transcripts) which represented 85,948 unique genes. Gene Ontology analysis indicated that 60% of the contigs matched proteins involved in biological process, cellular component or molecular function, while the remaining matched unknown proteins. We identified 42 P. lindheimeri genes involved in fatty acid and seed oil biosynthesis, and 39 of them shared 78–100% nucleotide identity with Arabidopsis orthologs. We manually annotated 16 key genes and 14 of them contained full-length protein sequences, indicating high coverage of clean reads to the assembled contigs. A detailed profiling of the 16 genes revealed various spatial and temporal expression patterns. The further comparison of their protein sequences uncovered amino acids conserved among HFA-producing species, but these varied among non-HFA-producing species. Our findings provide essential information for basic and applied research on HFA biosynthesis. Full article
(This article belongs to the Special Issue Biological Networks of Specialized Metabolites and Plants)
►▼ Show Figures

Figure 1

19 pages, 8892 KiB  
Article
The Predicted Functional Compartmentation of Rice Terpenoid Metabolism by Trans-Prenyltransferase Structural Analysis, Expression and Localization
by Min Kyoung You, Yeo Jin Lee, Ji Su Yu and Sun-Hwa Ha
Int. J. Mol. Sci. 2020, 21(23), 8927; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21238927 - 25 Nov 2020
Cited by 5 | Viewed by 2506
Abstract
Most terpenoids are derived from the basic terpene skeletons of geranyl pyrophosphate (GPP, C10), farnesyl-PP (FPP, C15) and geranylgeranyl-PP (GGPP, C20). The trans-prenyltransferases (PTs) mediate the sequential head-to-tail condensation of an isopentenyl-PP (C5) with [...] Read more.
Most terpenoids are derived from the basic terpene skeletons of geranyl pyrophosphate (GPP, C10), farnesyl-PP (FPP, C15) and geranylgeranyl-PP (GGPP, C20). The trans-prenyltransferases (PTs) mediate the sequential head-to-tail condensation of an isopentenyl-PP (C5) with allylic substrates. The in silico structural comparative analyses of rice trans-PTs with 136 plant trans-PT genes allowed twelve rice PTs to be identified as GGPS_LSU (OsGGPS1), homomeric G(G)PS (OsGPS) and GGPS_SSU-II (OsGRP) in Group I; two solanesyl-PP synthase (OsSPS2 and 3) and two polyprenyl-PP synthases (OsSPS1 and 4) in Group II; and five FPSs (OsFPS1, 2, 3, 4 and 5) in Group III. Additionally, several residues in “three floors” for the chain length and several essential domains for enzymatic activities specifically varied in rice, potentiating evolutionarily rice-specific biochemical functions of twelve trans-PTs. Moreover, expression profiling and localization patterns revealed their functional compartmentation in rice. Taken together, we propose the predicted topology-based working model of rice PTs with corresponding terpene metabolites: GPP/GGPPs mainly in plastoglobuli, SPPs in stroma, PPPs in cytosol, mitochondria and chloroplast and FPPs in cytosol. Our findings could be suitably applied to metabolic engineering for producing functional terpene metabolites in rice systems. Full article
(This article belongs to the Special Issue Biological Networks of Specialized Metabolites and Plants)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-5
Back to TopTop